title: hsdMS, 43°C, #2

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; hsdMS, 43°C, #2

data_processing:
Clean reads were then aligned to the P. aeruginosa PAO1 strain (assembly GCF_000006765.1) using the Hisat2-3n aligner software with default parameters, except for --no-spliced-alignment and --base-change A,G. 6mA sites were detected using the hisat-3n-table command, and the 6mA ratio was calculated as the number of unconverted reads over the total coverage at each A site.
Assembly: GCF_000006765.1
Supplementary files format and content: TSV

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: Pseudomonas Isolation Agar (PIA, Difco), and No salt Luria-Bertani (NSLB) supplemented with 10% sucrose. For DH5α heat shock, BHI (brain heart infusion broth, Difco) media was used. All strains were grown at 37 °C unless otherwise specified. Antibiotic concentrations used in this study were 300 μg/mL Carbenicillin (Crb) and 50 μg/ml Gentamicin (Gm) for P. aeruginosa.

extract_protocol:
Following cell lysis, the Zymo Genomic DNA Clean and ConcentratorTM kit was used as instructed to extract DNA.
For each DNA sample, 100 ng was fragmented using NEBNext® dsDNA Fragmentase (NEB, catalog no. M0348S) at 37 °C for 20 min and then denatured in 0.1 M NaOH at 37 °C for 5 min. The denatured DNA was neutralized by 10% HOAc, purified by the Oligo Clean & Concentrator kit (Zymo), and mixed with 0.001% (w:w) spike-in probes containing one 6mA site and one inosine site (GTG TCT GGT GTT CTG TCG TGT GCT ACT C/iN6Me-dA/T CCG ATC TCG CAT C/ideoxyI/T CAC AGT ATT CGT CGT ATG AGA CAC AAC TAC ATG CTT GTC CGC TCT TGT GTC GGC T).

treatment_protocol: Genomic DNA was extracted from cells cultured at 37 °C, 43 °C, or after 10 generations of recovery at 37 °C. Cells were 1:1 treated with Lysis Buffer (20mM Tris, 2mM EDTA, 1% SDS, 100µg/mL RNase A, and 100µg/mL Proteinase K) for incubation at 37 °C for 30 minutes, followed by 30 minutes at 55 °C.

value: bacterial cells


title: ∆hsdMSR, control

status: Public on Jun 03 2025

type: SRA

country: USA

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdMSR, control

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: genotype


title: Primed IgG ctrl rep3

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

library_source: transcriptomic

data_processing:
The base calling was done using bcl2fastq
Read alignment was done using  Rsubread (v. 2.0.0)
Genewise read counts were calculated using Rsubread (v. 2.0.0)
Assembly: human genome hg38
Supplementary files format and content: Processed data file is tab delimited text file containing the genewise read counts for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: Primed human induced pluripotent stem cells (hiPSC)

growth_protocol: Primed hiPSCs were cultured on Matrigel coated culture dishes in E8 medium. Naïve ctrl hiPSCs were cultured on inactivated mouse embryonic fibroblast (iMEF) monolayer in Naïve Cult expansion medium. The naïve anti-β1 hiPSCs were cultured as ctrl hiPSCs, but the culture medium was supplemented with integrin β1 function blocking antibody (MAb13; anti-β1).

extract_protocol:
RNA was isolated using NucleoSpin RNA -kit (#740955.250, Macherey-Nagel).
Illumina TruSeq® Stranded mRNA sample protocol

treatment_protocol: Primed hiPSCs were treated with IgG ctrl or anti-β1 (MAb13) antibodies for 12 hours, and naïve hiPSCs were treated with IgG ctrl or anti-β1 (MAb13) antibodies for 48 hours.

value: HEL 24.3 derived from fibroblasts

tag: treatment

value: treated with IgG for 12h


title: Sample 2_AN3CA

city: Dallas

first: Subhransu

middle: S

last: Sahoo

state: Texas

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Bcl files were demultiplexed with bcl2fastq (v2.20)
The paired-end reads were trimmed with Trim Galore (v.0.6.10)
Bismark (v.0.24.0) aligned the trimmed reads to human GRCh38 reference genome with Bowtie 2 (2.5.1)
The duplicates were removed from the alignment results with Bismark (v.0.24.0)
Bismark (v.0.24.0) identified the methylation on cytosines
Assembly: GRCh38
Supplementary files format and content: bedGraph files generated by bismark_methylation_extractor, containing the methylation percentages of the CpG cytosines

source_name: Uterus

growth_protocol: Endometrial cancer cell lines were cultured in ATCC recommended culture medium supplemented with 10% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol:
The DNA was isolated from the cell lines using the QIAamp DNA Mini Kit (Qiagen) per the manufacturer’s instructions.
The DNA samples underwent Agilent SureSelectXT Methyl-seq (Agilent Technologies) analysis to investigate their DNA methylation status across the entire PAX2, MLH1 and PAX8 loci using a custom designed capture panel for methyl-seq, per manufacturer’s instructions.
Targeted Methyl-seq

treatment_protocol: No treatment

tag: tissue

value: Uterus

tag: cell line

value: epithelial cells


title: Primed IgG ctrl rep1


title: Sample 1_Ishikawa

value: Ishikawa


title: Primed IgG ctrl rep2


title: Ovary_3

city: Beijing

first: SUN

last: WAN

state: Beijing

address: o. 2 Yuanmingyuan West Road, Haidian District

country: China

institute: China Agricultural University

description: Library name: Sample 14

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Triticum aestivum

source_name: wheat spikelet

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wheat spikelet

value: 21 days after terminal spikelet

value: central spikelet

value: untreated


title: hsdMS, 37°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; hsdMS, 37°C, #2


title: hsdMS, 43°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; hsdMS, 43°C, #1


title: Ovary_2

description: Library name: Sample 13


title: RNPC3_4_Illumina

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina: Quality assessment of the FASTQ files was conducted with FastQC  (version 0.11.8) and  MultiQC (version 1.10.1). ONT: Reads were basecalled in super-accuracy mode (dna_r9.4.1_450bps_sup_prom) with demultiplexing, using Guppy (version 6.0.6) and default parameters.
Illumina: Sequenced reads were mapped to the hg38 human reference genome using the align function in the Rsubread package (version 2.4.3). ONT: Sequenced reads were mapped to the CHM13v2 human reference genome with minimap2 (version 2.24).
Gene-level counts were summarised using the featureCounts function of Rsubread (version 2.10.2).
ONT: Transcript-level counts were generated using bambu (version 1.0.3).
ONT: Gene counts were filtered by expression level using edgeR (version 3.38.1).
Illumina: Gene counts were normalised using the trimmed mean of M-values (TMM) methods in edgeR (version 3.32.1). ONT: Gene counts were normalised using the trimmed mean of M-values (TMM) methods in edgeR (version 3.38.1).
Illumina: Differential expression analysis was conducted using limma (version 3.46.0). ONT: Differential expression analysis was conducted using edgeR's quasi-likelihood method.
Assembly: hg38 (Illumina), CHM13v2 (ONT)
Supplementary files format and content: Tab-delimited text files with columns representing gene IDs, gene length, and the number of reads mapping to that gene.

source_name: Human lung cancer cell line A549

growth_protocol: A549 cells were cultured in RPMI medium supplemented with 1X GlutaMAX (Gibco, Cat#35050061) and 5% FBS.

extract_protocol:
Total RNA was extracted using TRIsure™ reagent (Bioline, Cat#38033).
Illumina: Stranded Total RNA with Ribo-Zero for Illumina NovaSeq.   ONT: Long-read transcriptome libraries were prepared from 200 ng total RNA with the Oxford Nanopore Technologies PCR-cDNA (SQK-PCB109) kit, without poly(A) selection and according to the manufacturer’s instructions. 14 cycles of PCR were performed with an elongation time of 2 minutes and 30 seconds.  The pool of 8 indexed libraries was sequenced on 3 PromethION R9.4.1 flow cells (FLO-PRO002) on a PromethION 24 instrument running MinKNOW (version 22.03.2), refuelling the flow cells with Flush Buffer anytime the sequencing speed dropped below 300 bases per second.

treatment_protocol: Transfected with either human ON-TARGETplus siRNAs to RNPC3 (Dharmacon Inc., Cat#J-021646-18-0050) or Non-targeted (NT) siRNA (Dharmacon Inc., Cat#D-001810-01-05) using DharmaFECT 1 (Dharmacon  Inc.,  Cat#T-2001-03 according to the manufacturer’s protocol. Treatment was continued for 72h.

value: Human lung cancer cell line A549

value: RNPC3 siRNA

tag: molecule subtype

value: rRNA-depleted total RNA


title: RNPC3_3_Illumina


title: Primed anti-β1 rep3

value: treated with MAb13 for 12h


title: Ovary_1

description: Library name: Sample 12


title: HeLa_WT_HA-MCM3_CUT&RUN

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

data_processing:
Fastq files were mapped to the reference genome (hg19/mm10/dm3) using bowtie2.3.5.
The non-primary alignments, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was conducted by MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Bigwig files, heatmaps and averaged plotting of CUT&RUN and CUT&Tag signals were generated by deeptools (v3.3.0).
Assembly: hg19/dm3/mm10
Supplementary files format and content: bigWig files.
Library strategy: CUT&RUN

organism:
Drosophila melanogaster
Homo sapiens

source_name: HeLa cells/S2 cells

growth_protocol: HeLa cells were grown in high glucose DMEM base medium plus 10% FBS and 1% antibiotics.

extract_protocol:
Cells or nuclei were permeabilized by digitonin and genomic DNA were fragmented by specific antibody recruited MNase or Tn5. Then, the fragmented DNA was purified and subjected to multiplexed library preparation.
The multiplexed libraries were prepared for sequencing by using standard Illumina protocols.

treatment_protocol: HeLa cells with the homozygous BAHCC1 TTD-dead mutation (Y1993A) were generated via CRISPR-cas9 based genome editing. HA-tagged MCM3 or HA-tagged ORC1 was introduced into HeLa cells followed by selection for stable expression, which was then doxycycline induced (cells treated with 0.1μg/mL of doxycycline for 24 h).

tag: cell line (human)

value: HeLa

tag: cell line (drosophila)

tag: genotype (hela)

value: WT, HA-MCM

value: dox_0.1ug/mL for 24h

tag: antibody

value: anti-HA (Abcam, ab9110)


title: HeLa_Y1993A_HA-MCM3_CUT&RUN

value: BAHCC1 TTD-dead mutation Y1993A, HA-MCM3


title: hsdMS, 37°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; hsdMS, 37°C, #1

value: bacterial cells


title: RNA_seq_CREB3L2_rep1

first: Xinyu

address: 15 Datun Road

institute: Institute of Biophysics

data_processing:
For RNA-seq, use Fastp software to filter low-quality sequences, undetected sequences and linker sequences. Use Hisat2 algorithm for genome alignment. Using HTSeq, select the FPKM standardization method to count the gene expression.The DESeq2 algorithm is used for differential screening to obtain differential genes that meet the Fold Change and FDR thresholds. Based on the differential screening results and the FPKM or RPKM of the sample, Volcano Plot analysis and cluster map analysis (Heatmap) are performed.
For CUT&Tag, filtered reads were subject to software MACS to identify potential peaks.
Assembly: Hg38
Supplementary files format and content: For RNA-seq, a text file includes filtered reads count values for each sample.The first row indicates the name of each sample.For CUT&Tag,  a txt file includes peak location.

