title: dek2_Treated_H12

city: Gif Sur Yvette

first: Xiaoning

last: HE

address: 630,Rue Noetzlin

country: France

institute: universite-paris-saclay

data_processing:
Reads were quality checked using FASTQC v0.11.5
Adapters and reads with low sequencing quality were filtered using Trimmomatic 0.36, retaining first 100 bps and by using other default settings for paired-end sequences
The trimmed reads were then aligned to the Arabidopsis reference genome (TAIR10) using Tophat v2.1.1
MultibamSummary from deepTools2 package was used on the bam files derived from the previous step, to check for the correlation between the replicates
Counts reads:Count how many reads map to genomic features with FeatureCounts with the command "featureCounts -F GTF -t exon -g gene_id -a annotation.gff -T 8 -M -O -s 2 -Q 30 -o Count_reads_to_gene.txt input.bam"
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Arabidopsis thaliana

source_name: 14 days old seedlings

growth_protocol: For growing A.thaliana under sterile conditions seeds were surface sterilized in a solution of bleach: ethanol: H2O (V:V:V::1:4:3) for 10 min and washed four times with sterile water. The seeds were then stratified by placing them at 4 °C for 48 h. Seedlings were grown on half strength MS plates. Plates were sealed with Micropore tape and placed on grid-like shelves in a plant growth chamber for 14 days at 21 °C with 75% relative humidity under 16 h of daylight.

extract_protocol:
50-100 mg of Arabidopsis plant leaves or 14 days old seedling grown on ½ MS plates were taken in 2 ml tubes containing 2 steel beads, frozen in liquid Nitrogen and homogenized 2X using a Tissue Lyser (Eppendorf) for 1 min at 20 Hz to obtain a fine powder.  NucleoSpin® Plant RNA kit (Macherey Nagel, 7740949) was used to extract the total RNA from the plant.
mRNA libraries were prepared using the illumina Truseq Stranded mRNA Sample Preparation LS (low sample) kit following the manufacturer’s protocol. Briefly, the mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads then purified, fragmented and primed. Subsequently, both first and second strands of cDNA were synthesized using SuperScript II reverse transcriptase, followed by adenylation on the 3’ ends and ligation of adapters. The DNA fragments with adapters were amplified by 15 PCR cycles. Finally, the libraries were validated using the 1000 DNA kit on 2100 Bioanalyzer (Agilent Technologies), quantified using qubit (Life Technologies) then barcoded libraries were normalized and pooled in equal volumes. Stranded mRNA libraries were sequenced on an Illumina Hiseq 4000 system using paired-end method. The length of the read was around 150 bp. The RNA-seq was done on three independent biological replicates.

treatment_protocol: 14 day old seedling grown as described above were spray inoculated with Pst DC3000 hrcC- strain at an OD of 0.2 at 600nm and harvested after 24h and frozen in liq N2 prior to RNA extraction.

value: 14 days old seedlings

value: Pst DC3000 hrcC- strain


title: HUH7_antiKDM6A_siHNF4A_rep1

status: Public on Feb 19 2026

type: SRA

city: HUDDINGE

first: Lin

last: Chen

address: Blickagången 16, Flemingsberg,Neo

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: Library name: HUH7_antiKDM6A_siHNF4A_rep1

library_source: genomic

data_processing:
Sequencing data was processed using standard pipelines. Sequencing files (fastq files) provided by NOVOGENE (Cambridge, United Kingdom) were aligned to the GRCh38/hg38 version of the human reference genome using Bowtie2. Duplicate reads were removed, and peaks were called using the HOMER package to identify regions of significant enrichment. SEACR is used to call peaks and enriched regions from chromatin profiling data. ChIPseqSpikeInFree is used to normalize Data.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: HROHep03 cells were maintained in high-glucose DMEM/F12 medium, supplemented with 5% FBS and 1% antibiotics. Cells were incubated at 37°C in an atmosphere of 5% CO2.

extract_protocol:
CUT&TAG sample preparation was performed following protocols from the Fred Hutchinson Cancer Research Center. Approximately 50,000 harvested and counted cells were resuspended in Wash Buffer and mixed with Concanavalin A-coated magnetic beads. The mixture was incubated at room temperature to allow binding. Bead-bound cells were then washed and incubated with a primary antibody(anti-KDM6A, invitrogen, PA5-31828, 1μg) specific to the target protein, followed by a secondary antibody for bridging. Next, the bead-bound cells were incubated with Protein A-Tn5 transposase in the presence of digitonin for tethering. After a brief incubation to allow the transposome to tether to chromatin sites targeted by antibodies, cells were washed and subjected to magnesium activation to induce tagmentation. This step facilitated DNA cleavage and simultaneous tagging with sequencing adapters. Following tagmentation, DNA was purified using SPRI beads and quantified using a fluorometric method.
Libraries were PCR-amplified with barcoded primers, cleaned up, and subjected to quality control checks, including size selection and quantification.

tag: cell line


title: HUH7_antiKDM6A_siluc_rep3

description: Library name: HUH7_antiKDM6A_siluc_rep3


title: 15454, glucose, Replicate 3

city: Philadelphia

first: Marni

middle: J

last: Falk

state: PA

address: 3401 Civic Center Blvd

country: USA

institute: Children's Hospital of Philadelphia

library_source: transcriptomic

data_processing:
Sequencing quality was checked with FastQC
Adapter and quality trimming was performed with Trim Galore!
Samples were aligned to hg38 using STAR
Transcripts were quantified using RSEM
Assembly: hg38
Supplementary files format and content: RSEM isoform count files

molecule: polyA RNA

growth_protocol: Cells were cultured in 100mm dishes with 5.6mM glucoseDMEM-10% FBS-0.2% (v/v) uridine at37℃ with 5% CO2 until about 80% confluency.

extract_protocol:
Twenty-four hours later, cells were washed with cold PBS twice, then cold 1mL TRIzol® reagent (Invitrogen #15596026) was added. Cells were scraped with cell lifter and homogenized by pipetting up and down several times.
RNA was purified with RNeasy Kits (Qiagen, Hilden Germany, #74004).
Libraries were constructed with the TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: Media was then replaced with 10ml of fresh DMEM-10% FBS with 5.6 mM glucose, 10mM galactose, or 10mM galactose plus drug (cycloheximide, metformin, ONC201 or ONC206).

tag: cell type

value: metastatic osteosarcoma lung biopsy, same individual as Q2148

tag: treatment

value: 5.6 mM glucose media


title: age-1(hx546); rde-4(ne301), young adults, smallRNA-Seq, biol rep 3

city: Boston

first: Alla

last: Grishok

address: 72 E Concord

institute: Boston University

description: Library name: A1R4_3

data_processing:
Trimmed reads containing adapter contamination, with more than 10% uncertain bases, or with >50% low-quality bases. Performed by Novogene Corporation using perl scripts.
The remaining analysis utilized R. QuasR version 1.34 was used to align to the genome with qAlign(maxHits = 50) and counting was performed with qCount(orientation = "opposite") to obtain antisense reads
Assembly: WBcel235 (NCBI, GCF_000002985.6_WBcel235_genomic.fa)
Supplementary files format and content: csv files containing raw read counts (2 strains per file) for small RNAs mapping antisense to genes

molecule: total RNA

organism: Caenorhabditis elegans

source_name: bulk

growth_protocol: Starved L1 worms were chunked onto solid NGM plates with E. coli OP50 food at 20 °C. Once reaching egg-laying adults, alkaline hypochlorite solution was applied to synchronize L1 progeny, which were allowed to grow to young adults (first day of adulthood, before embryos are visible).

extract_protocol:
Populations of young adults were collected and washed in M9 and added to Trizol Reagent (Invitrogen). Worms in Trizol were lysed by freeze-thawing from -80 °C to 4 °C three times. Total RNA was purified from the lysate using the miRNeasy kit (Qiagen) according to manufacturer instructions, including the optional Buffer RWT wash step.
Libraries with insertions between 18 - 40 bp were size selected. Illumina sequencing was performed with SE50. Library preparation and sequencing performed by Novogene Corporation.

tag: tissue

value: bulk

tag: genotype


title: dek2_Treated_H11


title: 15454, glucose, Replicate 2


title: dek2_Treated_H10


title: HUH7_antiKDM6A_siHNF4A_rep2

description: Library name: HUH7_antiKDM6A_siHNF4A_rep2


title: age-1(hx546); rde-4(ne301), young adults, smallRNA-Seq, biol rep 2

description: Library name: A1R4_2


title: HUH7_antiKDM6A_siluc_rep2

description: Library name: HUH7_antiKDM6A_siluc_rep2


title: dek2_mock_H9

value: Mock


title: dek2_mock_H8


title: age-1(hx546); rde-4(ne301), young adults, smallRNA-Seq, biol rep 1

description: Library name: A1R4_1


title: 15454, glucose, Replicate 1


title: 15454, galactose, Replicate 3

value: 10 mM galactose media


title: 15454, galactose, Replicate 2


title: dek2_mock_H7


title: age-1(hx546), young adults, smallRNA-Seq, biol rep 3

description: Library name: A1_3


title: age-1(hx546), young adults, smallRNA-Seq, biol rep 2

description: Library name: A1_2


title: PBMCs, GBS and control cells, multiplexed

city: Richardson

first: Jayden

last: O'Brien

state: TX

address: 800 W Campbell Rd

department: Neuroscience

institute: The University of Texas at Dallas

description: Library name: Sample 1

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed and aligned to the GRCh38 human genome reference using Cell Ranger v7 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Seurat .Rds file containing all normalized per-cell counts and clustering annotations

source_name: Peripheral blood mononuclear cells

extract_protocol:
Frozen cryovials containing 107 PBMCs/mL were thawed in a 37°C water bath for 2 minutes. Following thawing, 1 mL of pre-warmed RPMI 1640 medium (Gibco, 11875-093) supplemented with 10% HyClone™ Fetal Bovine Serum (Thermo Fisher Scientific, SH3008803IR) and 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063) was added to each vial. The cell suspension was transferred to a 15 mL conical tube, and the cryovials were rinsed with additional RPMI media to maximize PBMC recovery. To aid in cell dissociation, Accumax (Thermo Fisher Scientific, 00-4666-56) was added at a 1:1 ratio to the sample volume, and cells were incubated at room temperature for 5 minutes. Samples were centrifuged at 350g for 5 minutes at room temperature. The supernatant was aspirated, and the cell pellets were resuspended in 1 mL of RPMI media containing 100 µg/mL DNase I and incubated at 37°C for 15 minutes.
Cells were washed once with 1X PBS and centrifuged at 500g for 5 minutes. The resulting cell pellets were fixed at 4 °C for 17 hours using the Chromium Single Cell Fixed RNA Sample Preparation Kit (10x Genomics). Fixed cells were subsequently hybridized with probes using the Fixed RNA Feature Barcode Kit (10x Genomics), following the manufacturer’s protocol. Remaining library preparation steps were carried out according to the standard 10x Genomics workflow.

