title: RNA MYOCD-FWYtoA_3

description: Library name: MYOCD-FWYtoA RNA-seq bio rep 3

value: MYOCD-FWYtoA retroviral transduction, SMC differentiation


title: RNA SRF-FUS_1

status: Public on Sep 02 2025

type: SRA

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

country: USA

institute: UTsouthwestern

description: Library name: SRF-FUS-seq bio rep 1

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
For RNA-seq analysis,reads were aligned to the mouse reference genome  GRCm38 (mm10) using the Hisat (version 2.0.0) aligner using default settings. Aligned reads were counted using featureCounts (version 1.4.6) per gene ID.
Assembly: GRCh38/mm10
Supplementary files format and content: Bigwig for ChIPseq, RNAseq Genome Tracks. Bed file for ChIP Peaks

molecule: polyA RNA

organism: Mus musculus

source_name: Cell Culture

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagents and Direct-zol RNA Miniprep Kits (Zymo Research, R2052) according to manufacturer’s protocol. For ChIP-seq, cells were fixed and crosslinked with 4% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
For RNA-seq, stranded mRNA-Seq libraries were generated using KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol. For ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB (NEB, E6177S). 10 ng of DNA was used as starting material for Input samples and 1 ng for IP samples. Libraries were amplified using 12 cycles for Input samples and 15 cycles for IP samples on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

tag: tissue

value: Cell Culture

tag: cell line

tag: cell type

value: Fibroblast-like cells from C3H mouse embryo

tag: genotype

value: WT

tag: treatment

value: SRF-FUS retroviral transduction, SMC differentiation


title: RNA MYOCD-FWYtoA_2

description: Library name: MYOCD-FWYtoA RNA-seq bio rep 2


title: Control, complete medium, rep1

city: Lausanne

first: Felix

last: Naef

address: EPFL SV IBI

country: Switzerland

institute: EPFL

description: Library name: Ctrl_1

data_processing:
Paired-end RNA-seq reads were aligned to the Ensembl GRCm38 primary assembly using STAR, with the Ensembl GTF (GRCm38.100) to build the index
Gene-level counts were generated via STAR --quantMode GeneCounts option
Normalization was performed using edgeR
Assembly: GRCm38 primary assembly
Supplementary files format and content: Tab-delimited text file include raw counts (unique mapping) for all samples
Supplementary files format and content: Tab-delimited text file include log2 CPM for all samples

growth_protocol: NIH3T3 mouse fibroblast cells were cultured in DMEM (high glucose, pyruvate) supplemented with 10% FBS and 100 U/ml penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Cells were washed with cold PBS containing cycloheximide and lysed in polysome lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl₂, 1% Triton X-100, 5 mM DTT, 100 µg/ml CHX, DNase, RNase inhibitor, protease/phosphatase inhibitors). Lysates were cleared by centrifugation and RNA was extracted via phenol-chloroform and ethanol precipitation.
NEBNext Ultra II Directional RNA Library Prep with PolyA selection

treatment_protocol: For amino acid starvation, cells were switched to custom DMEM/F-12 medium lacking specific branched-chain amino acids (leucine, isoleucine, valine) and supplemented with 10% dialyzed FBS for 6 hours. Different combinations of leucine, isoleucine, and valine were added back to create separate starvation conditions (single, double, or triple).

value: fibroblasts

tag: time


title: Leucine and Isoleucine deprivation, rep3

description: Library name: Double_3

value: amino acid starvation


title: ChIP_H3K27me3-Ab_WT_rep2

city: Clermont-Ferrand

first: Olivier

last: Mathieu

state: Auvergne

address: 28 Place Henri Dunant

department: UMR 6293 - iGReD

country: France

institute: CNRS

library_source: genomic

data_processing:
For all libraries, reads were trimmed and filtered for quality and adapter contamination using Trim Galore (v.0.6.7, Babraham Institute) with default parameters
RNA-seq: Filtered reads were aligned to the Arabidopsis reference genome (TAIR10) genome using STAR (v.2.7.9a). Reads aligning equally well to more than one position in the reference genome were discarded, and probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite. Sample tracks were generated using deeptools (v.3.5.1) bamCoverage with the option normalizeUsing CPM and binSize 1. Subsequent read counting for each gene and TE was performed using featureCounts (v.2.0.3) using the Araport11 genome annotation. Annotated TEs overlapping strongly (> 80%) with an annotated TE gene were considered TE genes, and the TE annotation was discarded. Differential expression analysis was performed using DESeq2 (v.1.36.0) with absolute fold-change ≥ 4 and Benjamini-Hochberg adjusted p-value < 0.05 were considered differentially expressed. For DEseq2 analysis of amiR-mail2 hypomorphic lines, criteria of absolute fold change ≥2 and Benjamini-Hochberg adjusted p-value < 0.05 were retained.
ChIP-seq: filtered reads were aligned to the TAIR10 Arabidopsis reference genome using bowtie2 (v.2.4.2), allowing only uniquely mapped reads with perfect matches. PCR duplicates were discarded using MarkDuplicates from the Picard Tools suite. Sample tracks were generated using deeptools (v.3.5.1) bamCoverage with the option normalizeUsing RPGC and binSize 1. Peaks calling was performed using MACS2 (v.2.2.7.1) using corresponding inputs as a background and --nomodel and –extsize 200 options, and peaks called in the anti-MYC or anti-FLAG WT controls were removed.
Assembly: TAIR10 (Araport11 annotation)
Supplementary files format and content: RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins.
Supplementary files format and content: ChIP-seq: bigWig format files with normalized read densities (Reads Per Genomic Content) calculated in 1 bp bins.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 14-day-old seedlings

growth_protocol: Plants were grown on soil in long-day conditions (16h light, 8h dark) at 23°C with 60% relative humidity.

extract_protocol:
RNA-seq : total RNA was extracted from aerial tissues of 12-day-old plants using RNAzol RT (RN190, Molecular Research Center, Inc). ChIP-seq : nuclei from 14-day-old plants were purified and chromatin was mainly sheared to 200-400 bp fragments using a Bioruptor UCD-200 (Diagenode) or a Covaris S220 Focused-ultrasonicator. Input and immunoprecipited fractions were purified for library construction.
RNA-seq: libraries were generated from about one µg total RNA at Beijing Genomics Institute (Hong Kong). ChIP-seq: libraries were generated from input or ChIPed DNAs at Beijing Genomics Institute (Hong Kong).

value: 14-day-old seedlings

tag: chip antibody

value: H3K27me3 Ab, Diagenode C15410069


title: RNA SRF-MYOCD-FWYtoA_3

description: Library name: SRF-MYOCD-FWYtoA RNA-seq bio rep 3

value: SRF-MYOCD-FWYtoA retroviral transduction, SMC differentiation


title: RNA SRF-MYOCD-FWYtoA_1

description: Library name: SRF-MYOCD-FWYtoA RNA-seq bio rep 1


title: ChIP_H3K27me3-Ab_mail1_rep2


title: RNA SRF-MYOCD-FWYtoA_2

description: Library name: SRF-MYOCD-FWYtoA RNA-seq bio rep 2


title: ChIP_H2Aub-Ab_mail1_rep1

value: H2AUb Ab, Cell Signaling Technology ref.8240


title: RNA MYOCD-FWYtoA_1

description: Library name: MYOCD-FWYtoA RNA-seq bio rep 1


title: Tongue19_5

city: Zürich

first: Ricardo

last: Frois-Martins

address: Winterthurerstrasse 260

department: Section of Immunology

institute: University of Zürich - Tierspital

data_processing:
Reads were aligned to a combined reference that consists of the concatenation of Mus musculus and Candida albicans. As mouse reference GRCm39 builds was used. As Candida reference, the SC5314_Assembly22 was used.
Expression values were computed using featureCounts, separate files for the mouse and the candida genes were generated.
Assembly: GRCm39 build was used. Gene annotation were from GENCODE Release M26.
Supplementary files format and content: Txt files with read counts; The files hold the mouse gene counts (.txt) and the candida genes (_candida.txt).

molecule: total RNA

source_name: Tongue

extract_protocol:
Initial step of isolation of total RNA from liquid YPD culture and murine tongue tissue was performed using TRI reagent (Sigma-Aldrich) according to the manufacturer’s protocol with the modification that the tissue was homogenized with steel ball using a TissueLyzer (Qiagen) for 6 minutes at 25 Hz and after homogenized with 0.5mm glass beads for 2 cycles of 2 minutes intercalated with 30 seconds of colling on ice before extraction of the nucleic acids with chloroform. After the TRI reagent/chloroform separation, the RNA extraction was performed using Direct-zol RNA MiniPrep Plus Kit (Qiagen) following manufacturer's protocol.
Illumina Truseq Total RNA (ribosomal depletion)

value: Tongue

value: (total tissue)

value: oral colonization (19 days)


title: ChIP_H2Aub-Ab_WT_rep1


title: RNA SRF-MYOCD-TAD_2

description: Library name: SRF-MYOCD-TAD RNA-seq bio rep 2

value: SRF-MYOCD-TAD retroviral transduction, SMC differentiation


title: ChIP_H3K27me3-Ab_ring1a-ring1b_rep1

value: ring1a-2 ring1b-3


title: Tongue19_4


title: RNA SRF_3

description: Library name: SRF RNA-seq bio rep 3

value: SRF retroviral transduction, SMC differentiation


title: RNA SRF-MYOCD-TAD_1

description: Library name: SRF-MYOCD-TAD RNA-seq bio rep 1


title: Tongue19_3_B


title: RNA SRF-MYOCD-TAD_3

description: Library name: SRF-MYOCD-TAD RNA-seq bio rep 3


title: RNA SRF_2

description: Library name: SRF RNA-seq bio rep 2


title: ChIP_H3K27me3-Ab_ndx_rep1


title: Tongue19_3_A


title: ChIP-Input MYOCD-FWYtoA

description: Library name: ChIP-Input MYOCD-FWYtoA

data_processing:
Basecalls performed using CASAVA version 1.8.2
For ChIP-seq analysis, raw sequencing reads with > 30% nucleotide with phred quality scores < 20 were filtered. Single-end sequencing reads were then aligned to the mouse reference genome GRCm38 (mm10) using bowtie2 aligner (v 2.3.4.3) with default parameters. For transcription factor ChIP-seq data, peaks were called using HOMER software package (version 4.9) findpeaks command, with parameter ‘-style factor’, peaks were called with >2 fold enrichment over input controls and > 4 fold enrichment over local tag counts and FDR threshold was set to 10-3. For histone marker ChIP-Seq data, peaks were called by findpeaks command with parameter ‘–style histone’, peaks were called with >2 fold enrichment over input controls and > 4 fold enrichment over local tag counts and FDR threshold set to 10-3. ChIP-seq peaks within a 1000 bp range were stitched together to form broad regions.
Assembly: GRCh38/mm10
Supplementary files format and content: Bigwig for ChIPseq, RNAseq Genome Tracks. Bed file for ChIP Peaks, TXT file for RNAseq RawCount

extract_protocol:
For ChIP-seq, cells were fixed and crosslinked with 4% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
For ChIP-seq, libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB (NEB, E6177S). 10 ng of DNA was used as starting material for Input samples and 1 ng for IP samples. Libraries were amplified using 12 cycles for Input samples and 15 cycles for IP samples on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.

