title: WT embryos, 24 hours post fertilization, biol rep 2

city: Lexington

first: Kaan Ihsan

last: Eskut

state: Kentucky

address: 195 Huguelet Dr.

department: Biology

institute: University of Kentucky

description:
Library name: hrs24_2
column name in raw counts:hrs24_2

data_processing:
RNA-seq reads from this study were aligned to the reference genome using HISAT2 v2.2.1
Gene expression was quantified from these alignments using StringTie v2.2.1
Assembly: UKy_Petmar_22M1.pri1.0
Supplementary files format and content: comma separated file with raw counts from stringtie v2.2.1

organism: Petromyzon marinus

source_name: Embryos

growth_protocol: Eggs and sperm were collected from mature adults by stripping gametes into crystallization dishes and containing 10% Holtfreter’s solution and incubated for 10 min to permit fertilization. After visually confirming activation, embryos were rinsed in distilled water to remove excess sperm and maintained in 10% Holtfreter’s solution at 18 °C throughout development.

extract_protocol:
Total RNA was extracted from two pools of approximately 100 snap frozen embryos for each condition, following the standard Trizol extraction protocol with the addition of 10 mM dithiothreitol(DTT) to the lysis reaction.
Library preparation and sequencing were conducted by Novogene using their "Plant and Animal Eukaryotic mRNA" pipeline.

tag: tissue

value: Embryos

value: Wildtype


status: Public on Aug 12 2026

type: SRA

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: LP_ATAC-NUP88-6h-1
library prep for ATAC-NUP88-6h-1 derived from ADLI-4-3-84-3-5__OCP_74G

library_source: transcriptomic

data_processing:
STAR Suite v1.6.1
https://github.com/morphic-bio/STAR-suite
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: .bed, .narrowPeak and unstranded.bw

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Paired-end libaries
ATAC-sequencing

tag: cell line

tag: cell type

value: iPSC

tag: editing strategy

value: Knock-in of inducible C-terminal degron

tag: altered gene_symbol

tag: time

tag: model system

tag: condition

value: Auxin

tag: parental cell_line


title: H23_DMSO_2

city: Shanghai

first: Shaofei

last: Wang

state: Shanghai

address: 131 Dongan Road, Xuhui District, Shanghai 200032, P.R. China

country: China

institute: Fudan University

description:
Library name: Sample2
H23_DMSO_2 FPKM

data_processing:
The raw sequencing reads were filtered and trimmed using SOAPnuke (v1.5.6) prior to alignment and the resultant clean reads were then mapped to the human genome GRCh38/hg38 with STAR (v2.5.3a). The quantification of expression levels of genes and transcripts was conducted by RSEM (v1.3.1)] and the differential expression analysis was performed using DESeq2 package (v1.4.5).
Assembly: GRCh38
Supplementary files format and content: NCI-H23_KRASi_24h_FPKMs.txt

source_name: lung

growth_protocol: The NCI-H23 human NSCLC cells, were cultured with RPMI 1640 medium containing 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from the cells using PureLink RNA Mini Kit (Cat. No. #12183025, Invitrogen) according to the manufacturer's instructions.
After the assessment of RNA quality by the Fragment Analyzer System (Alignment), cDNA libraries were prepared using MGIEasy Fast RNA Library Prep Kit (Cat. No. 940-000890-00, MGI) from RNA for sequencing on MGISEQ-2000RS platform (MGI Tech Co. Ltd.) to generate 50 bp single-end reads.

treatment_protocol: The NCI-H23 cells were treated with vehicle (DMSO) or KRAS inhibitor, either AMG-510 (1 μM) or MRTX849 (100 nM), for 24h. Three biological replicates were prepared for each condition.

value: lung

value: NSCLC

tag: genotype

value: KRAS-mutant

tag: treatment

value: DMSO (24h)

tag: batch


title: P134_26Sep

city: Stanford

first: Zhuoqing

last: Fang

state: California

address: 300 Pasteur Drive

country: USA

institute: Stanford

description:
Library name: P134_26Sep
Removed form analysis

data_processing:
CITE-seq files were demultipexed with cellranger mkfastq, and then processed by cellranger count pipeline
Assembly: GRCh38
Supplementary files format and content: cell ranger output files: barcodes.tsv.gz, matrix.mtx.gz, features.tsv.gz
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Blood

extract_protocol:
Live frozen PBMCs were thawed and washed twice with RPMI supplemented with 10% fetal bovine serum (FBS) and 20 µg/mL DNase I (Sigma-Aldrich), and resuspended in 1× PBS. Cells were washed with PBS and stained with Zombie Aqua Fixable Viability Dye according to the manufacturer’s recommendations. Live cells were fluorescence-activated cell sorted (FACS) into PBS supplemented with 5% FBS. Sorted cells were stained with a cocktail of TotalSeq™-A oligonucleotide-conjugated antibodies (BioLegend) in PBS containing 5% FBS, 2 mM EDTA, and 5 mg/mL human IgG, following the manufacturer’s recommendations, to enable cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq). Cells were washed twice with PBS supplemented with 5% FBS and resuspended in PBS supplemented with 1% BSA (Miltenyi) and 0.5 U/µL RNase inhibitor (Sigma-Aldrich). Approximately 9,000 cells were targeted for each experiment.
The PBMC suspension was used as input for automated microfluidic single-cell capture and barcoding using the 10x Genomics Chromium iX platform. Cells were mixed with the reverse transcription master mix and subjected to partitioning along with Chromium gel beads to generate single-cell gel beads in emulsion (GEMs) using the Chromium Single Cell 3′ Gene Expression v3 chemistry (10x Genomics). Feature Barcoding technology (10x Genomics) was used for generation of antibody-derived tag (ADT) libraries from TotalSeq™-A antibodies, according to the manufacturer’s protocol. Individual cells were uniquely barcoded during GEM generation and reverse transcription. Following reverse transcription, cDNA was recovered and purified using Dynabeads™ MyOne™ Silane beads (Thermo Fisher Scientific) and SPRIselect beads (Beckman Coulter). Gene expression and ADT libraries were constructed according to the manufacturer’s instructions. Constructed libraries underwent quality control assessment using a High Sensitivity D1000 DNA ScreenTape (Agilent) and were quantified using a Qubit Fluorometer (Thermo Fisher Scientific) and a KAPA Library Quantification Kit (KAPA Biosystems) on the AriaMx instrument (Agilent).

value: Blood

value: PBMCs

tag: cohort

value: AZ

tag: arm

tag: ethnicity

value: Black

tag: participant id

value: Secondary_Day 1

tag: particiant visit


title: Abomasum,Lactation,Goat-2

city: Cerdanyola del Vallès

first: Diego

middle: Alonso

last: Vargas Donayre

state: Barcelona

address: Carrer de la Vall Moronta

department: Plant and Animal Genomics

country: Spain

institute: Centre for Research in Agricultural Genomics (CRAG)

description: Library name: AB2

data_processing:
Raw reads with less than 100 bp and less than 85% of bases with Q>30 were discarded using Fastp. SILVA database rRNA database release 138.2 was used to eliminate rRNA contamination.
Filtered reads were mapped to the goat reference genome  with STAR and transcript structure recovery was conducted with StringTie. Novel lncRNAs were characterized with an internal protocol
Gene level estimated counts and offsets matrices were generated using tximport. Count data was normalized to CPM with edgeR. Genes with a CPM value greater than 0.5 in at least 3 samples in a tissue were considered as expressed. Null expressed genes were removed. Tissue-specificty of each gene was measured by the tau-index.
Assembly: ARS1.2
Supplementary files format and content: 33tissues_gene_counts.tsv.gz , tab-delimited text file includes raw gene count.
Supplementary files format and content: 33tissues_gene_length.tsv.gz , tab-delimited text file includes gene count offset.
Supplementary files format and content: 33tissues_CPM.tsv.gz , tab-delimited text file includes processed CPM
Supplementary files format and content: lncRNAs.gtf.gz , gtf file including novel lncRNA
Supplementary files format and content: 33tissues_tau.tsv.gz , tab-delimited text file includes tau-index for each expressed gene

organism: Capra hircus

source_name: Abomasum

extract_protocol:
RNA was extracted using the RiboPure™ Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol.
Strand-specific library construction was performed with VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina.

tag: tissue

value: Abomasum


title: OE21 cells, RNA-Seq, DMSO, 3 days, rep1

city: Cambridge

first: Harry

last: Fischl

address: Babraham Research Campus

institute: Storm Therapeutics

description: Library name: OE21_DMSO_3d_rep1

library_source: other

data_processing:
Paired-end reads were adapter trimmed using Trim Galore and counts per transcript and gene were determined using Salmon (Patro et al., 2027). Differential RNA, translation and translational efficency levels were determined using DESeq2 (Love et al., 2014, Chothani et al., 2019).
Assembly: GRCh38
Supplementary files format and content: csv file containing the RNA-seq count per gene for each replicate for both the 1 day and 3 day time point
Supplementary files format and content: csv file containing gene baseMean, log2FC and adjusted p-value for treated v control samples for differential Ribo-seq levels, RNA-seq levels and translational efficiency and associated integrated Ribo-seq and RNA-seq analysis translational efficiency class (Chothani et al., 2019)

molecule: other

extract_protocol:
Cell culture media was removed and cells were incubated (2 min, 37°C) with new media supplemented with 100 µg/mL cycloheximide (Merck, C4859), washed with PBS supplemented with 20 µg/mL cycloheximide, and lysed with 400 µL lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2 (Invitrogen, 89880), 1 mM DL-Dithiothreitol (DTT, Merck, 43815), 1% Triton X-100 (Thermo Scientific, 10671652), 0.1 % IGEPAL CA-630 (Merck, I8896), 100 µg/mL cycloheximide, 25 U/mL TURBO DNase (Invitrogen, AM2239) using a cell scraper. Lysate was triturated 10x through a 26-gauge needle and cell debris pelleted by centrifugation at 20,000 x g, 5 min, 4°C. Total RNA was purified from 100 µL cleared lysate using Trizol reagent according to the manufacturer’s instructions.
mRNA-seq libraries were generated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490S) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S).

treatment_protocol: OE21 cells were treated with DMSO or 1 µM STM9005 for 1 or 3 days

tag: cell line

value: Oesophageal carcinoma

value: DMSO 3 days


title: P135_26Sep

description: Library name: P135_26Sep

tag: cell type

value: Secondary_Day 7


title: P133_26Sep

description: Library name: P133_26Sep


title: H23_DMSO_1

description:
Library name: Sample1
H23_DMSO_1 FPKM


title: Frontal neocortex,Lactation,Goat-6

description: Library name: FN6

source_name: Frontal neocortex

value: Frontal neocortex


title: P132_26Sep

description: Library name: P132_26Sep

value: Primary_Day 7


title: OE21 cells, RNA-Seq, DMSO, 1 day, rep3

description: Library name: OE21_DMSO_1d_rep3

value: DMSO 1 day


title: OE21 cells, RNA-Seq, DMSO, 1 day, rep2

description: Library name: OE21_DMSO_1d_rep2


title: Myeloid (Cd11b+) cells from TNFR1 KO EO771 tumor, replicate 4

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

description: Library name: TNFR1_KO_4_CD11b

data_processing:
Raw data in fastq format were processed using the nf-core/rnaseq pipeline (v3.22.2), executed via Nextflow (v25.10.2). Quality control was performed with FastQC (v0.12.1), trimming with TrimGalore (v0.6.10) and Cutadapt (v4.9). Trimmed reads were pseudo-aigned and quantified against the mouse reference transcriptome (ENSEMBL GRCm39 release 113) using Salmon (v1.10.3) in quasi-mapping mode with a k-mer size of 20. Transcript-level abundance estimates were aggregated to gene-level counts using tximeta (v1.20.1).
Assembly: GRCm39.113
Supplementary files format and content: raw_counts.tsv - contains the raw counts for this RNAseq dataset

organism: Mus musculus

source_name: EO771 (tumor)

growth_protocol: Tumor cell lines were cultured in RPMI 1640 medium (Gibco) supplemented with 10%FBS (Sigma), 100U/ml penicillin, 100ug/ml streptomycin (Gibco), mouse cell lines were supplemented with 5x10-5 mol/L 2-mercaptoethanol (Gibco). All tumor cell lines were maintained in a humidified incubator at 5% CO2 and 37ᵒC for at least 7 days before being inoculated into mice. Mycoplasma contamination tests were routinely performed on all cell lines using the MycoAlert Mycoplasma Detection Kit (Lonza). To generate murine TNFR1 KO cell variants, each cell line was seeded at high cell density, one day prior to transfection with a customized vector from Genescript encoding a gRNA, Cas9, and GFP, using Lipofectamine 2000 (Thermo). gRNA was designed using several platforms (Benchling, Breaking-Cas, CHOP-CHOP, and Cas-Offinder), which predict the probability of on- and off-target gene editing. gRNA with the highest score across multiple platforms was selected. gRNA sequence is provided in supplementary figure 1. The gene-edited cells were sorted out twice using MoFlo Astrios EQ sorter (Beckman Coulter): first by GFP expression, and then by the absence of TNFR1 expression stained with anti-CD120a (Biolegend; 113003) to obtain several monoclonal TNFR1 KO cell lines.

