title: healthy control iMGs line 611, knockdown, aso, rep 4

description: Library name: 611_KD_aso_4


title: healthy control iMGs line 611, knockdown, aso, rep 3

status: Public on Mar 21 2026

type: SRA

city: Amsterdam

first: Dilara

last: Ayyildiz

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute For Neuroscience

description: Library name: 611_KD_aso_3

library_source: transcriptomic

data_processing:
High-quality reads were aligned to the reference genome GRCh38.p13 using the STAR aligner (version STAR-2.7.10b) with default settings. Aligned reads were counted using featureCounts from the Subread package (version 2.0.2). Counts were assigned to annotated features based on the GENCODE v42, and only reads overlapping exonic regions were included in downstream analyses.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: human iPSC

extract_protocol:
miRNeasy micro (Qiagen)
DNBSEQ platform at BGI

tag: cell line

value: human iPSC

tag: cell type

value: microglia

tag: sample group


title: healthy control iMGs line 611, knockdown, control, rep 5

description: Library name: 611_KD_ctr_5


title: 32D cell WT RPF rep1

city: Beijing

first: Yue

last: Huo

state: Beijing

address: Dongcheng District, Dongdan 3 Tiao 5 Hao

department: State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences

country: China

institute: Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
Raw reads were trimmed by Cutadapt with parameters "-e 0.1 -O 5 -n 2". Then, reads with distinct inline barcodes were demultiplexed using in-house scripts, and the 10-mer random sequence was appended to the reads name in bam file for later usage.
Low quality reads were filtered by Trimmomatic with parameter "SLIDINGWINDOW: 4:15".
In Ribo-seq library, reads length in 25-50 bp were retained for subsequent analysis. rRNA reads were removed by aligning reads with rRNA reference sequence on NCBI database by Bowtie2.
Cleaned reads were mapped to Mus musculus genome (Ensembl GRCm39.105) by STAR.
Uniquely mapped reads which with "NH: i:1" flag were retained for further analysis by SAMtools and PCR duplicate reads were removed by in-house script based on sharing identical random sequence. To quantify gene expression and translation abundance, we counted sequenced reads mapping to coding sequence (CDS) region by featureCounts.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include mRNA count value for each Sample
Library strategy: Ribo-seq

organism: Mus musculus

source_name: 32D cells

growth_protocol: Mouse 32D cells were cultured in RPMI1640 Medium supplemented with 10% FBS and mouse (m) IL-3 (10 ng/mL)

extract_protocol:
500 µl lysate was prepared as described. 100 µl lysate was used to prepare total RNA library, meanwhile, ribosome footprinting and subsequent library preparation of ribosome protected RNA fragments (RPFs) was performed with 400 µl lysate. Add 10 U RNase I to 400 µl lysate and incubate for 45 min at room temperature with gentle mixing. Then the nuclease digestion was stopped by adding 1 µl RNase inhibitor. RPFs were purified with MicroSpinS-400 columns (GE Healthcare Life Sciences) followed by size selection, which was conducted using 15% TBE-urea gel. rRNAs were depleted with the NEBNext rRNA depletion kit (New England BioLabs). Following end repair and 3'adaptor ligation, RNAs were reverse transcribed using SuperScript III (Thermo Fisher, USA).
cDNA libraries were prepared as described (Nat Protoc. 2012 Jul 26;7(8):1534-50) and sequenced with Illumina NovaSeq 6000 with strand-specific paired-end 150 bp read length.

treatment_protocol: Cells were incubated with 100 µg /ml cycloheximide (CHX, Sigma) at 37°C for 10 min, washed twice with ice-cold PBS containing 100 µg/ml of CHX and lysed in lysis buffer.

value: 32D cells

value: Mouse bone marrow lymphoblastocytes

tag: genotype

value: WT


title: healthy control iMGs line 611, overexpression, control, rep 3

description: Library name: 611_OE_ctr_3


title: FM232, DEK, replicate 1 (ChIP)

city: Suzhou

first: Gongjie

last: Wu

address: Renai Road

institute: Xi'an Jiaotong-Liverpool University

description: Library name: FM232-DEK-1

library_source: genomic

data_processing:
Bowtie2 aligner (v2.4.2), MACS2 peak caller (v.2.1.1.20160309)
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig

molecule: genomic DNA

source_name: Skin

growth_protocol: HeLa S3 and other melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, High glucose, Biosharp) supplemented with 10% fetal bovine serum (VivaCell), Penicillin-Streptomycin 100 X solution (Hyclone) in a standard incubator with 5% CO2 at 37°C. Cells were passaged every two to three days by Trypsin-EDTA solution (Sigma-Aldrich) after washing with 1 x PBS. Primary foreskin melanocytes FM232 were cultured in 254CF medium (Gibco) supplemented with human melanocyte growth supplement (HMGS-2, PMA free, Gibco), Penicillin-Streptomycin 100 X solution (Hyclone).

extract_protocol:
Nuclei were sonicated in a Bioruptor to yield chromatin fragments of ~200-500 bp, as confirmed by agarose gel electrophoresis.
ChIP-seq libraries were prepared and sequenced using single-end 50 bp sequencing (SE50) on the BGISEQ-500 platform (BGI, Wuhan, China).

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, washed in cold PBS and lysed in a high-salt lysis buffer.

tag: tissue

value: Skin

value: Primary melanocytes

tag: treatment


title: 32D cell eCLIP IP rep2

data_processing:
The hChe-RBPs CLIP-seq datasets were processed in accordance with previous studies, and the eCLIP-seq data processing pipeline was available at “https://github.com/YeoLab/eclip”.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include NAT10 eCLIP peak file

extract_protocol:
Cells were pelleted, flash frozen in liquid nitrogen and stored at -80°C. The pellet was lysed with lysis buffer (50 mM Tris–HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate and 1× protease inhibitor cocktail, Roche) followed by further RNase I, and Turbo DNase treatment as described. The lysate was incubated with specific 20 µg antibody overnight at 4°C for immunoprecipitation. eCLIP was performed as described previously (Nature methods, 2016, 13(6): 508-14.)
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7335S).

treatment_protocol: Cells were UV-crosslinked at 150 mJ and 254 nm wavelength in 10-cm plates with 3 ml of cold PBS.

tag: acrip antibody

value: NAT10 antibody


title: healthy control iMGs line 611, knockdown, aso, rep 1

description: Library name: 611_KD_aso_1


title: FM232, DEK, replicate 2 (Input)

description: Library name: FM232-Input-2


title: healthy control iMGs line 611, knockdown, aso, rep 5

description: Library name: 611_KD_aso_5


title: healthy control iMGs line 611, knockdown, control, rep 4

description: Library name: 611_KD_ctr_4


title: FM232, DEK, replicate 3 (ChIP)

description: Library name: FM232-DEK-3


title: FM232, DEK, replicate 2 (ChIP)

description: Library name: FM232-DEK-2


title: FM232, DEK, replicate 1 (Input)

description: Library name: FM232-Input-1


title: healthy control iMGs line 611, knockdown, aso, rep 2

description: Library name: 611_KD_aso_2


title: HeLa S3, DEK, replicate 2 (Input)

description: Library name: HeLaS3-Input-2

source_name: Cervix

value: Cervix

value: HeLa S3

value: Cervical carcinoma cell line


title: HeLa S3, DEK, replicate 1 (Input)

description: Library name: HeLaS3-Input-1


title: HeLa S3, DEK, replicate 2 (ChIP)

description: Library name: HeLaS3-DEK-2


title: healthy control iMGs line 611, knockdown, control, rep 2

description: Library name: 611_KD_ctr_2


title: AD iMGs line 607, baseline, rep 3

description: Library name: 607_OE_mock_3

value: AD iMGs line 607, baseline


title: HeLa S3, DEK, replicate 3 (ChIP)

description: Library name: HeLaS3-DEK-3


title: AD iMGs line 607, baseline, rep 4

description: Library name: 607_OE_mock_4


title: AD iMGs line 607, baseline, rep 5

description: Library name: 607_OE_mock_5


title: healthy control iMGs line 611, knockdown, control, rep 3

description: Library name: 611_KD_ctr_3


title: RPE1 in cell 7SK rep3 DMS

city: Houston

first: Anthony

last: Mustoe

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

description: Library name: RPE1_Incell_7SK_REP3_mod

library_source: other

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.3; https://github.com/Weeks-UNC/shapemapper2)
Parsed mutation files were analyzed using DanceMapper (v1.2; https://github.com/MustoeLab/DanceMapper)
Assembly: sequence files used for alignment are included as supplementary files
Supplementary files format and content: Archives (.tar.gz) include bernouli mixture save files (.bm), normalized N1/3 profiles (profile.txt), and normalized N7 profiles (profile.txtga). A complete description of these files is provided in the DanceMapper and Shapemapper documentation.

molecule: other

extract_protocol:
RNA was extracted from cells using TRIzol reagent (Ambion) or RNeasy Mini Kit (Qiagen).
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription. Amplicon libraries were prepared by 2-step PCR. Ribosomal libaries were prepared via Nextera.

treatment_protocol: RNA modified under variable folding conditions with DMS (or ethanol) for 6 minutes at 37 C, quenched with 20% 2-mercaptoethanol, and ethanol precipitated.

value: DMS treated


title: AD iMGs line 607, baseline, rep 2

description: Library name: 607_OE_mock_2


title: AD iMGs line 607, overexpression, mimic, rep 3

description: Library name: 607_OE_mim_3

value: AD iMGs line 607, overexpression, mimic


title: healthy control iMGs line 611, knockdown, control, rep 1

description: Library name: 611_KD_ctr_1


title: 1478, Mus musculus, Adrenal Gland,Adrenal Gland

status: Public on Mar 25 2026

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox001478

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

source_name: Adrenal Gland,Adrenal Gland

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

value: Adrenal Gland,Adrenal Gland

tag: batch


title: RPE1 in cell 7SK rep2 EtOH

description: Library name: RPE1_Incell_7SK_unmod

value: EtOH control


title: HEK293T 7SK SDA Replicate 1

description:
Library name: HEK293-7SK-V1-SDAUV-1
Cells were treated, RNA was extracted via proteinase K treatment, phenol-chloroform separation, and isopropanol precipitation. Gene specific libraries were amplified by MaP RT and PCR.

data_processing:
fastqs were processed, aligned, and had mutations counted by shapemapper2 software
mutation rates were used for downstream RNP-MaP site calling and z-scoring (see "Analysis of RNA–protein networks with RNP-MaP defines functional hubs on RNA", Weidmann et al. 2021 Nature Biotechnology)
Assembly: 7SK fasta files used for alignment are included as processed data files.
Supplementary files format and content: .fa files are fasta files containg the 7SK sequences (target and primers) used for alignment
Supplementary files format and content: profile.txt files are tab-separated value outputs of shapemapper2, which include mutation rates used for RNP-MaP processing
Supplementary files format and content: NT_thresholds.txt files include calculated thresholds required to be called an RNP-MaP protein binding site
Supplementary files format and content: RNPMaP_RESULTS.csv are comma separated values files containing RNP-MaP site calls and z-scoring, along with relevant depth and reactivity values
Library strategy: RNP-MaP

growth_protocol: HEK293T cells were cultured in DMEM medium supplemented with 10% FBS, 1% penicillin/streptomycin

extract_protocol:
Cells were lysed with proteinase K in an SDS-containing buffer, and RNA was extracted with PCA and precipitated with isopropanol, Total RNA was DNase-treated before purification with SPRI beads.
cDNA was generated by MaP RT with Superscript II including a 7SK-specific primer. Final sequencing libraries were generated by PCR using 7SK-specific primers, with indexing barcodes added in a second round of PCR.

treatment_protocol: Cells were washed twice with 1xPBS and re-covered in 0.5 growth volumes of PBS. 10 mM SDA (or DMSO control) was added and cells were incubated for 10 minutes at 37C before being crosslinked with 2J/cm2 365 nm ultraviolet light on ice

value: 10mM SDA (in DMSO) 37C 10min, 2J/cm2 365 nm UV on ice


title: HEK293T 7SK SDA Replicate 2

description:
Library name: HEK293-7SK-V1-SDAUV-2
Cells were treated, RNA was extracted via proteinase K treatment, phenol-chloroform separation, and isopropanol precipitation. Gene specific libraries were amplified by MaP RT and PCR.