value: Peripheral blood mononuclear cells


title: Col-0_Treated_H6

value: WT


title: GBS1, CD8

description: Library name: 356-16_S16

data_processing:
Raw FASTQ files were quality-controlled using Phred scores, per-base sequence, and duplication levels with FastQC v0.11.0. Reads were soft-clipped (12 bases per read) to remove adapters and low-quality bases, then aligned and sorted using STAR v2.7.6 with the GRCh38 human reference genome (GENCODE release 38, primary assembly). Sambamba v0.8.2 was used for deduplication. Prior to quantification, ENCODE blacklist genes were discarded using bedtools (v2.30.0). Data were then passed through StringTie v2.2.1 to obtain normalized transcripts per million (TPM) count values for each gene. The Rsubread (v2.14.2) featureCounts function was used to calculate raw counts for all genes.
Assembly: GRCh38
Supplementary files format and content: csv files include nTPM values for each sample

source_name: CD8+ peripheral blood mononuclear cells

extract_protocol:
Frozen cryovials containing 107 PBMCs/mL were thawed in a 37°C water bath for 2 minutes. Following thawing, 1 mL of pre-warmed RPMI 1640 medium (Gibco, 11875-093) supplemented with 10% HyClone™ Fetal Bovine Serum (Thermo Fisher Scientific, SH3008803IR) and 1% penicillin-streptomycin (Thermo Fisher Scientific, 15070063) was added to each vial. The cell suspension was transferred to a 15 mL conical tube, and the cryovials were rinsed with additional RPMI media to maximize PBMC recovery. To aid in cell dissociation, Accumax (Thermo Fisher Scientific, 00-4666-56) was added at a 1:1 ratio to the sample volume, and cells were incubated at room temperature for 5 minutes. Samples were centrifuged at 350g for 5 minutes at room temperature. The supernatant was aspirated, and the cell pellets were resuspended in 1 mL of RPMI media containing 100 µg/mL DNase I and incubated at 37°C for 15 minutes. Cells were washed with 10 mL of flow cytometry staining buffer (Invitrogen, 00-4222-26) and centrifuged at 350g for 5 minutes at room temperature. Cells were resuspended in 1X phosphate-buffered saline (PBS) and prepped for fluorescently activated cells sorting (FACS). First, cells were incubated with a Zombie UV viability stain for 10 minutes at room temperature. Then, 1 mL of flow cytometry staining buffer was added to each tube, cells were centrifuged, resuspended in flow cytometry staining buffer and treated with a human Fc receptor blocker for 10 minutes at room temperature protected from light. The cells were then treated with primary antibodies targeting CD45, CD3, CD4, CD8, and CD11b for 30 minutes, on ice, protected from light. Cells were then washed again with 1 mL of flow cytometry staining buffer, centrifuged, and resuspended in flow buffer and preserved on ice until sorting. FACS was performed on a BD FACSAria Fusion at the University of Texas at Dallas. Cells were gated to collect CD4+, CD8+, and CD11b+ cells in flow cytometry staining buffer. Tubes containing sorted cells were returned to the laboratory, centrifuged, resuspended in 1 mL of Qiazol (Qiagen, 1023537), transferred to a 1.5mL Eppendorf tube, and proceeded to RNA extraction. Next, 200 µL of chloroform (Fisher Scientific, C298-500) was added to each tube, manually shaken for 15 seconds, and allowed to incubate at room temperature for 2 minutes. Tubes were then centrifuged at 12,000g for 10 minutes at 4°C. The supernatant was collected, placed in a new 1.5 mL tube, and 500 µL of isopropanol (Fisher Scientific, A416-1) and 3 µg of GlycoBlue™ (Thermo Fisher Scientific, AM9515) were added. To maximize RNA precipitation, tubes were incubated overnight at -20°C. The next day, the cells were centrifuged at 12,000g for 30 minutes at 4°C. The supernatant was aspirated, and the resultant RNA pellet was washed with 1 mL of 75% ethanol (Fisher Scientific, BP2818-500). The tube was centrifuged at 7,500g for 5 minutes at 4°C and the supernatant was removed. The resultant RNA pellet was air dried for 10 minutes at room temperature and eluted in 20 µL of RNase-free water on a heat block at 55°C for 10 minutes.
Sequencing was performed using a NextSeq2000 for single-end total RNA sequencing at the University of Texas at Dallas Genome Core Research Facility.

value: CD8+ peripheral blood mononuclear cells


title: age-1(hx546), young adults, smallRNA-Seq, biol rep 1

description: Library name: A1_1


title: HUH7_antiKDM6A_siluc_rep1

description: Library name: HUH7_antiKDM6A_siluc_rep1


title: HC1, CD8

description: Library name: 356-15_S15


title: rde-4(ne301), young adults, smallRNA-Seq, biol rep 3

description: Library name: R4_3


title: Col-0_Treated_H5


title: Col-0_Treated_H4


title: 15454, cycloheximide, Replicate 3

value: cycloheximide


title: 15454, cycloheximide, Replicate 1


title: 15454, galactose, Replicate 1


title: rde-4(ne301), young adults, smallRNA-Seq, biol rep 2

description: Library name: R4_2


title: 15454, cycloheximide, Replicate 2


title: Col-0_Mock_A3


title: 15454, metformin, Replicate 1

value: metformin


title: rde-4(ne301), young adults, smallRNA-Seq, biol rep 1

description: Library name: R4_1


title: 15454, ONC206, Replicate 3


title: Col-0_Mock_A2


title: GBS3, CD8

description: Library name: 356-14_S14


title: HC3, CD8

description: Library name: 356-12_S12


title: HC2, CD8

description: Library name: 356-13_S13


title: N2 WT, young adults, smallRNA-Seq, biol rep 2

description: Library name: WT_2


title: 15454, ONC206, Replicate 2


title: GBS4, CD4

description: Library name: 356-11_S11

source_name: CD4+ peripheral blood mononuclear cells

value: CD4+ peripheral blood mononuclear cells


title: BH4-13: MIA Female, brain monocyte cells

type: genomic

city: Wilmington

first: Elizabeth

last: Wright-Jin

state: Delaware

address: 200 Powder Mill Road

department: Neurology

institute: Nemours Children's Health

description: Data from MIA Treated mice

hyb_protocol: Bisulfite conversion by: Qiagen and Epitect Bisulfite Kit on DNA was amplified, fragmented to Mouse Infinium Methylation EPIC BeadChIP (Illumina

scan_protocol: Tecan LIHA 1, iScan. Data Analysis: Total number of samples processed: 12. Normalization with Controls, Subtract background.

data_processing: Processed with GenomeStudio 2011.1, Name of ANnotation File: MouseMethylation-12v1-0_A2.bpm.

label: Cy3, Cy5

organism: Mus musculus

source_name: Brain

label_protocol: Standard Illumina MicroArray Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (50).

treatment_protocol: Maternal immune activation: Timed pregnant dams were exposed to lipopolysaccharide (LPS). Briefly, dams were given 50 ug/kg LPS or 0.05 ml 0.9% saline via intraperitoneal injection at E18.5. Hypoxia exposure: Mice were subjected to deep global hypoxia. Briefly, mice were subjected to 8 minutes of progressive hypoxia from 21% to 0% oxygen or normoxia (21% oxygen). Cell dissociation: Whole brains were collected from male and female pups on P7 and dissociated into a single cell solution using the Adult Brain Dissociation Kit and gentleMACS Octo Dissociator (Miltenyi Biotec) according to the manufacturer protocol.    Monocyte isolation: Brain monocytes were enriched via magnetic CD11b-coated beads (Miltenyi Biotec) according to manufacturer protocol. Cell pellets were flash frozen and stored at -80°C until genomic DNA extraction.

value: Brain

tag: Sex

value: Female

value: Monocytes

value: Maternal Immune Activation


title: Col-0_Mock_H1

value: 14 days old seedlings


title: 15454, ONC206, Replicate 1


title: HC1, CD4

description: Library name: 356-9_S9


title: N2 WT, young adults, smallRNA-Seq, biol rep 3

description: Library name: WT_3


title: BH4-11: MIA Female, brain monocyte cells

description: Data from MIA Treated mice


title: 15454, ONC201, Replicate 3


title: BH4-5: MIA Male, brain monocyte cells

description: Data from MIA Treated mice

value: Male


title: GBS3, CD4

description: Library name: 356-8_S8


title: age-1(hx546); rde-4(ne301), young adults, RNA-Seq, biol rep 2

description: Library name: A1R4_2

data_processing:
Trimmed reads containing adapter, poly-N or with low quality from raw data with Novogene perl scripts.
Index of the reference genome was built using Hisat2 v2.0.5
(Stringtie- 1.3.3b) was used to count the read numbers mapped to each gene
Assembly: WBcel235 (NCBI, GCF_000002985.6_WBcel235_genomic.fa)
Supplementary files format and content: xls file includes raw read counts for each sample

extract_protocol:
Populations of young adults were collected and washed in M9 and added to Trizol Reagent (Invitrogen). Worms in Trizol were lysed by freeze-thawing from -80 °C to 4 °C three times. Total RNA was purified from the lysate using the miRNeasy kit (Qiagen) according to manufacturer instructions, including the optional Buffer RWT wash step.
Strand-specific libraries were generated using NEBNextUltra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Ribosomal RNA was depleted. In order to select cDNA fragments of preferentially 250-300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then USER Enzyme (NEB, USA) was used to digest the second strand with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Library construction was performed by Novogene Corporation.


title: age-1(hx546); rde-4(ne301), young adults, RNA-Seq, biol rep 3

description: Library name: A1R4_3


title: GBS1, CD4

description: Library name: 356-10_S10


title: N2 WT, young adults, smallRNA-Seq, biol rep 1

description: Library name: WT_1


title: BH4-3: HIE Male, brain monocyte cells

description: Data from MIA Treated mice


title: age-1(hx546); rde-4(ne301), young adults, RNA-Seq, biol rep 1

description: Library name: A1R4_1


title: HC3, CD4

description: Library name: 356-6_S6


title: 143B, metformin, Replicate 3

value: osteosarcoma


title: 15454, ONC201, Replicate 1

value: metastatic osteosarcoma lung biopsy, same individual as Q2148


title: age-1(hx546), young adults, RNA-Seq, biol rep 3

description: Library name: A1_3

value: bulk


title: BH4-4: HIE Female, brain monocyte cells

description: Data from HIE Treated mice

value: Hypoxic-Ischemic Encephalopathy


title: GBS1, CD11b

description: Library name: 356-5_S5

source_name: CD11b+ peripheral blood mononuclear cells


title: 15454, ONC201, Replicate 2

value: 10 mM galactose media


title: HC1, CD11b

description: Library name: 356-4_S4

value: CD11b+ peripheral blood mononuclear cells


title: age-1(hx546), young adults, RNA-Seq, biol rep 2

description: Library name: A1_2


title: BH4-8: HIE Female, brain monocyte cells

description: Data from HIE Treated mice


title: GBS3, CD11b

description: Library name: 356-3_S3


title: 143B, glucose, Replicate 3

value: 5.6 mM glucose media


title: BH4-2: HIE male, brain monocyte cells

description: Data from HIE Treated mice


title: 143B, metformin, Replicate 1


title: HC2, CD11b

description: Library name: 356-2_S2


title: 143B, metformin, Replicate 2


title: 143B, glucose, Replicate 2


title: BH4-1: HIE Male, brain monocyte cells

description: Data from HIE Treated mice


title: age-1(hx546), young adults, RNA-Seq, biol rep 1

description: Library name: A1_1


title: rde-4(ne301), young adults, RNA-Seq, biol rep 3

description: Library name: R4_3


title: BH2-13: Control Female, brain monocyte cells

description: Data from Control Treated mice

value: Control


title: mRNAseq_YMEP_rep2

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description:
Library name: Sample 74
mRNAseq_YMEP_rep2

data_processing:
cutadapt
STAR alignment (RNA-seq)
featureCount, gene-level extraction (RNA-seq)
Assembly: mm10
Supplementary files format and content: gene count text file

source_name: Bone marrow

extract_protocol:
RNA was purified with TRIzol TM Reagent (Invitrogen, 15596026) and Direct-zol RNA microprep (Zymo R2060)
RNA-seq libraries were constructed using SMARTer Standard total RNA-seq kit v2

value: Bone marrow

value: MEP

value: WT

tag: batch


title: rde-4(ne301), young adults, RNA-Seq, biol rep 2

description: Library name: R4_2


title: BH2-5: Control Female, brain monocyte cells

description: Data from Control Treated mice

value: Brain


title: HC3, CD11b

description: Library name: 356-1_S1


title: rde-4(ne301), young adults, RNA-Seq, biol rep 1

description: Library name: R4_1


title: mRNAseq_YMEP_rep1

description:
Library name: Sample 73
mRNAseq_YMEP_rep1


title: 143B, glucose, Replicate 1


title: 143B, galactose, Replicate 1


title: BH2-2: Control Male, brain monocyte cells

description: Data from Control Treated mice


title: MEC1, siSrsf3 #2, biol rep 3

city: Oxford

first: Susann

last: Bruche

address: Institute of Developmental and Regenerative Medicine

department: Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

description:
Library name: 5C
siS3-2_ex3

data_processing:
Data was processed with the nf-core RNA-seq pipeline, v3.18.0 using fastp trimming and Star-Salmon alignment.
Assembly: GRCm39
Supplementary files format and content: *.txt files with output of featureCounts v2.0.6
Supplementary files format and content: *.tsv file of merged Salmon gene counts, column names equal "description" column.