source_name: Huvec

extract_protocol:
For RNA-seq, total RNA was extracted using TRIZOL.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. For CUT&Tag, a commercial kit (Cat. No. 53160) from Active Motif was used.
RNA-seq: After depleting rRNA,  RNA samples were further fragmented into 150-200 bp using divalent cations at 94 °C for 8 min. The cleaved RNA fragments were reverse-transcribed into double-strand cDNA. The resulting cDNA fragments were end-repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads. The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent 2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeq Xten by NovelBio Corp. Laboratory, Shanghai.
CUT&Tag: In brief, the cells were captured by ConA beads and incubated with proteinA-tn5 and corresponding primary antibodies. The genomic DNA was extracted with phenol chloroform extraction. The purified DNA was further amplified by barcoded primers to construct the library.

value: Huvec

value: epithelial

value: CREB3L2 stable expression


title: EV, 43°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; EV, 43°C, #2


title: RNPC3_2_Illumina


title: Sample 3_HEC1A

value: Uterus

value: epithelial cells


title: EV, 37°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; EV, 37°C, #2


title: Anther_2

description: Library name: Sample 10

value: wheat spikelet

value: 21 days after terminal spikelet

value: central spikelet


title: HeLa_KO_MCM2_CUT&Tag

data_processing:
Fastq files were mapped to the reference genome (hg19/mm10/dm3) using bowtie2.3.5.
The non-primary alignments, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively.
Peak calling was conducted by MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Bigwig files, heatmaps and averaged plotting of CUT&RUN and CUT&Tag signals were generated by deeptools (v3.3.0).
Assembly: hg19/dm3/mm10
Supplementary files format and content: bigWig files.
Library strategy: CUT&Tag

value: BAHCC1 KO

value: anti-MCM2 (Bethyl Laboratories, A300-191A)


title: HeLa_Y1993A_MCM2_CUT&Tag_rep2

value: BAHCC1 TTD-dead mutation Y1993A


title: Anther_1

description: Library name: Sample 9

value: untreated


title: NT_4_Illumina

value: Human lung cancer cell line A549

value: Non-targeted (NT) siRNA

value: rRNA-depleted total RNA


title: EV, 37°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; EV, 37°C, #1


title: HeLa_Y1993A_MCM2_CUT&Tag_rep1

value: HeLa


title: Lemma_3

description: Library name: Sample 8


title: NT_3_Illumina


title: EV, 43°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; EV, 43°C, #1

value: bacterial cells


title: NT_2_Illumina


title: HeLa_WT_MCM2_CUT&Tag

value: WT


title: ∆hsdR, 43°C→37°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdR, 43°C→37°C, #2


title: Anther_3

description: Library name: Sample 11


title: NT_1_Illumina


title: MCF10A Rep 2

type: RNA

city: Saskatoon

first: Deborah

last: Anderson

state: Saskatchewan

address: 107 Wiggins Road

country: Canada

institute: University of Saskatchewan

description: Replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R, followed by a per probe median centered normalization

label: biotin

source_name: ATCC Cell Line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: creb3l1 expression

value: Yes


title: HeLa_WT_H4K20me3_CUT&RUN

value: anti-H4K20me3 (Abcam 9503)


title: HeLa_KO_H4K20me1_CUT&RUN

value: anti-H4K20me1 (Abcam 9501)


title: ∆hsdR, 43°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdR, 43°C, #2


title: HeLa_Y1993A_H4K20me3_CUT&RUN


title: F5_2

description: Library name: Sample 5


title: Sample 4_HEC1B

value: Uterus

value: epithelial cells


title: F5_1

description: Library name: Sample 4

value: wheat spikelet

value: 21 days after terminal spikelet


title: ∆hsdR, 43°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdR, 43°C, #1


title: MCF10A

description: Replicate 1


title: ∆hsdR, 37°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdR, 37°C, #2


title: HeLa_Y1993A_H4K20me1_CUT&RUN


title: F1_3

description: Library name: Sample 3

value: central spikelet


title: Lemma_1

description: Library name: Sample 7


title: BT-20 Rep 2

description: Replicate 2

value: No


title: F1_2

description: Library name: Sample 2


title: HeLa_WT_H4K20me1_CUT&RUN


title: ∆hsdR, 37°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdR, 37°C, #1


title: T470 CREB3L1 Rep 2

description: Replicate 2


title: WT, 43°C→37°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; WT, 43°C→37°C, #2


title: ∆hsdR, 43°C→37°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; ∆hsdR, 43°C→37°C, #1


title: F1_1

description: Library name: Sample 1


title: HeLa_Y1993A_hBAHCC1_CUT&RUN

value: BAHCC1 TTD-dead mutation Y1993A

value: anti-hBAHCC1 (homemade; Fan et al., Nature Genetics, 2020)


title: HeLa_WT_hBAHCC1_CUT&RUN


title: F5_3

description: Library name: Sample 6

value: untreated


title: KO-E2

library_source: transcriptomic single cell

data_processing:
mkfastq module in cellranger was used to generate fastq files
cellrange count module was used to generate matrix containing cell-associated barcodes
cellranger loupe browser was used to run differentaial expression analysis
Assembly: mm10
Supplementary files format and content: feature tsv file
Supplementary files format and content: barcode tsv file
Supplementary files format and content: cell associated matrix file

organism: Mus musculus

extract_protocol:
The uterine horns from Pax2 cKO mouse were dissected, minced into 2-3 mm pieces and digested in a cocktail of Collagenase V and Dispase II. Following digestion, the cell suspension was centrifuged, washed and cells were harvested.
The isolated primary uterine cells were processed in the Chromium Single Cell Gene Expression platform (10x Genomics) to build the 3′ transcriptome libraries and sequenced.

value: uterine cells (mixed)

value: Pax2 cKO


title: T470 CREB3L1

description: Replicate 1


title: WT, 43°C→37°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; WT, 43°C→37°C, #1


title: T470 Rep 2

description: Replicate 2


title: WT, 43°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; WT, 43°C, #2


title: WT, 43°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; WT, 43°C, #1


title: BMDMs, LPS, BRD9 ChIP, pH7.4

city: Boston

first: Zhongyang

last: Wu

state: Massachusetts

address: 300 Longwood Ave,61 Binney Street, Enders building, EN622

institute: Boston Children's Hospital

data_processing:
Reads from Illumina paired end fastq files were mapped to the mouse genome (mm10) using Bowtie2
Read duplicates were removed and BAM files were generated with the Picard toolkit
Enriched atac regions were identified using MACS2 using the options “'-f BAMPE --bw 200 -B -g mm
Bigwig files were generated using deeptools software using the bamCoverage tool
Bigwig files were visualized with UCSC genome browser as well as used to generate heatmaps
Assembly: GRCm38 (mm10)
Supplementary files format and content: Bigwig

source_name: BMDMs

extract_protocol:
cells were crosslinked with 200 uM DSG-PBS for 30 mins, followed by 1% formaldehyde for 10 min at RT, after quenching  and cell lysis, chromatin was sonicated to an average DNA fragment of 300-400 bp.
NEB Next Ultra II DNA Library Prep Kit for Illumina (E7645L)

value: LPS, pH7.4

value: Bone-marrow derived macrophage

tag: chip antibody

value: BRD9 (Bethyl, A700153)


title: mus musculus, PDX tumor tissue, Control, biol repl3

city: Xi'an

first: Yongliang

last: Zheng

address: 157, West 5 Road, Department of Hematology, The Second Affiliated Hospital of Xi

institute: Xi'an Jiaotong University Second Affiliated Hospital

description: Library name: C01634

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.22.0 (the default parameters). Trimmed sequence reads were mapped to using hisat2 v2.2.0 (the default parameters). Read count was calculated and normalized by featurecount v2.0.6 (-p)
Assembly: mm39
Supplementary files format and content: table reads counts values of genes for each sample

source_name: PDX tumor tissue

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: PDX tumor tissue

value: Control


title: mus musculus, PDX tumor tissue, Control, biol repl2

description: Library name: C01631


title: BMDMs, LPS, BRD9 ChIP, pH6.5

value: LPS, pH6.5


title: T470

description: Replicate 1


title: RNPC3_1_Illumina

value: Human lung cancer cell line A549

value: RNPC3 siRNA

value: rRNA-depleted total RNA


title: WT, 37°C, #2

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; WT, 37°C, #2

value: bacterial cells


title: mus musculus, PDX tumor tissue, Control, biol repl1

description: Library name: C01627


title: BT20

description: Replicate 1


title: MDA MB 435 CREB3L1 Rep 2

description: Replicate 2

value: MDA MB 435

value: Yes


title: BMDMs, LPS, BRD4 ChIP, pH6.5


title: mus musculus, PDX tumor tissue, VPA-treated, biol repl3

description: Library name: C01625

value: VPA-treated


title: WT, 37°C, #1

description: Pseudomonas aeruginosa (PAO1) 6mA methylation sequencing; WT, 37°C, #1


title: BMDMs, LPS, BRD4 ChIP, pH7.4


title: MDA MB 435 Rep 2

description: Replicate 2

value: No


title: MDA MB 435 CREB3L1

description: Replicate 1


title: mus musculus, PDX tumor tissue, VPA-treated, biol repl1

description: Library name: C01608


title: BMDMs, LPS, input of LPS_BRD4 CHIP, pH6.5


title: Lung, with hUC-MSCs, KP A7818-infected, treat 3

city: Kaifeng

first: yue

last: ming

address: Henan University

institute: Henan University

description: Library name: MSC3

data_processing:
Illumina NovaSeq PE150
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(v0.20.0)
Trimmed sequence reads were mapped to Ensemble-GRCm38.94 using Hisat2(v2.2.1) (parameters--met-stderr --new-summary --dta --threads 10 --no-mixed--no-discordant)
DESeq2 R (v1.32.0) was used for differential expression analysis.
Assembly: Ensemble-GRCm38.94
Supplementary files format and content: Excel file include differential genes for each sample

source_name: Lung

extract_protocol:
Trizol reagent (Invitrogen) was used to isolate total RNA. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM  RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations.

value: Lung

value: WT


title: MDA MB 435

description: Replicate 1


title: mus musculus, PDX tumor tissue, VPA-treated, biol repl2

description: Library name: C01617


title: BMDMs, LPS, input of LPS_BRD9 CHIP, pH6.5


title: Lung, with hUC-MSCs, KP A7818-infected, treat 2

description: Library name: MSC2


title: LAM_EPR_rep2

first: Serdar

middle: E.

last: Bulun

state: IL

address: 303 E Superior Street

department: Obstetrics & Gynecology

institute: Northwestern Feinberg School of Medicine

description: Decoded transcripts (.zarr and .parquet files) and morphology images (ome.tif file) for E2+P4+RU486-treated LAM replicate 2.

data_processing: Imaging and signal decoding were performed on Xenium Analyzer.

source_name: Lower abdominal muscle

label_protocol: Samples were processed and labeled according to the manufacturers' protocol (CG000582 for Xenium In situ gene expression; CG000749 for Xenium in situ gene expression with cell segmentation; and CG000760 for Xenium Prime in situ gene expression with cell segmentation).

extract_protocol: LAM tissues were fixed in 4% PFA for 24 hours before paraffin embedding. 5um sections were mounted onto Xenium slides for further processing.