title: HeLa S3, DEK, replicate 1 (ChIP)

description: Library name: HeLaS3-DEK-1


title: AD iMGs line 607, baseline, rep 1

description: Library name: 607_OE_mock_1

value: human iPSC


title: HEK293T 7SK DMSO control

description:
Library name: HEK293-7SK-V1-UV-only
Cells were treated, RNA was extracted via proteinase K treatment, phenol-chloroform separation, and isopropanol precipitation. Gene specific libraries were amplified by MaP RT and PCR.

value: 0.5% DMSO 37C 10min, 2J/cm2 365 nm UV on ice


title: HeLa S3, DEK, replicate 3 (Input)

description: Library name: HeLaS3-Input-3


title: AD iMGs line 607, overexpression, mimic, rep 4

description: Library name: 607_OE_mim_4

value: microglia


title: AD iMGs line 607, overexpression, mimic, rep 2

description: Library name: 607_OE_mim_2


title: SK-Mel-103, DMSO treatment, DEK, replicate 1 (Input)

description: Library name: M9-DM-Input-1

value: Melanoma

value: DMSO


title: RPE1 in cell 7SK rep2 DMS

description: Library name: RPE1_Incell_7SK_REP2_mod


title: AD iMGs line 607, overexpression, mimic, rep 5

description: Library name: 607_OE_mim_5


title: SK-Mel-103, DMSO treatment, DEK, replicate 2 (ChIP)

description: Library name: M9-DM-DEK-2

value: Skin

value: WT


title: AD iMGs line 607, overexpression, mimic, rep 1

description: Library name: 607_OE_mim_1


title: SK-Mel-103, DMSO treatment, DEK, replicate 3 (ChIP)

description: Library name: M9-DM-DEK-3


title: AD iMGs line 607, overexpression, control, rep 2

description: Library name: 607_OE_ctr_2


title: RPE1 Cell free 7SK rep3 EtOH

description: Library name: RPE1_Cell_free_7SK_REP3_unmod


title: RPE1 in cell 7SK rep1 DMS

description: Library name: RPE1_Incell_7SK_REP1_mod


title: RPE1 in cell 7SK rep1 EtOH

description: Library name: RPE1_Incell_7SK_REP1_unmod


title: SK-Mel-103, DMSO treatment, DEK, replicate 1 (ChIP)

description: Library name: M9-DM-DEK-1


title: AD iMGs line 607, overexpression, control, rep 4

description: Library name: 607_OE_ctr_4


title: SK-Mel-103, DMSO treatment, DEK, replicate 2 (Input)

description: Library name: M9-DM-Input-2


title: AD iMGs line 605, baseline, rep 4

description: Library name: 605_OE_mock_4

value: AD iMGs line 605, baseline


title: AD iMGs line 607, overexpression, control, rep 1

description: Library name: 607_OE_ctr_1


title: AD iMGs line 605, baseline, rep 5

description: Library name: 605_OE_mock_5


title: AD iMGs line 607, overexpression, control, rep 3

description: Library name: 607_OE_ctr_3


title: RPE1 Cell free 7SK rep2 DMS

description: Library name: RPE1_Cell_free_7SK_REP2_mod


title: RPE1 Cell free 7SK rep3 DMS

description: Library name: RPE1_Cell_free_7SK_REP3_mod


title: SK-Mel-103, CX-4945 treatment, DEK, replicate 1 (Input)

description: Library name: M9-CX-Input-1


title: SK-Mel-103, CX-4945 treatment, DEK, replicate 2 (Input)

description: Library name: M9-CX-Input-2


title: SK-Mel-103, CX-4945 treatment, DEK, replicate 3 (Input)

description: Library name: M9-CX-Input-3


title: AD iMGs line 605, baseline, rep 1

description: Library name: 605_OE_mock_1


title: AD iMGs line 605, overexpression, mimic, rep 4

description: Library name: 605_OE_mim_4

value: AD iMGs line 605, overexpression, mimic


title: SK-Mel-103, DMSO treatment, DEK, replicate 3 (Input)

description: Library name: M9-DM-Input-3


title: RPE1 Cell free 7SK EtOH

description: Library name: RPE1_Cell_free_7SK_unmod


title: RPE1 Cell free 7SK rep1 DMS

description: Library name: RPE1_Cell_free_7SK_REP1_mod


title: AD iMGs line 605, overexpression, mimic, rep 5

description: Library name: 605_OE_mim_5


title: SK-Mel-103, CX-4945 treatment, DEK, replicate 3 (ChIP)

description: Library name: M9-CX-DEK-3


title: AD iMGs line 605, baseline, rep 3

description: Library name: 605_OE_mock_3


title: AD iMGs line 605, overexpression, mimic, rep 2

description: Library name: 605_OE_mim_2


title: HT-GmMYB21aOE-3

city: Nanjing

first: Jilei

last: Gan

address: No. 666, Binjiang Avenue, Jiangbei New District, Nanjing, Jiangsu Province

institute: Nanjing Agricultural University

description: Library name: HT-GmMYB21aOE-3

data_processing:
stringtie v2.1.3b
Align the Clean Reads of each sample with the specified reference genome for sequence comparison
Perform functional annotation of all genes, including alignment with NR, Swiss-Prot, KEGG, COG, KOG, GO, and Pfam databases.
Assembly: Glycine max Wm82.a4.v1
Supplementary files format and content: tab-delimited text file includes gene counts for each Sample

organism: Glycine max

source_name: flower buds

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: flower buds

value: high temperature


title: AD iMGs line 605, overexpression, control, rep 4

description: Library name: 605_OE_ctr_4


title: Mouse_kidney_NZB/WF1_30 weeks old_rep4

city: Bethesda

first: Kan

last: Jiang

state: MD

address: 9000 Rockville Pike

institute: NIAMS/NIH

description: Library name: s04_D1-well_com_outs

data_processing:
Raw sequencing data were processed with the 10X Genomics space ranger pipeline to generate  FASTQ files
Sequences were aligned to mm10 genome to gene expressin count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: tissue_hires_image.png
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: tissue_positions.csv
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: scalefactors_json.json
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
30 weeks old NZB/WF1 mouse kidney was immediately frozen in Optimal Cutting Temperature media. 15 µm frozen tissue sections were cut with cryostat
Spatial transcriptiome  sequencing libraries were prepared with Visium Spatial Gene Expression library preparation slide (10X Genomics) & Reagent kit according to manufatturer's construction

value: Kidney

tag: age

value: 30 weeks


title: Mouse_kidney_NZB/WF1_30 weeks old_rep3

description: Library name: s03_C1-well_com_outs


title: AD iMGs line 605, baseline, rep 2

description: Library name: 605_OE_mock_2


title: AD iMGs line 605, overexpression, mimic, rep 3

description: Library name: 605_OE_mim_3


title: in cell U1+U2 snRNA EtOH

description: Library name: Incell_U1+U2_unmod


title: AD iMGs line 607, overexpression, control, rep 5

description: Library name: 607_OE_ctr_5


title: HT-GmMYB21aOE-1

description: Library name: HT-GmMYB21aOE-1


title: AD iMGs line 605, overexpression, mimic, rep 1

description: Library name: 605_OE_mim_1


title: AD iMGs line 605, overexpression, control, rep 3

description: Library name: 605_OE_ctr_3


title: healthy control iMGs line 602, baseline, rep 5

description: Library name: 602_OE_mock_5

value: healthy control iMGs line 602, baseline


title: AD iMGs line 605, overexpression, control, rep 5

description: Library name: 605_OE_ctr_5


title: In cell U1+U2 snRNA rep2 DMS

description: Library name: In_cell_U1+U2_rep2_mod

value: DMS treated


title: SK-Mel-103, CX-4945 treatment, DEK, replicate 1 (ChIP)

description: Library name: M9-CX-DEK-1


title: HT-WT-3

description: Library name: HT-WT-3


title: AD iMGs line 605, overexpression, control, rep 1

description: Library name: 605_OE_ctr_1


title: in cell U2 rep3 DMS

description: Library name: Incell_U2_Rep3_mod


title: SK-Mel-103, CX-4945 treatment, DEK, replicate 2 (ChIP)

description: Library name: M9-CX-DEK-2


title: Human RnaseP rep2 EtOH

description: Library name: Human_RnaseP_rep2_unmod

value: EtOH control


title: in cell U1+U2 snRNA rep1 DMS

description: Library name: Incell_U1+U2_rep1_mod


title: AD iMGs line 605, overexpression, control, rep 2

description: Library name: 605_OE_ctr_2


title: in cell U2 rep3 EtOH

description: Library name: Incell_U2_Rep3_unmod


title: HT-GmMYB21aOE-2

description: Library name: HT-GmMYB21aOE-2


title: Mouse_kidney_NZB/WF1_30 weeks old_rep2

description: Library name: s02_B1-well_com_outs


title: healthy control iMGs line 602, baseline, rep 4

description: Library name: 602_OE_mock_4


title: healthy control iMGs line 602, baseline, rep 3

description: Library name: 602_OE_mock_3


title: HT-WT-1

description: Library name: HT-WT-1


title: NZBW_Kidney_30w_rep3

description: Library name: Sample9

data_processing:
Sequencing data were generated with an Illumina Novaseq6000 system.  The FastQ files were produced by processing raw sequencing data using bcl2fastq (v2.20.0)
Subsequently, the reads were aligned to the mouse reference genome mm10 using STAR (v2.7.8a) with default parameters.
Gene-level quantification was performed htseq-count (HTSeq v2.0.1) against the GRCm38 annotation.
The gene counts were used for differential gene expression was assessed using DESeq2 (v1.40.2)
Assembly: mm10
Supplementary files format and content: DeSeq2_metadata.xlsx
Supplementary files format and content: BulkRNA_rawcounts.txt

extract_protocol:
Tri Reagent (Sigma-Aldrich) was used followed by column-based purification with RNA Clean & Concentrator-5 Kit (Zymo Research).
NEBNext Poly(A) mRNA Magnetic Isolation kit (New England BioLabs) was used to generate cDNA libraries. Picogreen dsDNA quantitation assay (Thermo Fisher Scientific) was used to measure the cDNA concentration; cDNA was diluted to 3 nM, cDNA libraries were pooled together


title: NZBW_Kidney_30w_rep2

description: Library name: Sample8


title: Human RnaseP rep2 DMS

description: Library name: Human_RnaseP_rep2_mod


title: NZBW_Kidney_20w_rep3

description: Library name: Sample6


title: healthy control iMGs line 602, baseline, rep 2

description: Library name: 602_OE_mock_2


title: Mouse_kidney_NZB/WF1_30 weeks old_rep1

description: Library name: s01_A1-well_com_outs


title: HT-WT-2

description: Library name: HT-WT-2


title: HeLa in cell 7SK EtOH

description: Library name: HeLa_Incell_7SK_unmod

source_name: HeLa

value: HeLa


title: HeLa in cell 7SK rep2 DMS

description: Library name: HeLa_Incell_7SK_REP2_mod


title: healthy control iMGs line 602, baseline, rep 1

description: Library name: 602_OE_mock_1

value: human iPSC


title: NZBW_Kidney_20w_rep2

description: Library name: Sample5


title: NZBW_Kidney_30w_rep1

description: Library name: Sample7


title: NT-WT-2

description: Library name: NT-WT-2


title: NT-GmMYB21aOE-3

description: Library name: NT-GmMYB21aOE-3


title: healthy control iMGs line 602, overexpression, mimic, rep 1

description: Library name: 602_OE_mim_1


title: Cell free U2 Rep2 DMS

description: Library name: Cell_free_U2_Rep2_mod


title: NT-WT-3

description: Library name: NT-WT-3


title: healthy control iMGs line 602, overexpression, mimic, rep 4

description: Library name: 602_OE_mim_4


title: NZBW_Kidney_20w_rep1

description: Library name: Sample4


title: NT-GmMYB21aOE-2

description: Library name: NT-GmMYB21aOE-2


title: healthy control iMGs line 602, overexpression, mimic, rep 5

description: Library name: 602_OE_mim_5


title: NZBW_Kidney_10w_rep1

description:
Library name: Sample1
original runid: 221122_A00956_0621


title: healthy control iMGs line 602, overexpression, mimic, rep 3

description: Library name: 602_OE_mim_3


title: Cell Free U1 snRNA rep2 EtOH

description: Library name: Cell_Free_U1_snRNA_rep2_unmod


title: NZBW_Kidney_10w_rep2

description: Library name: Sample2


title: healthy control iMGs line 602, overexpression, control, rep 5

description: Library name: 602_OE_ctr_5


title: Cell Free U1 snRNA rep2 DMS

description: Library name: Cell_Free_U1_snRNA_rep2_mod


title: HeLa in cell 7SK rep1 DMS

description: Library name: HeLa_Incell_7SK_REP1_mod


title: NT-GmMYB21aOE-1

description: Library name: NT-GmMYB21aOE-1


title: Cell Free U1+U2 snRNA rep1 EtOH

description: Library name: Cell_Free_U1+U2_unmod


title: Human RnaseP rep1 DMS

description: Library name: Human_RnaseP_rep1_mod


title: NZBW_Kidney_10w_rep3

description: Library name: Sample3


title: snATAC-seq on adult Parhyale T4 and T5 legs, replicate 2

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 Av. Tony Garnier

country: France

institute: CNRS

description: Library name: SN2

library_source: genomic single cell

data_processing:
Sequencing data were processed using the Cell Ranger ATAC software (v1.2.0, 10x Genomics, Pleasanton, CA) to perform alignment, barcode filtering, and peak calling following the standard pipeline.
Assembly: updated version of Phaw_5.0 (GenBank GCA_001587735.2, see https://doi.org/10.5281/zenodo.6566786)
Supplementary files format and content: Filtered cell barcodes and peak locations

organism: Parhyale hawaiensis

source_name: T4 and T5 legs

growth_protocol: We used the Chicago-F inbred line of Parhyale hawaiensis (Dana, 1853). The animals were cultured and embryos were collected in artificial sea water (specific gravity 1.022) using standard methods.

