title: mRNA m6A IP WT rep2

description:
Library name: SAMPLES12
Normalized m6A matrix; Normalized mRNA expression matrix
mPWT-2

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
For comparison analysis, union peaks across samples were generated using bedtools, and reads under these peaks were counted using featureCounts95 for both IP and input samples. Raw counts were normalized to Counts Per Million (CPM). IP enrichment was calculated as CPMIP/CPMInput. A scaling factor (SF) was computed based on CPMIP m6A control RNA/CPMinput m6A control RNA. The final m6A quantification for each sample was calculated using IP enrichment/SF.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam
Library strategy: meRIP-seq

extract_protocol:
mRNA
RNA was fragmented using RNA Fragmentation Reagents (Invitrogen) by incubating at 70 °C for 6 minutes, followed by purification with the Oligo Clean & Concentrator Kit (Zymo Research).  RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) following the manufacturer’s protocol.


title: RNA-seq from 025-031 Pre Treatment Rep 3

status: Public on Mar 02 2026

type: SRA

city: Ann Arbor

first: Patrick

middle: J

last: Grohar

state: MI

address: 1600 Huron Parkway

country: USA

institute: University of Michigan Medical School

description:
Library name: 031_Pre3
E025_031Pre3

library_source: transcriptomic

data_processing:
Reads were aligned to hg38 with STAR v 2.7.3a and quantified with RSEM 1.3.3 using gencode 31 annotations. Following quantification, induced and repressed targets were identified and Log2FC was calculated.
Assembly: hg38
Supplementary files format and content: SARC037_expected_counts.txt: Expected count matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: Tumor

extract_protocol:
RNA was purified using mechanical disruption and column purification.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: tissue

value: Tumor


title: Downstream tandem hiPSC, uninduced, rep1

city: Cambridge

first: Christopher

middle: Patrick

last: Johnstone

state: Massachusetts

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description: Library name: downstream_tandem_uninduced_rep1

data_processing:
Reads trimmed with TrimGalore (v0.6.10) and aligned with Bowtie2 (v2.5.4) with setting --very-sensitive-local
Alignments deduplicated with MarkDuplicatesSpark / GATK4 (v4.6.2.0)
Reads that were duplicates, non-properly paired, or had a mapping quality under 3 were filtered with Sambamba (v1.0.1)
Reads aligned to the spike-in ERCC sequences to determine a cellular input normalization constant.
Normalized summary bigwigs computed with bamCoverage / deeptools (v3.5.6)
Assembly: GRCh38.p14, edited at the CLYBL locus according to genomic modifications
Supplementary files format and content: Bigwig files are provided for each condition, showing read mappings to the edited genomes.

source_name: LU99 STRAIGHT-IN DUAL

growth_protocol: Maintained in StemFlex™ Medium (Thermo Scientific A3349401) with 100 U/mL Penicillin-Streptomycin (Gibco 15140122) on plates coated with 5 ug/mL Laminin-521 (STEMCELL Technologies 200-0117).

extract_protocol:
Extracted with Monarch Total RNA purification kit (NEB T2010) . ERCC spike-in RNA (Mix 1, Thermo Fisher 4456740) was added during lysis.
Processed with NEB Ultra II Directional RNA with Poly(A) selection followed by library prep with unique dual indexes by a core facility.

treatment_protocol: Induced conditions treated with 1 ug/mL doxycycline for three days.

tag: cell line

value: LU99 STRAIGHT-IN DUAL

tag: cell type

value: hiPSC

tag: genetic modification

tag: treatment

value: control

tag: batch


title: RNA-seq from 032 Pre Treatment Rep 1

description:
Library name: 032_Pre1
E1_01032Pre1


title: Downstream tandem hiPSC, induced, rep2

description: Library name: downstream_tandem_induced_rep2

value: doxycycline


title: Downstream tandem hiPSC, induced, rep1

description: Library name: downstream_tandem_induced_rep1


title: YY1 Alkbh5 del-cIDR rep1

city: Chicago

first: Long

last: Zhao

state: Il

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description:
Library name: SAMPLES1
Peak files; Bigwig files

library_source: genomic

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam, bigwig
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: E14TG2a mES cells (ATCC) were cultured in DMEM (Gibco) supplemented with 15% FBS (Gibco), 1% EmbryoMax nucleosides (Sigma), 1% GlutaMAX supplement (Gibco), 1% MEM non-essential amino acids solution (Gibco), 1% Penicillin-Streptomycin (Gibco), 0.1 mM 2-Mercaptoethanol (Gibco), 1000 U/ml LIF (Sigma), 1 µM PD0325901 (Stemcell) and 3 µM CHIR99021 (Stemcell) at 37 °C in a humidified atmosphere with 5% CO2. HEK293T cells (ATCC) were maintained in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
mESCs nuclei were isolated by incubation with Complete Nuclei Isolation Buffer according to the manufacturer's instructions.
CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer's instructions.

value: mESC

tag: genotype

value: Alkbh5 del-cIDR


title: Mouse, Liver, E76R, rep 3

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description:
Library name: Mouse_Liver_E76R_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R3

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: No processed data files are included in this submission. Only raw FASTQ files are provided for each sample.

source_name: Liver

growth_protocol: Mice were housed five per cage and maintained under controlled temperature (22.5 °C) and a 12 h light/dark cycle, with food and water provided ad libitum.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit with xGEN Stubby adaptors and xGEN 10nt UDIs.

treatment_protocol: No treatment was applied prior to RNA extraction.

value: Liver

value: Whole tissue

value: H2B E76R


title: mRNA m6A IP WT rep1

description:
Library name: SAMPLES11
Normalized m6A matrix; Normalized mRNA expression matrix
mPWT-1

value: WT


title: RNA-seq from 025-031 Pre Treatment Rep 2

description:
Library name: 031_Pre2
E025_031Pre2


title: Divergent hiPSC, uninduced, rep1

description: Library name: divergent_uninduced_rep1


title: Mouse, Liver, E76R, rep 2

description:
Library name: Mouse_Liver_E76R_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R2


title: mRNA m6A IP Alkbh5 KO rep2

description:
Library name: SAMPLES10
Normalized m6A matrix; Normalized mRNA expression matrix
mPKO6-2

value: Alkbh5 KO


title: Convergent hiPSC, uninduced, rep3

description: Library name: convergent_uninduced_rep3


title: mRNA m6A IP Alkbh5 KO rep1

description:
Library name: SAMPLES9
Normalized m6A matrix; Normalized mRNA expression matrix
mPKO6-1


title: Mouse, Liver, E76R, rep 1

description:
Library name: Mouse_Liver_E76R_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R1


title: mRNA m6A IP Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES8
Normalized m6A matrix; Normalized mRNA expression matrix
mPKI-2


title: RNA-seq from 025-031 Post Treatment Rep 2

description:
Library name: 031_Post2
E025_031Po2


title: Mouse, Liver, E76K, rep 5

description:
Library name: Mouse_Liver_E76K_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver20_E76K

value: H2B E76K


title: Convergent hiPSC, induced, rep3

description: Library name: convergent_induced_rep3


title: Convergent hiPSC, uninduced, rep2

description: Library name: convergent_uninduced_rep2


title: Mouse, Liver, E76K, rep 4

description:
Library name: Mouse_Liver_E76K_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver16_E76K


title: RNA-seq from 025-031 Post Treatment Rep 1

description:
Library name: 031_Post1
E025_031Po1


title: mRNA m6A IP Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES7
Normalized m6A matrix; Normalized mRNA expression matrix
mPKI-1


title: RNA-seq from 013 Post Treatment Rep 2

description:
Library name: 013_Post2
C5_01013Po2


title: Mouse, Liver, E76K, rep 3

description:
Library name: Mouse_Liver_E76K_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver7_E76K


title: RNA-seq from 025-031 Post Treatment Rep 3

description:
Library name: 031_Post3
E025_031Po3


title: Convergent hiPSC, induced, rep2

description: Library name: convergent_induced_rep2


title: Mouse, Liver, E76K, rep 2

description:
Library name: Mouse_Liver_E76K_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver4_E76K


title: Convergent hiPSC, uninduced, rep1

description: Library name: convergent_uninduced_rep1


title: mRNA m6A Input WT rep2

description:
Library name: SAMPLES6
Normalized m6A matrix; Normalized mRNA expression matrix
mNWT-2


title: RNA-seq from 013 Post Treatment Rep 1

description:
Library name: 013_Post1
C4_01013Po1


title: mRNA m6A Input Alkbh5 KO rep2

description:
Library name: SAMPLES4
Normalized m6A matrix; Normalized mRNA expression matrix
mNKO6-2


title: mRNA m6A Input WT rep1

description:
Library name: SAMPLES5
Normalized m6A matrix; Normalized mRNA expression matrix
mNWT-1


title: RNA-seq from 025-031 Pre Treatment Rep 1

description:
Library name: 031_Pre1
E025_031Pre1


title: mRNA m6A Input Alkbh5 KO rep1

description:
Library name: SAMPLES3
Normalized m6A matrix; Normalized mRNA expression matrix
mNKO6-1


title: Mouse, Liver, D68N, rep 4

description:
Library name: Mouse_Liver_D68N_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver17_D68N

value: H2B D68N


title: RNA-seq from 013 Pre Treatment Rep 3

description:
Library name: 013_Pre3
C3_01013Pre3


title: RNA-seq from 013 Pre Treatment Rep 2

description:
Library name: 013_Pre2
C2_01013Pre2


title: WTC11_neuron_dTAG_R2_SLAM

first: Jesse

middle: R

last: Dixon

address: 10010 N. Torrey Pines Rd.

institute: Salk Institute for Biological Studies

description: Library name: TP659

data_processing:
Alignment was performed using HISAT-3N with a HISAT-3N index built to account for T>C conversions and with WTC11 SNPs substituted with N. For alignment purposes, read2 was treated as read1, and read1 was treated as read2.
Aligned data was de-duplicated using Picard MarkDuplicates.
A custom HTSeq Python script (SLAM_HTSeq.py) was used count read pairs that align to a gencode.v25 gene. Read pairs that HISAT-3N determine contain a T>C conversion (Yf>0) are counted as nascent, while all nascent and non-converted read pairs are counted as total.
Assembly: hg38
Supplementary files format and content: Nascent and total gene (gencode.v25) counts in .txt format

molecule: total RNA

source_name: hTERT RPE-1

growth_protocol: Prior to differentiation, WTC11 iNgn2 hiPSC cells  were maintained on Cultrex-coated plates in either Essential 8 Flex Medium (Gibco #A2858501) or mTeSR Plus (StemCell Technologies #100-0276). WTC11 iNgn2 hiPSC cells were differentiated into neurons using SMAD inhibition or into cardiomyocytes using STEMdiff Ventricular Cardiomyocyte Differentiation Kit (StemCell Technologies #05010).