extract_protocol:
For transcriptomic analyses, EO771 and HT29 tumor cell lines were collected at 6 and 24 hours after treatment with 1000 U/mL of TNFα. RNA was extracted using the RNeasy Mini Kit (Qiagen;74104)
RNA was sent to Dreamgenics (Asturias, Spain) for library construction.

value: EO771 (tumor)

value: Cd11b+ from tumor

value: TNFR1 KO


title: Hippocampus,Dry,Goat-54

description: Library name: HIC54

source_name: Hippocampus

value: Hippocampus


title: OE21 cells, RNA-Seq, DMSO, 3 days, rep2

description: Library name: OE21_DMSO_3d_rep2


title: Adrenal gland (cortex),Lactation,Goat-3

description: Library name: AGC3

source_name: Adrenal gland (cortex)

value: Adrenal gland (cortex)


title: P131_26Sep

description: Library name: P131_26Sep

value: Blood

value: Primary_Day 1


title: OE21 cells, RNA-Seq, DMSO, 1 day, rep1

description: Library name: OE21_DMSO_1d_rep1


title: Myeloid (Cd11b+) cells from TNFR1 WT EO771 tumor, replicate 3

description: Library name: TNFR1_WT_3_CD11b

value: TNFR1 WT


title: Myeloid (Cd11b+) cells from TNFR1 KO EO771 tumor, replicate 3

description: Library name: TNFR1_KO_3_CD11b


title: P130_26Sep

description: Library name: P130_26Sep

value: PBMCs

value: AZ

value: Black

value: Pre-vaccination


title: OE21 cells, STM9005, 3 days, rep3

description: Library name: OE21_STM9005_3d_rep3

data_processing:
Read 1 fastq files were adapter trimmed and filtered for reads with length between 20-40 nt using cutadapt. rRNA/tRNA/snoRNA/snRNA reads were removed using SortMeRNA (Kopylova et al., 2012). Reads were then aligned to a transcriptome index generated from the MANE Select transcript set (GRCh38, Ensembl release 108) using STAR (Dobin et al., 2013) (--alignEndsType EndToEnd, --outFilterMultimapNmax 1, --outFilterMismatchNmax 2, --alignIntronMax 1). Bam files were then processed using riboWaltz (Lauria et al., 2018) to determine the codon that was at the ribosome A-site for each RPF, filtering for read lengths from 26 to 32 nt and using the signal within a frame of -1 to +1 around the first nucleotide of each codon. Log2 fold changes (treated/control) in Ribo-seq Unit Step Transformation (RUST) ratios of observed/expected RPF density (O’Connor et al., 2016) for each A-site codon transcriptome-wide, excluding the first 40 and last 20 codons of transcripts and transcripts with fewer than 80 codons, were then calculated for each replicate.
Assembly: GRCh38
Supplementary files format and content: csv file containing log2 fold change (treated/control) a-sie codon RUST ratios for each replicate for both the 1 day and 3 day time point
Library strategy: Ribo-Seq

extract_protocol:
Cell culture media was removed and cells were incubated (2 min, 37°C) with new media supplemented with 100 µg/mL cycloheximide (Merck, C4859), washed with PBS supplemented with 20 µg/mL cycloheximide, and lysed with 400 µL lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2 (Invitrogen, 89880), 1 mM DL-Dithiothreitol (DTT, Merck, 43815), 1% Triton X-100 (Thermo Scientific, 10671652), 0.1 % IGEPAL CA-630 (Merck, I8896), 100 µg/mL cycloheximide, 25 U/mL TURBO DNase (Invitrogen, AM2239) using a cell scraper. Lysate was triturated 10x through a 26-gauge needle and cell debris pelleted by centrifugation at 20,000 x g, 5 min, 4°C. Total RNA was purified from 100 µL cleared lysate. Ribosome-protected RNA fragments (RPFs) were generated by incubating (45 min, 23 °C, 1400 rpm) cleared lysate (120 µL) with 3 µL RNase I (ThermoFisher, AM2294). Digestion was stopped with 4 µL SUPERase.In. Ribosomes were enriched by passing 100 µL through a pre-equilibrated Illustra MicroSpin S-400 HR column (GE Healthcare, 27-5140-01) and equilibrated by gravity flow with 3 mL equilibration buffer (20 mM Tris-HCl (pH 7.4), 150 mM NaCl, 5 mM MgCl2)). RNA was extracted from the flowthrough using Trizol reagent according to the manufacturer’s instructions.
rRNA was depleted from 6 µg of RNA using the Ribo-seq rRNA depletion kit (siTOOLs, dp-K024-000042) according to the manufacturer’s instructions and RNA was purified using an RNA Clean & Concentrator kit (Zymogen). RPFs were selected by excising RNAs between 27-32 nt following electrophoresis on a 15% TBE-Urea gel and extracted by incubating (15 min, 70 °C, 1400 rpm) gel pieces in RNA extraction buffer (0.3 M NaOAc (pH 5.2), 0.25 % SDS, 1 mM EDTA (pH 8.0)) and precipitating the RNA with isopropanol and GlycoBlue. RNA was resuspended incubated at 37°C for 30 min with 1 µL T4 PNK buffer, 1 µL T4 PNK and 1 µL SUPERase.In. RNA was purified using an RNA Clean & Concentrator column and generated into libraries using the NEBNext Small RNA-seq kit for Illumina (NEB, E7330S).

value: Oesophageal carcinoma

value: STM9005 3 days


title: Hippocampus,Dry,Goat-64

description: Library name: HIC64


title: P129_26Sep

description: Library name: P129_26Sep

value: NX

value: 3rd dose

value: Tertiary_Day 1


title: Myeloid (Cd11b+) cells from TNFR1 WT EO771 tumor, replicate 2

description: Library name: TNFR1_WT_2_CD11b

value: EO771 (tumor)


title: Hippocampus,Dry,Goat-73

description: Library name: HIC73


title: OE21 cells, STM9005, 3 days, rep2

description: Library name: OE21_STM9005_3d_rep2


title: P128_26Sep

description: Library name: P128_26Sep


title: Myeloid (Cd11b+) cells from TNFR1 WT EO771 tumor, replicate 1

description: Library name: TNFR1_WT_1_CD11b

value: Cd11b+ from tumor


title: Heart (left ventricle),Lactation,Goat-2

description: Library name: HLV2

source_name: Heart (left ventricle)

value: Heart (left ventricle)


title: P127_26Sep

description: Library name: P127_26Sep


title: Myeloid (Cd11b+) cells from TNFR1 KO EO771 tumor, replicate 1

description: Library name: TNFR1_KO_1_CD11b

value: TNFR1 KO


title: Myeloid (Cd11b+) cells from TNFR1 KO EO771 tumor, replicate 2

description: Library name: TNFR1_KO_2_CD11b


title: P126_26Sep

description: Library name: P126_26Sep

value: Tertiary_Day 7


title: OE21 cells, DMSO, 3 days, rep3

description: Library name: OE21_DMSO_3d_rep3

value: DMSO 3 days


title: OE21 cells, DMSO, 3 days, rep2

description: Library name: OE21_DMSO_3d_rep2


title: P125_26Sep

description: Library name: P125_26Sep

value: Blood


title: ChIP-seq for TRIM28 using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep2

city: Tokyo

first: Yosuke

last: Isota

address: Faculty of Science Bldg.3, Rm126, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, JAPAN

department: Graduate school of science

country: Japan

institute: The University of Tokyo

description: Library name: Trim28-Morc1dIDR-B

library_source: genomic

data_processing:
Adaptors of ChIP-seq reads were removed using Cutadapt, and reads were trimmed to 75 bp using SeqKit.
Trimmed reads were aligned to the mouse genome (mm10) using Bowtie2 in paired-end mode.
For aligned reads from both ChIP-seq, duplicates were removed using Picard, and only HighSignal regions within genomic blacklist regions (mm10-blacklist.v2) were removed.
BAM files from biological replicates were merged, and bigWig files were generated using the deepTools function bamCoverage with CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file

molecule: genomic DNA

growth_protocol: NIH3T3 cells were cultured at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% fetal bovine serum (Sigma) and Penicillin-Streptomycin-Glutamine (Gibco).

extract_protocol:
Cells were fixed with 1% FA. Chromatin fraction was extracted after processing with sonication and used for immunoprecipitation with TRIM28 antibody. DNA was purified from co-precipitaed fraction.
ChIP-seq library was prepared using NEBNext Ultra Ⅱ DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

treatment_protocol: Cells were treated with doxycycline (100 ng/mL) for 24 h prior to harvest.

value: fibroblast

value: TRE-3xFlag-MORC1 dIDR-bpNLS; rtTA

value: Doxycycline addition 100 ng/mL 24 h prior

tag: chip antibody

value: TRIM28 (GeneTex, AB_2037324)


title: Heart (left ventricle),Dry,Goat-54

description: Library name: HLV54


title: ChIP-seq for TRIM28 using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep1

description: Library name: Trim28-Morc1dIDR-A


title: OE21 cells, DMSO, 3 days, rep1

description: Library name: OE21_DMSO_3d_rep1


title: P124_26Sep

description: Library name: P124_26Sep

value: PBMCs

value: Black

value: Primary_Day 1


title: Heart (left ventricle),Dry,Goat-64

description: Library name: HLV64


title: OE21 cells, STM9005, 1 day, rep3

description: Library name: OE21_STM9005_1d_rep3

value: Oesophageal carcinoma

value: STM9005 1 day


title: ChIP-seq for TRIM28 using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep2

description: Library name: Trim28-Morc1-B

value: TRE-3xFlag-MORC1 WT; rtTA


title: P123_26Sep

description: Library name: P123_26Sep

value: NX


title: P122_26Sep

description: Library name: P122_26Sep

value: Primary_Day 7


title: OE21 cells, STM9005, 1 day, rep1

description: Library name: OE21_STM9005_1d_rep1


title: P121_26Sep

description: Library name: P121_26Sep

value: Pre-vaccination


title: OE21 cells, DMSO, 1 day, rep3

description: Library name: OE21_DMSO_1d_rep3

value: DMSO 1 day


title: ChIP-seq for TRIM28 using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep1

description: Library name: Trim28-Morc1-A


title: P114_19Sep

description: Library name: P114_19Sep

value: AZ

value: Secondary_Day 7


title: ChIP-seq for TRIM28 using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep1

description: Library name: Trim28-mCherry-A

value: TRE-3xFlag-mCherry; rtTA


title: OE21 cells, DMSO, 1 day, rep2

description: Library name: OE21_DMSO_1d_rep2


title: ChIP-seq for Flag using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep2