extract_protocol:
T4 and T5 legs were collected by anaesthetising adult animals in 0.02% clove oil in artificial seawater and cutting the legs at the proximal end of the merus (sample L1 and L2) or the basis (sample L3); 28 legs were collected for L1 and L3, 12 legs were collected for L2. Nuclei were isolated on a cold block, by opening each leg longitudinally and scraping the tissue from the cuticle using a surgical knife (Fine Science Tools #10316-14), followed by pipetting 25 times through a P200 micropipette tip in 250 µl of a lysis buffer consisting of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Igepal CA-630, 0.1% Tween-20, and 0.01% digitonin (for samples L1 and L3), or by 5 passes through a 25G x 5/8” needle using a 2.5 ml syringe (for sample L2). An equal volume of wash buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3mM MgCl2; 1% BSA; 0.1% Tween-20) was then added and cuticle pieces were removed by passing the lysate through a 10 μm pluriStrainer cell strainer (pluriSelect #43-10010). After lysis and filtering, nuclei were collected by centrifuging at 4˚C for 10 minutes at 600 rcf. Then,
Library preparation was performed using the 10x Genomics single-cell capturing system. Libraries were prepared using the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 according to the manufacturer’s instructions (User Guide Rev. C).  After extraction, the nuclear pellets were resuspended in 7 μl of 1X Nuclei Isolation Buffer provided by the kit. Nuclei suspensions containing 15,000 nuclei were used for the tagmentation reactions.

value: T4 and T5 legs

tag: Stage

value: Adult


title: healthy control iMGs line 602, overexpression, mimic, rep 2

description: Library name: 602_OE_mim_2

value: microglia


title: NT-WT-1

description: Library name: NT-WT-1


title: healthy control iMGs line 602, overexpression, control, rep 4

description: Library name: 602_OE_ctr_4


title: Human RnaseP rep1 EtOH

description: Library name: Human_RnaseP_rep1_unmod


title: snATAC-seq on adult Parhyale T4 and T5 legs, replicate 1

description: Library name: SN1


title: Whole adult

description:
Library name: nDNA
ATAC-seq assay performed not on dissociated nuclei, but on naked DNA

data_processing:
Reads were mapped to the P. hawaiensis genome (Phaw_5.0, GenBank GCA_001587735.2; updated in Almazán et al. 2022, download at: https://doi.org/10.5281/zenodo.6566786) using bowtie2 version 2.5.4 (Langmead and Salzberg 2012), using very-sensitive-local parameters.
Mapped reads were filtered to remove mitochondrial reads and low quality mapped reads (MAPQ≥20), using SAMtools version 1.21 (Danecek et al. 2021) and BEDtools version 2.31.1 (Quinlan and Hall 2010), and duplicates using Picard MarkDuplicates version 2.27.5 (https://broadinstitute.github.io/picard/).
ATACseq peaks were then identified using MACS2 version 2.2.7.1 (Zhang et al. 2008).
Assembly: updated version of Phaw_5.0 (GenBank GCA_001587735.2, see https://doi.org/10.5281/zenodo.6566786)
Supplementary files format and content: macs2 narrowPeak bed format (peak set called using macs2)

source_name: Whole adult

extract_protocol:
For whole embryo datasets E20, E23 and E24, single embryos at stages S20, S23 and S24, respectively, were collected and placed in the lid of an eppendorf tube, in 50 µl ice-cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). The egg membranes were removed, the cells were dissociated by gentle pipetting, and collected by centrifuging at 800 rcf for 10 min, at 4°C. The supernatant was discarded, the pellet was placed on ice and resuspended in 50 µl tagmentation mix, containing 25 μl 2x TD Buffer (Illumina #FC-121-1030) and 1.5 μl Tn5 Transposase (Illumina #FC-121-1030). Tagmentation was performed at 37°C for 30 minutes, shaking at 300 RPM. For embryonic leg datasets EL1, EL3 and EL3, developing embryonic T4 to T8 legs were collected from pools of stage S25-26 embryos, when white eyes are just starting to be visible. The embryos were dissected in artificial sea water on a cold block; egg membranes were removed and 30-40 legs were collected in ice-cold buffer consisting of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2 and 1% bovine serum albumin (BSA). The legs were then placed in 500 µl ice-cold lysis buffer consisting of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% Igepal CA-630 (Merck #I3021), 1 mM DTT (Roche #10197777001), 0.01% Tween-20 (Sigma #P1379), and 0.001% digitonin (Promega #G944A), and the leg tissue was mechanically dissociated by 5 passes through a 25G x 5/8” needle using a 2.5 ml syringe. The lysate was incubated for 5 minutes on ice and then cuticle debris was removed by filtering with a 10 μm pluriStrainer cell strainer (pluriSelect #43-10010). The nuclei were collected by centrifuging at 4˚C for 5 minutes at 500 rcf, washed in 400 µl ice-cold wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween-20, 1mM DTT), and collected again by centrifuging at 4˚C for 5 minutes at 500 rcf. For adult leg datasets L1, L2, and L3, uninjured T4 and T5 legs were collected by anaesthetising adult animals in 0.02% clove oil in artificial seawater and cutting the legs at the proximal end of the merus (sample L1 and L2) or the basis (sample L3); 28 legs were collected for L1 and L3, 12 legs were collected for L2. Nuclei were isolated on a cold block, by opening each leg longitudinally and scraping the tissue from the cuticle using a surgical knife (Fine Science Tools #10316-14), followed by pipetting 25 times through a P200 micropipette tip in 250 µl of a lysis buffer consisting of 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Igepal CA-630, 0.1% Tween-20, and 0.01% digitonin (for samples L1 and L3), or by 5 passes through a 25G x 5/8” needle using a 2.5 ml syringe (for sample L2). An equal volume of wash buffer (10 mM Tris-HCl pH 7.4; 10 mM NaCl; 3mM MgCl2; 1% BSA; 0.1% Tween-20) was then added and cuticle pieces were removed by passing the lysate through a 10 μm pluriStrainer cell strainer (pluriSelect #43-10010). Nuclei were collected by centrifuging at 4˚C for 5 minutes at 500 rcf (samples L1 and L2) or 10 minutes at 600 rcf centrifugation (sample L3). For the nDNA sample, we generated ATACseq data on genomic DNA from Parhyale hawaiensis that had been purified to remove histones and other proteins ('naked DNA'), to reveal intrinsic biases associated with tagmentation of DNA sequence rather than chromatin. Genomic DNA was extracted from single individuals that were flash frozen in liquid nitrogen, using the NucleoSpin Tissue kit (Macherey Nagel #740952) according to the manufacturer's recommendations.
For all samples except the nDNA sample, tagmentation was performed in 50 µl tagmentation mix, containing 25 µl 2X tagmentation buffer (Diagenode #C01019043) and 2.5 µl Tn5 loaded transposase (Diagenode #C01070012), at 37°C for 30 minutes, shaking at 300 RPM. Then the tagmented DNA was purified using the Qiagen MinElute kit (Qiagen #28204) and amplified by a total of 9-17 PCR cycles using Nextera XT Index kit v2 primers (5 initial cycles followed by qPCR reaction to determine the total number of PCR cycles needed for each library). After PCR amplification, the libraries were purified by AMPure XP beads (Beckman Coulter) and were resuspended in 20 μl nuclease-free water. Tagmention and library preparation for the nDNA sample were performed using the Nextera XT DNA Library kit (Illumina #FC-131-1024) according to the manufacturer's recommendations.

value: Whole adult


title: healthy control iMGs line 602, overexpression, control, rep 2

description: Library name: 602_OE_ctr_2


title: Cell Free U1+U2 snRNA rep1 DMS

description: Library name: Cell_Free_U1+U2_rep1_mod


title: healthy control iMGs line 602, overexpression, control, rep 3

description: Library name: 602_OE_ctr_3


title: healthy control iMGs line 602, overexpression, control, rep 1

description: Library name: 602_OE_ctr_1


title: EP6

city: Columbia

first: Jae-Wook

last: Jeong

state: MO

address: Rutland Drive

department: Obstetrics, Gynecology and Women’s Health

institute: University of Missouri

description: Library name: PtenEx3-4

data_processing:
The raw reads were initially filtered by removing low quality reads (average quality scores >50) and aligned to the mm39 genome and assembled using Star 2.7.9a
Differentially expressed genes (DEGs) were identified by the exact negative binomial test in the EdgeR software
Assembly: mm39
Supplementary files format and content: tab-delimited text file include normalized counts for each file

source_name: uterus

growth_protocol: Pgrcre/+Ptenf/fCtnnb1f(ex3)/+ female mice were generated by breeding Pgrcre/+ Ptenf/f  Rosa26mTmG/mTmG male with Ctnnb1f(ex3)/+Rosa26mTmG/mtmG females.

extract_protocol:
The total RNA from mouse uterus were isolated by QIAGEN RNeasy Mini Kit following the vendor's manual.
The library was prepared by University of Missouri Genomic Technology Coe Total RNA Library Preparation (rRNA depletion) service.

value: uterus

tag: Sex

value: Female

value: 2-weeks of age

value: Pgrcre/+ Pten f/f Ctnnb1 f/(ex3/+) Rosa26 mTmG/mTmG


title: EP1

description: Library name: PtenEx3-1


title: Adult legs T4 and T5, replicate 2

description: Library name: L2

source_name: Adult legs T4 and T5

value: Adult legs T4 and T5


title: P8

description: Library name: Ptend/d-4

value: Pgrcre/+ Pten f/f Rosa26 mTmG/mTmG


title: sample PITT-TN89

city: Pittsburgh

first: Xiaosong

last: Wang

state: Pennsylvania

address: 5150 Centre Ave

department: Pathology

institute: University of Pittsburgh

description:
Library name: PITT-TN89
Batch 1

data_processing:
Quality control test on the sequencing data was done with error rate calculation and a Phred Q20 and Q30 score. All samples passed with error rate (%) < 0.03, Q20 > 97%, and Q30 > 95%.
The preprocessed reads (fastq.gz) were mapped into reference genome (GRCh38.primary_assembly.genome.fa) using Rsubread R package (ver. 1.30.5, Liao et al. 2013).
The transcripts of each sample were assembled based on Transcripts Per Million (TPM) method (unlog values). Sequence read alignments were annotated using gencode.v47.annotation.gtf, mapping gene identifiers to HGNC IDs.
Transcripts of each sample were quantified using the Transcripts Per Million (TPM) method (unlogged values). TPM values for all samples were merged into a single tab-delimited file, where rows represent gene IDs and columns represent samples. Batch normalization was applied to correct for potential batch effects using ComBat (Johnson et al. 2007) from the sva R package (ver. 3.38.0)
Assembly: As reference genome, we downloaded "GRCh38.primary_assembly.genome.fa" file from Ensembl FTP. For gene ID annotation, we downloaded "gencode.v47.annotation.gtf" from GENCODE.
Supplementary files format and content: Tab-delimited file contains batch normalized unlog TPM values for all samples.