extract_protocol:
RNA was extracted using TRIzol and purified using Direct-zol RNA Miniprep Kit (Zymo #R2052). Iodoacetamide conversion was performed using SLAMseq Kinetics Kit – Anabolic Kinetics Module (Lexogen #061), with subsequent purification using either ethanol precipitation or RNA Clean & Concentrator-5 kit (Zymo #R1013).
Sequencing libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit (Zymo #R3003), according to manufacturer’s instructions.

treatment_protocol: Post-mitotic hiPSC-derived cells were treated with DMSO or dTAGV-1 for the stated times.

value: hTERT RPE-1

value: dTAG 4hr

tag: 4su labeling_period

value: 120 minutes


title: WTC11_neuron_dTAG_R1_SLAM

description: Library name: TP658


title: Mouse, Liver, D68N, rep 3

description:
Library name: Mouse_Liver_D68N_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver13_D68N


title: mRNA m6A Input Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES2
Normalized m6A matrix; Normalized mRNA expression matrix
mNKI-2


title: WTC11_neuron_DMSO_R2_SLAM

description: Library name: TP657

value: DMSO 4hr


title: RNA-seq from 016 Post Treatment Rep 3

description:
Library name: 016_Post3
B6_19016Po3

value: Tumor


title: RNA-seq from 013 Pre Treatment Rep 1

description:
Library name: 013_Pre1
C1_01013Pre1


title: Mouse, Liver, E76K, rep 1

description:
Library name: Mouse_Liver_E76K_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver3_E76K


title: Mouse, Liver, D68N, rep 2

description:
Library name: Mouse_Liver_D68N_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver10_D68N


title: caRNA KDM6A FL OE rep2

description:
Library name: SAMPLES16
carna-UTXWT-2
mRNA reads Count; repeat reads Count

library_source: other

data_processing:
Alignment: Reads were aligned to the mouse genome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam

molecule: other

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 uL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 ug non-ribosome RNA, followed by fragmentation using RNA Fragmentation Reagents (Invitrogen).
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer's protocol.

value: OE KDM6A FL


title: mRNA m6A Input Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES1
Normalized m6A matrix; Normalized mRNA expression matrix
mNKI-1


title: Mouse, Liver, D68N, rep 1

description:
Library name: Mouse_Liver_D68N_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver5_D68N


title: WTC11_neuron_DMSO_R1_SLAM

description: Library name: TP656


title: Convergent hiPSC, induced, rep1

description: Library name: convergent_induced_rep1

value: LU99 STRAIGHT-IN DUAL

value: hiPSC


title: RNA-seq from 016 Post Treatment Rep 1

description:
Library name: 016_Post1
B4_19016Po1


title: Mouse, Liver, WT, rep 5

description:
Library name: Mouse_Liver_WT_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver18_WT

value: H2B WT


title: RNA-seq from 016 Post Treatment Rep 2

description:
Library name: 016_Post2
B5_19016Po2


title: RNA-seq from 016 Pre Treatment Rep 3

description:
Library name: 016_Pre3
B3_19016Pre3


title: Mouse, Liver, WT, rep 3

description:
Library name: Mouse_Liver_WT_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver8_WT


title: WTC11_cardio_DMSO_R2_SLAM

description: Library name: TP653


title: Mouse, Liver, WT, rep 4

description:
Library name: Mouse_Liver_WT_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver14_WT


title: WTC11_cardio_dTAG_R2_SLAM

description: Library name: TP655


title: RNA-seq from 016 Pre Treatment Rep 2

description:
Library name: 016_Pre2
B2_19016Pre2


title: RNA-seq from 012 Pre Treatment Rep 1

description:
Library name: 012_Pre1
23U-GD-02243


title: WTC11_cardio_DMSO_R1_SLAM

description: Library name: TP652


title: caRNA KDM6A del-cIDR OE rep1

description:
Library name: SAMPLES13
carna-UTXL2-1
mRNA reads Count; repeat reads Count

value: mESC

value: OE KDM6A del-IDR


title: Mouse, Liver, WT, rep 2

description:
Library name: Mouse_Liver_WT_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver6_WT

value: Liver

value: Whole tissue


title: caRNA KDM6B FL OE rep2

description:
Library name: SAMPLES12
carna-6BWT-2
mRNA reads Count; repeat reads Count

value: OE KDM6B FL


title: WTC11_cardio_dTAG_R1_SLAM

description: Library name: TP654


title: caRNA KDM6B FL OE rep1

description:
Library name: SAMPLES11
carna-6BWT-1
mRNA reads Count; repeat reads Count


title: caRNA KDM6A FL OE rep1

description:
Library name: SAMPLES15
carna-UTXWT-1
mRNA reads Count; repeat reads Count


title: RNA-seq from 012 Post Treatment Rep 1

description:
Library name: 012_Post1
23U-GD-02245


title: Mouse, Liver, WT, rep 1

description:
Library name: Mouse_Liver_WT_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver1_WT


title: BMM Mtb-BB7 rep3

city: Stockholm

first: Martin

last: Rottenberg

address: Solna vägen 9

country: Sweden

institute: Karolinska Institutet

description:
Library name: Sample 9
Column name in Summary file.xlsx: Mtb BB73

data_processing:
Pre-processed reads were aligned to the standard mouse reference genome mm10 using the HISAT2 program
Hypergeometric Optimization of Motif EnRichment (HOMER, http://homer.salk.edu/homer) was used to create the tag directory and count tags in all exons.
For the gene expression analysis, unsupervised hierarchical clustering and principal component analysis of genes were performed in Qlucore Omics Explorer 3.2
Assembly: mm10
Supplementary files format and content: The Summary file.xlsx contains sheets with Salmon outputs, filtered TMPs and DEGs

source_name: Bone marrow derived macrophage

growth_protocol: Bone marrow cells were flushed from tibia and femurs with PBS, filtered through a 70μm cell strainer, resuspended in DMEM supplemented with 10% FCS and 30% L929 cell-conditioned medium (as a source of macrophage-colony stimulating factor) and incubated for 6 days at 37°C, 5% CO2. Bone marrow-derived macrophage (BMM) cultures were then washed with PBS, detached with 1%trypsin, and 5.105 cells were seeded to each well at (using 24 well plates). BMM were further incubated for 24 h at 37°C before infections or treatment with diverse compounds. BMM were F4/80+, CD11b+, CD11c- and SiglecF-.

extract_protocol:
RNA was isolated using miRNeasy micro kit (QIAGEN, Hilden, Germany)
Illumina TruSeq RNA Library Preparation Kit

treatment_protocol: triplicate independent cultures of BMM treated either with10 uM BB7 or NC and infected 4 h after with M. tuberculosis at a MOI of 3:1. RNA was extracted 4h after infection.

value: Bone marrow derived macrophage

value: M. tuberculosis- BB7


title: Mouse, Liver, Empty, rep 6

description:
Library name: Mouse_Liver_Empty_rep6
Normalized_counts_file_mRNA-seq_liver.tabular
Liver19_Empty

value: Empty


title: BMM Mtb-BB7 rep1

description:
Library name: Sample 7
Column name in Summary file.xlsx: Mtb BB71


title: Mouse, Liver, Empty, rep 5

description:
Library name: Mouse_Liver_Empty_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver15_Empty


title: RNA-seq from 003 Pre Treatment Rep 1

description:
Library name: 003_Pre1
001003_Pre1


title: caRNA KDM6B del-cIDR OE rep2

description:
Library name: SAMPLES10
carna-6BL1-2
mRNA reads Count; repeat reads Count

value: OE KDM6B del-IDR


title: caRNA KDM4B FL OE rep2

description:
Library name: SAMPLES8
carna-4BWT-2
mRNA reads Count; repeat reads Count

value: OE KDM4B FL


title: Mouse, Liver, Empty, rep 4

description:
Library name: Mouse_Liver_Empty_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver12_Empty


title: caRNA KDM6B del-cIDR OE rep1

description:
Library name: SAMPLES9
carna-6BL1-1
mRNA reads Count; repeat reads Count


title: BMM Mtb rep3

description:
Library name: Sample 6
Column name in Summary file.xlsx: Mtb3

value: M. tuberculosis-NC


title: RNA-seq from 003 Post Treatment Rep 3

description:
Library name: 003_Post3
001003_Post3


title: RNA-seq from 003 Pre Treatment Rep 3

description:
Library name: 003_Pre3
001003_Pre3


title: caRNA KDM4B FL OE rep1

description:
Library name: SAMPLES7
carna-4BWT-1
mRNA reads Count; repeat reads Count


title: caRNA KDM6A del-cIDR OE rep2

description:
Library name: SAMPLES14
carna-UTXL2-2
mRNA reads Count; repeat reads Count


title: caRNA KDM4B del-cIDR OE rep2

description:
Library name: SAMPLES6
carna-4BL1-2
mRNA reads Count; repeat reads Count

value: OE KDM4B del-IDR


title: BMM rep3

description:
Library name: Sample 3
Column name in Summary file.xlsx: Ctrl3

value: Untreated


title: Mouse, Liver, Empty, rep 3

description:
Library name: Mouse_Liver_Empty_rep3
Normalized_counts_file_mRNA-seq_liver.tabular
Liver11_Empty


title: Mouse, Liver, Empty, rep 2

description:
Library name: Mouse_Liver_Empty_rep2
Normalized_counts_file_mRNA-seq_liver.tabular
Liver9_Empty


title: RNA-seq from 003 Post Treatment Rep 1

description:
Library name: 003_Post1
001003_Post1

value: Tumor


title: RNA-seq from 003 Post Treatment Rep 2

description:
Library name: 003_Post2
001003_Post2


title: caRNA KDM4B del-cIDR OE rep1

description:
Library name: SAMPLES5
carna-4BL1-1
mRNA reads Count; repeat reads Count


title: BMM rep1

description:
Library name: Sample 1
Column name in Summary file.xlsx: Ctrl1


title: BMM Mtb-BB7 rep2

description:
Library name: Sample 8
Column name in Summary file.xlsx: Mtb BB72


title: BMM Mtb rep1

description:
Library name: Sample 4
Column name in Summary file.xlsx: Mtb1


title: Patient 033, post-treatment

description:
Library name: 033_posttreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)

data_processing:
BclConvert Software (Illumina) was used to generate de-multiplexed Fastq files. SpaceRanger v3.1.2 (10x Genomics) was used to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
Assembly: GRCh38 (used GRCh38-2020-A reference provided by 10x Genomics)
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene-barcode count matrix for tissue-associated barcodes in HDF5 format (8 micron bins)
Supplementary files format and content: cytassist_image.tiff: CytAssist image of H&E-stained tissue section
Supplementary files format and content: scalefactors_json.json: scaling factors used to map high- and low-resoution images to full-resolution image in json format
Supplementary files format and content: tissue_hires_image.png: high-resolution downsampled image of original tissue image
Supplementary files format and content: tissue_lowres_image.png: low-resolution downsampled image of original tissue image
Supplementary files format and content: tissue_positions.parquet: list of spot coordinates and corresponding spatial barcodes (8 micron bin)
Supplementary files format and content: probe_set.csv: list of probe sequences from Visium Human Transcriptome Probe Set v2.0
Library strategy: Spatial Transcriptomics

source_name: Tumor needle biopsy

extract_protocol:
FFPE 5µm tissue sections were deparaffinized, H&E stained and imaged. The tissue was permeabilized and 10x Genomics Human Transcriptome V2 probes were hybridized to the mRNA overnight. Probes were ligated before being placed in the 10x Genomics CytAssist instrument for probe release and capture by spatially barcoded spots on a Visium CytAssist HD Gene Expression slide.
Sequencing libraries were prepared following the 10x Genomics Visium HD Spatial Gene Expression Reagent Kits User Guide. Briefly, captured probes were subjected to extension and denaturation from slide, followed by real-time PCR quantification to determine optimal sample index PCR cycles to complete the Illumina-ready library. Final library quality was assessed using the LabChip GXII HT (PerkinElmer) and libraries were quantified by Qubit (ThermoFisher). Pooled libraries were subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeqX Plus for all samples except 013 samples, which were sequenced on an Illumina NovaSeq 6000).