treatment_protocol: WT mice 8-10 weeks of age were treated with with placebo/vehicle, E2+P4, or E2+P4+RU486 for 12 weeks before harvesting the LAM.

value: Lower abdominal muscle


title: LAM_EPR_rep1

description: Decoded transcripts (.zarr and .parquet files) and morphology images (ome.tif file) for E2+P4+RU486-treated LAM replicate 1.


title: Lung, with hUC-MSCs, KP A7818-infected, treat 1

description: Library name: MSC1


title: HCC 1954 CREB3L1 Rep 2

description: Replicate 2


title: HCC 1954 Rep 2

description: Replicate 2


title: BMDMs, unstimulated, BRD9 ChIP, pH7.4

value: unstimulated, pH7.4


title: Lung, no hUC-MSCs, KP A7818-infected, control 4

description: Library name: NC4


title: BMDMs, LPS, input, pH7.4

value: LPS, pH7.4

value: Bone-marrow derived macrophage


title: HCC 1954 CREB3L1

description: Replicate 1


title: BMDMs, unstimulated, BRD9 ChIP, pH6.5

value: unstimulated, pH6.5

value: BRD9 (Bethyl, A700153)


title: LAM_EP_rep1

description: Decoded transcripts (.zarr and .parquet files) and morphology images (ome.tif file) for E2+P4-treated LAM replicate 1.


title: LAM_EP_rep2

description: Decoded transcripts (.zarr and .parquet files) and morphology images (ome.tif file) for E2+P4-treated LAM replicate 2.


title: Lung, no hUC-MSCs, KP A7818-infected, control 3

description: Library name: NC3


title: LAM_Veh_rep2

description: Decoded transcripts (.zarr and .parquet files) and morphology images (ome.tif file) for Vehicle-treated LAM replicate 2.

value: Vehicle


title: Lung, with hUC-MSCs, KP A7818-infected, treat 4

description: Library name: MSC4


title: HCC 1806 CREB3L1 Rep 2

description: Replicate 2


title: HCC 1954

description: Replicate 1


title: Lung, no hUC-MSCs, KP A7818-infected, control 2

description: Library name: NC2


title: BMDMs, unstimulated, BRD4 ChIP, pH6.5


title: LAM_Veh_rep1

description: Decoded transcripts (.zarr and .parquet files) and morphology images (ome.tif file) for Vehicle-treated LAM replicate 1.


title: Lung, no hUC-MSCs, KP A7818-infected, control 1

description: Library name: NC1


title: HCC 1806 CREB3L1

description: Replicate 1


title: Hpb 3

city: Cardiff

first: Katherine

middle: Ann

last: Smith

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description: Library name: Sample 7

data_processing:
Low-quality bases and residual adapter contamination wese removed using Trim Galore! Script. Genome contaminants and ribosamal RNA were removed using the BBSplit and SortMeRNA tool (nf-core/rnaseq pipeline)
Assembly: Trimmed sequence reads were mapped to the GCA_001632525 Mus musculus BALB/cJ genome using Spliced Transcripts Alignment to a Reference (STAR) software
Supplementary files format and content: xlsl file contains raw counts for each Sample

source_name: Colon

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). Samples were made up to 20 ng/μL in nuclease-free water before library construction, quality control and Illumina next generation sequencing performed by Novogene
mRNA library construction was performed by Novogene using standard protocols (poly A enrichment).

treatment_protocol: Naive mice were fed a low omega-6 diet or a modified AIN-76A diet with a high omega-6:omega-3 ratio (mAIN-76A) for one week, then infected with 200 Heligmosomoides polygyrus bakeri L3 larvae for 14 days (Hpb), or maintained as naïve uninfected controls, before RNA-seq analysis of the colon.

value: Colon

value: Hpb


title: BMDMs, unstimulated, input of unstimulated_BRD9 CHIP, pH6.5


title: BMDMs, unstimulated, input, pH7.4


title: Hpb 5

description: Library name: Sample 8


title: Inguinal white adipose tissue, KO mice, replicate 2

city: Dalian

first: Haoan

address: No. 9, West Section, Lvshun South Road

institute: Dalian Medical University

description: Library name: KO2

data_processing:
Library quality was validated by Qubit 4.0 Fluorometer and Agilent 2100 Bioanalyzer. Pooled libraries were sequenced on an Illumina NovaSeq X Plus platform (PE150)Using NovaSeq X Plus Reagent Kits, generating  more than 20 million reads per sample.
Assembly: GRCm39
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Inguinal white adipose tissue

growth_protocol: IGF1R Floxed mice (B6;129-Igf1rtm2Arge/J, Jackson Laboratory, Stock No. 012251) were crossed with Adipoq-cre mice (B6; FVB-Tg (Adipoq-Cre)1Evdr/J, Jackson Laboratory, Stock No. 010803). Littermate Igf1r-Floxed (Flox) mice were used as controls. Mice were housed under a 12 h light/12 h dark cycle with ad libitum access to food and water. Mice were fed with NCD (D12450J, 10% kcal from fat, Research Diets, Inc., New Brunswick, NJ).

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 - 400bp use magnetic beads followed by PCR amplified for 10 - 15 PCR cycles.

treatment_protocol: Mice were fasted overnight prior to the experiment and anesthetized with Avertin before euthanasia.Tissues were rapidly dissected and snap-frozen in liquid nitrogen.

value: Inguinal white adipose tissue


title: BMDMs, unstimulated, BRD4 ChIP, pH7.4


title: HCC 1806

description: Replicate 1


title: Inguinal white adipose tissue, KO mice, replicate 3

description: Library name: KO3


title: BMDMs, unstimulated, input of unstimulated_BRD4 CHIP, pH6.5


title: HCC 1428 CREB3L1 Rep 2

description: Replicate 2


title: Inguinal white adipose tissue, Flox mice, replicate 3

description: Library name: LL3

value: IGF1R Flox


title: Hpb 2

description: Library name: Sample 6


title: Naive 5

description: Library name: Sample 4

value: Naïve


title: Inguinal white adipose tissue, KO mice, replicate 1

description: Library name: KO1


title: BMDMs, pH6.5 switch to pH7.4 2h, LPS

data_processing:
kallisto (v0.46.2) was used to pseudoalign samples to the GRCm38 (mm10) mouse transcriptome
kallisto abundance files were aggregated from transcript counts to gene counts with sleuth
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files containing sleuth-processed estimated gene counts for each set of experiments

extract_protocol:
RNA was harvested using RNAeasy mini plus kit (Qiagen) or TRIzol/BCP. 200 ng total RNA was used to for the construction of sequencing libraries.
Instruction manual of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: pH6.5 switch to pH7.4 2h, LPS


title: BMDMs, pH6.5 switch to pH7.4 4h, LPS

value: pH6.5 switch to pH7.4 4h, LPS


title: HCC 1428 CREB3L1

description: Replicate 1

value: Yes


title: Hpb 1

description: Library name: Sample 5


title: BMDMs, pH6.5 switch to pH7.4 0h, LPS

value: pH6.5 switch to pH7.4 0h, LPS


title: Naive 3

description: Library name: Sample 3


title: Inguinal white adipose tissue, Flox mice, replicate 2

description: Library name: LL2


title: HCC 1428 Rep 2

description: Replicate 2

value: No


title: BMDMs, pH6.5, LPS

value: WT

value: pH6.5, LPS


title: Naive 2

description: Library name: Sample 2


title: HCC 1806 Rep 2

description: Replicate 2


title: HCC 1428

description: Replicate 1


title: BMDMs, 1,6-hexanediol,LPS, rep2


title: Human_Chimpanzee hybrid with human mitochondria, Tetraploid3

first: Leijie

last: Li

address: 5323 Harry Hines Blvd.

department: Molecular Biology

institute: UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER

description:
HCh3
HC_human_count.txt
HC_chimp_count.txt

data_processing:
Hisat2 v 2.1.0 and Stringtie v 2.1.7 pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore v 0.6.10
Trimmed sequence reads were mapped to GRCh38/GRCm39 genomics by using Hisat2 v 2.1.0
Read count extraction using StringTie v 2.1.7
Assembly: GRCh38 for human;  Pan_tro 3.0 for chimpanzee; Susie_PAB v2 for orangutan
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism:
Pan troglodytes
Homo sapiens

source_name: Tetraploid

growth_protocol: All parental (contributor) and composite PSC lines were cultured in mTeSR Plus on Matrigel in a humidified atmosphere with 5% CO2 at 37*C.

extract_protocol:
RNA was harvested using the RNeasy Mini Plus Kit (Qiagen).
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit following the manufacturer's protocols.

treatment_protocol: Contributor and composite PSC lines were collected at ~70% confluency for lysis and RNA extraction.

value: Tetraploid

value: Hybrid tetraploid


title: Inguinal white adipose tissue, Flox mice, replicate 1

description: Library name: LL1


title: BMDMs, 1,6-hexanediol,LPS, rep1

value: Bone-marrow derived macrophage


title: BMDMs_CTBP1KD_LPS_rep4

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

description: Library name: 24L009960

data_processing:
NGS data quality was assessed with FastQC (RRID: SCR 014583, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Gene-level quantification was performed with Salmon version 1.9.0 (RRID: SCR_017036 ). Settings were: -libType A, -gcBias, -biasSpeedSamp 5 using the mm39 (M28, GRCm38, mm39) reference transcriptome provided by Gencode.
Gene count normalization and differential expression analysis were performed with DESeq2 version 1.44.0 (RRID: SCR_015687 ) after import of gene-level estimates with “tximport” version 1.32.0 (RRID: SCR_016752 ) in R (RRID: SCR_001905, R version 4.4.1 ).
For gene annotation, Ensembl gene IDs were mapped to MGI symbols using the Bioconductor package “AnnotationHub” version 3.12.0 (RRID: SCR_024227), and genome information was provided by Ensembl (GRCm39 release 105).
Assembly: mm39
Supplementary files format and content: TXT files with length-scaled TPMs and Differential Expression Analysis (DESeq2) results (Log2FoldChange, p-values) for BMDMs.
Supplementary files format and content: CSV file with counts and Differential Expression Analysis (DESeq2) results (Log2FoldChange, p-values) for J774.1 cells comparing LPS-stimulated Ctbp1,2dKO cells to wild type cells.