source_name: Human Breast Cancer Patient tissue

extract_protocol:
Total RNA was extracted from patient tissues using the standard procedure of Trizol RNA extraction. The primary quantitation and degradation or the extracted RNA were checked by nanodrop and TapeStation. The integrity and purity of RNA were examined by Agilent 2100.
The NovaSeq S4-300 Cycles-XP library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) or TruSeq coding RNA Access (Illumina) following the protocol provided by the manufacturer.

value: Human breast cancer tissue


title: EP2

description: Library name: PtenEx3-2


title: EP3

description: Library name: PtenEx3-3


title: Adult legs T4 and T5, replicate 3

description: Library name: L3


title: sample PITT-TN90_access

description:
Library name: PITT-TN90_access
Batch 1


title: healthy control iMGs line 205, baseline, rep 5

description: Library name: 205_OE_mock_5

value: healthy control iMGs line 205, baseline


title: sample PITT-TN98

description:
Library name: PITT-TN98
Batch 1


title: Embryonic leg stages 25 to 26, replicate 3

description: Library name: EL3

source_name: Embryonic legs

value: Embryonic legs

value: S25 to S26


title: Adult legs T4 and T5, replicate 1

description: Library name: L1


title: sample PITT-TN87

description:
Library name: PITT-TN87
Batch 1


title: healthy control iMGs line 205, baseline, rep 3

description: Library name: 205_OE_mock_3


title: healthy control iMGs line 205, baseline, rep 4

description: Library name: 205_OE_mock_4


title: Embryonic leg stages 25 to 26, replicate 1

description: Library name: EL1


title: P4

description: Library name: Ptend/d-1


title: healthy control iMGs line 205, baseline, rep 1

description: Library name: 205_OE_mock_1


title: Whole embryo, stage 24

description: Library name: E24

source_name: Whole embtyo

value: Whole embtyo


title: sample PITT-TN83

description:
Library name: PITT-TN83
Batch 1


title: P6

description: Library name: Ptend/d-2


title: Embryonic leg stages 25 to 26, replicate 2

description: Library name: EL2


title: shNT_2w_3

first: Yang

last: Zhao

address: Peking University, No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: Sample15

data_processing:
Prepared library was sequenced and mapped by Novogene.
Assembly: mm10
Supplementary files format and content: Comma separated values files

source_name: Cardiac fibroblast post myocardial infarction infected with Mef2c, Gata4, Tbx5, Myocd, Sall4 and shNT, day14

growth_protocol: For isolation of MICFs, hearts were excised from C57BL/6 mice at day 6 post-MI. The infarct region was dissected from surrounding viable myocardium and minced into fragments ≤1 mm³ using razor blades. Minced tissue was digested in 2 mL of digestion solution containing collagenase types I, II, and IV (Gibco, 2 mg/mL total) and dispase II (Sigma, 2 mg/mL) in 6-well plates at 37℃ for 2 hours. The resulting cell suspension was sequentially filtered through 70 µm and 40 µm cell strainers. Cells were pelleted by centrifugation, resuspended in red blood cell lysis buffer (Solarbio) to eliminate erythrocytes, washed, centrifuged again, and resuspended. MICFs were plated in 24-well plates.

extract_protocol:
Total RNA of MICFs was isolated with TRIzol (Thermo Fisher Scientific) followed by extraction using the Direct-Zol RNA Miniprep Kit (Zymo Research, R2062).
RNA from MICFs cells was submitted to Novogene for quantification, RNA-seq library preparation.

treatment_protocol: MICFs were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin-streptomycin.

value: Heart

value: male

value: Cardiac fibroblast

value: wild type


title: sample PITT-TN81

description:
Library name: PITT-TN81
Batch 1


title: sample PITT-TN79

description:
Library name: PITT-TN79
Batch 1


title: sample PITT-TN77

description:
Library name: PITT-TN77
Batch 1


title: healthy control iMGs line 205, overexpression, mimic, rep 3

description: Library name: 205_OE_mim_3

value: human iPSC

value: microglia


title: shNT_1w_2

description: Library name: Sample11

source_name: Cardiac fibroblast post myocardial infarction infected with Mef2c, Gata4, Tbx5, Myocd, Sall4 and shNT, day7


title: shNT_2w_2

description: Library name: Sample14


title: healthy control iMGs line 205, baseline, rep 2

description: Library name: 205_OE_mock_2

source_name: human iPSC


title: Whole embryo, stage 20

description: Library name: E20


title: Whole embryo, stage 23

description: Library name: E23


title: healthy control iMGs line 205, overexpression, mimic, rep 5

description: Library name: 205_OE_mim_5


title: sample PITT-TN76

description:
Library name: PITT-TN76
Batch 1


title: healthy control iMGs line 205, overexpression, mimic, rep 2

description: Library name: 205_OE_mim_2


title: shNT_1w_1

description: Library name: Sample10


title: hBMSCs, 14D OM

city: Seoul

first: Seung Cheol

last: Lee

address: Gwanak ro

country: South Korea

institute: Seoul National University

description:
Library name: Sample7
DEG 14Days_Treated_vs_Control.csv

data_processing:
Raw FASTQ files were processed with FastQC for adapter trimming and removal of low-quality reads. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 v2.2.1. Differential expression analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: CSV files including the DEGs

source_name: Bone marrow derived stromal cells

growth_protocol:
Osteogenic differentiation
hBMSCs (PCS-500-012, ATCC, USA) at passages 3–4 was cultured in α-MEM (Welgene, LM008-01) supplemented with 10% fetal bovine serum (FBS; Gibco, 16000-044) and 1% penicillin-streptomycin (Gibco, 15140-122). Cells were maintained at 37°C in a humidified 5% CO₂ incubator until reaching 80% confluency.

extract_protocol:
Total RNA was extracted using TRIzol® reagent (Thermo Fisher Scientific, Rockford, USA). Utilizing an Agilent Bioanalyzer RNA ScreenTape kit (Agilent, 5067–5576), the integrity of the RNA (RIN) was verified. All samples with RIN value > 8.0 were used for sequencing.
RNA-seq libraries were prepared using the SRSLY Library Prep kit (Claretbio, CBS-K155B-24) according to the manufacturer's instructions. First- and second-strand cDNA synthesis was performed using the SuperScript III First-Strand Synthesis System (Invitrogen, 18080-051) and E. coli DNA polymerase I (Enzynomics, DP002S), respectively. mRNA was enriched and fragmented using oligo(dT) selection, followed by adapter ligation and PCR amplification.

treatment_protocol: Osteogenic differentiation was induced at approximately 80% confluency by culturing the hADMSCs in a differentiation medium containing 10 mM β-glycerophosphate (Sigma-Aldrich, G9422), 50 µM ascorbic acid (Sigma-Aldrich, A4403), and 0.1 µM dexamethasone (Sigma-Aldrich, D4902). The medium was refreshed every 2 days, and DAB was applied 8 hours per day (18 Hz, 20 V).

value: Bone marrow derived stromal cells

value: hBMSCs

value: Mesenchymal stromal cells

value: 14D control


title: sample PITT-TN85

description:
Library name: PITT-TN85
Batch 1


title: hBMSCs, 7D OM+E

description:
Library name: Sample6
DEG Days7_Treated_vs_Control.csv

value: 7D DAB-stimulated


title: healthy control iMGs line 205, overexpression, mimic, rep 1

description: Library name: 205_OE_mim_1


title: shNT_1w_3

description: Library name: Sample12


title: healthy control iMGs line 205, overexpression, mimic, rep 4

description: Library name: 205_OE_mim_4


title: P7

description: Library name: Ptend/d-3

value: uterus

value: Female

value: 2-weeks of age

value: Pgrcre/+ Pten f/f Rosa26 mTmG/mTmG


title: sample PITT-TN74

description:
Library name: PITT-TN74
Batch 1

value: Human breast cancer tissue


title: hBMSCs, 14D OM+E

description:
Library name: Sample8
DEG 14Days_Treated_vs_Control.csv

value: 14D DAB-stimulated


title: shCalr_2w_3

description: Library name: Sample9

source_name: Cardiac fibroblast post myocardial infarction infected with Mef2c, Gata4, Tbx5, Myocd, Sall4 and shCalr, day14

value: Heart


title: shNT_2w_1

description: Library name: Sample13

value: male


title: shCalr_2w_2

description: Library name: Sample8

value: Cardiac fibroblast


title: hBMSCs, 7D OM

description:
Library name: Sample5
DEG Days7_Treated_vs_Control.csv

value: 7D control


title: sample PITT-TN71

description:
Library name: PITT-TN71
Batch 1


title: sample PITT-TN68

description:
Library name: PITT-TN68
Batch 1


title: sample PITT-TN61

description:
Library name: PITT-TN61
Batch 1


title: healthy control iMGs line 205, knockdown, control, rep 5

description: Library name: 205_KD_ctr_5

value: human iPSC


title: Hematopoietic stem cells, derived by bone marrow aspiration subject n

city: Be'er Sheva

first: Roy

last: Pollak

address: David Ben Gurion Blvd 1

department: Life sciences

country: Israel

institute: Ben Gurion University

description:
Library name: subject_n
Smart-seq2

library_source: transcriptomic single cell

data_processing:
Reads from each subject were mapped to the human genome (hg38) using HISAT2 (v2.0.5). The number of RNA molecules of each gene per each cell was calculated and normalized with SALMON (v0.12.0) employing transcript per million (TPM) normalization. Based on the TPM normalized values, an expression matrix was generated, representing the normalized expression level of each gene per cell.
Assembly: hg38
Supplementary files format and content: MDS_expression_matrix.csv file specifies gene expression level of each gene per cell normalized using TPM normalization.
Supplementary files format and content: metadata_MDS_GEO_submission.csv file specifies the relevant metadata.

molecule: polyA RNA

source_name: Bone marrow

extract_protocol:
To identify HSC, fresh BM samples were enriched over Lymphoprep™ (Ficoll with a density of 1.077 g/l). Cells of the mononuclear layer were collected and washed once with sample medium (phosphate-buffered saline supplemented with 2 mM EDTA and 2% serum). Cells were stained for 1 h on ice using the fluorescence-conjugated antibodies, CD34-FITC, CD38-ReCy7, CD90-PrcpCy5.5, and CD45RA-APC, and biotinylated lineage-antibodies, including anti-hCD3, hCD19, Mac1, and Ter119. After washing, DAPI and streptavidin, Pacific Blue™ conjugate were added, and HSC were sorted by FACS by immunophenotype Lin-CD34+, CD38-, CD90+, CD45RA-, CD49f. The population of HSC was then re-sorted as single cells into a 384-plate, using the same HSC gates. Each well of the plate contained Smart-Seq2 lysis-and-storage buffer. We estimated the FACS drop volume at roughly 0.001 µl (using a 70-µm nozzle).
Plates were frozen to -80°C. Processing of samples, library preparation, and sequencing were carried out at the INCPM facility (Rehovot, Israel). Sequencing of 1,150 cells was performed according to the Smart-seq2 protocol.

value: Bone marrow

value: Hematopoietic stem cell


title: hBMSCs, 4D OM

description:
Library name: Sample3
DEG Days4_Treated_vs_Control.csv

value: Bone marrow derived stromal cells

value: hBMSCs

value: 4D control


title: hBMSCs, 2D OM+E

description:
Library name: Sample2
DEG Days2_Treated_vs_Control.csv

value: Mesenchymal stromal cells

value: 2D DAB-stimulated


title: hBMSCs, 4D OM+E

description:
Library name: Sample4
DEG Days4_Treated_vs_Control.csv

value: 4D DAB-stimulated


title: healthy control iMGs line 205, overexpression, control, rep 5

description: Library name: 205_OE_ctr_5

data_processing:
High-quality reads were aligned to the reference genome GRCh38.p13 using the STAR aligner (version STAR-2.7.10b) with default settings. Aligned reads were counted using featureCounts from the Subread package (version 2.0.2). Counts were assigned to annotated features based on the GENCODE v42, and only reads overlapping exonic regions were included in downstream analyses.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each sample.

