title: 22Rv1-SF3B1-C1111S, BRM014, 1h, WX-02-23, 3h, biol rep 2

city: La Jolla

first: Lauren

last: Hargis

address: 10650 N Torrey Pines Road, BCC526

institute: Scripps Research Institute

description: Library name: WX-02-23_BRM014_3h_rep2

data_processing:
Sequencing reads were aligned to the human reference genome (hg19) and RefSeq gene annotations using Bowtie2 (v2.5.1) with the following parameters: bowtie2 --local --very-sensitive-local --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700 --threads 12 -x. Unmapped, duplicate, and low-quality reads were removed using Sambamba (v0.7.1). Reads mapping to the mitochondrial genome or ENCODE blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were excluded using SAMtools (v1.10). Peak calling was performed with MACS (v2.1.0) using the parameters: macs2 callpeak -q 0.01 --nomodel --shift -100 --extsize 150.
Assembly: hg19
Supplementary files format and content: Genome-wide chromatin accessibility signal tracks in bedGraph format (treat_pileup.bdg.gz) generated by MACS2 from hg19-aligned ATAC-seq data after removal of duplicate, low-quality, mitochondrial, and ENCODE blacklist reads. Files represent ATAC-seq read pileup across the genome and are compressed using gzip.

source_name: Prostate

growth_protocol: 22Rv1-SF3B1-C1111S cells (endogenous knock-in of C1111S mutation) were treated with DMSO or 1µM BRM014 for 1 hour, then treated with DMSO or 20µM WX-02-23 for an additional 3 hours (24-well plates, 70–80 % confluency).

extract_protocol:
ATAC-seq was performed using the Active Motif ATAC-Seq Buffer Set (Cat#: 53153) and 96-well Pre-Indexed Assembled Tn5 Transposomes (Cat#: 53152) according to the manufacturer’s protocol. After treatment, cells were washed twice with ice-cold PBS and lysed directly in-plate with 150 µL ATAC lysis buffer (Active Motif). Lysates were centrifuged at 500 × g for 10 min at 4 °C, and the supernatant was carefully removed to isolate nuclei. Each nuclei pellet was resuspended in 46 µL Tagmentation Master Mix (1× Tagmentation Buffer, 1× PBS, 0.01 % digitonin, 0.1 % Tween-20).
ATAC-seq was performed using the Active Motif ATAC-Seq Buffer Set and 96-well Pre-Indexed Assembled Tn5 Transposomes according to the manufacturer’s protocol. For indexing, each sample was combined with a distinct well of the Pre-Indexed Assembled Tn5 Transposome plate, ensuring unique barcode assignment per sample. Plates were sealed, gently vortexed, quick-spun, and incubated at 37 °C for 30 min with gentle mixing every 10 min. DNA was purified and libraries were prepared according to the manufacturer’s protocol. Libraries were cleaned by SPRI-bead purification and gel extraction to enrich for fragments < 1 kb, then multiplexed and sequenced on an Illumina NextSeq 2000 using 50-bp paired-end reads.

value: Prostate

value: prostate carcinoma epithelial cell

value: 1h pretreat, 3h


title: ChIP1, WT, H3K4me2, heat-treatment 5min, rep2

status: Public on Feb 25 2026

type: SRA

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: Cells were grown in YES medium until mid-log phase at 30 ºC.

extract_protocol:
Total RNA for mRNA-seq was extracted by the hot-phenol method, as previously described (Iyer,V. and Struhl,K. 1996). Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016). Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). mRNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.

treatment_protocol: The non-treated samples (0 min) were harvested immediately, and the heet-treated samples were moved from a 30 ºC water bath to 37.5 ºC and incuvated during the designated term (2.5, 5 and 25 min) with shaking.

tag: cell type

value: S.pombe cells

tag: genotype

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

tag: treatment

value: 5 min atter heat-treatment


title: 22Rv1-SF3B1-C1111S, BRM014, 1h, WX-02-23, 3h, biol rep 3

state: CA

country: USA

description: Library name: WX-02-23_BRM014_3h_rep3

organism: Homo sapiens

tag: tissue

tag: cell line

tag: batch


title: ChIP1, WT, H3K4me2, heat-treatment 25min, rep1

value: 25 min atter heat-treatment


title: 0.6_JE2_3

city: Guelph

first: Georgina

last: Cox

state: Ontario

address: Summerlee Science Complex

department: Molecular and Cellular biology

country: Canada

institute: University of Guelph

description: Library name: 0.6_JE2_3

library_source: transcriptomic

data_processing:
usegalaxy.org  (version 25.1.rc1)
Quality control of raw reads, demultiplexing and adapter trimming were completed in advance by the AAC.
Reads were aligned to the USA300 reference genome (GenBank: CP000255.1) using HISAT2 (Galaxy Version 2.2.1+galaxy1).
The number of reads mapped to the annotated genome (GCA_000013465, GFF3, EnsemblBacteria) were counted using featureCounts (Galaxy Version 2.0.8+galaxy0).
Analysis of differentially expressed genes was performed using the DESeq2 package (Galaxy Version 2.11.40.8+galaxy0)
Assembly: USA300_FPR3757
Supplementary files format and content: Text file containg raw counts for each sample

molecule: total RNA

organism: Staphylococcus aureus

growth_protocol: JE2 and JE2-saeS::Tn cells were grown in tryptic soy broth to an OD600nm of 0.3, 0.6 and 1.0

extract_protocol:
RNA was harvested using PuroSPIN Total RNA Purification Kit (Luna Nanotech).
Library preparation was conducted at the Advanced Analysis Centre (AAC) at the University of Guelph, Ontario, Canada

treatment_protocol: Cells were treated with or without 10 µM geranylgeranoic acid

value: Wildtype JE2


title: ChIP1, WT, H3K4me2, heat-treatment 0min, rep2

value: 0 min (non treated)


title: 33C_1

city: Callahagn

first: benjamin

last: Robinson

state: NSW

address: University Drive

department: School of Biomedical Science and Pharmacy

country: Australia

institute: University of Newcastle

description: Library name: Sample 1

data_processing:
FASTQ data generated by Illumina DRAGEN BCL Convert 07.021.609.3.9.3 pipeline
Adapters and poor quality bases/reads were trimmed with trim_galore (cutadapt)
Trimmed sequecne reads were mapped to GRCm38
Performed TEtranscripts to generate gene and TE counts
Assembly: mm10
Supplementary files format and content: Merged tab deliminated text file contains raw TE and gene counts

organism: Mus musculus

source_name: Round Spermatids

extract_protocol:
RNA was extracted using Rneasy Mini plus kit (Qiagen).
Ribo-zero stranded protocol performed by Australian Genome Research Facility (AGRF)

treatment_protocol: Mice were aneanesthetised with (5% isoflurane 2L/min) then placed on a floating block with a hole cut allowing the testis to be in contact with a thermally controlled water bath. Anestesia was maintained via nose cone (1.5-2% isoflurane 2L/min). Water temperature was maintaiend at 42°C or 33°C for 30 minutes. Mice were allowed to recover from anestesia then immediatley sacrificed and round spermatids isolated.

value: Round Spermatids

value: 33°C 30 minutes


title: 0.6_JE2_4

description: Library name: 0.6_JE2_4


title: Brain - Colon macrophage, Mafb KO, Multiplexing capture, 1

city: Liège

first: Thomas

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: Library name: 2-KO-Hashtag_NGS23-D645-1

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment to the mouse genome (GRCm38/mm10), filtering, unique molecular identifier counting and construction of gene-barcode matrices of the single cell RNA-Seq data were performed using Cell Ranger (7.1.0).
Single cell RNA-Seq data were further analyzed using R Bioconductor (4.2.3) and the Seurat package (4.3.0). Filtered matrices containing cell IDs and feature names for each sample were used to construct a Seurat object. All samples were merged and integrated with previously published single cell RNA-seq data containing CD45+SSCloCD11b+F4/80+CD64+ lung IM cells of Lyz2CreMafbfl/fl mice and Mafbfl/fl littermate controls (GSE193891). Quality control was performed by excluding cells with fewer than 200 detected genes, genes detected in fewer than three cells, and cells with more than 10% mitochondrial gene content. Gene counts for each sample were normalized using the default LogNormalize method, with a scale factor of 10,000 followed by log transformation. The top 2,000 highly variable features were identified using the vst method. Contaminating and actively proliferating cells were removed based on the expression of specific genes. Cells were clustered using the FindClusters function and the macrophage subsets were identified based on the expression of Hashtag barcodes and known macrophage subset specific genes. DEGs between macrophages subsets from Mafbfl/fl and Lyz2CreMafbfl/fl mice were determined using the FindMarkers method.
Assembly: GRCm38
Supplementary files format and content: barcode sequences corresponding to column indices
Supplementary files format and content: tsv files containing for each feature the feature ID, the name and the type of features
Supplementary files format and content: mtx files describing hte count of genes for all cells

molecule: polyA RNA

source_name: Brain and colon

extract_protocol:
Fifty thousand CD45+Lin−Ly6C−CD11b+CD115+ live cells from the peritoneal lavage, 50000 CD45+Lin−Ly6C−CD11bint/+F4/80+CD64+ live cells from the livers, 50000 CD45+Lin−CD11b+F4/80+CD64+ live cells from the colons and 50000 CD45+Lin−Ly6C−CD11b+F4/80+CD64+ live cells from the brains of Lyz2CreMafbfl/fl mice and Mafbfl/fl littermate controls were FACS-sorted in PBS with 5% FBS. Sorted cells were barcoded with TotalSeq™-B anti-mouse Hashtag antibodies (Biolegend). Hashtag barcoded cells were washed, pooled per genotype, spun down and resuspended in PBS with 0.04% UltraPure™ BSA (Invitrogen, AM2616) at an estimated final concentration of 1000 cells/μl. Cell suspensions were loaded into the Chromium Controller (10x Genomics) at a target recovery of 2000 cell per sorted population, to generate single-cell Gel Bead-in-EMulsion (GEMs).
Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, 1000128) according to manufacturer’s instructions. The libraries were sequenced on an NovaSeq 6000 (Illumina) sequencer on an S4 flow cell at 50000 reads per cell.