source_name: Epicardium

growth_protocol: The MEC1 epicardial cell line was cultured on 0.1% gelatine in DMEM high glucose with Glutamax, 10% FBS, 1% Penicillin/Streptomycin, at 37°C in 5% CO2.

extract_protocol:
RNA was isolated using a Qiagen RNAeasy kit.
Stranded RNAseq libraries with roughly 350bp inserts were generated by Azenta Life Sciences.

treatment_protocol: MEC-1 cells were transfected with 80pmol siRNA using Lipofectamine RNAiMAx for 48h.

value: Epicardium

value: epicardial

value: Srsf3 knockdown

value: siSrsf3, oligo 2


title: mRNAseq_YGMP_rep2

description:
Library name: Sample 72
mRNAseq_YGMP_rep2

value: GMP


title: N2 WT, young adults, RNA-Seq, biol rep 3

description: Library name: WT_3


title: 143B, cycloheximide, Replicate 3

value: osteosarcoma

value: cycloheximide


title: mRNAseq_YGMP_rep1

description:
Library name: Sample 71
mRNAseq_YGMP_rep1


title: HC2, CD4

description: Library name: 356-7_S7

value: CD4+ peripheral blood mononuclear cells


title: BH2-1: Control Male brain monocyte cells

description: Data from Control Treated mice

value: Male

value: Monocytes


title: 143B, galactose, Replicate 2

value: 10 mM galactose media


title: N2 WT, young adults, RNA-Seq, biol rep 2

description: Library name: WT_2

value: bulk


title: N2 WT, young adults, RNA-Seq, biol rep 1

description: Library name: WT_1


title: MEC1, siSrsf3 #2, biol rep 2

description:
Library name: 5B
siS3-2_ex2


title: control mammary tissue, sample 7

type: RNA

city: Araçatuba

first: Flavia

middle: Lombardi

last: Lopes

state: São Paulo

address: Rua Clovis Pestana, 793

department: DAPSA

country: Brazil

institute: FMVA-UNESP

hyb_protocol: Hybridization to the Affymetrix® miRNA 4.1 Array strips was carried out at 48ºC for 20 hours

scan_protocol: GeneAtlas® System (Affymetrix)

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Transcriptome Analysis Console (TAC) 4.0.1 (Thermo Fisher Scientific Co.) using the Robust Multi-array Average (RMA) algorithm

label: biotin

organism: Canis lupus familiaris

source_name: control mammary tissue

label_protocol: Total RNA (400 ng/sample) was labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Thermo Fisher Scientific Co.), according to the manufacturer’s instructions

growth_protocol: Samples were kept in RNAlater (Thermo Fisher Scientific®) before RNA extraction

extract_protocol: Total RNA was extracted using the miRVana kit from Thermo Fisher Scientific Co.

treatment_protocol: Four female dogs, aged between 2 and 4 years, were presented at Luiz Quintiliano de Almeida Veterinary Hospital at the School of Veterinary Medicine, São Paulo State University (Unesp) for mastectomy. Immediately after resection, samples (n = 12, 3 per animal) were collected under ethical approval #2008-007478. Subsequently, part of each tissue sample underwent histopathological analysis and immunophenotyping, while the remainder was preserved in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. Control samples (n = 4) were harvested from the mammary tissue of female dogs that were ethically euthanized from non-infectious unrelated conditions. These samples were kept in RNAlater (Thermo Fisher Scientific®) at 4ºC overnight and then stored at -80ºC. RNA extraction was performed using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific®), according to manufacturer’s instructions.

value: female

value: mammary


title: mRNAseq_YCMP_rep1

description:
Library name: Sample 69
mRNAseq_YCMP_rep1

value: Bone marrow

value: CMP


title: 143B, cycloheximide, Replicate 1


title: MEC1, siSrsf3 #2, biol rep 1

description:
Library name: 5A
siS3-2_ex1


title: MEC1, siSrsf3 #1, biol rep 3

description:
Library name: 4C
siS3-1_ex3

value: siSrsf3, oligo 1


title: control mammary tissue, sample 8


title: mRNAseq_YCMP_rep2

description:
Library name: Sample 70
mRNAseq_YCMP_rep2

value: WT


title: 143B, cycloheximide, Replicate 2


title: Nuclei from 6-weeks pooled from mouse kidneys

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

description:
Library name: mouse_p6w_kidney
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were performed  using the Cell Ranger software v5.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: Tab-delimited value files and matrix files.

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
The kidney pairs of two male and two female mice at each age (P0, P2, P7, P14, P21, 6wk) were dissected in cold PBS. Cortical regions were partially removed to enrich for medullary cell types. Kidneys were minced into small cubes, dounced 5 times with the loose pestle in Nuclei Lysis Buffer 1 (NLB1) (4 ml of nuclei EZ lysis buffer, 20 µl of RNasin Plus, 20 µl of SUPERaseIN, 1% BSA, cOmplete ULTRA tablet), and passed through a 200 µm strainer. The sample was then dounced 10 times with the tight pestle, incubated for 1 minutes in NLB1 on ice, passed through a 40 µm strainer, and centrifuged at 500g for 1 minutes at 4˚C. The pellet was resuspended in NLB2 (4 ml of Nuclei EZ Lysis Buffer, 4 µl of RNasin Plus, 4 µl of SUPERaseIN, 1% BSA, cOmplete ULTRA tablet), incubated on ice for 5 minutes, and centrifuged at 500g for 5 minutes at 4˚C. The pellet was resuspended in nuceli suspension buffer (2 ml of calcium/magnesium free PBS, 2 µl of RNasin Plus, 2% BSA) and passed through a 5 µm strainer. The nuclei were counted by hemocytometer and diluted to 1200 nuclei/uL.
The resulting nuclei suspensions were submitted to UTSW Next Gen Sequencing Core for library preparation and sequencing using the Chromium Single Cell 3' Prime Gene Expression kit (10x Genomics) on an Illumina NextSeq 2000.

value: Kidney

tag: age

value: Wild type

value: pooled male and female

tag: background


title: control mammary tissue, sample 6


title: 143B, galactose, Replicate 3


title: Nuclei from P14 pooled from mouse kidneys

description:
Library name: mouse_p14d_kidney
10x Genomics


title: 143B, ONC206, Replicate 3


title: Nuclei from P21 pooled from mouse kidneys

description:
Library name: mouse_p21d_kidney
10x Genomics


title: MEC1, siSrsf3 #1, biol rep 1

description:
Library name: 4A
siS3-1_ex1

value: Epicardium

value: epicardial

value: Srsf3 knockdown


title: 143B, ONC206, Replicate 1

value: osteosarcoma


title: 143B, ONC206, Replicate 2


title: Nuclei from P7 pooled from mouse kidneys

description:
Library name: mouse_p7d_kidney
10x Genomics


title: MEC1, siControl, biol rep 3

description:
Library name: 2C
siC_ex3

value: siCntl


title: tumor mammary tissue, sample 4

source_name: tumor mammary tissue


title: MEC1, siSrsf3 #1, biol rep 2

description:
Library name: 4B
siS3-1_ex2


title: 143B, ONC201, Replicate 3


title: tumor mammary tissue, sample 3


title: Nuclei from P2 pooled from mouse kidneys

description:
Library name: mouse_p2d_kidney
10x Genomics


title: tumor mammary tissue, sample 1


title: naïve lung cells

city: Kunming

first: Xiaolong

last: Zhang

state: Yunnan

address: 935 Jiaoling road

country: China

institute: Peking Union Medical College

description: Library name: sample 1

data_processing:
Genome alignment and data quality control were performed through dnbc4tools (version 2.1.0), and data were further analyzed using R package Seurat.
Assembly: Genome alignment and data quality control were performed through dnbc4tools (version 2.1.0), and data were further analyzed using R package Seurat.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: whole lung

extract_protocol:
Lung was excised and cut into small pieces followed by digestion with 1 mg/ml Collagenase I and 0.05 mg/ml DNase I at 37℃ for 45 mins. After passing through a 70 μm cell strainer, red blood cells were lysed.
The resulting single cell suspension was added to gel bead-in-emulsions in a DNBelab C4 system (BGI, China) to construct cDNA libraries.

value: whole lung

value: lung cells

tag: strain

value: untreated


title: tumor mammary tissue, sample 2

value: female


title: Nuclei from P0 pooled from mouse kidneys

description:
Library name: mouse_p0d_kidney
10x Genomics


title: 143B, ONC201, Replicate 1

value: 10 mM galactose media


title: control mammary tissue, sample 5

value: mammary


title: MEC1, siControl, biol rep 1

description:
Library name: 2A
siC_ex1


title: 143B, ONC201, Replicate 2


title: Wild-type dendritic cells type 2 without influenza infection [UNI_IRF7WT2DC2_06]

status: Public on Feb 18 2026

city: Singapore

first: Lina

middle: H K

last: Lim

state: Singapore

address: 28 medical drive

department: Department of Physiology

country: Singapore

institute: National University of Singapore

hyb_protocol: RNA samples were hybridized with NanoString nCounter reporter and capture probes according to the manufacturer’s protocol.

scan_protocol: Hybridized samples were processed and scanned using the NanoString nCounter system following the manufacturer’s standard protocol.

data_processing: Raw RCC files were generated by the NanoString nCounter system. Gene expression counts were extracted from RCC files using standard NanoString data processing procedures. Processed expression matrices were generated for downstream analysis.

label: not provided

source_name: conventional dendritic cells type 2

label_protocol: For NanoString nCounter analysis, sample preparation and labeling were performed according to the manufacturer’s instructions.

growth_protocol: Mice were maintained under specific pathogen–free conditions. Alveolar macrophages (AM), dendritic cells type 1 (DC1), and dendritic cells type 2 (DC2) were isolated from mouse lung tissue using standard immunological procedures.

extract_protocol: Total RNA was extracted from isolated cells following standard RNA extraction procedures suitable for NanoString nCounter analysis.

treatment_protocol: Cells were either left untreated or infected with influenza virus as indicated. Infection conditions were applied according to established experimental procedures.

value: uninfected

value: IRF7 wild-type


title: MEC1, siControl, biol rep 2

description:
Library name: 2B
siC_ex2

value: WT


title: Wild-type dendritic cells type 2 without influenza infection [UNI_IRF7WT3DC2_02]


title: IRF7 knockout dendritic cells type 2 without influenza infection [UNI_IRF7KO3DC2_08]

value: IRF7 knockout


title: IRF7 knockout dendritic cells type 2 under influenza infection [INF_IRF7KO2DC2_12]

value: influenza infection


title: IRF7 knockout dendritic cells type 2 without influenza infection [UNI_IRF7KO2DC2_06]


title: Wild-type dendritic cells type 2 under influenza infection [INF_IRF7WT2DC2_12]


title: IRF7 knockout dendritic cells type 2 without influenza infection [UNI_IRF7KO1DC2_03]


title: Wild-type dendritic cells type 2 under influenza infection [INF_IRF7WT1DC2_09]


title: Wild-type dendritic cells type 2 under influenza infection [INF_IRF7WT3DC2_06]


title: IRF3 knockout dendritic cells type 2 without influenza infection [UNI_IRF3KO3DC2_09]

value: IRF3 knockout


title: IRF7 knockout dendritic cells type 2 under influenza infection [INF_IRF7KO1DC2_09]


title: IRF7 knockout dendritic cells type 2 under influenza infection [INF_IRF7KO3DC2_11]


title: Wild-type dendritic cells type 2 without influenza infection [UNI_IRF3WT1DC2_12]

value: IRF3 wild-type


title: Wild-type dendritic cells type 2 without influenza infection [UNI_IRF7WT1DC2_03]


title: IRF3 knockout dendritic cells type 2 without influenza infection [UNI_IRF3KO2DC2_04]


title: Wild-type dendritic cells type 2 under influenza infection [INF_IRF3WT1DC2_12]


title: Wild-type dendritic cells type 1 without influenza infection [UNI_IRF7WT3DC1_01]

source_name: conventional dendritic cells type 1


title: IRF3 knockout dendritic cells type 2 without influenza infection [UNI_IRF3KO1DC2_01]


