title: MTN014_012_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_012 during tenofovir gel treatment to the Rectum


title: MTN014_001_Vagina_PreTreatment

status: Public on Jun 02 2025

type: RNA

city: Seattle

first: Sean

last: Hughes

state: WA

address: 850 Republican St

country: USA

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.

molecule: total RNA

organism: Homo sapiens

source_name: Vagina tissue from participant MTN014_001 at Baseline

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

tag: tissue

value: Vagina

tag: rin


title: BlaER subclone, BLaER d3_CTRL_r1

type: genomic

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

description:
d3_CTRL_r1
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

molecule: genomic DNA

source_name: B-ALL cell line

label_protocol: Standard Illumina Protocol

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: 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

tag: treatment

value: CEBPa Time:3 days


title: THP-1 cells, KD1_IN

type: SRA

city: Hefei

first: Chao

last: Hou

state: Anhui province

address: 81 Meishan Road

country: China

institute: Anhui Medical University

description: Library name: KD1_IN.R1.fq

library_source: transcriptomic

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.

molecule: polyA RNA

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.

tag: cell line

tag: cell type

value: Human monocytic leukemia cell

tag: genotype


title: THP-1 cells, NC3_IN

description: Library name: NC3_IN.R1.fq


title: THP-1 cells, NC1_IP

description: Library name: NC1_IP.R1.fq


title: THP-1 cells, KD1_IP

description: Library name: KD1_IP.R1.fq


title: MTN014_008_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_008 during tenofovir gel treatment to the Rectum

value: Rectum


title: THP-1 cells, NC2_IN

description: Library name: NC2_IN.R1.fq


title: THP-1 cells, NC1_IN

description: Library name: NC1_IN.R1.fq


title: THP-1 cells, NC3_IP

description: Library name: NC3_IP.R1.fq


title: RNA-seq_HEK293T_siRBFOX2_rep2

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

institute: Peking University

description:
Library name: Sample 40
HEK293T_included-upon-RBFOX2knockdown.txt.gz;HEK293T_excluded-upon-RBFOX2knockdown.txt.gz

library_source: other

data_processing:
Reads mapping to abundant RNA types were discarded using BWA-MEM (v0.7.17), retaining unmapped reads for further analysis. The processed reads were aligned to the human genome (hg38) via a two-round mapping strategy designed to capture more mismatches for RNA editing candidates, sequentially utilizing HISAT2 (v2.2.1) and BWA-MEM, with GENCODE (v40) as the transcriptome guide. Unique mapped reads with up to 0.04 mismatches per fragment relative to read length were selected using pysam (v0.22.1) (https://github.com/pysam-developers/pysam) for subsequent analysis. PCR duplicates were removed using Picard (v3.1.1) (https://github.com/broadinstitute/picard).
All usable reads spanning exon-exon junctions were segmented using the GATK (v4.5.0.0) SplitNCigarReads command. Base quality scores were recalibrated using two rounds of GATK BaseRecalibrator and ApplyBQSR commands. RNA variants were identified from BAM files of usable reads via the GATK HaplotypeCaller command. RNA single nucleotide variants were selected using the GATK SelectVariants command. Single nucleotide polymorphisms (SNPs) from dbSNP (v151), the 1000 Genomes Project, and the University of Washington Exome Sequencing Project were removed in SNVs. Raw counts were quantified using Subread featureCounts (v2.0.1) and normalized to transcripts per million (TPM) as gene expression levels.
The resulting MAPIT BAM files were each used as inputs to SAILOR workflow (https://github.com/YeoLab/FLARE/workflow_sailor) to determine C-to-U and A-to-G edit sites across genome. And, these C-to-U and A-to-G edit sites were filtered out the potential artifacts and known SNPs. The C-to-U and A-to-G editing sites called with a confidence score larger than 0.5(C-to-U)/0.9(A-to-G) and an editing fraction less than 0.7 were remained as the input to FLARE (https://github.com/YeoLab/FLARE) to identify edit clusters, with default parameters as described in INSCRIBE paper. Then, C-to-U or A-to-G edit clusters from two replicates were intersected through bedtools (v2.31.1). MAPIT high-confidence edit clusters were identified as the intersection of C-to-U edit clusters overlapped with A-to-G edit clusters with a maximum gap 100 nt.
For si-PTBP1 and si-RBFOX2 RNA-seq in HEK293T cells, trimmed reads were aligned to the human genome (hg38) using STAR (v2.7.11b) with the --twopassMode Basic parameter. Differential alternative splicing (AS) events were identified from the resulting BAM files using rMATS (v4.2.0), with included and excluded exons defined as those with |IncLevelDifference| > 0.1 and FDR < 0.1.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM
Supplementary files format and content: tab-delimited text including RNA editing data

molecule: other

source_name: HEK293T cell line

growth_protocol: HeLa and HEK293T cells were cultured in high glucose DMEM supplemented with 10% (v/v) FBS and 1% (v/v) PS.All cells were maintained at 37°C with 5% CO2.

extract_protocol:
For large samples, total RNA was extracted following the standard TRIzol protocol (Invitrogen) for bulk RNA library construction. For small samples, mRNA was isolated with Oligo d(T)25 Magnetic Beads (NEB, S1419S) and directly subjected to Smart-seq2 protocol, as detailed in Plate-based scMAPIT-seq.
RNA-seq library was generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604) or Smart-seq2 protocol.

