title: RSV-TMX rep4

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

description:
Library name: 236
10X Genomics

data_processing:
CellRanger v 8.0 was used to generate filtered barcode files.  The sequences were mapped to the Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv. Cells captured are listed in the 'captured_cells.txt'.
STAR (version 2.5.2a) was used for mapping. Reads were aligned to the mm10 reference genome (provided by the Dropseq group, GSE63269).  For barcode filtering, we excluded barcodes with <200 detected genes. Cells with >10% mitochondrial reads, and >5000 UMIs were filtered from further analysis.  Downstream analysis was in ScanPy (Python).  Doublets were identified and removed using nearest-neighbor classifier (Scrublet)(38).  Batch effects were corrected using SciV.  Counts were normalized to median total counts, log transformed and PCA clustered.  Highly variable genes were identified using Seurat.  Nearest neighbor clustering was using Leiden.  Cell annotation followed best practices manually validated using PanglaoDB.  Differential gene expression was using pseudobulk correcting for multiple hypothesis using moderated estimation in DESEQ2.
Assembly: Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv
Supplementary files format and content: features, barcodes and matrix as .tsv.gz files

organism:
Mus musculus
Human respiratory syncytial virus A strain Long

source_name: lung

growth_protocol: mouse experiments described below

extract_protocol:
The right lung was digested in Dispase II (100mg/mL), Collagenase A (10mg/mL), DNAse I (1500 kU/mL), and CaCl2 (0.25M) into a single cell solution using a 40 mm filter to create a single cell solution. Half the cells were separated for Single Cell Sequencing.
Libraries were constructed according to the Chromium NextGEM Fixed RNA Profiling Reagent Kits user guide (10x Genomics). Cells frozen in 10X Genomics Quenching Buffer were thawed and resuspended in 0.5X PBS with 0.02% BSA. The total cell number was quantified on the Luna-FX7 automated cell counter (Logos Biosystems, Anyang, South Korea) using acridine orange/propidium iodide stain. Aliquots of less than two million cells were used as input for the probe hybridization reaction and incubated at 42C overnight (21 hours 16 minutes). Following overnight incubation, subsets of four samples with unique probe barcodes were pooled together and washed three times with 10X Genomics Post-Hyb Wash Buffer. Samples were filtered through 30 μm Celltrics filters (Sysmex, Kobe, Japan) and the appropriate volume of cells was loaded onto a Single Cell Chip Q required for recovery of [enter captured cell number] cells.  Following the completion of the Chromium run the GEMs were transferred to emulsion safe strip tubes for the cell and UMI barcoding reaction using an Eppendorf MasterCycler Pro thermocycler (Eppendorf, Hamburg, Germany). After the GEM incubation, GEMs were broken, and the barcoded probe products were amplified by PCR. A portion of the amplified probe products was put into a second PCR reaction to add unique dual indexes to each library. The final libraries were quantified on the Qubit v4 fluorometer (ThermoFisher Scientific) and profiled on the Agilent 4200 Tapestation (Agilent Technologies, Santa Clara, CA). These libraries were sequenced on a NovaSeq X+ sequencer with paired-end, 150bp sequencing. Data was processed with bcl2fastq.

treatment_protocol: Scgb1a1-Cre X RelAfl/fl mice were Mock (PBS) or RSV-infected 3-5 weeks after birth (107 PFU).  Three days post-infection, when inflammation/viral replication resolved, mice were randomized into corn oil (10% ethanol and 90% corn oil; RelA WT) or tamoxifen (TMX) treatment (20 mg/kg/d i.p.; Sigma Aldrich, St. Louis, MO; T5648; RelA CKO) for 10 doses.  Animals were then rested for an additional week (21d post-RSV infection) before they were euthanized and lungs collected.

value: lung

value: scgb1a1-Cre X RelA fl/fl

value: TMX-RSV


title: SNI, 14DPA, Replicate 2

status: Public on Apr 01 2026

type: SRA

city: Guelph

first: Samantha

last: Payne

state: ON

address: 50 Stone Road East

country: Canada

institute: University of Guelph

description:
Library name: Sample 13
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 2).

library_source: transcriptomic

data_processing:
RNA integrity and quantity were assessed using an Agilent 4200 TapeStation prior to library preparation.
Libraries were sequenced on an Illumina NextSeq 2000 using a single-end 1×50 bp configuration
Assembly: GRCm39 (Mus musculus)
Supplementary files format and content: Raw read counts were analyzed in RStudio (v2024.12.1).

molecule: polyA RNA

organism: Mus musculus

source_name: distal left hindlimb regenerate digit, nail removed

extract_protocol:
After euthanasia, tissue distal to the metacarpophalangeal joint was collected, the nail was removed, and samples were stored at −80 degrees celsius. Frozen tissue was mechanically disrupted using rotational shearing blades, homogenized using QIAshredder columns, and total RNA was isolated with DNase treatment using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA-seq libraries were prepared from 500 ng of total RNA following poly(A) mRNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Strand-specific cDNA libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit, amplified for nine PCR cycles, and prepared according to the manufacturer’s protocol.

treatment_protocol: Spared nerve injury (SNI) mice received surgery in which the common peroneal and tibial branches of the sciatic nerve on the left hindlimb were transected. SHAM-operated mice underwent an identical surgical procedure without nerve transection. Five days following surgery mice underwent amputation through the third phalanx of the left hindlimb to induce regeneration of the digit tip.

tag: tissue

tag: time

value: 14 days post amputation

tag: treatment

value: SNI surgery denervation

tag: replicate

value: replicate 2


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_Dox_7d_Rep1

city: Miami

first: sanxiong

last: liu

state: FL

address: 1501 NW 10th Avenue

department: Human Genetics

country: USA

institute: University of Miami Miller School of Medicine

description: Library name: Sample 119

data_processing:
Raw sequencing reads (FASTQ files) were processed using the nf-core/slamseq pipeline (v1.0.0). Initial read quality was assessed with FastQC (v0.11.9). Adapters and low-quality sequences were trimmed using TrimGalore! (v0.6.4_dev). The core processing, including conversion-aware alignment, filtering, SNP masking, and quantification, was performed using Slamdunk (v0.4.3) with default parameters. Reads were aligned to the human genome reference (GRCh38), using gene and 3' UTR annotations derived from the UCSC Table Browser for GRCh38. Slamdunk was used to quantify reads at the gene level, specifically generating counts for total reads and counts for reads containing T>C conversions (indicative of newly synthesized RNA, defined in the analysis as reads with >2 T>C conversions). The submitted processed data files consist of these gene-level count matrices generated by Slamdunk.
Assembly: hg38
Supplementary files format and content: Each processed data file corresponds to a single experimental sample and is provided in comma-separated value (.csv) format. Within each file, rows represent individual transcripts identified by their RefSeq transcript ID. The columns contain transcript-level quantification and metric data generated by Slamdunk, including:
* readCount: Raw count of total reads mapping to the transcript.
* tcReadCount: Raw count of reads identified as containing T>C conversions (representing newly synthesized RNA, based on the pipeline's criteria, e.g., >2 T>C conversions per read).
* length: The length of the transcript.
* readsCPM: Reads Per Million mapped reads (calculated for total reads).
* conversionRate: The calculated T>C conversion rate for reads mapping to this transcript.
* Tcontent: The proportion of thymine bases within the transcript sequence.
* coverageOnTs: Coverage depth specifically over thymine bases.
* conversionsOnTs: Number of T>C conversions observed at thymine positions.
* multimapCount: Count related to multi-mapping reads assigned to the transcript.

molecule: total RNA

organism: Homo sapiens

growth_protocol: KMS-11 cells are cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
Cells were metabolically labeled with 100 µM 4-thiouridine (4sU) for 1 hour. Total RNA was extracted using TRIzol reagent followed by purification with the RNA Clean & Concentrator-5 kit (Zymo Research). 10 µg of RNA was then alkylated with iodoacetamide, followed by another cleanup using the RNA Clean & Concentrator-5 kit. 1 µg of the resulting RNA was used as input for library construction.
Sequencing libraries were prepared from 1 µg of alkylated total RNA using the QuantSeq 3’mRNA-Seq Library Prep FWD Kit for Illumina (Lexogen #015), following the manufacturer's protocol.

treatment_protocol: NSD2dTAG KMS-11 cells were treated with dTAGV-1 (100 nM) to induce NSD2 degradation. For specific experiments, NSD2-depleted cells were subsequently treated either with doxycycline (100 ng/ml) for reconstitution studies, or with the PRC2 inhibitors EPZ-6438 (200 nM) or MAK-658 (50 nM), or a DMSO vehicle control. The specific duration of each treatment varied according to the experimental condition and is indicated in the metadata associated with each sample.

tag: cell line

tag: genotype

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution

value: Doxycycline for 7d


title: RSV-TMX rep3

description:
Library name: 233
10X Genomics

library_source: transcriptomic single cell


title: SNI, 7DPA, Replicate 2

description:
Library name: Sample 10
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 2).

value: distal left hindlimb regenerate digit, nail removed

value: 7 days post amputation


title: RSV-corn oil rep4

description:
Library name: 225
10X Genomics

value: corn oil-RSV


title: SNI amputation, 7DPA, Replicate 2

description:
Library name: Sample 19
Bulk RNA-seq of regenerated mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 2).

value: SNI surgery denervation with amputation


title: SNI, 14DPA, Replicate 3

description:
Library name: Sample 14
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 3).

value: replicate 3


title: SNI, 7DPA, Replicate 3

description:
Library name: Sample 11
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 3).