treatment_protocol: 1mg/m2 trabectedin IV over 1h

value: Tumor needle biopsy

tag: treatment status

value: Post-treatment


title: BMM rep2

description:
Library name: Sample 2
Column name in Summary file.xlsx: Ctrl2


title: BMM Mtb rep2

description:
Library name: Sample 5
Column name in Summary file.xlsx Mtb2


title: Mouse, Liver, Empty, rep 1

description:
Library name: Mouse_Liver_Empty_rep1
Normalized_counts_file_mRNA-seq_liver.tabular
Liver2_Empty


title: Mouse, heart, E76R, rep 5

description:
Library name: Mouse_heart_E76R_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart22_E76R

source_name: Heart

value: Heart

value: H2B E76R


title: caRNA KDM4A FL OE rep2

description:
Library name: SAMPLES4
carna-4AWT-2
mRNA reads Count; repeat reads Count

value: mESC

value: OE KDM4A FL


title: Patient 033, pre-treatment

description:
Library name: 033_pretreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)

value: Pre-treatment


title: Mouse, heart, E76R, rep 4

description:
Library name: Mouse_heart_E76R_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart18_E76R

value: Whole tissue


title: caRNA KDM4A del-cIDR OE rep1

description:
Library name: SAMPLES1
carna-4AL2-1
mRNA reads Count; repeat reads Count

value: OE KDM4A del-IDR


title: Patient 032, post-treatment

description:
Library name: 032_posttreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)


title: EGFR KO Replicate 1

type: RNA

city: Shenzhen

first: Diansheng

last: Zhou

address: 1066 Xueyuan Road, Nanshan District

country: China

institute: Shenzhen University

description:
total RNA isolated from EGFR RNA immunoprecipitation
Biological replicate 1 of 2. EGFR KO MDA-MB-231 cells, transfected with EGFR CRISPR/Cas9 KO plasmid and EGFR HDR plasmid.

hyb_protocol: cRNAs were labeled with Cy3 or Cy5 dyes, fragmented, and hybridized (50 μL per array) for 17 hours at 65°C in an Agilent SureHyb chamber. Slides were washed and scanned using an Agilent DNA Microarray Scanner

scan_protocol: Scanned on an Agilent G2505C Scanner Array images were processed using Agilent Feature Extraction software v11.0.1.1

data_processing: For two-color data, within-array normalization was performed using locally weighted scatterplot smoothing (Lowess) to correct dye bias. Data processing were performed using GeneSpring GX v12.1 (Agilent Technologies)

source_name: EGFR KO MDA-MB-231 cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: Total RNA extracted using EZ-Magna RIP kit following manufacturer's instructions

value: MDA-MB-231 transfected with EGFR CRISPR/Cas9 KO plasmid and EGFR HDR plasmid


title: caRNA KDM4A del-cIDR OE rep2

description:
Library name: SAMPLES2
carna-4AL2-2
mRNA reads Count; repeat reads Count


title: EGFR WT Replicate 1

description:
total RNA isolated from EGFR RNA immunoprecipitation
Biological replicate 1 of 2. EGFR WT MDA-MB-231 cells, untreated.

source_name: EGFR WT MDA-MB-231 cells


title: Patient 029, post-treatment

description:
Library name: 029_posttreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)


title: caRNA KDM4A FL OE rep1

description:
Library name: SAMPLES3
carna-4AWT-1
mRNA reads Count; repeat reads Count


title: Mouse, heart, E76R, rep 3

description:
Library name: Mouse_heart_E76R_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart15_E76R


title: Patient 015, post-treatment

description:
Library name: 015_posttreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)


title: Mouse, heart, E76R, rep 2

description:
Library name: Mouse_heart_E76R_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart6_E76R


title: EGFR WT Replicate 2

description:
total RNA isolated from EGFR RNA immunoprecipitation
Biological replicate 2 of 2. EGFR WT MDA-MB-231 cells, untreated.


title: Patient 032, pre-treatment

description:
Library name: 032_pretreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)


title: Mouse, heart, E76K, rep 5

description:
Library name: Mouse_heart_E76K_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K5

value: H2B E76K


title: Mouse, heart, E76K, rep 4

description:
Library name: Mouse_heart_E76K_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K4


title: EGFR KO Replicate 2

description:
total RNA isolated from EGFR RNA immunoprecipitation
Biological replicate 2 of 2. EGFR KO MDA-MB-231 cells, transfected with EGFR CRISPR/Cas9 KO plasmid and EGFR HDR plasmid.


title: Patient 029, pre-treatment

description:
Library name: 029_pretreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)


title: Mouse, heart, E76R, rep 1

description:
Library name: Mouse_heart_E76R_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart4_E76R


title: H3K4me3 WT rep2

description:
Library name: SAMPLES18
Peak files; Bigwig files

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam, bigwig
Library strategy: CUT&Tag

extract_protocol:
mESCs nuclei were isolated by incubation with Complete Nuclei Isolation Buffer according to the manufacturer's instructions.
CUT&Tag was performed by using the CUT&Tag-IT® Core Assay Kit (Active Motif) following the manufacturer's instructions.
CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer's instructions.

value: WT


title: H3K4me3 Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES14
Peak files; Bigwig files

value: Alkbh5 del-cIDR


title: WT Biol Rep 1

city: Ithaca

first: Byron

last: Rusnak

email: bzr5@cornell.edu, ahr75@cornell.edu

state: NY

address: 237 Tower Rd

department: Plant Biology

institute: Cornell University

description:
Library name: Area4_WT-1
Visium 10x Genomics
instrument models: NextSeq 500 and NextSeq 2000

data_processing:
reads were converted to fastq format with spaceranger mkfastq and analyzed with spaceranger count v2.0 with default settings.
Assembly: TAIR10 v6.0.2 Arabidopsis genome
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: List of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in matrix
Supplementary files format and content: tissue_lowres_image.png: lowres image of tissue
Supplementary files format and content: tissue_hires_image.png: High res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and coordinates defining their location
Supplementary files format and content: Area2_scalefactors_json.json: scale factors in json format
Supplementary files format and content: Area2_detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: Area2_aligned_fiducials.jpg: aligned fiducials of the tissue image
Library strategy: Spatial Transcriptomics

organism: Arabidopsis thaliana

source_name: flower bud

growth_protocol: 16 degrees celsius, 24 hour light, 100 µmol m−2 s−1

extract_protocol:
Once ap1 cal AP1-GR  and drmy1 ap1 cal AP1-GR plants began to bolt, they were induced with 10 μM Dexamethasone in 0.015% Silwet (vol/vol) three times at roughly 24 hour intervals. About 108 hours (4 ½ days) after the first induction, when flower buds had reached stages 2-3, small pieces of the floral meristem cluster were carefully removed and submerged in Tissue Tek® O.C.T. Compound (Sakura®) in a 10 x 10 x 5 mm cryomold. Air bubbles were carefully removed with a 200 µL pipette tip and 9-12 cluster pieces were arranged on the bottom of the cryomold. O.C.T. embedded tissue was then flash frozen in liquid nitrogen cooled isopentane (2-methylbutane) and stored at -70°C until cryosectioning. Fresh frozen floral meristem clusters stored at -70°C were equilibrated to -10°C in a Thermofischer HM 525 NX cryostat for about 30 minutes. Tissue blocks were cut into 10 micron thick sections and placed on each capture area according to the instructions in the 10x Visium User Guide. Each capture area had a section from a separate block of frozen tissue. We used 2 sections from each genotype to serve as biological replicates.
Visium spatial RNAseq was performed according to the instructions in the user manual with the following notes and alterations. One cryosection slice was placed on each capture area of the Visium slide, each containing approximately 9-12 WT ap1 cal AP1-GR or drmy1 ap1 cal AP1-GR cauliflower-like clusters. After methanol fixation, H&E staining was replaced with toluidine blue staining as described above, then a coverslip was mounted with a solution of 85% glycerol, 10% RNAse free water, and 0.5% RNAseOUT, followed immediately by brightfield imaging as described above. Pre-permeabilization was performed as described above, and then the user manual was followed for the rest of the protocol using a 5 minute permeabilization time.

treatment_protocol: AP1-GR induced in 10 uM Dexamethasone once daily for 3 days (1 minute each day).

value: flower bud


title: Mouse, heart, E76K, rep 2

description:
Library name: Mouse_heart_E76K_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K2


title: H3K27ac WT rep2

description:
Library name: SAMPLES12
Peak files; Bigwig files


title: Patient 015, pre-treatment

description:
Library name: 015_pretreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)


title: H3K4me3 WT rep1

description:
Library name: SAMPLES17
Peak files; Bigwig files


title: 4285

city: Los Angeles

first: Chongyuan

last: Luo

address: 695 Charles E Young Drive South

department: Human Genetics

institute: University of California Los Angeles

description: Library name: Sample 8

data_processing:
snm3C-seq sequencing reads were mapped to hg38 using the map3C pipeline (https://github.com/luogenomics/map3C, doi: https://doi.org/10.1101/2025.10.10.681728)
Assembly: hg38
Supplementary files format and content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines). contact files are tab delimited files of contacts, columns in these files are: 1 - chromosome of first sequence, 2 - position of first sequence, 3 - chromosome of second sequence, 4 - position of second sequence, 5 strand of the first sequence , 6 strand of the second sequence .

source_name: brain

extract_protocol:
Each snm3C-seq reaction was performed with a brain tissue aliquot with a weight between 30-50 mg using methods described in Heffel et al,. 2024. All snm3C-seq reactions were carried out with anti-NeuN labelling using anti-NeuN antibody (PE-conjugated, clone A60, Millipore-Sigma number FCMAB317PE).
A detailed bench protocol for snm3C-seq is provided through protocol.io (https://doi.org/10.17504/protocols.io.kqdg3x6ezg25/v1). Snm3C-seq libraries were sequenced at the New York Genome Center using the Novaseq X Plus sequencer with 25B 300-cycle reagent kits.