title: Wild-type dendritic cells type 1 without influenza infection [UNI_IRF7WT1DC1_02]


title: IRF3 knockout dendritic cells type 2 under influenza infection [INF_IRF3KO3DC2_07]


title: IRF7 knockout dendritic cells type 1 without influenza infection [UNI_IRF7KO3DC1_07]


title: IRF7 knockout dendritic cells type 1 without influenza infection [UNI_IRF7KO1DC1_02]


title: IRF7 knockout dendritic cells type 1 without influenza infection [UNI_IRF7KO2DC1_05]


title: Wild-type dendritic cells type 1 without influenza infection [UNI_IRF7WT2DC1_05]


title: IRF3 knockout dendritic cells type 2 under influenza infection [INF_IRF3KO2DC2_06]


title: Wild-type dendritic cells type 1 under influenza infection [INF_IRF7WT3DC1_04]


title: IRF3 knockout dendritic cells type 2 under influenza infection [INF_IRF3KO1DC2_02]


title: IRF7 knockout dendritic cells type 1 under influenza infection [INF_IRF7KO3DC1_10]


title: Wild-type dendritic cells type 1 under influenza infection [INF_IRF7WT2DC1_11]


title: IRF7 knockout dendritic cells type 1 under influenza infection [INF_IRF7KO2DC1_11]


title: Wild-type dendritic cells type 1 under influenza infection [INF_IRF7WT1DC1_08]


title: Wild-type dendritic cells type 1 without influenza infection [UNI_IRF3WT1DC1_11]


title: IRF3 knockout dendritic cells type 1 under influenza infection [INF_IRF3KO3DC1_09]


title: Wild-type alveolar macrophages without influenza infection [UNI_IRF7WT3AM_03]

source_name: alveolar macrophages

value: AM


title: IRF3 knockout dendritic cells type 1 without influenza infection [UNI_IRF3KO3DC1_08]


title: Wild-type alveolar macrophages without influenza infection [UNI_IRF7WT2AM_04]


title: IRF3 knockout dendritic cells type 1 under influenza infection [INF_IRF3KO1DC1_01]


title: IRF3 knockout dendritic cells type 1 without influenza infection [UNI_IRF3KO2DC1_05]


title: IRF3 knockout dendritic cells type 1 without influenza infection [UNI_IRF3KO1DC1_02]


title: Wild-type alveolar macrophages without influenza infection [UNI_IRF7WT1AM_01]


title: IRF7 knockout dendritic cells type 1 under influenza infection [INF_IRF7KO1DC1_08]


title: IRF3 knockout dendritic cells type 1 under influenza infection [INF_IRF3KO2DC1_05]


title: IRF7 knockout alveolar macrophages without influenza infection [UNI_IRF7KO3AM_09]


title: Wild-type dendritic cells type 1 under influenza infection [INF_IRF3WT1DC1_10]


title: IRF7 knockout alveolar macrophages under influenza infection [INF_IRF7KO2AM_10]


title: Wild-type alveolar macrophages under influenza infection [INF_IRF7WT3AM_05]


title: IRF7 knockout alveolar macrophages without influenza infection [UNI_IRF7KO2AM_04]


title: Wild-type alveolar macrophages under influenza infection [INF_IRF7WT2AM_10]


title: IRF7 knockout alveolar macrophages without influenza infection [UNI_IRF7KO1AM_01]


title: Wild-type alveolar macrophages under influenza infection [INF_IRF7WT1AM_07]


title: Wild-type alveolar macrophages without influenza infection [UNI_IRF3WT1AM_10]


title: IRF7 knockout alveolar macrophages under influenza infection [INF_IRF7KO1AM_07]


title: IRF3 knockout alveolar macrophages without influenza infection [UNI_IRF3KO3AM_07]


title: IRF7 knockout alveolar macrophages under influenza infection [INF_IRF7KO3AM_12]


title: IRF3 knockout alveolar macrophages without influenza infection [UNI_IRF3KO1AM_03]


title: IRF3 knockout alveolar macrophages without influenza infection [UNI_IRF3KO2AM_06]


title: Wild-type alveolar macrophages under influenza infection [INF_IRF3WT1AM_11]


title: IRF3 knockout alveolar macrophages under influenza infection [INF_IRF3KO2AM_04]


title: Embryonic cells, strictly FACSed HNK-1 positive, 2

city: Plön

first: Robin

last: Pranter

address: August-Thienemann-Straße 2

country: Germany

institute: Max Plank Institute for Evolutionary Biology

description:
Library name: Strictly sorted 2
Smart-seq3

data_processing:
Count matrices were generated from the 10X Chromium data using the cellranger pipeline from 10X Genomics. And from the Smart-seq3 data using the zUMIs pipeline.
Assembly: PodMur_1.0
Supplementary files format and content: Rds-files

organism: Podarcis muralis

source_name: Embryo

extract_protocol:
Each embryo was photographed and then minced into fine pieces using a sterile scalpel. The minced embryo was incubated at 37°C with Trypsin (GibcoTM TrypLETM Express Enzyme (1X), phenol red) to dissociate the cells into a single cell suspension. Trypsin treatment was terminated after ten minutes by applying an inhibitor (GibcoTM Defined Trypsin Inhibitor). The suspension was triturated 50 times up and down through a 1ml pipet tip and then passed through a 70μm cell strainer (FlowmiTM Cell Strainer) to remove any remaining clumps. To stain the cells for viability the suspension was incubated for 12 minutes on ice with a Live/Dead stain (Invitrogen LIVE/DEADTM Fixable Near-IR Dead Cell Stain Kit; L34975). Suspended cells were washed once in nuclease-free PBS, fixed in methanol and stored in methanol at -80°C for up to several months. The fixed cell solutions were resuspended in a permeabilization buffer (PB; 2% BSA, 100U/ml RNase-inhibitor, 5mM 1,4-Ditiotreitol, 0.1M MOPS pH 7.5, 1mM EGTA, 2mM MgSO4, 125mM NaCl and 0.1% Saponin), and incubated on ice for 5min. Once permeabilized, the cells were stained with a mix of DAPI (1:1000; ThermoScientific 62248), which stains DNA, and a FITC-conjugated HNK-1 antibody (1:100; Anti-Hu CD57 eBioscience 11-057742) in MRDB (a buffer identical to PB but lacking saponin), followed by a washing step with the same buffer and passed through a 70μm cell strainer. Dissociated cells were sorted in a FACS ARIA III machine. Debris, doublets and cells that were dead before fixation were removed by three gates. The first gate excluded debris by excluding cells with low values in both forward and side scatter area. The second gate removed doublets by excluding cells with high values in forward scatter width, which can be clearly made out when forward scatter width and height are plotted against each other. The third gate further removed additional (large) debris, non-nucleated cells and cells that were dead before fixation by only selecting cells with high DAPI fluorescence and low Live/Dead fluorescence. The remaining cells were inspected and sorted based on their anti-HNK-1 (FITC) signal.
The unsorted and leniently sorted samples were processed into cDNA using 10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index). The strictly sorted sample was processed to cDNA following the Smart-seq3 protocol.

value: Embryo

tag: somite stage

value: Neural crest cells

tag: pooled

value: No

tag: fac-sorted

value: Yes

tag: top x%_of_hnk-1_signal


title: IRF3 knockout alveolar macrophages under influenza infection [INF_IRF3KO3AM_08]


title: Embryonic cells, strictly FACSed HNK-1 positive, 1

description:
Library name: Strictly sorted 1
Smart-seq3


title: IRF3 knockout alveolar macrophages under influenza infection [INF_IRF3KO1AM_03]


title: Embryonic cells, unsorted, 1

description:
Library name: Unsorted 1
10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index)

value: average 32

value: Whole embryo

value: Not sorted


title: Embryonic cells, unsorted, 2

description:
Library name: Unsorted 2
10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index)


title: Rrm4mR123-Gfp RNAseq replicate 4

city: Würzburg

first: Kathi

last: Zarnack

address: Biocenter, Am Hubland

department: Theodor Boveri Institute

institute: University Würzburg

description: Library name: Rrm4mR123G_rep4

data_processing:
The raw sequencing reads were quality filtered based on their quality score and length with Trimmomatic (Version 0.36; Bolger et al., 2014). Adapter sequences were first removed using the ILLUMINACLIP option. Next, a sliding window approach was employed to trim reads with an average Phred score below 15 within a 4-base window. Quality trimming was additionally performed to remove low-quality bases (Phred score <30) from the ends of the reads. Finally, reads shorter than 36 nucleotides after trimming were discarded.
STAR (version 2.7.11b) was used to align the trimmed reads to the U. maydis genome, allowing up to 4% mismatches in the mapped read length while limiting the mapping to one locus.
Uniquely mapped reads on each gene were counted using feature counts (version 2.0.1).
The resulting raw counts of mRNA libraries were used as input for the subsequent differential gene expression analysis. All differential gene expression analysis was performed using the R/Bioconductor package DESeq2 (version 1.42.0).
Assembly: Ustilago maydis genome assembly version Umaydis521 2.0.51
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Mycosarcoma maydis

source_name: hyphae

growth_protocol: The cultivation conditions for Ustilago maydis are detailed in Brachmann et al., Mol Genet Genomics, 2004 (DOI: 10.1007/s00438-004-1047-z). The starting cultures were grown in CM medium supplemented with glucose at 28°C.

extract_protocol:
To purify total RNA, 50 ml of hyphal cell culture with an OD600 of 0.5 was used. The cells from the 50 ml culture were collected and resuspended in 2 ml of 1x PBS, divided, and transferred into two 2 ml reaction tubes (1 ml each). The tubes were centrifuged at 16,200 g for 5 minutes at 4°C, and the supernatant was completely removed. The cell pellets were flash-frozen in liquid nitrogen. A 5 mm steel bead was added to each 2 ml tube, which were then placed in the pre-cooled TissueLyser Adapter (Qiagen). The samples underwent two rounds of mechanical disruption for 30 seconds at 30 Hz each, with a cooling step in liquid nitrogen between rounds.The cryogenically frozen cell powder was resuspended in 500 µl of TriZol (Invitrogen, 15596026) and incubated in a thermo block at room temperature for 5 minutes at 1000 rpm. Next, 500 µl of RNase-free water was added, and the mixture was manually shaken for 30 seconds. Subsequently, 400 μl of chloroform/isoamyl alcohol (24:1- BioChemica A1935,0500) was added. The samples were shaken vigorously by hand for 3 minutes, then incubated at room temperature for another 3 minutes. Following this, the samples were centrifuged for 10 minutes at 16,200 g. The aqueous phase was transferred to a fresh 1.5 ml tube pre-filled with 250 μl of chloroform/isoamyl alcohol (24:1- BioChemica A1935,0500). This extraction process was repeated, followed by centrifugation at 16,200 g for 5 minutes at 4°C.The aqueous phase was transferred to a solution containing 40 μl of sodium acetate (3 M, pH 5.2) and 1 ml of ice-cold ethanol (100%), then precipitated at -20°C for 2 hours. The RNA pellet was collected by centrifugation for 30 minutes at 16,200 g and 4°C, washed twice with 75% ice-cold ethanol, and centrifuged for 5 minutes at 16,200 g and 4°C. The pellet was briefly dried and resuspended in 50 μl of RNase-free water. RNA concentration was measured and adjusted accordingly.
Ribosomal RNA was depleted,   and the residual RNA was reverse transcribed into cDNA using the TruSeq library preparation kit with Ribo-Zero Gold (Illumina). Sequencing was performed on an Illumina NextSeq 500, generating 150-nt single-end reads.

treatment_protocol: Hyphal growth was induced by shifting the cells to Nitrate minimal medium supplement with 1% glucose at 28°C, 200 rpm for 6h post-induction.

value: hyphae

value: Strain expressing an Rrm4 version carrying a four amino acid block mutation in the RNP1 region of the third RRM domain, with C-terminal GFP tag.