value: MYOCD-FWYtoA retroviral transduction, SMC differentiation


title: ChIP-Input SRF-FUS

description: Library name: ChIP-Input SRF-FUS

value: Cell Culture


title: RNA SRF_1

description: Library name: SRF RNA-seq bio rep 1

value: Fibroblast-like cells from C3H mouse embryo


title: ChIP_H3K27me3-Ab_mail1-ring1a-ring1b_rep1

value: mail1-1 ring1a-2 ring1b-3


title: Tongue19_2_B


title: Tongue19_2_A


title: ChIP_H3K27me3-Ab_mail1-ndx_rep1

value: mail1-1 ndx-7


title: ChIP-Input SRF-MYOCD-TAD

description: Library name: ChIP-Input SRF-MYOCD-TAD

value: WT


title: Tongue19_6


title: ChIP-Input SRF-MYOCD-FWYtoA

description: Library name: ChIP-Input SRF-MYOCD-FWYtoA


title: ChIP_H3K27me3-Ab_mail1-main_rep1

value: mail1-1 main-2


title: ChIP-H3K27ac SRF-FUS

description: Library name: ChIP-H3K27ac SRF-FUS

value: SRF-FUS retroviral transduction, SMC differentiation


title: Tongue19_1_B


title: ChIP-H3K27ac SRF-MYOCD-TAD

description: Library name: ChIP-H3K27ac SRF-MYOCD-TAD


title: Tongue19_1_A


title: ChIP-H3K27ac SRF-MYOCD-FWYtoA

description: Library name: ChIP-H3K27ac SRF-MYOCD-FWYtoA


title: ChIP_H3K27me3-Ab_mail1_rep1

value: 14-day-old seedlings

value: H3K27me3 Ab, Diagenode C15410069


title: ChIP-Input SRF

description: Library name: ChIP-Input SRF


title: ChIP-H3K27ac SRF

description: Library name: ChIP-H3K27ac SRF


title: ChIP_H3K27me3-Ab_WT_rep1


title: ChIP-H3K27ac MYOCD-FWYtoA

description: Library name: ChIP-H3K27ac MYOCD-FWYtoA


title: amiR-mail2-5_rep4

source_name: 12-day-old seedlings

value: 12-day-old seedlings


title: ChIP-GFP SRF-FUS

description: Library name: ChIP-GFP SRF-FUS


title: ChIP-GFP MYOCD-FWYtoA

description: Library name: ChIP-GFP MYOCD-FWYtoA


title: Tongue3_6_B

value: Tongue

value: oral colonization (3 days)


title: ChIP-GFP SRF-MYOCD-FWYtoA

description: Library name: ChIP-GFP SRF-MYOCD-FWYtoA

value: SRF-MYOCD-FWYtoA retroviral transduction, SMC differentiation


title: amiR-mail2-5_rep3


title: Tongue3_6_A

value: (total tissue)


title: ChIP-GFP SRF-MYOCD-TAD

description: Library name: ChIP-GFP SRF-MYOCD-TAD

value: SRF-MYOCD-TAD retroviral transduction, SMC differentiation


title: Tongue3_5_B


title: amiR-mail2-4_rep4


title: Tongue3_5_A


title: Retinal_multiplexed_samples

city: Ottawa

first: Pierre

last: Mattar

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: Multiplexed_run
3′ Library & Gel Bead Kit v2, PN-120237, 10X Genomics

library_source: transcriptomic single cell

data_processing:
The resulting expression library FASTQs were processed using CellRanger (10X Genomics) and subjected to the deMULTIplex workflow. Output files were filtered and analyzed using Scanpy version 1.9.190 in Python (Python Core Team n.d.). Low-quality cells with few reads and high mitochondrial gene content were excluded. An unbiased deep-learning model using scDeepSort version 1.0 was used to identify cell types. Differential gene expression analyses were performed using Scanpy, or MAST version 1.24.042.
Assembly: mm10
Supplementary files format and content: processed H5ad file with embeddings, compressed filtered feature bc matrix tsv and mtx files

source_name: Retina

extract_protocol:
P1 retinae from 3 biological replicates each for control (Chd4 f/+Cre+) and mutant (Chd4 f/f Cre+) samples, for a total of 6 replicates were dissected, enzymatically dissociated using papain, and triturated in LO-OVO solution (1X LO-OVO (Bio Basic), 0.4% DNaseI in 1X PBS) following resuspension in 1X PBS.
Approximately 20,000 pooled cells were used in a single Chromium™ run (3′ Library & Gel Bead Kit v2, PN-120237, 10X Genomics).

value: Retina

value: Primary retinal cells

value: Chd4 f/+Cre+ and Chd4 f/f Cre+

tag: age

value: Postnatal day 1


title: Valine deprivation, rep3

description: Library name: Val_3

library_source: other

data_processing:
Raw reads were trimmed with cutadapt (parameter: -m 10, adapter: TGGAATTCTCGGGTGCCAAGG). Reads with identical UMIs (4 nt at both 5′ and 3′ ends) and inserts were removed using an in-house Perl script.
Reads were aligned to a combined mouse/human rRNA-tRNA reference with STAR. Unaligned reads were then mapped to the Ensembl GRCm38 reference genome
Only reads 25–35 nt long with a unique alignment (NH==1) were retained (samtools).
Filtered Ribo-seq reads were counted with htseq-count (intersection-strict mode) using the same Ensembl GTF annotation as RNA-seq.
Normalization was performed using edgeR.
Assembly: GRCm38 primary assembly
Supplementary files format and content: Tab-delimited text file include raw counts (unique mapping) for all samples
Supplementary files format and content: Tab-delimited text file include log2 CPM for all samples
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
Cells were washed with cold PBS containing cycloheximide and lysed in polysome lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl₂, 1% Triton X-100, 5 mM DTT, 100 µg/ml CHX, DNase, RNase inhibitor, protease/phosphatase inhibitors). Lysates were cleared by centrifugation. Ribosome-protected fragments were generated by RNase I digestion. Digested samples were purified using Microspin S-400 HR columns (Cytiva) equilibrated with polysome buffer, RNA extracted by phenol-chloroform extraction and ethanol precipitation,  and size-selected (26–34 nt) on 15% TBE-Urea gels. rRNA-depletion was performed with biotinylated oligos and Streptavidin Dynabeads.
Samples were purified using a RNA Clean & Concentrator kit (Zymo). End repair was performed by incubating RNA with T4 PNK (NEB) at 37°C for 1 hour, followed by ATP addition and another hour of incubation. Clean-up was performed using the  RNA Clean & Concentrator kit (Zymo). Libraries were prepared using the NEXTflex Small RNA-Seq Kit v3 (Revvity).

value: fibroblasts

value: amino acid starvation


title: Valine deprivation, rep2

description: Library name: Val_2


title: amiR-mail2-4_rep3


title: Valine deprivation, rep1

description: Library name: Val_1


title: ChIP-GFP SRF

description: Library name: ChIP-GFP SRF

value: Cell Culture

value: Fibroblast-like cells from C3H mouse embryo

value: WT

value: SRF retroviral transduction, SMC differentiation


title: Tongue3_4_A


title: ChIP_INPUT_main-MAIN-FLAG_rep4

value: 14-day-old seedlings


title: WT_RNA_rep4

value: 12-day-old seedlings


title: WT_RNA_rep3


title: Leucine, Isoleucine, and Valine deprivation, rep3

description: Library name: Triple_3


title: morc2_RNA_rep8


title: Tongue3_4_B

value: Tongue


title: ChIP_INPUT_mail1-MAIL1-FLAG_rep4


title: Tongue3_3_A

value: oral colonization (3 days)


title: morc2_RNA_rep7


title: ChIP_FLAG-Ab_mail1-MAIL1-FLAG_rep4

value: Anti-FLAG M2 Ab, Sigma F1804-1MG


title: Leucine, Isoleucine, and Valine deprivation, rep2

description: Library name: Triple_2


title: ChIP_FLAG-Ab_WT_rep4


title: ChIP_INPUTflag_WT_rep4


title: Tongue3_2_B

value: (total tissue)


title: mail1-ndx-morc2_RNA_rep8

value: mail1-1 ndx-7 morc2-1


title: Leucine deprivation, rep3

description: Library name: Leu_3


title: mail1-ndx-morc2_RNA_rep7


title: Tongue3_1_B


title: Leucine, Isoleucine, and Valine deprivation, rep1

description: Library name: Triple_1


title: mail1-ndx_RNA_rep8

value: mail1-1 ndx-7


title: Tongue3_1_A


title: Leucine deprivation, rep1

description: Library name: Leu_1


title: ChIP_INPUT_main-MAIN-MYC_rep2


title: ChIP_FLAG-Ab_main-MAIN-FLAG_rep4


title: mail1-ndx_RNA_rep7


title: ChIP_MYC-Ab_main-MAIN-MYC_rep2

value: Myc-Tag Ab, Cell Signaling Technology ref.2278


title: Tongue3_3_B


title: ChIP_INPUT_mail1-MAIL1-MYC_rep2


title: Isoleucine deprivation, rep3

description: Library name: Ile_3


title: Leucine deprivation, rep2

description: Library name: Leu_2


title: mail1_RNA_rep8


title: Isoleucine deprivation, rep2

description: Library name: Ile_2


title: Tongue3_2_A


title: ChIP_MYC-Ab_mail1-MAIL1-MYC_rep2


title: ChIP_INPUTmyc_WT_rep2


title: CD45- cells from conventional vein grafts

city: Hangzhou

first: Rong

last: Mou

address: 79 Qingchun Road

country: China

institute: Zhejiang University

description: 10x Genomics

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.1.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Assembly: mm10
Supplementary files format and content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: vein grafts

extract_protocol:
Mice were euthanized and perfused with PBS and vein grafts were harvested and placed in a petri dish containing DMEM with 10% fetal bovine serum (FBS) on ice. After collecting all grafts, to obtain single cell suspensions, arteries were washed with PBS for three times, cut into fine pieces and incubated with 1 mg/ml papain digesting solution [1 mg/ml papain (Sigma, P4762), 0.5 mg/ml 1,4-Dithioerythritol (Sigma, D8255), 0.156 mg/ml Taurine (Sigma, T8691), 0.25 mg/ml bovine serum albumin in PBS]. The digestion was performed at 37 ℃ water bath with reciprocal shaking. Detached cells in the supernatant were collected and suspended in DMEM with 10% FBS. Vascular allografts were then incubated with fresh digestion solutions every 10 min. After 3-4 digestions, the remaining tissues were incubated with 1 mg/ml papain digesting solution and 2 mg/ml collagenase I (Gibco, 17018029) and 1 mg/ml dispase II (Sigma, D4693) in Hank’s balanced salt solution containing calcium and magnesium. Detached cells were collected and fresh digestion solutions were added until the tissues dissolved completely. All digested cells from one sample were pooled together at the end of the digestion process. After sufficient digestion, cells were filtered through a 40-μm cell strainer, and the collected cells were centrifuged 8 min at 500 g speed at 4 ℃. Subsequently, cell pellet was suspended in PBS and stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit, Hoechst 33342 and CD45 (BD Pharmingen™, 553079) for 30 mins on ice. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+ & Dead Cell Stain- & CD45+/- or tdTomato+) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Samples were subjected to scRNA-seq. A ChromiumTM Single Cell 3' Reagent Kit v2 or V3 chemistry (10x Genomics) was used and a standard protocol was followed. The library was generated and sequenced on a Novaseq6000 PE150 platform (Illumina) with paired-end 150 bp sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: vein graft cells

value: vein grafts

tag: strain

value: 10-12 weeks old


title: mail1_RNA_rep7


title: H520,H3K27ac,rep1(ChIP)

city: Xi'an

first: Yihui

last: Zhang

state: Shanxi

address: No.229 Taibai North Road

institute: Northwest University

description: Library name: H520,H3K27ac,rep1

data_processing:
The ChIP-seq reads were mapped into the human reference genome (hg38) using Bowtie2 (version 2.5.0). Matching input control was used to call peaks. Peak calling was performed using MACS3. For cells H3K27ac data, a “--broad --broad-cutoff 0.1” was used for peak calling; For TP63, SOX2, GRHL2, KLF5 ChIP-seq data in HCC95, a “-q 0.01” was used for peak calling. Bigwig tracks were generated using deepTools (version 3.5.1) bamCoverage with (Reads Per Kilobase of transcript per Million mapped reads ( RPKM ) normalization and visualization with IGV( version 2.12.3).
Assembly: hg38
Supplementary files format and content: bigWig

organism: Homo sapiens

source_name: lung

extract_protocol:
Briefly, LUSC cells were fixed with 1% formaldehyde (F8775, Sigma) for 10 min at room temperature, and a final concentration of 125 mM glycine was used to quench the reaction. Cells were washed twice with cold PBS and collected in cold PBS by scraping, then resuspended in hypotonic lysis buffer (20 mM Hepes, pH 7.9, with 10 mM KCl, 10% glycerol, 1 mM DTT and a protease inhibitor cocktail (04693124001, Roche)). The pellet of nuclei was resuspended in RIPA buffer (10 mM Tris-HCl, pH 8.0, with 140 mM NaCl, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and Protease Inhibitor). Nuclear extracts were sonicated to generate chromatin fragment on a Covaris M220 Focused-ultrasonicator (Insert, microTUBE 130 µL; Temperature, 7°C; Peak Incident Power, 75W; Duty Factor, 5%; Treatment Time, 300s). The chromatin was cleaned by centrifugation at 14,000×g for 10 min at 4 °C and diluted with 1 mL RIPA buffer per reaction. Then the chromatin was precleared with Protein G Sepharose 4 Fast Flow (17061801, GE) for 2 hours, 30 µL of sample was set aside as an input and subjected to immunoprecipitation with antibody against H3K27ac (T59439M, Abmart), TP63 (13109S, Cell Signaling Technology), SOX2 (2748S, Cell Signaling Technology), KLF5 (ab137676, Abcam), GRHL2 (ab271023, Abcam) overnight. On the following day, Pierce Protein A/G Plus Agarose beads (Thermo Fisher Scientific, 20423) that were blocked with RIPA containing 0.5% bovine serum albumin (BSA) were added into the samples followed by incubation for 2 hour in cold room under rocking. The beads were then washed three times with RIPA buffer, followed by two times in RIPA buffer with 0.5 M NaCl, oncein LiCl buffer [250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630,0.1% sodium deoxycholate, and 10 mM tris-HCl (pH 8.0)], and twice in ice-cold Tris- EDTA (TE) buffer. Each time, the beads were sustaining for 5 min with a gentle rock. After washing, both the beads and input sample were added with 150 μL of extraction buffer (1% SDS in 1× TE, 12 μL of 5 M NaCl, and 10 μg of RNAse A) and incubated at 37°C for 1 hour with a shaking. Next, 20 μg of Proteinase K was added to the samples for incubation at 65°C overnight with thermoshaking.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit for Illumi-na (NEB, E7645).