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_0d_Rep2

description: Library name: Sample 116

value: No


title: SHAM, 21DPA, Replicate 2

description:
Library name: Sample 8
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 21 days post-amputation (biological replicate 2).

value: 21 days post amputation

value: SHAM surgery


title: SHAM, 21DPA, Replicate 1

description:
Library name: Sample 7
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 21 days post-amputation (biological replicate 1).

value: replicate 1


title: RSV-TMX rep1

description:
Library name: 231
10X Genomics

value: lung


title: RSV-TMX rep2

description:
Library name: 232
10X Genomics

value: scgb1a1-Cre X RelA fl/fl


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_7d_Rep2

description: Library name: Sample 118

value: dTAGv1 for 7d


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_7d_Rep1

description: Library name: Sample 117


title: SHAM, 14DPA, Replicate 3

description:
Library name: Sample 6
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 14 days post-amputation (biological replicate 3).

value: 14 days post amputation


title: RSV-corn oil rep3

description:
Library name: 223
10X Genomics


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_21d_Rep2

description: Library name: Sample 114

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: dTAGv1 and Doxycycline for 21d


title: SHAM, 14DPA, Replicate 2

description:
Library name: Sample 5
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 14 days post-amputation (biological replicate 2).

value: replicate 2


title: RSV-corn oil rep2

description:
Library name: 222
10X Genomics


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2Y1179A_dTAGv1_Dox_0d_Rep1

description: Library name: Sample 115

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution


title: SNI, 14DPA, Replicate 1

description:
Library name: Sample 12
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 14 days post-amputation (biological replicate 1).

value: distal left hindlimb regenerate digit, nail removed

value: SNI surgery denervation


title: RSV-corn oil rep1

description:
Library name: 221
10X Genomics

value: corn oil-RSV


title: Lin- cells, Luciferase control, IgG antibody, batch 4

city: Portland

first: Julia

last: Maxson

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description: Library name: mouse_batch4_LUC_IgG

library_source: genomic

data_processing:
Paired-end reads were trimmed using Fastp with adapter detection and poly-G trimming.
Trimmed reads from K562 samples were aligned to the human genome (GRCh38/hg38) and trimmed reads from mouse Lin- samples were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 with parameters “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”.
Duplicates were marked using the Sambamba “markdup” subcommand.
Peaks were called with GoPeaks using IgG samples as negative controls.
K562 CUT&RUN samples were sequenced across multiple batches. Samples from Batch 3 use an in-batch IgG control (K562_noDOX_IgG_3) for peak calling. K562 CUT&RUN samples from Batch 2 use the IgG control (K562_noDOX_IgG_1) from Batch 1 for peak calling. The IgG from Batch 2 yielded insufficient read depth to reliably model background signal and was therefore not used. The Batch 1 IgG sample used for peak calling was prepared using the same cell line and protocols as the experimental samples, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Mouse lineage-negative CUT&RUN samples were sequenced across multiple batches. Batch 1 samples (KAT7 and KMT2A samples) used the Batch 1 IgG control (mouse_batch1_LUC_IgG) for peak calling, which had similarly high read depth as the experimental samples in that batch, making it suitable for background modeling. Batches 2-3 used the Batch 4 IgG control (mouse_batch4_LUC_IgG) for peak calling. Batch 2 (sequenced on NovaSeq 6000) did not originally include an IgG control, and Batch 3 included an IgG control that had insufficient read depth and could not be used to reliably model background signal. The Batch 4 IgG control had read depth similar to samples in Batches 2-3, allowing for consistent background estimation and peak calling when in-batch controls were not usable.
Spike-in DNA from E. coli K-12 MG1655 was provided in the Epicypher CUT&RUN kit and used according to the manufacturer's protocols. To determine normalization factors for signal visualization, reads were aligned to host and E. coli reference genomes, and uniquely aligned reads were retained. Spike-in percentages were calculated as the proportion of reads mapping to E. coli relative to reads mapping to the host genome. Normalization factors were then calculated based on the relative spike-in percentages, scaled to the sample with the lowest spike-in recovery within each antibody target, consistent with Epicypher guidelines. Spike-in normalization was applied to the histone mark samples (H3K14ac, H3K23ac), as these samples had consistent spike-in recovery across replicates within each condition. BigWig coverage tracks for these samples were generated using spike-in derived scale factors with deepTools bamCoverage (--binSize 10 --smoothLength 50 --scaleFactor <sample-specific value>). Other antibody targets were not spike-in normalized due to variable spike-in recovery across replicates. For these samples, counts-per-million (CPM) normalized bigWig tracks were generated using deepTools bamCoverage with parameters “--binSize 10 --smoothLength 50 --normalizeUsing CPM”.
Assembly: GRCh38 (hg38) for samples from K562 cells, GRCm38 (mm10) for samples from mouse lineage-negative bone marrow cells
Supplementary files format and content: BigWig files include either spike-in normalized (for histone marks) or CPM-normalized (for other antibody targets) read signal for each sample.
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: K562 cells were grown in IMDM medium with 10% FBS, 2mM glutamine, 1x penicillin/streptomycin. Mouse lineage-negative (Lin-) bone marrow primary cells were grown in IMDM medium with 15% FBS, 2mM glutamine, 1x penicillin/streptomycin in the presence of SCF, IL6, and IL3.

extract_protocol:
Cells were harvested following the EpiCypher CUT&RUN kit protocol (EpiCypher CUTANA 14-1048).
CUT&RUN libraries were prepared using the New England Biolabs NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: K562 cells were either induced with 250ng/mL of doxycycline or not induced with any doxycycline for 24 hours. For mouse lineage-negative (Lin-) CUT&RUN, lentivirus were generated by co-transfecting psPAX2 (Addgene: 12260), pMD2.G (Addgene: 12259), and pSMAL_Luciferase (control) or pSMAL_SETBP1D868N into LentiX cells (Takara) with Fugene 6 (Promega E2691), according to the manufacturer's instructions. Mouse lineage-negative bone marrow cells were lentivirally transduced with either a control (luciferase) or SETBP1D868N mutant and then GFP-sorted.

value: Bone marrow

tag: cell type

value: lineage-negative bone marrow primary cells

value: wild-type

value: lentiviral transduction with control (luciferase)

tag: cutrun antibody

value: IgG (EpiCypher, 13-0042k)

tag: genome assembly

value: GRCm38 (mm10)

tag: sequencing batch


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_21d_Rep2

description: Library name: Sample 110

value: dTAGv1 for 21d


title: Lin- cells, Luciferase control, H3K23ac antibody, rep2

description: Library name: mouse_batch3_LUC_H3K23ac_2

value: H3K23ac (Cell Signaling Technology, 86664)


title: Lin- cells, Luciferase control, H3K23ac antibody, rep1

description: Library name: mouse_batch3_LUC_H3K23ac_1


title: SHAM, 7DPA, Replicate 1

description:
Library name: Sample 1
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 7 days post-amputation (biological replicate 1).

value: 7 days post amputation

value: SHAM surgery

value: replicate 1


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_21d_Rep1

description: Library name: Sample 113

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: dTAGv1 and Doxycycline for 21d


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_Dox_21d_Rep1

description: Library name: Sample 111

value: Doxycycline for 21d


title: Lin- cells, SETBP1D868N mutant, H3K23ac antibody, rep2

description: Library name: mouse_batch3_SETBP1-D868N_H3K23ac_2

value: lentiviral transduction with SETBP1D868N mutant


title: SHAM, 14DPA, Replicate 1

description:
Library name: Sample 4
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 14 days post-amputation (biological replicate 1).

value: distal left hindlimb regenerate digit, nail removed

value: 14 days post amputation


title: SNI, 21DPA, Replicate 1

description:
Library name: Sample 15
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 21 days post-amputation (biological replicate 1).

value: 21 days post amputation

value: SNI surgery denervation


title: Lin- cells, SETBP1D868N mutant, H3K23ac antibody, rep3

description: Library name: mouse_batch3_SETBP1-D868N_H3K23ac_3

value: Bone marrow

value: lineage-negative bone marrow primary cells

value: wild-type


title: SHAM, 7DPA, Replicate 3

description:
Library name: Sample 3
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 7 days post-amputation (biological replicate 3).

value: replicate 3


title: Control diet, no infection, 6

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: IT72

data_processing:
Adaptor sequences and low quality reads removed
Mapped to D. rerio genome (GRCz11_release100)
DEG determined using DESeq2
Assembly: GRCz11_release100
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Danio rerio

source_name: Intestine

extract_protocol:
RNA was extracted from 43 fish intestine using the RNAeasy minikits (Qiagen).
standard Illumina

value: Intestine


title: Control diet, infection, 9

description: Library name: IT66


title: Lin- cells, SETBP1D868N mutant, H3K23ac antibody, rep1

description: Library name: mouse_batch3_SETBP1-D868N_H3K23ac_1

value: H3K23ac (Cell Signaling Technology, 86664)

value: GRCm38 (mm10)


title: SHAM, 7DPA, Replicate 2

description:
Library name: Sample 2
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from a sham-operated animal at 7 days post-amputation (biological replicate 2).

value: 7 days post amputation

value: SHAM surgery

value: replicate 2


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_Dox_21d_Rep2

description: Library name: Sample 112

value: NSD2_dTAG knockin and NSD2WT reconstitution


title: Lin- cells, Luciferase control, H3K23ac antibody, rep3

description: Library name: mouse_batch3_LUC_H3K23ac_3

value: lentiviral transduction with control (luciferase)


title: Lin- cells, SETBP1D868N mutant, KMT2A antibody, rep3

description: Library name: mouse_batch1_SETBP1-D868N_KMT2A_3

value: lentiviral transduction with SETBP1D868N mutant

value: KMT2A (Cell Signaling Technology, 14689)


title: Control diet, no infection, 5

description: Library name: IT71


title: Control diet, infection, 8

description: Library name: IT65


title: Control diet, no infection, 4

description: Library name: IT70


title: Lin- cells, SETBP1D868N mutant, KMT2A antibody, rep2

description: Library name: mouse_batch1_SETBP1-D868N_KMT2A_2


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_21d_Rep1

description: Library name: Sample 109

value: dTAGv1 for 21d


title: Lin- cells, SETBP1D868N mutant, KMT2A antibody, rep1

description: Library name: mouse_batch1_SETBP1-D868N_KMT2A_1


title: Lin- cells, SETBP1D868N mutant, KAT7 antibody, rep3

description: Library name: mouse_batch1_SETBP1-D868N_KAT7_3

value: KAT7 (Cell Signaling Technology, 58418)


title: Lin- cells, SETBP1D868N mutant, KAT7 antibody, rep2

description: Library name: mouse_batch1_SETBP1-D868N_KAT7_2


title: Control diet, infection, 5

description: Library name: IT62


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_14d_Rep1

description: Library name: Sample 107

value: dTAGv1 and Doxycycline for 14d


title: Control diet, infection, 7

description: Library name: IT64


title: Lin- cells, Luciferase control, KMT2A antibody, rep2

description: Library name: mouse_batch1_LUC_KMT2A_2

value: Bone marrow


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_Dox_14d_Rep2

description: Library name: Sample 106

value: Doxycycline for 14d


title: Lin- cells, Luciferase control, KAT7 antibody, rep2

description: Library name: mouse_batch1_LUC_KAT7_2

value: lineage-negative bone marrow primary cells

value: wild-type


title: Lin- cells, Luciferase control, KAT7 antibody, rep1

description: Library name: mouse_batch1_LUC_KAT7_1


title: Control diet, infection, 6

description: Library name: IT63

value: Intestine


title: Lin- cells, Luciferase control, IgG antibody, batch 1

description: Library name: mouse_batch1_LUC_IgG

value: IgG (EpiCypher, 13-0042k)


title: Inulin diet, no infection, 6

description: Library name: IT60


title: Control diet, infection, 4

description: Library name: IT61


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_14d_Rep2

description: Library name: Sample 104

value: dTAGv1 for 14d


title: Lin- cells, SETBP1D868N mutant, KAT7 antibody, rep1

description: Library name: mouse_batch1_SETBP1-D868N_KAT7_1

value: GRCm38 (mm10)


title: Lin- cells, Luciferase control, KMT2A antibody, rep1

description: Library name: mouse_batch1_LUC_KMT2A_1


title: Inulin diet, no infection, 5

description: Library name: IT59


title: Lin- cells, Luciferase control, KAT7 antibody, rep3

description: Library name: mouse_batch1_LUC_KAT7_3


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_14d_Rep1

description: Library name: Sample 103


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_Dox_14d_Rep1

description: Library name: Sample 105


title: Lin- cells,  SETBP1D868N mutant, rep3

description:
Library name: pSmal_SETBP1-D868N_3
Column name in raw counts 241002_RNA-raw-counts.txt: SETBP1-D868N_3

data_processing:
Paired-end reads were trimmed using Fastp with adapter detection and poly-G trimming.
Trimmed reads were aligned to the mouse genome (GRCm38/mm10) using STAR.
For each experiment, a raw gene-level counts matrix was generated from STAR-aligned reads. DESeq2 was used for read count normalization and differential expression analysis.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text files contains raw counts for each sample.