value: switch from yeast to hyphal growth

tag: time

value: 6 hours post hyphal induction


title: Rrm4mR123-Gfp RNAseq replicate 5

description: Library name: Rrm4mR123G_rep5


title: Rrm4mR123-Gfp RNAseq replicate 1

description: Library name: Rrm4mR123G_rep1


title: Rrm4mR123-Gfp RNAseq replicate 3

description: Library name: Rrm4mR123G_rep3


title: Rrm4mR3-Gfp RNAseq replicate4

description: Library name: Rrm4mR3G_rep4


title: Rrm4mR3-Gfp RNAseq replicate5

description: Library name: Rrm4mR3G_rep5


title: Embryonic cells, leniently FACSed HNK-1 positive

description:
Library name: Leniently sorted
10X Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index)


title: Rrm4mR123-Gfp RNAseq replicate 2

description: Library name: Rrm4mR123G_rep2


title: Rrm4mR2-Gfp RNAseq replicate3

description: Library name: Rrm4mR2G_rep3


title: Rrm4mR3-Gfp RNAseq replicate2

description: Library name: Rrm4mR3G_rep2


title: Rrm4mR3-Gfp RNAseq replicate3

description: Library name: Rrm4mR3G_rep3


title: Rrm4mR2-Gfp RNAseq replicate4

description: Library name: Rrm4mR2G_rep4


title: Rrm4mR3-Gfp RNAseq replicate1

description: Library name: Rrm4mR3G_rep1


title: Rrm4mR2-Gfp RNAseq replicate1

description: Library name: Rrm4mR2G_rep1


title: Rrm4mR1-Gfp RNAseq replicate 5

description: Library name: Rrm4mR1G_rep5


title: Rrm4mR1-Gfp RNAseq replicate 1

description: Library name: Rrm4mR1G_rep1

value: Strain expressing an Rrm4 version carrying a four amino acid block mutation in the RNP1 region of the second RRM domain, with C-terminal GFP tag.


title: Rrm4mR2-Gfp RNAseq replicate2

description: Library name: Rrm4mR2G_rep2


title: Rrm4mR1-Gfp RNAseq replicate 3

description: Library name: Rrm4mR1G_rep3


title: Rrm4mR1-Gfp RNAseq replicate 2

description: Library name: Rrm4mR1G_rep2


title: rrm4Δ RNAseq replicate 4

description: Library name: rrm4Δ _rep4


title: Rrm4mR1-Gfp RNAseq replicate 4

description: Library name: Rrm4mR1G_rep4


title: rrm4Δ RNAseq replicate 5

description: Library name: rrm4Δ _rep5


title: Rrm4-Gfp RNAseq replicate 5

description: Library name: Rrm4G_rep5

value: Strain expressing an Rrm4 version carrying a four amino acid block mutation in the RNP1 region of the first RRM domain, with C-terminal GFP tag.


title: rrm4Δ RNAseq replicate 3

description: Library name: rrm4Δ _rep3


title: Rrm4-Gfp RNAseq replicate 1

description: Library name: Rrm4G_rep1


title: Rrm4-Gfp RNAseq replicate 2

description: Library name: Rrm4G_rep2


title: rrm4Δ RNAseq replicate 2

description: Library name: rrm4Δ _rep2


title: Rrm4-Gfp RNAseq replicate 4

description: Library name: Rrm4G_rep4


title: Rrm4-Gfp RNAseq replicate 3

description: Library name: Rrm4G_rep3


title: Rrm4mR3-Gfp iCLIP2 replicate5

library_source: other

data_processing:
Quality control: FastQC (v0.11.8)
Barcode and adapter trimming: Flexbar (v3.4.0) with non-default parameters: --zip-output GZ --threads 4 --stdout-log --adapter-seq AGATCGGAAGAGCGGTTCAG --adapter-min-overlap 1 --min-read-length 15 --length-dist --umi-tags --barcodes samplebarcodes.fasta (using sample barcodes: Rrm4mR1-Gfp iCLIP2 replicate 1: NNNNNCACTGTNNNN, Rrm4mR1-Gfp iCLIP2 replicate 2: NNNNNGATCTGNNNN, Rrm4mR1-Gfp iCLIP2 replicate 3: NNNNNACATCGNNNN, Rrm4mR1-Gfp iCLIP2 replicate 4: NNNNNTCAAGTNNNN, Rrm4mR1-Gfp iCLIP2 replicate 5: NNNNNAAGCTANNNN, Rrm4mR2-Gfp iCLIP2 replicate1: NNNNNACATCGNNNN, Rrm4mR2-Gfp iCLIP2 replicate2: NNNNNCACTGTNNNN, Rrm4mR2-Gfp iCLIP2 replicate3: NNNNNTCAAGTNNNN, Rrm4mR2-Gfp iCLIP2 replicate4: NNNNNGCTCATNNNN, Rrm4mR2-Gfp iCLIP2 replicate5: NNNNNGGAACTNNNN, Rrm4mR2-Gfp iCLIP2 replicate6: NNNNNTAGTTGNNNN, Rrm4mR3-Gfp iCLIP2 replicate1: NNNNNGCCTAANNNN, Rrm4mR3-Gfp iCLIP2 replicate2: NNNNNATTGGCNNNN, Rrm4mR3-Gfp iCLIP2 replicate3: NNNNNCTGATCNNNN, Rrm4mR3-Gfp iCLIP2 replicate4: NNNNNTACAAGNNNN, Rrm4mR3-Gfp iCLIP2 replicate5: NNNNNTGACATNNNN, Rrm4mR3-Gfp iCLIP2 replicate6: NNNNNGCGGACNNNN)
Mapping: STAR (v2.7.3a) with non-default parameters: --genomeDir Ensembl_release51_Umaydis521_2.0 --sjdbGTFfile Ustilago_maydis.Umaydis521_2.0.51.gtf --sjdbOverhang 76 --runThreadN 4 --alignEndsType Extend5pOfRead1 --outFilterMismatchNoverReadLmax 0.04 --outFilterMismatchNmax 999 --outFilterMultimapNmax 1 --outSAMattributes All --outReadsUnmapped Fastx --outSJfilterReads Unique --readFilesCommand zcat --outSAMtype BAM  SortedByCoordinate --limitBAMsortRAM 4000000000
Removal of reads directly mapped at chromosome ends (their upstream/crosslink position does not exist): Samtools (v1.9), Bedtools (v2.27.1): samtools view -H SAMPLE.mapped.bam > SAMPLE.header; samtools view SAMPLE.mapped.bam > SAMPLE.body; bedtools bamtobed -i SAMPLE.mapped.bam | sort -k1,1 > SAMPLE.mapped.bed; join -t $'\t' -j1 -e "NA" -a1 SAMPLE.mapped.bed CHROMOLENGTHTABLE > SAMPLE.mapped.len.bed; cat SAMPLE.mapped.len.bed | awk '{if(($2==0) || ($3>=$7)) printf "%s\t%s\t%s\t%s\t%s\t%s\n",$1,$2,$3,$4,$5,$6;}' > SAMPLE.idlist; awk 'FNR==NR && NF {a[$4];next} !($1 in a)' SAMPLE.idlist SAMPLE.body > SAMPLE.body.filtered; cat SAMPLE.header SAMPLE.body.filtered | samtools view -b - > SAMPLE.bam
Duplicate removal: UMI-tools (v1.0.0) with non-default parameter: umi_tools dedup --method unique (--random-seed=100 was set when removing duplicates in samples Rrm4mR2-Gfp iCLIP2 replicate1-6 and Rrm4mR3-Gfp iCLIP2 replicate1-6)
BAM to BED shifting one base upstream: bedtools (v2.27.1): bedtools bamtobed -i SAMPLE.duprm.bam | bedtools shift -m 1 -p -1 -i stdin -g CHROMOLENGTHTABLE | sort -k1,1 -k2,2n > SAMPLE.shifted1bp.bed
BED to bedGraph considering only 5' end positions: bedtools (v2.27.1): bedtools genomecov -bg -strand + -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.plus.bedgraph; bedtools genomecov -bg -strand - -5 -i SAMPLE.shifted1bp.bed -g CHROMOLENGTHTABLE > SAMPLE.duprm.minus.bedgraph
bedGraph to bigWig using bedGraphToBigWig of the UCSC tool suite (v365)
Processed reads from all five replicates were merged into a single dataset, and subjected to peak calling using PureCLIP (version 1.3.1) with default parameters.
The resulting crosslink sites were then used to define binding sites with the R/Bioconductor package BindingSiteFinder (version 1.7.9). Initially, a pre-filtering step was implemented to retain only the most significant sites. Specifically, crosslink sites ranked in the lowest 5% by PureCLIP score—a measure of binding affinity strength provided by PureCLIP—were excluded. To account for gene expression levels and to improve the binding site quality, crosslink sites with the lowest 10% PureCLIP score per gene were filtered out. For defining the binding sites, processed crosslink sites within a distance closer than 4-nt were merged, requiring at least 2 out of 5 sites to be covered by crosslink events. The centers of the binding sites were iteratively positioned at crosslink events with the highest PureCLIP score and extended by 2-nt on either side, resulting in binding sites with 5-nt width. Furthermore, binding sites were deemed reproducible if they harbored more crosslink events than the 5th percentile of the crosslink distribution across all binding sites, with at least 2 crosslink events per binding site, observed in n-1 biological replicates, where n is the number of replicates.
genome build/assembly Umaydis521_2.0 (Ensembl release 51)
processed data files format and content: bigWig files show all detected crosslink events for Rrm4mR1-Gfp, Rrm4mR2-Gfp and Rrm4mR3-Gfp, separated by minus and plus strands.
processed data files format and content: The BED file specifies  the coordinates of all 15311, 35438, and 10807 binding sites (5-nt width) detected for Rrm4mR1-Gfp, Rrm4mR2-Gfp, and Rrm4mR3-Gfp, respectively.

molecule: other

extract_protocol:
For a complete iCLIP2 experiment 150 mL shifted culture (OD600 = 0.5) was used. The cells were UV treated (254 nm, 1x 200 mJ/cm2, Biolink UV-Crosslinker, Vilber-Lourmat) and harvested, and lysed as detailed described before (see „Bead mill tube“). The cryogenic cell powder was resuspended in 2 mL iCLIP Lysis buffer (50 mM Tris–HCl, pH 7.4; 100 mM NaCl; 1% IGEPAL CA-630; 0.1% SDS, 0.5% sodium deoxycholate, 2 M urea (Roth) - in addition freshly added 2× Complete protease inhibitor EDTA-free (Merck, 11873580001), 1 mM DTT, 1 mM PMSF (+ 5 µl SUPERase-In Thermo Fisher) per 50 mL culture. Afterwards, the homogenisate was spun at 4°C, 10 min, and 16,200 g. The supernatant was carried into a fresh, pre-cooled tube and spun again. The respective supernatants were pooled and afterward separated into three fresh tubes containing 20 µl pre-washed GFP-Trap beads (Chromotek; gtma-20). The IP was conducted for 1 h, at 4°C under rotating conditions. Afterward, the beads were pooled in a 2 ml reaction tube and washed four times with 1 mL high-salt buffer (50 mM Tris–HCl, pH 7.4, 1 M NaCl, 1 mM EDTA, 1% IGEPAL CA-630, 0.1% SDS, 0.5% sodium deoxycholate). The beads were then washed twice within 1x PNK buffer (20 mM Tris–HCl, pH 7.4, 10 mM Mg2Cl, 0.2% Tween-20). The beads were then transferred into a fresh 1.5 mL reaction tube and again washed three times with 1x PNK buffer. The rest of the iCLIP2 procedure was adopted from the original iCLIP2 protocol including oligonucleotides (Buchbender et al., 2020). Running and blotting were performed as described before during Western blot analysis. Afterward, the respective membrane was washed with ice-cold 1x PBS buffer and then covered in a fresh transparent plastic bag and exposed to BAS Storage Phosphor Screen (GE Healthcare) for approximately 1 h or overnight at - 20°C. The screen was visualized by a TyphoonTM laser scanner (Cytiva), according to manufacturer information. An optional RNase I (Life Technologies, AM2295) treatment was performed after the immunoprecipitation. Various dilutions (ranging from 1:50 to 1:1500) were prepared in 1x PNK buffer and added to the beads.  The beads were incubated for 3 min, 37°C at 1000 rpm, and subsequently, washed with cold High-salt buffer and handled on ice.
Following immunoprecipitation, the remainder of the iCLIP2 procedure, including the use of oligonucleotides, was adopted from the original iCLIP2 protocol (Buchbender et al., 2020). cDNA libraries were quality controlled using a TapeStation system  (D1000 Sensitivity Kit), and their exact concentration was measured with a Qubit High Sensitivity Kit. The respective libraries were then pooled with equal molarity as described by Buchbender et al. (2020) to two separate pools, one of Rrm4mR1-Gfp samples and one of Rrm4mR2-Gfp and Rrm4mR3-Gfp samples. Sequencing was performed by NextSeq 500/550 Illumina.