extract_protocol:
miRNeasy micro (Qiagen)
DNBSEQ platform at BGI

value: microglia


title: shCalr_1w_1

description: Library name: Sample4

source_name: Cardiac fibroblast post myocardial infarction infected with Mef2c, Gata4, Tbx5, Myocd, Sall4 and shCalr, day7

value: wild type


title: sample PITT-TN72

description:
Library name: PITT-TN72
Batch 1

value: Human breast cancer tissue


title: healthy control iMGs line 205, overexpression, control, rep 2

description: Library name: 205_OE_ctr_2


title: sample PITT-TN64

description:
Library name: PITT-TN64
Batch 1


title: healthy control iMGs line 205, overexpression, control, rep 4

description: Library name: 205_OE_ctr_4


title: shCalr_1w_2

description: Library name: Sample5


title: healthy control iMGs line 205, overexpression, control, rep 3

description: Library name: 205_OE_ctr_3


title: healthy control iMGs line 205, knockdown, control, rep 4

description: Library name: 205_KD_ctr_4


title: shCalr_2w_1

description: Library name: Sample7


title: sample PITT-TN70

description:
Library name: PITT-TN70
Batch 1


title: shCalr_1w_3

description: Library name: Sample6


title: MICF_0w_3

description: Library name: Sample3

source_name: Cardiac fibroblast post myocardial infarction, day0


title: hBMSCs, 2D OM

description:
Library name: Sample1
DEG Days2_Treated_vs_Control.csv

value: 2D control


title: Hematopoietic stem cells, derived by bone marrow aspiration subject m

description:
Library name: subject_m
Smart-seq2


title: sample PITT-TN55

description:
Library name: PITT-TN55
Batch 1


title: healthy control iMGs line 205, knockdown, control, rep 3

description: Library name: 205_KD_ctr_3


title: healthy control iMGs line 205, overexpression, control, rep 1

description: Library name: 205_OE_ctr_1


title: Hematopoietic stem cells, derived by bone marrow aspiration subject l

description:
Library name: subject_l
Smart-seq2


title: sample PITT-TN54

description:
Library name: PITT-TN54
Batch 1


title: sample PITT-TN51

description:
Library name: PITT-TN51
Batch 1


title: Hematopoietic stem cells, derived by bone marrow aspiration subject k

description:
Library name: subject_k
Smart-seq2


title: MICF_0w_1

description: Library name: Sample1

value: Heart


title: MICF_0w_2

description: Library name: Sample2

value: male


title: healthy control iMGs line 205, knockdown, control, rep 1

description: Library name: 205_KD_ctr_1


title: healthy control iMGs line 205, knockdown, aso, rep 4

description: Library name: 205_KD_aso_4


title: Hematopoietic stem cells, derived by bone marrow aspiration subject h

description:
Library name: subject_h
Smart-seq2


title: healthy control iMGs line 205, knockdown, control, rep 2

description: Library name: 205_KD_ctr_2


title: meRIP IP rep2

description: Library name: Sample 2

data_processing:
Low-quality reads were removed by Trimmomatic software, and rRNA reads were filtered by Bowtie2 software. Clean reads were aligned to the Mus musculus genome (Ensembl GRCm39) using STAR software. The m6A-enriched peaks versus the immunoprecipitation (input) were detected using the R packages “MeTPeak” (p value < 10e-5 & fold-enrichment > 1.5). The distribution of peaks across the mRNA were plotted by R packages “Guitar”. Enrichment of m6A sites in the CDS and UTR regions was calculated by R package “ChIPseeker”. Analysis of motif was performed with HOMER findMotifsGenome.p1 with parameter “rna” (v4.10.3 version).  The repeatability between two biological replicates was evaluated by Pearson correlation coefficient with read coverages in m6A peak regions, which generated from deepTools “multiBamSummary BED-file”.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include meRIP peak file

source_name: BMDCs

extract_protocol:
Total RNAs extracted from the BMDCs were purified with PolyATract mRNA Isolation System. Chemically fragmented RNA (100 nucleotides) was incubated with an m6A antibody for immunoprecipitation by using the Magna methylated RNA immune precipitation (MeRIP) m'A Kit. The obtained m6A-containing mRNA was analyzed by high-throughput sequencing.
For high-throughput sequencing, the purified RNA fragments were applied for library construction using the TIANSeq Fast RNA Library Kit for Illumina (TIANGEN). The resulting libraries were sequenced on a Novaseq 6000 platform with paired-end 150-bp read length. The library preparation and high-throughput sequencing were conducted by TIANGEN (Beijing, China). Low-quality reads were removed by Trimmomatic software, and rRNA reads were filtered by Bowtie2 software.

value: BMDCs

value: Murine cells

value: m6A antibody


title: Hematopoietic stem cells, derived by bone marrow aspiration subject g

description:
Library name: subject_g
Smart-seq2

value: Bone marrow


title: sample PITT-TN49_access

description:
Library name: PITT-TN49_access
Batch 1


title: Hematopoietic stem cells, derived by bone marrow aspiration subject e

description:
Library name: subject_e
Smart-seq2

value: Hematopoietic stem cell


title: sample PITT-TN158

description:
Library name: PITT-TN158
Batch 2


title: healthy control iMGs line 205, knockdown, aso, rep 2

description: Library name: 205_KD_aso_2

value: human iPSC


title: meRIP Input rep1

description: Library name: Sample 3


title: sample PITT-TN49

description:
Library name: PITT-TN49
Batch 1


title: Hematopoietic stem cells, derived by bone marrow aspiration subject f

description:
Library name: subject_f
Smart-seq2


title: RIP IP rep1

description: Library name: Sample 1

data_processing:
Low-quality reads were removed by Trimmomatic software, and rRNA reads were filtered by Bowtie2 software. Clean reads were aligned to the Mus musculus genome (Ensembl GRCm39) using STAR software. The YTHDF1 RIP peaks versus the immunoprecipitation (input) were detected using the MACS software (p value < 10e-5 & fold-enrichment > 3).
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include RIP peak file

extract_protocol:
BMDCs were dissolved in RIP 1ysis buffer and incubated with magnetic bead-YTHDF1 antibody RIP immunoprecipitation buffer. Then the obtained immunoprecipitation was washed with RIP buffer and purified with proteinase K to get the immunoprecipitation RNAs. RIP lysis product and place without immunoprecipitation were applied as “input”. Co-immunoprecipitated and input RNAs were extracted with Trizol (Invitrogen).
For RIP-sequencing, rRNAs were depleted based on the NEBNext rRNA depletion kit, then was used for library construction with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp.

value: YTHDF1 antibody


title: healthy control iMGs line 205, knockdown, aso, rep 5

description: Library name: 205_KD_aso_5


title: sample PITT-TN50

description:
Library name: PITT-TN50
Batch 1


title: 32D cell WT 5hr rep2

data_processing:
Analysis of RNA-seq datasets, reads were aligned to Mus musculus genome (Ensembl GRCm39.105) using STAR PE mode with the default parameter, and uniquely mapped reads were retained for further analysis. FeatureCounts were used for calculating annotated gene counts.
For RNA lifetime profiling, the ERCC sequence were download from Thermofisher website (https://www.thermofisher.com). DESeq2 was used to calculate ERCC spike-in RNA size factors, which were then applied to normalize library size in each replicate.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include gene count value for each Sample

source_name: Mouse bone marrow

growth_protocol: Lineage-depleted bone marrow cells were cultured in StemSpan SFEM medium (Stem Cell Technologies) supplemented with 10 ng/mL rmSCF , 20 ng/mL rmTPO 10 μg/mL heparin (Sigma), and 0.5 × penicillin/streptomycin at 37 °C.

extract_protocol:
Total RNA was extracted and used for RNA-seq analysis.
For RNA sequencing, an equal amount of ERCC RNA spike-in control (Thermo Scientific, Waltham, MA) was added to the total RNA samples as internal control before library construction. RNA lifetime profiling was generated from two biological replicates. For RNA lifetime profiling in LT-HSCs, Smart seq II libraries were prepared by Annoroad Gene Technology (China).

treatment_protocol: Cells were treated with 5 μM actinomycin D (MCE) to inhibit mRNA transcription. HSCs were sorted at 0 h, 1h, 3h, 4h or 5 h post-treatment.

value: Mouse bone marrow

value: LT-HSCs


title: healthy control iMGs line 205, knockdown, aso, rep 3

description: Library name: 205_KD_aso_3


title: 32D cell WT 5hr rep1


title: sample PITT-TN157

description:
Library name: PITT-TN157
Batch 2


title: meRIP IP rep1

description: Library name: Sample 1


title: meRIP Input rep2

description: Library name: Sample 4


title: Hematopoietic stem cells, derived by bone marrow aspiration subject d

description:
Library name: subject_d
Smart-seq2


title: sample PITT-TN154

description:
Library name: PITT-TN154
Batch 2


title: sample PITT-TN159

description:
Library name: PITT-TN159
Batch 2


title: EV1-AN465_IP

city: Guangxi

first: Jun

last: Meng

address: ShuangYong Road

institute: Guangxi Medical University

description:
Library name: EV1-AN465_IP
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease

data_processing:
Sequencing reads were aligned to the hg38 genome using HISAT2, transcripts were quantified with StringTie, and m6A peaks were identified using sliding windows and analyzed with HOMER.
Assembly: The hg38 human genome was used as the reference for alignment.
Supplementary files format and content: Processed data included aligned reads, TPM values, m6A peak locations, and motif enrichment results, with peak distributions visualized on a 'mega gene.

source_name: RD cell line

extract_protocol:
Total RNA was extracted using Trizol reagent and assessed for quality with an Agilent Bioanalyzer.
mRNA was isolated, fragmented, enriched for m6A, and used to construct a strand-specific cDNA library.

treatment_protocol: EV71 infection was conducted in the RD cell line

value: RD cell line


title: RIP IP rep2

description: Library name: Sample 2


title: 32D cell WT 3hr rep2


title: sample PITT-TN144_access

description:
Library name: PITT-TN144_access
Batch 1


title: AN1-AN465_IP

description:
Library name: AN1-AN465_IP
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: healthy control iMGs line 205, knockdown, aso, rep 1

description: Library name: 205_KD_aso_1


title: sample PITT-TN153

description:
Library name: PITT-TN153
Batch 2


title: 1.5x dms Saturated TPP rep1 DMS

description: Library name: 1_5x_dms_Saturated_TPP_rep1_mod

data_processing:
Fastq files were aligned and parsed using ShapeMapper2 (v.2.3; https://github.com/Weeks-UNC/shapemapper2)
Parsed mutation files were analyzed using DanceMapper (v1.2; https://github.com/MustoeLab/DanceMapper)
Assembly: sequence files used for alignment are included as supplementary files
Supplementary files format and content: Archives (.tar.gz) include bernouli mixture save files (.bm), normalized N1/3 profiles (profile.txt), and normalized N7 profiles (profile.txtga). A complete description of these files is provided in the DanceMapper and Shapemapper documentation.

organism: Escherichia coli

source_name: in vitro transcript

extract_protocol:
RNA was extracted from cells using TRIzol reagent (Ambion) or RNeasy Mini Kit (Qiagen).
RNA was converted to cDNA using mutational profiling (MaP) reverse transcription. Amplicon libraries were prepared by 2-step PCR. Ribosomal libaries were prepared via Nextera.

value: DMS treated

value: in vitro transcript


title: Hematopoietic stem cells, derived by bone marrow aspiration subject c

description:
Library name: subject_c
Smart-seq2


title: sample PITT-TN156

description:
Library name: PITT-TN156
Batch 2


title: sample PITT-TN141

description:
Library name: PITT-TN141
Batch 1


title: 32D cell WT 1hr rep2

value: wild type


title: 32D cell WT 1hr rep1


title: sample PITT-TN140

description:
Library name: PITT-TN140
Batch 2

value: Human breast cancer tissue


title: 1x dms sub-saturated TPP rep 1 DMS

description: Library name: 100nM_TPP_REP1_mod


title: sample PITT-TN138_access

description:
Library name: PITT-TN138_access
Batch 1


title: AN2-AN465_input

description:
Library name: AN2-AN465_input
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: oePsbS_CA1_CA2 , bicarbonate, rep3

city: Warsaw

first: Piotr

last: Gawroński

address: Nowoursynowska Street 159

country: Poland

institute: Warsaw University of Life Sciences

description: Library name: CA1_23K

data_processing:
Raw sequencing reads were quantified using Salmon (Patro et al., 2017). Transcript-level abundances were estimated by quasi-mapping reads to the Arabidopsis thaliana reference transcriptome (TAIR10, Ensembl Plants release 52).
Assembly: Reads were mapped to Arabidopsis thaliana cDNAs (Ensembl, TAIR10, release 52).
Supplementary files format and content: Processed data files consist of transcript-level quantification tables generated by Salmon. Each file corresponds to a single RNA-seq sample and is provided in tab-delimited text format (quant.sf). The files contain estimated transcript abundances obtained by quasi-mapping reads to the Arabidopsis thaliana reference transcriptome (TAIR10). Each table includes the following columns: transcript identifier (Name), transcript length (Length), effective transcript length used for abundance estimation (EffectiveLength), transcripts per million (TPM), and the estimated number of reads assigned to the transcript (NumReads).