value: Brain and colon

value: Macrophages

value: Lyz2Cre Mafbfl/fl (Mafb KO)


title: 0.6_JE2_2

description: Library name: 0.6_JE2_2


title: 22Rv1-SF3B1-C1111S, BRM014, 1h, WX-02-23, 3h, biol rep 1

description: Library name: WX-02-23_BRM014_3h_rep1


title: Brain - Colon  macrophage, Mafb WT, Multiplexing capture

description: Library name: 1-WT-Hashtag_NGS23-D644-1

value: Mafbfl/fl (Mafb WT)


title: 22Rv1-SF3B1-C1111S, BRM014, 1h, DMSO, 3h, biol rep 2

description: Library name: DMSO_BRM014_3h_rep2

value: 1µM BRM014, DMSO


title: Brain - Colon - macrophage , Mafb KO, cDNA

description: Library name: 2-KO-cDNA_NGS23-D643


title: 22Rv1-SF3B1-C1111S, BRM014, 1h, DMSO, 3h, biol rep 1

description: Library name: DMSO_BRM014_3h_rep1


title: ChIP1, WT, H3K4me2, heat-treatment 5min, rep1


title: sae4_0.3

description: Library name: 0.3_saeS_4

value: JE2- saeS transposon


title: 22Rv1-SF3B1-C1111S, BRM014, 1h, DMSO, 3h, biol rep 3

description: Library name: DMSO_BRM014_3h_rep3

value: Prostate


title: Brain - Colon  macrophage, Mafb WT, cDNA

description: Library name: 1-WT-cDNA_NGS23-D642


title: ChIP1, WT, H3K4me2, heat-treatment 0min, rep1


title: ChIP1, WT, H3K4me1, heat-treatment 5min, rep2


title: sae3_0.3

description: Library name: 0.3_saeS_3


title: ChIP1, WT, H3K4me1, heat-treatment 25min, rep2


title: 22Rv1-SF3B1-C1111S, WX-02-23, 3h, biol rep 3

description: Library name: WX-02-23_3h_rep3

value: prostate carcinoma epithelial cell


title: 0.6_JE2_1

description: Library name: 0.6_JE2_1


title: Peritoneum - Liver macrophage, Mafb WT, cDNA

description: Library name: cDNA-WT_NGS23-B233

source_name: Peritoneum and liver

value: Peritoneum and liver


title: Peritoneum - Liver  macrophage, Mafb WT, Multiplexing capture

description: Library name: Hashtag-WT_NGS23-B235


title: sae1_0.3

description: Library name: 0.3_saeS_1


title: ChIP1, WT, H3K4me1, heat-treatment 0min, rep2

value: S.pombe cells


title: sae2_0.3

description: Library name: 0.3_saeS_2


title: Peritoneum - Liver - Spleen macrophage, Mafb KO, cDNA

description: Library name: cDNA-KO_NGS23-B234


title: 22Rv1-SF3B1-C1111S, WX-02-23, 3h, biol rep 1

description: Library name: WX-02-23_3h_rep1

value: 1h pretreat, 3h


title: 22Rv1-SF3B1-C1111S, WX-02-23, 3h, biol rep 2

description: Library name: WX-02-23_3h_rep2


title: G4_0.3

description: Library name: 0.3_JE2+GGA_4

value: GGA


title: G3_0.3

description: Library name: 0.3_JE2+GGA_3


title: Macro  Mafb KO, rep2, H3K27 antibody

description: Library name: KO-H3K27Ac-2_NGS24-E667

data_processing:
Preprocessing, alignment to the mouse genome (GRCm38/mm10), tag counting, and quality control of the CUT&RUN data were carried out with the nf-core/cutandrun pipeline. Normalized tag counts at MafB binding sites were quantified using the Homer’s annotatePeaks function.
Assembly: GRCm38/mm10
Supplementary files format and content: The mapped read are displayed in bigwig format for igv
Library strategy: CUT&Run

source_name: BMBM

extract_protocol:
Bone marrow monocytes from Mafbfl/fl or Lyz2CreMafbfl/fl mice were isolated using Monocyte Isolation Kit (BM) (Miltenyi Biotec, 130100629) and were seeded in tissue culture-treated 6-well plates (Greiner, 657160) and cultured for 4 days in RPMI supplemented with 10% FBS, 1 mM Sodium Pyruvate (Gibco, 11360070), 1X MEM Non-Essential Amino Acids Solution (Gibco, 11140050), 50 µM β-mercaptoethanol (Gibco, 31350010) and 40 ng/mL CSF-1 (Peprotech, 315-02) to differentiate them into bone marrow monocyte derived macrophages (BMDM). H3K27Ac CUT&RUN was performed with a CUTANA ChIC/CUT&RUN Kit (EpiCypher, 141048) according to manufacturer’s instructions, with modifications. BMDM from Mafbfl/fl or Lyz2CreMafbfl/fl mice were washed with ice-cold PBS and fixed with 0.1 % formaldehyde in PBS for 2 min at room temperature. Fixation was quenched by adding glycine (Merck, 104691000) to 0.125 M.  For each CUT&RUN sample, 1x 106 fixed cells and 0.5 µg antibodies were used. Anti-H3K27Ac (MA5-23516) and IgG Negative Control Antibody (EpiCypher, 13-0042) were used.
CUT&RUN libraries were prepared using were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645L) according to manufacturer’s instructions. These libraries were sequenced on an NovaSeq 6000 (Illumina) sequencer on an XP flow cell.

value: BMBM

tag: cut&run antibody


title: Macro  Mafb KO, rep2, IgG control

description: Library name: KO-IgG-2_NGS24-E665

value: H3K27Ac antibody (MA5-23516, Thermo Fisher Scientific)


title: ChIP1, WT, H3K4me1, heat-treatment 5min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min atter heat-treatment


title: 22Rv1-SF3B1-C1111S, DMSO, 3h, biol rep 3

description: Library name: DMSO_3h_rep3

value: DMSO, DMSO


title: 22Rv1-SF3B1-C1111S, DMSO, 3h, biol rep 1

description: Library name: DMSO_3h_rep1


title: 22Rv1-dTAG-FOXA1, dTAGv1, 1.5h, biol rep 3

description: Library name: dTAGv1_1.5h_rep3

growth_protocol: 22Rv1-dTAG-FOXA1 cells (endogenous knock-in, puro and blast resistant) were treated with DMSO or 500 nM dTAGv1 for 1.5 hours (24-well plates, 70–80 % confluency).

extract_protocol:
ATAC-seq was performed using the Active Motif ATAC-Seq Buffer Set (Cat#: 53153) and 96-well Pre-Indexed Assembled Tn5 Transposomes (Cat#: 53152) according to the manufacturer’s protocol. After treatment, cells were washed twice with ice-cold PBS and lysed directly in-plate with 150 µL ATAC lysis buffer (Active Motif). Lysates were centrifuged at 500 × g for 10 min at 4 °C, and the supernatant was carefully removed to isolate nuclei. Each nuclei pellet was resuspended in 46 µL Tagmentation Master Mix (1× Tagmentation Buffer, 1× PBS, 0.01 % digitonin, 0.1 % Tween-20).
ATAC-seq was performed using the Active Motif ATAC-Seq Buffer Set and 96-well Pre-Indexed Assembled Tn5 Transposomes according to the manufacturer’s protocol. For indexing, each sample was combined with a distinct well of the Pre-Indexed Assembled Tn5 Transposome plate, ensuring unique barcode assignment per sample. Plates were sealed, gently vortexed, quick-spun, and incubated at 37 °C for 30 min with gentle mixing every 10 min. DNA was purified and libraries were prepared according to the manufacturer’s protocol. Libraries were cleaned by SPRI-bead purification and gel extraction to enrich for fragments < 1 kb, then multiplexed and sequenced on an Illumina NextSeq 2000 using 50-bp single-end reads.

value: 500nM dTAGv1


title: G2_0.3

description: Library name: 0.3_JE2+GGA_2

value: Wildtype JE2


title: ChIP1, WT, H3K4me1, heat-treatment 0min, rep1

value: 0 min (non treated)


title: ChIP1, WT, H3, heat-treatment 25min, rep2

value: 25 min atter heat-treatment


title: 0.3_JE2_4

description: Library name: 0.3_JE2_4


title: Macro  Mafb KO, rep1, IgG control

description: Library name: KO-IgG-1_NGS24-E664

value: Macrophages

value: Lyz2Cre Mafbfl/fl (Mafb KO)


title: 0.3_JE2_3

description: Library name: 0.3_JE2_3


title: ChIP1, WT, H3, heat-treatment 5min, rep2


title: 22Rv1-dTAG-FOXA1, dTAGv1, 1.5h, biol rep 2

description: Library name: dTAGv1_1.5h_rep2

value: Prostate


title: Macro  Mafb WT, rep2, IgG control

description: Library name: WT-IgG-2_NGS24-E669

value: Mafbfl/fl (Mafb WT)


title: 22Rv1-dTAG-FOXA1, dTAGv1, 1.5h, biol rep 1

description: Library name: dTAGv1_1.5h_rep1

value: prostate carcinoma epithelial cell


title: ChIP1, WT, H3K4me1, heat-treatment 25min, rep1

value: S.pombe cells


title: ChIP1, WT, H3, heat-treatment 0min, rep2


title: ChIP1, WT, H3, heat-treatment 5min, rep1


title: G1_0.3

description: Library name: 0.3_JE2+GGA_1


title: Peritoneum - Liver  macrophage, Mafb KO, Multiplexing capture

description: Library name: Hashtag-KO_NGS23-B235

value: Peritoneum and liver


title: 0.3_JE2_1

description: Library name: 0.3_JE2_1


title: 22Rv1-dTAG-FOXA1, DMSO, 1.5h, biol rep 2

description: Library name: DMSO_1.5h_rep2

value: DMSO


title: 0.3_JE2_2

description: Library name: 0.3_JE2_2


title: ChIP1, WT, H3, heat-treatment 25min, rep1


title: 22Rv1-dTAG-FOXA1, DMSO, 1.5h, biol rep 3

description: Library name: DMSO_1.5h_rep3


title: 22Rv1-dTAG-FOXA1, DMSO, 1.5h, biol rep 1

description: Library name: DMSO_1.5h_rep1


title: Macro  Mafb WT, rep2, H3K27 antibody

description: Library name: WT-H3K27Ac-2_NGS24-E671

value: BMBM

value: IgG Negative Control Antibody (EpiCypher, 13-0042)


title: Macro  Mafb WT, rep1, IgG control

description: Library name: WT-IgG-1_NGS24-E668

value: H3K27Ac antibody (MA5-23516, Thermo Fisher Scientific)


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 9

city: Stanford

first: Yaereen

last: Dho

address: 443 Via Ortega, Shriram Center for Biological and Chemical Engineering Room 271

department: Chemistry

institute: Stanford University

description: Library name: Rt9

data_processing:
For processing of Illumina data, the quality of raw Illumina sequencing reads was evaluated using FastQC (Babraham Bioinformatics, Babraham Institute). These reads were processed to remove adapters, barcodes, and low-quality sequences using Trimmomatic68, using the following parameters: <ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:5 MINLEN:50>. The trimmed reads were then re-assessed with FastQC to confirm quality. These processed Illumina sequencing reads were used to quantify each transcript abundance against PacBio Iso-Seq transcriptome.
For PacBio Iso-Seq data, the raw data were processed using the Iso-Seq 3 pipeline in SMRT® Link software (PacBio) with default settings, resulting in generation of 357,877 high quality transcript isoforms. The quality of the Iso-seq transcriptome was assessed by mapping short read Ilumina short reads to the long read transcriptome assembly using bowtie2 and through BUSCO analysis for completeness. Peptide sequences, with longest ORF identified for each transcript, were then predicted using Transdecoder, resulting in 349,712 contigs. Redundant contigs were removed using CD-HIT-EST with a cut-off at 99% identity, yielding a final PacBio Iso-Seq transcriptome of 29,163 unique transcripts. Then this final processed PacBio Iso-seq transcriptome was annotated with best-hit Pfam terms, followed by all subsequent (lower-ranked) Pfam hits. Annotations also included the best Basic Local Alignment Search Tool (BLAST) hit from Arabidopsis thaliana proteomes (via UniProt), Taxus chinensis proteomes, and Cephalotaxus hainanensis proteomes, using BLASTP. Quantification of processed Illumina reads against the processed PacBio transcriptome was performed using Kallisto with default parameters. For all downstream expression analysis, log2-transformed, TMM-normalized CPM expression values were used.
Assembly: How the transcriptome was processed is described above in data processing step.
Supplementary files format and content: csv file includes expression values for all 36 samples, represented as TMM-normalized, log2-transformed counts per million.
Supplementary files format and content: fasta file includes 29,163 unique transcripts from processed PacBio Iso-Seq data.