value: HEK293T cell line

value: WT

tag: fixation

tag: primary antibody

tag: secondary antibody

tag: pag-deaminase


title: BlaER subclone, BLaER d3_sgIL1RN_r3

description:
d3_sgIL1RN_r3
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)

value: BLaER dCas9-DNMT3A sgIL1RN


title: BlaER subclone, BLaER B_CTRL_r4

description:
B_CTRL_r4
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)

value: CEBPa Time:0 days


title: BlaER subclone, BLaER B_sgIL1RN_r2

description:
B_sgIL1RN_r2
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: MTN014_004_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_004 during tenofovir gel treatment to the Rectum


title: MTN014_010_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_010 during tenofovir gel treatment to the Rectum


title: MTN014_006_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_006 during tenofovir gel treatment to the Vagina


title: RNA-seq_HEK293T_siRBFOX2_rep1

description:
Library name: Sample 39
HEK293T_included-upon-RBFOX2knockdown.txt.gz;HEK293T_excluded-upon-RBFOX2knockdown.txt.gz


title: MTN014_002_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_002 during tenofovir gel treatment to the Rectum


title: MTN014_003_Vagina_PreTreatment

source_name: Vagina tissue from participant MTN014_003 at Baseline


title: MTN014_004_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_004 during tenofovir gel treatment to the Vagina


title: MTN014_008_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_008 during tenofovir gel treatment to the Vagina


title: RNA-seq_HEK293T_siPTBP1_rep2

description:
Library name: Sample 38
HEK293T_included-upon-PTBP1knockdown.txt.gz;HEK293T_excluded-upon-PTBP1knockdown.txt.gz


title: MTN014_006_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_006 during tenofovir gel treatment to the Rectum


title: MTN014_002_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_002 during tenofovir gel treatment to the Vagina


title: RNA-seq_HEK293T_siPTBP1_rep1

description:
Library name: Sample 37
HEK293T_included-upon-PTBP1knockdown.txt.gz;HEK293T_excluded-upon-PTBP1knockdown.txt.gz


title: MTN014_010_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_010 during tenofovir gel treatment to the Vagina


title: RNA-seq_HEK293T_siNC_rep2

description:
Library name: Sample 36
HEK293T_included-upon-PTBP1knockdown.txt.gz;HEK293T_excluded-upon-PTBP1knockdown.txt.gz;HEK293T_included-upon-RBFOX2knockdown.txt.gz;HEK293T_excluded-upon-RBFOX2knockdown.txt.gz

value: si-NC


title: RNA-seq_HEK293T_siNC_rep1

description:
Library name: Sample 35
HEK293T_included-upon-PTBP1knockdown.txt.gz;HEK293T_excluded-upon-PTBP1knockdown.txt.gz;HEK293T_included-upon-RBFOX2knockdown.txt.gz;HEK293T_excluded-upon-RBFOX2knockdown.txt.gz


title: BlaER subclone, BLaER B_CTRL_r2

description:
B_CTRL_r2
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: RNA-seq_HeLa_untreated_rep2

description:
Library name: Sample 34
HeLa_Unreated-RNA_rep2_snpfiltered.SAILOR.ranked.bed.gz;HeLa_Unreated-RNA_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

source_name: HeLa cell line

value: HeLa cell line

tag: inhouseid


title: MTN014_012_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_012 at Baseline


title: MTN014_010_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_010 at Baseline


title: MAPIT_HeLa_IgGforYTHDF2_rep2

description:
Library name: Sample 32
MAPIT-IgGforYTHDF2_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforYTHDF2_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: rabbit IgG (CST, 2729S)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: BlaER subclone, BLaER B_CTRL r1

description:
B_CTRL_r1
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)


title: RNA-seq_HeLa_untreated_rep1

description:
Library name: Sample 33
HeLa_Unreated-RNA_rep1_snpfiltered.SAILOR.ranked.bed.gz;HeLa_Unreated-RNA_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_012_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_012 during tenofovir gel treatment to the Vagina


title: MTN014_008_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_008 at Baseline


title: MAPIT_HeLa_IgGforYTHDF2_rep1

description:
Library name: Sample 31
MAPIT-IgGforYTHDF2_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforYTHDF2_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MAPIT_HeLa_Anti-YTHDF2_rep1

description:
Library name: Sample 29
MAPIT-YTHDF2_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-YTHDF2_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: Anti-YTHDF2 (Proteintech, 24744-1-AP)


title: MAPIT_HeLa_IgGforSERBP1_rep2

description:
Library name: Sample 28
MAPIT-IgGforSERBP1_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforSERBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MAPIT_HeLa_IgGforSERBP1_rep1

description:
Library name: Sample 27
MAPIT-IgGforSERBP1_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforSERBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MAPIT_HeLa_Anti-SERBP1_rep2

description:
Library name: Sample 26
MAPIT-SERBP1_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-SERBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: Anti-SERBP1 (BETHYL, A303-938A)


title: BlaER subclone, BLaER B_CTRL_r3

description:
B_CTRL_r3
Infininium MethylationEPIC v2.0 Bead-Chip arrays (Illumina Cat #20087706)

source_name: B-ALL cell line


title: MTN014_002_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_002 at Baseline


title: THP-1 cells, NC2_IP

description: Library name: NC2_IP.R1.fq


title: MTN014_009_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_009 during tenofovir gel treatment to the Vagina


title: MTN014_004_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_004 at Baseline


title: MAPIT_HeLa_Anti-SERBP1_rep1

description:
Library name: Sample 25
MAPIT-SERBP1_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-SERBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: RNA-seq_HEK293T_untreated_rep2

description:
Library name: Sample 24
HEK293T_Unreated-RNA_rep2_snpfiltered.SAILOR.ranked.bed.gz;HEK293T_Unreated-RNA_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

source_name: HEK293T cell line


title: MTN014_011_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_011 during tenofovir gel treatment to the Vagina


title: RNA-seq_HEK293T_untreated_rep1

description:
Library name: Sample 23
HEK293T_Unreated-RNA_rep1_snpfiltered.SAILOR.ranked.bed.gz;HEK293T_Unreated-RNA_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_001_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_001 during tenofovir gel treatment to the Vagina


title: MAPIT_HeLa_Anti-YTHDF2_rep2

description:
Library name: Sample 30
MAPIT-YTHDF2_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-YTHDF2_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_005_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_005 during tenofovir gel treatment to the Vagina


title: MAPIT_HEK293T_IgGforRBFOX2PUM1_rep1

description:
Library name: Sample 21
MAPIT-IgGforRBFOX2PUM1_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforRBFOX2PUM1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_011_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_011 during tenofovir gel treatment to the Rectum