organism: Arabidopsis thaliana

source_name: rosette leaves

extract_protocol:
Total RNA was extracted from Arabidopsis thaliana rosette tissue using the Spectrum Plant Total RNA Kit (Sigma-Aldrich) according to the manufacturer’s instructions. Residual genomic DNA was removed by DNase I treatment using the DNA-free Kit (Ambion, Applied Biosystems) for 30 min. RNA concentration was measured using a NanoDrop UV–Vis spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed using the Experion Automated Electrophoresis System (Bio-Rad).
Strand-specific mRNA-seq libraries were prepared from total RNA using the TruSeq Stranded Sample Prep Kit (Illumina) according to the manufacturer’s instructions.

value: rosette leaves

value: oePsbS, oeCA1, oeCA2

value: bicarbonate


title: oePsbS_CA1_CA2 , bicarbonate, rep2

description: Library name: CA1_22K


title: 32D cell Nat10-/- 5hr rep1

value: Nat10 deficiency


title: 1x dms no ligand TPP DMS

description: Library name: unsatTPP_1x_mod


title: EV2-AN465_IP

description:
Library name: EV2-AN465_IP
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: 32D cell Nat10-/- 3hr rep2


title: Hematopoietic stem cells, derived by bone marrow aspiration subject b

description:
Library name: subject_b
Smart-seq2


title: TPP EtOH

description: Library name: TPP_unmod

value: EtOH control


title: sample PITT-TN137

description:
Library name: PITT-TN137
Batch 2


title: sample PITT-TN155

description:
Library name: PITT-TN155
Batch 2


title: 1x dms saturated TPP DMS

description: Library name: satTPP_1x_mod


title: EV2-AN465_input

description:
Library name: EV2-AN465_input
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: AN2-AN465_IP

description:
Library name: AN2-AN465_IP
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: oePsbS_CA1 , bicarbonate, rep2

description: Library name: CA12K

value: oePsbS, oeCA1


title: 1.5x dms Saturated TPP rep1 EtOH

description: Library name: 1_5x_dms_Saturated_TPP_rep1_unmod


title: sample PITT-TN136

description:
Library name: PITT-TN136
Batch 1


title: 1.5x dms Saturated TPP rep2 EtOH

description: Library name: 1_5x_dms_Saturated_TPP_rep2_unmod


title: 1.5x dms Saturated TPP rep2 DMS

description: Library name: 1_5x_dms_Saturated_TPP_rep2_mod


title: 32D cell Nat10-/- 1hr rep2


title: saturated TPP standard marathonRT EtOH

description: Library name: satTPP_mara_ph83_unmod


title: 1x dms sub-saturated TPP rep 2 DMS

description: Library name: 100nM_TPP_REP2_mod


title: sample PITT-TN144

description:
Library name: PITT-TN144
Batch 1


title: oePsbS_CA1, bicarbonate, rep1

description: Library name: CA11K


title: 32D cell WT 3hr rep1


title: 1x dms sub-saturated TPP rep 3 DMS

description: Library name: 100nM_TPP_REP3_mod


title: EV1-AN465_input

description:
Library name: EV1-AN465_input
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: 32D cell WT 0hr rep2


title: oePsbS, bicarbonate, rep2

description: Library name: oePsbS2K

value: oePsbS


title: saturated TPP standard marathonRT 1.5x DMS

description: Library name: satTPP_mara_ph83_mod


title: 1x dms sub-saturated TPP EtOH

description: Library name: 100nM_TPP_REP1_unmod


title: AN1-AN465_input

description:
Library name: AN1-AN465_input
A Novel Therapeutic Targeting METTL3 Inhibition in Hand, Foot, and Mouth Disease


title: oePsbS_CA1 , bicarbonate, rep3

description: Library name: CA13K


title: sample PITT-TN138

description:
Library name: PITT-TN138
Batch 1


title: sample PITT-TN134

description:
Library name: PITT-TN134
Batch 1


title: oePsbS, bicarbonate, rep1

description: Library name: oePsbS1K


title: 32D cell Nat10-/- 5hr rep2


title: 32D cell Nat10+/- KO2 9hr rep2

source_name: 32D cells

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen).
For RNA sequencing, an equal amount of ERCC RNA spike-in control (Thermo Scientific, Waltham, MA) was added to the total RNA samples as internal control before library construction. Sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit.  RNA lifetime profiling was generated from two biological replicates.

treatment_protocol: Cells were treated with 0.05 µg/ml actinomycin D and collected at indicated time points.

value: 32D cells

value: Mouse bone marrow lymphoblastocytes


title: npq4, bicarbonate, rep3

description: Library name: npq4-13K


title: 32D cell Nat10+/- KO2 9hr rep1


title: sample PITT-TN139

description:
Library name: PITT-TN139
Batch 1

source_name: Human Breast Cancer Patient tissue


title: 32D cell WT 0hr rep1


title: sample PITT-TN131

description:
Library name: PITT-TN131
Batch 1


title: Ecoli in cell tmRNA rep1 EtOH

description: Library name: Ecoli_incell_tmRNA_rep1_unmod


title: oePsbS_CA1_CA2 , bicarbonate, rep1

description: Library name: CA1_21K


title: 32D cell Nat10-/- 0hr rep2


title: 32D cell Nat10-/- 1hr rep1


title: 32D cell Nat10-/- 3hr rep1


title: sample PITT-TN127

description:
Library name: PITT-TN127
Batch 1


title: oePsbS, bicarbonate, rep3

description: Library name: oePsbS3K


title: 32D cell Nat10+/- KO2 6hr rep1


title: 32D cell Nat10+/- KO2 3hr rep1


title: 32D cell Nat10+/- KO2 3hr rep2


title: sample PITT-TN122

description:
Library name: PITT-TN122
Batch 1


title: Ecoli cell free tmRNA rep1 DMS

description: Library name: Ecoli_cellfree_tmRNA_rep1_mod


title: Ecoli in cell tmRNA rep2 EtOH

description: Library name: Ecoli_incell_tmRNA_rep2_unmod


title: Col0, bicarbonate, rep3

description: Library name: Col-03K


title: sample PITT-TN135

description:
Library name: PITT-TN135
Batch 1


title: 32D cell Nat10+/- KO2 6hr rep2


title: Col0, bicarbonate, rep2

description: Library name: Col-02K


title: npq4, bicarbonate, rep1

description: Library name: npq4-11K


title: ecoli tmRNA EtOH

description: Library name: ecoli_tmRNA_unmod


title: Ecoli in cell tmRNA rep1 DMS

description: Library name: Ecoli_incell_tmRNA_rep1_mod


title: npq4, bicarbonate, rep2

description: Library name: npq4-12K


title: sample PITT-TN134_access

description:
Library name: PITT-TN134_access
Batch 1


title: 32D cell Nat10+/- KO2 0hr rep1


title: 32D cell Nat10-/- 0hr rep1


title: sample PITT-TN133

description:
Library name: PITT-TN133
Batch 2


title: 32D cell Nat10+/- KO2 0hr rep2


title: oePsbS_CA1_CA2 , water, rep3

description: Library name: CA1_23

value: control


title: sample PITT-TN132

description:
Library name: PITT-TN132
Batch 1


title: 23S rRNA amplicon 3 mM MnCl pH8.3 RT

description: Library name: 23s_rRNA_amplicon_3mmph83

value: Untreated


title: sample PITT-TN121

description:
Library name: PITT-TN121
Batch 1


title: sample PITT-TN120

description:
Library name: PITT-TN120
Batch 1


title: 32D cell WT 9hr rep2


title: Col0, bicarbonate, rep1

description: Library name: Col-01K


title: Ecoli in cell tmRNA rep2 DMS

description: Library name: Ecoli_incell_tmRNA_rep2_mod


title: 23S rRNA amplicon 2.5 mM MnCl pH8.3 RT

description: Library name: 23s_rRNA_amplicon_25mmph83


title: 32D cell WT 9hr rep1


title: sample PITT-TN116_access

description:
Library name: PITT-TN116_access
Batch 1


title: 32D cell WT 6hr rep1


title: Ecoli cell free tmRNA rep2 DMS

description: Library name: Ecoli_cellfree_tmRNA_rep2_mod


title: 23S rRNA amplicon 1 mM MnCl pH8.3 RT

description: Library name: 23s_rRNA_amplicon_1mmph83


title: sample PITT-TN108

description:
Library name: PITT-TN108
Batch 1


title: 23S rRNA amplicon 1 mM MnCl pH7.5 RT

description: Library name: 23s_rRNA_amplicon_1mmph75


title: denatured ecoli tmRNA DMS

description: Library name: denatured_ecoli_tmRNA_mod


title: oePsbS_CA1_CA2 , water, rep2

description: Library name: CA1_22


title: sample PITT-TN117

description:
Library name: PITT-TN117
Batch 1


title: oePsbS_CA1, water, rep1

description: Library name: CA11


title: sample PITT-TN107

description:
Library name: PITT-TN107
Batch 1


title: 23S rRNA amplicon 0.5 mM MnCl pH8.3 RT

description: Library name: 23s_rRNA_amplicon_05mmph83


title: oePsbS, water, rep2

description: Library name: oePsbS2


title: 32D cell WT 0hr rep2


title: oePsbS, water, rep1

description: Library name: oePsbS1


title: 23S rRNA amplicon 1 mM MnCl pH8 RT

description: Library name: 23s_rRNA_amplicon_1mmph8


title: 32D cell WT 6hr rep2


title: oePsbS_CA1_CA2 , water, rep1

description: Library name: CA1_21


title: sample PITT-TN106

description:
Library name: PITT-TN106
Batch 1


title: sample PITT-TN115

description:
Library name: PITT-TN115
Batch 1


title: sample PITT-TN118

description:
Library name: PITT-TN118
Batch 1


title: 23S rRNA amplicon 2 mM MnCl pH8.3 RT

description: Library name: 23s_rRNA_amplicon_2mmph83


title: sample PITT-TN125

description:
Library name: PITT-TN125
Batch 1


title: 23S rRNA amplicon 1 mM MnCl pH8.5 RT

description: Library name: 23s_rRNA_amplicon_1mmph85


title: sample PITT-TN111

description:
Library name: PITT-TN111
Batch 2


title: 16S rRNA amplicon 3 mM MnCl pH8.3 RT

description: Library name: 16s_rRNA_amplicon_3mmph83


title: oePsbS_CA1 , water, rep3

description: Library name: CA13


title: oePsbS, water, rep3

description: Library name: oePsbS3


title: 32D cell WT 3hr rep1


title: npq4, water, rep3

description: Library name: npq4-13


title: 32D cell Nat10+/- KO1 9hr rep2


title: sample PITT-TN102

description:
Library name: PITT-TN102
Batch 1


title: sample PITT-TN105

description:
Library name: PITT-TN105
Batch 1


title: npq4, water, rep1

description: Library name: npq4-11


title: 32D cell WT 0hr rep1


title: 32D cell WT 3hr rep2


title: 16S rRNA amplicon 1 mM MnCl pH8 RT

description: Library name: 16s_rRNA_amplicon_1mmph8


title: Col0, water, rep3

description: Library name: Col-03


title: oePsbS_CA1, water, rep2

description: Library name: CA12


title: sample PITT-TN100

description:
Library name: PITT-TN100
Batch 1


title: 16S rRNA amplicon 2.5 mM MnCl pH8.3 RT

description: Library name: 16s_rRNA_amplicon_25mmph83


title: 32D cell Nat10+/- KO1 6hr rep1


title: 23S rRNA amplicon 2 mM MnCl pH9 RT

description: Library name: 23s_rRNA_amplicon_2mmph9


title: 16S rRNA amplicon 2 mM MnCl pH8.3 RT

description: Library name: 16s_rRNA_amplicon_2mmph83


title: Col0, water, rep2

description: Library name: Col-02


title: 16S rRNA amplicon 1 mM MnCl pH8.3 RT

description: Library name: 16s_rRNA_amplicon_1mmph83


title: 16S rRNA amplicon 2 mM MnCl pH9 RT

description: Library name: 16s_rRNA_amplicon_2mmph9


title: WGBS,ESC,WT2_BS

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: WT2_BS

data_processing:
For analysis of the raw data, bismark was used to generate the coverage file
Assembly: mm10
Supplementary files format and content: Text based tab separated coverage file

source_name: mESC

growth_protocol: Embryonic stem cells (ESCs) were derived from Uhrf1Fx/Fx mice and cultured in 2i/LIF as described (Kunath et al., 2007; Mulas et al., 2017). Uhrf1-/- ESCs were obtained by transfecting Uhrf1Fx/Fx ESCs with a linearized CreERT2-IRES-Blasticidin plasmid (Betschinger et al., 2013) using Lipofectamine 2000 and cells were selected with 2 μg/ml puromycin. Stably transfected and resistant clones were picked and expanded.  Established ESC lines were cultured for two weeks with 1 μg/ml 4-hydroxytamoxifen (4-OHT) to induce CRE recombination and selected 48h with 1 μg/ml blasticidin to obtain UHRF1-null colonies.