organism: Cephalotaxus harringtonia

source_name: root tips

growth_protocol: The plants were purchased from Forest Farms (forestfarm.com). They were grown in pots with soil, watered approximately once every week. Growth conditions consisted of ambient laboratory temperature and lighting.

extract_protocol:
Various tissues from C. harringtonia var. Fastigiata were excised from the whole plant using ethanol-sterilized scissors. For young inner needles (YIN), actively growing inner young light-green yellowish needles of 0.5-2 cm in length were harvested. Young outer needles (YON) were actively growing outer light-green needles, 1.5-3 cm in length. For young stems (YSt), light-green stems with YIN and YON of 2-3 cm in length from the tip of the stem (meristem) was harvested; all the surrounding needles were removed using a sterile scalpel. Old needles (ON) were mature, dark green needles (≥1-2 years old), 4-7 cm in length. For old stems (OSt), at least 1-2 year-old mature dark green stems (4-5 cm in length) with ON removed were collected. Before harvesting root tips (Rt), they were thoroughly washed with water, quickly rinsed with 30% ethanol, and washed again with water as a final washing step. Then, roots of 5-8 cm in length from the root tip, including the root meristem, were collected. Needles and roots, due to their thin structure, were latitudinally split into equally sized sections for paired metabolomics (feeding experiments) and transcriptomics (RNA-seq). Stems were longitudinally sectioned into equal halves for the same paired analyses. All the tissues were immediately flash frozen in liquid nitrogen and were homogenized to a fine powder under liquid nitrogen using a chilled mortar and pestle that were pre-treated with RNAse Zap RNAse Decontamination Solution (Thermo Fisher Scientific). RNA from the powdered tissue samples were extracted using RNeasy Plant Mini Kit (Qiagen) with on-column DNase digestion. RLC buffer was used as the lysis buffer. For root samples, the extracted RNA was further cleaned up using the same kit. RNA concentration and purity were measured using a NanoDrop and Qubit (Qubit® 2.0 Fluorometer), and quality was further assessed using an Agilent 2100 Bioanalyzer.
Library preparation for Illumina NovaSeq 6000 (S4 Flow cell – PE150) sequencing was performed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (non-directional; New England Biolabs), as per the manufacturer instructions. Individual libraries were barcoded with internal index sets at Novogene. For fragmentation, Diagenode Bioruptor Pico was used, and inserts were size selected with NEBNext beads to have an average insert size of 150-200 bp. The PCR products were purified (AMPure XP system). The quality and size distribution of each library were confirmed with analysis using a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent). Each library was quantified using Qubit (Qubit® 2.0 Fluorometer) and real-time PCR (Kapa). Equimolar amounts of libraries for each sample (36 total, from May 2023 feeding experiments) were pooled for paired-end sequencing within a single Novaseq 6000 lane (S4 Flow cell – PE150). For PacBio Iso-Seq libraries, only a subset of tissues from the 36 total samples was sequenced: Rt1 (root tips), Rt6 (root tips), an equal combination of Rt4 and Rt8 (root tips), an equal combination of YIN3 and YIN4 (young inner needles), an equal combination of YSt3 and OSt3 (young and old stems), and an equal combination of ON1 and ON2 (old needles). Inclusion of Rt1, Rt,6 and Rt8—tissues with active CET biosynthesis—ensured that the transcriptome contained CET biosynthetic genes. Additional tissues were included to represent all other major tissue types beyond root tips, enabling capture of complete transcripts from C. harringtonia. PacBio SMRT library preparation and sequencing were performed by QB3 Genomics, UC Berkeley, Berkeley, CA (RRID: SCR_022170) on the PacBio Sequel II System using the Sequel II 3.1 binding kit with a 30-hour movie time. RNA concentration was adjusted to <5 ng/μL using the Qubit HS RNA Kit, and RNA quality was assessed via capillary electrophoresis on an Agilent Bioanalyzer 2100 using the Eukaryotic Total RNA Pico Assay, as per the manufacturer instructions, with a 2 min denaturation at 70 C followed by a 2 min cold shock on ice in a freezer. PacBio SMRT sequencing library was prepared as described in the Iso-Seq™ Template Preparation for Sequel® Systems manual using the NEBNext® Single Cell/Low Input cDNA Synthesis & Amplification Module and the Pacific Biosciences Iso-Seq Express Oligo Kit with the barcoded primers provided in the manufacturer’s protocol for first-strand cDNA synthesis (standard purification) and PCR amplification. Barcoded cDNAs from six representative samples (containing 10 unique tissue samples as discussed above) were pooled in equimolar amounts, and a single library was prepared from this pooled cDNA using the SMRTbell Prep Kit 3.0 following the standard protocol.

value: root tips


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 10

description: Library name: Rt10


title: 22Rv1-dTAG-FOXA1, BMS-986365, 24h, biol rep 2

description: Library name: BMS986365_24h_rep2

data_processing:
Raw sequencing data (FASTQ format) were processed using the SLAMdunk pipeline for alignment to the human genome (hg19) and counts-per-million (CPM) quantification. Reads were aligned to a composite reference genome consisting of the human genome (UCSC hg19) supplemented with ERCC and SIRV spike-in sequences. Transcript quantification was performed using RefSeq-curated 3′ UTR annotations.Transcripts with substantial expression (average >3 CPM in at least one treatment group) were retained for downstream analysis. All downstream analyses were performed in R, and code is available upon request.
Assembly: UCSC hg19 + ERCC + SIRV
Supplementary files format and content: Tab-delimited text files (tcount.tsv) generated by SLAM-Dunk containing per-transcript read counts and normalized counts per million (CPM) values derived from hg19-aligned sequencing data. These files were used for RNA-seq–based gene expression analysis.

extract_protocol:
22Rv1-dTAG-FOXA1 cells (70 % confluency; 6-well plates) were treated with the indicated compounds for the specified durations. Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with 0.1 % (v/v) β-mercaptoethanol (BME) added to all buffers. RNA concentration was quantified using the Qubit Broad Range RNA Assay Kit (Thermo Fisher Scientific).
For library preparation, 500 ng of total RNA per sample was processed using the QuantSeq 3′ mRNA-seq V2 Library Prep Kit FWD with UDI (Lexogen) according to the manufacturer’s instructions. Samples were purified using the magnetic bead purification module (Lexogen). Libraries were multiplexed and sequenced on an Illumina NextSeq 2000 platform to generate 100 bp single-end reads.

tag: timepoint


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 8

description: Library name: Rt8


title: Macrophage, Mafb WT Male, rep2

description:
Library name: WT-M-2_NGS23-A777
WT.M_2

data_processing:
Preprocessing, alignment to the mouse genome (GRCm38/mm10), sequence counting, and quality control of the bulk RNA-Seq data were carried out with the nf-core/rnaseq pipeline. RNA-Seq data were further analyzed using R Bioconductor (4.2.3) and the DESeq2 package (1.38.3). DEGs were calculated using the DESeq function.
Assembly: GRCm38/mm10
Supplementary files format and content: tsv file containing the gene count of each sample

source_name: BMDM

extract_protocol:
Two hundred fifty thousand bone marrow monocytes from Mafbfl/fl or Lyz2CreMafbfl/fl mice were isolated using Monocyte Isolation Kit (BM) (Miltenyi Biotec, 130100629) and were seeded in tissue culture-treated 6-well plates (Greiner, 657160) and cultured for 4 days in RPMI supplemented with 10% FBS, 1 mM Sodium Pyruvate (Gibco, 11360070), 1X MEM Non-Essential Amino Acids Solution (Gibco, 11140050), 50 µM β-mercaptoethanol (Gibco, 31350010) and 40 ng/mL CSF-1 (Peprotech, 315-02) to differentiate them into bone marrow monocyte derived macrophages (BMDM). After 4 days of differentiation, non-adherent cells were washed off with ice-cold PBS and total RNA was isolated with the standard TRIzol (Invitrogen, 15596018) RNA extraction protocol. Total RNA was further purified and concentrated using a RNA Clean & Concentrator Kit (Zymo Research, R1013) according to manufacturer’s instructions. RNA quality and quantity were evaluated using a 5200 Fragment Analyzer (Agilent). Samples with a RIN > 9.9 were selected for sequencing.
One hundred nanograms of RNA was used to generate the libraries using the TruSeq Stranded mRNA kit (Illumina, 20020594). These libraries were sequenced on an NovaSeq 6000 (Illumina) sequencer on an S4 flow cell.

value: BMDM


title: Macrophage, Mafb WT Male, rep1

description:
Library name: WT-M-1_NGS23-A776
WT.M_1


title: Organoid patient 57

city: Pozuelo de Alarcon

first: Angel

middle: Ayuso

last: Sacido

state: Madrid

address: Ctra. Pozuelo-Majadahonda KM 1.800.

department: Faculty of Experimental Sciences

country: Spain

institute: Universidad Francisco de Vitoria

description: Library name: Sample 21

data_processing:
Reads were filtered and aligned to genome via HISAT
Aligned reads were mapped with Bowtie2.
Alignment was checked by standard quality control means of coverage, saturation and randomness
Figures were produced with Dr.Tom BGI Bioinformatics tool suite
Assembly: GRCh38
Supplementary files format and content: We include 2 xls files that contain the TPM values of all samples.

source_name: GBM

growth_protocol: GO samples were isulated from fresh GBM tissue, and cultured for 2 weeks in ultra low attatchment plates with a custom media.

extract_protocol:
Qiagen RNA extraction kit, following manufacturer instructions
Rna libraries were constructed with the D-Plex Small RNA-seq Library Prep Kit, following manufacturers instructions

treatment_protocol: No treatment, samples are fresh.