title: MTN014_009_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_009 during tenofovir gel treatment to the Rectum


title: MAPIT_HEK293T_Anti-PUM1_rep2

description:
Library name: Sample 20
MAPIT-PUM1_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-PUM1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: PUM1 (Abcam, ab92545)


title: MTN014_007_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_007 during tenofovir gel treatment to the Rectum


title: MAPIT_HEK293T_Anti-PUM1_rep1

description:
Library name: Sample 19
MAPIT-PUM1_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-PUM1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_005_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_005 during tenofovir gel treatment to the Rectum


title: MAPIT_HEK293T_Anti-RBFOX2_rep2

description:
Library name: Sample 18
MAPIT-RBFOX2_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-RBFOX2_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: RBFOX2 (BETHYL, A300-864A)


title: MTN014_003_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_003 during tenofovir gel treatment to the Rectum


title: MAPIT_HEK293T_IgGforRBFOX2PUM1_rep2

description:
Library name: Sample 22
MAPIT-IgGforRBFOX2PUM1_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforRBFOX2PUM1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MAPIT_HEK293T_Anti-RBFOX2_rep1

description:
Library name: Sample 17
MAPIT-RBFOX2_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-RBFOX2_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_001_15cmRectum_TfvGelToRectum

source_name: 15cmRectum tissue from participant MTN014_001 during tenofovir gel treatment to the Rectum


title: MAPIT_HEK293T_IgGforPTBP1_rep2

description:
Library name: Sample 16
MAPIT-IgGforPTBP1_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforPTBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: mouse IgG (Santa Cruz, sc-2025)

value: rabbit anti-mouse (Abcam, catalog no. ab46450)


title: MTN014_007_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_007 during tenofovir gel treatment to the Vagina

value: Vagina


title: MAPIT_HEK293T_IgGforPTBP1_rep1

description:
Library name: Sample 15
MAPIT-IgGforPTBP1_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-IgGforPTBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz


title: MTN014_011_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_011 at Baseline


title: MAPIT_HEK293T_Anti-PTBP1_rep2

description:
Library name: Sample 14
MAPIT-PTBP1_rep2_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-PTBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: Anti-PTBP1 (Milipore, MABE986)


title: Ptch1, MycN, Control, CUT&RUN, rep 1

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: Library name: sample_id_8

library_source: genomic

data_processing:
Paired-end FASTQ files were processed using the nf-core CUT&RUN pipeline (v3.1).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCm38 (NCBI, p.6, release 108) and duplicates were removed for only control samples using picard.
Peaks were called with macs2 (normalization mode: CPM).
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

organism: Mus musculus

source_name: Cerebellum

extract_protocol:
Cut&Run assays were performed with CUTANATM ChIC/CUT&RUN kit according to the manufacturer’s protocol (EpiCypher, #14-1048). Briefly, fresh 500,000 cells were collected with a cell lifter (Corning, #3008) and resuspended in wash buffer (Pre-wash buffer (EpiCypher, #21-1002), protease inhibitor, and 0.5 mM spermidine and bound to activated Concanavalin A beads. Cells conjugated with beads were incubated with Antibody buffer (Cell permeabilization buffer and 2 mM EDTA) and antibodies at 4°C overnight. After extensive washing with Cell permeabilization buffer (Wash buffer and 0.01% digitonin), the cells were incubated with pAG-MNase (EpiCypher, #15-1016) for 10 min at room temperature, and then chromatin digestion was performed with calcium chloride for 2 h at 4°C. SNAP CUTANA™ Spike-in Controls for CUT&RUN (Cat: SKU-19-1002) panels of modified DNA-barcoded Designer Nucleosomes (dNucs™) carrying an array of widely studied histone post-translational modifications (PTMs) were used. After chromatin digestion, the stop buffer and E. coli spike-in DNA (EpiCypher, #18-1401) were added and incubated for 10 min at 37°C. Chromatin fragments were purified with DNA cleanup columns.
Library preparation on samples was conducted using manufacturer’s protocols for NEBNext Ultra II Dna Library Prep Kit (New England BioLabs, CAT#E7645) and NEB Multiplex Dual Index oligos (New England BioLabs, CAT#E7600, #E7780) with the following modifications. We input approximately 10ng of sample for half reactions, we diluted the NEBNext Illumina adaptor 1:25, we used the following PCR cycling conditions: 1 cycle of Initial Denaturation at 98C for 30 seconds, 12+ cycles of Denaturation at 98C for 10 seconds then Annealing/Extension at 65C for 10 seconds, and 1 final cycle of extension at 65C for 5 minutes. Following library preparation, double size selection was performed using Ampure beads and quality and concentration of libraries were determined by an Agilent 4200 Tapestation with High-Sensitivity D1000 reagents before pooling for sequencing.

value: Cerebellum

value: Medulloblastoma

value: Ptch+/-

tag: cut&run antibody

value: MycN


title: Ptch1, NCOR2, Control, CUT&RUN, rep 1

description: Library name: sample_id_9


title: MAPIT_HEK293T_Anti-PTBP1_rep1

description:
Library name: Sample 13
MAPIT-PTBP1_rep1_snpfiltered.SAILOR.ranked.bed.gz;MAPIT-PTBP1_high-confidence_editclusters.bed.gz;RBP-MAPIT_and_untreatedRNA-seq_TPM_in_ED-Fig2.csv.gz

value: HEK293T cell line

value: WT


title: Ptch1, KMT2D, Control, CUT&RUN, rep 1

description: Library name: sample_id_7


title: MTN014_003_15cmRectum_TfvGelToVagina

source_name: 15cmRectum tissue from participant MTN014_003 during tenofovir gel treatment to the Vagina


title: SingleADAR_HEK293T_IgG_rep2

description:
Library name: Sample 12
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz


title: MTN014_003_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_003 at Baseline


title: MTN014_006_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_006 at Baseline