extract_protocol:
DNeasy Blood and Tissue Kits for DNA Isolation
The 5mC and 5hmC libraries were prepared using TrueMethyl oxBS Module (NuGEN) following the manufacture's protocol

value: 5mC & 5hmC called as Cytosine, unmethylated Cytosine converted to Thymidine.

value: mESC


title: sample PITT-TN104

description:
Library name: PITT-TN104
Batch 2


title: sample PITT-TN090

description:
Library name: PITT-TN090
Batch 2


title: 32D cell Nat10+/- KO1 9hr rep1


title: 16S rRNA amplicon 1 mM MnCl pH7.5 RT

description: Library name: 16s_rRNA_amplicon_1mmph75


title: sample PITT-TN093

description:
Library name: PITT-TN093
Batch 2


title: 32D cell Nat10+/- KO1 6hr rep2


title: sample PITT-TN099

description:
Library name: PITT-TN099
Batch 2


title: 32D cell Nat10+/- KO1 3hr rep2


title: npq4, water, rep2

description: Library name: npq4-12


title: Col0, water, rep1

description: Library name: Col-01


title: sample PITT-TN097

description:
Library name: PITT-TN097
Batch 2


title: denatured ecoli rRNA DMS

description: Library name: denatured_ecoli_rRNA_mod

value: DMS treated


title: sample PITT-TN086

description:
Library name: PITT-TN086
Batch 2


title: 32D cell IgG rep2

data_processing:
Raw reads were pre-processed to remove low quality bases and adapter sequences by Cutadapt. rRNA reads were removed by aligning reads with rRNA reference sequence on NCBI database by Bowtie2. Filtered reads were aligned to mouse transcript sequences using Bowtie2 software in local alignment mode.
MACS2 was used for peak calling, with parameters selected to optimize performance with transcript mapped reads (i.e., turning off the shifting model and local lambda, and using transcript bases as the genome size). Input samples were used as controls for peak calling. In MACS2 peak calling results, each of these summits is a putative “ac4C site”.
Assembly: Ensembl GRCm39.105
Supplementary files format and content: tab-delimited text files include ac4C peak file

extract_protocol:
Total RNA was purified from 32D cells using Trizol (Thermo Scientific) and enrichment of polyadenylated RNA [poly(A) RNA] was achieved through PolyATtract mRNA Isolation Systems (Promega) for acRIP-seq. Then, acRIP was performed as described previously (Cell. 2018 Dec 13;175(7):1872-1886.e24. ) with minor modifications.
Libraries were prepared according to NEB's instructions accompanying the NEBNext Ultra II DNA Library Prep Kit (E7103S) and NEBNext Multiplex Oligos for Illumina (E7335S).

value: WT

value: IgG antibody


title: cell free ecoli rRNA rep2 DMS

description: Library name: cellfree_ecoli_rRNA_rep2_mod


title: 16S rRNA amplicon 1 mM MnCl pH8.5 RT

description: Library name: 16s_rRNA_amplicon_1mmph85


title: WGBS,ESC,MT2_BS

description: Library name: MT2_BS


title: WGBS,ESC,MT1_BS

description: Library name: MT1_BS


title: sample PITT-TN091

description:
Library name: PITT-TN091
Batch 2

value: Human breast cancer tissue


title: cell free ecoli rRNA rep1 EtOH

description: Library name: ecoli_rRNA_unmod


title: sample PITT-TN058

description:
Library name: PITT-TN058
Batch 2


title: 32D cell IgG rep1


title: 32D cell Nat10+/- KO1 0hr rep2


title: 32D cell ac4C Input rep2


title: cell free ecoli rRNA rep1 DMS

description: Library name: cell_free_ecoli_rRNA_rep1_mod


title: WGBS,ESC,WT1_BS

description: Library name: WT1_BS

value: wild type


title: 32D cell ac4C IP rep2

value: ac4C antibody


title: 32D cell ac4C Input rep1


title: 32D cell Nat10+/- KO1 0hr rep1


title: WGBS,ESC,WT2_OX_BS

description: Library name: WT2_OX_BS

value: Additional oxidation of 5hmC. Only 5mCs are Cytosine, 5hmCs are Thymidine.


title: cell free ecoli rRNA rep2 EtOH

description: Library name: cellfree_ecoli_rRNA_rep2_unmod


title: WGBS,ESC,WT1_OX_BS

description: Library name: WT1_OX_BS


title: 32D cell Nat10+/- KO1 3hr rep1

value: Nat10 deficiency


title: 32D cell ac4C IP rep1


title: Neurons, RNA, Replicate 3

status: Public on Mar 20 2026

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: Neuron_MPRA3_RNA

data_processing:
DNA and RNA Counts as well as DNA and RNA annotations were generated using the MPRAflow count utility as specified in Gordon et al. 2020 using the --mpranalyze flag
The design file was created using custom scripts (https://github.com/HudsonAlpha/Hauser_MAPT_MPRAs). Briefly, reads were alligned to hg38 chr17 using bwa mem. A unique bed file was generated using samtools/bedtools and fasta sequences were obtained from the bedfile using bedtools getfasta.
The barcode association dictionary was created using custom scripts (https://github.com/HudsonAlpha/Hauser_MAPT_MPRAs). Briefly, reads were alligned to hg38 chr17 using bwa mem, and unique barcodes were identified. Barcodes were sorted into 100bp bins based on the location of their associatied insert sequence.
For merged fastqs for replicate 1, fastqs from sequencing runs 1 and 2 were combined into a single file. Because the UMI read was in the header for sequencing run 1 MPRAflow requires reads in fastq format, the UMI seuence was extracted from the header and faux fastqs were generated using a script in (https://github.com/HudsonAlpha/Hauser_MAPT_MPRAs) before merging with the UMI fastqs from sequencing run 2.
Assembly: hg38
Supplementary files format and content: DNA and RNA counts are total barcode counts in csv format
Supplementary files format and content: DNA and RNA annotations are label files for use with mpranalyze in tsv format
Supplementary files format and content: The design file is a fasta file used for MPRAflow's count utility.
Supplementary files format and content: Barcode association dictionary is used for MPRAflow's count utility and is a python pickle file

extract_protocol:
Qiagen Allprep RNA/DNA mini kit for MPRA output sequencing, Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

value: Neurons


title: Neurons, DNA, Replicate 3

description: Library name: Neuron_MPRA3_DNA


title: WT-HeLa, HSV-1 infection 9h,rep 3

first: jie

address: 5 Summer Palace Road, Haidian District, Beijing

institute: school of Life science

description: Library name: HSV240913_WT9

data_processing:
To simultaneously consider both host and HSV genomes, we created a fusion reference genome by combining GRCh38 and NC_001806.2 sequences. We then processed Hi-C data using the distiller-nf pipeline (https://github.com/open2c/distiller-nf). Briefly, we mapped Hi-C reads to the fusion reference genome using BWA (v.0.7.17). Next, we used Pairtools (v.0.2) to filter out reads with MAPQ scores < 30 to remove PCR duplications and extract Hi-C contacts. To show interactions between HSV-1 and the host genome, we divided the host genome into uniform bins of 500 kb in size and calculated the number of contacts between each bin and any HSV region. To visually represent interactions between HSV, host centromeres, and surrounding areas, we created plots using contact matrices generated without MAPQ filtering. We also used these matrices to quantitatively assess HSV-1 enrichment in centromeric regions. Specifically, we calculated HSV-1-related contact ratios in centromeric regions to those in remaining regions, resulting in an odds ratio to measure enrichment.
Assembly: GRCh38/hg38
Supplementary files format and content: .mcool format (multi-resolution cooler files) containing genome-wide Hi-C contact matrices mapped to GRCh38/hg38, at resolutions including 1000 bp. Files represent chromatin interaction frequencies for 3D genome analysis.

source_name: HeLa

extract_protocol:
Cells were fixed in 1.75% formaldehyde, quenched in a 0.1% BSA solution, washed, and resuspended in 200 μL ice-cold wash buffer (10 mM Tris (pH 8.0), 10 mM NaCl, and 0.1 mg/mL BSA with 20 μL of a protease inhibitor (Sigma P8340). Then, cells were treated in sodium dodecyl sulfate (SDS) and Triton X-100 and digested with the restriction enzyme MboI. After deactivating the enzyme, cells underwent biotinylation and ligation reactions, after which 50 ng of the Hi-C sample was used for library preparation.
Library construction protocol Hi-C DNA was purified using the DNA Clean & Concentrator®-5 kit (Zymo Research) and eluted in nuclease-free water. A total of 50 ng DNA was subjected to tagmentation using Vazyme TTE Mix V50 at 55 °C for 10 min, followed by purification. Tagmented DNA was amplified using Nextera i5 and i7 unique dual indices with an initial limited-cycle PCR (2 cycles) to introduce sequencing adapters. Biotin-labeled ligation products were then captured using Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher Scientific) according to the manufacturer’s instructions. The bead-bound DNA was further amplified by PCR (10 cycles) to enrich Hi-C fragments. Libraries were purified and size-selected using AMPure XP beads with double-sided selection (0.6×/0.15×). Final libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: HeLa

value: tumor cell

value: HSV-1 infection 9h


title: WGBS,ESC,MT2_OX_BS

description: Library name: MT2_OX_BS


title: KD-HeLa, HSV-1 infection 20h,rep 1

description: Library name: KD-Hela20h

data_processing:
Paired-end RNA-seq libraries from HSV-1-infected wild-type and RAP80-knockdown cells were aligned to the human reference genome GRCh37d5 with STAR, and gene-level expression was quantified with RSEM.
Assembly: GRCh38/hg38
Supplementary files format and content: counts.matrix: Tab-delimited gene expression matrix. Rows = Ensembl gene IDs, columns = KD/WT samples, values = gene expression levels.

extract_protocol:
Cells with RAP80 knockdown were infected with HSV-1, and total RNA was extracted at indicated time points using a standard kit. After quality validation, mRNA was enriched via oligo(dT) beads, and strand-specific RNA-seq libraries were constructed. Libraries were quantified, pooled, and sequenced on a NovaSeq 6000 (Illumina) platform according to the manufacturer’s instructions, generating paired-end 150 bp reads.
Total RNA was extracted and DNase-treated. Poly(A) mRNA was isolated, fragmented, and used to construct a stranded RNA-seq library via first- and second-strand cDNA synthesis, adapter ligation, and PCR amplification. Libraries were sequenced on an Illumina platform (paired-end 150 bp) following standard Illumina protocols.

value: RAP80 KD

value: HSV-1 infection 20h


title: WT-HeLa, HSV-1 infection 20h,rep 2

description: Library name: WT-seq


title: HEK293FT, RNA, Replicate 3

description: Library name: HEK_MPRA3_RNA

value: human embryonic kidney cells


title: HEK293FT, DNA, Replicate 3

description: Library name: HEK_MPRA3_DNA


title: WT-HeLa, HSV-1 infection 6h,rep 3

description: Library name: HSV240913_WT6

value: HSV-1 infection 6h


title: sample PITT-TN046

description:
Library name: PITT-TN046
Batch 2

extract_protocol:
Total RNA was extracted from patient tissues using the standard procedure of Trizol RNA extraction. The primary quantitation and degradation or the extracted RNA were checked by nanodrop and TapeStation. The integrity and purity of RNA were examined by Agilent 2100.
The NovaSeq S4-300 Cycles-XP library for DNA sequencing was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) or TruSeq coding RNA Access (Illumina) following the protocol provided by the manufacturer.