growth_protocol: For mouse bone marrow lineage-negative cells: IMDM medium with 15% FBS, 2mM glutamine, 1x penicillin/streptomycin in the presence of SCF, IL6, and IL3.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen, 74106). 500ng of total RNA (or 100ng of total RNA for MYST inhibitor experiment) was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Watchmaker mRNA Library Prep Kit (7K0105-024) following manufacturer's protocols. For MYST inhibitor profiling, 100 ng of total RNA was submitted to Novogene for library preparation and sequencing.

treatment_protocol: Lentivirus were generated by co-transfecting psPAX2 (Addgene: 12260), pMD2.G (Addgene: 12259), and pSMAL_Luciferase (control) or pSMAL_SETBP1D868N into LentiX cells (Takara) with Fugene 6 (Promega E2691), according to the manufacturer's instructions. Mouse lineage-negative (Lin-) bone marrow primary cells were lentivirally transduced with either a control (luciferase) or SETBP1D868N mutant. To assess transcriptional changes following MYST inhibitor treatment, RNA-seq analysis was also conducted in mouse bone marrow lineage-negative (Lin⁻) primary cells lentivirally transduced with the SETBP1D868N mutant, followed by treatment with DMSO or PF-9363 (2.5uM) for 4 days.


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_14d_Rep2

description: Library name: Sample 108


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_7d_Rep2

description: Library name: Sample 102

value: dTAGv1 and Doxycycline for 7d


title: Lin- cells, Luciferase control, KMT2A antibody, rep3

description: Library name: mouse_batch1_LUC_KMT2A_3


title: Lin- cells,  SETBP1D868N mutant, rep2

description:
Library name: pSmal_SETBP1-D868N_2
Column name in raw counts 241002_RNA-raw-counts.txt: SETBP1-D868N_2


title: Inulin diet, no infection, 4

description: Library name: IT58


title: Lin- cells,  SETBP1D868N mutant, rep1

description:
Library name: pSmal_SETBP1-D868N_1
Column name in raw counts 241002_RNA-raw-counts.txt: SETBP1-D868N_1


title: Lin- cells, Luciferase control, rep3

description:
Library name: pSmal_LUC_3
Column name in raw counts 241002_RNA-raw-counts.txt: LUC_3


title: Inulin diet, infection, 8

description: Library name: IT54


title: SNI, 7DPA, Replicate 1

description:
Library name: Sample 9
Bulk RNA-seq of mouse digit tissue distal to the metacarpophalangeal joint from an SNI denervated animal at 7 days post-amputation (biological replicate 1).

value: distal left hindlimb regenerate digit, nail removed

value: 7 days post amputation

value: SNI surgery denervation

value: replicate 1


title: Lin- cells, Luciferase control, rep2

description:
Library name: pSmal_LUC_2
Column name in raw counts 241002_RNA-raw-counts.txt: LUC_2

value: lentiviral transduction with control (luciferase)


title: Lin- cells, Luciferase control, rep1

description:
Library name: pSmal_LUC_1
Column name in raw counts 241002_RNA-raw-counts.txt: LUC_1


title: Inulin diet, infection, 6

description: Library name: IT51


title: T-ALL cell line 2696, Vincristine treated resistant cells

city: New haven

first: Dengchao

last: cao

state: CT

address: 300 george st, room6122

institute: Yale university

description:
Library name: 23_VR2696
Column name in FPKM_All_samples.csv:23_VR2696_S23

data_processing:
Raw sequencing reads were trimmed to remove adapter sequences and low-quality bases using Cutadapt. Trimmed reads were aligned to the mouse reference genome (mm10) and annotated transcripts using the STAR aligner. Read quantification was performed against RefSeq release dated 2/8/17 using the Partek Flow expectation/maximization (E/M) algorithm. Expression levels were normalized and reported as fragments per kilobase of transcript per million mapped reads (FPKM). Lowly expressed genes were filtered out using a geometric mean cutoff of 1.0 to reduce noise. Differential gene expression analysis between groups was conducted using the GSA statistical method.
Assembly: mm10
Supplementary files format and content: csv. files includes FPKM values for each sample

source_name: Thymus

growth_protocol: Mcm2hypo T-ALL cells were maintained in DMEM supolemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using the RNeasy Kit (Qiagen, catalog no. 13323) according to the manufacturer’s instructions.
RNA libraries were prepared using the Illumina Stranded mRNA Prep kit (Illumina) following manufacturer’s instructions.

value: Thymus

value: precursor T cell lymphoblastic leukemia/lymphoma

value: Vincristine

tag: batch


title: T-ALL cell line 2883, Methotrexate treated resistant cells

description:
Library name: 16_MTX2883
Column name in FPKM_All_samples.csv:16_MTX2883_S16

value: Methotrexate


title: Egg diet, no infection, 6

description: Library name: IT48


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_0d_Rep1

description: Library name: Sample 95

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: No


title: Egg diet, no infection, 4

description: Library name: IT46


title: Inulin diet, infection, 7

description: Library name: IT52


title: T-ALL cell line 2883, Prednisone treated resistant cells

description:
Library name: 19_PD2883
Column name in FPKM_All_samples.csv:19_PD2883_S19

value: Prednisone


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_7d_Rep2

description: Library name: Sample 98

value: dTAGv1 for 7d


title: Egg diet, no infection, 5

description: Library name: IT47

value: Intestine


title: T-ALL cell line 2883, Etoposide treated resistant cells

description:
Library name: 13_EP2883
Column name in FPKM_All_samples.csv:13_EP2883_S13

value: Etoposide


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_Dox_7d_Rep1

description: Library name: Sample 99

value: Doxycycline for 7d


title: T-ALL cell line 2869, Vincristine treated resistant cells

description:
Library name: 24_VR2869
Column name in FPKM_All_samples.csv:24_VR2869_S24


title: T-ALL cell line 2696, Etoposide treated resistant cells

description:
Library name: 14_EP2696
Column name in FPKM_All_samples.csv:14_EP2696_S14


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_7d_Rep1

description: Library name: Sample 101

value: dTAGv1 and Doxycycline for 7d


title: T-ALL cell line 2883, Vincristine treated resistant cells

description:
Library name: 22_VR2883
Column name in FPKM_All_samples.csv:22_VR2883_S22


title: T-ALL cell line 2641, Prednisone treated resistant cells

description:
Library name: 20_PD2641
Column name in FPKM_All_samples.csv:20_PD2641_S20


title: Inulin diet, infection, 5

description: Library name: IT49


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_Dox_0d_Rep2

description: Library name: Sample 96


title: SLAMseq_KMS11_NSD2dTAG#11_NSD2WT_dTAGv1_7d_Rep1

description: Library name: Sample 97


title: T-ALL cell line 2869, Cytarabine treated resistant cells

description:
Library name: 12_CR2869
Column name in FPKM_All_samples.csv:12_CR2869_S12

value: Cytarabine


title: T-ALL cell line 2869, parental control

description:
Library name: 6_Par2869
Column name in FPKM_All_samples.csv:6_Par2869_S6

value: PBS


title: T-ALL cell line 2883, Cytarabine treated resistant cells

description:
Library name: 11_CR2883
Column name in FPKM_All_samples.csv:11_CR2883_S11


title: T-ALL cell line 2641, parental control

description:
Library name: 5_Par2641
Column name in FPKM_All_samples.csv:5_Par2641_S5


title: Egg diet, infection, 6

description: Library name: IT39


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_Dox_21d_Rep2

description: Library name: Sample 92

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution

value: Doxycycline for 21d


title: Egg diet, infection, 7

description: Library name: IT40


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_21d_Rep2

description: Library name: Sample 94

value: dTAGv1 and Doxycycline for 21d


title: T-ALL cell line 7298, Cytarabine treated resistant cells

description:
Library name: 7_CR7298
Column name in FPKM_All_samples.csv:7_CR7298_S7

value: Thymus

value: T cell lymphoblastic leukemia/lymphoma

value: SCL/LMO1 transgenic


title: T-ALL cell line 2883, parental control

description:
Library name: 3_Par2883
Column name in FPKM_All_samples.csv:3_Par2883_S3

value: precursor T cell lymphoblastic leukemia/lymphoma


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_21d_Rep1

description: Library name: Sample 89

value: dTAGv1 for 21d


title: Egg diet, infection, 5

description: Library name: IT38


title: H2AK119ub1 WT 14dGOs rep2

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Library name: Sample11

data_processing:
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: ovary

extract_protocol:
After ZP of SN-type FGOs were removed by acid tyrodes’ solution, ZP-free oocytes were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80C until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21C or 37C for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021).
CATCH-seq is an improved method of the ultra-low-input native ChIP-seq (ULI-NChIP). The original protocol of CATCH-seq was described in Zhu et al., and we have made some modifications to improve its usability. For each immunoprecipitation reaction, 0.25 µL of rabbit anti-H3K4me3 (Active Motif 39159, 70 oocytes/library), 500 ng of rabbit anti-H3K27me3 (Diagenode C15410069, 50-80 oocytes/library), 1.0 µg of mouse anti-H3K36me2 (MBL, MABI0332, 100 oocytes/library) or 1.0 µL of rabbit anti-H3K36me3 antibody (Active Motif 61022, MABI0333, 100 oocytes/library) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. CUT&RUN libraries were prepared as previously described (Hayashi, R. & Inoue, A). The antibodies used were rabbit anti-H3K27me3 (1/100, Diagenode C15410069, 150-170 oocytes/library). Protein A-MNase was provided by Dr. Steven Henikoff’s laboratory (Skene et al.). CUT&RUN libraries were sequenced on a NextSeq500 or Nextseq2000 with paired-end or single-end reads (Illumina).

value: ovary

tag: developmental stage

value: 14d growing oocyte

value: wild type


title: H3K4me3_P1P6MLL_matDKO_blastocyst_Rep2

description: Library name: Sample7

source_name: Blastocyst embryos

value: Blastocyst embryos

value: Blastocyst

value: maternal Pcgf1/6 double knockout


title: Input_P1P6MLL_matDKO_blastocyst_Rep1

description: Library name: Sample9


title: Egg diet, no infection, 3

description: Library name: IT36

value: Intestine


title: H2AK119ub1 WT 14dGOs rep1

description: Library name: Sample10


title: Egg diet, infection, 8

description: Library name: IT41


title: Egg diet, no infection, 2

description: Library name: IT35


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_21d_Rep1

description: Library name: Sample 93


title: T-ALL cell line 2696, parental control

description:
Library name: 4_Par2696
Column name in FPKM_All_samples.csv:4_Par2696_S4


title: H3K4me3_P1P6MLL_matDKO_blastocyst_Rep1

description: Library name: Sample6


title: T-ALL cell line 7298, parental control

description:
Library name: 1_Par7298
Column name in FPKM_All_samples.csv:1_Par7298_S1