value: brain

tag: Sex

value: Female

value: neurotypical


title: H3K4me3 Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES13
Peak files; Bigwig files


title: Mouse, heart, E76K, rep 3

description:
Library name: Mouse_heart_E76K_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K3


title: Mouse, heart, E76K, rep 1

description:
Library name: Mouse_heart_E76K_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_E76K1


title: H3K27ac WT rep1

description:
Library name: SAMPLES11
Peak files; Bigwig files


title: WT Biol Rep 2

description:
Library name: Area2_WT-2
Visium 10x Genomics
instrument models: NextSeq 500 and NextSeq 2000


title: drmy1 Biol Rep 2

description:
Library name: Area1_drmy1-2
Visium 10x Genomics
instrument models: NextSeq 500 and NextSeq 2000


title: 4458

description: Library name: Sample 9


title: H3K27ac Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES8
Peak files; Bigwig files


title: 6419

description: Library name: Sample 6

value: Male


title: 6145

description: Library name: Sample 5


title: Mouse, heart, D68N, rep 3

description:
Library name: Mouse_heart_D68N_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N3

value: H2B D68N


title: Mouse, heart, D68N, rep 4

description:
Library name: Mouse_heart_D68N_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N4

value: Heart


title: 4438

description: Library name: Sample 7


title: H3K9me3 WT rep1

description:
Library name: SAMPLES5
Peak files; Bigwig files


title: UF_pool11A

city: Montreal

first: Naguib

last: Mechawar

address: 6875 Boulevard LaSalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: lib11_UF
pooled library for subjects R1_225, R1_257, R2_409, R1_502

library_source: transcriptomic single cell

data_processing:
Process library using CellRanger
Call cells and remove ambient RNA with CellBender
Demultiplex with genotype with Demuxlet
Dedoublet with genotype with scDblFinder
Combine demuxafy results
Process data with Seurat, normalize with scTransform, integrate with harmony
Assembly: GRCh38
Supplementary files format and content: gene expression matrices for each library in csv and associated subject assignment in csv

source_name: Brain

extract_protocol:
Before beginning the nuclei extraction procedure, all buffers were filtered through 0.22 mm filters to eliminate bacteria, and RNAseInhibitor (Sigma, cat# 3335402001, 1:1000) was added. In each experiment, 4 subjects (2 subjects from each DS-CA and 2 subjects from CTRL) were processed. On average 40-60 mg of tissue was placed in a glass douncer with 3 mL of lysis buffer (5% bovine serum albumin (BSA) wash buffer with 0.05 % NP40 detergent). The tissue was dounced 10 times with a thin pestle and 5 times with the thick pestle, and then incubated in the lysis buffer for the remainder of 4 minutes. Next, 10 mL of 5% BSA wash buffer was added to the homogenate, which was all filtered through a 30 mm MACS SmartStrainer (Miltenyi Biotec cat#130-098-463), and spun in a spin bucket centrifuge at 500 g at 4°C for 6 minutes. The supernatant was decanted, the pellet was resuspended in 5mL of 2% BSA wash buffer, filtered through a second 30 mm MACS SmartStrainer, and then spun again at 500 g at 4°C for 6 minutes. The supernatant was decanted, and the pellet was resuspended in 1 mL of 2% BSA wash buffer, then filtered again through a 30 mm MACS SmartStrainer. DRAQ5 (or Hoescht, depending on availability) was added to stain nuclei, and RNaseInhibitor (1:1000) was added to preserve RNA integrity. The nuclei were placed on ice until ready to fluorescence-assisted nuclear sorting (FANS) on a BD FACSAria, at 4°C, using a 130 mm nozzle on “purity” mode. We gated narrowly on singlets based on forward scatter (particle size) and DRAQ5 fluorescence (see Supplementary Figure 1 for example), in order to remove as much debris as possible, which serves to effectively minimize ambient RNA (Caglayan et al., 2022). The singlets were sorted into a tube containing 2% BSA with RNaseInhibitor (1:1000). Wide bore pipette tips were used whenever possible to avoid excessive force on the nuclei.
After obtaining concentrations, the 4 sorted nuclei samples were pooled, with the volume contributed by each sample calculated to account for 25% of the nuclei in the pool. The pool was filtered one final time through a 30 mm MACS filter, and a final concentration of the pool was taken before nuclei capture with the 10X Chromium system. The 10X Genomics 3’ v3.1 Dual Index Gene Expression chemistry was used for nuclei capture, cDNA synthesis, and library preparation. Concentrations and fragment sizes for cDNA and libraries were measured with High Sensitivity RNA Screen Tape on an Agilent Tape Station. Each library was sequenced on an S4 flow cell on the NovaSeq6000 sequencer at the McGill Genome Center.

value: Brain

value: Seq batch 2


title: H3K27ac Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES7
Peak files; Bigwig files

value: mESC


title: Patient 013, post-treatment

description:
Library name: 013_posttreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)

value: Tumor needle biopsy

value: Post-treatment


title: UF_pool12B

description:
Library name: lib12_UF
pooled library for subjects R1_152, R1_216, R2_360, R22_485


title: UF_pool9A

description:
Library name: lib9_UF
pooled library for subjects R1_268, R1_309, R1_502, R2_527


title: Patient 013, pre-treatment

description:
Library name: 013_pretreatment
FFPE spatial transcriptome sequencing (10x Genomics Visium HD)

value: Pre-treatment


title: Mouse, heart, D68N, rep 2

description:
Library name: Mouse_heart_D68N_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N2

value: Whole tissue


title: UCSF2303

description: Library name: Sample 3


title: H3K9me3 WT rep2

description:
Library name: SAMPLES6
Peak files; Bigwig files


title: Mouse, heart, D68N, rep 1

description:
Library name: Mouse_heart_D68N_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_D68N1


title: UCSF2302

description: Library name: Sample 2


title: UF_pool10B

description:
Library name: lib10_UF
pooled library for subjects R1_90, R1_138, R2_276, R1_447


title: drmy1 Biol Rep 1

description:
Library name: Area3_drmy1-1
Visium 10x Genomics
instrument models: NextSeq 500 and NextSeq 2000


title: UCSF2301

description: Library name: Sample 1


title: UF_pool8A

description:
Library name: lib8_UF
pooled library for subjects R2_245, R1_250, R2_278, R4_289


title: H3K9me3 Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES2
Peak files; Bigwig files


title: 4267

description: Library name: Sample 4


title: Mouse, heart, WT, rep 5

description:
Library name: Mouse_heart_WT_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT5

value: H2B WT


title: H3K9me3 Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES1
Peak files; Bigwig files


title: Mouse, heart, WT, rep 2

description:
Library name: Mouse_heart_WT_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT2


title: Mouse, heart, WT, rep 4

description:
Library name: Mouse_heart_WT_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT4


title: Caco2_interacted_with_Entamoeba_histolytica_KERP2gs_Trial3

city: Tokyo

first: Ruofan

last: Peng

state: Tokyo

address: 7-3-1 Hongo, Bunkyo-ku

department: International Health

country: Japan

institute: University of Tokyo

description:
Library name: Sample 12
KERP2gs_T3

data_processing:
Sequence reads were quality-checked using FastQC (v0.11.8) and trimmed using Trimmomatic (v0.39).
Trimmed reads were aligned to the E. histolytica reference genome assembly (AmoebaDB-68) or the human reference genome (GRCh38.p14) using STAR (v2.7.10a).
Mapped reads were indexed and sorted using Samtools (v1.15.1)
Read count quantification at the gene level was performed using FeatureCounts (v2.0.1) with strand-specific parameters.
Differential gene expression analysis was conducted using the DESeq2 R package (v1.36.0)
Assembly: GRCh38.p14
Supplementary files format and content: CSV formats

source_name: Colon epithelium

growth_protocol: Caco-2 cells (ATCC) were cultured in Eagle's Minimum Essential Medium (EMEM; ATCC 30-2003) supplemented with 20% heat-inactivated fetal bovine serum (FBS; Sigma-Aldrich, St. Louis, MO, USA.) as complete EMEM. The medium was replaced every two days, and cells were incubated under standard cell culture conditions at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA from E. histolytica trophozoites was extracted using the TRIzol reagent (Invitrogen) following the manufacturer’s protocol.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: Caco-2 cells were seeded in 6-well plates and cultured for 21 days. E. histolytica strains were harvested, washed with pre-warmed EMEM, and co-cultured with Caco-2 cells for 4 hours at a host-to-parasite ratio of 1:10. The experimental conditions included: Untreated Control: Caco-2 cells cultured without parasites (Caco-2 wildtype). HA-KERP2: Caco-2 cells co-cultured with E. histolytica HA-KERP2-overexpressing trophozoites. Wild-type G3: Caco-2 cells co-cultured with E. histolytica wild-type (G3) trophozoites. psAP-KERP2gs: Caco-2 cells co-cultured with E. histolytica KERP2 knockdown trophozoites.

value: Colon epithelium

value: Caco-2 (ATCC HTB-37)

value: Caco-2 interacted with KERP2-knockdown E. histolytica Trial 3


title: Mouse, heart, WT, rep 3

description:
Library name: Mouse_heart_WT_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT3


title: eCLIP-seq IP ALKBH5 FL rep2

description:
Library name: SAMPLES8
Peak file; bigwig

data_processing:
Quality Control: Sequencing reads were quality-controlled using cutadapt.
Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed.
Peak Calling: Peaks were identified with MACS2.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam,bigwig

extract_protocol:
mESCs were UV crosslinked at 400 mJ/cm² (254 nm) once and nuclei were isolated following the cell fractionation protocol.
library construction protocol: eCLIP-seq

value: WT


title: Xenograft Bone Marrow TARGET-seq RNA

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

description: Library name: Xenograft_BM_TARGETseq_RNA

data_processing:
RNA sequencing data were pre-processed with a custom pipeline (https://github.com/asgerjakobsen/TARGET-seq-plus-RNA) to trim and demultiplex reads into single-cell barcodes using cutadapt (v3.4) and then map them to the hg38 reference genome and ERCC92 transcripts with STARsolo (v2.7.10a) using the GENCODE v38 reference gene annotation.
Genotyping amplicon data were demultiplexed and processed to generate tables of allelic counts, which were used to call cell genotypes as described in Jakobsen et al. 2024.
FACS indexing, genotyping and transcriptome data were integrated for downstream analysis in Seurat.
The following QC filters were applied to the starting dataset of 10,640 cells: minimum 5000 RNA reads per cell, minimum 1000 genes per cell, maximum % mitochondrial reads = 15%, and maximum % ERCC reads = 65%, leaving 8,998 cells remaining. The filtered data were integrated with the 13,247 primary BM cells from the original TARGET-seq+ dataset (Jakobsen et al. 2024).
Assembly: hg38
Supplementary files format and content: RDS file containing Seurat object with quality controlled TARGET-seq+ data from 13 primary bone marrow samples (Jakobsen et al. 2024) integrated with data from 5 xenografted bone marrow samples and 1 control primary sample (this study).
Supplementary files format and content: Table of tab-separated values for TARGET-seq+ genotyping data from 5 xenografted bone marrow samples and 1 control sample. For each mutation and each single cell, data are provided for the genomic DNA amplicon and the heterozygous germline SNP.