title: mAdu_3

city: Heidelberg

first: Stephanie

last: Gehrs

address: Im Neuenheimer Feld

country: Germany

institute: DKFZ

description:
Library name: M8_3
mAdu_3

data_processing:
For all samples, low-quality bases were removed with the Fastq_quality_filter from the FASTX Toolkit 0.0.13 (FASTX-Toolkit) with 90% of the reads needing a quality phred score > 20. Homertools 4.7 (Heinz et al., 2010) were used for PolyA-tail trimming, and reads with a length < 17 were removed. Filtered reads were quantified with Kallisto (Bray et al., 2016) using RefSeq transcripts of the mouse mm10 reference (McGarvey et al., 2015) (kallisto parameters -b 10 -t 3 --plaintext --single -l 292 -s 50). Later, in the customized analysis, the gene identifiers were converted to Ensembl IDs with the org.Mm.eg.db R package, and the Gencode vM4 annotation, which included only protein-coding genes, was used for transcriptome annotation. TPM was used as the normalization method.
Assembly: mm10
Supplementary files format and content: txt file with tpm values per sample.

source_name: lung

extract_protocol:
RNA from FACS-sorted EC was isolated with an Arcturus PicoPure RNA Isolation Kit. The frozen pellet was resuspended in 50 μl of Arcturus PicoPure extraction buffer, and RNA was isolated according to the manufacturer’s instructions. The RNA was eluted in 13 μl of RNase-free water, and the concentration was measured using a high-sensitivity RNA assay with a Qubit Fluorometer according to the manufacturer’s instructions.
A sequencing library was generated with 10 ng of total RNA using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech) according to the manufacturer’s protocol. Sequencing reads (100 bp paired-end reads) were generated on the HiSeq platform (Illumina).

value: lung

value: endothelial cell

value: wt


title: Whole Blood, F11_144

city: London

first: Paula

last: Longhi

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary, University of London

description: Gene expression data from human whole blood

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: rma

label: biotin

source_name: Whole Blood

label_protocol: Affymetrix protocol

extract_protocol: RNA from whole blood was extracted using the PAXgene blood RNA isolation kit.

value: Whole Blood

tag: age

tag: surgery

value: Valve

tag: gender

value: Male


title: MTN014_007_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_007 at Baseline

tag: ptid

tag: visit


title: MTN014_005_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_005 at Baseline

tag: tissue

tag: rin


title: Whole Blood, F10_195

value: Both


title: Whole Blood, F08_132

value: CABG

value: Female


title: Whole Blood, F06_141


title: MTN014_001_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_001 at Baseline


title: Whole Blood, F07_128


title: SingleADAR_HEK293T_IgG_rep1

description:
Library name: Sample 11
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

source_name: HEK293T cell line

tag: treatment

value: rabbit IgG (CST, 2729S)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: Whole Blood, F12_125


title: Whole Blood, F09_120


title: SingleADAR_HEK293T_Anti-G3BP1_rep2

description:
Library name: Sample 10
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

tag: cell line

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: mAdu_2

description:
Library name: M8_2
mAdu_2

tag: cell type


title: MTN014_009_15cmRectum_PreTreatment

source_name: 15cmRectum tissue from participant MTN014_009 at Baseline


title: Whole Blood, G01_105


title: SingleADAR_HEK293T_Anti-G3BP1_rep1

description:
Library name: Sample 9
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

tag: genotype


title: Aged_3

description:
Library name: M18_3
Aged_3


title: Whole Blood, F05_167


title: Whole Blood, F01_80


title: Whole Blood, F04_111


title: Whole Blood, E12_114


title: SingleAPOBEC_HEK293T_IgG_rep2

description:
Library name: Sample 8
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

tag: fixation


title: Whole Blood, F02_118


title: Whole Blood, E10_123


title: Whole Blood, E09_106


title: Aged_1

description:
Library name: M18_1
Aged_1


title: Aged_2

description:
Library name: M18_2
Aged_2


title: mAdu_1

description:
Library name: M8_1
mAdu_1


title: SingleAPOBEC_HEK293T_Anti-G3BP1_rep1

description:
Library name: Sample 5
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

tag: primary antibody


title: Dual_HEK293T_IgG_rep2

description:
Library name: Sample 4
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

tag: secondary antibody


title: AKP, H3K27ac, Knockout, ChIP, rep1

data_processing:
Paired-end FASTQ files were processed using the nf-core ChIP-seq pipeline (v2.0.0).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCm38 (NCBI, p.6, release 108) and duplicates were marked and removed from all samples with picard.
Peaks were called with macs2 (peak mode: narrow) using a p-value threshold of 0.00001 and an effective genome size of 2.65e9.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: bigWig

extract_protocol:
Cerebellar tissues were processed for ChIP using Ren lab's protocol from Roadmap Epigenome (https://www.encodeproject.org).
Library preparation on samples was conducted using manufacturer’s protocols for NEBNext Ultra II Dna Library Prep Kit (New England BioLabs, CAT#E7645) and NEB Multiplex Dual Index oligos (New England BioLabs, CAT#E7600, #E7780) with the following modifications. We input approximately 10ng of sample for half reactions, we diluted the NEBNext Illumina adaptor 1:25, we used the following PCR cycling conditions: 1 cycle of Initial Denaturation at 98C for 30 seconds, 12+ cycles of Denaturation at 98C for 10 seconds then Annealing/Extension at 65C for 10 seconds, and 1 final cycle of extension at 65C for 5 minutes. Following library preparation, double size selection was performed using Ampure beads and quality and concentration of libraries were determined by an Agilent 4200 Tapestation with High-Sensitivity D1000 reagents before pooling for sequencing.