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_Dox_21d_Rep1

description: Library name: Sample 91


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_14d_Rep2

description: Library name: Sample 88

value: dTAGv1 and Doxycycline for 14d


title: Egg diet, no infection, 1

description: Library name: IT34


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_21d_Rep2

description: Library name: Sample 90


title: H3K4me3_P1P6MLL_WT_blastocyst_Rep2

description: Library name: Sample5


title: H3K4me3_P1P6MLL_WT_blastocyst_Rep1

description: Library name: Sample4


title: H2AK119ub1 CR P1P6MLL_TKO FGOs

description: Library name: Sample3

data_processing:
CATCH-seq and CUT&RUN sequencing reads were aligned to the mouse reference genome (mm10) using Bowtie2 (version 2.3.5) with the parameters “-q -N 1 -L 25”. After removing PCR duplicates and filtering out multiple mapping reads, uniquely mapped reads were used for the downstream analysis. Spike-in normalization of CATCH-seq reads was performed as previously described. The reads were aligned to the mouse (mm10) and D. melanogaster (dm6) reference genome. All the H2A.Z and histone modification peaks were called by MACS2 (version 2.1.2) with the parameters ‘-g mm –nomodel --nolambda’.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Run

value: Full-grown oocyte

value: Pcgf1/6/Mll2 triple knockout


title: H2AK119ub1 CR P1P6MLL_WT FGOs

description: Library name: Sample1


title: H2AK119ub1 CR P1P6MLL_DKO FGOs

description: Library name: Sample2

value: Pcgf1/6 double knockout


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_Dox_14d_Rep2

description: Library name: Sample 86

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution

value: Doxycycline for 14d


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_14d_Rep1

description: Library name: Sample 87


title: Egg diet, infection, 3

description: Library name: IT29


title: Hippocampal tissue, 5xFAD/p75NTRko, biol rep3

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: 3291
Column name in raw_counts_all_samples.txt: NGS3291

data_processing:
The quality of the FASTQ files was assessed with the FastQC software, reads were aligned to the mouse (mm10) genome with Hisat2 (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). The BAM files were sorted by genomic coordinates and indexed using samtools. Htseq-count was utilized to summarize reads at the gene level (htseq-count -f bam -s yes -i gene_id bam/$FILE_ID.bam data/refs/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf > $COUNTS_DIR/NGS$FILE_ID). Differential expression analysis (DEA) was conducted using EdgeR and a significance threshold of adjusted p-value (padj) < 0.05 was applied. Two designs were employed, both accounting for gender differences between the mice (gender included as a covariate). The first design also included disease and genotype as covariates (~ disease + genotype + gender), with healthy WT mice treated as the reference. The second design accounted for mouse line as a group covariate (~ group + gender, groups: WT, 5xFAD, p75NTRko, 5xFAD/p75NTRko), with WT mice as the reference.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file contains the raw counts of each sample.

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent (15596018, Thermo Scientific) as per the manufacturer’s protocol. The quantity and quality of extracted RNA samples were analyzed using RNA 6000 Nano kit on a bioanalyzer (Agilent).
RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled by qPCR for obtaining optimal unbiased libraries across samples by assessing the number of cycles (14) required for amplification of the library. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on a Nextseq 2000 at the genomics facility of IMBB FORTH according to the manufacturer’s instructions.

value: Hippocampus

value: BrdU injections


title: Input_P1P6MLL_WT_blastocyst_Rep1

description: Library name: Sample8


title: Egg diet, infection, 4

description: Library name: IT30


title: Hippocampal tissue, 5xFAD/p75NTRko, biol rep2

description:
Library name: 3290
Column name in raw_counts_all_samples.txt: NGS3290


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_Dox_14d_Rep1

description: Library name: Sample 85


title: Hippocampal tissue, 5xFAD/p75NTRko, biol rep1

description:
Library name: 3289
Column name in raw_counts_all_samples.txt: NGS3289


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_14d_Rep2

description: Library name: Sample 84

value: dTAGv1 for 14d


title: Hippocampal tissue, p75NTRko, biol rep3

description:
Library name: 3288
Column name in raw_counts_all_samples.txt: NGS3288


title: Egg diet, infection, 2

description: Library name: IT28


title: Hippocampal tissue, p75NTRko, biol rep2

description:
Library name: 3287
Column name in raw_counts_all_samples.txt: NGS3287


title: Hippocampal tissue, 5xFAD, biol rep3

description:
Library name: 3285
Column name in raw_counts_all_samples.txt: NGS3285


title: Inulin diet, no infection, 3

description: Library name: IT26


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_14d_Rep1

description: Library name: Sample 83


title: Hippocampal tissue, p75NTRko, biol rep1

description:
Library name: 3286
Column name in raw_counts_all_samples.txt: NGS3286


title: Hippocampal tissue, 5xFAD, biol rep2

description:
Library name: 3284
Column name in raw_counts_all_samples.txt: NGS3284


title: Hippocampal tissue, WT, biol rep3

description:
Library name: 3282
Column name in raw_counts_all_samples.txt: NGS3282


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_7d_Rep1

description: Library name: Sample 81

value: dTAGv1 and Doxycycline for 7d


title: Hippocampal tissue, 5xFAD, biol rep1

description:
Library name: 3283
Column name in raw_counts_all_samples.txt: NGS3283


title: Inulin diet, no infection, 1

description: Library name: IT24


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_7d_Rep2

description: Library name: Sample 82


title: Egg diet, infection, 1

description: Library name: IT27


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_Dox_7d_Rep1

description: Library name: Sample 79

value: Doxycycline for 7d


title: Inulin diet, infection, 4

description: Library name: IT20


title: H3K36me3_P1P6MLL_TKO_FGO_Rep2

description: Library name: Sample33

value: ovary

value: Pcgf1/6 & Mll2 triple knockout


title: Inulin diet, no infection, 2

description: Library name: IT25


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_Dox_7d_Rep2

description: Library name: Sample 80


title: H3K36me3_P1P6MLL_DKO_FGO_Rep2

description: Library name: Sample31


title: H3K36me3_P1P6MLL_TKO_FGO_Rep1

description: Library name: Sample32


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_7d_Rep2

description: Library name: Sample 78

value: dTAGv1 for 7d


title: Hippocampal tissue, WT, biol rep2

description:
Library name: 3281
Column name in raw_counts_all_samples.txt: NGS3281


title: Hippocampal tissue, WT, biol rep1

description:
Library name: 3280
Column name in raw_counts_all_samples.txt: NGS3280


title: H3K36me3_P1P6MLL_WT_FGO_Rep2

description: Library name: Sample29

value: wild type


title: Inulin diet, infection, 3

description: Library name: IT18


title: H3K36me3_P1P6MLL_DKO_FGO_Rep1

description: Library name: Sample30


title: Inulin diet, infection, 2

description: Library name: IT16


title: H3K36me3_P1P6MLL_WT_FGO_Rep1

description: Library name: Sample28


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_7d_Rep1

description: Library name: Sample 77


title: Inulin diet, infection, 1

description: Library name: IT15


title: H3K36me2_P1P6MLL_DKO_FGO_Rep2

description: Library name: Sample25


title: Control diet, no infection, 2

description: Library name: IT13


title: H3K36me2_P1P6MLL_DKO_FGO_Rep1

description: Library name: Sample24


title: Input_H3K4me3_P1P6MLL_WT_FGO

description: Library name: Sample19


title: H3K27me3_CR_P1P6MLL_DKO_FGO_Rep2

description: Library name: Sample10


title: H3K27me3_CR_P1P6MLL_WT_FGO_Rep2

description: Library name: Sample8


title: Control diet, infection, 2

description: Library name: IT4


title: Control diet, infection, 3

description: Library name: IT6


title: wk3_KrasWT_Saline_B0504

city: New York

first: Rohit

last: Chandwani

state: NY

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

data_processing:
Reads were processed with the ENCODE ATAC-seq pipeline v2.2.2 (https://github.com/ENCODE-DCC/atac-seq-pipeline/) and were aligned to the human genome build mm10
Briefly, adapters were trimmed with cutadapt v2.5 and aligned to Encode mm10 with Bowtie2 v2.3.4.3.
Duplicate reads and reads mapping to the mitochondrial chromosome were removed.
Signal files and peak calls were generated using MACS2 v2.2.4.
Peaks overlapping ENCODE blacklisted regions (ENCFF547MET.bed) were excluded.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Adult Pancreas

extract_protocol:
tdTomato+ acinar cells, tdTomato+ progenitor cells or CD133+ CD49f+ ductal cells were FACS sorted as applicable. Standard ATAC-seq protocol was followed (Buenrostro et al. 2013).
Illumina Nextera kit

value: Adult Pancreas

value: KrasWT

value: Tamoxifen

value: Saline


title: Control diet, infection, 1

description: Library name: IT1

value: Intestine


title: wk3_KrasWT_Saline_B0237


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_Dox_21d_Rep1

description: Library name: Sample 71

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: Doxycycline for 21d


title: wk3_KrasWT_Saline_B0234


title: wk3_KrasWT_Caerulein_B0508

value: Caerulein


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_21d_Rep2

description: Library name: Sample 70

value: dTAGv1 for 21d


title: H3K36me2_P1P6MLL_TKO_FGO_Rep2

description: Library name: Sample27

value: Full-grown oocyte


title: PacC {delta} - Keratin - 96 hours, replicate III

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

description: Library name: PacCKer96h_III

data_processing:
FastQC v0.12.0 was used to visualize the libraries quality before and after trimming.
Trimmomatic v0.39 was used to remove adapters and quality filtered setting the cutoff threshold for average base quality score at 15 over a window of 4 bases. Reads shorter than 36 bases post-trimming were excluded.
Filtered reads were mapped onto the T. interdigitale H6 genome using the STAR v2.7.10b.
Gene level read-counts were quantified using STAR’s –quantMode GeneCounts parameter.
The data were analyzed using the R package DESeq2. The samples were normalized, and the dispersions were estimated using the default settings. The package was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.05 and a log2(foldchange) >= 1.0 (upregulation) or <= -1.0 (downregulation) were called as differentially expressed.
Assembly: Broad T. interdigitale strain H6 genome
Supplementary files format and content: tab-delimited text files include reads count values for each sample and DESeq output in CSV format containing mean expression, fold changes and p value.

organism: Trichophyton interdigitale

growth_protocol: T. interdigitale strains H6 WT and pacC-1 were cultured on malt extract agar [2% glucose, 2% malt extract, 0.1% peptone (w/v), pH 5.7].