source_name: Bone Marrow

extract_protocol:
FACS sorting into 384-well plates containing lysis buffer, as per the TARGET-seq+ protocol (Jakobsen et al. 2024).
TARGET-seq+ protocol (Jakobsen et al. 2024) for 3' RNA sequencing and targeted genotyping from single cells.

value: Bone Marrow


title: Caco2_interacted_with_Entamoeba_histolytica_KERP2gs_Trial2

description:
Library name: Sample 11
KERP2gs_T2

value: Caco-2 interacted with KERP2-knockdown E. histolytica Trial 2


title: UF_pool7A

description:
Library name: lib7_UF
pooled library for subjects R1_268, R1_309, R1_502, R2_527


title: UF_pool6b

description:
Library name: lib6_UF
pooled library for subjects R2_158, R2_342, R2_409, R2_413

value: Seq batch 1


title: UF_pool5

description:
Library name: lib5_UF
pooled library for subjects R1_117, R2_527, R1_184, R1_441


title: eCLIP-seq Input ALKBH5 FL rep2

description:
Library name: SAMPLES6
Peak file; bigwig


title: Mouse, heart, WT, rep 1

description:
Library name: Mouse_heart_WT_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_WT1


title: eCLIP-seq Input ALKBH5 FL rep1

description:
Library name: SAMPLES5
Peak file; bigwig


title: Caco2_interacted_with_Entamoeba_histolytica_G3_Trial3

description:
Library name: Sample 9
G3_T3

value: Caco-2 interacted with E. histolytica_G3 Trial 3


title: UF_pool4

description:
Library name: lib4_UF
pooled library for subjects R22_125, R22_485, R1_216, R2_360


title: Caco2_interacted_with_Entamoeba_histolytica_KERP2gs_Trial1

description:
Library name: Sample 10
KERP2gs_T1

value: Caco-2 interacted with KERP2-knockdown E. histolytica Trial 1


title: Mouse, heart, Empty, rep 5

description:
Library name: Mouse_heart_Empty_rep5
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty5

value: Heart

value: Empty


title: UF_pool3

description:
Library name: lib3_UF
pooled library for subjects R2_334, R1_167, R1_133, R1_134

value: Brain


title: Caco2_interacted_with_Entamoeba_histolytica_G3_Trial2

description:
Library name: Sample 8
G3_T2

value: Caco-2 interacted with E. histolytica_G3 Trial 2


title: Mouse, heart, Empty, rep 6

description:
Library name: Mouse_heart_Empty_rep6
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty6


title: eCLIP-seq IP ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES4
Peak file; bigwig

value: mESC

value: Alkbh5 del-cIDR


title: eCLIP-seq IP ALKBH5 FL rep1

description:
Library name: SAMPLES7
Peak file; bigwig


title: Mouse, heart, Empty, rep 4

description:
Library name: Mouse_heart_Empty_rep4
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty4

value: Whole tissue


title: eCLIP-seq Input ALKBH5 del-cIDR rep2

description:
Library name: SAMPLES2
Peak file; bigwig


title: Caco2_interacted_with_Entamoeba_histolytica_G3_Trial1

description:
Library name: Sample 7
G3_T1

value: Caco-2 interacted with E. histolytica_G3 Trial 1


title: Caco2_interacted_with_Entamoeba_histolytica_HA-KERP2_Trial3

description:
Library name: Sample 6
HAKERP2_T3

value: Colon epithelium

value: Caco-2 interacted with HA-KERP2 expressing E. histolytica Trial 3


title: eCLIP-seq IP ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES3
Peak file; bigwig


title: Mouse, heart, Empty, rep 2

description:
Library name: Mouse_heart_Empty_rep2
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty2


title: Mouse, heart, Empty, rep 3

description:
Library name: Mouse_heart_Empty_rep3
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty3


title: caRNA m6A IP WT rep2

description:
Library name: SAMPLES12
Normalized m6A matrix; Normalized repeat expression matrix

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
For comparison analysis, union peaks across samples were generated using bedtools, and reads under these peaks were counted using featureCounts95 for both IP and input samples. Raw counts were normalized to Counts Per Million (CPM). IP enrichment was calculated as CPMIP/CPMInput. A scaling factor (SF) was computed based on CPMIP m6A control RNA/CPMinput m6A control RNA. The final m6A quantification for each sample was calculated using IP enrichment/SF.
Assembly: GRCm39
Supplementary files format and content: tsv
Library strategy: meRIP-seq

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 uL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 ug non-ribosome RNA, followed by fragmentation using RNA Fragmentation Reagents (Invitrogen). 5% of the fragmented RNA was saved as input. m6A immunoprecipitation was performed using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) according to the manufacturer's instructions.
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer's protocol.

value: m6A IP


title: UF_pool2

description:
Library name: lib2_UF
pooled library for subjects R1_90, R1_138, R1_250, R2_278


title: Caco2_interacted_with_Entamoeba_histolytica_HA-KERP2_Trial1

description:
Library name: Sample 4
HAKERP2_T1

value: Caco-2 (ATCC HTB-37)

value: Caco-2 interacted with HA-KERP2 expressing E. histolytica Trial 1


title: eCLIP-seq Input ALKBH5 del-cIDR rep1

description:
Library name: SAMPLES1
Peak file; bigwig


title: Caco2_interacted_with_Entamoeba_histolytica_HA-KERP2_Trial2

description:
Library name: Sample 5
HAKERP2_T2

value: Caco-2 interacted with HA-KERP2 expressing E. histolytica Trial 2


title: Xenograft_Cord Blood_Myeloid_TNF_RNA

description: Library name: Xenograft_CB_Myeloid_TNF_RNA

data_processing:
Data was processed using Cell Ranger 2.0.0 using default parameters. RNA reads were aligned to the human reference genome. Downstream analysis and QC done on Seurat v.4. Doublet filtering using scdblfinder and souporcell on select samples. Peak calling using MACS2.
Assembly: hg38
Supplementary files format and content: RDS file containing seurat object with quality controlled raw data
Supplementary files format and content: RDS object containing metadata for which genetic clade the cells in this dataset belong to. Genetic clades were inferred from SouporCell analysis as described in Zeng et al. 2026

source_name: Cord Blood

extract_protocol:
Per manufacturer's instructions for 10x genomics Multiome (RNA+ATAC) kit; or for the BD Rhapsody platform. Either low input or standard protocols were followed for the samples sequenced on the 10x platform.
Per manufacturer's instructions for 10x genomics Multiome (RNA+ATAC) kit; or the BD Rhapsody platform.

value: Cord Blood

value: TNF


title: Mouse, ske, E76R, rep 5

description:
Library name: Mouse_ske_E76R_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R5

source_name: Quadriceps

value: Quadriceps

value: H2B E76R


title: caRNA m6A IP WT rep1

description:
Library name: SAMPLES11
Normalized m6A matrix; Normalized repeat expression matrix

value: WT


title: caRNA m6A IP Alkbh5 KO rep2

description:
Library name: SAMPLES10
Normalized m6A matrix; Normalized repeat expression matrix

value: Alkbh5 KO


title: Caco-2_wildtype_Trial3

description:
Library name: Sample 3
Negative_T3

value: Caco-2 wildtype control Trial 3


title: UF_pool1

description:
Library name: lib1_UF
pooled library for subjects R1_227, R22_247, R1_391

value: Brain

value: Seq batch 1


title: Mouse, ske, E76R, rep 3

description:
Library name: Mouse_ske_E76R_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R3

value: Whole tissue


title: Xenograft_Cord Blood_Myeloid_LPS_RNA

description: Library name: Xenograft_CB_Myeloid_LPS_RNA

value: LPS


title: Xenograft_Cord Blood_Progenitor_LPS_RNA

description: Library name: Xenograft_CB_Progenitor_LPS_RNA


title: Caco-2_wildtype_Trial2

description:
Library name: Sample 2
Negative_T2

value: Colon epithelium

value: Caco-2 wildtype control Trial 2


title: Xenograft_Cord Blood_Progenitor_TNF_RNA

description: Library name: Xenograft_CB_Progenitor_TNF_RNA


title: caRNA m6A IP Alkbh5 KO rep1

description:
Library name: SAMPLES9
Normalized m6A matrix; Normalized repeat expression matrix

value: mESC

value: m6A IP


title: Mouse, heart, Empty, rep 1

description:
Library name: Mouse_heart_Empty_rep1
Normalized_counts_file_mRNA-seq_heart.tabular
Heart_Empty1

value: Heart

value: Empty


title: caRNA m6A IP Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES8
Normalized m6A matrix; Normalized repeat expression matrix

value: Alkbh5 del-cIDR


title: Caco-2_wildtype_Trial1

description:
Library name: Sample 1
Negative_T1

value: Caco-2 (ATCC HTB-37)

value: Caco-2 wildtype control Trial 1


title: Xenograft_Cord Blood_Progenitor_PBS_RNA

description: Library name: Xenograft_CB_Progenitor_PBS_RNA

value: Cord Blood

value: PBS


title: Mouse, ske, E76R, rep 2

description:
Library name: Mouse_ske_E76R_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R2

value: Quadriceps

value: H2B E76R


title: Xenograft_Cord Blood_Myeloid_PBS_RNA

description: Library name: Xenograft_CB_Myeloid_PBS_RNA


title: SYD_H_rep3_IP

city: Beijing

first: Shuaijie

last: Guo

state: None Selected

address: 23 Art Museum Back Street, Dongcheng District, Beijing, China

institute: Beijing Hospital of Traditional Chinese Medicine

description:
Library name: H3_IP
m6A immunoprecipitated fraction for SYD High replicate 3

data_processing:
Paired-end reads were quality controlled by Q30. 3' adaptor-trimming and low quality reads removing were performed by cutadapt software (v1.9.3).
The high quality clean reads were aligned to the Rattus norvegicus reference genome using HISAT2 software (v2.0.4) to obtain expression profile data.
HTSeq (v0.9.1) was used to get the raw count, and edgeR (v3.16.5) was used to perform normalization and identify differentially expressed mRNAs. Methylated peaks were called using MACS.
GO and KEGG Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: rn6
Supplementary files format and content: Excel file containing normalized count matrix, peak coordinates (BED format), and differential expression results.