title: Rrm4mR3-Gfp iCLIP2 replicate4


title: rrm4Δ RNAseq replicate 1

description: Library name: rrm4Δ _rep1


title: Rrm4mR3-Gfp iCLIP2 replicate3


title: Rrm4mR3-Gfp iCLIP2 replicate6


title: Rrm4mR3-Gfp iCLIP2 replicate2


title: Rrm4mR3-Gfp iCLIP2 replicate1


title: Rrm4mR2-Gfp iCLIP2 replicate5


title: Rrm4mR2-Gfp iCLIP2 replicate6


title: Rrm4mR2-Gfp iCLIP2 replicate3


title: Rrm4mR2-Gfp iCLIP2 replicate4


title: Rrm4mR1-Gfp iCLIP2 replicate 5


title: Rrm4mR1-Gfp iCLIP2 replicate 3


title: Rrm4mR1-Gfp iCLIP2 replicate 2


title: S2536.2_Rosa26KO_Old

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
Library name: S2536.2
column name in Raw_Counts_Formatted.tsv: S2536.2_Rosa26KO_Old

data_processing:
raw reads were quality-checked with FastQC v0.11.8. Experiments containing adaptor sequences were trimmed with Trim Galore v0.4.4_dev.
Reads were aligned to the mm10 reference genome with STAR aligner v2.5.3a, and converted to gene counts with HOMER's analyzeRepeats.pl.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole liver

extract_protocol:
RNA was harvested using Direct-zol RNA Miniprep Plus Kit (Zymo Research). 250 ng of total RNA was used for the construction of sequencing libraries.
polyA RNA isolation and library preparation was performed with the Watchmaker mRNA Library Prep Kit (Watchmaker Genomics: 7BK0001 ) with xGEN Stubby adaptors (IDT, Cat: 336338420) and xGEN 10nt UDIs (IDT, Cat: 336338436). Libraries were sequenced with the Element Biosciences AVITI Sequencing platform using the AVITI 2x75 High Output Cloudbreak Freestyle Kit (Element Biosciences, Cat: 860-00015).

value: whole liver

value: 25 months


title: Rrm4mR2-Gfp iCLIP2 replicate1


title: S2361_Cd44KO_Old_g2

description:
Library name: S2361
column name in Raw_Counts_Formatted.tsv: S2361_Cd44KO_Old_g2


title: Rrm4mR1-Gfp iCLIP2 replicate 4


title: S2359_Cd44KO_Old_g4

description:
Library name: S2359
column name in Raw_Counts_Formatted.tsv: S2359_Cd44KO_Old_g4


title: S2352_Rosa26KO_Young

description:
Library name: S2352
column name in Raw_Counts_Formatted.tsv: S2352_Rosa26KO_Young

value: 9 months


title: S2357_Cd44KO_Old_g4

description:
Library name: S2357
column name in Raw_Counts_Formatted.tsv: S2357_Cd44KO_Old_g4


title: S2354_Rosa26KO_Old

description:
Library name: S2354
column name in Raw_Counts_Formatted.tsv: S2354_Rosa26KO_Old


title: Rrm4mR2-Gfp iCLIP2 replicate2


title: S2362_Cd44KO_Old_g2

description:
Library name: S2362
column name in Raw_Counts_Formatted.tsv: S2362_Cd44KO_Old_g2


title: S2353_Rosa26KO_Young

description:
Library name: S2353
column name in Raw_Counts_Formatted.tsv: S2353_Rosa26KO_Young


title: S2351_Rosa26KO_Young

description:
Library name: S2351
column name in Raw_Counts_Formatted.tsv: S2351_Rosa26KO_Young


title: Cd8+ P14 cells (young), old mouse

first: K. Garrett

last: Evensen

institute: The Salk Institute for Biological Studies

description: Library name: S2_Old

data_processing:
Raw fastq files were processed using cellranger v8.0.1 count
Assembly: Mouse mm10
Supplementary files format and content: h5 files with matrix data for each cell

source_name: Liver

extract_protocol:
Whole liver was dissected out and placed on a 40 or 70 um cell strainer mounted on 50 mL tube. Single cell suspension was obtained by mashing using 3 mL syringe plunger while passing 10 % FBS in RPMI. Liver samples were centrifuged ar 60 r.c.f., 4 degC for 2 min with no brake to pellet hepatocytes. The supernatant was collected and centrifuged at 420 r.c.f, 4 degC for 4 min. Immune cells were enriched with 40 % Percoll (Cytiva) in HBSS. The pellet was resuspended in ACK lysis buffer (KD Medical) for red blood cell lysis. The the lysis buffer was neutralised and removed by centrifugation. Cells were then counted with trypan blue and haemocytometer. Immune cells from 7 young and 7 old mice were combined to enrich for adoptively transferred P14 CD8+ T cells. First, T cells were enriched using Invitrogen T cell enrichment kit (Invitrogen 8804-6822). The enriched T cells were then stained for the congenic marker Thy1.1, CD8, DAPI. Antigen-specific response was confirmed by anti-PD1 staining observed during sorting. Cells were sorted out using flow cytometer at the SBP flow core. All Thy1.1+ CD8+ T cells were collected in 0.05% BSA in PBS. Cells were counted for viability and then loaded onto 10X scRNAseq Chip. For single-cell sequencing, T-cell suspensions were processed using the GEM-X Universal 3' Gene Expression v4 kit (10x Genomics, Pleasanton, CA, USA; Cat. Nos. 1000686, 1000690, 1000215) according to the manufacturer’s user guide (CG000731, Rev B).
Single-cell libraries were sequenced on the Element Biosciences AVITI platform (San Diego, CA, USA) using the Cloudbreak FS High Output kit (Cat. No. 860-00015) with paired-end reads of 28 bp for Read 1 and 90 bp for Read 2. Raw sequencing data were processed with Cell Ranger (vX.X, 10x Genomics) using the mm10 (GRCm38) mouse reference genome to generate gene–cell count matrices for downstream analysis.

value: Liver

value: P14 CD8+ T cells

value: Old


title: Cd8+ P14 cells (young), young mouse

description: Library name: S1_Young

value: Young


title: rbbp5_ko_ebss.brep.3

first: William

last: Dion

address: 10550 N Torrey Pines Rd

institute: Scripps Research

description: Library name: rbbp5_ko_ebss_3

data_processing:
Galaxy online platform was used for quantification
Salmon quant was used for quantification
3D RNA-Seq App online platform was used for normalization and diffferential gene expression analysis
Assembly: mm10
Supplementary files format and content: csv file with TPM values

source_name: mouse embroynic fibroblasts

growth_protocol: Rbbp5 (flox/flox); Rosa26 CRE (+/+) MEFs were cultured in full DMEM supplemented with 10% FBS, treated with (RBBP5 KO) or without tamoxifen for seven days before subject to full medium or EBSS treatment for 16 hours.

extract_protocol:
Total mRNA was isolated from murine embryonic fibroblasts (MEFs) with PureLink RNA mini kit (Life Technologies) with additional on-column DNase digestion step to remove genomic DNA per the manufacturer’s instructions.
Illumina TruSeq kit (#20020594)

value: mouse embroynic fibroblasts

value: Rbbp5 (flox/flox); Rosa26 CRE (+/+)

value: tamoxifen for 7 days followed by EBSS


title: Rrm4mR1-Gfp iCLIP2 replicate 1


title: S2358_Rosa26KO_Old

description:
Library name: S2358
column name in Raw_Counts_Formatted.tsv: S2358_Rosa26KO_Old


title: rbbp5_ko_ebss.brep.2

description: Library name: rbbp5_ko_ebss_2

treatment_protocol: Rbbp5 (flox/flox); Rosa26 CRE (+/+) MEFs were cultured in full DMEM supplemented with 10% FBS, treated with (RBBP5 KO) or without tamoxifen for seven days before subject to full medium or EBSS treatment for 16 hours.


title: rbbp5_ko_full.brep.3

description: Library name: rbbp5_ko_full_3

value: tamoxifen for 7 days followed by full DMEM medium


title: wildtype_full.brep.3

description: Library name: wt_full_3

value: full DMEM medium


title: rbbp5_ko_full.brep.2

description: Library name: rbbp5_ko_full_2


title: wildtype_full.brep.2

description: Library name: wt_full_2


title: wildtype_ebss.brep.1

description: Library name: wt_ebss_1

value: EBSS for 16h


title: wildtype_full.brep.1

description: Library name: wt_full_1


title: wildtype_ebss.brep.3

description: Library name: wt_ebss_3


title: wildtype_ebss.brep.2

description: Library name: wt_ebss_2


title: Hypoxia EPIC V2, Replicate 2

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

hyb_protocol: With the use of the EZ DNA Methylation kit (Zymo Research), the extracted DNA was sodium bisulfite converted. Bisulfite-treated samples were subsequently processed using the Illumina Infinium MethylationEPIC v2.0 array (Illumina), as per the manufacturer's instructions.

scan_protocol: Array was imaged using HiScan and standard Illumina scanner setting.

data_processing:
Raw IDAT files were processed using the minfi cross-package workflow in R studio. The probes in the array were annotated using the Illumina Human Methylation EPIC v2 anno.20a1.hg38 and Illumina Human Methylation EPIC v2 manifest R packages. Normalization of probes was performed using the functional normalization method. CpG probes with a detection p-value >0.05, those located on sex chromosomes, as well as probes containing SNPs and cross-hybridizing probes obtained from, were excluded from downstream analysis. After this filtering, the resulting dataset included 888,670 CpG probes. Both β-values was computed for analysis.
EPIC_processed_GEO.csv represents Average Beta values
EPIC_Signal_GEO.csv represents raw values

label: Cy3 and Cy5

source_name: IOMM-Lee

label_protocol: Standard Illumina protocol

growth_protocol: IOMM-Lee cells were cultured in DMEM media enriched with 10% Fetal Bovine Serum, 100 U/ml Penicillin, and 100 g/ml Streptomycin. The cells were incubated at 37°C with 5% CO2.

extract_protocol: Genomic DNA was extracted using QIAamp DNA Mini Kit (QIAGEN).

treatment_protocol: Cells were grown in for 48h in a hypoxia workstation maintained at 37°C with 0.2% O2 and 5% CO2

value: IOMM-Lee

value: malignant (grade 3) meningioma cells

tag: group

value: Test

value: Hypoxic (0.2% O2)


title: Normoxia EPIC V2, Replicate 2

value: Control

value: Normoxic


title: Normoxia EPIC V2, Replicate 1


title: Hypoxia EPIC V2, Replicate 1


title: rbbp5_ko_full.brep.1

description: Library name: rbbp5_ko_full_1


title: Cd4_T_Cell_iPrimer-seq_data

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

description: Library name: Cd4_T_Cell_iPrimer-seq_data

data_processing:
The raw data was quality control using fastqc and then trimmed of the Nextera adaptor. Following trimming, the Drop-seq-Tools pipeline was used to filter the data with a Phred quality score threshold of 30 for sample barcode and UMI identify and poly(A) trimming. The filtered data was mapped to the mouse genome(mm10) using STAR 2.5.1a, and the reads counted using Drop-seq-Tools.
Assembly: mm10

source_name: Colon & Lymph node

extract_protocol:
RNA were extrat from the cell using the magic-beads combined with poly T
RNAs were extracted with oligo-dT magnetic beads. The isolated RNA was incubated with the 20 μL reverse transcription mix consisting of 100 unit Hiscript III Reverse Transcriptase (Vazyme, R303), 40 unit RNase Inhibitor (Vazyme, R301),1 μL 25 mM dNTP mix, 1 μL 100 mM DTT, 1 μL 1 val Betaine (Sigma, B0300-1VL), 0.5 μL 5% Digitonin, 0.5 μL TSO-LNA and 0.5 μL 5 μM Probe. The reaction was incubated at 42℃ for 90 min. Following cDNA synthesis, the sample were pooled, cleaned and concentrated with cleanup beads at a 1:0.8 of DNA to beads ration and eluted in 30 μL of ddH2O. Second-strand synthesis and pre-amplification were performed in a 50 μL reaction, consisting of 2 X KAPA HiFi Ready mix and 0.5 μM TSO-PCR primer, with the following PCR setup initial denaturation at 98 °C for 3 min, (denaturation at 98 °C for 15 s, annealing at 65 °C for 30 s, elongation at 72 °C for 6 min) repeated for 8 cycle, and a final elongation at 72 °C for 10 min. The DNA was cleanup using DNA cleanup beads at a ratio of 1:0.8 of DNA to beads and eluted with 30 μL of ddH2O. The library was prepared with the TruePrep DNA Library Prep Kit V2 for Illumina according to the manufacturer. Probe was designed by TSO, sample barcode(7-mer), UMI(8-mer) and Oligo(dT).