extract_protocol:
Three independent RNA biological replicates for each condition were used for the synthesis of cDNA using the Illumina Stranded mRNA Prep Kit (Illumina, USA)
Equal amounts of RNA from three independent biological replicates at each time point (24 and 96 h) were used for the synthesis of cDNA with the TruSeq RNA library Kit (Illumina, San Diego, CA, USA) and cDNA libraries were sequenced on Illumina NovaSeq 6000 System (Illumina, USA) using the SP 300 cycle flow cell configuration to generate 150 bp paired-end reads.

treatment_protocol: Approximately 1 × 10^6 conidia were inoculated into 100 mL of Sabouraud medium and cultured at 28 °C for 96 h (120 rpm). Mycelia were filtered and transferred to 100 mL of minimal medium supplemented with 0.5% bovine keratin (m/v). Cultures were incubated for 24 or 96 h at 28°C under agitation. The mycelial mass was weighed, and the liquid medium was collected and stored at −80 °C after pH measurement. Culture conditions were performed in three biological replicates.

value: fungal cells

value: PacC knockdown

value: keratin

value: 96 hours


title: PacC {delta} - Keratin - 96 hours, replicate II

description: Library name: PacCKer96h_II


title: H3K36me2_P1P6MLL_WT_FGO_Rep2

description: Library name: Sample23

value: ovary


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_21d_Rep2

description: Library name: Sample 74

value: dTAGv1 and Doxycycline for 21d


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_0d_Rep1

description: Library name: Sample 75

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution

value: No


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_14d_Rep2

description: Library name: Sample 68

value: dTAGv1 and Doxycycline for 14d


title: H3K36me2_P1P6MLL_WT_FGO_Rep1

description: Library name: Sample22

value: wild type


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_21d_Rep1

description: Library name: Sample 73


title: Input_H3K4me3_P1P6MLL_TKO_FGO

description: Library name: Sample21

value: Pcgf1/6 & Mll2 triple knockout


title: PacC {delta} - Keratin - 96 hours, replicate I

description: Library name: PacCKer96h_I


title: Control diet, no infection, 1

description: Library name: IT12

value: Intestine


title: Input_H3K4me3_P1P6MLL_DKO_FGO

description: Library name: Sample20

value: Pcgf1/6 double knockout


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_14d_Rep1

description: Library name: Sample 67

value: NSD2_dTAG knockin and NSD2WT reconstitution


title: wk3_KrasWT_Caerulein_B0244

value: Adult Pancreas

value: KrasWT

value: Tamoxifen

value: Caerulein


title: wk3_KrasWT_Caerulein_4988


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_Dox_14d_Rep2

description: Library name: Sample 66

value: Doxycycline for 14d


title: wk3_KrasG12Vgeo_Saline_B0231

value: Saline


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_Dox_14d_Rep1

description: Library name: Sample 65


title: wk3_KrasWT_Caerulein_B0165


title: PacC {delta} - Keratin - 24 hours, replicate I

description: Library name: PacCKer24h_I

value: fungal cells

value: PacC knockdown

value: keratin

value: 24 hours


title: PacC {delta} - Keratin - 24 hours, replicate III

description: Library name: PacCKer24h_III


title: wk3_KrasWT_Caerulein_4986


title: PacC {delta} - Keratin - 24 hours, replicate II

description: Library name: PacCKer24h_II


title: wk3_KrasWT_Caerulein_4946


title: wk3_KrasG12Vgeo_Caerulein_B0538


title: H6 - Keratin - 96 hours, replicate III

description: Library name: H6Ker96h_III

value: WT

value: 96 hours


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_14d_Rep1

description: Library name: Sample 63

value: dTAGv1 for 14d


title: wk3_KrasG12Vgeo_Saline_B0066


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_14d_Rep2

description: Library name: Sample 64


title: wk3_KrasG12Vgeo_Saline_B0341


title: wk3_KrasG12Vgeo_Caerulein_B0493


title: H6 - Keratin - 96 hours, replicate II

description: Library name: H6Ker96h_II


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_21d_Rep1

description: Library name: Sample 69

value: dTAGv1 for 21d


title: H3K36me2_P1P6MLL_TKO_FGO_Rep1

description: Library name: Sample26

value: ovary

value: Full-grown oocyte

value: Pcgf1/6 & Mll2 triple knockout


title: wk3_KrasWT_Saline_4953

value: Adult Pancreas


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2Y1179A_dTAGv1_Dox_0d_Rep2

description: Library name: Sample 76

value: NSD2_dTAG knockin and NSD2Y1179A reconstitution

value: No


title: wk3_KrasWT_Saline_4952

value: KrasWT

value: Tamoxifen


title: wk3_KrasWT_Saline_4947

value: Saline


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_7d_Rep2

description: Library name: Sample 62

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: dTAGv1 and Doxycycline for 7d


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_Dox_7d_Rep2

description: Library name: Sample 60

value: Doxycycline for 7d


title: wk3_KrasG12R_Saline_B0170


title: wk3_KrasG12R_Saline_B0503


title: wk3_KrasG12Vgeo_Caerulein_B0232

value: Caerulein


title: H6 - Keratin - 96 hours, replicate I

description: Library name: H6Ker96h_I

value: fungal cells

value: WT

value: keratin


title: wk3_KrasG12R_Saline_B0238


title: H6 - Keratin - 24 hours, replicate III

description: Library name: H6Ker24h_III

value: 24 hours


title: wk3_KrasG12R_Saline_4948


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_7d_Rep1

description: Library name: Sample 61


title: wk3_KrasG12R_Saline_B0240


title: wk3_KrasG12R_Saline_B0507


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_Dox_7d_Rep1

description: Library name: Sample 59


title: H6 - Keratin - 24 hours, replicate I

description: Library name: H6Ker24h_I


title: wk3_KrasG12R_Caerulein_B0235


title: H6 - Keratin - 24 hours, replicate II

description: Library name: H6Ker24h_II


title: wk3_KrasG12R_Caerulein_B0505


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_7d_Rep2

description: Library name: Sample 58

value: dTAGv1 for 7d


title: wk3_KrasG12R_Caerulein_4954


title: wk3_KrasG12R_Caerulein_B0163


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_0d_Rep1

description: Library name: Sample 55


title: wk3_KrasG12D_Saline_4991


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep2

description: Library name: Sample 54

value: NSD2_dTAG knockin

value: dTAGv1 for 21d


title: wk3_KrasG12D_Saline_4913

value: Adult Pancreas


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_Dox_0d_Rep2

description: Library name: Sample 56


title: wk3_KrasG12D_Saline_B0473


title: wk3_KrasG12D_Saline_4987


title: wk3_KrasG12D_Saline_B0474


title: Human EGR1 (334-423)

type: protein

city: rehovot

first: irina

last: miodownik

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Microarray was self-hybridized on IDT duplex buffer on a temperature gradient

scan_protocol: GenePix 4400A array scanner. Multiple scans at different intensities were performed and the optimal per protein was selected for further analysis.

data_processing: For each probe area, the median of pixels was calculated. Then, the data was spatially detrended according to the local background.

molecule: protein

source_name: E coli

extract_protocol: Purified from E. coli or obtained commercially

tag: tag

value: GST-tagged protein


title: Full-length human RUNX1

value: HIS-tagged protein


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_dTAGv1_7d_Rep1

description: Library name: Sample 57


title: wk3_KrasG12R_Caerulein_B0162


title: Full-length human RUNX3

description: Obtained commercially (Prospec cat# PRO-836)


title: wk3_KrasG12D_Caerulein_B0560


title: Full-length human STAT1

value: mNeonGreen


title: Full-length human HOXB13

description: Obtained commercially (Prospec cat# pro-1765)


title: Control diet, no infection, 3

description: Library name: IT14

value: Intestine


title: wk3_KrasG12D_Saline_4911

value: Tamoxifen

value: Saline


title: H3K27me3_CR_P1P6MLL_TKO_FGO_Rep2

description: Library name: Sample12

value: ovary

value: Full-grown oocyte

value: Pcgf1/6 & Mll2 triple knockout


title: wk3_KrasG12D_Caerulein_B0565

value: Caerulein


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_21d_Rep1

description: Library name: Sample 53


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_14d_Rep1

description: Library name: Sample 51

value: dTAGv1 for 14d


title: wk3_KrasG12D_Caerulein_B0109


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_14d_Rep2

description: Library name: Sample 52


title: wk3_KrasG12D_Caerulein_B0511


title: SLAMseq_KMS11_NSD2dTAG#8_NSD2WT_Dox_21d_Rep2

description: Library name: Sample 72

value: NSD2_dTAG knockin and NSD2WT reconstitution

value: Doxycycline for 21d


title: wk3_KrasG12R_Caerulein_B0233


title: Human IRF1 (1-114)

description: Obtained commercially (Prospec, cat# CYT-449)


title: lateProgenitor_PT39B-2

source_name: developing pancreas

value: developing pancreas


title: Human FOXA2 (142-269)


title: wk3_KrasG12D_Caerulein_B0107


title: wk3_KrasG12D_Caerulein_B0559


title: lateProgenitor_PT39B-1


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_7d_Rep1

description: Library name: Sample 49

value: NSD2_dTAG knockin

value: dTAGv1 for 7d


title: Human FOXO3A (31-264)


title: Full-length human KLF3

description: Obtained commercially (Prospec, cat# PRO-1632)


title: lateProgenitor_PT27B-2


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_7d_Rep2

description: Library name: Sample 50


title: lateProgenitor_PT38B-1


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep2

description: Library name: Sample 48

value: No


title: earlyProgenitor_PT43A_2_2


title: earlyProgenitor_PT42A-1


title: HFF-1 cells,infected HSV-2,24h,m6A IP,Control3

city: kun ming

first: Li ji xiong

last: Li

country: China

institute: Institute of Medical Biology, Chinese Academy of Medicine

description: Library name: HSV-2-3.IP

data_processing:
Raw reads (Raw Data) are generated after sequencing on a sequencer, image analysis, base identification and QC. Q30 was first used for quality control. Then, cutadapt software (v1.9.3) was used to remove splice information and remove low quality reads to obtain high quality clean reads. The clean reads were matched to the reference genome using Hisat2 software (v2.0.4). Methylated peaks in each sample were then identified using MACS software (1.4.2). Differential methylation peaks identification was performed using diffReps software (1.55.6). The peaks located on exons of sequences which gene biotypes were mRNA were screened using our own programs and annotated accordingly. GO and Pathway analyses were performed for differentially methylated
Assembly: HG38
Supplementary files format and content: Human Gene_Expression_Profiling.xlsx
Supplementary files format and content: Human Methylated_RNA_sites.mRNA.xlsx
Library strategy: MeRIP-Seq

source_name: Human foreskin tissue

extract_protocol:
HFF-1 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Vivacell, cat. no. C3113-0500) containing 20% fetal bovine serum (FBS; Cell-Box, cat. no. AU3-01S-02-S) and penicillin-streptomycin (100 U/mL) at 37°C under 5% CO₂. HFF cells were seeded into T225 flasks and cultured until reaching approximately 90% confluence after 24 hours. The cells were then washed twice with phosphate-buffered saline (PBS), and three flasks were infected with HSV-2 G at an MOI of 0.1 to form the infection group, while three other flasks remained uninfected as negative controls. After adsorption for 1 hour at 37°C, fresh DMEM supplemented with 20% FBS was added, and the cells were further cultured for 24 hours before harvesting the cell samples.
following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified. RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer (Agilent) and then sequenced in a DNBSEQT7 platform (MGI Tech).