organism: Rattus norvegicus

growth_protocol: H9c2 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's protocol, and RNA quality was evaluated using NanoDrop ND-1000 and agarose gel electrophoresis.
Total RNA was randomly fragmented to ~200 nt. Protein A/G beads were coupled to the m6A antibody, and the RNA fragments were incubated with the bead-linked antibodies at 4°C for 4 h. RNA libraries for IP and Input samples were then constructed with the GenSeq Low Input Whole RNA Library Prep Kit by following the manufacturer's instructions.

treatment_protocol: Cells were divided into Control group (no intervention), Model group (induced with 50 µM Phenylephrine for 24 h), and SYD-H group (treated with 2 mg/mL SYD and 50 µM Phenylephrine for 24 h).

value: cardiomyocyte

value: wild type

value: 2 mg/mL SYD + 50 uM PE for 24 h


title: Mouse, ske, E76R, rep 1

description:
Library name: Mouse_ske_E76R_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R1

value: Whole tissue


title: Primary stromal cells, undifferentiated, ITGA11 siRNA, donor YM07

city: Odense

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

description:
Library name: YM07_siRNA
YM07_siRNA

data_processing:
Raw base calls of 10x libraries were demultiplexed into fastq files and then aligned and quantified at the exon and intron level using zUMI (Parekh S, et al., Gigascience 7:giy059) and STAR (Dobin A, et al., Bioinformatics 29:15-21) with genome GRCh38. Quality control, merging, and normalization were done in Seurat (Butler A, et al. 2018. Nature Biotechnology 36: 411) to yield a gene count matrix for 136,014 cells. The seurat object ("SeuratObject") of the article can be found at OSF (https://osf.io/s8nfb/) and as processed data in this series.
Bulk RNA-seq reads were aligned to GRCh378(hg38) genome using STAR (Dobin A, et al., Bioinformatics 29:15-21) and default settings. Bam files were used to quantify tag distribution at gene bodies using featureCounts from the Subread package (Liao Y,  et al. 2014. Bioinformatics 30: 923) . Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing treatment conditions (siITGA11 vs. siCTR, ITGA11high vs ITGA11low) and including donor information in the model.
Assembly: GRCh38
Supplementary files format and content: 8524.dgecounts.rds, 8525.dgecounts.rds, 8890.dgecounts.rds, 8983.dgecounts.rds, 8984.dgecounts.rds, 8985.dgecounts.rds, 9171.dgecounts.rds, 9172.dgecounts.rds, 9173.dgecounts.rds, 9174.dgecounts.rds, 9294.dgecounts.rds, 9295.dgecounts.rds, 9296.dgecounts.rds, A174.dgecounts.rds, A175.dgecounts.rds, A176.dgecounts.rds, A177.dgecounts.rds, A178.dgecounts.rds, A323.dgecounts.rds, A324.dgecounts.rds, s1.dgecounts.rds, s2.dgecounts.rds, s3.dgecounts.rds, s4.dgecounts.rds, s6.dgecounts.rds, s8.dgecounts.rds, tab delimited files to retrieve zUMI derrived raw gene count matrices of the individual 10x scRNA-seq libraries.
Supplementary files format and content: SeuratObject.qs, serialized and compressed seurat object using R package "qs"
Supplementary files format and content: Bulk_Counts.txt, tab delimited file with featureCounts derrived raw gene counts from bulk RNA-seq as well as DESeq derived rlog values, normalized counts, fold changes and adjusted p-values for the comparisons from bulk RNA-seq

source_name: cultured primary stromal cells from iliac crest aspirate

growth_protocol: Cells were seeded in tissue culture flasks and expanded in culture medium consisting of minimum essential medium (MEM, 32561-094, Invitrogen) supplemented with 10% fetal bovine serum (FBS, 16000044, Life Technologies) and 1% penicillin/streptomycin (P/S, 15140-130, Invitrogen). They were incubated at 37 °C with 5% CO2 and 95% humidity. The culture medium was changed three times a week, and the cells were either passaged or set out for differentiation when reaching 80-90% confluency.

extract_protocol:
For 10x scRNA-seq, cells have been trypsinized and spun down at 200 g and washed twice in culture media. Cells were separated using a 40 µm mesh, washed 3 times in PBS with 0.04% non-acetylated BSA, and cell numbers were adjusted to 0.7 million cells per ml followed by a final transfer through a 40 µm mesh.
Bulk RNA was extracted from cultured cells using Trizol combined with Econo Spin columns (Epoch Life Sciences).
scRNA-seq: Libraries were prepared according to manufactures instructions (10x Genomics).
Bulk RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol:
For 10x scRNA-seq libraries, cells were trypsinised at 90 % confluency.
For bulk-RNA-seq on siRNA transfected primary, reverse transfection was done 3 days prior to differentiation, using a final concentration of 30 nM siRNA, 0.15% lipofectamin 2000 and 140,000 cells per ml using alphaMEM without additives. For a single 12-well, 1.5 µl of 20 µM siRNA stock was mixed with 150 µl alphaMEM, 1.5 µl lipofectamin 200 was mixed with 150 µl alphaMEM, and both mixtures were united after 5 minutes incubation. After additional 20 minutes incubation, 140,000 cells in 0.7 ml were added and 1 ml of cell-transfection-mix was plated to a 12-well, yielding 40,000 cells per squar-cm.
For bulk-RNA-seq on sorted primary cells, cells at passge 2 or 3  with unconjugated primary ITGA11 antibody (0519-100/ITGA11-203E3, Nanotools) followed by secondary FITC-conjugated anti-mouse immunoglobulin (F0261, Dako Denmark A/S) and sorted on a BD FACSAria III  to capture the lowest 30% and highest and 30% of ITGA11 expresison. Cells were plated at a density of either 50.000 or 5.000 cells per square-cm and harvested in Trizol three or 7 days after, respectively.

value: ITGA11 siRNA


title: Mouse, ske, E76K, rep 5

description:
Library name: Mouse_ske_E76K_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske20_E76K

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: No processed data files are included in this submission. Only raw FASTQ files are provided for each sample.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit with xGEN Stubby adaptors and xGEN 10nt UDIs.

value: H2B E76K


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, proliferated, donor YM07

description:
Library name: YM07_Low_5000
YM07_Low_5000

value: cultured primary stromal cells from iliac crest aspirate

value: ITGA11 sorted low, proliferated


title: Mouse, ske, E76R, rep 4

description:
Library name: Mouse_ske_E76R_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske_E76R4


title: caRNA m6A IP Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES7
Normalized m6A matrix; Normalized repeat expression matrix

value: mESC

value: m6A IP


title: SYD_H_rep2_IP

description:
Library name: H2_IP
m6A immunoprecipitated fraction for SYD High replicate 2


title: caRNA m6A Input WT rep1

description:
Library name: SAMPLES5
Normalized m6A matrix; Normalized repeat expression matrix

value: WT

value: input


title: Mouse, ske, E76K, rep 4

description:
Library name: Mouse_ske_E76K_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske15_E76K


title: caRNA m6A Input WT rep2

description:
Library name: SAMPLES6
Normalized m6A matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, D0, donor YM07

description:
Library name: YM07_Low_D0
YM07_Low_D0

value: ITGA11 sorted low, D0


title: SYD_H_rep2_Input

description:
Library name: H2_Input
Input fraction (total RNA control) for SYD High replicate 2


title: Mouse, ske, E76K, rep 3

description:
Library name: Mouse_ske_E76K_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske9_E76K


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, D0, donor YM07

description:
Library name: YM07_High_D0
YM07_High_D0

value: ITGA11 sorted high, D0


title: caRNA m6A Input Alkbh5 KO rep2

description:
Library name: SAMPLES4
Normalized m6A matrix; Normalized repeat expression matrix

value: Alkbh5 KO


title: SYD_H_rep3_Input

description:
Library name: H3_Input
Input fraction (total RNA control) for SYD High replicate 3


title: SYD_H_rep1_IP

description:
Library name: H1_IP
m6A immunoprecipitated fraction for SYD High replicate 1


title: caRNA m6A Input Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES2
Normalized m6A matrix; Normalized repeat expression matrix

value: Alkbh5 del-cIDR


title: Mouse, ske, E76K, rep 1

description:
Library name: Mouse_ske_E76K_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske3_E76K

value: Quadriceps


title: SYD_H_rep1_Input

description:
Library name: H1_Input
Input fraction (total RNA control) for SYD High replicate 1

value: cardiomyocyte


title: caRNA m6A Input Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES1
Normalized m6A matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, control siRNA, donor YM07

description:
Library name: YM07_CT
YM07_CT

value: control siRNA


title: caRNA m6A Input Alkbh5 KO rep1

description:
Library name: SAMPLES3
Normalized m6A matrix; Normalized repeat expression matrix


title: Model_rep3_IP

description:
Library name: M3_IP
m6A immunoprecipitated fraction for Model replicate 3

value: wild type

value: 50 uM Phenylephrine (PE) for 24 h


title: Primary stromal cells, undifferentiated, ITGA11 siRNA, donor YM04

description:
Library name: YM04_siRNA
YM04_siRNA

value: ITGA11 siRNA


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, proliferated, donor YM07

description:
Library name: YM07_High_5000
YM07_High_5000

value: ITGA11 sorted high, proliferated


title: Mouse, ske, D68N, rep 4

description:
Library name: Mouse_ske_D68N_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske17_D68N

value: Whole tissue

value: H2B D68N


title: Model_rep3_Input

description:
Library name: M3_Input
Input fraction (total RNA control) for Model replicate 3


title: Mouse, ske, D68N, rep 3

description:
Library name: Mouse_ske_D68N_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske16_D68N


title: ATAC WT rep2

description:
Library name: SAMPLES6
Peak files; Bigwig files

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam, bigwig

extract_protocol:
For mESCs, 5 × 104 cells were collected, mixed with 10 µl of ATAC-Seq Spike-In Nuclei (Active Motif), and proceeded to the transposition reaction.
ATAC-seq was performed by using the ATAC-Seq Kit (Active Motif) according to the manufacturer's instructions.

value: mESC


title: ATAC WT rep1

description:
Library name: SAMPLES5
Peak files; Bigwig files


title: Model_rep2_Input

description:
Library name: M2_Input
Input fraction (total RNA control) for Model replicate 2


title: Mouse, ske, D68N, rep 2

description:
Library name: Mouse_ske_D68N_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske11_D68N