value: lung

value: human lung epithelial cells


title: WT_RNA_rep8


description: Library name: Double_3

value: fibroblasts

value: amino acid starvation


title: H520(Input), rep2

description: Library name: H520,input


title: ChIP_INPUT_main-MAIN-FLAG_rep3


title: Leucine and Isoleucine deprivation, rep2

description: Library name: Double_2


title: WT_RNA_rep7


title: ChIP_MYC-Ab_WT_rep2


title: ChIP_FLAG-Ab_main-MAIN-FLAG_rep3


title: swn-7_RNA_rep5


title: HCC95, siTP63b, rep3

description: Library name: siTP63b, rep3

data_processing:
The RNA-seq reads were aligned to the human reference genome (hg38) using HISAT2 (2.2.1) with default settings. Uniquely aligned reads were counted at gene regions using the package featureCounts (version 2.0.1) based on Gencode v40 annotations.
Assembly: hg38
Supplementary files format and content: txt files include raw counts of each sample

extract_protocol:
Total RNA was isolated with TRIzol reagent (15596018, Invitrogen) from cultured cells
For RNA-seq library preparation, poly (A)+ RNA was selected using the NEB-Next Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) to perform the LM-seq procedure. including that isolated mRNA is fragmented in reverse transcription buffer with heat and then reverse-transcribed with SmartScribe reverse transcriptase (Clontech) using a random hexamer oligo (HZG883). After reverse transcription, RNA is removed by RNaseA and RNaseH treatment. A partial adaptor (HZG885) is then ligated to the single stranded cDNA using T4 RNA ligase 1 (NEB) and incubated overnight at 22℃. After purification, ligated cDNA is amplified by 18 cycles of PCR using oligos that contain full BGI adaptors. Last, the resultant libraries were purified using the DNA Clean Beads, followed by sequencing using the DNBSEQ-T7 PE150  platform  (Biopharmaceutical PublicService Platform, Nanjing).


title: Leucine and Isoleucine deprivation, rep1

description: Library name: Double_1


title: swn-7_RNA_rep6


title: CD45- cells from No-Touch vein grafts

description: 10x Genomics


title: Control, complete medium, rep3

description: Library name: Ctrl_3


title: HCC95, siTP63b, rep2

description: Library name: siTP63b, rep2


title: ChIP_INPUT_mail1-MAIL1-FLAG_rep3


title: Control, complete medium, rep2

description: Library name: Ctrl_2


title: mail1-swn_RNA_rep6

value: mail1-1 swn-7


title: Isoleucine deprivation, rep1

description: Library name: Ile_1


title: mail1-swn_RNA_rep5


title: H520,H3K27ac,rep2(ChIP)

description: Library name: H520,H3K27ac,rep2


title: Control, complete medium, rep1

description: Library name: Ctrl_1


title: HCC95, siSOX2b, rep3

description: Library name: siSOX2b, rep3


title: ChIP_INPUTflag_WT_rep3

value: 14-day-old seedlings


title: P33_post_TCR

city: Seoul

first: Junha

last: Cha

address: Yonsei-Ro 50

department: Department of Biotechnology

country: South Korea

institute: Yonsei University

description:
Library name: P33_post_TCR
10X Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GEX: GRCh 1.2.0 (TCR: GRCh38-alts-ensembl-3.1.0)
Supplementary files format and content: Tab separated value files and matrix files

source_name: Hypopharynx

extract_protocol:
We collected fresh tumor tissues on the day of surgery, which were mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929), following the manufacturer's instructions. After incubation for 1 hour at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat#130-098-462) into RPMI-1640 medium (Corning, Inc., Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 × g for 10 minutes. The pellet was suspended in PBS containing 2% fetal bovine serum. Tissue-infiltrating lymphocytes were enriched using a Ficoll gradient (Sigma-Aldrich), and the resulting single-cell suspensions were subsequently counted using trypan blue.
Libraries were constructed using the Chromium controller, adhering to the protocol described in the 10x Chromium Next GEM Single Cell 5′ v2 Cell Surface Protein User Guide (CG000330). Initially, cell suspensions were diluted with nuclease-free water to achieve a target cell count of 10,000. These suspensions were then combined with a master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip K. Within the droplets, RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed. Following this, the cDNA molecules were pooled and subjected to PCR enrichment. The amplified cDNA underwent size selection for the 5′ Gene Expression libraries, V(D)J Enriched Libraries, and Cell Surface Protein libraries. For the Cell Surface Protein Library, the cDNA pool was enriched through index PCR. In the case of the V(D)J Enriched Library, the enriched cDNA pool was amplified through two rounds using specific primers. For the 5′ Gene Expression Library, the cDNA pool underwent end repair, addition of a single 'A' base, and ligation of adapters, followed by purification and PCR enrichment. The purified libraries were quantified using qPCR in accordance with the qPCR Quantification Protocol Guide (KAPA) and assessed for quality using the Agilent Technologies 4200 TapeStation. Finally, the libraries were sequenced on the HiSeq platform (Illumina) following the specified read length outlined in the user guide.

treatment_protocol: Patients who were pathologically diagnosed with head and neck cancer and underwent surgical resection at Severance Hospital (Seoul, Republic of Korea) between January 2019 and December 2020 were enrolled. Patients received a single cycle of either intravenous D (1,500 mg) or D+T (1,500 mg + 75 mg) before curative surgical resection. Surgery was planned within 2 to 8 weeks after administration. Radiologic evaluations were conducted at baseline and after neoadjuvant immunotherapy using CT or MRI, prior to surgical resection. All patients underwent surgical resection based on the original clinical and radiological extent of the disease. Adjuvant chemoradiotherapy was planned based on the multidisciplinary team's assessment. Clinical and radiologic surveillance, including physical examinations and cross-sectional imaging, was performed every 3 months for the first 2 years after surgical resection, and then every 6 months. Dose reduction was not permitted for neoadjuvant D+/-T or adjuvant D.

value: Hypopharynx

tag: hpv p16

value: negative

tag: ici duration_days

value: D+T


title: P33_pre_TCR

description:
Library name: P33_pre_TCR
10X Genomics


title: mail1_RNA_rep6

value: 12-day-old seedlings


title: HCC95, siSOX2b, rep2

description: Library name: siSOX2b, rep2


title: mail1-clf_RNA_rep6

value: mail1-1 clf-29


title: mail1-clf_RNA_rep5


title: ChIP_INPUT_main-MAIN-MYC_rep1


title: P32_pre_TCR

description:
Library name: P32_pre_TCR
10X Genomics

source_name: Oropharynx

value: Oropharynx


title: mail1_RNA_rep5


title: HCC95, siTP63b, rep1

description: Library name: siTP63b, rep1


title: ChIP_FLAG-Ab_mail1-MAIL1-FLAG_rep3

value: Anti-FLAG M2 Ab, Sigma F1804-1MG


title: HCC95, siGRHL2a, rep2

description: Library name: siGRHL2a, rep2


title: P31_pre_TCR

description:
Library name: P31_pre_TCR
10X Genomics

value: positive


title: P31_post_TCR

description:
Library name: P31_post_TCR
10X Genomics


title: ChIP_INPUT_mail1-MAIL1-MYC_rep1


title: WT_RNA_rep6


title: ChIP_FLAG-Ab_WT_rep3


title: HCC95, siGRHL2a, rep1

description: Library name: siGRHL2a, rep1


title: WT_RNA_rep5


title: HCC95, siNC1, rep3

description: Library name: siNC1, rep3


title: P30_post_TCR

description:
Library name: P30_post_TCR
10X Genomics

value: D


title: HCC95, siSOX2b, rep1

description: Library name: siSOX2b, rep1


title: ChIP_MYC-Ab_main-MAIN-MYC_rep1

value: Myc-Tag Ab, Cell Signaling Technology ref.2278


title: ChIP_INPUT_WT_rep1


title: HCC95, siGRHL2a, rep3

description: Library name: siGRHL2a, rep3


title: P30_pre_TCR

description:
Library name: P30_pre_TCR
10X Genomics


title: ChIP_MYC-Ab_WT_rep1


title: clf29_RNA_rep5


title: clf29_RNA_rep6


title: HCC95, siNC1, rep1

description: Library name: siNC1, rep1


title: ChIP_INPUT_main_rep4


title: HCC95, siKLF5b, rep3

description: Library name: siKLF5b, rep3


title: P29_pre_TCR

description:
Library name: P29_pre_TCR
10X Genomics


title: HCC95, siNC1, rep2

description: Library name: siNC1, rep2


title: HCC95, siKLF5b, rep2

description: Library name: siKLF5b, rep2


title: ring1a-ring1b_RNA_rep1

value: ring1a-2 ring1b-3


title: P28_post_TCR

description:
Library name: P28_post_TCR
10X Genomics


title: P29_post_TCR

description:
Library name: P29_post_TCR
10X Genomics


title: ChIP_H3K27me3-Ab_main_rep4

value: H3K27me3 Ab, Millipore 07-449


title: P28_pre_TCR

description:
Library name: P28_pre_TCR
10X Genomics


title: ChIP_H3K27me3-Ab_WT_rep4


title: ndx-7_RNA_rep1


title: P27_post_TCR

description:
Library name: P27_post_TCR
10X Genomics


title: ChIP_MYC-Ab_mail1-MAIL1-MYC_rep1


title: HCC95, KLF5(ChIP)

description: Library name: HCC95, KLF5

extract_protocol:
Briefly, LUSC cells were fixed with 1% formaldehyde (F8775, Sigma) for 10 min at room temperature, and a final concentration of 125 mM glycine was used to quench the reaction. Cells were washed twice with cold PBS and collected in cold PBS by scraping, then resuspended in hypotonic lysis buffer (20 mM Hepes, pH 7.9, with 10 mM KCl, 10% glycerol, 1 mM DTT and a protease inhibitor cocktail (04693124001, Roche)). The pellet of nuclei was resuspended in RIPA buffer (10 mM Tris-HCl, pH 8.0, with 140 mM NaCl, 1% Triton X-100, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate and Protease Inhibitor). Nuclear extracts were sonicated to generate chromatin fragment on a Covaris M220 Focused-ultrasonicator (Insert, microTUBE 130 µL; Temperature, 7°C; Peak Incident Power, 75W; Duty Factor, 5%; Treatment Time, 300s). The chromatin was cleaned by centrifugation at 14, 000×g for 10 min at 4 °C and diluted with 1 mL RIPA buffer per reaction. Then the chromatin was precleared with Protein G Sepharose 4 Fast Flow (17061801, GE) for 2 hours, 30 µL of sample was set aside as an input and subjected to immunoprecipitation with antibody against  H3K27ac (T59439M, Abmart), TP63 (13109S, Cell Signaling Technology), SOX2 (2748S, Cell Signaling Technology), KLF5 (ab137676, Abcam), GRHL2 (ab271023, Abcam) overnight. On the following day, Pierce Protein A/G Plus Agarose beads (Thermo Fisher Scientific, 20423) that were blocked with RIPA containing 0.5% bovine serum albumin (BSA) were added into the samples followed by incubation for 2 hour in cold room under rocking. The beads were then washed three times with RIPA buffer, followed by two times in RIPA buffer with 0.5 M NaCl, oncein LiCl buffer [250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate, and 10 mM tris-HCl (pH 8.0)], and twice in ice-cold Tris- EDTA (TE) buffer. Each time, the beads were sustaining for 5 min with a gentle rock. After washing, both the beads and input sample were added with 150 μL of extraction buffer (1% SDS in 1× TE, 12 μL of 5 M NaCl, and 10 μg of RNAse A) and incubated at 37°C for 1 hour with a shaking. Next, 20 μg of Proteinase K was added to the samples for incubation at 65°C overnight with thermoshaking.
DNA was isolated by performing a phenol/chloroform/isoamyl alcohol extraction to prepare the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit for Illumi-na (NEB, E7645).