description: Library name: Flag-Morc1dIDR-B

extract_protocol:
Cells were fixed with 1% FA. Chromatin fraction was extracted after processing with sonication and used for immunoprecipitation with Flag antibody. DNA was purified from co-precipitaed fraction.
ChIP-seq library was prepared using NEBNext Ultra Ⅱ DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

value: fibroblast

value: Flag (Sigma-Aldrich, #AB_259529)


title: Liver,Lactation,Goat-6

description: Library name: LI6

source_name: Liver

value: Liver


title: P112_19Sep

description: Library name: P112_19Sep

value: Blood


title: OE21 cells, DMSO, 1 day, rep1

description: Library name: OE21_DMSO_1d_rep1


title: ChIP-seq for Flag using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep1

description: Library name: Flag-Morc1dIDR-A

value: TRE-3xFlag-MORC1 dIDR-bpNLS; rtTA

value: Doxycycline addition 100 ng/mL 24 h prior


title: Liver,Dry,Goat-54

description: Library name: LI54


title: ChIP-seq for Flag using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep2

description: Library name: Flag-Morc1-B


title: Liver,Dry,Goat-64

description: Library name: LI64


title: P110_19Sep

description: Library name: P110_19Sep

value: PBMCs

value: Black

value: Primary_Day 1


title: ChIP-seq for Flag using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep1

description: Library name: Flag-Morc1-A

value: TRE-3xFlag-MORC1 WT; rtTA


title: Lung,Lactation,Goat-6

description: Library name: LU6

source_name: Lung

value: Lung


title: P109_19Sep

description: Library name: P109_19Sep


title: ATAC-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep2

description: Library name: Morc1dIDR_2

data_processing:
Adaptors of ATAC-seq reads were removed using Cutadapt, and reads were trimmed to 75 bp using SeqKit.
Trimmed reads were aligned to the mouse genome (mm10) using Bowtie2 in paired-end mode with the options -N 1 -X 2000 --no-mixed --no-discordant.
For aligned reads from ATAC-seq, duplicates were removed using Picard, and only HighSignal regions within genomic blacklist regions (mm10-blacklist.v2) were removed.
BAM files from biological replicates were merged, and bigWig files were generated using the deepTools function bamCoverage with CPM normalization.
Assembly: mm10
Supplementary files format and content: bigWig : read coverage file

extract_protocol:
Cells were gently lysed in 50 µL of ice-cold lysis buffer to release nuclei, which were subsequently pelleted and transferred into a transposition mixture composed of 2× TD buffer (25 µL; Illumina), TDE1 transposase (1.5 µL; Illumina), and nuclease-free water (23.5 µL).
DNA fragments generated by TDE1 insertion were then purified using MinElute PCR Purification Kit (Qiagen). Libraries were produced by PCR amplification using barcoded primer sets (0.125 µM).

treatment_protocol: Cells were treated with doxycycline (100 ng/mL) for 48 h prior to harvest.

value: Doxycycline addition 100 ng/mL 48 h prior


title: MIR155_NEURO7

city: New York

first: Michelle E.

last: Ehrlich

state: NY

address: 1 Gustave L. Levy Pl, New York, NY 10029

department: Department of Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired-end RNA sequencing FASTQ files for all samples were aligned to Homo sapiens Reference genome (Grch38) using STAR read aligner and mapped reads were summarized to gene counts using subread function of FeatureCounts. Genes with expression (< 1 FPKM) across all samples were filtered from all subsequent analysis. Hierarchical clustering and Principal component analysis (PCA) were preformed as part of quality control to visualize biological variance between replicates, which were further exhibited by Volcano plots and Venn diagrams. We then performed differential gene expression analysis to compare all cell types with each other on normalized counts with EdgeR. Multiple biological replicates were used for all comparative analysis. Differentially expressed genes (DEGs) were identified at a false discovery rate (FDR) of 0.05. To identify biological pathways that may be differentially dysregulated by MIR155KO or MIR155 overexpression, we performed gene set enrichment analysis (GSEA) on the identified DEGs by using Enrichr, GSEA-MSIGDB and IPA (Ingenuity Pathways Analysis), where we identified enriched biological pathways, gene ontology sets, and mRNA targets of miRNA at an adjusted p-value < 0.05.
Assembly: Homo sapiens Reference genome (Grch38)

source_name: Differentiated human Induced pluripotent stem cells

growth_protocol: hiPSCs were maintained in 6-well plates (Corning) in feeder-free conditions using Geltrex in complete mTeSR1 medium in a humidified incubator (5% CO2, 37°C).

extract_protocol:
RNA isolation was performed on the lysates of WT, MIR155KO Clone 5 and MIR155KO Clone 25 hiPSC-derived cells, and MIR155-overexpressing NSCs and cortical neurons, according to the manufacturer’s protocol (miRNeasy mini-kit, Qiagen). Isolated RNA samples were submitted to Novogene Corporation Inc. for analysis of RNA quality and integrity.
All samples passed quality control, and RNA-seq libraries were prepared for sequencing using NovaSeq

treatment_protocol:
For neural differentiation to generate NSCs, hiPSCs were dissociated with Accutase and replated on 12-well tissue culture plates coated with Geltrex in complete mTeSR1 medium with 10 µM ROCK inhibitor. When cells were 100% confluent, the medium was replaced with Neural Induction medium (NIM, 50% DMEM/F12 medium, 50% Neurobasal medium, 2% B27 minus Vitamin A, 1% N2 supplement, 2 mM GlutaMAX and 100 U/mL Penicillin-Streptomycin) (day in vitro 0 (DIV0)) and maintained for 15 days. Inhibitors used in dual-SMAD inhibition protocol (LDN/SB/XAV, DIV0-10; XAV, DIV11-15;) included LDN193189 (100 nM), SB431542 (10 µM) and XAV939 (1.0 µM). On DIV15 hiPSC-derived NSCs were dissociated using Accutase and can be stocked in Synth-a-Freeze™ Cryopreservation Medium (Thermo Fisher Scientific) in liquid Nitrogen tank.
For terminal differentiation to generate functional cortical neurons, hiPSC-derived NSCs (DIV15) were replated at 200,000-300,000 cells/cm2 in NIM medium with 10 µM ROCK inhibitor on dried poly-l-ornithine (Sigma-Aldrich) and laminin-coated 6-well plates or 8-well slide chambers. Cells were left to adhere overnight and on DIV16 NIM medium with ROCK inhibitor was replaced with Neuron Maturation media (BrainPhys™ Neuronal Medium, 2% B27 with Vitamin A, 2 mM GlutaMAX and 100 U/mL Penicillin-Streptomycin) supplemented with PD0325901 (10 µM), SU5402 (10 µM), DAPT (10 µM), BDNF (40 ng/mL), GDNF (40 ng/mL), Laminin (1.0 µg/mL), dBcAMP (250 µM) and L-Ascorbic acid (200 µM). During DIV16-23 Neuron Maturation media were half-changed every other day. After DIV24, the medium was replaced with Neuronal Maintenance media (BrainPhys™ Neuronal Medium, 2% B27 with Vitamin A, 2 mM GlutaMAX and 100 U/mL Penicillin-Streptomycin) supplemented with BDNF (40 ng/mL), GDNF (40 ng/mL), Laminin (1.0 µg/mL), dBcAMP (250 µM) and L-Ascorbic acid (200 µM). After DIV32, hiPSC-derived cortical neurons were active at this stage which can be confirmed with Ca2+ imaging. Between DIV50 and DIV60 hiPSC-derived cortical neurons were used for electrophysiological recordings.

value: MIR155-overexpressing neurons

value: hiPSC differentiation


title: Lung,Dry,Goat-54

description: Library name: LU54


title: CONTR_NEURO7

value: Differentiated human Induced pluripotent stem cells

value: Control neurons


title: P108_19Sep

description: Library name: P108_19Sep

value: NX

value: 3rd dose

value: Tertiary_Day 1


title: Kidney (medulla),Dry,Goat-73

description: Library name: KM73

source_name: Kidney (medulla)

value: Kidney (medulla)


title: ATAC-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 dIDR-bpNLS, rep1

description: Library name: Morc1dIDR_1

value: fibroblast


title: ChIP-seq for TRIM28 using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep2

description: Library name: Trim28-mCherry-B

value: TRE-3xFlag-mCherry; rtTA

value: TRIM28 (GeneTex, AB_2037324)


title: CONTR_NEURO6


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 trpL_W18A_W20A 2

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

country: Germany

institute: Helmholtz Center for Infection Research

description: Library name: PA14_wt_trpL_W18A_W20A_2

data_processing:
cutadapt
bowtie2
featureCounts
Assembly: NC_008463.1
Supplementary files format and content: bed files - reads per gene (featureCounts)

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: bacteria

growth_protocol: Planktonic growth in LB medium at 37°C. Harvest in early stationary phase at OD600 = 2.0.

extract_protocol:
RNeasy Plus kit (Qiagen) in combination with QIAshredder columns (Qiagen) was used according to the manufacturer’s manual. Modifications:  Cell lysis was performed with 8 mg/mL lysozyme in Tris-EDTA-buffer (pH 8.0). RLT buffer with mecaptoethanol was added. Samples were frozen at -70°C for 60 min and then processed with QIAshredder columns. The remaining steps were performed according to the manufacturer's manual. After RNA elution, samples were treated with DNase (DNA-free Kit DNase Treatment & Removal, ambion).
RNA was fragmented (150–350 bp) by FastAP buffer (Thermo). End repair was performed with DNase (Thermo) and FastAP. Barcodes were ligated to each sample by T4 RNA ligase 1 (NEB). Samples were purified with the RNA Clean & Concentrator-25 Kit (Zymo). The RiboZero Bacteria Kit (Illumina) was used to remove ribosomal RNA. cDNA libraries were generated using SMARTscribe reverse transcriptase (Clonetech). Enrichment was done by AccuPrime HiFi Taq (Thermo) and all purification steps using RNAClean XP beads (Agencourt). Libraries were sequenced in paired-end mode on an Illumina Novaseq 6000 device (2 x 50 bp)

value: bacteria

value: planctonic growth in LB, OD600= 2


title: ATAC-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep2

description: Library name: Morc1WT_2


title: MIR155_NSC8

value: MIR155-overexpressing NSCs


title: P107_19Sep

description: Library name: P107_19Sep

value: Blood

value: PBMCs

value: Black


title: P106_19Sep

description: Library name: P106_19Sep

value: Tertiary_Day 7


title: MIR155_NSC7

value: hiPSC differentiation


title: P105_19Sep

description: Library name: P105_19Sep


title: ATAC-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep2

description: Library name: mCherry_2

value: Doxycycline addition 100 ng/mL 48 h prior


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 wild type 2

description: Library name: PA14_wt_2

value: WT


title: MIR155_NEURO6

value: Differentiated human Induced pluripotent stem cells

value: MIR155-overexpressing neurons


title: MIR155_NSC6


title: ATAC-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-mCherry, rep1

description: Library name: mCherry_1


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 wild type 1

description: Library name: PA14_wt_1


title: P104_19Sep

description: Library name: P104_19Sep

value: NX

value: Primary_Day 1


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14  dmiaA and trpL_W18A_W20A 2

description: Library name: PA14_dmiaA_trpLW18A_W20A_2

value: dmiaA and trpL_W18A_W20A


title: P103_19Sep

description: Library name: P103_19Sep

value: Pre-vaccination


title: CONTR_NSC8

value: Control NSCs


title: Suprasylvian sulcus outer subventricular zone, 15 day old ferret brain_5

city: Bundoora

first: Mary

last: Tolcos

state: VIC

address: 225-245 Plenty Rd

country: Australia

institute: RMIT University

description: Library name: 10-19F21P15_Sulcus_OSVZ

data_processing:
Raw data was pre-processed using Trimmomatic (v0.38) with standard paired-reads settings to remove residual Illumina adapters and to set length between 36 and 100 bases. QC was performed on both untrimmed raw data and trimmed data using FastQC (v0.11.9).Trimmed sequencing data were mapped and aligned to the reference genome using STAR (v2.7.9a) and summarised in Rstudio (v2023.06.1, Build 524) using the featureCounts function from the Rsubread package (v2.16.0). Differential expression analysis was performed using the edgeR package (v3.42.4) within the R environment (v4.3.1) via Rstudio.
Assembly: Genome: MusPutFur1.0, Toplevel unmasked; Annotations: MusPutFur1.0.108
Supplementary files format and content: Excel .xlsx file. Contains Ensembl Gene IDs, Gene annotations (where annotations were mapped), and batch matrix counts for each sample and region of interest.