value: Human foreskin tissue

value: Fibroblast


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_21d_Rep1

description: Library name: Sample 45

value: dTAGv1 for 21d


title: earlyProgenitor_PT43A_2_1


title: earlyProgenitor_PT42A_2_1


title: d2_KrasWT_Caerulein_B2261

value: Adult Pancreas

value: KrasWT


title: earlyProgenitor_PT42A_2_2


title: HFF-1 cells,infected HSV-2,24h,m6A IP,Control2

description: Library name: HSV-2-2.IP


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_0d_Rep1

description: Library name: Sample 47


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_14d_Rep2

description: Library name: Sample 44


title: HFF-1 cells,infected HSV-2,24h,Control3

description: Library name: HSV-2-3.Input


title: earlyProgenitor_PT42A_1_2


title: earlyProgenitor_PT43A_1_2


title: d2_KrasWT_Caerulein_B2259

value: Tamoxifen


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_21d_Rep2

description: Library name: Sample 46


title: Full-length human P53

description: Obtained commercially (Abcam, cat# ab-84768-50)

value: GST-tagged protein


title: Full-length human HOXC11

description: Obtained commercially (Prospec, cat# pro-1658)

value: HIS-tagged protein


title: d2_KrasWT_Caerulein_B2068


title: Full-length human POU6F1

description: Obtained commercially (Prospec, cat# PRO-1484)


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_14d_Rep1

description: Library name: Sample 43


title: HFF-1 cells,infected HSV-2,24h,Control2

description: Library name: HSV-2-2.Input


title: d2_KrasWT_Caerulein_B2058


title: earlyProgenitor_PT43A_1_1


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_7d_Rep2

description: Library name: Sample 42


title: d2_KrasG12Vgeo_Caerulein_B2165


title: d2_KrasG12R_Caerulein_B2260


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_0d_Rep1

description: Library name: Sample 39


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_7d_Rep1

description: Library name: Sample 41


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_0d_Rep2

description: Library name: Sample 40


title: HFF-1 cells,infected HSV-2,24h,Control1

description: Library name: HSV-2-1.Input


title: d2_KrasG12R_Caerulein_B2066


title: SLAMseq_KMS11_dTAGparental_dTAGv1_21d_Rep2

description: Library name: Sample 38

value: WT


title: d2_KrasG12R_Caerulein_B2067

value: Caerulein


title: HFF-1 cells,uninfected HSV-2,24h,m6A IP,Control3

description: Library name: Mock3.IP


title: d2_KrasG12Vgeo_Caerulein_B2059


title: HFF-1 cells,infected HSV-2,24h,m6A IP,Control1

description: Library name: HSV-2-1.IP


title: HFF-1 cells,uninfected HSV-2,24h,m6A IP,Control2

description: Library name: Mock2.IP


title: d2_KrasG12R_Caerulein_B2257


title: d2_KrasG12D_Caerulein_B2242


title: SLAMseq_KMS11_dTAGparental_dTAGv1_21d_Rep1

description: Library name: Sample 37


title: HFF-1 cells,uninfected HSV-2,24h,Control2

description: Library name: Mock2.Input


title: d2_KrasG12D_Caerulein_B2104


title: SLAMseq_KMS11_dTAGparental_dTAGv1_14d_Rep2

description: Library name: Sample 36

value: dTAGv1 for 14d


title: d2_KrasG12D_Caerulein_B2243


title: GS-C-VA2_2

city: Golden

first: Davinia

last: Salvachua

state: CO

address: 15013 Denver West Parkway

institute: National Renewable Energy Laboratory

description: Library name: sample17

data_processing:
Read quality was assessed using FastQC from Babraham Institute (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read- trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters trimq=10, qtrim="rl", maq=10.
Reads were aligned to genomes using STAR (PMID: 23104886), using --outMultimapperOrder Random --outFilterMatchNminOverLread 0 --outSAMmultNmax 1.
Aligned reads were mapped to genes using htseq-count (https://pubmed.ncbi.nlm.nih.gov/25260700/) with parameters -a=1, --mode="union".
Assembly: G. subvermispora FP105752 RP-B in NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCA_000320605.2)
Assembly: Trametes versicolor v1.0 (Trametes versicolor FP-101664 SS1 (basidiomycetes) (5)) in NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000271585.1/)
Supplementary files format and content: tab-delimited text file with gene names and raw counts. Samples 13 - 24 are techinical replicates of samples 1 - 12. Counts from the technical replicates were summed to produce one file of counts for each sample.

organism: Gelatoporia subvermispora

source_name: monokaryon

growth_protocol: An agar square (~0.5 cm2) with fungal mycelia was taken from agar plates maintained at 4 °C from our strain collection, deposited on a fresh YMPG-agar plate (mycelia in contact with the agar), and incubated for 5 days at 28 °C for G. subvermispora, or 7 days at 28 °C for T. versicolor. These plates were utilized as the starter for the submerged cultivations. 4-5 agar squares (~0.5 cm2) with mycelia from the fungal mat edges of seed agar plate cultivations were added to non-baffled 250 mL flasks containing 50 mL of YMPG and incubated at 220 rpm and 28 °C for 7 days (seed 1). This was done in duplicate. Seed 1 was homogenized (10 seconds, speed 6) in sterile conditions using an Omni Mixer 115V with a 50 mL SS Chamber PTFE (Omni International, GA, USA). The fungal suspension (2 mL) was re-inoculated in YMPG under the same conditions as the seed 1 culture for 5 days (seed 2). Seed 2 was homogenized as described previously and a ratio of 1:12.5 (v:v) of fungal suspension per media volume was used to inoculate the corresponding cultivations. T. versicolor and G. subvermispora cultivations (12 per fungi) were conducted in 250 mL flasks containing 25 mL of M7 with cellobiose (5 g/L) and incubated statically at 28 °C, 75% humidity using a humidity-controlled incubator in the dark for 5 days (T. versicolor) or 12 days (G. subvermispora).

extract_protocol:
Transcriptomic samples were generated by centrifugation at 6,000 x g for 10 min at 4°C, followed by flash freezing the pellets in liquid nitrogen after discarding the supernatants. Samples were stored at -80°C. Frozen fungal cultures (100-200 mg) were transferred to a pre-chilled mortar and ground to a fine powder in liquid nitrogen. The liquid nitrogen was allowed to evaporate and the sample was transferred to a pre-chilled 15 mL centrifuge tube. All steps were performed on dry ice to ensure samples remained frozen. RLT buffer (700 μL)(Qiagen) containing 10% β- mercaptoethanol was added to the frozen samples and the samples were allowed to thaw with periodic vortexing at high speed. Samples were vortexed at high speed continuously for 1 min or until the sample was completely homogenous. Samples were transferred to a QIAshredder column (Qiagen) and processed using the RNeasy mini kit and subjected to DNase gDNA digestion according to the manufacturers protocol (Qiagen). The RNA samples are assessed using the Agilent 2100 Bioanalyzer, RNA with RIN >7 proceed with cDNA library.
TruSeq Stranded Total RNA (cat#20020596) is used to generate cDNA library for illumina NextSeq550 platform according to the manufacture protocol. Single- read sequencing of the cDNA libraries with a read length of 150 is performed on NextSeq 500 Sequencing System using NextSeq 500/550 High Output v2 kit 150 cycles (cat#20024907).

treatment_protocol: All the flasks were supplemented with filter-sterilized ascorbic acid (5 mM in water) and α-tocopherol (1 mM in ethanol). After 30 min, three flasks of each fungus were induced with vanillate (100 mM stock), for a final concentration of 2 mM. Vanillate stock was prepared by solubilizing vanillic acid powder in DI water, adjusted to pH 8 with 4N NaOH, and filtering through 0.2 μm sterile PES filter. A second pulse of vanillate (100 mM stock) was added to the same flasks 12 h after the first pulse. For samples without vanillate, 2 pulses of autoclaved water (equal volume to the added vanillate solution) was added in lieu of vanillate solution at the same timepoints. Cultivations were harvested 12 h after the second pulse, corresponding to 6 days for T. versicolor and 13 days for G. subvermispora. A set of control samples was also generated where the media was not inoculated with fungi, but all other conditions were held the same. Media not inoculated with fungi served as controls for the extracellular fractions. All cultivations and controls were performed in triplicate.

tag: strain

value: monokaryon

tag: incubation time1

value: 12 days

value: 5mM ascorbic acid, 1mM alpha-tocopherol

tag: incubation time2

value: 30 min

value: 100 mM vanillate

value: 12 hr

tag: incubation time3


title: HFF-1 cells,uninfected HSV-2,24h,m6A IP,Control1

description: Library name: Mock1.IP

tag: tissue

value: Human foreskin tissue


title: GS-C3_2

description: Library name: sample15

value: water


title: HFF-1 cells,uninfected HSV-2,24h,Control1

description: Library name: Mock1.Input

value: Fibroblast


title: d2_KrasG12D_Caerulein_B2106

value: Adult Pancreas

tag: time


title: SLAMseq_KMS11_dTAGparental_dTAGv1_14d_Rep1

description: Library name: Sample 35

tag: treatment


title: GS-C-VA3_2

description: Library name: sample18


title: GS-C-VA1_2

description: Library name: sample16


title: HFF-1 cells,uninfected HSV-2,24h,Control3

description: Library name: Mock3.Input


title: GS-C1_2

description: Library name: sample13


title: SLAMseq_KMS11_dTAGparental_dTAGv1_7d_Rep1

description: Library name: Sample 33

value: dTAGv1 for 7d


title: GS-C2_2

description: Library name: sample14


title: Chicken SPs, St 36 ventral, 4

city: Fukuoka

first: Seung June

last: Kwon

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Graduate School of Systems Life Sciences

institute: Kyushu University

description: Library name: Sample 12

data_processing:
Sequences were separated by sample barcodes with UMI-tools and aligned to reference genome using HISAT2.
featureCounts was used to generate raw count data assigned to genes.
DESeq2 was used to extract differentially expressed genes.
UMI-tools was used to demultiplex the raw fastq files (now should be treated as a single-end file).
Assembly: chicken: GRCg6a, GCA_000002315.5; emu: ZJU2.0, GCA_016128335.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Gallus gallus

source_name: Sternal progenitors from LPM

extract_protocol:
After UV irradiation, total tissue lysate was collected and purified. 2nd strand DNA was synthesized using Rnase H, DNA pol I, and DNA ligase mix.
Only cDNAs from UV-irraidated region are filled-in to 5' end of T7 promotoer, being linearly amplified as RNAs via IVT reaction. RNA libraries were then reverse-transcribed and sequenced on Illumina NovaSeq 6000 (R1: UMI and barcode, R2: cDNA).