value: lung

value: human lung epithelial cells


title: ChIP_INPUT_main_rep3


title: P27_pre_TCR

description:
Library name: P27_pre_TCR
10X Genomics


title: HCC95, H3K27ac(ChIP)

description: Library name: HCC95, H3K27ac


title: ChIP_INPUT_WT_rep3


title: mail1-ring1a-ring1b_RNA_rep2

value: mail1-1 ring1a-2 ring1b-3


title: mail1-ring1a-ring1b_RNA_rep1


title: HCC95, TP63(ChIP)

description: Library name: HCC95, TP63


title: ring1a-ring1b_RNA_rep2


title: mail1-ndx_RNA_rep2

value: mail1-1 ndx-7


title: P26_pre_TCR

description:
Library name: P26_pre_TCR
10X Genomics

source_name: Oral cavity

value: Oral cavity


title: ChIP_INPUT_WT_rep4

value: 14-day-old seedlings


title: HCC95, SOX2(ChIP)

description: Library name: HCC95, SOX2


title: mail1-ndx_RNA_rep1


title: P25_post_TCR

description:
Library name: P25_post_TCR
10X Genomics


title: ChIP_H3K27me3-Ab_main_rep3


title: ChIP_H3K27me3-Ab_WT_rep3


title: mail1_RNA_rep2


title: P25_pre_TCR

description:
Library name: P25_pre_TCR
10X Genomics


title: HCC95, siKLF5b, rep1

description: Library name: siKLF5b, rep1


title: ndx-7_RNA_rep2


title: HCC95(Input)

description: Library name: HCC95, input


title: MDA-MB-231 cells, FLAG-tagged RBMS3, biol rep 1

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: Library name: RBMS3-1

data_processing:
Raw sequencing data from RBMS3-1 and RBMS3-2 samples were first processed by appending unique molecular identifiers (UMIs) to reads using a custom Python script (append_umi.py)
The processed reads were then analyzed using the CLIP Tool Kit (CTK) pipeline. The CTK pipeline included alignment to the human reference genome (hg38), filtering, and peak calling. CIMS (Crosslinking-Induced Mutation Sites) analysis was performed to identify nucleotide deletions that represent direct protein-RNA crosslinking sites. These analyses resulted in 27,706 high-confidence RBMS3 binding sites (FDR < 10%, fold change > 10) that were stored in the BED format file RBMS3_eclairCLIP.pool.tag.uniq.del.CIMS.fdr10.f10.bed.
Assembly: hg38
Supplementary files format and content: bed file with CIMS CLIP peaks from both replicates

growth_protocol: MDA-MB-231 cells RBMS3 were maintained in DMEM supplemented with 10% FBS and antibiotics at 37C and 5% CO2.

extract_protocol:
First, cells were irradiated using a 254nm UV-crosslinker at 400mJ/cm2. Cells were then lysed on ice before Immunoprecipitaiton of RNA-RBP complexes with FLAG Magnetic Agarose Beads (Pierce, Anti-DYKDDDDK).
Library preparation was performed as detailed in: Integrative analysis of mRNA stability regulation uncovers a metastasis-suppressive program in breast cancer. Heather Karner, Tabea Mittmann, Vicky W. Chen, Ashir A. Borah, Andreas Langen, Hassan Yousefi, Lisa Fish, Balyn W. Zaro, Albertas Navickas, Hani Goodarzi bioRxiv 2025.06.06.658309; doi: https://doi.org/10.1101/2025.06.06.658309

value: Breast cancer cells

value: FLAG-tagged RBMS3


title: mail1_RNA_rep1

value: 12-day-old seedlings


title: P24_post_TCR

description:
Library name: P24_post_TCR
10X Genomics

source_name: Larynx

value: Larynx

value: negative

value: D+T


title: H520, H3K27ac, rep2(ChIP)

description: Library name: H520, H3K27ac, rep2


title: MDA-MB-231 cells, DNA, shRBMS3-C, biol rep 3

description: Library name: shRBMS3-C-DNA-3

data_processing:
We first collated sequence reads with identical sequences using the fastq2collapse.pl program (CTK tools) to remove PCR duplicates, generating collapsed FASTQ files. UMIs were extracted from these collapsed sequences using UMI-tools. The adapter sequence (TGGTCTGGATCCACCGGTCCGGT) was then removed from the UMI-extracted reads using cutadapt (parameters: --trimmed-only -e 0.2 -g TGGTCTGGATCCACCGGTCCGGT -m 25), retaining only reads that contained the adapter and were at least 25 nucleotides long after trimming.
The processed RNA reads were then reverse-complemented using seqkit to align them with the reference sequences. For DNA libraries, a similar processing pipeline was used, but with a different adapter sequence (GTGGTCTGGATCCACCGGTCCGGTTTA), and a minimum length filter of 35 nucleotides.
A reference sequence file containing all candidate regulatory elements was indexed using BWA. Both RNA and DNA processed reads were aligned to this reference using BWA-MEM. Aligned reads were sorted and indexed using SAMtools. For RNA libraries, we performed UMI-based deduplication to account for PCR duplicates by collapsing reads with identical UMIs mapping to the same position using UMICollapse (parameters: -k 1 --algo adj --merge avgqual). Counts for each candidate regulatory element were obtained by extracting the reference sequence names from the alignment files and counting their occurrences using SAMtools and standard Unix tools.
Assembly: hg38
Supplementary files format and content: text file with raw counts of each candidate regulatory element for all samples

growth_protocol: MDA-MB-231 cells were grown in DMEM supplemented with 10% FBS and antibiotics at 37C and 5%CO2.

extract_protocol:
DNA and RNA co-extraction were performed using the Quick DNA/RNA kit (Zymo) with DNAse I digestion for RNA samples.
Libraries were prepared as detailed in: Khoroshkin, M., Asarnow, D., Zhou, S. et al. A systematic search for RNA structural switches across the human transcriptome. Nat Methods 21, 1634–1645 (2024). https://doi.org/10.1038/s41592-024-02335-1

treatment_protocol: RBMS3 knockdown and control cells were subject to lentiviral transduction with the MPRA reporter library of RBMS3 binding sites. After 72h, cells were sorted on for expression of mCherry and ~300k cells per replicate were immediately collected for RNA and DNA extraction.

value: RBMS3 KD2

value: Transfection with RBMS3-reporter library


title: HCC95, GRHL2(ChIP)

description: Library name: HCC95, GRHL2


title: P24_pre_TCR

description:
Library name: P24_pre_TCR
10X Genomics


title: P26_post_TCR

description:
Library name: P26_post_TCR
10X Genomics

value: D


title: MDA-MB-231 cells, DNA, shRBMS3-C, biol rep 2

description: Library name: shRBMS3-C-DNA-2


title: WT_RNA_rep1


title: P23_post_TCR

description:
Library name: P23_post_TCR
10X Genomics

value: Oropharynx

value: positive


title: H520(Input)

description: Library name: H520, input

value: lung


title: W53_KO1_leaf_Rep

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads using Trimmomatic.
The processed reads were aligned to the rice genome using HISAT2.
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Assembly: Oryza sativa japonica nipponbare genome – IRGSP1
Supplementary files format and content: Text delimited files including FPKM for each sample.

organism: Oryza sativa Indica Group

source_name: Six-week-old leaf

growth_protocol: The plants were grown in green house with natural day-night cycles with temperature maintained around 28 degrees celsius.

extract_protocol:
Total RNA was isolated from leaves using TRIzol method.
Libraries were prepared for sequencing using standard Novaseq protocols. The kit used is NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalog no-E7765L) and the adapter sequences are Read 1- AGATCGGAAGAGCACACGTCTGAACTCCAGTCA and for read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: For OsPep2 and PSK treatment, 2 cm leaf strips were maintained overnight in sterile water to wash away residual wound signals. Peptides were dissolved in water and treatment was given in six well plates. Wounding was performed on six-week-old leaves as described in the text.

value: Six-week-old leaf

value: Rice, Indica, Pusa Basmati 1 (PB1), WRKY53-KO1


title: H226(Input)

description: Library name: H226, input

value: human lung epithelial cells


title: MDA-MB-231 cells, FLAG-tagged RBMS3, biol rep 2

description: Library name: RBMS3-2


title: H520, H3K27ac, rep1(ChIP)

description: Library name: H520, H3K27ac, rep1


title: MDA-MB-231 cells, DNA, shRBMS3-B, biol rep 2

description: Library name: shRBMS3-B-DNA-2

value: RBMS3 KD1


title: H226, H3K27ac, rep2(ChIP)

description: Library name: H226, H3K27ac, rep2


title: P22_post_TCR

description:
Library name: P22_post_TCR
10X Genomics

value: Oral cavity


title: MDA-MB-231 cells, DNA, shRBMS3-B, biol rep 1

description: Library name: shRBMS3-B-DNA-1

value: Breast cancer cells


title: P23_pre_TCR

description:
Library name: P23_pre_TCR
10X Genomics


title: W53_KO1_mock_Rep

source_name: Six-week-old leaf strips

value: Six-week-old leaf strips


title: H226, H3K27ac, rep1(ChIP)

description: Library name: H226, H3K27ac, rep1


title: BEAS-2B(Input)

description: Library name: BEAS-2B, input


title: MDA-MB-231 cells, DNA, shCTRL, biol rep 2

description: Library name: shCTRL-DNA-2

value: WT


title: W53_KO1_Pep2_2h_Rep


title: MDA-MB-231 cells, DNA, shCTRL, biol rep 3

description: Library name: shCTRL-DNA-3


title: P20_post_TCR

description:
Library name: P20_post_TCR
10X Genomics


title: MDA-MB-231 cells, DNA, shCTRL, biol rep 1

description: Library name: shCTRL-DNA-1


title: W53_KO1_mock


title: P22_pre_TCR

description:
Library name: P22_pre_TCR
10X Genomics


title: BEAS-2B, H3K27ac, rep2(ChIP)

description: Library name: BEAS-2B, H3K27ac, rep2


title: W53_KO1_Pep2_2h


title: P19_post_TCR

description:
Library name: P19_post_TCR
10X Genomics

value: Larynx


title: BEAS-2B, H3K27ac, rep1(ChIP)

description: Library name: BEAS-2B, H3K27ac, rep1


title: W53_KO1_Pep2_30min_Rep


title: MDA-MB-231 cells, DNA, shRBMS3-C, biol rep 1

description: Library name: shRBMS3-C-DNA-1


title: W53_KO1_leaf


title: P19_pre_TCR

description:
Library name: P19_pre_TCR
10X Genomics

value: negative


title: EoL-1 ATF3/JUN double knockout rep 3

city: Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: UNSW Sydney

description: Library name: EoL-1 ATF3/JUN double knockout rep 3

data_processing:
Read quality of the trimmed fastq files was assessed by FastQC v.0.11.9. Fastq files were then quantified using Salmon v1.6.0 in mapping-based mode using the partial hg38 transcriptome.
Assembly: hg38
Supplementary files format and content: salmon quantification output file (.sf)

growth_protocol: EoL-1 were incubated in a 37°C 5% CO2 water-jacketed incubator. EoL-1 cells were grown in RPMI 1640 (Gibco Life Technologies) supplemented with 10% Fetal Bovine Serum (Interpath Services Pty Ltd, Australia) and 1% Penicillin-Streptomycin-Glutamine (Gibco Life Technologies). The EoL-1 cell line was supplied by the European Collection of Cell Cultures (ECACC; Salisbury, United Kingdom) as catalogue number 94042252, and purchased from Sigma Aldrich.