organism: Mustela putorius furo

source_name: brain

extract_protocol:
Laser capture microdissection and RNeasy Micro Kit (Qiagen)
Tecan Celero EZ DNA-Seq Library kit

value: brain

tag: age

value: 15 day old


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA and trpL_W18A_W20A 1

description: Library name: PA14_dmiaA_trpL_W18A_W20A_1

value: bacteria

value: planctonic growth in LB, OD600= 2


title: CONTR_NSC7


title: Coronal gyrus outer subventricular zone, 15 day old ferret brain_5

description: Library name: 10-19F21P15_Gyrus_OSVZ

value: Coronal gyrus outer subventricular zone


title: P102_19Sep

description: Library name: P102_19Sep

value: Blood

value: PBMCs

value: Black

tag: time

value: Primary_Day 7


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 trpL_W18A_W20A 1

description: Library name: PA14_wt_trpL_W18A_W20A_1


title: CONTR_NSC6

value: hiPSC differentiation


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 2

description: Library name: PA14_dmiaA_2

value: dmiaA


title: Adrenal gland (cortex),Lactation,Goat-2

description: Library name: AGC2

value: Adrenal gland (cortex)


title: P101_19Sep

description: Library name: P101_19Sep

value: NX


title: OE21 cells, RNA-Seq, STM9005, 1 day, rep1

description: Library name: OE21_STM9005_1d_rep1

value: Oesophageal carcinoma

value: STM9005 1 day


title: Suprasylvian sulcus outer subventricular zone, 15 day old ferret brain_4

description: Library name: 9-19F20P15_Sulcus_OSVZ


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 1

description: Library name: PA14_dmiaA_1


title: MIR155_NEURO5

value: Differentiated human Induced pluripotent stem cells

value: MIR155-overexpressing neurons


title: Coronal gyrus outer subventricular zone, 15 day old ferret brain_4

description: Library name: 9-19F20P15_Gyrus_OSVZ

value: brain


title: Ethiopian CL lesion; 4mm; P2

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

institute: Hull York Medical School, University of York

description:
Library name: PK_393_3_4-SCI5E156-AK34706
10x Visium for FFPE spatial transcriptomics

data_processing:
Raw sequencing data was used to generate FASTQ files using default settings.
Spatial 3' v1 chemistry using spaceranger-1.3.0 was used to align reads to GrCh38-2020-A genome using the Visium Human Transcriptome Probe Set to obtain gene expression matrices
Assembly: GRCh38-2020-A
Supplementary files format and content: _aligned_fiducials.jpg: Shows fiducials and spot co-localisation
Supplementary files format and content: _detected_tissue_image.jpg: Image showing spots over tissue section
Supplementary files format and content: .h5: Feature barcode matrices file in the HDF5 format
Supplementary files format and content: _scalefactors_json.json: Json file for scalefactors
Supplementary files format and content: _spatial_enrichment.csv: shows spatial enrichment of genes
Supplementary files format and content: _tissue_hires_image.png: tissue section image in high resolution
Supplementary files format and content: _tissue_lowres_image.png: tissue section image in low resolution
Supplementary files format and content: _tissue_positions_list.csv: spatial barcodes and their xy co-ordinates on tissue
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Frozen tissue blocks were sectioned at 10 μm thickness and initial sections from each sample was assessed for RNA quality (RNA Integrity Number, RIN; 2.2-8.7).  Due to low RIN values, we adapted the 10x Genomics Visium FFPE protocol for frozen sections
Manufacturer's instructions (10x Visium for FFPE) were followed to prepare sequencing libraries

value: Skin

value: Clinical infection


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14  trpL1_W10A_W20A and trpl2_W18A_W20A 2

description: Library name: PA14_wt_trpL1_W10A_W20A_trpl2_W18A_W20A_2

value: bacteria

value: trpL1_W10A_W20A and trpl2_W18A_W20A

value: planctonic growth in LB, OD600= 2


title: MIR155_NEURO4


title: Ethiopian non-lesional skin; 2mm; P2

description:
Library name: PK_393_3_2-SCI5E144-SCI5E232
10x Visium for FFPE spatial transcriptomics

value: non-lesional


title: OE21 cells, STM9005, 3 days, rep1

description: Library name: OE21_STM9005_3d_rep1

value: STM9005 3 days


title: Suprasylvian sulcus outer subventricular zone, 15 day old ferret brain_3

description: Library name: 8-19F19P15_Sulcus_OSVZ

value: 15 day old


title: Heart (left ventricle),Lactation,Goat-3

description: Library name: HLV3

value: Heart (left ventricle)


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 trpL1_W10A_W20A and trpl2_W18A_W20A 1

description: Library name: PA14_wt_trpL1_W10A_W20A_trpl2_W18A_W20A_1


title: Heart (left ventricle),Lactation,Goat-6

description: Library name: HLV6


title: MIR155_NEURO3

value: hiPSC differentiation


title: Ethiopian CL lesion; 4mm; P4

description:
Library name: PK_392_5_4-SCI5E157-SCI5E244
10x Visium for FFPE spatial transcriptomics


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 trpL1_W10A_W20A 2

description: Library name: PA14_wt_trpL1_W10A_W20A_2


title: CONTR_NEURO5

value: Control neurons


title: Suprasylvian sulcus outer subventricular zone, 15 day old ferret brain_2

description: Library name: 7-19F18P15_Sulcus_OSVZ


title: Coronal gyrus outer subventricular zone, 15 day old ferret brain_3

description: Library name: 8-19F19P15_Gyrus_OSVZ

value: Coronal gyrus outer subventricular zone


title: Ethiopian non-lesional skin; 2mm; P4

description:
Library name: PK_392_5_2-SCI5E145-SCI5E233
10x Visium for FFPE spatial transcriptomics


title: Heart (left ventricle),Dry,Goat-73

description: Library name: HLV73


title: CONTR_NEURO4


title: Coronal gyrus outer subventricular zone, 15 day old ferret brain_2

description: Library name: 7-19F18P15_Gyrus_OSVZ


title: Ethiopian CL lesion; 4mm; P1

description:
Library name: PK_392_1_4-SCI5E181-SCI5E268
10x Visium for FFPE spatial transcriptomics


title: OE21 cells, STM9005, 1 day, rep2

description: Library name: OE21_STM9005_1d_rep2

value: Oesophageal carcinoma


title: Hypothalamus,Dry,Goat-73

description: Library name: HYT73

source_name: Hypothalamus

value: Hypothalamus


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA and trpL1_W10A_W12A and trpL2_W18A_W20A 1

description: Library name: PA14_∆miaA_trpL1_W10A_W12A_trpL2_W18A_W20A_1


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 trpL1_W10A_W20A 1

description: Library name: PA14_wt_trpL1_W10A_W20A_1


title: Coronal gyrus outer subventricular zone, 15 day old ferret brain_1

description: Library name: 6-19F17P15_Gyrus_OSVZ


title: Ethiopian non-lesional skin; 2mm; P1

description:
Library name: PK_392_1_2-SCI5E169-SCI5E256
10x Visium for FFPE spatial transcriptomics


title: Suprasylvian sulcus outer subventricular zone, 15 day old ferret brain_1

description: Library name: 6-19F17P15_Sulcus_OSVZ


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA and trpL1_W10A_W12A and trpL2_W18A_W20A 2

description: Library name: PA14_∆miaA_trpL1_W10A_W12A_trpL2_W18A_W20A_2


title: Liver,Lactation,Goat-3

description: Library name: LI3

value: Liver


title: MIR155_NSC5

value: Differentiated human Induced pluripotent stem cells

value: MIR155-overexpressing NSCs


title: CONTR_NEURO3


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA and trpL1_W10A_W12A 2

description: Library name: PA14_∆miaA_trpL1_W10A_W12A_2

value: dmiaA and trpL1_W10A_W12A


title: MIR155_NSC4


title: Ethiopian CL lesion; 4mm; P5

description:
Library name: PK_391_7_4-SCI5E134-SCI5E221
10x Visium for FFPE spatial transcriptomics

value: Skin

value: Clinical infection


title: Suprasylvian sulcus outer subventricular zone, 5 day old ferret brain_5

description: Library name: 5-19F44P5_Sulcus_OSVZ

value: brain

value: 5 day old


title: Ethiopian non-lesional skin; 2mm; P5

description:
Library name: PK_391_7_2-SCI5E122-SCI5E209
10x Visium for FFPE spatial transcriptomics

value: non-lesional


title: RNA-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA and trpL1_W10A_W12A 1

description: Library name: PA14_∆miaA_trpL1_W10A_W12A_1

value: bacteria

value: planctonic growth in LB, OD600= 2


title: MIR155_NSC3


title: Ethiopian CL lesion; 4mm; P3

description:
Library name: PK_391_4_4-SCI5E110-SCI5E197
10x Visium for FFPE spatial transcriptomics


title: Ethiopian non-lesional skin; 2mm; P3

description:
Library name: PK_391_4_2-SCI5E098-SCI5E185
10x Visium for FFPE spatial transcriptomics


title: Suprasylvian sulcus outer subventricular zone, 5 day old ferret brain_4

description: Library name: 4-19F42P5_Sulcus_OSVZ


title: RNA-Seq control of Pseudomonas aeruginosa UCBPP-PA14 wild type 3

description: Library name: PA14WT_PL04_3_PA14

growth_protocol: Planktonic growth in LB medium at 37°C. Harvest at OD600 = 0.4 (exponential phase).