source_name: bone marrow-derived macrophages

growth_protocol: For bone marrow-derived macrophages (BMDMs): Humerus, femur and tibia were isolated from 6-12 weeks old C57BL6/N mice (RRID:MGI:7466658), disinfected with ethanol and transferred to the cell culture hood. Using scissors, tweezers and a syringe with G27 needle, bones were opened and bone marrow was flushed into a 50 ml conical tube filled with cold RPMI 1640. Cells were collected by centrifugation (300 xg, 5 min), supernatant was aspirated and cells were suspended in AKC lysis buffer (1M NH4Cl, 1M KHCO3, 0.5M EDTA) to lyse red blood cells. Subsequently, cells were suspended in PBS, carefully layered over Ficoll Paque (GE Healthcare 17144002) and subjected to density centrifugation (500xg, 45 min, slow acceleration and deceleration). The top layer was aspirated and middle fraction was collected in a fresh conical tube filled with Differentiation medium (30% L929 supernatant, 20% FBS, 1% Penicillin/ Streptomycin, 49% DMEM high glucose). Cells were pelleted by centrifugation, supernatant was aspirated and cells were suspended and plated in Differentiation medium on 15 cm bacterial plates. After 3 days of incubation at 5% CO2 and 37 °C in a humidified incubator, half of the medium was exchanged by fresh Differentiation medium and differentiation was continued until day 6. Cells were detached by incubation in Versene (Thermo Fisher Scientific, 11518876 ) and subjected to counting using a Neubauer chamber. Finally, differentiated cells in macrophage serum free medium (Thermo Fisher Scientific, 12065074) were seeded at 905000 cells/cm2 in tissue culture treated dishes and incubated at 5% CO2 and 37 °C in a humidified incubator.; For J774.1: J774.1 (RRID: CVCL_4770) cells were cultured in DMEM high glucose (Sigma, #D6429) supplemented with 10% FBS (Sigma, #S0615) and 1% Penicillin/Streptomycin (Sigma, #P4333) at 5% CO2 and 37 °C in a humidified incubator on tissue-culture treated dishes. At approximately 70-80 % confluence cells were passaged by scraping and suspending in fresh medium pre-warmed to 37 °C. J774.1 wt and CTBP1,2dKO cells were generated by transfection of fluorescently-labeled RNP complexes with guid RNAs against CTBP1 and CTBP2, followed by FACS sorting and single cell outgrowth. Single cell clones were genotyped and knockouts were confirmed by western blot. A non-mutated single cell clone from these single cell outgrowth was used as wild type (wt) and a mutated single cell clone was used as Ctbp1/2 dKO.

extract_protocol:
RNA was isolated using the ReliPrep RNA miniprep system (Promega) following the manufacturers instructions. In brief, cells were lysed in BL+TG buffer and lysates stored at -70 °C. For isolation of RNA, lysates were mixed with 2-propanol, bound to a silica membrane washed and DNA was digested by DNAseI. After additional washes RNA was eluted in nuclease-free water. RNA concentration was measured using a Nanophotometer (Implen) and 100-1000 ng of RNA were reverse transcribed using the  Reverse Transcription System with random hexamers (Promega) following the manufacturers instructions. Thereby a control without reverse transcription was included to assess potential DNA contaminations during qPCR.
The RNA quality was determined on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano kit, following the manufacturer’s instructions. Library preparation and rRNA depletion were conducted using the TruSeq unstranded mRNA Library Prep kit (Illumina) starting with 500 ng of RNA for each biological triplicate. The samples were sequenced on the Illumina NovaSeq 6000 or NovaSeq X PLUS.

treatment_protocol: Cells were seeded and incubated over night at normal growth condition. Then vehicle (PBS) or LPS (#LPS25 Sigma, 100ng/mL) were added and cells were incubated for 4 h for RNAseq experiments

value: bone marrow-derived macrophages

tag: Sex

value: male

value: Ctbp1 siRNA

value: 4 h 100 ng/ml LPS

tag: replicate

tag: strain


title: Human_Chimpanzee hybrid with human mitochondria, Tetraploid2

description:
HCh2
HC_human_count.txt
HC_chimp_count.txt


title: G1E-ER4 SMC2-AID RCMC, Auxin 8 hr, Biological Replicate 2

city: Cambridge

first: Viraat

middle: Yogi

last: Goel

department: Biological Engineering

institute: Massachusetts Institute of Technology (MIT)

description: Processed data file merges biological replicates 1 & 2

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. Remaining reads were indexed (pairix v0.3.7) and filtered to retain only those reads where both read mates lie in a locus of interest. These filtered reads were subsequently converted to .cool format using cooler (v0.8.11) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Loops were manually annotated within each captured locus.
Assembly: mm39
Supplementary files format and content: mcool:multi-resolution contact map
Library strategy: Region Capture Micro-C

growth_protocol: The G1E-ER4 cell line and its sublines were cultured in IMDM supplemented with 2% penicillin/streptomycin, 15% fetal bovine serum, Kit ligand, erythropoietin, and monothioglycerol. Cells were maintained at a density less than 1 million cells per 1mL.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified using a DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size-selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 5-7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. 80-mer biotinylated probes were designed end-to-end to tile across regioins of interest with Twist Bioscience. Capture was performed using the custom target enrichment panels using Twist Bioscience's Standard Hybridization Target Enrichment Protocol (Twist Bioscience, 104178) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution. The library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 4 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

value: proerythroblast

value: Auxin, 8hr


title: Human_Chimpanzee hybrid with human mitochondria, Tetraploid1

description:
HCh1
HC_human_count.txt
HC_chimp_count.txt


title: BMDMs_ctrl_LPS_rep4

description: Library name: 24L009959

value: control siRNA


title: G1E-ER4 SMC2-AID RCMC, Auxin 8 hr, Biological Replicate 1


title: BMDMs_CTBP2KD_veh_rep4

description: Library name: 24L009957

value: Ctbp2 siRNA

value: vehicle (PBS)


title: BMDMs, 1,6-hexanediol, rep1


title: G1E-ER4 SMC2-AID RCMC, Auxin 4 hr, Biological Replicate 4

description: Processed data file merges biological replicates 1-4

value: Auxin, 4hr


title: BMDMs, MS645,LPS, rep2


title: BMDMs_CTBP2KD_LPS_rep4

description: Library name: 24L009961


title: Human_Chimpanzee hybrid with chimpanzee mitochondria, Tetraploid3

description:
HCc3
HC_human_count.txt
HC_chimp_count.txt


title: Human_Chimpanzee hybrid with chimpanzee mitochondria, Tetraploid2

description:
HCc2
HC_human_count.txt
HC_chimp_count.txt


title: BMDMs_CTBP1KD_veh_rep4

description: Library name: 24L009956


title: BMDMs, MS645,LPS, rep1


title: Human_Chimpanzee hybrid with chimpanzee mitochondria, Tetraploid1

description:
HCc1
HC_human_count.txt
HC_chimp_count.txt


title: G1E-ER4 SMC2-AID RCMC, Auxin 4 hr, Biological Replicate 2


title: BMDMs_CTBP2KD_LPS_rep3

description: Library name: 24L009953


title: G1E-ER4 SMC2-AID RCMC, Auxin 4 hr, Biological Replicate 1


title: P18,CiPDO,replicate2,scRNA-seq,oligo

first: Ying

last: Xu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

description: Library name: P18-CiPDO-replicate2-oligo

data_processing:
The raw sequencing data was processed by DNBelab_C_Series_HT_scRNA-analysis-software to obtain gene expression profiles used for downstream analysis.
We filtered out cells expressing less than 500 genes, and cells with more than 30% transcripts mapped to mitochondrial genes.
Doublets were predicted with the package Scrublet, and then removed from the data.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: colorectal cancer PDO

extract_protocol:
To isolate single cells, patient-derived organoids or CRC tissues were incubated with TrypLE Express at 37°C for 20-30 min. The cells were then filtered through a 20 μm cell strainer, after which live cells were counted using a hemocytometer.
According to the manufacture ’ s introduction, Single-cell RNA-seq libraries wereconstructed using Single Cell 3 ’ Library andGel Bead Kit V3.1

value: colorectal cancer PDO

tag: age


title: P18,CiPDO,replicate1,scRNA-seq,oligo

description: Library name: P18-CiPDO-replicate1-oligo


title: BMDMs, 1,6-hexanediol, rep2


title: Naive 1

description: Library name: Sample 1

value: Colon

value: Naïve


title: BMDMs, MS645, rep1

value: WT


title: BMDMs, MS645, rep2


title: BMDMs_ctrl_LPS_rep3

description: Library name: 24L009951


title: G1E-ER4 SMC2-AID RCMC, Auxin 1 hr, Biological Replicate 3

value: Auxin, 1hr


title: G1E-ER4 SMC2-AID RCMC, Auxin 1 hr, Biological Replicate 4


title: BMDMs_ctrl_veh_rep4

description: Library name: 24L009955


title: G1E-ER4 SMC2-AID RCMC, Auxin 1 hr, Biological Replicate 2


title: G1E-ER4 SMC2-AID RCMC, Auxin 4 hr, Biological Replicate 3


title: P18,CiPDO,replicate1,scRNA-seq,cDNA

description: Library name: P18-CiPDO-replicate1-cDNA


title: BMDMs, iBET, rep2

value: iBET


title: G1E-ER4 SMC2-AID RCMC, Auxin 1 hr, Biological Replicate 1


title: BMDMs, iBET, rep1

value: Bone-marrow derived macrophage


title: G1E-ER4 SMC2-AID RCMC, Auxin 0.5 hr, Biological Replicate 2

value: Auxin, 0.5hr


title: BMDMs_CTBP1KD_LPS_rep3

description: Library name: 24L009952

value: bone marrow-derived macrophages

value: male


title: WT, +auxin, Rep 3

first: Nicholas

middle: K

last: Conrad

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

description: Library name: wplus3

library_source: other

data_processing:
Adapter sequences were trimmed from reads using Flexbar (v. 3.5.0), and the sequences were aligned to the hg38 genome using STAR (v.2.7.5c). m6A sites were identified with GLORI-tools (https://github.com/liucongcas/GLORI-tools) by reporting the A-to-G conversion rate. Incomplete conversions and false positives were eliminated with the following filters: ≥5 variant nucleotides, ≥15 coverage of A + G, and ≥0.1 A rate.
Assembly: hg38
Supplementary files format and content: CSV files include called m6A sites with adjusted P-values

molecule: other

growth_protocol: HCT116-derived cell lines were grown at 37°C with 5% CO2 in DMEM (Sigma D5796) supplemented with 10% tetracycline tested FBS (bio-techne R&D Systems S10350), penicillin-streptomycin (Sigma P0781), and 2mM L-glutamine (Fisher BP379-100). The EV, K163A, and WT complemented METTL16-AID cell lines were maintained in 50 ug/ml hygromycin (Sigma H3274) and 100 ug/ml G418 (Fisher BP673).

extract_protocol:
RNA was extracted using TRIzol (MRC Cat#TR 118). RNA was then treated with RQ1 DNase, and then rRNA was removed using the RiboMinus Eukaryote System V2.
GLORI-Seq was performed as described in Shen et al Nature Protocols, 2024. In brief, RNA was fragmented at 94°C for 4 min using the NEBNext Magnesium RNA Fragmentation Module to ~100-200 nt. Then, guanosines were protected, non-methylated adenosines were deaminated to inosines, and guanosines were deprotected. End repair was performed using Antarctic phosphatase and T4 PNK. Then, libraries were made using the NEBNext Small RNA Library Prep Set for Illumina with the NEBNext Multiplex Oligos for Illumina, Index primers set 1 and 2. Libraries were purified using the Monarch Spin PCR & DNA Cleanup Kit and a 1.5X KAPA Pure Beads cleanup. Finally, 150x150 paired-end sequencing was done on a NovaSeq X 1.5B flow cell with 10% PhiX added to diversify. Note 3 biological replicates were performed for each experiment.

treatment_protocol: To induce TIR1 and exogenous METTL16 expression, cells were treated overnight with 1 µg/ml of doxycycline (dox, Fisher BP2653). Then, to degrade endogenous METTL16, cells were treated for 72 hrs with 1 mM auxin (Sigma I5148). Note that media with fresh drugs was changed/added daily.