extract_protocol:
For extraction of RNA from EoL-1 cells, cells were washed with PBS and then lysed and homogenized in TRI-Reagent (Sigma Aldrich) followed by phenol/chloroform extraction to isolate RNA. RNA was washed with isopropanol with added GlycoBlue Co-Precipitant (Invitrogen) and pelleted by centrifugation at 12,000 x g for 10 min at 4°C, the pellet was washed with 70% ethanol, before the RNA was pelleted by centrifugation at 7,500 x g for 5 min at 4°C. The pellet was dried at room temperature for 20 min and resuspended in 20 - 50 µL MQW.
Illumina Stranded mRNA Prep kit

treatment_protocol: CRISPR/Cas9 was used to generate ATF3 knockout EoL-1 cells

value: Eosinophil

value: ATF3/JUN double knockout


title: MDA-MB-231 cells, RNA, shRBMS3-C, biol rep 2

description: Library name: shRBMS3-C-RNA-2

value: RBMS3 KD2

value: Transfection with RBMS3-reporter library


title: W53_KO1_Pep2_30min


title: P18_post_TCR

description:
Library name: P18_post_TCR
10X Genomics

value: Oropharynx

value: D+T


title: EoL-1 ATF3/JUN double knockout rep 2

description: Library name: EoL-1 ATF3/JUN double knockout rep 2


title: MDA-MB-231 cells, RNA, shRBMS3-C, biol rep 1

description: Library name: shRBMS3-C-RNA-1


title: P18_pre_TCR

description:
Library name: P18_pre_TCR
10X Genomics

value: positive


title: W53_KO1_PSK_2h_Rep

value: PSK


title: MDA-MB-231 cells, RNA, shRBMS3-B, biol rep 2

description: Library name: shRBMS3-B-RNA-2


title: P20_pre_TCR

description:
Library name: P20_pre_TCR
10X Genomics


title: WT_RNA_rep2

value: 12-day-old seedlings


title: W53_KO1_PSK_2h

value: Rice, Indica, Pusa Basmati 1 (PB1), WRKY53-KO1


title: EoL-1 JUN knockout rep 3

description: Library name: EoL-1 JUN knockout rep 3

value: JUN knockout


title: W53_KO1_PSK_30min_Rep


title: MDA-MB-231 cells, RNA, shRBMS3-B, biol rep 1

description: Library name: shRBMS3-B-RNA-1

value: RBMS3 KD1


title: EoL-1 JUN knockout rep 2

description: Library name: EoL-1 JUN knockout rep 2


title: MDA-MB-231 cells, RNA, shCTRL, biol rep 3

description: Library name: shCTRL-RNA-3

value: Breast cancer cells


title: P33_post_GEX

description:
Library name: P33_post_GEX
10X Genomics

value: Hypopharynx


title: EoL-1 ATF3/JUN double knockout rep 1

description: Library name: EoL-1 ATF3/JUN double knockout rep 1


title: W53_KO1_PSK_30min

value: Six-week-old leaf strips


title: P33_pre_GEX

description:
Library name: P33_pre_GEX
10X Genomics


title: EoL-1 JUN knockout rep 1

description: Library name: EoL-1 JUN knockout rep 1


title: MDA-MB-231 cells, RNA, shCTRL, biol rep 2

description: Library name: shCTRL-RNA-2

value: WT


title: W53_KO1_unwounded_Rep

value: Six-week-old leaf


title: P32_pre_GEX

description:
Library name: P32_pre_GEX
10X Genomics

value: negative


title: MDA-MB-231 cells, RNA, shCTRL, biol rep 1

description: Library name: shCTRL-RNA-1


title: EoL-1 ATF3 knockout rep 3

description: Library name: EoL-1 ATF3 knockout rep 3

value: Eosinophil

value: ATF3 knockout


title: EoL-1 ATF3 knockout rep 2

description: Library name: EoL-1 ATF3 knockout rep 2


title: W53_KO1_unwounded


title: ZR-75-1 cells, biol rep 2

description: Library name: ZR-75-2

data_processing:
We first used Salmon (v0.14.1) to align the reads to the human transcriptome (gencode v28). Transcripts with average expression >1 TPM across the cell lines were selected for further analysis (i.e. transcripts that are ‘expressed’). Bowtie2 (v2.3.5) was then used to align reads to these annotated major isoforms. Samtools mpileup command was used next to generate read stacks, which were then processed to count the number of T to C conversions. For every gene, we required the coverage to be at least 10 reads at counted Ts, filtered abundant variant calls (as they imply germline variant rather than chemical conversion), and finally calculated a C to T ratio (allowing for a pseudo-count of 1). We filtered outlier transcripts, using the 3×IQR above or below median as thresholds. Note that biological replicates were combined at this stage by combining the counts prior to calculating the C to T ratio. Since the cells were pulsed with 4sU for 4hr, 4sU incorporation, and therefore the resulting C to T ratio, are driven by the rate of transcription. At steady state, decay rate is equal to transcription rate normalized by the steady state expression. So, we used this rule to estimate a decay rate (log transformed) for every gene across all cell lines, based on its SLAM-seq C to T ratio and its baseline expression (AU).
Assembly: hg38
Supplementary files format and content: text file with SLAM-Seq C to T ratios of every gene for all samples

growth_protocol: HCC1806, HCC38 and ZR-75-1 cell lines were maintained in RPMI-1640 supplemented with 10% FBS and antibiotics. MCF7, MDA-MB-231 and MDA-MB-453 cell lines were cultivated in DMEM supplemented with 10% FBS and antibiotics. All cell lines were incubated in humidified air at 37C and 5% CO2.

extract_protocol:
RNA was extracted using Trizol Reagent (Invitrogen) and Iodoacetamide labeling was performed using the SLAMseq Explorer and Kinetics Kit (Lexogen) while keeping samples protected from light.
Library construction was performed using the Quant-Seq 3' mRNA-Seq Library Prep Kit (Lexogen).

treatment_protocol: All cells were incubated with 100 µM 4-thiouridine (4sU) added in their respective culture medium for 4 hours before washing 2x with PBS and collecting cells.

value: 4-thiouridine (4sU)


title: P31_post_GEX

description:
Library name: P31_post_GEX
10X Genomics

value: Oropharynx


title: P31_pre_GEX

description:
Library name: P31_pre_GEX
10X Genomics

value: D+T


title: W53_KO1_wound_2h_Rep

value: Wounding


title: EoL-1 ATF3 knockout rep 1

description: Library name: EoL-1 ATF3 knockout rep 1


title: ZR-75-1 cells, biol rep 1

description: Library name: ZR-75-1


title: P8_post2_TCR

description:
Library name: P8_post2_TCR
10X Genomics

value: positive

value: D


title: W53_KO1_wound_2h

value: Rice, Indica, Pusa Basmati 1 (PB1), WRKY53-KO1


title: EoL-1 wild type rep 3

description: Library name: EoL-1 wild type rep 3

value: Wild type


title: MDA-MB-453 cells, biol rep 2

description: Library name: MDA-MB-453-2


title: MDA-MB-453 cells, biol rep 1

description: Library name: MDA-MB-453-1


title: P30_pre_GEX

description:
Library name: P30_pre_GEX
10X Genomics


title: EoL-1 wild type rep 2

description: Library name: EoL-1 wild type rep 2


title: W53_KO1_wound_12h_Rep


title: P29_post_GEX

description:
Library name: P29_post_GEX
10X Genomics


title: W53_KO1_wound_15min_Rep


title: EoL-1 wild type rep 1

description: Library name: EoL-1 wild type rep 1


title: MDA-MB-231 cells, biol rep 2

description: Library name: MDA-MB-231-2


title: P29_pre_GEX

description:
Library name: P29_pre_GEX
10X Genomics


title: MCF7, sciATAC-seq of untreated cycling cells

city: New York

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

data_processing:
Libraries were demultiplexed using custom scripts to assign reads to individual cells based on indices from PCR, ligation, and Tn5 combinatorial barcoding. BCL files were converted to fastq and demultiplexed with the bcl2fastq software (version 2.19.0), based on PCR libraries and their unique 10 bp index.
Fastq files were further demultiplexed by ligation adapter index with the cutadapt software (version 1.18): cutadapt -e 0.15 --no-indels -g file:P5_barcodes.fasta -o BC1_A1_ligation_{name}-1.fastq.gz -p BC1_A1_{name}_R1.fastq.gz BC1_A1_S1_R2_001.fastq.gz BC1_A1_S1_R1_001.fastq.gz. Finally, individual cells were demultiplexed from each library:ligation file based on tagmentation adapters found in the 5’ ends of read pairs: cutadapt -e 0.15 --no-indels -g ^file:$N5_barcode -G ^file:$N7_barcode -o BC1-{name1}-{name2}.1.fastq.gz -p BC1-{name1}-{name2}.2.fastq.gz. The remaining 19 bp of adapter sequence was trimmed from all reads: cutadapt -u 19 -o $OUTPUT_R1\.trimmed.fastq.gz $INPUT_R1. Reads were then aligned to the GRCh38 human genome using Bowtie2 with the following parameters: -k 4 -p 6 -X2000 --local --mm --seed 23
Cells were filtered based on 1) a read depth of at least 1,000 fragments, and 2) an overall alignment rate of 80%.
The SnapATAC2 (version 2.3.1) analysis framework was followed to generate the TSS enrichment score vs. unique fragments plot, perform doublet removal, dimensional reduction, and Leiden algorithm derived from Traag et al, 2019 (https://doi.org/10.1038/s41598-019-41695-z) clustering analysis.
Gene body accessibility was counted using Gencode v38 basic gene annotation, and subsequently used for visualizing gene accessibility as a proxy for expression after applying the MAGIC algorithm for imputation and data smoothing.
Assembly: hg38
Supplementary files format and content: Cycling_p5.bams.fragments.2672 are the genomic coordinates for fragments from each cell

source_name: Breast; Mammary gland

growth_protocol: MCF7 cells were cultured in 75 cm2 flasks in DMEM/F-12 supplemented with GlutaMAX (Gibco 10565018) at 37C and 5% CO2. Cells were subcultured at a 1:3 ratio every 3 days. Prior to their use, MCF7 cell identity was verified by STR profiling through LabCorp Cell Line Authentication service. For harvesting, flasks were washed with ice cold PBS then cells were dissociated with TrypLE Express enzyme.

extract_protocol:
Nuclei were extracted and single-cell indexing was performed following the EasySci-ATAC protocol, as described in Supplemental protocol 2 of Sziraki, et al., 2023: https://doi.org/10.1038/s41588-023-01572-y. Briefly, cells were resuspended in 1 mL Nuclei Isolation Buffer (NIB) + 0.1% IGEPAL CA-630 and filtered through a 40 µm filter. Nuclei were stained with Trypan Blue and counted with the EVE Automated Cell Counter; the final concentration was adjusted to 1,000 nuclei/µL using NIB.
For each barcode combination, 5,000 nuclei were mixed with 4 µL of barcoded Tn5 and tagmentation was carried out in a thermomixer at 55C for 10 minutes with gentle shaking at 350 RPM.  Following tagmentation, nuclei were put directly on ice to prevent over tagmentation, followed by addition of a stop buffer consisting of spermidine-EDTA. Nuclei were then pooled and redistributed to 96-wells to allow multiplexing via barcoded ligation, followed by a third round of pooling and redistribution to a final barcoding reaction via eight separately barcoded PCR amplifications for library preparation and sequencing on an Illumina NextSeq.

treatment_protocol: None.