value: Cerebellum

value: Medulloblastoma

value: AtohI-Cre Kmt2dfl/+ Ptch+/-

tag: chip antibody

tag: group

value: Knockout


title: AKP, H3K27ac, Knockout, ChIP, rep2


title: Ptch1, H3K27ac, Control, ChIP, rep2

value: Ptch+/-

value: Control


title: Dual_HEK293T_IgG_rep1

description:
Library name: Sample 3
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz

value: HEK293T cell line

value: WT

tag: pag-deaminase

tag: inhouseid


title: Whole Blood, E06_98

value: Whole Blood

tag: age

tag: surgery


title: Whole Blood, E11_83

tag: gender


title: SingleAPOBEC_HEK293T_IgG_rep1

description:
Library name: Sample 7
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz


title: Whole Blood, E04_176


title: Whole Blood, E08_108

value: Valve


title: Dual_HEK293T_Anti-G3BP1_rep2

description:
Library name: Sample 2
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz


title: SingleAPOBEC_HEK293T_Anti-G3BP1_rep2

description:
Library name: Sample 6
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz


title: Ptch1, H3K27ac, Control, ChIP, rep1


title: Whole Blood, E07_180

value: Male


title: Whole Blood, E05_192


title: Whole Blood, D09_101


title: AKP, IgG, Knockout, Input sample


title: Whole Blood, E01_151


title: Whole Blood, E02_163


title: Whole Blood, D08_190


title: Dual_HEK293T_Anti-G3BP1_rep1

description:
Library name: Sample 1
HEK293T_DualSingleEnzyme_G3BP1_editing.tsv.gz


title: Ptch1, IgG, Control, Input sample


title: HeLa_untreated_FRISCR_cell15

description: FRISCR_untreated_editing.tsv.gz;FRISCR_untreated_TPM.tsv.gz

data_processing:
Reads mapping to abundant RNA types were discarded using BWA-MEM (v0.7.17), retaining unmapped reads for further analysis. The processed reads were aligned to the human genome (hg38) via a two-round mapping strategy designed to capture more mismatches for RNA editing candidates, sequentially utilizing HISAT2 (v2.2.1) and BWA-MEM, with GENCODE (v40) as the transcriptome guide. Unique mapped reads with up to 0.04 mismatches per fragment relative to read length were selected using pysam (v0.22.1) (https://github.com/pysam-developers/pysam) for subsequent analysis. PCR duplicates were removed using Picard (v3.1.1) (https://github.com/broadinstitute/picard).
All usable reads spanning exon-exon junctions were segmented using the GATK (v4.5.0.0) SplitNCigarReads command. Base quality scores were recalibrated using two rounds of GATK BaseRecalibrator and ApplyBQSR commands. RNA variants were identified from BAM files of usable reads via the GATK HaplotypeCaller command. RNA single nucleotide variants were selected using the GATK SelectVariants command. Single nucleotide polymorphisms (SNPs) from dbSNP (v151), the 1000 Genomes Project, and the University of Washington Exome Sequencing Project were removed in SNVs. Raw counts were quantified using Subread featureCounts (v2.0.1) and normalized to transcripts per million (TPM) as gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM for each single cell
Supplementary files format and content: tab-delimited text including RNA editing data for each single cell
Library strategy: FRISCR_MAPIT-seq

source_name: HeLa cell line

growth_protocol: HeLa cells were cultured in high glucose DMEM supplemented with 10% (v/v) FBS and 1% (v/v) PS.All cells were maintained at 37°C with 5% CO2.

extract_protocol:
mRNA was isolated with Oligo d(T) Magnetic Beads (NEB, S1419S) and directly subjected to Smart-seq2 protocol.
RNA-seq library was generated according to the Smart-seq2 protocol.

treatment_protocol: Other

value: HeLa cell line


title: AKP, H3K4me3, Knockout, CUT&RUN, rep2

data_processing:
Paired-end FASTQ files were processed using the nf-core-cutandrun pipeline (v3.0).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCm38 (NCBI, p.6, release 108) and duplicates were removed for only control samples using picard.
Peaks were called with macs2 (normalization mode: CPM).
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

tag: cut&run antibody


title: Whole Blood, D10_138

tag: tissue

value: Both


title: HeLa_untreated_FRISCR_cell14


title: AKP, H3K4me3, Knockout, CUT&RUN, rep1


title: HeLa_untreated_FRISCR_cell13


title: Whole Blood, D07_89

value: CABG


title: Whole Blood, D04_179


title: Whole Blood, E03_100


title: Whole Blood, D05_115


title: Ptch1, H3K4me3, Control, CUT&RUN, rep2


title: Whole Blood, D03_85


title: Whole Blood, D01_194


title: Whole Blood, D12_126


title: HeLa_untreated_FRISCR_cell12


title: HeLa_untreated_FRISCR_cell10


title: HeLa_untreated_FRISCR_cell11


title: Whole Blood, D06_116


title: Ptch1, H3K4me3, Control, CUT&RUN, rep1


title: AKP, IgG, Knockout, Input


title: Whole Blood, C12_104


title: Whole Blood, D02_119


title: HeLa_untreated_FRISCR_cell9


title: Ptch1, IgG, Control, Input


title: Whole Blood, C10_113


title: Whole Blood, C09_124


title: Whole Blood, C11_95

value: Female


title: Yoda1 -treated AGM # 2

city: Chestnut Hill

first: DHVANIT

last: SHAH

state: MA

address: 72 Gerry Rd

institute: Dhvanit Shah Lab

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: counts

source_name: AGM

extract_protocol: none provided by the submitter

value: Yoda1 -treated


title: Whole Blood, C06_136


title: Whole Blood, C05_97


title: HeLa_untreated_FRISCR_cell8


title: Yoda1 -treated AGM # 1


title: Whole Blood, C04_147


title: HeLa_untreated_FRISCR_cell7


title: Whole Blood, C08_88


title: Cyclic stretch-treated AGM # 3

value: Cyclic stretch-treated


title: Whole Blood, C01_86

value: AVR


title: Whole Blood, C03_94


title: HeLa_untreated_FRISCR_cell6


title: Whole Blood, C02_91


title: Static Control AGM # 3

value: Static Control


title: HeLa_untreated_FRISCR_cell3


title: HeLa_untreated_FRISCR_cell4


title: Static Control AGM # 2


title: Whole Blood, B12_188


title: HeLa_untreated_FRISCR_cell2


title: Whole Blood, C07_161


title: Whole Blood, B11_158


title: HeLa_untreated_FRISCR_cell5


title: Cyclic stretch-treated AGM # 1


title: HeLa_untreated_FRISCR_cell1


title: Cyclic stretch-treated AGM # 2


title: Static Control AGM # 1


title: cholangiocarcinoma cells, siZDHHC5-3

first: Li

address: No. 443, Mount Huangshan Road, Shushan District

institute: University of Science and Technology of China

description:
Library name: Sample 6
Column name in raw counts All Samples.txt: B2