extract_protocol:
Ribo-Seq: RNA footprints were isolated from monosome fractions with Tri-Reagent (Zymo clean and concentrator). Total bacterial RNA from the same culture was extracted using the RNeasy Mini Kit from Qiagen. RNA-Seq: RNeasy Plus kit (Qiagen) in combination with QIAshredder columns (Qiagen) was used according to the manufacturer’s manual. Modifications:  Cell lysis was performed with 8 mg/mL lysozyme in Tris-EDTA-buffer (pH 8.0). RLT buffer with mecaptoethanol was added. Samples were frozen at -70°C for 60 min and then processed with QIAshredder columns. The remaining steps were performed according to the manufacturer's manual. After RNA elution, samples were treated with DNase (DNA-free Kit DNase Treatment & Removal, ambion).
Ribo-Seq: NEBNext Multiplex small RNA library prep for Illumina (E7300) using custom multiplex primers. RNA-Seq: RNA was fragmented (150–350 bp) by FastAP buffer (Thermo). End repair was performed with DNase (Thermo) and FastAP. Barcodes were ligated to each sample by T4 RNA ligase 1 (NEB). Samples were purified with the RNA Clean & Concentrator-25 Kit (Zymo). The RiboZero Bacteria Kit (Illumina) was used to remove ribosomal RNA. cDNA libraries were generated using SMARTscribe reverse transcriptase (Clonetech). Enrichment was done by AccuPrime HiFi Taq (Thermo) and all purification steps using RNAClean XP beads (Agencourt). Libraries were sequenced in paired-end mode on an Illumina Novaseq 6000 device (2 x 50 bp)

value: WT

value: planctonic growth in LB, OD600= 0.4


title: CONTR_NSC5

value: Control NSCs

value: hiPSC differentiation


title: MIR155_NEURO8

value: MIR155-overexpressing neurons


title: RNA-Seq control of Pseudomonas aeruginosa UCBPP-PA14 wild type 2

description: Library name: PA14WT_PL04_2_PA14


title: HT29 WT, TNF treated, 6h, replicate 3

description: Library name: HT29_T-6h-3

data_processing:
QC - fastQC
Adapter trimming - Trimmomatic
Alignment to ref genome - STAR
Quantification and raw counts matrix obtention - featureCounts
Assembly: hg28 GENCODE ref 39
Supplementary files format and content: Raw counts matrix

growth_protocol: Tumor cell lines were cultured in RPMI 1640 medium (Gibco) supplemented with 10%FBS (Sigma), 100U/ml penicillin, 100ug/ml streptomycin (Gibco), mouse cell lines were supplemented with 5x10-5 mol/L 2-mercaptoethanol (Gibco), and B16-OVA cell line was also supplemented with 400μg/mL of geneticin (Gibco). All tumor cell lines were maintained in a humidified incubator at 5% CO 2 and 37ᵒC for at least 7 days before being inoculated into mice. Mycoplasma contamination tests were routinely performed on all cell lines using the MycoAlert Mycoplasma Detection Kit (Lonza). To generate murine TNFR1 KO cell variants, each cell line was seeded at high cell density, one day prior to transfection with a customized vector from Genescript encoding a gRNA, Cas9, and GFP, using Lipofectamine 2000 (Thermo). gRNA was designed using several platforms (Benchling, Breaking-Cas, CHOP-CHOP, and Cas-Offinder), which predict the probability of on- and off-target gene editing. gRNA with the highest score across multiple platforms was selected. gRNA sequence is provided in supplementary figure 1. The gene-edited cells were sorted out twice using MoFlo Astrios EQ sorter (Beckman Coulter): first by GFP expression, and then by the absence of TNFR1 expression stained with anti-CD120a (Biolegend; 113003) to obtain several monoclonal TNFR1 KO cell lines. To analyse the tumour engraftment capability following TNFR1 silencing, C57BL/6, Rag1 -/- or Batf3 -/- [35] mice were subcutaneously injected on day 0 with 0.5x10 6 of wild-type or TNFR1 KO tumour cell lines suspended in 50μl of saline buffer.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen;74104) and sent for RNA-seq sequencing analysis to Macrogen (South Korea).
Done by Macrogen (South Korea)

treatment_protocol: For transcriptomic analyses, EO771 and HT29 tumor cell lines were collected at 6 and 24 hours after treatment with 1000 U/mL of TNFα.

value: TNF treated, 6h


title: CONTR_NSC4


title: P111_19Sep

description: Library name: P111_19Sep

value: Blood

value: PBMCs

value: AZ

value: Black

value: Primary_Day 7


title: Coronal gyrus outer subventricular zone, 5 day old ferret brain_5

description: Library name: 5-19F44P5_Gyrus_OSVZ

value: Coronal gyrus outer subventricular zone


title: HT29 WT, TNF treated, 6h, replicate 2

description: Library name: HT29_T-6h-2


title: Coronal gyrus outer subventricular zone, 5 day old ferret brain_4

description: Library name: 4-19F42P5_Gyrus_OSVZ

value: brain


title: RNA-Seq control of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 3

description: Library name: PA14miaA_PL04_3_PA14

value: dmiaA


title: P113_19Sep

description: Library name: P113_19Sep

value: Secondary_Day 1


title: RNA-Seq control of Pseudomonas aeruginosa UCBPP-PA14 wild type 1

description: Library name: PA14WT_PL04_1_PA14

value: bacteria


title: CONTR_NSC3

value: Differentiated human Induced pluripotent stem cells


title: Suprasylvian sulcus outer subventricular zone, 5 day old ferret brain_3

description: Library name: 3-19F40P5_Sulcus_OSVZ

value: 5 day old


title: MIR155_NEURO2


title: Coronal gyrus outer subventricular zone, 5 day old ferret brain_3

description: Library name: 3-19F40P5_Gyrus_OSVZ


title: RNA-Seq control of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 1

description: Library name: PA14miaA_PL04_1_PA14

value: planctonic growth in LB, OD600= 0.4


title: MIR155_NEURO1


title: HT29 WT, TNF treated, 24h, replicate 2

description: Library name: HT29_T-24h-3

value: WT

value: TNF treated, 24h


title: CONTR_NEURO2

value: Control neurons

value: hiPSC differentiation


title: HT29 WT, TNF treated, 6h, replicate 1

description: Library name: HT29_T-6h-1

value: TNF treated, 6h


title: Coronal gyrus outer subventricular zone, 5 day old ferret brain_2

description: Library name: 2-19F39P5_Gyrus_OSVZ


title: Ribo-Seq of Pseudomonas aeruginosa UCBPP-PA14 wild type 2

description: Library name: 2210_RiboSeq_PA14_PL04_2

data_processing:
cutadapt
bowtie2
featureCounts
Assembly: NC_008463.1
Supplementary files format and content: bed files - reads per gene (featureCounts)
Library strategy: Ribo-Seq


title: Suprasylvian sulcus outer subventricular zone, 5 day old ferret brain_2

description: Library name: 2-19F39P5_Sulcus_OSVZ


title: MIR155_NSC1

value: MIR155-overexpressing NSCs


title: CONTR_NEURO1


title: Coronal gyrus outer subventricular zone, 5 day old ferret brain_1

description:
Library name: 1-19F38P5_Gyrus_OSVZ
Column name in 'file name': "name"


title: HT29 WT, TNF treated, 24h, replicate 1

description: Library name: HT29_T-24h-2


title: ORv01, D49FNA

city: Minneapolis

first: Grace

last: Walker

state: Minnesota

address: 425 East River Parkway

department: Masonic Cancer Center

institute: University of Minnesota

description:
Library name: ORv01D49FNA
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated day 49 FNA biopsy

library_source: transcriptomic single cell

data_processing:
10x Genomics 3' GEX library FASTQs were processed with Cellranger v8.0.1 using the CanFam4 genome modified with the Y chromosome (ROS_Cfam_1.0 and NC_051844.1) and the mitochondrial genome taken from CanFam3.1. The decomposed counts matrix was processed downsteam in R v4.4.3.
Assembly: canFam4 genome + Y chromosome from ROS_Cfam_1.0 (NC_051844.1) + MT chromosome from canFam3.1
Supplementary files format and content: Archived and compressed (.tar.gz) cellranger folders containing decomposed count matrices per sample

organism: Canis lupus familiaris

source_name: Marginal zone lymphoma

growth_protocol: Longitudinal lymph node biopsies (including a pre-treatment Tru-Cut, fine-needle aspirates, and a nodal resection) were harvested prior to drug administration on treatment days. Samples were collected into cold RPMI 1640 media (Gibco, Cat. 21870-084) supplemented with 10% fetal bovine serum (FBS; SeraPrime, Cat. F31016-500), Primocin (InvivoGen, Cat. ant-pm-1), 2 mM L-glutamine (Quality Biological, Cat. QB-118-084-721EA), 2 mM sodium pyruvate (Gibco, Cat. 11360-070), 10 mM HEPES (Cat. 25-060-CI), 1% (v/v) MEM Non-Essential Amino Acids Solution (100x; Gibco, Cat. 11140-050), and 50 µM 2-mercaptoethanol (Sigma-Aldrich, Cat. M3148). Samples were immediately processed for single-cell suspension.

extract_protocol:
Lymph node biopsies were subjected to manual mechanical disaggregation by gentle mincing, followed by trituration using a wide-bore tip, and passage through a sterile 70-µm cell strainer into cold collection media. The resulting cell suspension was washed, passed through a 40-µm mesh filter to remove remaining debris and cell clumps, and resuspended in PBS containing 0.04% BSA. Cell concentration and viability were determined prior to single-cell capture. Single-cell suspensions were maintained at 4°C and transported on ice for cell concentration and viability assessment prior to same-day single-cell capture.
Single-cell sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3' GEX Reagent Kit according to the manufacturer's protocol. Single cells were partitioned into Gel Beads-in-emulsion (GEMs) for cell lysis and reverse transcription, followed by cDNA amplification and library construction (fragmentation, adapter ligation, and index PCR).

treatment_protocol: On the first day of the trial (day 0), the study dog received a single intravenous dose of 2 × 109 TCID50 / kg VSV. Stable disease was maintained for 28 days without further intervention. On day 30 the owners elected to withdraw from the trial to pursue conventional cytotoxic chemotherapy. A standard multi-agent CHOP protocol was initiated as follows: vincristine 0.63-0.7 mg/m2 (days 30, 44, 65, 79, 100, 114, 135, and 149), cyclophosphamide 250-270 mg/m2 (days 37, 72, 107, and 142), and doxorubicin 25-30 mg/m2 (days 51, 86, 121, and 156). A complete response per VCOG-RECIST criteria was achieved at day 100 of the study (70 days post-CHOP initiation), with a five-month duration of response. Following disease progression on day 243, the dog received palliative oral prednisolone at a dose of 1.1 mg/kg q24h, for another four months. The dog was euthanized due to declining quality of life, with 365 days total survival time from study screening.

value: Marginal zone lymphoma

tag: disease state

value: Tumor

tag: breed

value: Goldendoodle

tag: Sex

value: Male

tag: neuter status

value: Neutered

tag: age (yr)

value: VSV + CHOP

tag: biopsy type

value: Fine needle aspirate


title: HT29 WT, untreated, 6h, replicate 3

description: Library name: HT29_6h-4

tag: treatment

value: Untreated, 6h


title: Suprasylvian sulcus outer subventricular zone, 5 day old ferret brain_1

description: Library name: 1-19F38P5_Sulcus_OSVZ

value: brain


title: Ribo-Seq of Pseudomonas aeruginosa UCBPP-PA14 wild type 1

description: Library name: 2210_RiboSeq_PA14_PL04_1

value: bacteria

tag: genotype

tag: batch


title: Ribo-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 3

description: Library name: 2210_RiboSeq_PA14dmiaA_PL04_3

value: dmiaA

value: planctonic growth in LB, OD600= 0.4


title: MIR155_NSC2

value: Differentiated human Induced pluripotent stem cells


title: ATAC-seq using doxycycline-inducible NIH3T3 cell lines expressing 3xFlag-MORC1 WT, rep1

description: Library name: Morc1WT_1

value: fibroblast

value: TRE-3xFlag-MORC1 WT; rtTA

value: Doxycycline addition 100 ng/mL 48 h prior


title: Ribo-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 2

description: Library name: 2210_RiboSeq_PA14dmiaA_PL04_2


title: CONTR_NSC2

value: Control NSCs

value: hiPSC differentiation


title: HT29 WT, untreated, 24h, replicate 2

description: Library name: HT29_24h-2

value: WT

value: Untreated, 24h


title: ORv01, D10resect

description:
Library name: ORv01D10resect
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated day 10 tumor resection

value: Marginal zone lymphoma

value: Tumor

value: Goldendoodle

value: Male

value: VSV

value: Resection


title: EsANAC029-OE_25d_RNAseq_rep1

city: MianYang

first: Chanjuan

last: Wu

state: Si Chuan

address: No. 59, Middle Section of Qinglong Avenue, Fucheng District

institute: Southwest University of Science and Technology

description: Library name: Sample 4

data_processing:
Basecalling performed using Illumina Casava 1.8.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown in a growth chamber for 25 days, under a 16 h light/8 h dark photoperiod at 25°C.

extract_protocol:
Total RNA was extracted from 25-day-old Arabidopsis seedlings with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq X plus, paired-end 150bp).