value: Breast; Mammary gland

value: breast cancer cell line

value: wildtype


title: MDA-MB-231 cells, biol rep 1

description: Library name: MDA-MB-231-1

value: Breast cancer cells


title: W53_KO1_wound_15min


title: P28_post_GEX

description:
Library name: P28_post_GEX
10X Genomics


title: MCF7, H3K27me3, in-house pG-Tn5, replicate 2

data_processing:
Reads were aligned to hg38 genome using bowtie230 using the following parameters--end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700  for mapping of inserts 10-700 bp in length.
Duplicate reads, reads mapping to the mitochondrial genome and blacklisted regions were removed using picardtools to generate the final bam file. Bam files were then sorted using picardtools.
Using bedtools, bam files were converted to bedpe files which were then converted to bedgraph format. Bedgraph files were used as input into SEACR peak caller, where peaks were called with parameters specified to non-normalized and stringent threshold set to 0.01.
Technical replicates were combined into a single bam file using samtools merge command. Bigwig files were generated using deepTools’ bamCoverage command with the following parameters to normalize:  --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads.  Afterwards, a master peak set between technical replicates was created keeping only peaks that overlapped with each other between technical replicates and merging overlapping peaks into a single peak. A master non-redundant peak set was created by merging overlapping peaks of master peaksets from different Tn5 conditions (Epicypher’s pAG-Tn5 vs in house pG-Tn5) using GenomicRanges package in R.
Assembly: hg38
Supplementary files format and content: stringent.0.01.output.stringent.bed files are peaks called by SEACR
Supplementary files format and content: overlap.bed files are merged overlapping peaks betweeen replicates tagmented and profiled with the same enzyme Histone mark condition
Supplementary files format and content: bigwig files are coverage from merged replicates for Genome Browser visualization.
Library strategy: CUT&Tag

growth_protocol: MCF-7 cells were cultured in in 75 cm2 flasks DMEM/F-12 (ThermoFisher 10565018) supplemented with GlutaMAX (Gibco 10565018), 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin at 37 °C and 5% CO2. Cells were subcultured at a 1:3 ratio every 3 days. Prior to their use, MCF7 cell identity was verified by STR profiling through LabCorp Cell Line Authentication service.

extract_protocol:
MCF7 cells were briefly centrifuged followed by incubation with Nuclear Extraction buffer on ice for 10 minutes. After resuspension in Wash Buffer, nuclei were slow frozen in cryogenic vials with 10% DMSO for storage at –80 °C before resuming the rest of the protocol.
Approximately 100,000 cells were used per sample for overnight incubation with primary antibody (1:100 CST #9733T or 1:100 ab4729). Secondary antibody ( 1:100 ABIN101961) was incubated for 30 minutes at room temperature followed by addition of commercial pAG-Tn5 (EpiCypher SKU: 15-1017) or in-house pG-Tn5 preloaded with adapters. Phenol chloroform DNA extraction was performed using Qiagen’s Maxtract High Density phase-lock tubes. Libraries were PCR amplified for 12 cycles with Illumina i5 or i7 barcoded primers and Ampure XP beads were used for post-PCR cleanup.

treatment_protocol: None. Cycling cells were harvested


title: MCF7 cells, biol rep 2

description: Library name: MCF7-2

value: WT


title: MCF7, H3K27me3, in-house pG-Tn5, replicate 1


title: P28_pre_GEX

description:
Library name: P28_pre_GEX
10X Genomics


title: P30_post_GEX

description:
Library name: P30_post_GEX
10X Genomics


title: MCF7 cells, biol rep 1

description: Library name: MCF7-1


title: HCC38 cells, biol rep 2

description: Library name: HCC38-2


title: W53_KO1_wound_30min

value: Six-week-old leaf


title: P27_post_GEX

description:
Library name: P27_post_GEX
10X Genomics


title: MCF7, H3K27me3, Epicypher pAG-Tn5, replicate 2


title: W53_KO2_leaf_Rep

value: Rice, Indica, Pusa Basmati 1 (PB1), WRKY53-KO2


title: HCC38 cells, biol rep 1

description: Library name: HCC38-1


title: W53_KO1_wound_12h


title: MCF7, H3K27me3, Epicypher pAG-Tn5, replicate 1


title: P26_post_GEX

description:
Library name: P26_post_GEX
10X Genomics

value: Oral cavity

value: negative


title: MCF7, H3K27ac, in-house pG-Tn5, replicate 2

value: H3K27ac (Abcam ab4729)


title: MCF7, H3K27ac, in-house pG-Tn5, replicate 1


title: HCC1806 cells, biol rep 1

description: Library name: HCC1806-1

value: 4-thiouridine (4sU)


title: W53_KO2_mock

value: Six-week-old leaf strips


title: P26_pre_GEX

description:
Library name: P26_pre_GEX
10X Genomics


title: W53_KO2_mock_Rep


title: MCF7, H3K27ac, Epicypher pAG-Tn5, replicate 2


title: P25_post_GEX

description:
Library name: P25_post_GEX
10X Genomics

value: Oropharynx

value: D+T


title: W53_KO2_leaf


title: Colon tumour, APC-KI, week6, recovered 3

city: Singapore

first: Christiane

last: Ruedl

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Data was processed with nf-core/rnaseq (v1.4.2) pipeline
Sequence reads were trimmed with TrimGalore! (v0.6.4) and Cutadapt (v2.5)
Trimmed sequence reads were mapped to GrCM38/mm10 with STAR (vSTAR_2.6.1d)
Read count normalization was performed with DeSeq2 (v1.37.6)
Assembly: GrCM38/mm10
Supplementary files format and content: Matrix with merged gene counts of all samples as a tab delimited text file

source_name: colon tumour

extract_protocol:
Colon tumours were pinched from underlying muscle layer and homogenised in Trizol (Invitrogen), before purifying total RNA with phase seperation and RNAsimple Total RNA Kit (Tiangen). DNase I digest was performed on-column.
cDNA libraries for RNA-seq were prepared with Illumina TruSeq Stranded mRNA HT Sample prep Kit

value: colon tumour

value: 6 weeks

tag: group

value: repressed Tcf7l2 expression

value: APC-KI

value: 100 mg/kg doxycycline in food pellets


title: W53_KO2_Pep2_2h_Rep


title: P25_pre_GEX

description:
Library name: P25_pre_GEX
10X Genomics

value: positive


title: MDA-MB-231 cells, RNA, shRBMS3-C, biol rep 3

description: Library name: shRBMS3-C-RNA-3

value: Breast cancer cells

value: RBMS3 KD2

value: Transfection with RBMS3-reporter library


title: W53_KO1_wound_30min_Rep

value: Six-week-old leaf

value: Rice, Indica, Pusa Basmati 1 (PB1), WRKY53-KO1

value: Wounding


title: MCF7, H3K27ac, Epicypher pAG-Tn5, replicate 1

value: Breast; Mammary gland

value: breast cancer cell line

value: wildtype

value: H3K27ac (Abcam ab4729)


title: P24_post_GEX

description:
Library name: P24_post_GEX
10X Genomics

value: Larynx

value: negative

value: D+T


title: Colon tumour, APC-KI, week6, recovered 2

value: colon tumour

value: 6 weeks

value: repressed Tcf7l2 expression


title: MCF7, ATAC-seq with in-house pG-Tn5 Lot 2, replicate 2

data_processing:
Reads were aligned using -X 2000 parameters on bowtie2. Reads were shifted to account for Tn5 insertion bias using deepTools alignmentSieve command with –-ATACshift parameter set.
Duplicate reads, reads mapping to the mitochondrial genome and blacklisted regions were removed using picardtools to generate the final bam file. Bam files were then sorted using picardtools.
Peaks were called from bam files with MACS2 using the following parameters -B --SPMR --nomodel --shift -37 --extsize 73 --nolambda --keep-dup all --call-summits --slocal 10000. Next, a non-redundent master peakset was made by intersecting technical replicate narrowPeaks in bedtools, then merging intersected narrowPeak files in bedtools for each cell type. Cell-type masterpeak sets were merged in bedtools to create a non-redundant peakset across all ATAC samples.
Technical replicates were combined into a single bam file using samtools merge command. Bigwig files were generated using deepTools’ bamCoverage command with the following parameters to normalize: --binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads
Assembly: hg38
Supplementary files format and content: atac_peaks.narrowPeak files are peaks called by MACS2
Supplementary files format and content: overlap.bed files are merged overlapping peaks betweeen replicates tagmented with the same enzyme
Supplementary files format and content: bigwig files are coverage from merged replicates for Genome Browser visualization.

extract_protocol:
Prior to tagmentation, cells were treated in culture medium with DNase (Worthington cat# LS002007) at a final concentration of 200 U/mL at 37 °C for 30 mins, then washed twice with PBS at 500g, RT.
For Illumina enzyme tagmented material, 2.5 µL of Illumina TDE1 enzyme was used. K562 transposome titration experiment: pG-Tn5 tagmentation was titrated with the following amounts of loaded transposome: 1.0, 2.5, 5.0, 7.0 µL. Libraries were PCR amplified  with Illumina i5 or i7 barcoded primers, with 7 cycles of PCR were performed during library preparation for the K562 experiment and 8 cycles performed during library preparation for the MCF7 experiment.


title: W53_KO2_Pep2_2h

value: Six-week-old leaf strips

value: Rice, Indica, Pusa Basmati 1 (PB1), WRKY53-KO2


title: P27_pre_GEX

description:
Library name: P27_pre_GEX
10X Genomics

value: Oropharynx

value: positive

value: D


title: W53_KO2_Pep2_30min_Rep


title: HCC1806 cells, biol rep 2

description: Library name: HCC1806-2

value: Breast cancer cells

value: WT

value: 4-thiouridine (4sU)


title: P24_pre_GEX

description:
Library name: P24_pre_GEX
10X Genomics


title: Colon tumour, APC-WT, day10, cachectic 3

value: 10 days

value: endogenous Tcf7l2 expression

value: APC-WT

value: 100 mg/kg doxycycline in food pellets


title: W53_KO2_Pep2_30min


title: P23_post_GEX

description:
Library name: P23_post_GEX
10X Genomics


title: MCF7, ATAC-seq with in-house pG-Tn5 Lot 2, replicate 1

value: Breast; Mammary gland

value: breast cancer cell line

value: wildtype


title: Colon tumour, APC-WT, day10, cachectic 2

value: colon tumour


title: MCF7, ATAC-seq with in-house pG-Tn5 Lot 1, replicate 2


title: MCF7, ATAC-seq with in-house pG-Tn5 Lot 1, replicate 1


title: Colon tumour, APC-WT, day10, cachectic 1


title: P23_pre_GEX

description:
Library name: P23_pre_GEX
10X Genomics


title: P22_post_GEX

description:
Library name: P22_post_GEX
10X Genomics

value: Oral cavity

value: negative


title: WT_PB1_leaf_Rep

value: Six-week-old leaf

value: Rice, Indica, Pusa Basmati 1 (PB1)


title: WT_PB1_leaf


title: MCF7, ATAC-seq with Illumina TDE1, replicate 2


title: Gallus gallus, retina, rep1

city: guangzhou

first: Zhibin

last: Li

address: tianhe road 600

institute: The Third Affiliated Hospital of Sun Yat-Sen University

data_processing:
Raw data were filtered using a custom script in Cell Ranger v3.0.2 (10X Genomics) and Seurat.
Assembly: GRCh38.p14,MFA1912RKSv2,F.catus_Fca126_mat1.0,UU_Cfam_GSD_1.0,CU_Pguttatus_1,ASM1899790v1,HZGC01,Bangor_MerUng_6.1,serCan2020,bMelUnd1.mat.Z,ASM2559416v1,ASM1176430v1.1,mEriEur2.1,mRatBN7.2,bGalGal1.mat.broiler.GRCg7b,Oreochromis_mossambicus_EIV1,ZJU1.0,GRCm39,Sscrofa11.1,pvi1.1,CAS_Tse_1.0,Cavpor3.0,BCM_Maur_2.0,AmbMex60DD.
Supplementary files format and content: Tab-separated values files and matrix files.

molecule: nuclear RNA

organism: Gallus gallus

extract_protocol:
Eyeballs were excised and preserved in ice-cold, oxygenated Hanks Balanced Salt Solution (HBSS). Using fine scissors, the cornea was removed with a circular incision along the ora serrata. The lens and vitreous body were then extracted as thoroughly as possible. The detachment of the retina from the scleral cup was performed using ophthalmic forceps, followed by the careful removal of any retinal pigment epithelium (RPE) adhering to the retina. The isolated retina was washed once with fresh HBSS and immediately frozen in liquid nitrogen. For subsequent dissociation, the samples were transported on dry ice. The dissociated retinal tissue was washed with phosphate-buffered saline (PBS) and cut into smaller pieces, followed by the addition of 100 μL of precooled 0.1 × Lysis Buffer, thorough mixing, and incubation on ice for 5 min. The sample was then washed with 1 mL of precooled wash buffer, and cell debris and larger tissues were removed using 40-μm MACS Smart Strainer filtration. The sample was then centrifuged at 4 °C and 500 ×g for 5 min, after which the supernatant without nuclear particles was discarded. The sample underwent three wash cycles with wash buffer. The pellet was resuspended on ice in cooled, diluted nuclei buffer. Nuclear concentration was determined using a Countess II FL automatic cell counter, ensuring the nuclear suspension concentration was within the appropriate range.
The human retinal cells underwent library construction using a 10X Chromium Single-Cell 3’ Library Kit v3 (PN-1000078) following the guidelines provided by the manufacturer.The other 24 retina cells underwent library construction using DNBelab C4.