treatment_protocol: Mice were irradiated with a laser device (LaserMedix1500, Fotonmedix Mecal Laser, China) with an output power of 1.22 W, a wavelength of 980 nm, 80% duty, covering 4 square centimeters of spots, and each treatment was performed for five minutes every two days.

value: Colon & Lymph node

value: CD4 T cell

value: Control & light treatment


title: rbbp5_ko_ebss.brep.1

description: Library name: rbbp5_ko_ebss_1


title: CIN Tumor CIN Micronuclei 2

city: Edmonton

first: Kristi

last: Baker

state: AB

address: 11560 University Ave NW, Room 2308

country: Canada

institute: University of Alberta

description:
Library name: SRM14
CIN Tumor CIN Micronuclei 2

data_processing:
2. Bioinformatics Analysis Pipeline 2.1 Data quality control. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. 2.2 Reads mapping to the reference genome.  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools. 2.3 Quantification of gene expression level. 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCm39
Supplementary files format and content: gene_count.xls = gene counts in excel file for all samples
Supplementary files format and content: gene_fpkm.xls = gene fpkm in excel file for all samples

source_name: Orthotopic colorectal cancer tissue

extract_protocol:
Standard Trizol extraction procedure.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. For the non strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the strand specific library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Orthotopic colorectal cancer tissue

value: colorectal cancer


title: CIN Tumor MSI Free 2

description:
Library name: SRM15
CIN Tumor MSI Free 2


title: MSI Tumor CIN Micronuclei 2

description:
Library name: SRM10
MSI Tumor CIN Micronuclei 2


title: MSI Tumor MSI Free 2

description:
Library name: SRM11
MSI Tumor MSI Free 2


title: CIN Tumor MSI Micronuclei 2

description:
Library name: SRM13
CIN Tumor MSI Micronuclei 2


title: CIN Tumor CIN Free 1

description:
Library name: SRM8
CIN Tumor CIN Free 1


title: MSI Tumor CIN Free 2

description:
Library name: SRM12
MSI Tumor CIN Free 2


title: CIN Tumor MSI Micronuclei 1

description:
Library name: SRM5
CIN Tumor MSI Micronuclei 1


title: CIN Tumor CIN Micronuclei 1

description:
Library name: SRM6
CIN Tumor CIN Micronuclei 1


title: MSI Tumor CIN Free 1

description:
Library name: SRM4
MSI Tumor CIN Free 1


title: CIN Tumor CIN Free 2

description:
Library name: SRM16
CIN Tumor CIN Free 2


title: MSI Tumor MSI Free 1

description:
Library name: SRM3
MSI Tumor MSI Free 1


title: CIN Tumor MSI Free 1

description:
Library name: SRM7
CIN Tumor MSI Free 1


title: MSI Tumor MSI Micronuclei 1

description:
Library name: SRM1
MSI Tumor MSI Micronuclei 1


title: 1242_24mo

description:
Library name: 1242
Column name in raw_counts.txt: 1242 (23445170.0 total)

data_processing:
Alignment to GrCM38/mm10 using STAR aligner, tag counting using HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: txt files include raw count values for each Sample

source_name: Hepatocytes

extract_protocol:
Trizol-Chloroform extraction method
P_Stranded Library&Seq(PE100) BGI

value: Hepatocytes

value: WT

tag: date of_birth

tag: cull day

value: Male


title: 1244_5mo

description:
Library name: 1244
Column name in raw_counts.txt: 1244 (22893387.0 total)

tag: cell type


title: MSI Tumor MSI Micronuclei 2

description:
Library name: SRM9
MSI Tumor MSI Micronuclei 2

tag: cell line


title: MSI Tumor CIN Micronuclei 1

description:
Library name: SRM2
MSI Tumor CIN Micronuclei 1

tag: tissue


title: 1240_24mo

description:
Library name: 1240
Column name in raw_counts.txt: 1240 (23410670.0 total)

tag: genotype


title: 1238_24mo

description:
Library name: 1238
Column name in raw_counts.txt: 1238 (23215608.0 total)

tag: Sex


title: 1237_5mo

description:
Library name: 1237
Column name in raw_counts.txt: 1237 (21200659.0 total)


title: 1243_5mo

description:
Library name: 1243
Column name in raw_counts.txt: 1243 (22521788.0 total)


title: 1189_24mo

description:
Library name: 1189
Column name in raw_counts.txt: 1189 (23561851.0 total)


title: 1235_5mo

description:
Library name: 1235
Column name in raw_counts.txt: 1235 (21064074.0 total)


title: 1186_5mo

description:
Library name: 1186
Column name in raw_counts.txt: 1186 (21794507.0 total)


title: 1187_24mo

description:
Library name: 1187
Column name in raw_counts.txt: 1187 (23781337.0 total)


title: 1184_5mo

description:
Library name: 1184
Column name in raw_counts.txt: 1184 (21211055.0 total)


title: 1185_24mo

description:
Library name: 1185
Column name in raw_counts.txt: 1185 (23223159.0 total)


title: 1239_5mo

description:
Library name: 1239
Column name in raw_counts.txt: 1239 (22573937.0 total)


title: 1181_24mo

description:
Library name: 1181
Column name in raw_counts.txt: 1181 (23650119.0 total)


title: 1180_5mo

description:
Library name: 1180
Column name in raw_counts.txt: 1180 (22487980.0 total)


title: KO_274rep1,KO_274rep2

city: Shanghai

first: Qian

last: Wen

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

description: Library name: Sample8

data_processing:
fastp
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
The clear reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each Sample

source_name: liver

extract_protocol:
Collect the livers of mice from each treatment group and extract RNA using Trizol.
Total RNA was extracted and assessed for quality and quantity. mRNA was enriched using poly(A) selection with Oligo(dT) beads. The mRNA was then fragmented and reverse transcribed into cDNA using random primers. After second-strand synthesis, end repair and adapter ligation were performed. The resulting libraries were purified and amplified by PCR. Sequencing was carried out on the Illumina NovaSeq  platform.

value: liver

value: AF6 fl/fl, Alb cre

tag: treatment

value: HFHC diet for 16 weeks


title: KO_289rep1,KO_289rep2

description: Library name: Sample10


title: KO_202rep1,KO_202rep2

description: Library name: Sample7


title: 1188_5mo

description:
Library name: 1188
Column name in raw_counts.txt: 1188 (21038999.0 total)

tag: age


title: 1236_24mo

description:
Library name: 1236
Column name in raw_counts.txt: 1236 (23560035.0 total)


title: HF_KO52rep1,HF_KO52rep2

description: Library name: Sample6


title: KO_287rep1,KO_287rep2

description: Library name: Sample9


title: HM_278rep1,HM_278rep2

description: Library name: Sample5

value: AF6 fl/fl


title: HM_204rep1,HM_204rep2

description: Library name: Sample3


title: HF_HM51rep1,HF_HM51rep2

description: Library name: Sample2


title: HM_273rep1,HM_273rep2

description: Library name: Sample4


title: C207.5: CD8b+/CD45.1/+CD45.2+ lymph node T cells bearing the NP207 TCR

first: Jonathan

middle: S.

last: Duke-Cohan

state: MA

address: 450 Brookline Avenue JF517

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: Sample mouse C207.5
Column name in processed data files: C207.5

data_processing:
The paired output fasta files for each sample were checked for quality using FastQC, and adapters trimmed using FastqMcf and Cutadapt
Contaminating non-polyA-tailed RNA sequence, mitochondrial genome sequences, ribosomal RNAs and transfer RNAs were then removed using Bowtie2
The resulting filtered reads were aligned to the mouse reference genome assembly GRCm39 using STAR v2.7.3a
HTSeq-count was then used to count the reads aligned to each gene
Differential gene expression was performed using DESeq2
Assembly: GRCm39
Supplementary files format and content: "raw_read_counts_all.csv" contains raw gene reads for all samples in CSV format
Supplementary files format and content: "normalized_TPM_all.csv" contains normalized TPM for all samples in CSV format

extract_protocol:
Total RNA from the samples was isolated using the BD Arcturus PicoPure kit with on-column DNase digestion.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input kit with Tagmentation (Takara Bio USA, Inc.), Illumina adapters were added, and each sample library sequenced on the NovaSeq X Plus platform (2 x 250 bp paired end sequencing, 40 x 106 reads/sample).

treatment_protocol: Source cells are retrogenic CD8 T cells, each bearing a unique transduced TCR specific for the NP366 peptide of influenza A virus, that have been adoptively transferred into normal mice that are then infected with influenza virus. Following resolution of infection, at about 4 weeks, the retrogenic cells bearing congenic surface markers are separated by FACS away from host T cells in the mediastinal lymph nodes and deposited directly into lysis buffer for RNA extraction and transcriptome analysis

value: Mediastinal lymph node CD8+ T cells

value: retrogenic NP207 TCR

value: post-influenza response

tag: sample group


title: HF_HM47rep1,HF_HM47rep2

description: Library name: Sample1


title: C204.6: CD8b+/CD45.1+/+ lymph node T cells bearing the NP204 TCR

description:
Library name: Sample mouse C204.6
Column name in processed data files: C204.6

value: retrogenic NP204 TCR


title: C204.2: CD8b+/CD45.1+/+ lymph node T cells bearing the NP204 TCR

description:
Library name: Sample mouse C204.2
Column name in processed data files: C204.2


title: C202.3: CD8b+/Thy1.1+ lymph node T cells bearing the NP202 TCR

description:
Library name: Sample mouse C202.3
Column name in processed data files: C202.3

value: retrogenic NP202 TCR


title: C204.5: CD8b+/CD45.1+/+ lymph node T cells bearing the NP204 TCR

description:
Library name: Sample mouse C204.5
Column name in processed data files: C204.5


title: C202.7: CD8b+/Thy1.1+ lymph node T cells bearing the NP202 TCR

description:
Library name: Sample mouse C202.7
Column name in processed data files: C202.7


title: C207.2: CD8b+/CD45.1/+CD45.2+ lymph node T cells bearing the NP207 TCR

description:
Library name: Sample mouse C207.2
Column name in processed data files: C207.2


title: C207.4: CD8b+/CD45.1/+CD45.2+ lymph node T cells bearing the NP207 TCR

description:
Library name: Sample mouse C207.4
Column name in processed data files: C207.4


title: C202.6: CD8b+/Thy1.1+ lymph node T cells bearing the NP202 TCR

description:
Library name: Sample mouse C202.6
Column name in processed data files: C202.6


title: C204.3: CD8b+/CD45.1+/+ lymph node T cells bearing the NP204 TCR

description:
Library name: Sample mouse C204.3
Column name in processed data files: C204.3


title: C202.2: CD8b+/Thy1.1+ lymph node T cells bearing the NP202 TCR

description:
Library name: Sample mouse C202.2
Column name in processed data files: C202.2


title: C207.3: CD8b+/CD45.1/+CD45.2+ lymph node T cells bearing the NP207 TCR

description:
Library name: Sample mouse C207.3
Column name in processed data files: C207.3


title: 1182_5mo

description:
Library name: 1182
Column name in raw_counts.txt: 1182 (22301368.0 total)