value: seedlings


title: HT29 WT, untreated, 6h, replicate 1

description: Library name: HT29_6h-2

value: Untreated, 6h


title: ORv01, D28FNA

description:
Library name: ORv01D28FNA
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated day 28 FNA biopsy

value: Neutered

value: Fine needle aspirate


title: MIR155KO Clone 25 NSC-22

value: Differentiated human Induced pluripotent stem cells

value: MIR155KO Clone 25 NSC


title: ORv01, D7FNA

description:
Library name: ORv01D7FNA
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated day 7 FNA biopsy


title: HT29 WT, untreated, 24h, replicate 1

description: Library name: HT29_24h-1


title: MIR155KO Clone 25 NSC-21


title: ORv01, D10FNA

description:
Library name: ORv01D10FNA
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated day 10 FNA biopsy


title: EsANAC029-OE_25d_RNAseq_rep2

description: Library name: Sample 5


title: HT29 WT, untreated, 24h, replicate 3

description: Library name: HT29_24h-3


title: MIR155KO Clone 25 NSC-23


title: CONTR_NSC1


title: Col-0_25d_RNAseq_rep1

description: Library name: Sample 1

value: wild type


title: Col-0_25d_RNAseq_rep2

description: Library name: Sample 2


title: ORv01, PreTx

description:
Library name: ORv01PreTx_TruCut
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated Pretx TruCut lymph node biopsy

value: PreTx

value: TruCut


title: Control4, Visium

city: BETHESDA

first: Veronica

last: Gomez-Lobo

state: MD

address: 10 Central Dr. Bldg10, Rm 8N248

institute: NIH

description:
Library name: C1
ovary tissue from sarcoma patient

data_processing:
Raw sequencing files generated by Illumina sequencing were demultiplexed & processed using the Space Ranger default pipeline to obtain fastq files for each sample.
Alignment of reads (genome hg38), filtering and UMI counting was performed to obtain gene barcode matrix file (gene counts per nucleus) using Space Ranger software from 10x Genomics.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5 file : The "matrix.h5 file contains information about the features (genes) and cell-barcodes associated with the matrix rows and columns
Supplementary files format and content: scalefactors_json.json : scale factors in json format
Supplementary files format and content: tissue_positions.csv :  list of barcodes and coordinate specifying visium spots
Supplementary files format and content: tissue_hires_image.png : high-resolution images of the ovarian sections
Library strategy: Spatial Transcriptomics

source_name: Ovary

extract_protocol:
FFPE ovary sections (5 microns) were mounted onto a positively charged slide followed by staining with hematoxylin and eosin. Slides were mounted in 75% glycerol and brightfield images were taken using microscope.  The tissue sections were transferred immediately onto 6.5 × 6.5mm or 11mm x 11mm capture areas on a Visium gene expression slide using Visium CysAssist (10x Genomics). The tissue sections were then subjected to permeabilization followed by reverse transcription for cDNA synthesis. Subsequently, the cDNA amplification was performed, and spatial libraries were constructed. The libraries were pooled and paired-end sequencing was performed on SP flow cell using an Illumina NovaSeq 6000 platform.
Spatial transcriptome sequencing libraries from ovarian tissue were constructed using 10x Genomics Visium spatial gene expression slide & reagent kit

value: Ovary


title: Control6, Visium

description:
Library name: C5
ovary tissue from Medullablastoma patient


title: X31_TCR

city: Salt Lake City

first: Tracey

last: Lamb

address: 15 N Medical Drive

department: Pathology

institute: University of Utah

description: Library name: X31_TCR

data_processing:
10x Genomics Cell Ranger 9.0.1 software
Assembly: GRCm39
Supplementary files format and content: Cell ranger output .tsv and .mtx files
Supplementary files format and content: TCR data output in .csv
Library strategy: TCR-Seq

extract_protocol:
Lungs were minced (Miltenyi gentleMACS program m_lung_01) then subject to a 30 minute enzymatic digestion (37°C, 5 mL iRPMI, 2.5 mg Collagenase D, 2000 U DNase I) prior to mechanical homogenization (Miltenyi gentleMACS program m_lung_02). Cells underwent a 3-minute RBC lysis prior to resuspension in MACS buffer (D-PBS, 0.5% BSA, 2 mM EDTA) then filtered through a 100-micron cell strainer. T cells were isolated via Miltenyi Biotec's Pan T Cell Isolation Kit II, mouse (CAT 130-095-130) according to manufacturer instructions and resuspended in MACS buffer.
10x Genomics 5' standard library protocol for Gene expression and TCR

treatment_protocol: Plasmodium infections were performed by injecting 5x10^5 parasitized red blood cells (pRBCs) of PbE intraperitoneally (200 μL). Injection of 200 μL Krebs-Ringer solution was performed in control mice. Influenza infections were performed by administering 3x10^4 plaque-forming units (PFU) intranasally (40 μL) under anesthesia. 1X PBS was administered in control mice. Mice were administered one or both infections at day 0 (PbE+X31, PbE+PBS, Krebs+X31).

value: Lung

value: T Cells

tag: strain


title: MIR155KO Clone 25 NSC-13

value: hiPSC differentiation


title: Mtb 2x MIC Corramycin rep 3, 24 h

city: Saarbrücken

first: Franziska

last: Fries

state: Saarland

address: Campus E8 1

department: Microbial Natural Products

institute: Helmholtz Institute for Pharmaceutical Research Saarland

description:
Library name: Sample 47
Forward and reverse reads are denoted by R1 and R2.

data_processing:
Raw sequencing data was analyzed using Geneious Prime (version 2023.1.1). Reads were mapped to the reference sequence (NCBI NZ_CP009072.1 and NC_000962.3) and mRNA abundances were quantified as transcripts per million (TPM) prior to differential gene expression analysis with DESeq2.
Assembly: NCBI NZ_CP009072.1 (E. coli ATCC25922), NCBI NC_000962.3 (Mtb H37Rv)
Supplementary files format and content: csv files include raw transcript counts and normalized counts RPKM, TPM
Supplementary files format and content: xlsx files contain differential expression tables for the different samples, organized by organism (each with different sheets for the different conditions).

organism: Mycobacterium tuberculosis

growth_protocol: E. coli ATCC25922 was grown overnight in cation-adjusted Mueller-Hinton broth (MHB2) at 37 °C with shaking. The next morning, the culture was sub-cultured 1:100 in fresh MHB2 and grown until log-phase, after which the culture was adjusted to an OD600 of 0.5. M. tuberculosis H37Ra was grown in Middlebrook 7H9 medium supplemented with 10% OADC until log-phase was reached. Single cells were prepared by syringing and the culture was adjusted to an OD600 of 0.5.

extract_protocol:
For E. coli, 500 µL of samples were centrifuged at 5,000 g, RT, 10 min. The supernatant was removed and pellets were dissolved in TE buffer (100 mM Tris, 1 mM EDTA, pH 8.0) containing 15 mg/mL lysozyme and 20 µL of proteinase K (Qiagen). Samples were mechanically disrupted with acid-washed glass beads (one spatula tip of sizes 150-212 µm, 212-300 µm and 425-600 µm, respectively) using the TissueLyser II (Qiagen) at a frequency of 1/s for 5 min. 700 µL QIAzol lysis reagent (Qiagen) were added and samples were disrupted for another two cycles with the TissueLyser II. Subsequently, total RNA was extracted using the RNeasy mini kit (Qiagen). For Mtb, 7 mL of samples were drawn and total RNA was extracted following a protocol consisting of mechanical disruption with the FastPrep machine (MP Biomedicals, Irvine, CA, USA) and extraction using the RNeasy mini kit (Qiagen).
Library preparation was performed using NEBNext Ultra II Directional RNA Library Preparation Kit.

treatment_protocol: For E. coli, bacteria were treated with 0.125x, 0.25x or 0.5x MIC of corramycin, or DMSO (control) for either 15 min or 45 min. Each condition was performed in triplicates. For M. tuberculosis, bacteria were exposed to 0.5x, 1x or 2x MIC of corramycin, or DMSO (control) for either 6 h or 24 h. Each condition was performed in triplicates.

value: bacterial strain


title: Control5, Visium

description:
Library name: C2
ovary tissue from Medullablastoma patient


title: CG5, Visium

description:
Library name: CG5
ovary tissue from CG patient


title: MIR155KO Clone 25 NSC-11


title: MIR155KO Clone 5 NSC-23

value: MIR155KO Clone 5 NSC


title: Mtb 2x MIC Corramycin rep 2, 24 h

description:
Library name: Sample 46
Forward and reverse reads are denoted by R1 and R2.


title: PbE_TCR

description: Library name: PbE_TCR

value: PbE


title: HT29 WT, TNF treated, 24h, replicate 3

description: Library name: HT29_T-24h-4

value: WT

value: TNF treated, 24h


title: CG4, Visium

description:
Library name: CG4
ovary tissue from CG patient


title: PbE_X31_TCR

description: Library name: PbE_X31_TCR


title: Mtb 2x MIC Corramycin rep 1, 24 h

description:
Library name: Sample 45
Forward and reverse reads are denoted by R1 and R2.


title: CG3, Visium

description:
Library name: CG3
ovary tissue from CG patient


title: X31

description: Library name: X31_GEX

data_processing:
10x Genomics Cell Ranger 9.0.1 software
Assembly: GRCm39
Supplementary files format and content: Cell ranger output .tsv and .mtx files
Supplementary files format and content: TCR data output in .csv


title: Mtb 1x MIC Corramycin rep 3, 24 h

description:
Library name: Sample 44
Forward and reverse reads are denoted by R1 and R2.


title: MIR155KO Clone 5 NSC-22


title: MDA-MB-231 cells, USP7

city: Chongqing

first: Tianshu

last: Yang

state: --- Select One ---

address: No. 83, Xinqiao Zhengjie, Shapingba District, Chongqing City

institute: Xinqiao Hospital

description: Library name: USP7

data_processing:
Basecells were performed using  NovoNGS CUT&Tag 2.0 high-sensitivity kit.
Assembly: hg38
Supplementary files format and content: bed
Library strategy: CUT&Tag

molecule: protein

extract_protocol:
For each CUT&Tag assay, approximately 10⁴ cells were prepared and processed according to the protocol provided with the NovoNGS CUT&Tag 2.0 high-sensitivity kit (Novoprotein, China). Whole genome DNA sequencing was conducted by Sangon Corporation, Beijing.
Library were constructed by using  NovoNGS CUT&Tag 2.0 high-sensitivity kit.

value: Human breast cancer cells

value: cell line

value: scan data


title: MIR155KO Clone 5 NSC-21

value: Differentiated human Induced pluripotent stem cells


title: PbE

description: Library name: PbE_GEX


title: Mtb 1x MIC Corramycin rep 2, 24 h

description:
Library name: Sample 43
Forward and reverse reads are denoted by R1 and R2.


title: HT29 WT, untreated, 6h, replicate 2

description: Library name: HT29_6h-3

value: Untreated, 6h


title: Mtb 1x MIC Corramycin rep 1, 24 h

description:
Library name: Sample 42
Forward and reverse reads are denoted by R1 and R2.


title: PbE_X31

description: Library name: PbE_X31_GEX


title: MIR155KO Clone 5 NSC-13


title: HemSC,Vehicle treated, rep3, H3K27Ac CUT&Tag

first: Qian

last: Bian

address: Jinzun Road No.115

department: Shanghai Institute of Precision Medicine, Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Vehicle_H3K27Ac_rep3
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.