value: Retina


title: P22_pre_GEX

description:
Library name: P22_pre_GEX
10X Genomics

value: D


title: MCF7, ATAC-seq with Illumina TDE1, replicate 1


title: WT_PB1_Rep

data_processing:
Adaptor trimming was performed using cutadapt.
The reads obtained were trimmed using cutadapt and aligned to IRGSP1 rice genome with parameters -q -v 3 -k 1 -y -a --best –strata
The alignment files are converted to coverage files using bam coverage tool of Deeptools with the 5bp bin size.
Assembly: Oryza sativa japonica Nipponbare genome – IRGSP1
Supplementary files format and content: The processed coverage files of the ChIP-seq alignments are provided in bigwig format.

growth_protocol: The plants were grown in small pots in greenhouse under natural day light conditions at 28 degree celsius

extract_protocol:
Snap frozen samples were ground into powder and nuclei were extracted. Sheared chromatin from all the treated samples and control samples were used for immunoprecipitation using GFP trap beads from chromotek. Washes, elution, de-crosslinking and DNA  purification was done as described in the manuscript. The purified DNA was taken for library preparation.
The library was prepared using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (Catalog no-E7103L). Adapter sequences used for sequencing: Read1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA Read2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

treatment_protocol: Leaf strips of six-week-old plants were maintained in sterile water overnight and the peptide treatment was administered in six well plates.

value: Six-week-old leaf strips


title: parental101_3

data_processing:
Reads were aligned to a combined reference that consists of the concatenation of Mus musculus and Candida albicans. As mouse reference GRCm39 builds was used. As Candida reference, the SC5314_Assembly22 was used.
Expression values were computed using featureCounts, separate files for the mouse and the candida genes were generated.
Assembly: GRCm39 build was used. Gene annotation were from GENCODE Release M26.
Supplementary files format and content: Txt files with read counts; The files hold the mouse gene counts (.txt) and the candida genes (_candida.txt).

organism: Candida albicans

source_name: (pure yeast cell culture)

extract_protocol:
Initial step of isolation of total RNA from liquid YPD culture and murine tongue tissue was performed using TRI reagent (Sigma-Aldrich) according to the manufacturer’s protocol with the modification that the tissue was homogenized with steel ball using a TissueLyzer (Qiagen) for 6 minutes at 25 Hz and after homogenized with 0.5mm glass beads for 2 cycles of 2 minutes intercalated with 30 seconds of colling on ice before extraction of the nucleic acids with chloroform. After the TRI reagent/chloroform separation, the RNA extraction was performed using Direct-zol RNA MiniPrep Plus Kit (Qiagen) following manufacturer's protocol.
Illumina Truseq Total RNA (ribosomal depletion)

value: (pure yeast cell culture)

value: strain 101

value: Fungus grown overnight in 10 ml YPD broth


title: Colon tumour, APC-KI, week6, recovered 1

value: 6 weeks

value: repressed Tcf7l2 expression

value: APC-KI


title: WT_PB1


title: P20_post_GEX

description:
Library name: P20_post_GEX
10X Genomics

value: Oropharynx

value: positive

value: D+T


title: parental101_2


title: K562, ATAC-seq with 2.5uL Illumina's Tn5, replicate 3

source_name: Bone; Marrow

value: Bone; Marrow

value: immortalized myelogenous leukemia cell line

value: wildtype


title: K562, ATAC-seq with 2.5uL Illumina's Tn5, replicate 2


title: WRKY53-GFP_Pep2_30min_Rep


title: P20_pre_GEX

description:
Library name: P20_pre_GEX
10X Genomics


title: K562, ATAC-seq with 2.5uL Illumina TDE1, replicate 1


title: WRKY53-GFP_Pep2_30min


title: Mus musculus, retina, rep2


title: WRKY53-GFP_Pep2_2h_Rep


title: P19_post_GEX

description:
Library name: P19_post_GEX
10X Genomics

value: Larynx

value: negative


title: WRKY53-GFP_Pep2_2h

value: Rice, Indica, Pusa Basmati 1 (PB1)


title: P19_pre_GEX

description:
Library name: P19_pre_GEX
10X Genomics


title: K562, ATAC-seq with 7.5uL in-house pG-Tn5, replicate 3


title: P18_post_GEX

description:
Library name: P18_post_GEX
10X Genomics


title: K562, ATAC-seq with 7.5uL in-house pG-Tn5, replicate 2


title: WRKY53-GFP_normal_Rep


title: Tamias sibiricus, retina, rep1

organism: Tamias sibiricus

value: Retina


title: WRKY53-GFP_normal

value: Six-week-old leaf strips


title: K562, ATAC-seq with 7.5uL in-house pG-Tn5, replicate 1


title: Channa argus, retina, rep1

organism: Channa argus


title: P18_pre_GEX

description:
Library name: P18_pre_GEX
10X Genomics


title: K562, ATAC-seq with 5uL in-house pG-Tn5, replicate 3


title: P16_post_GEX

description:
Library name: P16_post_GEX
10X Genomics

value: D


title: P16_pre_GEX

description:
Library name: P16_pre_GEX
10X Genomics


title: Mossambicus, retina, rep1

organism: Oreochromis mossambicus


title: WRKY53-GFP_mock_Rep


title: Pogona vitticeps, retina, rep1

organism: Pogona vitticeps


title: WRKY53-GFP_mock


title: oreochromis, retina, rep1

city: guagnzhou

address: tianhe

description: Library name: AM3G1174

data_processing:
Raw data were filtered using a custom script in Cell Ranger v3.0.2 (10X Genomics).
Assembly: F.catus_Fca126_mat1.0, Oreochromis_mossambicus_EIV1, ASM1899790v1, bMelUnd1.mat.Z, bGalGal1.mat.broiler.GRCg7b, ZJU1.0
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Oreochromis

extract_protocol:
Eyeballs were excised and preserved in ice-cold, oxygenated Hanks Balanced Salt Solution (HBSS). Using fine scissors, the cornea was removed with a circular incision along the ora serrata. The lens and vitreous body were then extracted as thoroughly as possible. The detachment of the retina from the scleral cup was performed using ophthalmic forceps, followed by the careful removal of any retinal pigment epithelium (RPE) adhering to the retina. The isolated retina was washed once with fresh HBSS and immediately frozen in liquid nitrogen. For subsequent dissociation, the samples were transported on dry ice. The dissociated retinal tissue was washed with phosphate-buffered saline (PBS) and cut into smaller pieces, followed by the addition of 100 μL of precooled 0.1 × Lysis Buffer, thorough mixing, and incubation on ice for 5 min. The sample was then washed with 1 mL of precooled wash buffer, and cell debris and larger tissues were removed using 40-μm MACS Smart Strainer filtration. The sample was then centrifuged at 4 °C and 500 ×g for 5 min, after which the supernatant without nuclear particles was discarded. The sample underwent three wash cycles with wash buffer. The pellet was resuspended on ice in cooled, diluted nuclei buffer. Nuclear concentration was determined using a Countess II FL automatic cell counter, ensuring the nuclear suspension concentration was within the appropriate range.
The retinal cells underwent library construction using a 10X Chromium Single-Cell 3’ Library Kit v3 (PN-1000078) following the guidelines provided by the manufacturer.

value: Retinal cells


title: P15_post_GEX

description:
Library name: P15_post_GEX
10X Genomics


title: K562, ATAC-seq with 5uL in-house pG-Tn5, replicate 1


title: Input_WT_PB1_Rep


title: Mus musculus, retina, rep1


title: P15_pre_GEX

description:
Library name: P15_pre_GEX
10X Genomics


title: K562, ATAC-seq with 2.5uL in-house pG-Tn5, replicate 3


title: Melopsittacus undulatus, retina, rep1

description: Library name: AM3G1173

organism: Melopsittacus undulatus


title: K562, ATAC-seq with 2.5uL in-house pG-Tn5, replicate 2


title: Input_WT_PB1


title: P14_post_GEX

description:
Library name: P14_post_GEX
10X Genomics


title: Melopsittacus undulatus, retina, rep1


title: rim101 strain T=60 min (pH 8.0), replicate 2

city: CERDANYOLA DEL VALLES

first: JOAQUIN

last: ARINO

state: Barcelona

address: ED. IBB

department: Biochemistry & Mol. Biol.

country: Spain

institute: UNIVERSITAT AUTONOMA BARCELONA

description: Library name: rim101_T60_rep2

data_processing:
Mapping of fastq files to generate SAM files was carried out with the Bowtie2 software (Langmead & Salzberg, 2012) in local / sensitive mode against the GCA_000027005.1 assembly (an average of 92.3% of mapped reads).
The SeqMonk software v1.48.1 (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was employed to analyze the SAM files. Mapped reads were counted using the RNA-Seq pipeline on gene features and differentially expressed genes with respect to time zero were identified using the built-in EdgeR package
Assembly: GCA_000027005.1
Supplementary files format and content: file "All_Datasets_RPKM.xlsx", excel file with "Reads Per Kilobase Million" data for each sample.
Supplementary files format and content: file "Table S3 full Transcriptomics TC.xlsx", excel file conaining the diferentially expressed genes for each condition as defined by the EdgeR package (fold-change log2 >1 or <-1 and p-value < 0.01) plus functional annotations

organism: Komagataella phaffii

source_name: whole cell

growth_protocol: K. phaffii X-33 and its isogenic PJA-001 (crz1) and PJA-007 (rim101) derivatives were grown at 28 °C in YP medium (10 g/L yeast extract, 20 g/L peptone) supplemented with a 20 g/L of glycerol (YP-Gly)

extract_protocol:
Total RNA was extracted with the Ribo Pure™-Yeast kit (Ambion) following the manufacturer’s instructions. The quality was assessed by capillary electrophoresis in a Bioanalyzer equipment and RNA amounts quantified by measuring the A260 in a Nanodrop ND-1000 Spectrophotometer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP (non-directional library). The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification, and was checked by Qubit™ assay (Thermofisher) and real-time PCR for quantification and size distribution monitored with a Bioanalyzer.

treatment_protocol: For the analysis of the transcriptional response of K. phaffii to alkalinization of the medium cells were grown overnight on YP-Gly medium, and then cultures were diluted in 100 ml of fresh medium at OD600=0.2 and grown until the OD600 of the cultures reached around 0.6. Then two 50 ml-aliquots were centrifuged (5 min at 1000xg). One aliquot was resuspended in the same volume of  fresh YPGly medium plus 50 mM TAPS pH 5.5 (control cells) or in YPGly supplemented with 50 mM TAPS adjusted to pH 8.0 (stressed cells). Samples (15 ml) were taken immediately after resuspension in medium at pH 5.5 (time=0) and, for each stressed culture, after 15, 30 and 60 min. In all cases samples were placed on ice and immediately centrifuged at 4 °C.