tag: strain


title: C202.1: CD8b+/Thy1.1+ lymph node T cells bearing the NP202 TCR

description:
Library name: Sample mouse C202.1
Column name in processed data files: C202.1


title: C202.5: CD8b+/Thy1.1+ lymph node T cells bearing the NP202 TCR

description:
Library name: Sample mouse C202.5
Column name in processed data files: C202.5


title: C105.6: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.6
Column name in processed data files: C105.6

value: retrogenic NP105 TCR


title: C101.7: CD8b+/CD45.1+/CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.7
Column name in processed data files: C101.7

value: retrogenic NP101 TCR


title: C105.4: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.4
Column name in processed data files: C105.4


title: C105.7: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.7
Column name in processed data files: C105.7


title: C105.5: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.5
Column name in processed data files: C105.5


title: C101.5: CD8b+/CD45.1+/CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.5
Column name in processed data files: C101.5


title: C105.2: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.2
Column name in processed data files: C105.2


title: C101.6: CD8b+/CD45.1+/CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.6
Column name in processed data files: C101.6


title: 1183_24mo

description:
Library name: 1183
Column name in raw_counts.txt: 1183 (23177456.0 total)


title: C101.4: CD8b+/CD45.1+/CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.4
Column name in processed data files: C101.4


title: C105.1b: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.1b
Column name in processed data files: C105.1b


title: C101.3: CD8b+/CD45.1+/CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.3
Column name in processed data files: C101.3


title: C101.1: CD8b+/CD45.1/+CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.1
Column name in processed data files: C101.1


title: C101.2: CD8b+/CD45.1+/CD45.2+ lymph node T cells bearing the NP101 TCR

description:
Library name: Sample mouse C101.2
Column name in processed data files: C101.2


title: C105.1a: CD8b+/CD45.1+/+ lymph node T cells bearing the NP105 TCR

description:
Library name: Sample mouse C105.1a
Column name in processed data files: C105.1a


title: PD-L1

city: Changchun

first: Simiao

last: Wang

state: other

address: Jilin university

institute: Simiao Wang

description: Library name: PD_L1

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (v.3.0.2) for de-multiplexing, sequence alignment, quality control, and universal molecular identifiers (UMIs) quantification.
Assembly: rattus_norvegicus__ensembl-97
Supplementary files format and content: Raw

source_name: non-small cell lung cancer

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3.1 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and  sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics) according to the manufacturer’s  instructions. Sequencing was performed with Illumina  NovaSeq 6000  according to the manufacturer’s instructions (Illumina).
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3.1 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and  sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v3.1 reagent kit (10X Genomics) according to the manufacturer’s  instructions. Sequencing was performed with Illumina  NovaSeq 6000  according to the manufacturer’s instructions (Illumina).

value: non-small cell lung cancer


title: PBS

description: Library name: PBS


title: AI-Exo

description: Library name: AI_Exo


title: scRNA, mouse lymph node tissues with vector rep3

city: ChengDu

first: yucui

last: shang

address: No. 12 Linyin Street, Wuhou District

department: State Key Laboratory of Biotherapy and Cancer Center

institute: SiChuan University

description: Library name: Ren3

data_processing:
To identify tumor cells, we added the exogenous plasmid sequence into the mm10 genome reference. Cellranger (v7.0.1) was used to generate the index of the genome reference and align the raw data with the mm10 genome reference for the murine model.
Assembly: Mouse mm10
Supplementary files format and content: Tap-separated values files and matrix files

source_name: lymph node

extract_protocol:
The ground lymph node tissue was filtered through a 100-μm filter to obtain a single-cell suspension. The cell numbers were quantified, and the concentration was adjusted to 800-1200 cells/μl, with cell activity > 85%. Single-cell suspensions were subjected to scRNA-seq within an hour of acquisition, using the 10x genomics platform to construct the single-cell library of samples.
Single-cell RNA sequencing libraries were generated using the Chromium Single Cell 3’ Reagent Kits v3 (10x Genomics).

value: lymph node


title: scRNA, mouse lymph node tissues with vector rep2

description: Library name: Ren2


title: scRNA, Alox15b-knockdown mouse lymphoma tumor tissues treated with tucidinostat rep1

description: Library name: Chidamide1

source_name: lymphoma tumor tissues

value: lymphoma tumor tissues

value: tucidinostat


title: scRNA, Alox15b-knockdown mouse lymphoma tumor tissues treated with tucidinostat rep2

description: Library name: Chidamide2


title: scRNA, Alox15b-knockdown mouse lymphoma tumor tissues rep2

description: Library name: Vehicle2

value: vehicle


title: scRNA, Alox15b-knockdown mouse lymphoma tumor tissues rep1

description: Library name: Vehicle1


title: Larp1 KO Cortex rep 3.2

city: New Haven

first: Carson

middle: C

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

description: Library name: Nestin-Cre;Larp1-flox/flox Mouse 3.2

data_processing:
FASTQ files were trimmed using cutadapt.
Adapter trimmed files were aligned to the mm10 genome using STAR.
Gene level quantification was performed using rsem and UCSC gene annotations.
Assembly: mm10
Supplementary files format and content: FASTQ
Supplementary files format and content: RSEM

source_name: cortex

extract_protocol:
RNA was extracted from fresh cortex by homogenization and trizol.
Libraries were constructed from rRNA-depleted RNA using the NEB Ultra II Directional RNA-seq kit.

value: cortex

value: KO


title: Larp1 KO Cortex rep 3.1

description: Library name: Nestin-Cre;Larp1-flox/flox Mouse 3.1


title: scRNA, Alox15b-knockdown mouse lymphoma tumor tissues treated with tucidinostat rep3

description: Library name: Chidamide3


title: Larp1 KO Cortex rep 2.2

description: Library name: Nestin-Cre;Larp1-flox/flox Mouse 2.2


title: Larp1 KO Cortex rep 2.1

description: Library name: Nestin-Cre;Larp1-flox/flox Mouse 2.1


title: Larp1 KO Cortex rep 1.1

description: Library name: Nestin-Cre;Larp1-flox/flox Mouse 1.1


title: Larp1 WT Cortex rep 3.2

description: Library name: Nestin-Cre Mouse 3.2

value: WT


title: Larp1 WT Cortex rep 2.2

description: Library name: Nestin-Cre Mouse 2.2


title: Larp1 WT Cortex rep 3.1

description: Library name: Nestin-Cre Mouse 3.1


title: Larp1 WT Cortex rep 2.1

description: Library name: Nestin-Cre Mouse 2.1


title: Larp1 WT Cortex rep 1.1

description: Library name: Nestin-Cre Mouse 1.1


title: Larp1 KO Cortex rep 1.2

description: Library name: Nestin-Cre;Larp1-flox/flox Mouse 1.2


title: 3i_PAL_Day14_scATAC

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

description: Library name: Sample 3

data_processing:
The generated fastq files were processed with dnbc4tools (v2.1.2). We aligned the reads to the human genome hg38 assembly after creating the genome index file together with the GENCODE v32 annotation GTF file.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file listing the unique cell barcodes detected in the dataset. A sparse matrix in Matrix Market (MTX) format, containing accessibility count values for each peak across all barcoded cells.
Supplementary files format and content: A BED-formatted file listing the genomic regions (peaks) identified as open chromatin regions.

growth_protocol: The MACS-isolated iPSC-derived lung progenitor cells (LPs) were seeded in the 24-well micro-patterned plates for "2.5-dimensional culture" (Tosoh Co., Ltd.) with multiple round shaped cell-attachment areas in 100 μm diameter pre-coated with 0.5 ug/cm2 of iMatrix-511 silk (TaKaRa bio, 892021) at the cell densities 1x10^5 cells/well. These cells were cultured in "DCIK+3i" (CHIR99021, SB431542, and Y27632) medium for 7 days to induce AT2 cells, followed by an additional 7-day maintenance with DCIK+3i medium to induce AT2 cells, DCI+LATS medium to induce AT1 cells, and PAL medium to induce iATCs

extract_protocol:
The cell suspension after CPM MACS sorting was used as "CPM_MACS_progenitor". The micro-patterned cultured cells were dissociated by  0.5 mM EDTA/PBS and Accutase treatment and subjected to scRNA-seq.
Single-cell ATAC-seq libraries were prepared using DNBelab C Series High-throughput Single-cell ATAC Library Preparation Set (MGI, #940-000793-00), following the manufacturer’s protocol. After making the nuclei suspension, we subjected 100,000 nuclei to transposition reaction and 20,000 nuclei to droplet formation for each sample using DNBelab C-TaiM 4RS (MGI, #900-000637-00). PCR was first performed in droplets for 10 cycles. Then, after the subsequent demulsification and beads purification, PCR amplification was performed with scATAC Barcode primers for 12 cycles. We then converted the generated libraries to DNB through single-stranded circularization and rolling amplification.

value: iPSC-derived alveolar epithelial cells


title: Larp1 WT Cortex rep 1.2

description: Library name: Nestin-Cre Mouse 1.2


title: 3i_Day14_scATAC

description: Library name: Sample 1


title: 3i_LATS_Day14_scATAC

description: Library name: Sample 2


title: 9. GM1301 (PD-T4-8) T4 Phage DNA

city: Boston

first: Amy

middle: Si-Ying

last: Lee

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

description: Library name: 9. GM1301 (PD-T4-8) T4 Phage DNA

data_processing:
Paired-end reads were quality and adapter trimmed using Cutadapt to remove adapter sequences, poly-A/T, and low-quality bases (Q<30), retaining only reads ≥20 nt in length.
Cutom genome indices were built from FASTA files using bowtie2-build. Reads were aligned to either pGEM9z plasmid or T4 phage reference genomes using Bowtie2 to produce SAM alignment files.
SAM files were converted to sorted and indexed BAM format using Samtools (1.21)
Fragment lengths and strand-specific 5 prime end counts were extracted using the Bioconductor Rsamtools package in R (4.3.1).
The top 100 5 prime ends were used to extract ±10 nucleotide windows from the reference genome using Bsgenome and GenomicRanges R packages. Fasta sequences were saved for downstream WebLogo motif analysis.
Assembly: pGEM9z plasmid
Assembly: T4 phage
Supplementary files format and content: BigWig (.bw) files for each sample contain read coverage tracks generated from BAM files.

organism: Escherichia coli

source_name: bacteria

extract_protocol:
1 M Tris-HCl pH 8.0, 10% SDS, and 0.5 M EDTA pH 8.0 were added to the cleavage reaction followed by 10% SDS to reach 500 µL total volume. 500 µL of Phenol:Chlorofom:Isoamyl Alchol 25:24:1 Saturated with 10 mM Tris, pH 8.0, 1 mM EDTA (Sigma Aldrich) was added, vortexed, centrifuged, and the resulting aqueous phage was added to 50 µL 3M NaOAc and 1 µL 20 mg mL−1 glycogen. 1 mL of 100% ethanol was added, vortexed, and samples were stored at −20°C overnight. The following day, samples were pelleted and washed with 70% ethanol three times before resuspension in RNase-free dH2O.
Sequencing libraries were made from single stranded DNA fragments using a xGEN kit (IDT) and sequenced on a NextSeq500

treatment_protocol: Nuclease-NTPase protein concentrations were optimized to generate 100–600 bp DNA fragments required for DNA sequencing. 25 nM PaAbpAB, 75 nM BtHachiman, 1 µM EcPD-T4-8 were individually incubated with 400 ng pGEM9Z plasmid in a 40 µL reactions with DNA cleavage buffer (20 mM Tris-HCl pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM MnCl2, 1 mM DTT). 25 nM PaAbpAB, 1 µM BmAzaca, 25 nM BtHachiman, and 1 µM EcPD-T4-8 were individually incubated with 400 ng phage T4 DNA in 40 µL reactions with DNA cleavage buffer. Proteins were diluted in gel filtration buffer supplemented with 10% glycerol. Reactions were incubated at 37°C for 30 min followed by 100 µg mL−1 Proteinase K treatment at 50°C for 30 min.

value: bacteria


title: 8. GM1301 (PD-T4-8) pGEM9z

description: Library name: 8. GM1301 (PD-T4-8) pGEM9z