data_processing:
For RNA-seq analysis, sequencing data were mapped to reference (hg38) with STAR (version 2.7.3a). Mapped reads were processed with HTSeq and normalized with DESeq2. DEGs were identified under the threshold of adjusted P value <0.01 and |log2Foldchange| > 1.5. Volcano plot showing top DEGs was generated with R package ggplot2 (version 3.4.1). GO enrichment and GSEA analysis of DEGs was performed with the clusterProfiler (version 4.7.1.3) package in R. Cell type enrichment was performed with xCell based on FPKM values in SAHA and Vehicle-treated HemSCs.CUT&Tag analysis was performed as previously described (Zheng Y et al (2020). Protocol.io). After adaptor trimming with cutadapt (version), fastq files were mapped to reference genome (hG38) and spike-in genome (e.coli) with bowtie2. Duplicated reads were marked and removed for mapped reads. Scaling factor of each sample was determined based on the fragments mapped to E.coli genome for spike-in normalization. Peak calling was performed with SEACR to identify top 1% regions based on spike-in normalized fragment counts. DiffBind (version 3.0) was applied to identify differential H3K27Ac peaks in SAHA and Vehicle groups at the genome-wide scale. Pearson correlation between H3K27Ac strength alterations and gene expression changes was performed in R.
Assembly: hg38
Supplementary files format and content: 1. For RNA-seq, processed data files include mapped counts (*.counts) genenrated by htseq-count. 2. For CUT&Tag, processed data files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.
Library strategy: CUT&Tag

source_name: Infantile hemangioma

growth_protocol: HemSCs isolated from proliferating IH specimens in our previous study were cultured in Endothelial Cell Growth Medium-2 (EGM-2, Lonza, Cat #CC-3162) supplemented with 20% FBS (Gibco).

extract_protocol:
1. For RNA-seq, total RNA was extracted with FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme, Cat #RC112-01). 2. For CUT&Tag, genomic DNA was extracted with DNA extractiong beads as supplied in Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat #TD903)  kit.
1. After passing quality controls for RNA integrity and confirming the absence of RNA degradation and contaminations, RNA-seq libraries were generated by Annoroad (Beijing, China) with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, Cat #NR604-01/02) following the manufacturer’s protocols. RNA-seq libraries from three biological replicates of each group were sequenced on an Illumina NovaSeq 6000 platform at PE150 mode. 2. CUT&Tag was performed as previously described using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, Cat #TD903) with spike-in modifications. In brief, 50,000 cells were harvested, washed with PBS and incubated with activated Concanavalin A-coated beads at room temperature for 10 min, followed by overnight incubation with primary antibody (H3K27Ac, Abcam, Cat #ab4729, 1:50 dilution) at 4°C. Samples were then incubated with the secondary antibody for 1 hr at room temperature, washed twice with Dig-wash buffer, and incubated with pA/G Tn5 at a final concentration of 0.04 μM for 1 hr at room temperature. Tagmentation was then performed at 37°C for 1 hr. For spike-in calibration, control DNA template (Hyperactive DNA Spike-in Control for CUT&Tag, Vazyme, Cat #NS101-01) was added during DNA extraction of each sample at the concentration of 0.5 pg/50,000 cells. PCR amplification and purification was performed for sequencing on Illumina platform.

treatment_protocol: RNA-seq and H3K27Ac CUT&Tag libraries were constructed in HemSCs treated with 1 μM SAHA or Vehicle control (0.1% DMSO) for 16 hr

value: Infantile hemangioma

value: Hemangioma stem cell

value: Antibody:H3K27Ac, Abcam, Cat #ab4729, 1:50 dilution

value: Vehicle treated


title: MIR155KO Clone 5 NSC-12


title: MIR155KO Clone 5 NSC-11


title: Ribo-Seq of Pseudomonas aeruginosa UCBPP-PA14 dmiaA 1

description: Library name: 2210_RiboSeq_PA14dmiaA_PL04_1

value: bacteria

value: dmiaA

value: planctonic growth in LB, OD600= 0.4


title: ko3

city: Suzhou

first: Rongchuan

last: Zhao

address: Keling road 88

institute: Suzhou Institute of Biomedical Engineering and Technology

description:
Library name: ko3
knockdown group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene count and FPKM value for each Sample

source_name: tumor tissue

extract_protocol:
RNA was extracted from tumor tissue using TRIzol reagent. Briefly, tumor tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: tumor tissue

value: knockdown


title: HemSC,Vehicle treated, rep2, H3K27Ac CUT&Tag

city: Shanghai

description:
Library name: Vehicle_H3K27Ac_rep2
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.


title: Mtb 0.5x MIC Corramycin rep 2, 24 h

description:
Library name: Sample 40
Forward and reverse reads are denoted by R1 and R2.

value: bacterial strain


title: EsANAC029-OE_25d_RNAseq_rep3

description: Library name: Sample 6

value: seedlings


title: HemSC,SAHA treated, rep3, H3K27Ac CUT&Tag

description:
Library name: SAHA_H3K27Ac_rep3
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.

value: SAHA treated


title: ko2

description:
Library name: ko2
knockdown group, replicate biosample 2


title: HemSC,Vehicle treated, rep1, H3K27Ac CUT&Tag

description:
Library name: Vehicle_H3K27Ac_rep1
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.


title: ko1

description:
Library name: ko1
knockdown group, replicate biosample 1


title: Wild type NSC-22

value: Wild type NSC

value: hiPSC differentiation


title: HemSC,SAHA treated, rep2, H3K27Ac CUT&Tag

description:
Library name: SAHA_H3K27Ac_rep2
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.


title: Mtb 0.5x MIC Corramycin rep 1, 24 h

description:
Library name: Sample 39
Forward and reverse reads are denoted by R1 and R2.


title: Mtb control rep 3, 24 h

description:
Library name: Sample 38
Forward and reverse reads are denoted by R1 and R2.


title: Mtb control rep 2, 24 h

description:
Library name: Sample 37
Forward and reverse reads are denoted by R1 and R2.


title: Col-0_25d_RNAseq_rep3

description: Library name: Sample 3

value: wild type


title: wt3

description:
Library name: wt3
wt group, replicate biosample 3

value: wt


title: Wild type NSC-23

value: Differentiated human Induced pluripotent stem cells


title: Wild type NSC-21


title: HemSC,SAHA treated, rep1, H3K27Ac CUT&Tag

description:
Library name: SAHA_H3K27Ac_rep1
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.

value: Infantile hemangioma


title: Wild type NSC-13


title: wt2

description:
Library name: wt2
wt group, replicate biosample 2


title: HemSC,Vehicle treated, rep3, RNA-seq

description:
Library name: Vehicle_RNA_seq_rep3
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.

data_processing:
For RNA-seq analysis, sequencing data were mapped to reference (hg38) with STAR (version 2.7.3a). Mapped reads were processed with HTSeq and normalized with DESeq2. DEGs were identified under the threshold of adjusted P value <0.01 and |log2Foldchange| > 1.5. Volcano plot showing top DEGs was generated with R package ggplot2 (version 3.4.1). GO enrichment and GSEA analysis of DEGs was performed with the clusterProfiler (version 4.7.1.3) package in R. Cell type enrichment was performed with xCell based on FPKM values in SAHA and Vehicle-treated HemSCs.CUT&Tag analysis was performed as previously described (Zheng Y et al (2020). Protocol.io). After adaptor trimming with cutadapt (version), fastq files were mapped to reference genome (hG38) and spike-in genome (e.coli) with bowtie2. Duplicated reads were marked and removed for mapped reads. Scaling factor of each sample was determined based on the fragments mapped to E.coli genome for spike-in normalization. Peak calling was performed with SEACR to identify top 1% regions based on spike-in normalized fragment counts. DiffBind (version 3.0) was applied to identify differential H3K27Ac peaks in SAHA and Vehicle groups at the genome-wide scale. Pearson correlation between H3K27Ac strength alterations and gene expression changes was performed in R.
Assembly: hg38
Supplementary files format and content: 1. For RNA-seq, processed data files include mapped counts (*.counts) genenrated by htseq-count. 2. For CUT&Tag, processed data files include bigwig (*.bw) files normalized with spike-in control and peak (*.bed) files generated by SEACR.

value: Hemangioma stem cell

value: WT


title: Mtb 0.5x MIC Corramycin rep 3, 24 h

description:
Library name: Sample 41
Forward and reverse reads are denoted by R1 and R2.


title: Mtb control rep 1, 24 h

description:
Library name: Sample 36
Forward and reverse reads are denoted by R1 and R2.


title: wt1

description:
Library name: wt1
wt group, replicate biosample 1


title: Wild type NSC-12


title: HemSC,Vehicle treated, rep2, RNA-seq

description:
Library name: Vehicle_RNA_seq_rep2
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.

value: Vehicle treated


title: Mtb 2x MIC Corramycin rep 3, 6 h

description:
Library name: Sample 35
Forward and reverse reads are denoted by R1 and R2.


title: ORv01, D3FNA

description:
Library name: ORv01D3
NEXT GEM Single Cell 3’ Gene Expression of mechanically dissociated day 3 FNA biopsy

value: Marginal zone lymphoma

value: Tumor

value: Goldendoodle

value: Male

value: Neutered

value: VSV

value: Fine needle aspirate


title: X740_Irrad_F

city: Charlottesville

first: Anita

last: Salamon

state: VA

address: 415 Lane Road

department: Robert M. Berne Cardiovascular Research Center

institute: University of Virginia

description:
Library name: X740
10x Genomics

data_processing:
Fastq files were aligned to a custom reference mouse genome (GRCm39) with the tdTomato and ZsGreen reporter gene sequences using Cell Ranger pipeline v9.0.1.
Filtered gene–barcode matrices were imported to R v4.4.3 utilizing Seurat package v5.3.0.
Filtering: Cells were retained for analysis only if they checked more than 200 and fewer than 5,000 detected genes and displayed mitochondrial transcript levels below 10%.
Assembly: mouse genome (GRCm39) with the reporter gene tdTomato and ZsGreen
Supplementary files format and content: The filtered_feature_bc_matrix.h5 files are outputs from the 10x Genomics Cell Ranger count pipeline.

source_name: BCA

growth_protocol: Mice (SMC-EC dual Apoe-/-) were housed under standard conditions. At 9 weeks of age, mice were placed on antibiotic drinking water (sulfamethoxazole/trimethoprim) for 6 weeks. Following this 6-week period, mice were placed on a Western diet (Inotiv, TD.88137) ad libitum for 18-20 weeks to induce advanced atherosclerosis.

extract_protocol:
BCA regions were harvested, minced, and dissociated using 4 U/mL Liberase  and 0.744 U/mL Elastase for 60 min at 37°C.  Individual samples were pooled and stained for viability with Fixable Viability Dye eFluor™ 780. Live cells were sorted (BD Influx™ Cell Sorter), counted (DeNovix Celldrop™) and submitted directly for library preparation.
Library construction was performed at the Genome Analysis and Technology Core at the University of Virginia, in accordance with the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1, 10x Genomics).

treatment_protocol: Irradiated group: Received lethal irradiation (two 600 cGy doses, 3 hours apart) using a cesium-137 irradiator. Bone marrow (BM) was reconstituted 30–60 minutes post-irradiation with >1 × 106 unfractionated BM cells via tail vein injection. BM was harvested from the femur and tibia from CD45.1 Apoe-/-  donor mice aged 4 to 8 weeks. Control group: Received no irradiation and sterile saline tail vein injection in lieu of donor bone marrow to parallel the experimental cohort.

value: BCA

value: female

value: Irradiated

tag: time on_wd

value: 18 weeks


title: MIR155KO Clone 25 NSC-12

data_processing:
Paired-end RNA sequencing FASTQ files for all samples were aligned to Homo sapiens Reference genome (Grch38) using STAR read aligner and mapped reads were summarized to gene counts using subread function of FeatureCounts. Genes with expression (< 1 FPKM) across all samples were filtered from all subsequent analysis. Hierarchical clustering and Principal component analysis (PCA) were preformed as part of quality control to visualize biological variance between replicates, which were further exhibited by Volcano plots and Venn diagrams. We then performed differential gene expression analysis to compare all cell types with each other on normalized counts with EdgeR. Multiple biological replicates were used for all comparative analysis. Differentially expressed genes (DEGs) were identified at a false discovery rate (FDR) of 0.05. To identify biological pathways that may be differentially dysregulated by MIR155KO or MIR155 overexpression, we performed gene set enrichment analysis (GSEA) on the identified DEGs by using Enrichr, GSEA-MSIGDB and IPA (Ingenuity Pathways Analysis), where we identified enriched biological pathways, gene ontology sets, and mRNA targets of miRNA at an adjusted p-value < 0.05.
Assembly: Homo sapiens Reference genome (Grch38)

value: MIR155KO Clone 25 NSC

value: hiPSC differentiation


title: HemSC,Vehicle treated, rep1, RNA-seq

description:
Library name: Vehicle_RNA_seq_rep1
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.