title: WT-HeLa, HSV-1 infection 12h,rep 3

description: Library name: HSV240913_WT12

value: HSV-1 infection 12h


title: sample PITT-TN088

description:
Library name: PITT-TN088
Batch 2


title: KD-HeLa, HSV-1 infection 15h,rep 3

description: Library name: HSV240913_KD15

value: HSV-1 infection 15h


title: KD-HeLa, HSV-1 infection 9h,rep 3

description: Library name: HSV240913_KD9


title: WT-HeLa, HSV-1 infection 18h,rep 3

description: Library name: HSV240913_WT18

value: WT

value: HSV-1 infection 18h


title: WT-HeLa, HSV-1 infection 9h,rep 2

description: Library name: HSV240715_WT9


title: KD-HeLa, HSV-1 infection 20h,rep 2

description: Library name: KD-seq


title: 16S rRNA amplicon 0.5 mM MnCl pH8.3 RT

description: Library name: 16s_rRNA_amplicon_05mmph83

value: Untreated


title: WT-HeLa, HSV-1 infection 15h,rep 2

description: Library name: HSV240715_WT15


title: WT-HeLa, HSV-1 infection 12h,rep 2

description: Library name: HSV240715_WT12


title: KD-HeLa, HSV-1 infection 24h,rep 3

description: Library name: HSV240913_KD24

value: HSV-1 infection 24h


title: KD-HeLa, HSV-1 infection 24h,rep 2

description: Library name: HSV240715_KD24


title: KD-HeLa, HSV-1 infection 12h,rep 2

description: Library name: HSV240715_KD12


title: KD-HeLa, HSV-1 infection 18h,rep 2

description: Library name: HSV240715_KD18


title: KD-HeLa, HSV-1 infection 6h,rep 2

description: Library name: HSV240715_KD6


title: sample PITT-TN062

description:
Library name: PITT-TN062
Batch 2

value: Human breast cancer tissue


title: WT-HeLa, HSV-1 infection 18h,rep 1

description: Library name: WT18


title: WT-HeLa, HSV-1 infection 24h,rep 1

description: Library name: WT24


title: KD-HeLa, HSV-1 infection 6h,rep 1

description: Library name: KD6H


title: KD-HeLa, HSV-1 infection 9h,rep 1

description: Library name: KD9H


title: WT-HeLa, HSV-1 infection 12h,rep 1

description: Library name: WT12


title: WGBS,ESC,MT1_OX_BS

description: Library name: MT1_OX_BS

value: Additional oxidation of 5hmC. Only 5mCs are Cytosine, 5hmCs are Thymidine.

value: mESC


title: WT-HeLa, HSV-1 infection 24h,rep 3

description: Library name: HSV240913_WT24


title: WT-HeLa, HSV-1 infection 20h,rep 1

description: Library name: WT-Hela20h


title: KD-HeLa, HSV-1 infection 9h,rep 2

description: Library name: HSV240715_KD9


title: KD-HeLa, HSV-1 infection 12h,rep 3

description: Library name: HSV240913_KD12


title: WT-HeLa, HSV-1 infection 6h,rep 2

description: Library name: HSV240715_WT6


title: Induced FUS + Sp1 DNA binding domain chimera line, anti-FLAG, replicate 2

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description: Library name: FUS-Sp1 DBD, FLAG, R2

data_processing:
Reads trimmed with Cutadapt (version 2.6) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Reads aligned with Bowtie2 (version 2.3.5.1) with the following options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Bowtie2 .sam output converted to .bam with samtools (version 1.9)
.bam files sorted and indexed with samtools (version 1.9)
duplicates removed with samtools (version 1.9)
bigWig coverage files generated with deepTools bamCoverage (version 3.5.4) with the following options: --binSize 10 --samFlagInclude 64 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads --ignoreDuplicates, using the hg38 blacklist file published in Doi: 10.1186/s13059-023-03027-3
Irreproducible Discovery Rate (IDR) analysis: macs3 (version 2.2.7.1) peak calling with a liberal p-value cutoff (-p 1e-3) and --nolambda; merged control replicates (CTRL, mAb, R1 + CTRL, mAb, R2; or CTRL, rAb, R1 + CTRL, mAb, R2) used as a control; peaks sorted by pValue before running IDR (version 2.0.4.2) with the following options: --input-file-type narrowPeak --rank p.value
MACS3 bedGraph files used to combine replicates with macs3 cmbreps (--method mean)
Combined bedGraph outputs used for differential peak calling with macs3 bdgdiff with the following options: --cutoff 1.0 --depth1 1.0 --depth2 1.0 -l 120 -g 60, using merged control replicates as a control
Peak coordinates merged and/or intersected with bedtools (version 2.27.1) or bedops (version 2.4.39)
ChIP-Seq heatmaps generated with deepTools (version 3.5.4) computeMatrix and plotHeatmap tools
Assembly: hg38
Supplementary files format and content: *IDR_0.1.txt: peaks highly reproducible between replicates 1 and 2 (IDR score <=0.01). See https://github.com/nboley/idr for a detailed explanation of the output fields
Supplementary files format and content: bdgdiff .bed files: contain coordinates of unchanged (common), depleted (cond 1) or enriched (cond2) ChIP-seq peaks in EPC1 mutants (HSA-6mut or Delta-TRRAP) compared to WT EPC1. The last column in the file represent the log10 likelihood ratio to show how likely the observed signal in one or the other condition in a particular region is from that condition comparing to the other condition.The higher the value, the greater the difference. Only highly reproducible peaks (IDR score <=0.01) are included in the list (reproducible IDR and bdgdiff peaks intersected with bedops --element-of 1)
Supplementary files format and content: *.bw files: coverage files generated with deepTools
Library strategy: CUT&Run

source_name: U-2 OS

growth_protocol: U-2 OS cells were cultured at 37 °C with 5% CO2 in high-glucose Dulbecco's Modified Eagle Medium (DMEM; Thermo Fisher #12800082) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
CUT&Run was performed as previously described (dx.doi.org/10.17504/protocols.io.zcpf2vn), using 0.5x10^6 cells per antibody, 0.02% digitonin and pA/G-MNase digestion (30 minutes on ice). After phenol:chloroform extraction DNA was purified with home-made serapure beads (Doi:10.1101/gr.128124.111).
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, adapted for short fragments (dx.doi.org/10.17504/protocols.io.bagaibse); adaptors diluted 1:20; 11 PCR cycles

treatment_protocol: Cells were induced for 36 hours with 1 µg/mL doxycycline while also stained with 5 nM of JF549 Halo ligand and 5 nM of JFX650 SNAP ligand. Following induction, cells were trypsinized and resuspended in medium containing 1 µg/mL doxycycline, then subjected to fluorescence-activated cell sorting (FACS) to select for transgene-expressing cells (induction levels typically ranged from ~10% to 50%). Sorted cells were plated into individual wells of six-well plates and cultured for an additional 36 hours in medium with 1 µg/mL doxycycline prior to initiation of the CUT&RUN protocol.

value: U-2 OS

value: Osteosarcoma

tag: antibody

value: Sigma F3165

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible FUS-Sp1 DBD chimera integrated at the AAVS1 safe harbor locus

value: 36 hrs dox induction + cell sorting


title: Induced Sp1 activation domain + CTCF DNA binding domain chimera line, mouse anti-V5, replicate 2

description: Library name: Sp1AD-CTCF DBD, mV5, R2

value: Thermo Fisher R960-25

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1 AD-CTCF DBD chimera integrated at the AAVS1 safe harbor locus


title: KD-HeLa, HSV-1 infection 12h,rep 1

description: Library name: KD12

value: HeLa

value: tumor cell

value: RAP80 KD


title: KD-HeLa, HSV-1 infection 6h,rep 3

description: Library name: HSV240913_KD6

value: HSV-1 infection 6h


title: KD-HeLa, HSV-1 infection 15h,rep 1

description: Library name: KD15

value: HSV-1 infection 15h


title: KD-HeLa, HSV-1 infection 18h,rep 3

description: Library name: HSV240913_KD18

value: HSV-1 infection 18h


title: Induced Sp1 activation domain + CTCF DNA binding domain chimera line, anti-FLAG, replicate 2

description: Library name: Sp1AD-CTCF DBD, FLAG, R2


title: Induced Sp1 activation domain + CTCF DNA binding domain chimera line, rabbit anti-V5, replicate 2

description: Library name: Sp1AD-CTCF DBD, rV5, R2

value: Abcam ab9116


title: KD-HeLa, HSV-1 infection 15h,rep 2

description: Library name: HSV240715_KD15


title: WT-HeLa, HSV-1 infection 18h,rep 2

description: Library name: HSV240715_WT18

value: WT


title: WT-HeLa, HSV-1 infection 15h,rep 3

description: Library name: HSV240913_WT15


title: WT-HeLa, HSV-1 infection 9h,rep 1

description: Library name: WT9H

value: HSV-1 infection 9h


title: Induced wild type Sp1 line, mouse anti-V5, replicate 2

description: Library name: Sp1 WT, mV5, R2

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible wild type Sp1 integrated at the AAVS1 safe harbor locus


title: WT-HeLa, HSV-1 infection 24h,rep 2

description: Library name: HSV240715_WT24

value: HSV-1 infection 24h


title: Induced wild type Sp1 line, anti-FLAG, replicate 2

description: Library name: Sp1 WT, FLAG, R2

value: U-2 OS

value: Osteosarcoma


title: Parental cell line, mouse anti-V5, replicate 2

description: Library name: CTRL, mV5, R2

value: Endogenous knock-in V5-Halo-SP1


title: Induced Sp1 mutant line, anti-FLAG, replicate 2

description: Library name: Sp1 mut, FLAG, R2

value: Sigma F3165

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible mutant Sp1 integrated at the AAVS1 safe harbor locus

value: 36 hrs dox induction + cell sorting


title: Parental cell line, rabbit anti-V5, replicate 2

description: Library name: CTRL, rV5, R2


title: Induced FUS + Sp1 DNA binding domain chimera line, anti-FLAG, replicate 1

description: Library name: FUS-Sp1 DBD, FLAG, R1

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible FUS-Sp1 DBD chimera integrated at the AAVS1 safe harbor locus


title: KD-HeLa, HSV-1 infection 24h,rep 1

description: Library name: KD24

value: HeLa

value: tumor cell


title: WT-HeLa, HSV-1 infection 6h,rep 1

description: Library name: WT6H

value: HSV-1 infection 6h


title: WT-HeLa, HSV-1 infection 15h,rep 1

description: Library name: WT15

value: HSV-1 infection 15h


title: Induced Sp1 activation domain + CTCF DNA binding domain chimera line, anti-FLAG, replicate 1

description: Library name: Sp1AD-CTCF DBD, FLAG, R1

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1 AD-CTCF DBD chimera integrated at the AAVS1 safe harbor locus


title: Induced EWS + Sp1 DNA binding domain chimera line, anti-FLAG, replicate 1

description: Library name: EWS-Sp1 DBD, FLAG, R1

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible EWS-Sp1 DBD chimera integrated at the AAVS1 safe harbor locus


title: Induced Sp1 activation domain + LacI chimera line, mouse anti-V5, replicate 1

description: Library name: Sp1AD-LacI, mV5, R1

value: Thermo Fisher R960-25

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1 AD-LacI chimera integrated at the AAVS1 safe harbor locus


title: Induced Sp1 activation domain + CTCF DNA binding domain chimera line, rabbit anti-V5, replicate 1

description: Library name: Sp1AD-CTCF DBD, rV5, R1

value: Abcam ab9116


title: Induced CTCF DNA binding domain line, anti-FLAG, replicate 1

description: Library name: CTCF DBD, FLAG, R1

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible CTCF DBD integrated at the AAVS1 safe harbor locus


title: KD-HeLa, HSV-1 infection 18h,rep 1

description: Library name: KD18

value: RAP80 KD

value: HSV-1 infection 18h


title: Induced Sp1 activation domain + LacI chimera line, mouse anti-V5, replicate 2

description: Library name: Sp1AD-LacI, mV5, R2

value: U-2 OS

value: Osteosarcoma