value: Sternal progenitors from LPM


title: GS-C-VA3

description: Library name: sample6


title: GS-C-VA2

description: Library name: sample5


title: SLAMseq_KMS11_dTAGparental_dTAGv1_7d_Rep2

description: Library name: Sample 34


title: Chicken SPs, St 36 ventral, 3

description: Library name: Sample 11


title: d2_KrasG12Vgeo_Caerulein_B2167

value: Tamoxifen


title: SLAMseq_KMS11_dTAGparental_dTAGv1_0d_Rep2

description: Library name: Sample 32

value: No


title: GS-C-VA1

description: Library name: sample4


title: Chicken SPs, St 36 ventral, 2

description: Library name: Sample 10


title: GS-C3

description: Library name: sample3


title: GS-C2

description: Library name: sample2


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_72h_Rep1

description: Library name: Sample 29

value: NSD2_dTAG knockin

value: dTAGv1 for 72h


title: TV-C-VA2_2

description: Library name: sample23

organism: Trametes versicolor

value: 5 days


title: TV-C-VA3_2

description: Library name: sample24

value: monokaryon


title: SLAMseq_KMS11_dTAGparental_dTAGv1_0d_Rep1

description: Library name: Sample 31

value: WT


title: GS-C1

description: Library name: sample1

value: 12 days

value: 5mM ascorbic acid, 1mM alpha-tocopherol


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_72h_Rep2

description: Library name: Sample 30


title: Chicken SPs, St 36 dorsal, 3

description: Library name: Sample 7


title: TV-C-VA1_2

description: Library name: sample22

value: 30 min

value: 100 mM vanillate


title: TV-C1_2_2

description: Library name: sample19

value: 12 hr


title: Chicken SPs, St 36 dorsal, 2

description: Library name: Sample 6


title: TV-C2_2

description: Library name: sample20

value: water


title: Chicken SPs, St 36 dorsal, 4

description: Library name: Sample 8


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_24h_Rep2

description: Library name: Sample 28

value: dTAGv1 for 24h


title: Chicken SPs, St 36 dorsal, 1

description: Library name: Sample 5


title: TV-C3_2

description: Library name: sample21


title: Chicken SPs, St 36 ventral, 1

description: Library name: Sample 9


title: TV-C-VA3

description: Library name: sample12


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_24h_Rep1

description: Library name: Sample 27


title: TV-C3

description: Library name: sample9


title: TV-C-VA2

description: Library name: sample11


title: TV-C2

description: Library name: sample8


title: TV-C-VA1

description: Library name: sample10


title: Chicken SPs, St 24, 3

description: Library name: Sample 3


title: Chicken SPs, St 24, 2

description: Library name: Sample 2


title: Chicken SPs, St 24, 1

description: Library name: Sample 1


title: h-, rsm1∆::natMX, biol_rep_2

first: Ana

middle: M

last: Sanchez

address: 430 E 67th Street, RRL-865

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: Library name: rsm1_knockout, Strain ASY240, biol_rep_2

data_processing:
Base calls from Illumina NovaSeq X Plus (FASTQ files)
Each replicate was processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: PomBase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicated were generated with HTSeq-0.10.0 using exon annotations from PomBase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold-change analysis were performed using DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq2 output files that include average (avg) normalized counts

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Log phase cultures grown at 30°C in YES medium.

extract_protocol:
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq X Plus instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

value: Strain ASY240

tag: growth condition

value: log phase culture, YES medium

value: Vegetative growth

value: rsm1 knockout

value: Schizosaccharomyces pombe


title: h-, nup211-1435* asp1-WT::kanMX, biol_rep_1

description: Library name: nup211_1435, Strain IAP105, biol_rep_1

value: Strain IAP105


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_2h_Rep2

description: Library name: Sample 24

tag: cell line

value: NSD2_dTAG knockin

value: dTAGv1 for 2h


title: h-, nup211-1435* asp1-WT::kanMX, biol_rep_2

description: Library name: nup211_1435, Strain IAP105, biol_rep_2

tag: genotype


title: h-,nup211-1435* asp1-WT::kanMX, biol_rep_3

description: Library name: nup211_1435, Strain IAP105, biol_rep_3

tag: cell type


title: h-, rsm1∆::natMX, biol_rep_3

description: Library name: rsm1_knockout, Strain ASY240, biol_rep_3


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_2h_Rep1

description: Library name: Sample 23


title: Chicken SPs, St 24, 4

description: Library name: Sample 4

value: Sternal progenitors from LPM


title: 29hpf-ef1a-mCherry_07

city: San Francisco

first: Nicole

last: Aponte Santiago

state: CA

address: 35 Medical Center Way

institute: UCSF

description: Library name: NAS017

data_processing:
Libraries were sequenced on NextSeq 2000 P2 FlowCell with cycle allocations as follows. Read 1: 16 cycles (Cell Barcode Part 1); Read 2: 65 cycles (cDNA); I5 Index Read: 8 cycles (Cell Barcode Part 2); I7 Index Read: 6 cycles (Sample Index).
Sequencing reads were mapped to GRCz11 with StarSolo using the Lawson Lab v4.3.2 GTF file, which extended to include common transgenic sequences (e.g., mCherry2).
Counts matrices were QC-filtered based on total transcripts per cell, mitochondrial transcript content, and putative doublets.
Assembly: The dataset was aligned to a common zebrafish reference genome (GRCz11) using the Lawson Lab v4.3.2 GTF file. Reference transcriptome and gene annotations were extended to comprise common transgenic sequences: mCherry2, mNeonGreen, mScarlet, mTagBFP2, kikGR1, mEOS4b, miRFP670, EGFP, sfGFP, Cas9, CRE, ERT2, Gal4ff, Tol2.
Supplementary files format and content: h5ad

source_name: whole embryos

growth_protocol: Tg(eef1a1l1:h2b-mCherry2)/+ zebrafish embryos were collected and kept at 28.5 °C in 0.3x Danieau buffer [17.4 mM sodium chloride, 0.21 mM potassium chloride, 0.12 mM magnesium sulfate, 0.18 mM calcium nitrate, 1.5 mM HEPES, pH 7.6] until dechoreonation and dissociation at 29hpf.

extract_protocol:
29 hpf dechorionated embryos were enzymatically dissociated into a single cell suspension. Samples were washed twice before resuspending in 400 µL of Resuspension Buffer (10% OptiPrep (Sigma, D1556), 1x PBS, and 0.1% BSA in ddH2O) for single-cell microfluidic barcoding. An ONYX microfluidics platform (Droplet Genomics, DG-ONYX), V2 barcoding PDMS chips (Droplet Genomics DG-CBC2-80-10), and inDrops V3 hydrogel beads were used to encapsulate single cells for cDNA barcoding.
Droplet Genomics protocol was followed for library preparation.

treatment_protocol: Before dissociation, embryos were dechorionated with a 1x pronase solution at 1 mg/mL and sorted for mCherry+ signal.

value: whole embryos


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_0h_Rep2

description: Library name: Sample 22

value: No


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_8h_Rep2

description: Library name: Sample 26

value: dTAGv1 for 8h


title: h-, rsm1∆::natMX, biol_rep_1

description: Library name: rsm1_knockout, Strain ASY240, biol_rep_1


title: TV-C1

description: Library name: sample7

value: monokaryon

value: 5 days

value: 5mM ascorbic acid, 1mM alpha-tocopherol

value: 30 min


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_8h_Rep1

description: Library name: Sample 25


title: 29hpf-ef1a-mCherry_08

description: Library name: NAS018


title: h-, WT, biol_rep_3

description: Library name: WT, Strain Sp1, biol_rep_3

value: Strain Sp1

value: WT


title: h-, WT, biol_rep_1

description: Library name: WT, Strain Sp1, biol_rep_1

value: log phase culture, YES medium


title: h-, WT, biol_rep_2

description: Library name: WT, Strain Sp1, biol_rep_2

value: Vegetative growth


title: SLAMseq_KMS11_NSD2dTAG#11_dTAGv1_0h_Rep1

description: Library name: Sample 21


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 2h, biol_rep_3

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 2h_biol_rep_3

growth_protocol: Log phase cultures of wild-type and HASX cells were grown at 30°C in ePMGT(+PO4),  transferred to phosphate-free medium, and incubated in ePMGT(–PO4) medium for 1, 2 or 4 h.

value: Strain BS1453

value: 2h phosphate starved culture, ePMGT(-PO4) medium

value: asp1-H397A, aps1 knockout, siw14 knockout, spx1 knockout


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 2h, biol_rep_2

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 2h_biol_rep_2

value: Schizosaccharomyces pombe


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 4h, biol_rep_2

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 4h_biol_rep_2

value: 4h phosphate starved culture, ePMGT(-PO4) medium


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 2h, biol_rep_1

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 2h_biol_rep_1


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 4h, biol_rep_3

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 4h_biol_rep_3


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_72h_Rep1

description: Library name: Sample 19

value: NSD2_dTAG knockin

value: dTAGv1 for 72h


title: 29hpf-ef1a-mCherry_05

description: Library name: NAS015

value: whole embryos


title: 29hpf-ef1a-mCherry_06

description: Library name: NAS016


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 4h, biol_rep_1

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 4h_biol_rep_1


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_24h_Rep1

description: Library name: Sample 17

value: dTAGv1 for 24h


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_72h_Rep2

description: Library name: Sample 20


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 1h, biol_rep_3

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 1h_biol_rep_3

value: 1h phosphate starved culture, ePMGT(-PO4) medium


title: 29hpf-ef1a-mCherry_02

description: Library name: NAS012


title: 29hpf-ef1a-mCherry_04

description: Library name: NAS014


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_24h_Rep2

description: Library name: Sample 18


title: 29hpf-ef1a-mCherry_03

description: Library name: NAS013


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_8h_Rep1

description: Library name: Sample 15

value: dTAGv1 for 8h


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 1h, biol_rep_2

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 1h_biol_rep_2


title: 29hpf-ef1a-mCherry_01

description: Library name: NAS011


title: h-, WT, 2h, biol_rep_3

description: Library name: WT, Strain Sp1, 2h_biol_rep_3


title: d2_KrasG12Vgeo_Caerulein_B2057

value: Adult Pancreas

value: Tamoxifen

value: Caerulein


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_8h_Rep2

description: Library name: Sample 16


title: h-, asp1-H397A::natMX aps1∆::kanMX siw14∆::hygMX spx1∆::ura4MX, 1h, biol_rep_1

description: Library name: HASX_asp1-H397A aps1 knockout siw14 knockout spx1 knockout, Strain BS1453, 1h_biol_rep_1