data_processing:
Clean reads were aligned to the hg38 reference genome with HISAT2 using default parameters. Gene expression levels were determined via HT-seq via default parameters. Differential expression analysis between the two groups was performed via the DESeq2 (1.38.3) R package. Genes with p < 0.05 and |fold change| > 1 were identified as differentially expressed genes (DEGs). Hierarchical clustering analysis of these DEGs was conducted via the p heatmap package (version 1.0.12).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cholangiocarcinoma cells

extract_protocol:
RNA from various groups was extracted with TRIzol reagent (Genesand).
RNA-Seq was performed via the BGISEQ platform (BGI) and Illumina HiSeq 2500.

value: cholangiocarcinoma cells


title: Whole Blood, B08_166


title: Whole Blood, B10_152


title: Whole Blood, B05_149


title: cholangiocarcinoma cells, siZDHHC5-2

description:
Library name: Sample 5
Column name in raw counts All Samples.txt: B1


title: Whole Blood, B09_135


title: Whole Blood, B04_133


title: Whole Blood, B03_130


title: HeLa_DSP_FRISCR_IgG_cell16

description: FRISCR_DSP_editing.tsv.gz;FRISCR_DSP_TPM.tsv.gz

value: DSP

value: rabbit IgG (CST, 2729S)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: Whole Blood, B02_153


title: Whole Blood, B01_160


title: Whole Blood, B06_173


title: Whole Blood, B07_137


title: Whole Blood, A11_121


title: Whole Blood, A09_127


title: Whole Blood, A10_142


title: HeLa_DSP_FRISCR_IgG_cell14


title: HeLa_DSP_FRISCR_IgG_cell15


title: Whole Blood, A12_150


title: cholangiocarcinoma cells, siZDHHC5-1

description:
Library name: Sample 4
Column name in raw counts All Samples.txt: B0


title: cholangiocarcinoma cells, siControl-3

description:
Library name: Sample 3
Column name in raw counts All Samples.txt: A2


title: Whole Blood, A07_196

description: Gene expression data from human whole blood


title: cholangiocarcinoma cells, siControl-2

description:
Library name: Sample 2
Column name in raw counts All Samples.txt: A1


title: HeLa_DSP_FRISCR_IgG_cell12


title: cholangiocarcinoma cells, siControl-1

description:
Library name: Sample 1
Column name in raw counts All Samples.txt: A0


title: HeLa_DSP_FRISCR_IgG_cell11


title: MDS27_2016

city: Birmingham

first: Peter

last: Keane

address: Vincent Drive

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

description: Library name: MDS27_2016

data_processing:
Raw sequencing reads were processed to remove low-quality bases and Nextera ATAC adapter sequences using Trimmomatic v0.39 (Bolger et al. 2014; PMID:24695404)
Reads were then aligned to the human genome (version hg38) using Bowtie2 v2.2.5 (Langmead and Salzburg, 2012; PMID:22388286) with the --very-sensitive-local parameter.
Potential PCR duplicates were removed from the alignments using Picard MarkDuplicates v2.16.10 (http://broadinstitute.github.io/picard).
Peaks were called using MACS2 v2.2.7.1 (Zhang et al. 2008; PMID:18798982) with the options --nomodel --call-summits -q 0.05 -B --trackline.
Assembly: hg38
Supplementary files format and content: Read pileups in bedGraph format

source_name: HSPCs CD34+CD45+

extract_protocol:
Freshly collected cells were collected and sort based on the positive expression of CD45 and CD34.
Fragment transposition ATAC libraries were generated following the Omni-ATAC protocol. doi: 10.1038/nmeth.4396

value: HSPCs CD34+CD45+

value: CEBPA mutant


title: Patient7_Alveolar_Tconv

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

description: Sorted Treg cells from BAL fluid obtained from a patient with severe SARS-CoV-2 pneumonia within 48 hours of intubation

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: RREM-seq

source_name: Tconv cells(CD4+)

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. For WGEM-seq libraries, gDNA was first fragmented to a size of 240–290-bp using the Covaris E220 sonicator and then enzymatically converted with TET2 and APOBEC (New England Biolabs) per the manufacturer’s instructions. For WGBS libraries, gDNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Additional restriction enzyme digestion step was included for RRBS and RREM-seq libraries, in which gDNA was fragmented with MspI (New England Biolabs) and then size-selected for 100- to 250-bp fragments using solid-phase reversible immobilization beads (MagBio Genomics). CG-enriched gDNA was then bisulfite converted for RRBS libraries and enzymatically converted for RREMseq libraries. Random priming, adaptor ligation, PCR product clean-up, and final library amplification were performed using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs) for WGEM-seq libraries and the Pico Methyl-Seq Library Prep Kit (Zymo Research) was used for WGBS, RRBS, and RREM-seq libraries. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and four pooled libraries per run were sequenced on an Illumina NextSeq 2000 instrument using the 200 cycles NextSeq 2000 P3 reagent kit (whole-genome libraries) or the 100 cycles NextSeq 2000 P2 reagent kit (reduced representation libraries).
EM-seq (whole-genome and reduced representation) and Bisulfite-seq (whole-genome and reduced representation)

value: Tconv cells(CD4+)

tag: disease state

value: severe SARS-CoV-2 pneumonia


title: Patient6_Alveolar_Treg

description: Sorted Tconv cells from BAL fluid obtained from a patient with severe SARS-CoV-2 pneumonia within 48 hours of intubation

source_name: Treg cells (CD4+CD127lowCD25+)

value: Treg cells (CD4+CD127lowCD25+)