value: colorectal carcinoma

value: METTL16-AID + WT METTL16

value: +dox +auxin

tag: time

value: 72 hrs


title: BMDMs_ctrl_veh_rep3

description: Library name: 24L009947

value: control siRNA


title: BMDMs_CTBP2KD_LPS_rep1

description: Library name: 24L009945

value: Ctbp2 siRNA

value: 4 h 100 ng/ml LPS


title: BMDMs, JQ1,LPS, rep2

tag: cell type


title: P18,CiPDO,replicate2,scRNA-seq,cDNA

description: Library name: P18-CiPDO-replicate2-cDNA

value: colorectal cancer PDO


title: BMDMs_CTBP1KD_veh_rep3

description: Library name: 24L009948

tag: genotype

value: Ctbp1 siRNA

value: vehicle (PBS)


title: K163A, +auxin, Rep 3

description: Library name: kplus3

value: METTL16-AID + K163A METTL16

tag: treatment


title: BMDMs, JQ1,LPS, rep1

value: WT


title: BMDMs, iBET,LPS, rep1

value: iBET,LPS


title: G1E-ER4 SMC2-AID RCMC, Auxin 0.5 hr, Biological Replicate 1

value: proerythroblast


title: K163A, -auxin, Rep 3

description: Library name: k-3

value: -dox -auxin


title: WT, -auxin, Rep 3

description: Library name: w-3


title: G1E-ER4 SMC2-AID RCMC, Auxin 0 hr, Biological Replicate 3

description: Processed data file merges biological replicates 2-4

value: Auxin, 0hr


title: BMDMs, iBET,LPS, rep2

value: Bone-marrow derived macrophage


title: EV, +auxin, Rep 3

description: Library name: eplus3

value: colorectal carcinoma

value: METTL16-AID + Empty Vector (EV)


title: BMDMs, JQ1, rep2


title: BMDMs_CTBP2KD_veh_rep1

description: Library name: 24L009941

tag: tissue

value: bone marrow-derived macrophages

value: male


title: BMDMs_ctrl_LPS_rep1

description: Library name: 24L009943

value: control siRNA


title: BMDMs_CTBP1KD_LPS_rep1

description: Library name: 24L009944


title: G1E-ER4 SMC2-AID RCMC, Auxin 0 hr, Biological Replicate 4

tag: cell line


title: BMDMs, JQ1, rep1


title: EV, -auxin, Rep 3

description: Library name: e-3

value: 72 hrs


title: BMDMs_CTBP1KD_veh_rep1

description: Library name: 24L009940


title: G1E-ER4 SMC2-AID RCMC, Auxin 0 hr, Biological Replicate 2


title: G1E-ER4 Async RCMC, Biological Replicate 2

description: Processed data file merges biological replicates 1 & 2. Raw data files from the NovaSeq 6000 contain "NovaS1" in their filename while raw data files from the NovaSeq X contain "NovaX" in their filename.


title: WT, +auxin, Rep 2

description: Library name: wplus2

value: METTL16-AID + WT METTL16

value: +dox +auxin


title: G1E-ER4 Async RCMC, Biological Replicate 1, NovaSeqX


title: WT, -auxin, Rep 2

description: Library name: w-2


title: BMDMs_ctrl_veh_rep1

description: Library name: 24L009939


title: BMDMs, untreated, LPS, rep1

value: untreated, LPS


title: G1E-ER4 Late G1 RCMC, Biological Replicate 2


title: K163A, +auxin, Rep 2

description: Library name: kplus2


title: BMDMs, untreated, rep2

value: untreated


title: BMDMs, untreated, rep1


title: 10- EC

type: protein

city: University Park

first: Pak kin

last: Wong

state: State College

address: 513 Chemical and Biomedical Engineering Building

institute: the Pennsylvania State university

hyb_protocol: manufacture's protocol 012623 QAH-CAA-1200 SA10 Penn S069889

label: Cy3 equivalent dye

molecule: protein

source_name: primary bladder cancer PPS3 treated with MPC5

extract_protocol: Cell culture supernatants were collected.

value: primary bladder cancer


title: K163A, -auxin, Rep 2

institute: UT Southwestern Medical Center

description: Library name: k-2

value: METTL16-AID + K163A METTL16


title: BMDMs_CTBP2KD_veh_rep3

description: Library name: 24L009949

value: Ctbp2 siRNA

value: vehicle (PBS)


title: EV, +auxin, Rep 2

description: Library name: eplus2


title: G1E-ER4 Mid G1 RCMC, Biological Replicate 2

value: proerythroblast


title: BMDMs, pH 6.5 4h, LPS 4h, rep1

value: WT

value: pH 6.5 4h, LPS 4h


title: G1E-ER4 Late G1 RCMC, Biological Replicate 1, NovaSeqX


title: G1E-ER4 Mid G1 RCMC, Biological Replicate 1, NovaSeqX


title: 9- C

scan_protocol: manufacture's protocol 012623 QAH-CAA-1200 SA10 Penn S069889

source_name: primary bladder cancer PPS3 treated with serum free DMEM control


title: EV, -auxin, Rep 2

description: Library name: e-2

value: colorectal carcinoma

value: -dox -auxin


title: WT, +auxin, Rep 1

description: Library name: wplus1


title: G1E-ER4 Early G1 RCMC, Biological Replicate 2


title: BMDMs, pH 6.5 4h, rep2

value: Bone-marrow derived macrophage


title: BMDMs, pH 6.5 4h, rep1


title: WT, -auxin, Rep 1

description: Library name: w-1


title: G1E-ER4 Early G1 RCMC, Biological Replicate 1, NovaSeqX


title: BMDMs, pH 7.4 0h, LPS 4h, rep2

value: pH 7.4 0h, LPS 4h


title: G1E-ER4 AnaTelophase RCMC, Biological Replicate 2


title: 8- L+Efs

data_processing: manufacture's protocol 012623 QAH-CAA-1200 SA10 Penn S069889

source_name: primary bladder cancer PPS2 treated with MPC9


title: K163A, +auxin, Rep 1

description: Library name: kplus1


title: 6- B+L

source_name: primary bladder cancer PPS2 treated with MPC12

label_protocol: manufacture's protocol 012623 QAH-CAA-1200 SA10 Penn S069889


title: 7- EC

source_name: primary bladder cancer PPS2 treated with MPC5


title: BMDMs, pH 6.5 4h, LPS 4h, rep2


title: 4- L+Efs

source_name: primary bladder cancer PPS1 treated with MPC9


title: 5- C

source_name: primary bladder cancer PPS2 treated with serum free DMEM control


title: K163A, -auxin, Rep 1

description: Library name: k-1


title: BMDMs, pH 7.4 0h, LPS 4h, rep1


title: BMDMs, pH 7.4 0h, rep2


title: EV, +auxin, Rep 1

description: Library name: eplus1

value: METTL16-AID + Empty Vector (EV)


title: BMDMs, untreated, LPS, rep2


title: G1E-ER4 AnaTelophase RCMC, Biological Replicate 1, NovaSeqX


title: G1E-ER4 Prometaphase RCMC, Biological Replicate 2


title: 2- B+L

source_name: primary bladder cancer PPS1 treated with MPC12


title: 3- EC

source_name: primary bladder cancer PPS1 treated with MPC5


title: Cas9-SOC1 3'UTR bio rep 4

status: Public on Jun 02 2025

city: St. Louis

first: Richard

middle: Keith

last: Slotkin

state: Missouri

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

description:
Library name: sRNA_T1_Cas9-SOC1_3UTR_bio_rep_4
small RNA-seq library

data_processing:
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt. Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Assembly: TAIR10
Supplementary files format and content: Normalized read counts are provided for each filtered small-RNA read.

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: All Arabidopsis plants were grown at 22°C on Pro-Mix FPX soil in Conviron MTPS-120 growth chambers under the long day (16 hours light / 8 hours dark) in the Plant Growth Facility at the Donald Danforth Plant Science Center.

extract_protocol:
Total RNA was extracted using TRIzol
Small RNAs is enriched using the miRVana miRNA isolation kit (Life Technologies), and the libraries are prepared using TruSeq Small RNA Library Preparation Kit (Illumina).

value: Inflorescence


title: Cas9-SOC1 3'UTR bio rep 6

description:
Library name: sRNA_T1_Cas9-SOC1_3UTR_bio_rep_6
small RNA-seq library


title: EV, -auxin, Rep 1

description: Library name: e-1

value: 72 hrs


title: Cas9-SOC1 3'UTR bio rep 1

description:
Library name: sRNA_T1_Cas9-SOC1_3UTR_bio_rep_1
small RNA-seq library


title: Cas9-SOC1 3'UTR bio rep 5

description:
Library name: sRNA_T1_Cas9-SOC1_3UTR_bio_rep_5
small RNA-seq library


title: Cas9-SOC1 3'UTR bio rep 2

description:
Library name: sRNA_T1_Cas9-SOC1_3UTR_bio_rep_2
small RNA-seq library


title: Cas9-4xBS bio rep 5

description:
Library name: sRNA_T1_Cas9-4xBS_bio_rep_5
small RNA-seq library


title: Cas9-4xBS bio rep 3

description:
Library name: sRNA_T1_Cas9-4xBS_bio_rep_3
small RNA-seq library


title: Cas9-4xBS bio rep 2

description:
Library name: sRNA_T1_Cas9-4xBS_bio_rep_2
small RNA-seq library


title: BMDMs, pH 7.4 0h, rep1

source_name: BMDMs


title: 1- C

source_name: primary bladder cancer PPS1 treated with serum free DMEM control


title: Cas9-4xBS bio rep 4

description:
Library name: sRNA_T1_Cas9-4xBS_bio_rep_4
small RNA-seq library


title: Cas9-4xBS bio rep 1

description:
Library name: sRNA_T1_Cas9-4xBS_bio_rep_1
small RNA-seq library


title: Cas9-1xBS bio rep 5

description:
Library name: sRNA_T1_Cas9-1xBS_bio_rep_5
small RNA-seq library


title: Cas9-1xBS bio rep 6

description:
Library name: sRNA_T1_Cas9-1xBS_bio_rep_6
small RNA-seq library


title: Cas9-1xBS bio rep 2

description:
Library name: sRNA_T1_Cas9-1xBS_bio_rep_2
small RNA-seq library


title: Cas9-1xBS bio rep 1

description:
Library name: sRNA_T1_Cas9-1xBS_bio_rep_1
small RNA-seq library


title: Cas9-1xBS bio rep 3

description:
Library name: sRNA_T1_Cas9-1xBS_bio_rep_3
small RNA-seq library


title: TTchemDRBseq, CFAP20-KO + TY-CFAP20-R100C, 60min, rep2

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: Library name: TTchemDRBseq_TYCFAP20-R100C_60min_rep2

data_processing:
*library strategy: nascent RNA-seq
A sequencing quality profile was generated using FastQC (Version 0.11.9). Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the Human Genome 38 using STAR (Version 2.7.7a) with genome file GCA_000001405.15_GRCh38 and splice junction file Homo_sapiens.GRCh38.94.correctedContigs.gtf. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
A list of 49,948 gene-coordinates was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene (Karolchik et al., 2004). To prevent contamination of binding profiles, genes were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). From this, a set of 3,000 actively transcribed genes was selected by calculating gene size-corrected read-densities of BrU-seq data in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. These 3,000 actively transcribed genes were used in downstream analyses, unless stated otherwise. Read-density profiles of transcribed strands around TSS coordinates were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10 million reads. Subsequently, to properly compare the shape of the profiles, the average read-densities at the peak of the profile (average of density at 0.2-1kb after the TSS) was put to 1. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.0.5) and Rstudio (Version 1.1.423) (Team, 2019).
Assembly: hg38
Supplementary files format and content:
TSScoordinates_InclBrUseqInWTmock.txt: tab-delimited text file containing coordinates of 9,944 TSSs including associated BrUseq signal in WT cells
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_WT_60m_rep*_DeDup_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20KO_60m_rep*_DeDup_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20resc_60m_rep2_Dedup_FragLength150_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS
TTchemDRBseq_ReadDensityAroundTSS_200KbWindow_Above3kb_2kbGap_CFAP20R100C_60m_rep2_Dedup_FragLength150_TranscStrand.txt: tab-delimited text file containing the read-density/10M total reads of the transcribed strand at the indicated distance from the TSS