value: GBM


title: 22Rv1-dTAG-FOXA1, BMS-986365, 24h, biol rep 1

description: Library name: BMS986365_24h_rep1


title: Macro  Mafb WT, rep1, H3K27 antibody

description: Library name: WT-H3K27Ac-1_NGS24-E670


title: ChIP1, WT, H3, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: Organoid patient 54

description: Library name: Sample 20


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 7

description: Library name: Rt7


title: Macrophage, Mafb WT Female, rep2

description:
Library name: WT-F-2_NGS23-A775
WT.F_2


title: Organoid patient 58

description: Library name: Sample 22


title: Organoid patient 43

description: Library name: Sample 19


title: Macrophage, Mafb WT Female, rep1

description:
Library name: WT-F-1_NGS23-A774
WT.F_1


title: Organoid patient 42

description: Library name: Sample 18


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 6

description: Library name: Rt6


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 5

description: Library name: Rt5


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 4

description: Library name: Rt4


title: Macrophage, Mafb KO Male, rep2

description:
Library name: KO-M-2_NGS23-A781
KO.M_2


title: 22Rv1-dTAG-FOXA1, DMSO, 24h, BMSstudy, biol rep 1

description: Library name: DMSO_24h_BMSstudy_rep1


title: 22Rv1-dTAG-FOXA1, DMSO, 24h, BMSstudy, biol rep 2

description: Library name: DMSO_24h_BMSstudy_rep2


title: Macrophage, Mafb KO Male, rep1

description:
Library name: KO-M-1_NGS23-A780
KO.M_1


title: 22Rv1-dTAG-FOXA1, DMSO, 24h, BMSstudy, biol rep 3

description: Library name: DMSO_24h_BMSstudy_rep3


title: Macrophage, Mafb KO Female, rep2

description:
Library name: KO-F-2_NGS23-A779
KO.F_2


title: 22Rv1-dTAG-FOXA1, BMS-986365, 8h, biol rep 3

description: Library name: BMS986365_8h_rep3


title: Organoid patient 39

description: Library name: Sample 16


title: Hepatic Stellate Cells, NTN1-3

city: Shanghai

first: Jiahui

last: Zhao

address: Dongan road 130

country: China

institute: Fudan university

description:
Library name: Sample6
Column name in processed data.txt:T3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore
Trimmed sequence reads were mapped to mm10 using Hisat2
Read count extraction were performed using featureConts
Read count normalization and differential expression analysis were performed using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Hepatic Stellate Cells

growth_protocol: Immortalized HSCs were maintained in DMEM medium containing 10% fetal growth serum (BGS) at 37°C and 5% CO2. Cells were switched to serum-free DMEM for 12 hours before treatments.

extract_protocol:
Total RNA was extracted from using Trizol. 200ng of total RNA was used for the construction of  sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS® Universal V8 RNA-seg Library Prep Kit for Illumina

treatment_protocol: Cells were treated with 300ng/ml Netrin1 recombinant protein(R&D System, 1109-N1-025) and equal volum of PBS in the presence of serum-free DMEM for 12h.

value: Hepatic Stellate Cells

value: WT

value: 300ng/ml Netrin-1 recombinant protein

tag: time


title: Organoid patient 37

description: Library name: Sample 14


title: 22Rv1-dTAG-FOXA1, BMS-986365, 8h, biol rep 2

description: Library name: BMS986365_8h_rep2


title: 22Rv1-dTAG-FOXA1, DMSO, 8h, BMSstudy, biol rep 3

description: Library name: DMSO_8h_BMSstudy_rep3


title: Macrophage, Mafb KO Female, rep1

description:
Library name: KO-F-1_NGS23-A778
KO.F_1

value: Macrophages

value: Lyz2Cre Mafbfl/fl (Mafb KO)


title: Organoid patient 36

description: Library name: Sample 13


title: 22Rv1-dTAG-FOXA1, BMS-986365, 8h, biol rep 1

description: Library name: BMS986365_8h_rep1

value: Prostate


title: Hepatic Stellate Cells, NTN1-2

description:
Library name: Sample5
Column name in processed data.txt:T2


title: Hepatic Stellate Cells, NTN1-1

description:
Library name: Sample4
Column name in processed data.txt:T1


title: Organoid patient 41

description: Library name: Sample 17


title: RNA-seq of Cephalotaxus harringtonia: old stem, replicate 2

description: Library name: OSt2

source_name: old stem

value: old stem


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 3

description: Library name: Rt3


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 2

description: Library name: Rt2


title: RNA-seq of Cephalotaxus harringtonia: old stem, replicate 3

description: Library name: OSt3


title: 22Rv1-dTAG-FOXA1, DMSO, 8h, BMSstudy, biol rep 1

description: Library name: DMSO_8h_BMSstudy_rep1

value: prostate carcinoma epithelial cell


title: Tumor patient 57

description: Library name: Sample 10


title: Organoid patient 38

description: Library name: Sample 15


title: RNA-seq of Cephalotaxus harringtonia: old stem, replicate 1

description: Library name: OSt1


title: 22Rv1-dTAG-FOXA1, DMSO, 8h, BMSstudy, biol rep 2

description: Library name: DMSO_8h_BMSstudy_rep2


title: Hepatic Stellate Cells, PBS-3

description:
Library name: Sample3
Column name in processed data.txt:C3

value: PBS


title: 22Rv1-dTAG-FOXA1, dTAGv1, 24h, biol rep 3

description: Library name: dTAGv1_24h_rep3

value: 500nM dTAGv1


title: 22Rv1-dTAG-FOXA1, dTAGv1, 24h, biol rep 1

description: Library name: dTAGv1_24h_rep1


title: Organoid patient 17

description: Library name: Sample 12


title: RNA-seq of Cephalotaxus harringtonia: old stem, replicate 4

description: Library name: OSt4


title: Tumor patient 43

description: Library name: Sample 8


title: Vestibule, 22 Months, Bio rep 5

city: Omaha

first: David

middle: Z

last: He

state: NE

address: 2500 California Plaza

department: Biomedical Science

institute: Creighton University

description:
Library name: CBA/J 22 months Vestibular Bio rep 5
10X Genomics

data_processing:
Standard 10x Genomics CellRanger pipeline (version 6.1.2) was used for demultiplexing, alignment (10x reference genome mm10), barcode processing, and UMI counting to obtain the filtered count matrices. Processing and visualization of the scRNA-seq data from cochlear and vestibular were performed in R. Ten filtered count matrices obtained from 5 biological replicates of cochlear and vestibular samples were loaded into R, converted to Seurat Objects, and pre-processed to eliminate the poor-quality cells using parameters such as counts, features, percentage of mitochondria, ribosomes, and blood gene content. Cells with at least 200 features, 1000 UMI counts, and less than 25% mitochondrial genes were included for the downstream analysis. Individual Seurat Objects were integrated into a single Seurat Object for cochlea and vestibule.
Assembly: Mouse mm10
Supplementary files format and content: Filtered barcode, matrix and features(genes) files

source_name: Vestibular Sensory Epithelium

extract_protocol:
Whole cochlear and vestibular organs were microdissected from the inner ears of 22-month-old CBA/J mice in petri dishes containing cold L-15 media (Gibco #11320033). The sensory epithelia were subjected to enzymatic digestion by transferring into 1.5 ml eppendorf tubes containing 1 ml/mg collagenase IV (Sigma) in L-15 medium for 10 minutes at room temperature. Then the cells were resuspended in 400 µL of enzyme-free DMEM containing 10% FBS and single-cell suspensions were obtained by trituration using a trimmed 200 ul pipette tip followed by filtering with a 40 uM strainer. The cells were pelleted by centrifuging at 300 xg for 5 mins at 4°C, then resuspended in media and subsequently quantified the number of cells. 7-8 mice were used for each biological replicate, and 5 biological replicates were obtained for cochlea and vestibule for the two age groups respectively.
Single-cell capture and library preparation were performed using droplet-based microfluidic technology, following the manufacturer’s instructions for the Chromium Next GEM Single Cell 3ʹ v3.1 dual index kit. The quality of the obtained libraries was assessed via high-sensitivity DNA kits (Agilent Technologies) using Agilent 2100 Bioanalyzer prior to sequencing with Illumina NovaSeq 6000.

treatment_protocol: Animals were bred and aged to assess the biological aging

value: Vestibular Sensory Epithelium

value: Wild-type


title: 22Rv1-dTAG-FOXA1, dTAGv1, 24h, biol rep 2

description: Library name: dTAGv1_24h_rep2


title: Tumor patient 54

description: Library name: Sample 9


title: RNA-seq of Cephalotaxus harringtonia: root tips, replicate 1

description: Library name: Rt1


title: RNA-seq of Cephalotaxus harringtonia: old needles, replicate 6

description: Library name: ON6

source_name: old needles

value: old needles


title: Hepatic Stellate Cells, PBS-1

description:
Library name: Sample1
Column name in processed data.txt:C1


title: Tumor patient 58

description: Library name: Sample 11


title: RNA-seq of Cephalotaxus harringtonia: old needles, replicate 3

description: Library name: ON3


title: Vestibule, 22 Months, Bio rep 3

description:
Library name: CBA/J 22 months Vestibular Bio rep 3
10X Genomics


title: Tumor patient 39

description: Library name: Sample 5


title: RNA-seq of Cephalotaxus harringtonia: old needles, replicate 5

description: Library name: ON5


title: 22Rv1-dTAG-FOXA1, dTAGv1, 8h, biol rep 3

description: Library name: dTAGv1_8h_rep3


title: Hepatic Stellate Cells, PBS-2

description:
Library name: Sample2
Column name in processed data.txt:C2


title: RNA-seq of Cephalotaxus harringtonia: old needles, replicate 2

description: Library name: ON2


title: Tumor patient 42

description: Library name: Sample 7


title: 22Rv1-dTAG-FOXA1, DMSO, 24h, biol rep 3

description: Library name: DMSO_24h_rep3

value: DMSO


title: Tumor patient 38

description: Library name: Sample 4


title: 22Rv1-dTAG-FOXA1, dTAGv1, 8h, biol rep 2

description: Library name: dTAGv1_8h_rep2


title: RNA-seq of Cephalotaxus harringtonia: old needles, replicate 4

description: Library name: ON4


title: Tumor patient 41

description: Library name: Sample 6


title: 22Rv1-dTAG-FOXA1, DMSO, 24h, biol rep 1

description: Library name: DMSO_24h_rep1


title: 22Rv1-dTAG-FOXA1, DMSO, 24h, biol rep 2

description: Library name: DMSO_24h_rep2


title: Vestibule, 22 Months, Bio rep 4

description:
Library name: CBA/J 22 months Vestibular Bio rep 4
10X Genomics


title: Cochlea, 22 Months, Bio rep 5

description:
Library name: CBA/J 22 months Cochlear Bio rep 5
10X Genomics

source_name: Cochlear Sensory Epithelium

value: Cochlear Sensory Epithelium


title: 22Rv1-dTAG-FOXA1, dTAGv1, 8h, biol rep 1

description: Library name: dTAGv1_8h_rep1


title: Vestibule, 22 Months, Bio rep 2

description:
Library name: CBA/J 22 months Vestibular Bio rep 2
10X Genomics


title: Tumor patient 37

description: Library name: Sample 3

value: GBM


title: RNA-seq of Cephalotaxus harringtonia: old needles, replicate 1

description: Library name: ON1


title: Tumor patient 17

description: Library name: Sample 1


title: Vestibule, 22 Months, Bio rep 1

description:
Library name: CBA/J 22 months Vestibular Bio rep 1
10X Genomics


title: RNA-seq of Cephalotaxus harringtonia: young stem, replicate 6

description: Library name: YSt6

source_name: young stem

value: young stem


title: Tumor patient 36

description: Library name: Sample 2


title: 22Rv1-dTAG-FOXA1, DMSO, 8h, biol rep 2

description: Library name: DMSO_8h_rep2


title: Cochlea, 22 Months, Bio rep 4

description:
Library name: CBA/J 22 months Cochlear Bio rep 4
10X Genomics


title: RNA-seq of Cephalotaxus harringtonia: young stem, replicate 5

description: Library name: YSt5


title: TSq7

city: Athens

first: Vasilis

last: Aidinis

state: Vari

address: Fleming 34

country: Greece

institute: Institute for Fundamental Biomedical Research, BSRC Alexander Fleming

description: Library name: Sample 21

data_processing:
Base calling was performed using bcl2fastq software.
Fastq files were mapped to the Genome Reference Consortium Human Build 38 (GRCh38), using a two-step alignment process. Firstly, reads were mapped with hisat2, using default parameters. Next, the unmapped reads were mapped with bowtie2 using the --local and --very-sensitive parameters.
Counting the reads on the 3’ UTRs was performed with metaseqR2  and were normalized with DESEQ. For the differential expression analysis, we employed the PANDORA algorithm within the metaseqR2 package by integrating the DESEQ, DESEQ2, edgeR, limma, NBPSeq, and NOISeq algorithms. Differentially expressed genes were identified based on a meta p-value threshold of < 0.05 and an absolute log2 fold change > 0.58.
Assembly: hg38
Supplementary files format and content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for Quant-Seq data.