value: whole cell


title: K562, ATAC-seq with 2.5uL in-house pG-Tn5, replicate 1


title: P14_pre_GEX

description:
Library name: P14_pre_GEX
10X Genomics


title: P13_post_GEX

description:
Library name: P13_post_GEX
10X Genomics

value: Hypopharynx


title: K562, ATAC-seq with 1uL in-house pG-Tn5, replicate 2


title: Serinus canaria, retina, rep1

organism: Serinus canaria


title: rim101 strain T=60 min (pH 8.0), replicate 1

description: Library name: rim101_T60_rep1


title: Trachemys scripta elegans, retina, rep1

organism: Trachemys scripta elegans


title: K562, ATAC-seq with 5uL in-house pG-Tn5, replicate 2


title: rim101 strain T=30 min (pH 8.0), replicate 2

description: Library name: rim101_T30_rep2


title: rim101 strain T=30 min (pH 8.0), replicate 1

description: Library name: rim101_T30_rep1


title: K562, ATAC-seq with 1uL in-house pG-Tn5, replicate 1


title: P12_post_GEX

description:
Library name: P12_post_GEX
10X Genomics


title: Macaca fascicularis, retina, rep1

organism: Macaca fascicularis


title: rim101 strain T=15 min (pH 8.0), replicate 2

description: Library name: rim101_T15_rep2


title: Meriones unguiculatus, retina, rep1

organism: Meriones unguiculatus


title: P12_pre_GEX

description:
Library name: P12_pre_GEX
10X Genomics


title: Ctenopharyngodon idella, retina, rep1

organism: Ctenopharyngodon idella


title: rim101 strain T=15 min (pH 8.0), replicate 1

description: Library name: rim101_T15_rep1


title: skin, wild-type, rep2

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

institute: CSIC

description: Library name: Sample5_WT

data_processing:
Quality control of RNA-seq raw data was performed using FastQC v0.12.0 (Andrews, 2010). High-quality clean data were obtained by removing adapters and low-quality reads using fastp v0.20.0 (Chen, 2023). Only reads longer than 100 bp were aligned to the Danio rerio reference genome (GCA_000002035.4) using STAR v2.7.9a (Dobin et al., 2013), followed by gene count assignment with HTseq v0.10.0 (Anders, Pyl and Huber, 2015). Genes with low counts were excluded from further analysis using the filterByExpr function in the R package edgeR v4.0.16 (Chen et al., 2024).
Assembly: GCA_000002035.4
Supplementary files format and content: txt file includes gene count assignment using HTseq v0.10.0

organism: Danio rerio

source_name: skin

extract_protocol:
A maximum of 30 mg of skin tissue was employed for total RNA extraction from each individual using the RNeasy Mini Kit (QIAGEN GmbH, Germany), in accordance with the manufacturer's instructions. The integrity of the extracted RNA was verified to ensure that the RNA integrity number (RIN) was greater than 8.
Strand-specific mRNA libraries were then sequenced on an Illumina NovaSeq X Plus platform at Novogene CO (China), generating paired-end reads of 150 base pairs (bp) in length (23M reads on average).

value: skin

value: wild-type


title: P11_post_GEX

description:
Library name: P11_post_GEX
10X Genomics

organism: Homo sapiens

extract_protocol:
We collected fresh tumor tissues on the day of surgery, which were mechanically and enzymatically dissociated using a gentleMACS dissociator (Miltenyi Biotec, Gladbach Bergisch, Germany, Cat#130-093-235) and the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929), following the manufacturer's instructions. After incubation for 1 hour at 37℃, the resuspended samples were filtered through a 70-µm MACS SmartStrainer (Miltenyi Biotec, Cat#130-098-462) into RPMI-1640 medium (Corning, Inc., Corning, NY, USA) supplemented with 10% fetal bovine serum (Biowest, Riverside, MO, USA) and centrifuged at 300 × g for 10 minutes. The pellet was suspended in PBS containing 2% fetal bovine serum. Tissue-infiltrating lymphocytes were enriched using a Ficoll gradient (Sigma-Aldrich), and the resulting single-cell suspensions were subsequently counted using trypan blue.
Libraries were constructed using the Chromium controller, adhering to the protocol described in the 10x Chromium Next GEM Single Cell 5′ v2 Cell Surface Protein User Guide (CG000330). Initially, cell suspensions were diluted with nuclease-free water to achieve a target cell count of 10,000. These suspensions were then combined with a master mix and loaded with Single Cell 5′ Gel Beads and Partitioning Oil into a Next GEM Chip K. Within the droplets, RNA transcripts from individual cells were uniquely barcoded and reverse-transcribed. Following this, the cDNA molecules were pooled and subjected to PCR enrichment. The amplified cDNA underwent size selection for the 5′ Gene Expression libraries, V(D)J Enriched Libraries, and Cell Surface Protein libraries. For the Cell Surface Protein Library, the cDNA pool was enriched through index PCR. In the case of the V(D)J Enriched Library, the enriched cDNA pool was amplified through two rounds using specific primers. For the 5′ Gene Expression Library, the cDNA pool underwent end repair, addition of a single 'A' base, and ligation of adapters, followed by purification and PCR enrichment. The purified libraries were quantified using qPCR in accordance with the qPCR Quantification Protocol Guide (KAPA) and assessed for quality using the Agilent Technologies 4200 TapeStation. Finally, the libraries were sequenced on the HiSeq platform (Illumina) following the specified read length outlined in the user guide.

value: Oropharynx


title: skin, wild-type, rep3

description: Library name: Sample6_WT


title: rim101 strain T=0 (pH 5.5), replicate 2

description: Library name: rim101_T0_rep2


title: Atelerix algirus, retina, rep1

organism: Atelerix algirus


title: P11_pre_GEX

description:
Library name: P11_pre_GEX
10X Genomics

value: positive


title: Mustela putorius furo, retina, rep1

organism: Mustela putorius furo


title: skin, wild-type, rep1

description: Library name: Sample4_WT


title: skin, mc2rKO, rep3

description: Library name: Sample3_KO

value: mc2r knockout


title: P13_pre_GEX

description:
Library name: P13_pre_GEX
10X Genomics

value: D+T


title: Sus scrofa, retina, rep1

organism: Sus scrofa


title: skin, mc2rKO, rep2

description: Library name: Sample2_KO


title: Gallus gallus, retina, rep1

description: Library name: AM3G1172

organism: Gallus gallus


title: P9_pre_GEX

description:
Library name: P9_pre_GEX
10X Genomics


title: P9_post_GEX

description:
Library name: P9_post_GEX
10X Genomics


title: parental101_1

organism: Candida albicans

value: (pure yeast cell culture)

value: strain 101

value: Fungus grown overnight in 10 ml YPD broth


title: crz1 strain T=60 min (pH 8.0), replicate 1

description: Library name: crz1_T60_rep1


title: P8_post2_GEX

description:
Library name: P8_post2_GEX
10X Genomics


title: skin, mc2rKO, rep1

description: Library name: Sample1_KO


title: female kd ip, rep3

city: Shanghai

first: Guofeng

last: Cheng

state: Shanghai

address: #500, Zhennan Road, Shanghai

institute: Tongji University

description: Library name: Femalekd-3-ip

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore (parameters -q 25 --paired --length 50 --trim-n)
Trimmed sequence reads were mapped to S. japonicum reference genome (Assembly PRJNA520774) using STAR (parameters --outFilterMultimapNmax 30 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --genomeLoad NoSharedMemory --sjdbOverhang 140).Then, reads that mapped to ribosomal RNA (rRNA) were excluded.
Assembly: S. japonicum reference genome (Assembly PRJNA520774)
Supplementary files format and content: bed
Library strategy: MeRIP-Seq

organism: Schistosoma japonicum

source_name: Anhui

extract_protocol:
regular method for RNA isolation
regular protocol for library construction

tag: Sex

value: female

value: mettl3 KD


title: P8_post_GEX

description:
Library name: P8_post_GEX
10X Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GEX: GRCh 1.2.0 (TCR: GRCh38-alts-ensembl-3.1.0)
Supplementary files format and content: Tab separated value files and matrix files


title: crz1 strain T=60 min (pH 8.0), replicate 2

description: Library name: crz1_T60_rep2


title: Trem2-Treated-4

city: Indianapolis

first: Joshua

last: Kulas

state: IN

address: 1210 Waterway Blvd Ste. 2000

institute: IBRI

description: Library name: Trem2-4

data_processing:
Fastq files were aligned with STAR version 2.7.11a and quantified by the featureCounts program from Subread version 2.0.4. Ensembl IDs were converted to gene symbols wih biomaRt. DEGs were found by using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: a text file containing the raw counts matrix, csv files containing the relevant DESeq2 results tables with average normalized counts, log2FoldChange, and p-value

source_name: blood

extract_protocol:
Zymo Research Quick-RNA miniprep kit (Zymo Research, R1054, R1055)
Clontech SMARTer Stranded Total RNA-Seq Kit v3 – Pico

value: blood

value: IMG

value: microglia differentiated from iPSC-derived HPCs


title: female kd input, rep3

description: Library name: Femalekd-3-input


title: Trem2-Treated-3

description: Library name: Trem2-3


title: female kd ip, rep2

description: Library name: Femalekd-2-ip


title: P8_pre_GEX

description:
Library name: P8_pre_GEX
10X Genomics

value: D


title: Trem2-Treated-2

description: Library name: Trem2-2


title: crz1 strain T=30 min (pH 8.0), replicate 2

description: Library name: crz1_T30_rep2

value: whole cell


title: female kd input, rep2

description: Library name: Femalekd-2-input


title: crz1 strain T=30 min (pH 8.0), replicate 1

description: Library name: crz1_T30_rep1


title: Trem2-Treated-1

description: Library name: Trem2-1


title: crz1 strain T=60 min (pH 8.0), replicate 3

description: Library name: crz1_T60_rep3


title: rim101 strain T=0 (pH 5.5), replicate 1

description: Library name: rim101_T0_rep1


title: female kd ip, rep1

description: Library name: Femalekd-1-ip


title: crz1 strain T=15 min (pH 8.0), replicate 3

description: Library name: crz1_T15_rep3


title: crz1 strain T=15 min (pH 8.0), replicate 2

description: Library name: crz1_T15_rep2


title: female wt ip, rep3

description: Library name: 28F-3-ip

value: wt


title: Myelin-Treated-2

description: Library name: Myelin2


title: crz1 strain T=30 min (pH 8.0), replicate 3

description: Library name: crz1_T30_rep3


title: Myelin-Treated-1

description: Library name: Myelin1


title: P6_post_GEX

description:
Library name: P6_post_GEX
10X Genomics

value: negative


title: P4_post_GEX

description:
Library name: P4_post_GEX
10X Genomics

value: Larynx


title: P5_pre_GEX

description:
Library name: P5_pre_GEX
10X Genomics

value: Hypopharynx


title: P4_pre_GEX

description:
Library name: P4_pre_GEX
10X Genomics


title: female wt ip, rep2

description: Library name: 28F-2-ip


title: IgG-Treated-IMG-4

description: Library name: IgG4


title: crz1 strain T=0 (pH 5.5), replicate 2

description: Library name: crz1_T0_rep2


title: crz1 strain T=0 (pH 5.5), replicate 1

description: Library name: crz1_T0_rep1


title: IgG-Treated-IMG-3

description: Library name: IgG3


title: P2_post_GEX

description:
Library name: P2_post_GEX
10X Genomics

value: Oropharynx

value: positive


title: female wt ip, rep1

description: Library name: 28F-1-ip


title: wild-type strain T=60 min (pH 8.0), replicate 3

description: Library name: WT_T60_rep3

value: wild-type


title: IgG-Treated-IMG-2

description: Library name: IgG2


title: female kd input, rep1

description: Library name: Femalekd-1-input


title: Myelin-Treated-3

description: Library name: Myelin3


title: female wt input, rep1

description: Library name: 28F-1-input


title: P2_pre_GEX

description:
Library name: P2_pre_GEX
10X Genomics

value: D+T


title: P5_post_GEX

description:
Library name: P5_post_GEX
10X Genomics


title: crz1 strain T=15 min (pH 8.0), replicate 1

description: Library name: crz1_T15_rep1


title: wild-type strain T=60 min (pH 8.0), replicate 2

description: Library name: WT_T60_rep2


title: crz1 strain T=0 (pH 5.5), replicate 3

description: Library name: crz1_T0_rep3


title: P1_post_GEX

description:
Library name: P1_post_GEX
10X Genomics


title: female wt input, rep3

description: Library name: 28F-3-input


title: Control-IMG-4

description: Library name: Control4


title: wild-type strain T=60 min (pH 8.0), replicate 1

description: Library name: WT_T60_rep1


title: male wt ip, rep3

description: Library name: 28d-M-3-ip

value: male


title: P3_post_GEX

description:
Library name: P3_post_GEX
10X Genomics


title: P1_pre_GEX

description:
Library name: P1_pre_GEX
10X Genomics


title: wild-type strain T=30 min (pH 8.0), replicate 3

description: Library name: WT_T30_rep3


title: IgG-Treated-IMG-1

description: Library name: IgG1


title: Control-IMG-3

description: Library name: Control3


title: male wt ip, rep2

description: Library name: 28d-M-2-ip


title: wild-type strain T=30 min (pH 8.0), replicate 2

description: Library name: WT_T30_rep2


title: Control-IMG-2

description: Library name: Control2


title: female wt input, rep2

description: Library name: 28F-2-input


title: male wt input, rep2

description: Library name: 28d-M-2-input


title: Control-IMG-1

description: Library name: Control1


title: male wt ip, rep1

description: Library name: 28d-M-1-ip


title: wild-type strain T=15 min (pH 8.0), replicate 3

description: Library name: WT_T15_rep3