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO + TY-CFAP20(WT)

growth_protocol: All cell lines were cultured at 37°C with 5% CO2 in DMEM GlutaMAX (Gibco), supplemented with 10% fetal calf serum (Avantor, VWR) and penicillin/streptomycin (Sigma).

extract_protocol:
Immediately after 4SU labeling, cells were washed with PBS and lysed in TRIzol reagent (Invitrogen). Total RNA was isolated by TRIzol/chloroform isolation and ethanol precipitation. 110 μg RNA (in a total volume of 116 μl) was fragmented by adding 4 μl of 5 M NaOH and left on ice for 30 min. Fragmentation was stopped by the addition of 80 μl of 1 M Tris pH 7 and cleaned up twice using the Micro Bio-Spin P-30 Gel Columns (BioRad, 7326223) according to the manufacturer’s instructions. Biotinylation of 4SU-residues was performed in a total volume of 250 μl, containing 10 mM Tris-HCl pH 7.4, 1 mM EDTA and 5 μg of MTSEA biotin-XX linker (Biotium, BT90066) for 30 min at room temperature in the dark. RNA was then purified by phenol-chloroform extraction, denatured by 10 min incubation at 65 °C and added to 150 μl μMACS Streptavidin MicroBeads (Milentyl, 130-074-101). RNA was incubated with beads for 15 min at room temperature and beads were applied to a μColumn in the magnetic field of a μMACS magnetic separator. The beads were washed tree times with 55°C pull-down wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween-20). Biotinylated RNA was eluted twice by addition of 100 mM DTT and cleaned up using the RNeasy MinElute kit (Qiagen, 74204) using 1,050 μl ethanol (≥99%) per 200 μl reaction after addition of 700 μl of RLT buffer to precipitate RNA of less than 200 nucleotides.
For WT and CFAP-KO cells, purified 4SU-labelled RNA was then depleted of rRNAs using the QIAseq FastSelect -rRNA depletion kit (Qiagen), followed by library preparation using the TruSeq Stranded Total RNA kit (Illumina, 20020596). The libraries were amplified according to the manufacturer’s instructions, pooled and paired-end sequenced on a DNBSEQ-G400 (BGI) system. For CFAP20-KO cells expressing GFP-CFAP20(WT) or GFP-CFAP20(R100C), no ribodepletion was performed.

treatment_protocol: Cells were exposed to 100 μM DRB (Sigma) for 4 hours. Following removal of DRB, cells were either immediately metabolically labeled with 1 mM 4-thio-uridine (4SU; Glentham Life Sciences) for 30 min, or released in regular medium for 30 min followed by 30 min labeling with 1 mM 4-thio-uridine.

tag: genome used_to_map_to

value: DRB treated, 30 min DRB release, followed by 30 min DRB-release + 4SU labeling

tag: pulldown antibody

value: Streptavidin-Biotin-based pulldown

tag: type of_material

value: Nascent RNA


title: Cas9-1xBS bio rep 4

description:
Library name: sRNA_T1_Cas9-1xBS_bio_rep_4
small RNA-seq library


title: Cas9-0xBS bio rep 5

description:
Library name: sRNA_T1_Cas9-0xBS_bio_rep_5
small RNA-seq library


title: Cas9-0xBS bio rep 6

description:
Library name: sRNA_T1_Cas9-0xBS_bio_rep_6
small RNA-seq library


title: G1E-ER4 Prometaphase RCMC, Biological Replicate 1, NovaSeqX

description: Processed data file merges biological replicates 1 & 2. Raw data files from the NovaSeq 6000 contain "NovaS1" in their filename while raw data files from the NovaSeq X contain "NovaX" in their filename.


title: Cas9-SOC1 3'UTR bio rep 3

description:
Library name: sRNA_T1_Cas9-SOC1_3UTR_bio_rep_3
small RNA-seq library


title: Cas9-0xBS bio rep 4

description:
Library name: sRNA_T1_Cas9-0xBS_bio_rep_4
small RNA-seq library


title: dCas9-DNMT3A_ChIP_sgIL1RN_ r1

city: Badalona

first: José

middle: Luis

last: Sardina

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
ChIP-seq libraries were prepared by an external sequencing service provider. In brief, the following steps were followed: (1) Take IPed-DNA and Input DNA for sample qualification. (2) DNA-end repair, 3'-dA overhang and adaptor ligation. (3) PCR amplification and size selection. (4) Library quality control; (5) Library circularization; (6) The library was amplified to make DNA nanoball (DNB); (7) Sequencing on DNBSEQ (DNBSEQ Technology) platform. Sequencing read Length: SE50
Quality control of sequenced reads was assesed by FastQC
TrimGalore was used to remove adapter sequences. Trimmed reads were aligned using Bowtie2 and filtered with samtools
Duplicates reads were removed using picard and peak calling was performed using MACS2
Differential enrichment analysis was performed using the option edge, from the R package diffBind
bigwig tracks were generated using DeepTools bamCoverage (-normalizeUsing RPKM  -binSize 10)
Assembly: GRCh38
Supplementary files format and content: bigWig files used for browser exploration data; narrowPeak

source_name: B-ALL cell line

growth_protocol: BlaER cells and subclones were grown in suspension in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1X Penicillin-Streptomycin, 1X L-glutamine and 0,1X β-mercaptoethanol.

extract_protocol:
ChIP experiments were performed as previously described (Sardina et al. Cell Stem Cell. 2018). Briefly, 30 million cells were cross-linked with 1% formaldehyde (Sigma).  Chromatin was sheared to 100-300bp fragments and conjugated with 10ug of anti-Cas9 antibody (Active Motif Cat #61757) rotating ON at 4ºC.Finally, DNA was purified by phenol: chloroform:isoamyl alcohol (25:24:1) extraction and ethanol precipitated.
For ChIP-seq, IP and Input DNA samples were quantified with Agilent 2100 before library preparation. BGI Genomics (Hong Kong, China) performed the library construction and sequencing process. For ligation, DNA-end repair and 3’-dA overhang was used. Then PCR amplification and size selection was performed. Library quality control and circularization was performed prior amplification to make DNA nanoball (DNB). Sequencing was done on the DNBSEQ platform using 50-nucleotide paired-end mode.

value: B-ALL cell line

value: BLaER subclone harboring dCas9-DNMT3A

value: B cell


title: Cas9-0xBS bio rep 3

description:
Library name: sRNA_T1_Cas9-0xBS_bio_rep_3
small RNA-seq library


title: dCas9-DNMT3A_ChIP_CTRL_r2

value: CTRL


title: dCas9-DNMT3A_ChIP_CTRL_r1


title: Cas9-4xBS bio rep 6

description:
Library name: sRNA_T1_Cas9-4xBS_bio_rep_6
small RNA-seq library


title: BlaER subclone, BLaER d7_sgIL1RN_r2

description:
d7_sgIL1RN_r2
Cell line: dCas9-DNMT3A sgIL1RN Treatment: CEBPa Days: 7

data_processing:
Reads were aligned using STAR, default mode for paired-end data
Gene expression was quantified using featureCounts
Differential expression analysis was performed using the R package DESeq2
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the ClusterProfiler R package. GO terms with corrected P-value less than 0.05 were considered significantly enriched.
Assembly: GRCh38
Supplementary files format and content: Non-normalized raw counts are provided as .txt files

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. In brief, the following protocol was followed: mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE150 (read length).

treatment_protocol: To induce transdifferentiation, the BlaER cells with dCas9-DNMT3A targeting with IL1RN were continuously treated with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Cells were collected at 0, 3 and 7 days.

value: BLaER cell line with dCas9-DNMT3A

value: iMac

value: dCas9-DNMT3A sgIL1RN

value: CEBPa Days:7


title: BlaER subclone, BLaER d7_sgIL1RN_r1

description:
d7_sgIL1RN_r1
Cell line: dCas9-DNMT3A sgIL1RN Treatment: CEBPa Days: 7


title: Mouse islets, β cell-specific knockout control, Male, rep1

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

description: Library name: 644M-betaWT

data_processing:
BCLConvert v4.3.13 was used for base-calling.
Skewer v0.1.123 was used for adapter trimming.
Trimmed reads were aligned to mm10 using STAR v2.5.3a and Ensembl annotation release 104.
Expression estimation was performed with RSEM v1.3.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of each knockout condition includes TPM values for each sample

source_name: Pancreas

extract_protocol:
Mouse islets were digested from pancreata with collagenase and purified by Histopaque gradiant centrifugation. The RNA extraction was performed on isolated islets via Qiagen silica gel spin column.
500 ng total RNA sample was enriched for mRNA by oligo (dT) selection followed by fragmentation using divalent cations under elevated temperature.  Double-stranded cDNA was synthesized using SuperScript II RT (Invitrogen, Carlsbad, California) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and then RNAse H for mRNA removal.  Double-stranded cDNA was purified with SPRI beads (Beckman Coulter Genomics, CA), followed by incubation with Klenow DNA Polymerase and Adenine to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments.  DNA fragments were ligated to Illumina unique molecular index (UMI) adapters, which have a single ‘T’ base (Thymine) overhang at their 3’end.  Following ligation, cDNA was purified with SPRI beads, and PCR-amplified (13 cycles) with PhusionTM DNA Polymerase using Illumina's genomic DNA primer set and purified with SPRI beads.