source_name: Bronchoalveolar Lavage fluid cells

extract_protocol:
Total RNA was isolated using the mirVanaTM miRNA iolation kit (Ambion) with minor modifications. 350μl of TriReagent was used for cell lysis and storage of samples, followed by addition of 350μl of mirVana cell lysis solution and 35μl of mirVana miRNA additive. All further steps for the isolation of total RNA were performed as recommended by the manufacturer. Quality and quantity of isolated RNA was assessed by agarose gel electrophoresis and spectrophotometry (Nanodrop) respectively.
For library preparation, the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI (Lexogen) was used according to manufacturer’s instructions. Briefly, 150-400 ng of RNA from each sample were used for 1 st strand synthesis, followed by RNA template removal. 2 nd strand synthesis was initiated by random primers containing compatible linker sequences at their 5’ end. In-line barcodes were introduced during second-strand synthesis, followed by magnetic bead-based purification. The resulting products were amplified for up to 15 cycles and re-purified. Library quality was assessed using the Agilent Tapestation 4150 and the High Sensitivity D1000 assay kit, while quantity was assessed using the Invitrogen Qubit 4 Fluorometer and the Invitrogen Qubit dsDNA HS Assay. The quantified libraries were pooled equimolarly, and a total of 25ng were used for Adapter Conversion PCR Amplification using the Universal Library Conversion Kit (App-A), Version: V1.0 (MGI Tech Co., Ltd.), following the Universal Library Conversion Kit (App-A) User Manual (Version: A3).

treatment_protocol: No treatment

value: Bronchoalveolar Lavage fluid cells

tag: disease state

value: IPF post COVID-19


title: RNA-seq of Cephalotaxus harringtonia: young stem, replicate 3

description: Library name: YSt3


title: 22Rv1-dTAG-FOXA1, DMSO, 8h, biol rep 1

description: Library name: DMSO_8h_rep1


title: RNA-seq of Cephalotaxus harringtonia: young stem, replicate 2

description: Library name: YSt2


title: RNA-seq of Cephalotaxus harringtonia: young stem, replicate 4

description: Library name: YSt4


title: 22Rv1-dTAG-FOXA1, DMSO, 8h, biol rep 3

description: Library name: DMSO_8h_rep3


title: Cochlea, 22 Months, Bio rep 2

description:
Library name: CBA/J 22 months Cochlear Bio rep 2
10X Genomics


title: Cochlea, 22 Months, Bio rep 3

description:
Library name: CBA/J 22 months Cochlear Bio rep 3
10X Genomics


title: Cochlea, 22 Months, Bio rep 1

description:
Library name: CBA/J 22 months Cochlear Bio rep 1
10X Genomics


title: 22Rv1-dTAG-FOXA1, dTAGv1, 3h, biol rep 1

description: Library name: dTAGv1_3h_rep1


title: RNA-seq of Cephalotaxus harringtonia: young stem, replicate 1

description: Library name: YSt1


title: TSq6

description: Library name: Sample 20

value: resolved post-COVID-19 ILD


title: TSq4

description: Library name: Sample 18


title: 22Rv1-dTAG-FOXA1, dTAGv1, 3h, biol rep 2

description: Library name: dTAGv1_3h_rep2


title: TSq3

description: Library name: Sample 17


title: TSq5

description: Library name: Sample 19


title: RNA-seq of Cephalotaxus harringtonia: young outer needles, replicate 5

description: Library name: YON5

source_name: young outer needles

value: young outer needles


title: IRI, ANXA13-3, Day 1

city: Guangzhou

first: Jiaxiao

last: Li

state: Guangdong

address: Guangdong, China

institute: The Third Affiliated Hospital of Southern Medical University

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene.
Assembly: -
Supplementary files format and content: tab-delimited text file includes raw counts for each group
Supplementary files format and content: tab-delimited text file includes normalized gene counts for each group

source_name: kidney

extract_protocol:
Total RNA was extracted from the kidney using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapterligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, the library preparations were sequenced on an Illumina Novaseq 6000 and 150 bp paired-end reads were generated.

value: kidney

tag: strain

value: ANXA13 + IRI


title: IRI, ANXA13-2, Day 1


title: 22Rv1-dTAG-FOXA1, DMSO, 3h, biol rep 3

description: Library name: DMSO_3h_rep3

source_name: Prostate

value: Prostate


title: 22Rv1-dTAG-FOXA1, DMSO, 3h, biol rep 1

description: Library name: DMSO_3h_rep1

value: prostate carcinoma epithelial cell


title: RNA-seq of Cephalotaxus harringtonia: young outer needles, replicate 3

description: Library name: YON3


title: TSq25

description: Library name: Sample 15

value: persistent post-COVID-19 ILD


title: IRI, ANXA13-1, Day 1


title: RNA-seq of Cephalotaxus harringtonia: young outer needles, replicate 6

description: Library name: YON6


title: 22Rv1-dTAG-FOXA1, DMSO, 3h, biol rep 2

description: Library name: DMSO_3h_rep2


title: LCMV_CL13_Gp33

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

data_processing:
sequencing data was first alligned and reads per gene counted using Cellranger 7 (10x genomics).  Count data was normalized and analyzed using the Seurat 4 R package.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: spleen

extract_protocol:
8 days after the treatment, splenocytes were isolated from the mice and resuspended in ice cold FACS buffer (Ca2+/Mg2+ PBS supplemented with 4% FBS and 2mM EDTA). Splenocytes were stained with antibodies and LCMV-GP33 Tetramer in FACS buffer on ice for 30min. Cells were washed and resuspended in FACS buffer, LCMV-GP33 Tet+ CD8 T cells were sorted using FACSAria II(BD)
Library was contructed using manufactures protcol for single cell 5' v2 10x genomics

treatment_protocol: C57Bl/6J mice were intravenously infected with 2x10^6 LCMV clone-13 with transient CD4 depletion. >45 days post infection, mice were treated with a single dose of injection buffer or 200ug NT-I7, a hybrid Fc-fused recombinant human IL-7 (hIL-7-hyFc, efineptakin alfa, NeoimmuneTech).

value: spleen

value: T cells

value: buffer


title: RNA-seq of Cephalotaxus harringtonia: young outer needles, replicate 2

description: Library name: YON2


title: TSq23

description: Library name: Sample 13

value: CPFE post-COVID-19


title: RNA-seq of Cephalotaxus harringtonia: young outer needles, replicate 1

description: Library name: YON1


title: RNA-seq of Cephalotaxus harringtonia: young outer needles, replicate 4

description: Library name: YON4


title: HEV-infected organoid sample 1

city: Heidelberg

first: Carl

last: Herrmann

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University

description:
Library name: HEV-1
10x Genomics

data_processing:
The demultiplexing and and gene counting were made by Cell Ranger software (cellranger-7.1.0)
Assembly: GRCh38
Assembly: Hepatitis E virus (JQ679013.1)
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Small intestine

growth_protocol: The iPSC line iPSC.3A (a kind gift from Stephen Duncan) was maintained in feeder-free conditions using mTeSR1 medium (STEMCELL Technologies) on Matrigel (Corning, ref 354230) coated plates as per the manufacturers instructions. iPSC.3A cells were differentiated to small intestinal organoids using the STEMdiffTM Intestinal organoids Kit (STEMCELL Technologies, ref 05140) according to the manufacturers protocol.

extract_protocol:
hIOs were harvested and dissociated by incubation with TrpLEX (Gibco, ref 12604013) 37 °C for 20min.
Single-cell suspensions were loaded onto the 10x Chromium controller according to manufacturers instructions of the Chromium Next GEM Single Cell 3 Kit v3.1 (10x Genomics, ref 1000269) with a targeted cell recovery of 10,000. Sequencing libraries were prepared according to the manufacturers instructions. Resulting libraries were pooled and sequenced on an Illumina NextSeq2000.

treatment_protocol: hIOs weretreated similar to the infected hIOs by breaking them up and  supplementing with 10 M Y27632 (STEMCELL Technologies, ref 72304). After 8 h on a rolling platform at 37 °C and 5% CO2, they were washed 3 times with PBS and hIOs were re-embedded into 100% gelated Matrigel.

value: Small intestine

value: iPSC

value: organoids

value: HEV genotype 3


title: LCMV_CL13_Gp33_IL7

value: Fc-fused IL-7 (NT-I7)


title: Non-infected organoid

description:
Library name: Mock
10x Genomics

data_processing:
The demultiplexing and and gene counting were made by Cell Ranger software (cellranger-7.1.0)
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

growth_protocol: The iPSC line iPSC.3A (a kind gift from Stephen Duncan) was maintained in feeder-free conditions using mTeSR1 medium (STEMCELL Technologies) on Matrigel (Corning, ref 354230) coated plates as per the manufacturer’s instructions. iPSC.3A cells were differentiated to small intestinal organoids using the STEMdiffTM Intestinal organoids Kit (STEMCELL Technologies, ref 05140) according to the manufacturer’s protocol.

extract_protocol:
hIOs were harvested and dissociated by incubation with TrpLEX (Gibco, ref 12604013) 37 °C for 20min.
Single-cell suspensions were loaded onto the 10x Chromium controller according to manufacturer’s instructions of the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics, ref 1000269) with a targeted cell recovery of 10,000. Sequencing libraries were prepared according to the manufacturer’s instructions. Resulting libraries were pooled and sequenced on an Illumina NextSeq2000.

treatment_protocol: hIOs weretreated similar to the infected hIOs by breaking them up and supplementing with 10 μM Y27632 (STEMCELL Technologies, ref 72304). After 8 h on a rolling platform at 37 °C and 5% CO2, they were washed 3 times with PBS and hIOs were re-embedded into 100% gelated Matrigel.