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, D0, donor YM04

description:
Library name: YM04_Low_D0
YM04_Low_D0

value: cultured primary stromal cells from iliac crest aspirate


title: Mouse, ske, E76K, rep 2

description:
Library name: Mouse_ske_E76K_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske6_E76K

value: H2B E76K


title: Mouse, ske, D68N, rep 1

description:
Library name: Mouse_ske_D68N_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske7_D68N


title: Model_rep2_IP

description:
Library name: M2_IP
m6A immunoprecipitated fraction for Model replicate 2


title: ATAC Alkbh5 KO rep2

description:
Library name: SAMPLES4
Peak files; Bigwig files


title: Model_rep1_IP

description:
Library name: M1_IP
m6A immunoprecipitated fraction for Model replicate 1


title: Mouse, ske, WT, rep 5

description:
Library name: Mouse_ske_WT_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske18_WT

value: H2B WT


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, proliferated, donor YM04

description:
Library name: YM04_High_5000
YM04_High_5000


title: Mouse, ske, WT, rep 4

description:
Library name: Mouse_ske_WT_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske13_WT


title: Primary stromal cells, undifferentiated, control siRNA, donor YM04

description:
Library name: YM04_CT
YM04_CT


title: ATAC Alkbh5 del-cIDR rep2

description:
Library name: SAMPLES2
Peak files; Bigwig files


title: Control_rep3_IP

description:
Library name: C3_IP
m6A immunoprecipitated fraction for Control replicate 3


title: ATAC Alkbh5 del-cIDR rep1

description:
Library name: SAMPLES1
Peak files; Bigwig files


title: Control_rep3_Input

description:
Library name: C3_Input
Input fraction (total RNA control) for Control replicate 3


title: Mouse, ske, WT, rep 2

description:
Library name: Mouse_ske_WT_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske8_WT


title: Mouse, ske, WT, rep 3

description:
Library name: Mouse_ske_WT_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske10_WT


title: Primary stromal cells, undifferentiated, ITGA11 siRNA, donor OF13AT

description:
Library name: OF13AT_siRNA
OF13AT_siRNA


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, proliferated, donor YM04

description:
Library name: YM04_Low_5000
YM04_Low_5000

value: ITGA11 sorted low, proliferated


title: Nascent RNA WT 60min rep2

description:
Library name: SAMPLES24
Normalized mRNA expression matrix; Normalized repeat expression matrix

data_processing:
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq X platform in paired-end mode (150 bp per read) at Azenta.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Quantification: For each time point, the relative transcription rates were normalized to the 10-minute sample. Log2 fold changes (log2FC) relative to the 10-minute sample were calculated for each time point using edgeR96. These log2FC values were used to represent the transcription rates for subsequent data analysis.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam
Library strategy: EU labelled RNA profiling

extract_protocol:
After EU incubation, cells were lysed with TRIzol (Invitrogen), and total RNA was extracted. An equal amount of RNA extracted from EU-labeled Drosophila cells was added to each sample as a spike-in for further normalization. Nascent RNA was captured using the Click-iT Nascent RNA Capture Kit (Invitrogen) according to the manufacturer's instructions.
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer's protocol.

treatment_protocol: mESCs were seeded into eight 6-cm dishes at equal cell densities one day before EU labeling. The following day, cells were incubated in media containing 1 mM EU for 10, 20, 40, or 60 minutes.

value: WT

tag: eu treatment time (min)


title: Primary stromal cells, undifferentiated, control siRNA, donor OF13AT

description:
Library name: OF13AT_CT
OF13AT_CT


title: Mouse, ske, WT, rep 1

description:
Library name: Mouse_ske_WT_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske1_WT


title: Nascent RNA WT 60min rep1

description:
Library name: SAMPLES23
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: ATAC Alkbh5 KO rep1

description:
Library name: SAMPLES3
Peak files; Bigwig files

value: Alkbh5 KO


title: Primary stromal cells, undifferentiated, ITGA11 siRNA, donor OF01

description:
Library name: OF01_siRNA
OF01_siRNA


title: Model_rep1_Input

description:
Library name: M1_Input
Input fraction (total RNA control) for Model replicate 1


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, D0, donor YM04

description:
Library name: YM04_High_D0
YM04_High_D0

value: ITGA11 sorted high, D0


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, D0, donor OF01

description:
Library name: OF01_Low_D0
OF01_Low_D0

value: ITGA11 sorted low, D0


title: Mouse, ske, Empty, rep 5

description:
Library name: Mouse_ske_Empty_rep5
Normalized_counts_file_mRNA-seq_ske.tabular
Ske14_Empty

value: Quadriceps

value: Empty


title: Nascent RNA WT 40min rep1

description:
Library name: SAMPLES21
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, proliferated, donor OF01

description:
Library name: OF01_Low_5000
OF01_Low_5000


title: Nascent RNA WT 40min rep2

description:
Library name: SAMPLES22
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Mouse, ske, Empty, rep 4

description:
Library name: Mouse_ske_Empty_rep4
Normalized_counts_file_mRNA-seq_ske.tabular
Ske12_Empty


title: Control_rep2_IP

description:
Library name: C2_IP
m6A immunoprecipitated fraction for Control replicate 2

value: cardiomyocyte

value: wild type


title: Mouse, ske, Empty, rep 6

description:
Library name: Mouse_ske_Empty_rep6
Normalized_counts_file_mRNA-seq_ske.tabular
Ske19_Empty


title: Nascent RNA WT 20min rep2

description:
Library name: SAMPLES20
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: CUMC_E172

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

country: Germany

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 2.1.7) was used to convert BCL to fastq format, coupled with adaptor trimming
Salmon v1.3.0 was used to quantify transcript abundance after generating a full decoy-aware transcriptome index.
tximport v1.18.0 was used to import transcript level count estimates from Salmon and summarize them at the gene level using the "lengthScaledTPM" option for the countsFromAbundance argument.
Genome_build: GENCODE Release 34 (GRCh38.p5)
Supplementary_files_format_and_content: tab-delimited text file containing estimated counts per gene for each sample

source_name: PDAC

extract_protocol:
Qiagen RNAeasy Plus Micro Kit
NuGEN Ovation RNA-Seq System V2

tag: compartment

value: Epithelium

tag: group

value: Primary


title: Control_rep1_IP

description:
Library name: C1_IP
m6A immunoprecipitated fraction for Control replicate 1


title: Mouse, ske, Empty, rep 2

description:
Library name: Mouse_ske_Empty_rep2
Normalized_counts_file_mRNA-seq_ske.tabular
Ske4_Empty

value: Whole tissue


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, proliferated, donor OF01

description:
Library name: OF01_High_5000
OF01_High_5000

value: ITGA11 sorted high, proliferated


title: Primary stromal cells, undifferentiated, control siRNA, donor OF01

description:
Library name: OF01_CT
OF01_CT

value: control siRNA


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, D0, donor OF01

description:
Library name: OF01_High_D0
OF01_High_D0

value: cultured primary stromal cells from iliac crest aspirate


title: Mouse, ske, Empty, rep 3

description:
Library name: Mouse_ske_Empty_rep3
Normalized_counts_file_mRNA-seq_ske.tabular
Ske5_Empty


title: CUMC_E171


title: CUMC_E170


title: Nascent RNA WT 10min rep1

description:
Library name: SAMPLES17
Normalized mRNA expression matrix; Normalized repeat expression matrix

source_name: mESC

value: mESC


title: Control_rep1_Input

description:
Library name: C1_Input
Input fraction (total RNA control) for Control replicate 1


title: CUMC_E169


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, D0, donor EF02

description:
Library name: EF2_Low_D0
EF2_Low_D0


title: CUMC_E168


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, proliferated, donor EF02

description:
Library name: EF2_Low_5000
EF2_Low_5000


title: HSPCs, E76R, rep 3

description: Library name: HSPCs_E76R_rep3

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample by DESeq2.

source_name: HSPCs

growth_protocol: HSPCs were cultured in DMEM supplemented with 15% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin, 20 ng/ml mouse SCF, 10 ng/ml mouse IL-6 and 6 ng/ml mouse IL-3 at 37°C in 5% CO₂ and 5% O₂.

treatment_protocol: The cells were subjected to differentiation into myeloid and megakaryocyte/erythroid lineages using MethoCult GF M3434 supplemented with 20 ng/ml mouse FLT3L and 50 ng/ml mouse TPO. After 9 days, cells were collected.

value: HSPCs


title: Nascent RNA Alkbh5 KO 60min rep2

description:
Library name: SAMPLES16
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Nascent RNA Alkbh5 KO 40min rep2

description:
Library name: SAMPLES14
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: HSPCs, E76R, rep 2

description: Library name: HSPCs_E76R_rep2

value: MethoCult GF M3434 supplemented with 20 ng/ml mouse FLT3L and 50 ng/ml mouse TPO.


title: Nascent RNA WT 20min rep1

description:
Library name: SAMPLES19
Normalized mRNA expression matrix; Normalized repeat expression matrix

value: WT


title: CUMC_E167


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, D0, donor EF02

description:
Library name: EF2_High_D0
EF2_High_D0


title: Nascent RNA Alkbh5 KO 60min rep1

description:
Library name: SAMPLES15
Normalized mRNA expression matrix; Normalized repeat expression matrix

value: Alkbh5 KO


title: HSPCs, E76R, rep 1

description: Library name: HSPCs_E76R_rep1


title: Nascent RNA WT 10min rep2

description:
Library name: SAMPLES18
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Nascent RNA Alkbh5 KO 40min rep1

description:
Library name: SAMPLES13
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, proliferated, donor EF02

description:
Library name: EF2_High_5000
EF2_High_5000


title: HSPCs, E76K, rep 3

description: Library name: HSPCs_E76K_rep3


title: Control_rep2_Input

description:
Library name: C2_Input
Input fraction (total RNA control) for Control replicate 2