value: Pancreas

value: Pancreatic islets

value: Cpeb1 +/+; Ins1-Cre/+

value: male

value: adult day 111

tag: batch


title: Mouse islets, β cell-specific knockout of Cpeb1, Male, rep2

description: Library name: 747M-betaKO

value: Cpeb1 flx/flx; Ins1-Cre/+

value: adult day 80


title: Cas9-0xBS bio rep 1

description:
Library name: sRNA_T1_Cas9-0xBS_bio_rep_1
small RNA-seq library

value: Inflorescence


title: Mouse islets, β cell-specific knockout control, Male, rep2

description: Library name: 748M-betaWT


title: BlaER subclone, BLaER d3_sgIL1RN_r2

description:
d3_sgIL1RN_r2
Cell line: dCas9-DNMT3A sgIL1RN Treatment: CEBPa Days: 3

value: B cell intermediate to iMac

value: CEBPa Days:3


title: BlaER subclone, BLaER d3_sgIL1RN_r1

description:
d3_sgIL1RN_r1
Cell line: dCas9-DNMT3A sgIL1RN Treatment: CEBPa Days: 3

value: B-ALL cell line


title: Mouse islets, β cell-specific knockout of Cpeb1, Male, rep1

description: Library name: 645M-betaKO


title: BlaER subclone, BLaER B_sgIL1RN_r2

description:
B_sgIL1RN_r2
Cell line: dCas9-DNMT3A sgIL1RN Treatment: no treat

value: B cell

value: no treat


title: Mouse islets, β cell-specific knockout control, Female, rep2

description: Library name: 667F-betaWT

value: female

value: adult day 107


title: BlaER subclone, BLaER B_sgIL1RN_r1

description:
B_sgIL1RN_r1
Cell line: dCas9-DNMT3A sgIL1RN Treatment: no treat

value: BLaER cell line with dCas9-DNMT3A

value: dCas9-DNMT3A sgIL1RN


title: BlaER subclone, BLaER d7_CTRL_r1

description:
d7_CTRL_r1
Cell line: dCas9-DNMT3A sgCTRL Treatment: CEBPa Days: 7

value: iMac

value: dCas9-DNMT3A sgCTRL

value: CEBPa Days:7


title: Mouse islets, Whole-body knockout control, Male, rep3

description: Library name: 661M-wholeWT

value: Pancreas

value: Pancreatic islets

value: Cpeb1 +/+

value: male


title: Mouse islets, β cell-specific knockout of Cpeb1, Female, rep1

description: Library name: 648F-betaKO

value: Cpeb1 flx/flx; Ins1-Cre/+

value: adult day 108


title: Cas9-0xBS bio rep 2

description:
Library name: sRNA_T1_Cas9-0xBS_bio_rep_2
small RNA-seq library

value: Inflorescence


title: Mouse islets, Whole-body knockout control, Male, rep2

description: Library name: 654M-wholeWT

value: adult day 122


title: BlaER subclone, BLaER d3_CTRL_r1

description:
d3_CTRL_r1
Cell line: dCas9-DNMT3A sgCTRL Treatment: CEBPa Days: 3

value: B-ALL cell line

value: B cell intermediate to iMac

value: CEBPa Days:3


title: BlaER subclone, BLaER d3_CTRL_r2

description:
d3_CTRL_r2
Cell line: dCas9-DNMT3A sgCTRL Treatment: CEBPa Days: 3


title: BlaER subclone, BLaER B_CTRL_r2

description:
B_CTRL_r2
Cell line: dCas9-DNMT3A sgCTRL Treatment: no treat

value: B cell

value: no treat


title: BlaER subclone, BLaER B_CTRL r1

description:
B_CTRL_r1
Cell line: dCas9-DNMT3A sgCTRL Treatment: no treat

value: BLaER cell line with dCas9-DNMT3A


title: Mouse islets, Whole-body knockout of Cpeb1, Male, rep3

description: Library name: 693M-wholeKO

value: Cpeb1 KO/KO

value: adult day 139


title: BlaER subclone, BLaER 16h_sgIL1RN_r2

description:
16h_sgIL1RN_r2
Cell line: dCas9-DNMT3A sgIL1RN Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 16

growth_protocol: C/EBPa-B cell-derived iMacs were grown in DMEM supplemented with 10% heat-inactivated FBS, 1X Penicillin-Streptomycin and 1X L-glutamine.

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit. Then, was converted using cDNA kit. The library and sequencing was done by BGI Genomics.
RNA-seq libraries were prepared by an external sequencing service provider. In brief, the following protocol was followed: mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE150 (read length).

treatment_protocol: C/EBPa-B cell-derived iMacs were either untreated or treated with IL-1β (1 ng/mL) for 3 h and 16 h.

value: iMac

value: dCas9-DNMT3A sgIL1RN

value: Treatment1:CEBPa Days:9 Treatment 2:IL1B Hours:16


title: Mouse islets, Whole-body knockout control, Male, rep1

description: Library name: 648M-wholeWT

value: Pancreas

value: Pancreatic islets

value: Cpeb1 +/+

value: adult day 123


title: BlaER subclone, BLaER 16h_sgIL1RN_r1

description:
16h_sgIL1RN_r1
Cell line: dCas9-DNMT3A sgIL1RN Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 16


title: Mouse islets, Whole-body knockout of Cpeb1, Male, rep2

description: Library name: 659M-wholeKO

value: male

value: adult day 111


title: BlaER subclone, BLaER 0h_sgIL1RN_r2

description:
0h_sgIL1RN_r2
Cell line: dCas9-DNMT3A sgIL1RN Treatment1: CEBPa Days: 9

value: B-ALL cell line

value: Treatment1:CEBPa Days:9


title: Mouse islets, β cell-specific knockout control, Female, rep1

description: Library name: 650F-betaWT

value: Cpeb1 +/+; Ins1-Cre/+

value: female

value: adult day 108


title: Mouse islets, Whole-body knockout control, Female, rep2

description: Library name: 579F-wholeWT

value: adult day 188


title: Mouse islets, β cell-specific knockout of Cpeb1, Female, rep2

description: Library name: 664F-betaKO

value: Cpeb1 flx/flx; Ins1-Cre/+

value: adult day 107


title: Mouse islets, Whole-body knockout control, Female, rep1

description: Library name: 578F-wholeWT


title: BlaER subclone, BLaER 3h_sgIL1RN_r2

description:
3h_sgIL1RN_r2
Cell line: dCas9-DNMT3A sgIL1RN Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 3

value: BLaER cell line with dCas9-DNMT3A

value: iMac

value: Treatment1:CEBPa Days:9 Treatment 2:IL1B Hours:3


title: Mouse islets, Whole-body knockout of Cpeb1, Male, rep1

description: Library name: 613M-wholeKO

value: Pancreas

value: Cpeb1 KO/KO

value: adult day 155


title: BlaER subclone, BLaER 3h_sgIL1RN_r1

description:
3h_sgIL1RN_r1
Cell line: dCas9-DNMT3A sgIL1RN Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 3

value: dCas9-DNMT3A sgIL1RN


title: BlaER subclone, BLaER d7_CTRL_r2

description:
d7_CTRL_r2
Cell line: dCas9-DNMT3A sgCTRL Treatment: CEBPa Days: 7

value: dCas9-DNMT3A sgCTRL

value: CEBPa Days:7


title: BlaER subclone, BLaER 16h_CTRL_r2

description:
16h_CTRL_r2
Cell line: dCas9-DNMT3A sgCTRL Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 16

value: B-ALL cell line

value: Treatment1:CEBPa Days:9 Treatment 2:IL1B Hours:16


title: BlaER subclone, BLaER 16h_CTRL_r1

description:
16h_CTRL_r1
Cell line: dCas9-DNMT3A sgCTRL Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 16


title: BlaER subclone, BLaER 3h_CTRL_r2

description:
3h_CTRL_r2
Cell line: dCas9-DNMT3A sgCTRL Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 3


title: BlaER subclone, BLaER 3h_CTRL_r1

description:
3h_CTRL_r1
Cell line: dCas9-DNMT3A sgCTRL Treatment1: CEBPa Days: 9 Treatment 2: IL1B Hours: 3


title: Mouse islets, Whole-body knockout of Cpeb1, Female, biol rep1

description: Library name: 577F-wholeKO

value: Pancreatic islets


title: BlaER subclone, BLaER 0h_CTRL_r2

description:
0h_CTRL_r2
Cell line: dCas9-DNMT3A sgCTRL Treatment1: CEBPa Days: 9

value: Treatment1:CEBPa Days:9


title: WT EAE Replicate 1

city: detroit

first: Shailendra

last: Giri

state: MI

address: 2799 W grand boul

department: Neurology Research

institute: henry ford hospital

description: Library name: WT_1

data_processing:
aligned & generated raw matrices with Pipseeker which were piped with Seurat
Assembly: MM10
Supplementary files format and content: MATRIX FILES

source_name: spinal cord

extract_protocol:
Fluent Pipseek V5
Fluent Pipseek V5 pip-seq(scRNA-seq)

treatment_protocol: Irg1KO & WT mice subjected to EAE

value: spinal cord

value: male

value: WT


title: Irg1 KO EAE Replicate 1

description: Library name: Irg1_KO1

value: Irg1 KO


title: dCas9-DNMT3A_ChIP_sgIL1RN_ r2

value: BLaER subclone harboring dCas9-DNMT3A

value: B cell


title: WT EAE Replicate 2

description: Library name: WT_2


title: BlaER subclone, BLaER 0h_sgIL1RN_r1

description:
0h_sgIL1RN_r1
Cell line: dCas9-DNMT3A sgIL1RN Treatment1: CEBPa Days: 9

value: BLaER cell line with dCas9-DNMT3A

value: iMac


title: Mouse islets, Whole-body knockout of Cpeb1, Female, biol rep2

description: Library name: 607F-wholeKO

value: Pancreas

value: Cpeb1 KO/KO

value: female

value: adult day 165


title: Irg1 KO EAE Replicate 2

description: Library name: Irg1_KO2


title: BlaER subclone, BLaER 0h_CTRL r1

description:
0h_CTRL_r1
Cell line: dCas9-DNMT3A sgCTRL Treatment1: CEBPa Days: 9

value: dCas9-DNMT3A sgCTRL


title: MTN014_006_Vagina_TfvGelToVagina

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

institute: University of Washington

hyb_protocol: standard as recommended by illumina

scan_protocol: standard Illumina protocol using Illumina iScan system

data_processing:
The data was preprocessed by Bioconductor lumi package (version 2.34.0). It was vst transformed and rsn normalized. Only probes with detection threshold < 0.05 in at least 10 samples were included in the analysis.
Matrix normalized table: This table contains detection p-values and signal intensity data that were transformed with a variance stabilizing transformation and normalized with a robust spline normalization using the Bioconductor lumi package (version 2.34.0). The normalized data was filtered to only include probes with a detection threshold p value <0.05 in at least 10 samples. Matrix non-normalized table: This table contains raw signal intensity values and detection p-values for each sample.

source_name: Vagina tissue from participant MTN014_006 during tenofovir gel treatment to the Vagina

label_protocol: Labeling was performed using 50 ng total RNA and the Life Technologies/Ambion Illumina TotalPrep RNA Amplification kit

extract_protocol: Total RNA was extracted using the Qiagen Fibrous Tissue RNeasy mini kit

tag: ptid

tag: visit

value: Vagina

tag: rin


title: MTN014_012_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_012 during tenofovir gel treatment to the Vagina


title: MTN014_004_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_004 during tenofovir gel treatment to the Rectum

value: Rectum


title: MTN014_008_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_008 during tenofovir gel treatment to the Vagina


title: MTN014_010_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_010 during tenofovir gel treatment to the Vagina


title: MTN014_012_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_012 during tenofovir gel treatment to the Rectum


title: MTN014_004_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_004 during tenofovir gel treatment to the Vagina


title: MTN014_010_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_010 during tenofovir gel treatment to the Rectum


title: MTN014_012_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_012 at Baseline


title: MTN014_006_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_006 during tenofovir gel treatment to the Rectum


title: MTN014_002_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_002 during tenofovir gel treatment to the Vagina


title: Mouse islets, Whole-body knockout control, Female, rep3

description: Library name: 650F-wholeWT

value: Pancreatic islets

value: Cpeb1 +/+

tag: Sex

value: adult day 109


title: MTN014_010_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_010 at Baseline


title: MTN014_008_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_008 during tenofovir gel treatment to the Rectum


title: MTN014_006_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_006 at Baseline


title: adult zebrafish retinal ganglion cells, day 7 uninjured, fish set #2

city: Austin

first: Anna

last: Battenhouse

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

description:
Library name: Library-7DCtrl-2
Column name in BulkRNAseq_raw_counts.tsv:  U_7DPI_2

data_processing:
Raw read data were imported to the CLC Genomics Workbench (Qiagen Digital Insights) licensed through the Molecular Biology Information Service of the Health Sciences Library System at the University of Pittsburgh.
Differential gene expression analysis was performed on Injured versus Uninjured groups, after genes with TPM=0 in one or more replicates were excluded.
DEGs from 1, 5 and 7 dpi  time points were identified using the following filter: the maximum of the average group RPKM value >1.5, absolute fold change >1.5, FDR P-value <0.05.
Pathway enrichment analyses were performed using DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov) and using the KEGG database.
Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl, version 106
Supplementary files format and content: Tab-delimited BulkRNAseq_raw_counts.tsv file has raw gene counts for each Sample

organism: Danio rerio

source_name: retina

growth_protocol: isl2b:GFP transgenic zebrafish (Danio rerio) used in this study were 3-6 maintained on a 14:10 hour light:dark cycle at 28C.