title: IRI-3, empty vector, Day 1

value: empty vetor + IRI


title: TSq22

description: Library name: Sample 12

value: Bronchoalveolar Lavage fluid cells


title: TSq26

description: Library name: Sample 16


title: TSq21

description: Library name: Sample 11

value: resolved post-COVID-19 ILD


title: RNA-seq of Cephalotaxus harringtonia: young inner needles, replicate 4

description: Library name: YIN4

source_name: young inner needles

value: young inner needles


title: HEV-infected organoid sample 2

description:
Library name: HEV-2
10x Genomics


title: TSq2

description: Library name: Sample 10


title: sham-2, Day 1

value: kidney

value: sham


title: RNA-seq of Cephalotaxus harringtonia: young inner needles, replicate 1

description: Library name: YIN1


title: sham-1, Day 1


title: TSq24

description: Library name: Sample 14


title: human T cells from bone marrow of NSG mice, BiTE, rep5

city: Munich

first: Lisa

last: Rohrbacher

address: Marchioninistraße 15

department: MED III

institute: LMU University Hospital

description: Library name: human T cells from bone marrow of NSG mice, BiTE5

data_processing:
Quality assesment of the fastq data files was conducted using fastqc (v0.11.5), followed by poly A trimming using cutadapt (v4.1). Subsequent read filtering, mapping, and conducting were performed using the zUMIs pipeline (v.2.9.7), with reads mapped to the human genome (hg38). Bulk-fastq data was sample-demultiplexed using deML.
Assembly: hg38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: csv files

source_name: bone marrow

growth_protocol: Human T cells were given to AML-bearing NSG mice IV. After 18 days, T cells were isolated from the bone marrow of these mice.

extract_protocol:
RNA isolation and library preparation were performed according to the Prime-seq protocol. RNA was isolated from cell lysates and cDNA synthesized using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0753) with barcoded oligo-dT primers (E3V7NEXT) and a custom template-switching oligo. Libaries were prepared from 30 ng of pooled cDNA.
Libraries were prepared using the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, E7805S) using a prime-seq specific custom ligation-adapter and dual-indexing with TruSeq i5 and Nextera i7 primers via PCR.

treatment_protocol: Part of the T cells were transduced with a CAR vector. The other part was redirected to the tumor by BiTE molecule

value: bone marrow

value: BiTE


title: TSq17

description: Library name: Sample 8

value: persistent post-COVID-19 ILD


title: human T cells from bone marrow of NSG mice, CAR, rep8

description: Library name: human T cells from bone marrow of NSG mice, CAR8

value: T cells

value: CAR+


title: IRI-1, empty vector, Day 1


title: TETA_7W_4

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

data_processing:
Bulk RNA-seq reads were aligned with STAR v2.7.1a to the reference sequence (mm10 from UCSC).
Mouse reference was used for gene annotation and counting (gencode M25).
Uniquely mapped reads were quantified using featureCounts v2.0.1 suite using protein coding genes by gene.
Supplementary files format and content: mm10
Supplementary files format and content: Input tables are included as tab separated files.

source_name: Mouse brain

extract_protocol:
Total RNA was extracted from prefrontal cortex (PFC) of male mice at 7 weeks with the AllPrep DNA/RNA Mini Kit (#80204, Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
RNA was harvested using RNeasy Mini Kit (Qiagen). 500 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep following manufacturer's protocols.

value: Mouse brain

value: Copper-chelating Trientine (TETA)

tag: age

value: 7 weeks post-natal

tag: condition

value: Copper-deficient


title: RNA-seq of Cephalotaxus harringtonia: young inner needles, replicate 3

description: Library name: YIN3


title: human T cells from bone marrow of NSG mice, CAR, rep10

description: Library name: human T cells from bone marrow of NSG mice, CAR10

value: CAR++


title: TSq19

description: Library name: Sample 9

value: SSC-ILD post-COVID-19


title: RNA-seq of Cephalotaxus harringtonia: young inner needles, replicate 2

description: Library name: YIN2


title: IRI-2, empty vector, Day 1

value: empty vetor + IRI


title: sham-3, Day 1


title: human T cells from bone marrow of NSG mice, CAR, rep9

description: Library name: human T cells from bone marrow of NSG mice, CAR9


title: TETA_7W_3


title: human T cells from bone marrow of NSG mice, CAR, rep7

description: Library name: human T cells from bone marrow of NSG mice, CAR7


title: TSq16

description: Library name: Sample 7

value: Bronchoalveolar Lavage fluid cells


title: spleen_5dpi_infection_rep4

city: Nanjing

first: Tailong

last: Wang

state: Jiangsu

address: Xuanwu

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description: Library name: Sample36

data_processing:
The raw data in ASTQ format were filtered by fastp (v0.20.1).The clean reads of each sample were then aligned to the reference genome GRCg7b using HISAT2 (v2.2.1) software to obtain the raw counts of the reads aligned to each gene.
Assembly: Genome assembly bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab-delimited tex file includes raw counts for each Sample

organism: Gallus gallus

extract_protocol:
Total RNA was extracted with TRIzol reagent.RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
After the total RNA samples were tested to be qualified, the MGIEasy RNA library preparation kit was used for library construction. Magnetic beads with oligo (DT) were used for enrichment and purification; Fragment buffer was added to the purified mRNA to make its fragment into a short fragment; the fragment mRNA was used as a template for reverse transcription into double stranded cDNA with six base random primers, and then the product was purified. The purified double stranded cDNA was subjected to end repair, addition of dA tail, linker connection and PCR amplification. After the amplified product was qualified, it was denatured and single stranded cyclized, and the cyclized product was inspected.

treatment_protocol: infection and non-infection

value: spleen

tag: time point

value: infection


title: TSq15

description: Library name: Sample 6

value: resolved post-COVID-19 ILD


title: spleen_5dpi_infection_rep2

description: Library name: Sample34


title: human T cells from bone marrow of NSG mice, BiTE, rep4

description: Library name: human T cells from bone marrow of NSG mice, BiTE4


title: TETA_7W_2


title: spleen_5dpi_infection_rep5

description: Library name: Sample37


title: human T cells from bone marrow of NSG mice, BiTE, rep3

description: Library name: human T cells from bone marrow of NSG mice, BiTE3


title: human T cells from bone marrow of NSG mice, CAR, rep6

description: Library name: human T cells from bone marrow of NSG mice, CAR6


title: 22Rv1-SF3B1-C1111S, DMSO, 3h, biol rep 2

description: Library name: DMSO_3h_rep2

data_processing:
Sequencing reads were aligned to the human reference genome (hg19) and RefSeq gene annotations using Bowtie2 (v2.5.1) with the following parameters: bowtie2 --local --very-sensitive-local --no-mixed --no-discordant --dovetail --phred33 -I 10 -X 700 --threads 12 -x. Unmapped, duplicate, and low-quality reads were removed using Sambamba (v0.7.1). Reads mapping to the mitochondrial genome or ENCODE blacklist regions (wgEncodeDacMapabilityConsensusExcludable.bed.gz) were excluded using SAMtools (v1.10). Peak calling was performed with MACS (v2.1.0) using the parameters: macs2 callpeak -q 0.01 --nomodel --shift -100 --extsize 150.
Assembly: hg19
Supplementary files format and content: Genome-wide chromatin accessibility signal tracks in bedGraph format (treat_pileup.bdg.gz) generated by MACS2 from hg19-aligned ATAC-seq data after removal of duplicate, low-quality, mitochondrial, and ENCODE blacklist reads. Files represent ATAC-seq read pileup across the genome and are compressed using gzip.

extract_protocol:
ATAC-seq was performed using the Active Motif ATAC-Seq Buffer Set (Cat#: 53153) and 96-well Pre-Indexed Assembled Tn5 Transposomes (Cat#: 53152) according to the manufacturer’s protocol. After treatment, cells were washed twice with ice-cold PBS and lysed directly in-plate with 150 µL ATAC lysis buffer (Active Motif). Lysates were centrifuged at 500 × g for 10 min at 4 °C, and the supernatant was carefully removed to isolate nuclei. Each nuclei pellet was resuspended in 46 µL Tagmentation Master Mix (1× Tagmentation Buffer, 1× PBS, 0.01 % digitonin, 0.1 % Tween-20).
ATAC-seq was performed using the Active Motif ATAC-Seq Buffer Set and 96-well Pre-Indexed Assembled Tn5 Transposomes according to the manufacturer’s protocol. For indexing, each sample was combined with a distinct well of the Pre-Indexed Assembled Tn5 Transposome plate, ensuring unique barcode assignment per sample. Plates were sealed, gently vortexed, quick-spun, and incubated at 37 °C for 30 min with gentle mixing every 10 min. DNA was purified and libraries were prepared according to the manufacturer’s protocol. Libraries were cleaned by SPRI-bead purification and gel extraction to enrich for fragments < 1 kb, then multiplexed and sequenced on an Illumina NextSeq 2000 using 50-bp paired-end reads.

value: Prostate

value: prostate carcinoma epithelial cell

value: DMSO, DMSO

value: 1h pretreat, 3h


title: TSq14

description: Library name: Sample 5


title: spleen_5dpi_infection_rep3

description: Library name: Sample35


title: TSq10

description: Library name: Sample 2

value: CPFE post-COVID-19


title: CTL_7W_4

value: water

value: Control


title: TSq13

description: Library name: Sample 4

value: persistent post-COVID-19 ILD


title: human T cells from bone marrow of NSG mice, CAR, rep5

description: Library name: human T cells from bone marrow of NSG mice, CAR5

value: bone marrow

value: T cells

value: CAR+


title: CTL_7W_5

value: Mouse brain

value: 7 weeks post-natal


title: TSq1

description: Library name: Sample 1

value: Bronchoalveolar Lavage fluid cells


title: spleen_5dpi_non-infection_rep4

description: Library name: Sample32

value: spleen

value: non-infection


title: CTL_7W_3


title: human T cells from bone marrow of NSG mice, CAR, rep4

description: Library name: human T cells from bone marrow of NSG mice, CAR4

value: CAR++


title: CTL_7W_2


title: human T cells from bone marrow of NSG mice, CAR, rep3

description: Library name: human T cells from bone marrow of NSG mice, CAR3


title: spleen_5dpi_infection_rep1

description: Library name: Sample33

value: infection


title: CTL_7W_1


title: Macro  Mafb KO, rep1, H3K27 antibody

description: Library name: KO-H3K27Ac-1_NGS24-E666

source_name: BMBM

extract_protocol:
Bone marrow monocytes from Mafbfl/fl or Lyz2CreMafbfl/fl mice were isolated using Monocyte Isolation Kit (BM) (Miltenyi Biotec, 130100629) and were seeded in tissue culture-treated 6-well plates (Greiner, 657160) and cultured for 4 days in RPMI supplemented with 10% FBS, 1 mM Sodium Pyruvate (Gibco, 11360070), 1X MEM Non-Essential Amino Acids Solution (Gibco, 11140050), 50 µM β-mercaptoethanol (Gibco, 31350010) and 40 ng/mL CSF-1 (Peprotech, 315-02) to differentiate them into bone marrow monocyte derived macrophages (BMDM). H3K27Ac CUT&RUN was performed with a CUTANA ChIC/CUT&RUN Kit (EpiCypher, 141048) according to manufacturer’s instructions, with modifications. BMDM from Mafbfl/fl or Lyz2CreMafbfl/fl mice were washed with ice-cold PBS and fixed with 0.1 % formaldehyde in PBS for 2 min at room temperature. Fixation was quenched by adding glycine (Merck, 104691000) to 0.125 M.  For each CUT&RUN sample, 1x 106 fixed cells and 0.5 µg antibodies were used. Anti-H3K27Ac (MA5-23516) and IgG Negative Control Antibody (EpiCypher, 13-0042) were used.
CUT&RUN libraries were prepared using were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645L) according to manufacturer’s instructions. These libraries were sequenced on an NovaSeq 6000 (Illumina) sequencer on an XP flow cell.