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, D0, donor CHS140

description:
Library name: CHS140_Low_D0
CHS140_Low_D0


title: Mouse, ske, Empty, rep 1

description:
Library name: Mouse_ske_Empty_rep1
Normalized_counts_file_mRNA-seq_ske.tabular
Ske2_Empty


title: CUMC_E165


title: Nascent RNA Alkbh5 KO 20min rep2

description:
Library name: SAMPLES12
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, ITGA11 sorted low, proliferated, donor CHS140

description:
Library name: CHS140_Low_5000
CHS140_Low_5000

value: ITGA11 sorted low, proliferated


title: CUMC_E164


title: HSPCs, E76K, rep 2

description: Library name: HSPCs_E76K_rep2


title: CUMC_E166


title: CUMC_E163


title: Nascent RNA Alkbh5 KO 20min rep1

description:
Library name: SAMPLES11
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: HSPCs, D68N, rep 3

description: Library name: HSPCs_D68N_rep3


title: HSPCs, E76K, rep 1

description: Library name: HSPCs_E76K_rep1


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, proliferated, donor CHS140

description:
Library name: CHS140_High_5000
CHS140_High_5000


title: CUMC_E162


title: Primary stromal cells, undifferentiated, ITGA11 sorted high, D0, donor CHS140

description:
Library name: CHS140_High_D0
CHS140_High_D0

value: ITGA11 sorted high, D0


title: Primary stromal cells, undifferentiated, ITGA11 siRNA, donor CHS101

description:
Library name: CHS101_siRNA
CHS101_siRNA

value: ITGA11 siRNA


title: HSPCs, D68N, rep 1

description: Library name: HSPCs_D68N_rep1


title: HSPCs, WT, rep 3

description: Library name: HSPCs_WT_rep3


title: CUMC_E161


title: Nascent RNA Alkbh5 del-cIDR 60min rep1

description:
Library name: SAMPLES7
Normalized mRNA expression matrix; Normalized repeat expression matrix

value: Alkbh5 del-cIDR


title: Nascent RNA Alkbh5 del-cIDR 60min rep2

description:
Library name: SAMPLES8
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: CUMC_E160


title: Primary stromal cells, undifferentiated, donor OF11

description:
Library name: s8
OF11


title: Primary stromal cells, undifferentiated, control siRNA, donor CHS101

description:
Library name: CHS101_CT
CHS101_CT


title: CUMC_E159


title: HSPCs, D68N, rep 2

description: Library name: HSPCs_D68N_rep2


title: HSPCs, WT, rep 2

description: Library name: HSPCs_WT_rep2


title: Nascent RNA Alkbh5 KO 10min rep2

description:
Library name: SAMPLES10
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Nascent RNA Alkbh5 KO 10min rep1

description:
Library name: SAMPLES9
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Nascent RNA Alkbh5 del-cIDR 40min rep2

description:
Library name: SAMPLES6
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: CUMC_E158


title: HSPCs, WT, rep 1

description: Library name: HSPCs_WT_rep1


title: Primary stromal cells, undifferentiated, donor OF07

description:
Library name: s6
OF07


title: CUMC_E157


title: HSPCs, Empty, rep 3

description: Library name: HSPCs_Empty_rep3

value: Empty


title: Nascent RNA Alkbh5 del-cIDR 20min rep2

description:
Library name: SAMPLES4
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Nascent RNA Alkbh5 del-cIDR 40min rep1

description:
Library name: SAMPLES5
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, donor OF10

description:
Library name: s4
OF10


title: Primary stromal cells, undifferentiated, donor OF09

description:
Library name: s3
OF09


title: CUMC_E156


title: HSPCs, Empty, rep 2

description: Library name: HSPCs_Empty_rep2


title: Nascent RNA Alkbh5 del-cIDR 20min rep1

description:
Library name: SAMPLES3
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: HSPCs, Empty, rep 1

description: Library name: HSPCs_Empty_rep1


title: Nascent RNA Alkbh5 del-cIDR 10min rep2

description:
Library name: SAMPLES2
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, donor OF02

description:
Library name: s2
OF02


title: Primary stromal cells, undifferentiated, donor OF01

description:
Library name: s1
OF01


title: Nascent RNA Alkbh5 del-cIDR 10min rep1

description:
Library name: SAMPLES1
Normalized mRNA expression matrix; Normalized repeat expression matrix


title: Primary stromal cells, undifferentiated, donor YF01

description:
Library name: A324
YF01


title: CUMC_E153


title: CUT&tag H3K27ac ALKBH5 del-cIDR rep3

description: Library name: CHe-LJ-38s-T14

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: CUT&Tag

source_name: Whole seedling

extract_protocol:
For caRNA MeRIP-seq, caRNA was isolated and non-ribosome RNA was further enriched using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL of 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 0.5-1 μg non-ribosome RNA, followed by fragmentation using RNA Fragmentation Reagents (Invitrogen). 5% of the fragmented RNA was saved as input. m6A immunoprecipitation was performed using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) according to the manufacturer’s instructions. For nascent RNA-seq in mESCs, cells were incubated in media containing 1 mM EU with different time points and lysed with TRIzol (Invitrogen) for total RNA extraction. An equal amount of RNA extracted from EU-labeled Drosophila cells was added to each sample as a spike-in for further normalization. Nascent RNA was captured using the Click-iT™ Nascent RNA Capture Kit (Invitrogen) according to the manufacturer’s instructions. For CLIP-seq in mESCs, cells were UV crosslinked at 400 mJ/cm² (254 nm) once and nuclei were isolated following the cell fractionation protocol. For ATAC-seq, CUT&Tag, CUT&RUN in mESCs, nuclei were isolated by incubation with complete nuclei isolation buffer (Active Motif) according to the manufacturer’s instructions. For ATAC-seq, CUT&Tag, CUT&RUN in Arabidopsis, nuclei were extracted from 10-day-old seedlings after germination.
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer’s protocol. ATAC-seq was performed by using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s instructions. CUT&Tag was performed by using the CUT&Tag-IT® Core Assay Kit (Active Motif) following the manufacturer’s instructions. CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer’s instructions.

treatment_protocol: All wild-type (WT) and transgenic Arabidopsis lines used in this study were in the Arabidopsis thaliana Columbia (Col-0) background. Seeds were surface sterilized in 10% sodium hypochlorite solution for 10 minutes, washed five times with sterile water, and grown on Murashige and Skoog (MS) medium (PhytoTech Labs) supplemented with 1.5% sucrose and 0.8% agar (pH 5.8). Seedlings were grown under controlled conditions in either a growth chamber or a growth room at 21 °C with a 16-hour light/8-hour dark photoperiod.                                                                                E14TG2a mES cells (ATCC) were cultured in DMEM (Gibco) supplemented with 15% FBS (Gibco), 1% EmbryoMax nucleosides (Sigma), 1% GlutaMAX supplement (Gibco), 1% MEM non-essential amino acids solution (Gibco), 1% Penicillin-Streptomycin (Gibco), 0.1 mM 2-Mercaptoethanol (Gibco), 1000 U/ml LIF (Sigma), 1 µM PD0325901 (Stemcell) and 3 µM CHIR99021 (Stemcell) at 37 °C in a humidified atmosphere with 5% CO2.

value: Whole seedling

tag: ecotype

value: OE ALKBH5 del-cIDR


title: CUMC_E152

value: Epithelium

value: Primary


title: CUMC_E155


title: Primary stromal cells, undifferentiated, donor P42

description:
Library name: A323
P42


title: CUT&tag H3K4me3 ALKBH5 FL rep3

description: Library name: CHe-LJ-38s-T11

value: OE ALKBH5 FL


title: Primary stromal cells, undifferentiated, donor L37

description:
Library name: A178
L37


title: CUMC_E150


title: CUMC_E149


title: Primary stromal cells, undifferentiated, donor L29

description:
Library name: A176
L29


title: CUMC_E154


title: Subject_038_second dose

type: protein

city: Manchester

first: Fidel

last: Ramirez Bencomo

state: England

address: Michael Smith Building

department: FBMH/SBS/EIGen

country: United Kingdom

institute: The University of Manchester

description: Individual participant of trial NCT00962700

hyb_protocol: Slides were blocked with 200 µL of SuperG Blocking Buffer (Grace Biolabs, US) per well and incubated for one hour at room temperature (RT). Washes were done three times with 300μL TBS‐T (0.05% Tween‐20) and once in TBS for 10 min, slides were incubated in the dark for 1hr at 20°C with 100μL of Goat Anti-Human IgG Fc (DyLight 650) pre-adsorbed secondary antibody (ab98622, Abcam, UK), using a working dilution of 1:5000 in blocking agent. The arrays were incubated for IgA detection with 100 μL of Goat Anti-Human IgA alpha chain (DyLight 650) pre-adsorbed secondary antibody (ab96998, Abcam, UK), using a working dilution of 1:5000 in blocking agent. Slides were rinsed in de-ionised water and dried by centrifugation at 200 x g for 2 min.

scan_protocol: Slides were scanned in an InnoScan 710 (Innopsys, France) with the photomultiplier tube set to 100% for 635 nm. Image analysis and data quantification were carried out using Mapix v9.1.0 - Microarray image acquisition and analysis software (Innopsys, France).

data_processing: Microarray spot intensities were quantified using Mapix v9.1.0 Microarray Image Analysis software (Innopsys, France), which utilises automatic background subtraction for each spot. The spot intensities for each protein were recorded in quintuplicate; arithmetic means were determined, and spot intensities for buffer-only controls were subtracted

molecule: protein

source_name: MenOccy Trial

label_protocol: Secondary antibody was purchased from Abcam: Goat anti-human IgG Fc (DyLight® 650) preadsorbed secondary antibody (ab98622, Abcam, UK)

extract_protocol: Human sera collected from an open-label phase II study NCT00962624

value: Blood

value: Serum


title: CUMC_E151


title: CUT&tag H3K4me3 ALKBH5 del-cIDR rep3

description: Library name: CHe-LJ-38s-T13


title: Primary stromal cells, undifferentiated, donor L35

description:
Library name: A177
L35

value: cultured primary stromal cells from iliac crest aspirate


title: CUT&tag H3K4me3 Col-0 rep3

description: Library name: CHe-LJ-38s-T09


title: Subject_038_Pre-immune

description: Individual participant of trial NCT00962699

label: Goat anti-human IgG Fc (DyLight® 650) preadsorbed secondary antibody


title: Subject_038_third dose

description: Individual participant of trial NCT00962701


title: Subject_037_second dose

description: Individual participant of trial NCT00962697


title: Primary stromal cells, undifferentiated, donor L20

description:
Library name: A175
L20


title: Subject_037_third dose

description: Individual participant of trial NCT00962698


title: CUT&RUN Flag ALKBH5 del-cIDR rep3

description: Library name: CHe-LJ-38s-R19

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: CUT&Run


title: Primary stromal cells, undifferentiated, donor L12

description:
Library name: A174
L12


title: CUT&tag H3K27ac ALKBH5 FL rep3

description: Library name: CHe-LJ-38s-T12


title: CUMC_E147


title: Subject_035_third dose

description: Individual participant of trial NCT00962695


title: Primary stromal cells, undifferentiated, donor P36

description:
Library name: 9295
P36


title: CUT&tag H3K27ac Col-0 rep3

description: Library name: CHe-LJ-38s-T10


title: Subject_037_Pre-immune

description: Individual participant of trial NCT00962696


title: CUT&RUN Flag Col-0 rep3

description: Library name: CHe-LJ-38s-R17


title: CUT&RUN Flag ALKBH5 FL rep3

description: Library name: CHe-LJ-38s-R18


title: CUMC_E146


title: Primary stromal cells, undifferentiated, donor P26

description:
Library name: 9294
P26


title: Primary stromal cells, undifferentiated, donor P62

description:
Library name: 9174
P62


title: CUMC_E145


title: caRNA MeRIP-seq IP ALKBH5 del-cIDR mutant rep3

description: Library name: CHe-LJ-38s-P05

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: MeRIP-Seq

value: OE ALKBH5 del-cIDR H204A


title: CUMC_E148


title: Subject_035_second dose

description: Individual participant of trial NCT00962694


title: caRNA MeRIP-seq IP ALKBH5 FL mutant rep3

description: Library name: CHe-LJ-38s-P03

value: OE ALKBH5 FL H204A


title: CUMC_E143


title: CUMC_E144


title: caRNA MeRIP-seq IP ALKBH5 del-cIDR rep3

description: Library name: CHe-LJ-38s-P04