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_2h_Rep1

description: Library name: Sample 13

value: dTAGv1 for 2h


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_0h_Rep2

description: Library name: Sample 12

value: No


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_2h_Rep2

description: Library name: Sample 14


title: h-, WT, 2h, biol_rep_2

description: Library name: WT, Strain Sp1, 2h_biol_rep_2

value: Strain Sp1

value: Vegetative growth

value: WT


title: h-, WT, 4h, biol_rep_2

description: Library name: WT, Strain Sp1, 4h_biol_rep_2


title: h-, WT, 4h, biol_rep_3

description: Library name: WT, Strain Sp1, 4h_biol_rep_3


title: h-, WT, 1h, biol_rep_3

description: Library name: WT, Strain Sp1, 1h_biol_rep_3


title: MDSCs, arglabin, 1

city: Nanjing

first: Di

last: Kang

address: 138 Xianlin Ave

department: School of Pharmacy

institute: Nanjing University of Chinese Medicine

description: Library name: Sample 4

data_processing:
The sequencing data was filtered with SOAPnuke.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.12) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0).
To take insight to the change of phenotype, GO and KEGG enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test.
Assembly: NCBI/GCF_000001653.26_GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample

source_name: MDSCs

growth_protocol: RPIM-1640, 10% fetal bovine serum, 2 mM β-mercaptoethanol, 10 ng/mL IL-4, 10 ng/mL GM-CSF. MDSCs were cultured at 37C at 5% CO2.

extract_protocol:
RNA was harvested using RNA-easyTM Isolation Reagent (Vazyme). Approximately 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China) following manufacturer’s protocols.

treatment_protocol: MDSCs were treated with Vehicle control (DMSO) or arglabin (10 μM) for 2 hours.

value: MDSCs

value: Arg


title: SLAMseq_KMS11_NSD2dTAG#8_dTAGv1_0h_Rep1

description: Library name: Sample 11

data_processing:
Raw sequencing reads (FASTQ files) were processed using the nf-core/slamseq pipeline (v1.0.0). Initial read quality was assessed with FastQC (v0.11.9). Adapters and low-quality sequences were trimmed using TrimGalore! (v0.6.4_dev). The core processing, including conversion-aware alignment, filtering, SNP masking, and quantification, was performed using Slamdunk (v0.4.3) with default parameters. Reads were aligned to the human genome reference (GRCh38), using gene and 3' UTR annotations derived from the UCSC Table Browser for GRCh38. Slamdunk was used to quantify reads at the gene level, specifically generating counts for total reads and counts for reads containing T>C conversions (indicative of newly synthesized RNA, defined in the analysis as reads with >2 T>C conversions). The submitted processed data files consist of these gene-level count matrices generated by Slamdunk.
Assembly: hg38
Supplementary files format and content: Each processed data file corresponds to a single experimental sample and is provided in comma-separated value (.csv) format. Within each file, rows represent individual transcripts identified by their RefSeq transcript ID. The columns contain transcript-level quantification and metric data generated by Slamdunk, including:
* readCount: Raw count of total reads mapping to the transcript.
* tcReadCount: Raw count of reads identified as containing T>C conversions (representing newly synthesized RNA, based on the pipeline's criteria, e.g., >2 T>C conversions per read).
* length: The length of the transcript.
* readsCPM: Reads Per Million mapped reads (calculated for total reads).
* conversionRate: The calculated T>C conversion rate for reads mapping to this transcript.
* Tcontent: The proportion of thymine bases within the transcript sequence.
* coverageOnTs: Coverage depth specifically over thymine bases.
* conversionsOnTs: Number of T>C conversions observed at thymine positions.
* multimapCount: Count related to multi-mapping reads assigned to the transcript.


title: MDSCs, Vehicle control, 3

description: Library name: Sample 3

value: DMSO


title: h-, WT, 1h, biol_rep_1

description: Library name: WT, Strain Sp1, 1h_biol_rep_1

value: Schizosaccharomyces pombe


title: MDSCs, arglabin, 2

description: Library name: Sample 5


title: h-, WT, 0h, biol_rep_3

description: Library name: WT, Strain Sp1, 0h_biol_rep_3

value: Log phase culture, ePMGT(+PO4) medium


title: MDSCs, arglabin, 3

description: Library name: Sample 6


title: h-, WT, 4h, biol_rep_1

description: Library name: WT, Strain Sp1, 4h_biol_rep_1

value: 4h phosphate starved culture, ePMGT(-PO4) medium


title: h-, WT, 0h, biol_rep_1

description: Library name: WT, Strain Sp1, 0h_biol_rep_1


title: h-, WT, 0h, biol_rep_2

description: Library name: WT, Strain Sp1, 0h_biol_rep_2


title: SLAMseq_KMS11_dTAGparental_dTAGv1_72h_Rep1

description: Library name: Sample 9

value: dTAGv1 for 72h


title: 3CL pro (Cys145Ala) (48 h) biol rep 1

city: Vancouver

first: Christopher

last: Overall

state: BC

address: 2350 Health Sciences Mall

institute: UBC

description: Library name: 48_4_1-PB-042424

data_processing:
Sequencing data was demultiplexed using Illumina's BCL Convert. Alignment and quantification were performed using the DRAGEN RNA app on Basespace Sequence Hub
Assembly: Homo sapiens (hg38 no Alts, with decoys) reference.
Supplementary files format and content: tab delimited text file includes TPM for each sample

source_name: HEK293 Flp-In T-REx

extract_protocol:
RNA purification using the RNeasy mini kit (Qiagen, 74104) with QIAShredder columns (Qiagen, 79656).
samples were prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina).

value: HEK293 Flp-In T-REx


title: SLAMseq_KMS11_dTAGparental_dTAGv1_72h_Rep2

description: Library name: Sample 10

extract_protocol:
Cells were metabolically labeled with 100 µM 4-thiouridine (4sU) for 1 hour. Total RNA was extracted using TRIzol reagent followed by purification with the RNA Clean & Concentrator-5 kit (Zymo Research). 10 µg of RNA was then alkylated with iodoacetamide, followed by another cleanup using the RNA Clean & Concentrator-5 kit. 1 µg of the resulting RNA was used as input for library construction.
Sequencing libraries were prepared from 1 µg of alkylated total RNA using the QuantSeq 3’mRNA-Seq Library Prep FWD Kit for Illumina (Lexogen #015), following the manufacturer's protocol.


title: 3CL pro (48 h) biol rep 2

description: Library name: 48_2_3-PB-042424


title: MDSCs, Vehicle control, 2

description: Library name: Sample 2


title: 3CL pro (Cys145Ala) (48 h) biol rep 2

description: Library name: 48_4_3-PB-042424


title: MDSCs, Vehicle control, 1

description: Library name: Sample 1


title: G1685D_3

city: Houston

first: Nick

last: Newkirk

state: TX

department: Genetics and Epigenetics

institute: MD Anderson UTHealth Graduate School of Biomedical Sciences

description:
Library name: AUM1630_3
corresponds to AUM1630-3

data_processing:
tinyRNA (https://github.com/MontgomeryLab/tinyRNA) run using default runconfig.yml trimming of raw read files, bowtie alignment and deseq parameters
HQAlign (github.com/FireLabSoftware/HQAlign) used on raw sequencing data trimmed using cutadapt (https://cutadapt.readthedocs.io/en/) default settings and aligned to WS290: WGS, ncRNA, piRNA, mRNA, miRNA. Alignments analyzed in RStudio using the following significance cutoffs for identifying differentially expressed mappings: log2 fold change >(±)2 and >10 total RPM between the two samples being compared. Filtering for 26G (mRNA and ncRNA) and 21U (piRNA) mapped reads was performed using HQAlignSubset.py (github.com/ArurLab) and differentially expressed mappings were identified using the same significance cutoffs
Assembly: tinyRNA:  WS279; HQAlign: WS290
Supplementary files format and content: tinyRNA - .csv; feature GeneID, small RNA type and deseq data for each WS279 feature
Supplementary files format and content: HQAlign - .xlsx; aligned reads to each feature (see tab for feature), number of sense and anit-sense reads aligned and size and base histogram data provided for each replicate

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: hermaphrodite animals were shifted to 25C at the mid-L4 stage (after spermatogensis had completed) for 24 hours for oocytes to development

extract_protocol:
TRIzol with chloroform extraction and ethanol precipitation
TruSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: M9 wash to collect and frozen in Trizol at -80C

value: whole worm


title: h-, WT, 2h, biol_rep_1

description: Library name: WT, Strain Sp1, 2h_biol_rep_1

value: 2h phosphate starved culture, ePMGT(-PO4) medium


title: SLAMseq_KMS11_dTAGparental_dTAGv1_24h_Rep2

first: sanxiong

last: liu

institute: University of Miami Miller School of Medicine

description: Library name: Sample 8

value: dTAGv1 for 24h


title: 3CL pro (48 h) biol rep 1

description: Library name: 48_2_1-PB-042424


title: 3CL pro (Cys145Ala) (24 h) biol rep 2

description: Library name: 24_4_3-PB-042424


title: RNase L (1–409) biol rep 2

description: Library name: 2_4b-PB-062824


title: SLAMseq_KMS11_dTAGparental_dTAGv1_8h_Rep1

description: Library name: Sample 5

value: dTAGv1 for 8h


title: h-, WT, 1h, biol_rep_2

description: Library name: WT, Strain Sp1, 1h_biol_rep_2

value: 1h phosphate starved culture, ePMGT(-PO4) medium


title: 3CL pro (24 h) biol rep 2

description: Library name: 24_2_3-PB-042424


title: 3CL pro (24 h) biol rep 1

description: Library name: 24_2_1-PB-042424


title: G1685D_1

description:
Library name: AUM1630_1
corresponds to AUM1630-1


title: RNaseL biol rep 2

description: Library name: 1_1b-PB-062824


title: SLAMseq_KMS11_dTAGparental_dTAGv1_8h_Rep2

description: Library name: Sample 6


title: 3CL pro (Cys145Ala) (24 h) biol rep 1

description: Library name: 24_4_1-PB-042424


title: RNase L (410–741) biol rep 1

description: Library name: 1_3b-PB-062824


title: RNase L (410–741) biol rep 2

description: Library name: 2_3b-PB-060624


title: SLAMseq_KMS11_dTAGparental_dTAGv1_2h_Rep2

description: Library name: Sample 4

value: dTAGv1 for 2h


title: RNase L (1–409) biol rep 1

description: Library name: 1_4b-PB-060624


title: RNaseL biol rep 1

description: Library name: 1_1b-PB-060624


title: R3K_2

description: Library name: R3K_2


title: G1685D_2

description:
Library name: AUM1630_2
corresponds to AUM1630-2


title: SLAMseq_KMS11_dTAGparental_dTAGv1_24h_Rep1

description: Library name: Sample 7


title: R3K_1

description: Library name: R3K_1


title: R3K_3

description: Library name: R3K_3


title: SLAMseq_KMS11_dTAGparental_dTAGv1_2h_Rep1

description: Library name: Sample 3


title: SLAMseq_KMS11_dTAGparental_dTAGv1_0h_Rep2

description: Library name: Sample 2

value: No