value: BMBM

value: Macrophages

value: Lyz2Cre Mafbfl/fl (Mafb KO)


title: human T cells from bone marrow of NSG mice, BiTE, rep2

description: Library name: human T cells from bone marrow of NSG mice, BiTE2

value: BiTE


title: TSq11

description: Library name: Sample 3

value: resolved post-COVID-19 ILD


title: TETA_E18_3-2

value: Copper-chelating Trientine (TETA)

value: Embryonic day 18.5

value: Copper-deficient


title: CD11b-MD12

city: Jinan

first: Xiaofei

address: Duanxing Road 4

institute: Shandong Provincial ENT Hospital, Shandong University

description:
tpm_MD12_11b_ne
read_count_MD12_11b_ne

data_processing:
Data filtering  The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Structure variation detection The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5)  and rMATS (V3.2.5)  were used to detect fusion genes and differential splicing genes (DSGs), respectively Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: MD, female, 52 yrs old

extract_protocol:
1. Introduction This procedure is suitable for Total RNA extraction of animal tissues, cells and other samples to provide high quality RNA for library preparation. 2. Experimental Procedures 2.1 Tissue Sample Fragmentation and Lysis 2.1.1 Grinding Machine 2.1.1.1 Transfer appropriate sample to corresponding grinding tube, 2.1.1.2 Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min 2.1.2 Liquid Nitrogen Grinding and Crushing 2.1.2.1 Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. 2.1.2.2 Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer.  Stand flat for 5 min for the fully lysis of tissue cells. 2.1.3 Cell Sample Lysis Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells) 2.2 Sample Purification 2.2.1 Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. 2.2.2 Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking； 2.2.3 Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). 2.2.4 Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. 2.2.5 Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. 2.2.6 Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃)。 2.2.7 Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. 2.2.8 Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
1. Introduction RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.  Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly. 2.Experimental Procedure 2.1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2.2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 2.3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 2.4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 2.5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 2.6 PCR The PCR reaction system and program are configured and set up to amplify the product. 2.7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 2.8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 2.9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: blood cell

value: CD11b- cell

tag: gender

value: female

value: 52 yrs old

value: MD


title: spleen_2dpi_infection_rep5

description: Library name: Sample28

value: spleen


title: spleen_2dpi_infection_rep4

description: Library name: Sample27


title: spleen_5dpi_non-infection_rep2

description: Library name: Sample30

value: non-infection


title: spleen_5dpi_non-infection_rep3

description: Library name: Sample31


title: TETA_7W_1

value: Mouse brain

value: 7 weeks post-natal


title: human T cells from bone marrow of NSG mice, CAR, rep1

description: Library name: human T cells from bone marrow of NSG mice, CAR1

value: bone marrow

value: T cells

value: CAR+


title: spleen_2dpi_infection_rep2

description: Library name: Sample25

value: infection


title: human T cells from bone marrow of NSG mice, BiTE, rep1

description: Library name: human T cells from bone marrow of NSG mice, BiTE1

value: BiTE


title: CD11b-MD6

description:
tpm_MD06_11b_ne
read_count_MD06_11b_ne

source_name: MD, female, 53 yrs old

value: 53 yrs old


title: spleen_5dpi_non-infection_rep1

description: Library name: Sample29


title: human T cells from bone marrow of NSG mice, CAR, rep2

description: Library name: human T cells from bone marrow of NSG mice, CAR2

value: CAR++


title: CD11b-MD5

description:
tpm_MD05_11b_ne
read_count_MD05_11b_ne

source_name: MD, female, 48 yrs old

value: 48 yrs old


title: CD11b-MD15

description:
tpm_MD15_11b_ne
read_count_MD15_11b_ne

source_name: MD, female, 55 yrs old

value: blood cell

value: 55 yrs old


title: TETA_E18_1-1

value: Copper-chelating Trientine (TETA)

value: Embryonic day 18.5

value: Copper-deficient


title: CD11b-MD7

description:
tpm_MD07_11b_ne
read_count_MD07_11b_ne

source_name: MD, female, 62 yrs old

value: CD11b- cell

value: female

value: 62 yrs old

value: MD


title: TETA_E18_3-1

value: Mouse brain


title: spleen_2dpi_infection_rep3

description: Library name: Sample26

value: spleen


title: CD11b-MD1

description:
tpm_MD01_11b_ne
read_count_MD01_11b_ne

source_name: MD, female, 38 yrs old

value: 38 yrs old


title: spleen_2dpi_infection_rep1

description: Library name: Sample24

value: infection


title: CD11b-MD17

description:
tpm_MD17_11b_ne
read_count_MD17_11b_ne

source_name: MD, male, 59 yrs old

value: male

value: 59 yrs old


title: spleen_2dpi_non-infection_rep2

description: Library name: Sample22

value: non-infection


title: TETA_E18_2-2


title: HEK293T MLL1 KO replicate 1

city: Boston

first: Parmit

middle: Kumar

last: Singh

state: MA

address: 450 Brookline Avenue

department: Department of Cancer Immunology and Virology

institute: Dana-Farber Cancer Institute

description: PCR products were sequenced

library_source: other

data_processing:
Raw reads were trimmed for LTR and linker sequenced from read1 and read2, respectively. Trimmed reads were aligned to the hg19 genome to get sam files; a Python script processed sam files to generate unique sites. Sites from uninfected cells were removed, and then they were converted to bed files. These bed files were used to analyze the distribution of integration sites with respect to various human genomic annotations, such as genes, transcription start sites, CpG, average gene density, lamina-associated domains, and speckle-associated domains.
Assembly: hg19
Supplementary files format and content: bed files containing HIV-1 integration sites

molecule: other

source_name: human embryonic kidney

extract_protocol:
Infected genomic DNA was isolated from human cell lines.
Ligation-mediated PCR was done to amplify virus-host junction sequences.
PCR products were sequenced at Illumina NextSeq -2000 for 150 bp paired-end sequencing.

value: human embryonic kidney

value: cells lacking MLL1

value: Infected by wild type HIV-1 virus


title: CD11b-CON13

description:
tpm_HC13_11b_ne
read_count_HC13_11b_ne

source_name: healthy control, female, 52 yrs old

value: blood cell

value: 52 yrs old

value: Control


title: CTL_E18_3-1

value: water

value: Embryonic day 18.5


title: CD11b-CON11

description:
tpm_HC11_11b_ne
read_count_HC11_11b_ne

source_name: healthy control, female, 55 yrs old

value: CD11b- cell

value: female

value: 55 yrs old


title: MLL1 KO replicate 2

description: PCR products were sequenced


title: TETA_E18_1-2

value: Mouse brain

value: Copper-chelating Trientine (TETA)

value: Copper-deficient


title: TETA_E18_2-1


title: HEK293T WT replicate 2

description: PCR products were sequenced

value: Wild type


title: WT HEK293T MLL1 replicate 2

description: PCR products were sequenced


title: CD11b-MD3

description:
tpm_MD03_11b_ne
read_count_MD03_11b_ne

source_name: MD, male, 63 yrs old

value: male

value: 63 yrs old

value: MD


title: WT HEK293T replicate 1 for MLL1

description: PCR products were sequenced

value: human embryonic kidney


title: spleen_2dpi_non-infection_rep3

description: Library name: Sample23

source_name: spleen

value: spleen

value: non-infection


title: liver_5dpi_infection_rep4

description: Library name: Sample19

source_name: liver

value: liver

value: infection


title: SET2D KO replicate 1

description: PCR products were sequenced

value: cell lacking SET2D

value: Infected by wild type HIV-1 virus


title: CTL_E18_3-2

value: water

value: Embryonic day 18.5

value: Control


title: CD11b-CON4

description:
tpm_HC4_11b_ne
read_count_HC4_11b_ne

source_name: healthy control, male, 59 yrs old

value: blood cell

value: CD11b- cell

value: 59 yrs old


title: SET2D KO replicate 2

description: PCR products were sequenced

value: cells lacking SET2D


title: liver_5dpi_infection_rep3

description: Library name: Sample18


title: PEA 6

city: Liverpool

first: Daniel

middle: John

last: Owens

address: Byrom Street

department: Research Institute for Sport and Exercise Science

country: United Kingdom

institute: Liverpool John Moores University

description:
Library name: PEA6_S15_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_10um_6

data_processing:
Partek® Flow® Genomic Analysis Software
Pre-alignment QA/QC was performed on all reads prior to read trimming. STAR alignment 4.4.1d was used to align trimmed reads to the Mus musculus genome
Aligned reads were then quantified to the Ensembl transcriptome annotation model associated with Mus musculus mm39 genome.
Filtered raw counts were used for normalisation and differential analysis with DESeq2
Assembly: Mus musculus mm39 genome
Supplementary files format and content: Matrix table, raw counts (quantification)
Supplementary files format and content: Matrix table, normalized counts (normalization)

growth_protocol: C2C12 murine myoblasts were cultured on gelatin (0.2%) coated 6-well culture plates in humidified 5% CO2 at 37°C in growth media comprising DMEM, 10% FBS, 10% NBCS and 1% of a pen-strep solution. Upon reaching ~80% confluence, monolayers were washed twice with pre-warmed PBS and switched to low serum differentiation media (DM), DMEM, 2% HS and 1% pen-strep. Every 48h thereafter, DM was removed from monolayers via aspiration and was replaced with fresh media. Cells were terminally differentiated by day-8 of low serum DM exposure

extract_protocol:
Following a 24-hour treatment with PEA or vehicle control, terminally differentiated C2C12 monolayers were lysed with buffer RLT from the Qiagen RNeasy kit (Qiagen Ltd). RNA was then extracted from cell lysates using the RNeasy kit with proteinase K digestion, as per the manufacturer’s guidelines. Eluted RNA was stored at -80oC until required for determination of total RNA and library processing.
Libraries were constructed from 100 ng of total RNA with Poly-A tail enrichment of mRNA using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® with Agencourt AMPureXP Sample Purification Beads (Beckman Coulter. Wycombe, UK) as per manufacturers guidelines, by Bart's and the London Genome Centre at Queen Mary, University of London.

treatment_protocol: We terminally differentiated C2C12 myotubes as described above. On day 8 of differentiation, DM was removed and swapped with DM containing vehicle (DMSO) or PEA (10 µM). Myotubes were then cultured in the respective treatments for 24 hours before being harvested for RNA extraction. Duplicate wells for each treatment were used and the experiment repeated three times to generate an n=6 samples per treatment.

value: Myotube

value: WT

value: 10uM palmitoylethanolamide 24h


title: CD11b-CON3

description:
tpm_HC3_11b_ne
read_count_HC3_11b_ne

source_name: healthy control, male, 65 yrs old

value: male

value: 65 yrs old


title: PEA 5

description:
Library name: PEA5_S2_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_10um_5


title: liver_5dpi_infection_rep5

description: Library name: Sample20


title: CD11b+MD17

description:
tpm_MD17_11b_po
read_count_MD17_11b_po

value: CD11b+Myeloid cell

value: MD


title: CD11b-CON10

description:
tpm_HC10_11b_ne
read_count_HC10_11b_ne

source_name: healthy control, female, 36 yrs old

value: female

value: 36 yrs old


title: BY4741 Thiolutin (3 µg/mL, 3 h) biological replicate 2

city: Rzeszów

first: Mateusz

last: Mołoń

state: Rzeszów

address: Aleksandra Zelwerowicza 4

country: Poland

institute: University of Rzeszów

description:
Library name: BY4741 THIOII rep2
YPD medium, 28°C, exponential phase; RNA extracted after treatment; Saccharomyces cerevisiae BY4741.

data_processing:
Raw reads were quality-checked.
Reads were aligned to the Saccharomyces cerevisiae reference genome.
Gene-level read counts were generated.
Differential expression analysis was performed using DESeq2 with Benjamini–Hochberg correction (FDR < 0.05).
GO enrichment analysis was performed on differentially expressed genes (optional supplementary outputs).
Assembly: Saccharomyces cerevisiae (S288C) reference genome assembly (e.g., R64-1-1).
Supplementary files format and content: Processed data files include a gene-level raw count matrix and a complete DESeq2 results table for all annotated genes.
Supplementary files format and content: gene_raw_counts_matrix.txt: rows = genes, columns = 5 samples; DESeq2_full_results_all_genes.csv: gene-level statistics including baseMean, log2FoldChange, pvalue, and padj (FDR).