extract_protocol:
1, 5 and 7 days post injury (dpi), the retina were harvested, cells dissociated using papain digestion, and RGCs were FACS isolated into SmartSeq HT lysis buffer (Takara Bio) for mRNA extraction.
cDNA sequencing libraries were prepared using a SmartSeq HT kit (Takara Bio) and Illumina Nextera XT kit (Illumina Inc).

treatment_protocol: Optic nerve transection (ONT) was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured (sham) control.

value: retina

value: adult retinal ganglion cells from isl2b:eGFP transgenic fish line

value: retinal ganglion cells

value: isl2b:eGFP transgenic fish line

value: uninjured

value: day 7


title: adult zebrafish retinal ganglion cells, day 7 uninjured, fish set #3

description:
Library name: Library-7DCtrl-3
Column name in BulkRNAseq_raw_counts.tsv:  U_7DPI_3


title: MTN014_004_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_004 at Baseline


title: MTN014_008_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_008 at Baseline


title: adult zebrafish retinal ganglion cells, day 7 uninjured, fish set #1

description:
Library name: Library-7DCtrl-1
Column name in BulkRNAseq_raw_counts.tsv:  U_7DPI_1


title: MTN014_002_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_002 at Baseline


title: adult zebrafish retinal ganglion cells, 7 days post injury, fish set #3

description:
Library name: Library-7DPI-3
Column name in BulkRNAseq_raw_counts.tsv:  I_7DPI_3

value: optic nerve transection

value: day 7 post-injury


title: MTN014_011_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_011 during tenofovir gel treatment to the Vagina


title: MTN014_009_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_009 during tenofovir gel treatment to the Vagina


title: adult zebrafish retinal ganglion cells, 7 days post injury, fish set #1

description:
Library name: Library-7DPI-1
Column name in BulkRNAseq_raw_counts.tsv:  I_7DPI_1


title: adult zebrafish retinal ganglion cells, day 5 uninjured, fish set #3

description:
Library name: Library-5DCtrl-3
Column name in BulkRNAseq_raw_counts.tsv:  U_5DPI_3

value: day 5


title: MTN014_007_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_007 during tenofovir gel treatment to the Rectum


title: MTN014_005_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_005 during tenofovir gel treatment to the Vagina


title: Mouse islets, Whole-body knockout of Cpeb1, Female, biol rep3

description: Library name: 655F-wholeKO

source_name: Pancreas

value: Pancreas

value: Cpeb1 KO/KO

value: female

value: adult day 98


title: MTN014_003_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_003 during tenofovir gel treatment to the Rectum

value: Rectum

value: Vagina


title: adult zebrafish retinal ganglion cells, day 5 uninjured, fish set #1

description:
Library name: Library-5DCtrl-1
Column name in BulkRNAseq_raw_counts.tsv:  U_5DPI_1


title: MTN014_001_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_001 during tenofovir gel treatment to the Vagina


title: MTN014_002_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_002 during tenofovir gel treatment to the Rectum


title: adult zebrafish retinal ganglion cells, 7 days post injury, fish set #2

description:
Library name: Library-7DPI-2
Column name in BulkRNAseq_raw_counts.tsv:  I_7DPI_2


title: TTchemDRBseq, CFAP20-KO + TY-CFAP20-WT, 60min, rep2

description: Library name: TTchemDRBseq_TYCFAP20-WT_60min_rep2

source_name: RPE1 iCas9 p53/puro-dKO CFAP20-KO + TY-CFAP20(WT)

value: DRB treated, 30 min DRB release, followed by 30 min DRB-release + 4SU labeling

value: Streptavidin-Biotin-based pulldown

value: Nascent RNA


title: adult zebrafish retinal ganglion cells, 5 days post injury, fish set #3

description:
Library name: Library-5DPI-3
Column name in BulkRNAseq_raw_counts.tsv:  I_5DPI_3

value: retina

value: adult retinal ganglion cells from isl2b:eGFP transgenic fish line

value: day 5 post-injury


title: MTN014_011_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_011 during tenofovir gel treatment to the Rectum


title: adult zebrafish retinal ganglion cells, 5 days post injury, fish set #2

description:
Library name: Library-5DPI-2
Column name in BulkRNAseq_raw_counts.tsv:  I_5DPI_2

value: retinal ganglion cells

value: isl2b:eGFP transgenic fish line


title: MTN014_007_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_007 during tenofovir gel treatment to the Vagina


title: adult zebrafish retinal ganglion cells, 5 days post injury, fish set #1

description:
Library name: Library-5DPI-1
Column name in BulkRNAseq_raw_counts.tsv:  I_5DPI_1

value: optic nerve transection


title: adult zebrafish retinal ganglion cells, day 5 uninjured, fish set #2

description:
Library name: Library-5DCtrl-2
Column name in BulkRNAseq_raw_counts.tsv:  U_5DPI_2

value: uninjured


title: MTN014_009_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_009 during tenofovir gel treatment to the Rectum


title: adult zebrafish retinal ganglion cells, day 1 uninjured, fish set #3

description:
Library name: Library-1DCtrl-3
Column name in BulkRNAseq_raw_counts.tsv:  U_1DPI_3

value: day 1


title: MTN014_003_Vagina_TfvGelToVagina

source_name: Vagina tissue from participant MTN014_003 during tenofovir gel treatment to the Vagina


title: BlaER subclone, BLaER d3_CTRL_r3

type: genomic

description:
d3_CTRL_r3
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC v2.0 Bead-Chip arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Methylation data were analyzed using the minfi package in R. Data was imported into R and normalized (noob and quantile normalization). Probes were removed if they did not pass the detection cut-off (p < 0.01), and if were associated with known SNPs or with the X and Y chromosomes

label: Cy5 and Cy3

source_name: B-ALL cell line

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using Bllood & Cell Culture DNA Mini Kit (QIAGEN).

treatment_protocol: To induce transdifferentiation, the BlaER cells and subclones were continuously treated with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml).

tag: subclone

value: BLaER dCas9-DNMT3A sgCTRL

value: CEBPa Time:3 days


title: adult zebrafish retinal ganglion cells, day 1 uninjured, fish set #2

description:
Library name: Library-1DCtrl-2
Column name in BulkRNAseq_raw_counts.tsv:  U_1DPI_2

source_name: retina


title: BlaER subclone, BLaER d3_sgIL1RN_r4

description:
d3_sgIL1RN_r4
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)

value: BLaER dCas9-DNMT3A sgIL1RN


title: BlaER subclone, BLaER d3_sgIL1RN_r1

description:
d3_sgIL1RN_r1
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: BlaER subclone, BLaER d3_CTRL_r4

description:
d3_CTRL_r4
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: MTN014_001_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_001 during tenofovir gel treatment to the Rectum


title: adult zebrafish retinal ganglion cells, day 1 uninjured, fish set #1

description:
Library name: Library-1DCtrl-1
Column name in BulkRNAseq_raw_counts.tsv:  U_1DPI_1


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #1

description:
Library name: Library-1DPI-1
Column name in BulkRNAseq_raw_counts.tsv:  I_1DPI_1

value: day 1 post-injury


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #2

description:
Library name: Library-1DPI-2
Column name in BulkRNAseq_raw_counts.tsv:  I_1DPI_2


title: BlaER subclone, BLaER B_sgIL1RN_r3

description:
B_sgIL1RN_r3
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)

value: CEBPa Time:0 days


title: BlaER subclone, BLaER d3_CTRL_r2

description:
d3_CTRL_r2
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: MTN014_005_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_005 at Baseline

value: Vagina


title: MTN014_005_Vagina_TfvGelToRectum

source_name: Vagina tissue from participant MTN014_005 during tenofovir gel treatment to the Rectum

value: Rectum


title: MTN014_011_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_011 at Baseline


title: MTN014_007_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_007 at Baseline


title: THP-1 cells, KD3_IP

city: Hefei

first: Chao

last: Hou

state: Anhui province

address: 81 Meishan Road

institute: Anhui Medical University

description: Library name: KD3_IP.R1.fq

data_processing:
RNA extraction, methylated RNA immunoprecipitation (MeRIP) experiments, library preparation, high-throughput sequencing, and data analysis were performed by SeqHealth Technology Co., Ltd. (Wuhan, China). The KC-Digital™ Stranded mRNA Library Prep Kit (DR08502; Wuhan Kangce Technology Co., Ltd., China) was used to construct an RNA sequencing library. This kit mitigates artificial repeat bias during PCR and sequencing by labelling pre-amplified cDNA molecules with a unique molecular identifier composed of 12 random bases. The resulting library products, ranging from 200 to 500 bp in length, were enriched, quantified, and subsequently subjected to high-throughput sequencing using [Sequencer Automatic Selection]. Raw sequencing data were initially filtered using fastp (version 0.23.4) to eliminate low-quality reads and adapter sequences. The clean reads were subsequently processed using internal scripts from Wuhan Kangce Technology Co., Ltd. to mitigate the duplication bias introduced during library preparation and sequencing.
Assembly: GRCh38
Supplementary files format and content: The FASTQ format is a text file format for storing biological sequencing data, including the sequence identifier of read, base sequence, separated lines, and the sequencing quality fraction corresponding to each base pair.

growth_protocol: THP-1 cells were maintained in medium 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
mRNA was enriched using Oligo d(T) magnetic beads.
RNA libraries for m7G meRIP-seq were prepared using DNBSEQ-T7 following manufacturer's protocols.

treatment_protocol: THP-1 cells were induced as adherent cells by 100ng/ml PMA for 48 hours.

value: Human monocytic leukemia cell


title: BlaER subclone, BLaER B_sgIL1RN_r4

description:
B_sgIL1RN_r4
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: THP-1 cells, KD3_IN

description: Library name: KD3_IN.R1.fq


title: MTN014_009_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_009 at Baseline


title: BlaER subclone, BLaER B_sgIL1RN_r1

description:
B_sgIL1RN_r1
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: adult zebrafish retinal ganglion cells, 1 day post injury, fish set #3

description:
Library name: Library-1DPI-3
Column name in BulkRNAseq_raw_counts.tsv:  I_1DPI_3


title: THP-1 cells, KD2_IP

description: Library name: KD2_IP.R1.fq


title: BlaER subclone, BLaER d3_sgIL1RN_r2

description:
d3_sgIL1RN_r2
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: THP-1 cells, KD2_IN

description: Library name: KD2_IN.R1.fq