tag: tissue

value: Infantile hemangioma


title: Mtb 2x MIC Corramycin rep 2, 6 h

description:
Library name: Sample 34
Forward and reverse reads are denoted by R1 and R2.

tag: cell line

value: bacterial strain


title: MIR155KO Clone 25 neurons-23

tag: cell type

value: Differentiated human Induced pluripotent stem cells

value: MIR155KO Clone 25 neurons


title: Wild type NSC-11

value: Wild type NSC


title: HemSC,SAHA treated, rep3, RNA-seq

description:
Library name: SAHA_RNA_seq_rep3
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.

value: Hemangioma stem cell

value: WT

value: SAHA treated


title: Mtb 2x MIC Corramycin rep 1, 6 h

description:
Library name: Sample 33
Forward and reverse reads are denoted by R1 and R2.


title: X738_Sham_F

description:
Library name: X738
10x Genomics

value: Control


title: HemSC,SAHA treated, rep2, RNA-seq

description:
Library name: SAHA_RNA_seq_rep2
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.


title: MIR155KO Clone 25 neurons-22


title: BETHip3

city: Taiyuan

first: Yuan

last: Fu

state: Shanxi

address: No. 56, Xinjian South Road, Yingze District

department: Department of Biochemistry and Molecular Biology, School of Basic Medicine

institute: Shanxi Medical University

description: Library name: Sample 9

data_processing:
RNA was extracted according to the manufacturer's instructions, and RNA integrity was checked using an Agilent 2100 Bioanalyzer.
Libraries were constructed using an Illumina NovaSeq X Plus, and 150 bp paired-end reads were generated on the platform.
Fastp (version 0.19.7) was used for quality control. Clean reads for subsequent analysis were obtained after raw data filtering, sequencing error rate check, and GC content distribution check. Clean reads were aligned with the reference genome using HISAT2 (v2.1.0) under default parameters to obtain the positioning information of reads on the reference genome.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hippocampus

growth_protocol: C57BL/6 male mice (6-8 weeks old) were purchased from the Experimental Animal Center of Shanxi Medical University. The mice were divided into three groups: (1) the Con group was fed a standard diet; (2) the HMD group was fed a high-methionine diet for 8 weeks; and (3) the Bet+HMD group was fed a high-methionine diet for 8 weeks, after which betaine (2.5% w/v) was supplemented in the drinking water (for 2 weeks).

extract_protocol:
The hippocampus of the three groups were isolated after being euthanized by cervical dislocation.
RNA libraries for RNA-seq were prepared using Agilent 2100 RNA Nano 6000 Assay Kit following manufacturer's protocols and the NanoPhotometer® spectrophotometer following  the purity of the samples.

treatment_protocol: Two mice per cage were housed at a stable temperature (24±2℃), with 12h/12h light/dark time alternation, and constant humidity. Free food and drinks available at all times.

value: hippocampus

value: High methionine feeding combined with betaine supplementation


title: Mtb 1x MIC Corramycin rep 3, 6 h

description:
Library name: Sample 32
Forward and reverse reads are denoted by R1 and R2.


title: BETHip2

description: Library name: Sample 8


title: HemSC,SAHA treated, rep1, RNA-seq

description:
Library name: SAHA_RNA_seq_rep1
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.


title: BETHip1

description: Library name: Sample 7


title: MIR155KO Clone 25 neurons-21


title: MIR155KO Clone 25 neurons-13


title: Mtb 1x MIC Corramycin rep 2, 6 h

description:
Library name: Sample 31
Forward and reverse reads are denoted by R1 and R2.


title: Mtb 1x MIC Corramycin rep 1, 6 h

description:
Library name: Sample 30
Forward and reverse reads are denoted by R1 and R2.


title: PMN_IfnarKO_3

city: St Louis

first: Shuying

last: Xu

state: MO

address: 425 South Euclid Ave

institute: Washington University in St. Louis

description: Library name: 2.9_1_PMN_IFNARKO

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Differential expression analysis was performed in R version 4.5.1 using DESeq2 BioC 3.22 Version 1.50.2 to analyze differences between conditions, and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: mm10
Supplementary files format and content: Tab separated file for raw counts at gene level for all samples

source_name: Primary mouse neutrophils

extract_protocol:
RNA samples were collected using Trizol Reagent (Invitrogen), followed by extraction using chloroform. RNA was isolated as per the manufacturer’s instruction using Direct-zol RNA Miniprep Plus kit (Zymo Research).
RNA was fragmented in reverse transcriptase buffer while ribosomal RNA was blocked using FastSelect reagents (Qiagen), and mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies), indexed, pooled, and sequenced on an Illumina NovaSeq X Plus (Illumina, USA) using paired end reads extending 150 bases.

treatment_protocol: Naïve or Mycobacterium tuberulosis infection

value: Primary mouse neutrophils

value: Ifnar-/-

value: Mycobacterium tuberulosis infection


title: HemSC,untreated, rep2, RNA-seq

description:
Library name: HemSC_RNA_seq_rep2
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.

value: untreated


title: HemSC,untreated, rep3, RNA-seq

description:
Library name: HemSC_RNA_seq_rep3
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.


title: MIR155KO Clone 25 neurons-12

extract_protocol:
RNA isolation was performed on the lysates of WT, MIR155KO Clone 5 and MIR155KO Clone 25 hiPSC-derived cells, and MIR155-overexpressing NSCs and cortical neurons, according to the manufacturer’s protocol (miRNeasy mini-kit, Qiagen). Isolated RNA samples were submitted to Novogene Corporation Inc. for analysis of RNA quality and integrity.
All samples passed quality control, and RNA-seq libraries were prepared for sequencing using NovaSeq


title: PMN_IfnarKO_2

description: Library name: 2.6_1_PMN_IFNARKO


title: HemSC,untreated, rep1, RNA-seq

description:
Library name: HemSC_RNA_seq_rep1
Raw files include pair-ended zipped fastq files (*.fq.gz), processed files include counts (*.counts) files generated by htseq-count.


title: MIR155KO Clone 25 neurons-11


title: Mtb 0.5x MIC Corramycin rep 1, 6 h

description:
Library name: Sample 28
Forward and reverse reads are denoted by R1 and R2.


title: PMN_IfnarKO_1

description: Library name: 2.5_1_PMN_IFNARKO


title: Mtb 0.5x MIC Corramycin rep 2, 6 h

description:
Library name: Sample 29
Forward and reverse reads are denoted by R1 and R2.


title: MIR155KO Clone 5 neurons-22

value: MIR155KO Clone 5 neurons


title: Mtb control rep 3, 6 h

description:
Library name: Sample 27
Forward and reverse reads are denoted by R1 and R2.


title: U937 cells+DMSO_rep3

city: guiyang

first: 李

middle: 瑞

last: 引

address: Guiyang City, Guizhou Province

institute: 贵州医科大学

description: Library name: NC_3

data_processing:
Sequence was trimmed using Fastp v0.20 to remove adaptor and low quality reads
Hisat2 2.0.4 mapping to reference genome.
Count counting.
Assembly: GRCh_38
Supplementary files format and content: Supplementary files format and content: gene_count_matrix.txt: Tab-delimited text file contains counts for each sample.

source_name: Homo sapiens

growth_protocol: 1640,10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Total RNA was isolated and purified from cultured cells using TRIzol reagent following the manufacturer's procedure.
cDNA

treatment_protocol: U937 cells were cultured in RPMI-1640 medium without serum. For the experimental group, cells were treated with 1 µM B2 for 36 hours. The control group was treated with an equal concentration of DMSO for 36 hours. Following treatment, cells were harvested for subsequent analyses.

value: Homo sapiens

value: Acute myeloid leukemia


title: PMN_WT_3

description: Library name: 1.6_1_PMN_WT

value: wildtype


title: MIR155KO Clone 5 neurons-21

value: Differentiated human Induced pluripotent stem cells

value: hiPSC differentiation


title: PMN_WT_2

description: Library name: 1.5_1_PMN_WT


title: Mtb control rep 2, 6 h

description:
Library name: Sample 26
Forward and reverse reads are denoted by R1 and R2.

value: bacterial strain


title: U937 cells+DMSO_rep2

description: Library name: NC_2


title: U937 cells+DMSO_rep1

description: Library name: NC_1


title: MIR155KO Clone 5 neurons-13


title: Mtb control rep 1, 6 h

description:
Library name: Sample 25
Forward and reverse reads are denoted by R1 and R2.


title: PMN_WT_1

description: Library name: 1.2_1_PMN_WT


title: MIR155KO Clone 5 neurons-12


title: U937 cells+B2_rep3

description: Library name: B2_3


title: Male_C26-Cisplatin_8

city: Fayetteville

first: Ana

middle: Regina

last: Cabrera

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

description: Library name: 75

data_processing:
Raw sequencing reads were assessed for quality using the software FastQC and summarized using MultiQC.
Adapter sequences and low-quality bases (Phred score < 25) were removed using fastp. Reads shorter than 20 bp after trimming were discarded.
Transcript abundances were quantified using the mapping-based mode of Salmon.
Transcript-level estimates were imported into R using the tximport package to summarize expression at the gene level.
Raw counts were processed using edgeR. Counts per million (CPM) were calculated and lowly expressed genes were filtered based on CPM thresholds. Data were normalized using trimmed mean of M-values (TMM) and differential gene expression analysis was performed using limma with the voom transformation. Genes with an adjusted p-value (FDR) < 0.05 were considered significantly differentially expressed.
Assembly: Mus musculus genome assembly mm39 (GRCm39).
Supplementary files format and content: Processed data files include normalized gene expression per sample

source_name: Gastrocnemius

extract_protocol:
TRI-zol and PureLink RNA Mini Kit
Total RNA was extracted from gastrocnemius muscle and RNA libraries were prepared by the Clinical Genomics Center at the Oklahoma Medical Research Foundation (OMRF, USA). Libraries were constructed for Illumina sequencing and sequenced using 150-bp paired-end reads to a depth of approximately 20 million reads per sample on an Illumina platform.

value: Gastrocnemius

value: Male

tag: cancer

tag: chemotherapy

value: Cisplatin


title: MIR155KO Clone 5 neurons-11

city: New York

first: Michelle E.

last: Ehrlich

address: 1 Gustave L. Levy Pl, New York, NY 10029

institute: Icahn School of Medicine at Mount Sinai


title: U937 cells+B2_rep2

description: Library name: B2_2

value: WT


title: APACT3

type: RNA

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

hyb_protocol: 15 µg of fragmented biotin-labeled cRNA was hybridized to Affymetrix Human Genome U13 Plus 2.0 Array

scan_protocol: standard Affymetrix protocol

data_processing: Raw data was normalized by the MAS5.0 algorithm and log2-transformed (log2(x+1))

label: biotin

label_protocol: total RNA was used to prepare biotin-labeled cRNA using the Affymetrix GeneChip Kit according to the manufacturer’s protocol

extract_protocol: RNA was isolated from the tumor tissue with the DNA/RNA AllPrep Mini Kit (Qiagen) according to the manufactors instruction

tag: dna methylation-based risk group

value: Low Risk 1

value: pediatric adrencocortical tumor


title: Male_C26-Cisplatin_7

description: Library name: 74


title: Wild type neurons-24

value: Wild type neurons


title: U937 cells+B2_rep1

description: Library name: B2_1


title: Wild type neurons-23


title: APACT28

value: High Risk


title: Male_C26-Cisplatin_6

description: Library name: 73