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Cells were cultured in YPD medium at 28°C with agitation to exponential phase prior to treatment.

extract_protocol:
Total RNA was extracted from approximately 2 × 10^6 cells using the Invitrogen RNA extraction kit according to the manufacturer’s instructions.
Poly(A)-selected RNA libraries were prepared using the MGIEasy RNA Library Prep Set (MGI Tech) following the manufacturer’s protocol.

treatment_protocol: Cells were exposed to thiolutin at a final concentration of 3 µg/mL for 3 hours during exponential growth. Control cultures were maintained without treatment.

value: yeast

value: MATa his3 leu2 met15 ura3

value: thiolutin 3 µg/mL for 3 hours

value: yeast cell


title: CTL_E18_1-2

source_name: Mouse brain

value: Mouse brain

value: water

value: Embryonic day 18.5

value: Control


title: CTL_E18_2-2


title: wild type HEK293T replicate 1

description: PCR products were sequenced

value: human embryonic kidney

value: Wild type

value: Infected by wild type HIV-1 virus


title: liver_5dpi_infection_rep2

description: Library name: Sample17

value: liver

value: infection


title: CD11b+MD15

description:
tpm_MD15_11b_po
read_count_MD15_11b_po

value: blood cell

value: CD11b+Myeloid cell

value: 55 yrs old


title: CTL_E18_1-1


title: CTL_E18_2-1


title: liver_5dpi_infection_rep1

description: Library name: Sample16


title: PEA 4

description:
Library name: PEA4_S18_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_10um_4

value: Myotube

value: WT

value: 10uM palmitoylethanolamide 24h


title: CD11b-CON2

description:
tpm_HC2_11b_ne
read_count_HC2_11b_ne

source_name: healthy control, female, 62 yrs old

value: CD11b- cell

value: female

value: 62 yrs old


title: liver_5dpi_non-infection_rep5

description: Library name: Sample15

value: non-infection


title: liver_5dpi_non-infection_rep3

description: Library name: Sample13


title: PEA 2 top up

description:
Library name: PEA2_S27_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_10um_2


title: BY4741 Thiolutin (3 µg/mL, 3 h) biological replicate 1

description:
Library name: BY4741 THIOI rep1
YPD medium, 28°C, exponential phase; RNA extracted after treatment; Saccharomyces cerevisiae BY4741.

value: yeast

value: MATa his3 leu2 met15 ura3

value: thiolutin 3 µg/mL for 3 hours

value: yeast cell


title: liver_5dpi_non-infection_rep4

description: Library name: Sample14


title: liver_5dpi_non-infection_rep2

description: Library name: Sample12


title: PEA 1

description:
Library name: PEA1_S22_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_10um_1


title: BY4741 Control biological replicate 2

description:
Library name: BY4741 rep2
YPD medium, 28°C, exponential phase; RNA extracted after treatment; Saccharomyces cerevisiae BY4741.

value: untreated


title: PEA 3

description:
Library name: PEA3_S4_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_10um_3


title: PEA 2

description:
Library name: PEA2_S16_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt: PEA_10um_2


title: CD11b+MD7

description:
tpm_MD07_11b_po
read_count_MD07_11b_po

value: MD


title: CD11b+MD12

description:
tpm_MD12_11b_po
read_count_MD12_11b_po

source_name: MD, female, 52 yrs old

value: 52 yrs old


title: liver_5dpi_non-infection_rep1

description: Library name: Sample11

value: liver


title: mirr>ND-42 RNAi , brain and eye disc

city: Paris

first: Francois

last: SCHWEISGUTH

address: 25 rue du Dr Roux

country: France

institute: CNRS - Institut Pasteur

description: Library name: ND-42

data_processing:
Raw data mapping and primary analysis was performed in the Cell Ranger pipeline.
Secondary analysis for marker gene expression pattern was performed with Seurat (Butler et al., 2018).
Assembly: GCF_000001215.4
Supplementary files format and content: normalized.csv

organism: Drosophila melanogaster

source_name: brain and eye disc

growth_protocol: Around 50 embryos with indicated genotypes were collected within 3 hours  and raised until 120 hours in 25°C .

extract_protocol:
The brain with eye discs  were dissociated in 0.25% Trypsin-EDTA solution at 37 ℃ for 10 min. Cells were then washed in DPBS and passed through 35μm filter before library preparation.
Construction of 10x single cell libraries and sequencing on Illumina Hiseq platform were performed by Novogene.

value: brain and eye disc

value: mirr>ND-42 RNAi BL28894


title: mirr>OreR, brain and eye disc

description: Library name: OreR

value: mirr>OreR


title: liver_2dpi_infection_rep5

description: Library name: Sample10

value: infection


title: CD11b+MD6

description:
tpm_MD06_11b_po
read_count_MD06_11b_po

source_name: MD, female, 53 yrs old

value: blood cell

value: CD11b+Myeloid cell

value: 53 yrs old


title: BY4741 Control biological replicate 1

description:
Library name: BY4741 rep1
YPD medium, 28°C, exponential phase; RNA extracted after treatment; Saccharomyces cerevisiae BY4741.


title: CD11b+MD5

description:
tpm_MD05_11b_po
read_count_MD05_11b_po

source_name: MD, female, 48 yrs old

value: female

value: 48 yrs old


title: SKOV3, TK208 treated, rep3

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: SKOV3_TK208_3

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat2 algorithm (v2.0.8b)
gene count measurements were obtained using HTSeq algorithm using refseq annotation
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contains the read counts of the gene using htseq-count

growth_protocol: SKOV3 cells were cultured in RPMI medium supplented with 10% FBS.

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen, Cat#74004) and quantified using nanodrop and Agilent bioanalyzer.
Total RNA samples  were used for sequencing library preparation according to Illumina stranded mRNA sample preparation guide. Each library was bar-coded and then pooled for sequencing run with 50bp single-read sequencing protocol.

treatment_protocol: SKOV3 cells treated with vehicle, and ERX-208 (1000 nM) for 48 hours

value: Human

value: Ovarian cancer


title: Control 5

description:
Library name: Control5_S17_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_Control_5

value: Myotube

value: WT

value: Control (vehicle DMSO)


title: CD11b+MD3

description:
tpm_MD03_11b_po
read_count_MD03_11b_po

value: male

value: 63 yrs old

value: MD


title: Control 6

description:
Library name: Control6_S3_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_Control_6


title: CD11b+MD1

description:
tpm_MD01_11b_po
read_count_MD01_11b_po

source_name: MD, female, 38 yrs old

value: 38 yrs old


title: liver_2dpi_infection_rep2

description: Library name: Sample7

value: liver


title: liver_2dpi_infection_rep4

description: Library name: Sample9


title: Control 4

description:
Library name: Control4_S8_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_Control_4


title: SKOV3 Vehicle, rep3

description: Library name: SKOV3_C3

value: Vehicle control


title: liver_2dpi_infection_rep3

description: Library name: Sample8

value: infection


title: SKOV3, TK208 treated, rep2

description: Library name: SKOV3_TK208_2


title: spleen_2dpi_non-infection_rep1

description: Library name: Sample21

value: spleen

value: non-infection


title: SKOV3, TK208 treated, rep1

description: Library name: SKOV3_TK208_1


title: CD11b+CON13

description:
tpm_HC13_11b_po
read_count_HC13_11b_po

value: blood cell

value: CD11b+Myeloid cell

value: 52 yrs old

value: Control


title: CD11b+CON11

description:
tpm_HC11_11b_po
read_count_HC11_11b_po

value: female

value: 55 yrs old


title: Control 2

description:
Library name: Control2_S19_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_Control_2

value: Myotube

value: WT


title: SKOV3 Vehicle, rep2

description: Library name: SKOV3_C2

value: Human

value: Ovarian cancer


title: Control 1

description:
Library name: Control1_S9_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt: PEA_Control_1

value: Control (vehicle DMSO)


title: CD11b+CON10

description:
tpm_HC10_11b_po
read_count_HC10_11b_po

value: 36 yrs old


title: liver_2dpi_non-infection_rep5

description: Library name: Sample5

value: liver


title: CD11b+CON4

description:
tpm_HC4_11b_po
read_count_HC4_11b_po

value: male

value: 59 yrs old


title: Control 3

description:
Library name: Control3_S21_001
Column name in Partek_PEA_Dan_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts.txt:  PEA_Control_3


title: liver_2dpi_non-infection_rep4

description: Library name: Sample4


title: E3_47A_DOXTPP1_KO

city: Bethesda

first: Eros

last: Lazzerini Denchi

address: 9000 Rockville Pike

institute: NCI

description: Library name: Library 13

data_processing:
Telomeric reads were isolated from the fastq files using the following command: zcat XXX.fastq.gz | grep -E "CTAACCCTAACC|CAAACCCAAACC|GTTAGGGTTAGG|GTTTGGGTTGG">XXX.txt The resulting txt files were analyzed in RStudio to quantify number of reads containing mutants repeats and number of consecutive mutant repeats. In the manuscript associated with this file we report the quantifications.
Assembly: mm10
Supplementary files format and content: The .txt files contain reads corresponding to the telomeric reads

source_name: mESC

growth_protocol: mESCs (E14) were grown on 0.1% gelatin-coated plates in DMEM medium containing LIF (1,000 U/ml) and 2i (1 μM PD03259010 and 3 μM CHIR99021). Cell lines were tested for mycoplasma contamination.

extract_protocol:
Cells were washed with PBS, treated with Trypsin/EDTA, and neutralized with growth media. Genomic DNA was isolated, digested, and telomere sequences were enriched following the same protocol described for the dot blot assay. A total of 100-150 ng of enriched telomeric DNA was then sonicated using a Covaris S220 Ultrasonicator to generate DNA fragments ranging from 300-500 bp.
Library preparation for Illumina sequencing was performed using the NEBNext Ultra II kit, following the manufacturer’s instructions.

value: mESC

value: TPP1 knockout

value: 1 μg/ml of doxycycline for 72 hours