title: Patient7_Alveolar_Treg


title: HeLa_DSP_FRISCR_IgG_cell10

value: HeLa cell line

value: WT


title: HeLa_DSP_FRISCR_IgG_cell13


title: Whole Blood, A04_117

value: Whole Blood

value: Valve

value: Male


title: Patient5_Alveolar_Treg


title: HeLa_DSP_FRISCR_IgG_cell9


title: FaDu cells, Compound4, control, biol repl2

city: Jinan City

first: Wu

last: Huina

state: Shandong Province

address: No.4, Duanxing West Road, Huaiyin District

department: Department of Pharmacy

institute: Shandong Second Provincial General Hospital

description:
Library name: Sample5
Column name in gene_count.xls:RPt_2

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 GrCM38 using hisat2 v2.2.0 (the default parameters). Read count was calculated and normalized by featurecount v2.0.6 (-p)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: throat

growth_protocol: FaDu cells were maintained in DMEM/F12 supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Add 1 ml of Trizol reagent to each well, pipette up and down to fully lyse the cells and mix them with the Trizol Then place in liquid nitrogen to quickly freeze, and store at -80℃.
The library was constructed using fragmented mRNA templates according to the standard procedure of Novogene.

treatment_protocol: Fadu cells were seeded into 6-well plates and incubated overnight at 37℃, 5% CO₂. Then drug-t for 48h,

value: throat

value: FaDu

value: Hypopharyngeal squamous carcinoma cells


title: Whole Blood, A03_157

value: Both


title: Whole Blood, A02_191

value: Female


title: Patient5_Alveolar_Tconv


title: FaDu cells, Compound4, control, biol repl1

description:
Library name: Sample4
Column name in gene_count.xls:RPt_1


title: Patient4_Alveolar_Tconv


title: HeLa_DSP_FRISCR_IgG_cell8

value: DSP

value: rabbit IgG (CST, 2729S)


title: Whole Blood, A01_162


title: HeLa_DSP_FRISCR_IgG_cell7

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: MDS27_2013

description: Library name: MDS27_2013

value: HSPCs CD34+CD45+

value: CEBPA mutant


title: Whole Blood, A05_96


title: FaDu cells, Control, control, biol repl2

description:
Library name: Sample2
Column name in gene_count.xls:NC_2


title: Patient3_Alveolar_Tconv

value: Tconv cells(CD4+)

value: severe SARS-CoV-2 pneumonia


title: Patient6_Alveolar_Tconv


title: FaDu cells, Compound4, control, biol repl3

description:
Library name: Sample6
Column name in gene_count.xls:RPt_3


title: Patient2_Alveolar_Treg

value: Treg cells (CD4+CD127lowCD25+)


title: HeLa_DSP_FRISCR_IgG_cell6

value: HeLa cell line

value: WT


title: FaDu cells, Control, control, biol repl1

description:
Library name: Sample1
Column name in gene_count.xls:NC_1


title: CS_Mated_03

city: Athens

first: Cordula

last: Schulz

state: ga

address: 136 Cedar Street

institute: University of Georgia, Athens

description: Library name: CSM3

data_processing:
Sequences aligned using TopHat 2.0.12
Assembly: iso-1
Supplementary files format and content: Comparison of FPKM values between all groups

organism: Drosophila melanogaster

source_name: Tesitis

extract_protocol:
Testes were dissected from male flies in tissue isolation buffer and apical tips seperated using surgical needles. Isolated tips were placed in Trizol and stored at -80C until tRNA extraction.
Library was was constructed using Invitrogen Purelink RNA Mini Kit (12183025) as per instructions.

value: Tesitis

value: gonadal cells

value: CS

tag: treatment

value: mated


title: MSKG5191_5day_scRNAseq_Combo

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: Library name: MSKG5191_5day_scRNAseq_Combo

library_source: transcriptomic single cell

data_processing:
CUT&RUN data were mapped to hg38 human genome reference with BWA mem (0.7.12-r1039), then converted to BAM format and deduplicated with biobambam2 (v2.0.87). Uniquely mapped properly paired reads were extracted with samtools (v1.2) and fragments were extracted with bedtools (v2.17.0).  Single-cell RNA-seq data were aligned and quantified using the Cell Ranger (v7.0.1) pipeline (http://www.10xgenomics.com) against the human genome GRCh38 (refdata-gex-GRCh38-2020-A).
Assembly: hg38
Supplementary files format and content: BigWig and Peaks in bed format for CUT&RUN, CellRanger output for scRNAseq

source_name: spleen

growth_protocol: CHRF-288-11 cells were cultured in RPMI + 20% FBS + PSG [CUT&RUN] 0.5-1 million MSKG5191 (NUP98::NSD1) PDX cells were transplanted via tail vein injection into NSG mice.  Spleens were harvested and human leukemic cells were isolated using the human/mouse chimera kit (StemCell Technologies).  Two spleens per sample were combined for scRNAseq, and spleens from three mice were pooled for each sample. [scRNAseq]

extract_protocol:
CUT&RUN samples were prepared using the CUTANA ChIC/CUT&RUN kit. For scRNAseq, leukemic cells were human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 5 days, washed three times in PBS + 0.04% BSA, and counted.  The volume of cells to load to have a desired recovery target of 8,000-10,000 cells was calculated and cells were loaded on Chromium Next GEM Chip K (10X Genomics).  Samples were processed using the 10X Genomics 5' kit (v2).
CUT&RUN libraries were prepared using the CUTANA CUT&RUN library prep kit.  Single cell RNA-seq libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v2 (10X Genomics) according to manufacturer's protocols.

treatment_protocol: After the percentage of human leukemia cells in the peripheral blood reached ~30%, treatment was started.  Mice were treated for 5-days with vehicle, 3 mg/kg PF9363 (QD, IP), 75 mg/kg SNDX-5613 (BID, PO), or combination. [scRNAseq]

value: spleen

value: leukemia


title: CS_Mated_02

description: Library name: CSM2


title: HeLa_DSP_FRISCR_IgG_cell4

tag: cell line


title: CS_Mated_01

description: Library name: CSM1

tag: cell type


title: MSKG5191_5day_scRNAseq_PF

description: Library name: MSKG5191_5day_scRNAseq_PF


title: CS_Single_03

description: Library name: CS3

tag: genotype

value: non-mated


title: HeLa_DSP_FRISCR_IgG_cell2

tag: fixation

value: DSP


title: Treg_Smarcc1_RNP_edited_3

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Library name: Treg_Smarcc1_RNP_edited_3

data_processing:
Sequencing data were converted to fastq files, aligned to the mm10 reference genome using bowtie2, shifted for Tn5 offset using deeptools, and quantified using subread featurecounts.
Assembly: mm10
Supplementary files format and content: .txt files have peak locations and ATAC counts within each peak for each library

source_name: Spleen, Lymph Nodes

extract_protocol:
We adapted a previous protocol for gene editing using CRISPR/Cas9 ribonucleoprotein (RNP) complex nucleofection(Seki & Rutx, 2018) for application to primary mouse Tregs for editing at the Smarcc1 locus. We isolated CD4 T cells from pooled spleen and lymph nodes of 6-8-week-old Foxp3IRES-GFP mice and using magnetic negative selection using the Dynabeads Untouched Mouse CD4 Cells Kit (ThermoFisher Scientific, cat#11415D), resting cells for at least 30 min at 4°C prior to electroporation. We freshly prepared gRNA duplexes by combining crRNA (pre-designed validated crRNA, IDT) and tracrRNA oligos (IDT) at equimolar concentrations to a final duplex18 concentration of 40 μM, heating the duplex at 95°C for 5 min in a PCR thermocycler and cooling down at RT for 15 minutes before keeping on ice. For every reaction, we used 12x106 CD4 T cells, washed with Ca/Mg free PBS and spun down at 200G for 10 min at RT to remove FBS. During this spin, immediately prior to nucleofection, we assembled RNP complexes by thoroughly mixing 2.25 μl of 5 μg/μl TrueCut Cas9 Protein V2 (Thermo Fisher) with 5ul 40μM gRNA duplex and incubating at RT for 15 minutes. For each target, we used a pool of two RNPs carrying different gRNAs duplexes (assembled separately). Cells were resuspended in 100 ul of Electroporation Solution P4 (Lonza) with the pool of both targeting RNPs or with RNPs carrying control non-targeting gRNAs for 2 min at RT and transferred into Large Lonza cuvettes for nucleofection with a Lonza Amaxa 4D Nucleofector (Program DS137). 150 μl of pre-warmed complete T cell medium (RPMI-1640, 10% FBS, supplemented with L-Glutamine, NEAA, beta- mercaptoethanol, and 10mM HEPES) with pre-equilibrated cytokine (10ng/mL recombinant mouse IL7 and 2000 IU/mL recombinant human IL2) was added immediately afterwards and cells were rested for 1h at 37°C. Cells from each cuvette reaction were subsequently transferred to separate wells of a 12 well plate containing 1mL of pre-warmed complete medium, adding another 750 μl of media used to wash residual cells from cuvettes. After 2 additional hours of rest, cells were expanded with anti-CD3/anti-CD28 beads (Thermo Fisher) at a 1:1 ratio for 3 days. All cells in culture were transferred into separate Treg-depleted Foxp3DTR hosts, injected with DT (Sigma) at 20 ng/g mouse body weight for two consecutive days prior to transfer and again on the day following transfer. Cells were parked in vivo for 1 week prior to sorting 10,000 GFP+ Tregs from pooled spleen and lymph nodes for bulk ATAC-seq. 3 biological replicates passing quality-control were used for targeting conditions and 2 biological replicates passing quality-control for non- targeting condition
Bulk ATAC-seq libraries were prepared using the ImmGen ATAC-seq protocol as described in Yoshida et al, Cell, 2019

value: Spleen, Lymph Nodes

value: Treg

value: FOXP3-IRES-GFP, Smarcc1 targeting gRNA RNP

tag: strain

tag: Sex

value: Female


title: HeLa_DSP_FRISCR_IgG_cell3

tag: primary antibody

value: rabbit IgG (CST, 2729S)

tag: secondary antibody

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: Patient4_Alveolar_Treg

value: Treg cells (CD4+CD127lowCD25+)

value: severe SARS-CoV-2 pneumonia


title: MSKG5191_5day_scRNAseq_vehicle

description: Library name: MSKG5191_5day_scRNAseq_vehicle

value: vehicle


title: HeLa_DSP_FRISCR_IgG_cell1

value: HeLa cell line

value: WT

tag: pag-deaminase


title: CHRF_CUTRUN_Menin

description: Library name: CHRF_CUTRUN_Menin

data_processing:
CUT&RUN data were mapped to hg38 human genome reference with BWA mem (0.7.12-r1039), then converted to BAM format and deduplicated with biobambam2 (v2.0.87). Uniquely mapped properly paired reads were extracted with samtools (v1.2) and fragments were extracted with bedtools (v2.17.0).  Single-cell RNA-seq data were aligned and quantified using the Cell Ranger (v7.0.1) pipeline (http://www.10xgenomics.com) against the human genome GRCh38 (refdata-gex-GRCh38-2020-A).
Assembly: hg38
Supplementary files format and content: BigWig and Peaks in bed format for CUT&RUN, CellRanger output for scRNAseq
Library strategy: CUT&RUN

value: no treatment


title: CS_Single_02

description: Library name: CS2

value: Tesitis

value: gonadal cells

value: CS


title: FaDu cells, Control, control, biol repl3

description:
Library name: Sample3
Column name in gene_count.xls:NC_3

value: throat

value: FaDu

value: Hypopharyngeal squamous carcinoma cells


title: Treg_Smarcc1_RNP_edited_1

description: Library name: Treg_Smarcc1_RNP_edited_1

value: Spleen, Lymph Nodes

value: Treg

value: Male


title: CS_Single_01

description: Library name: CS1

value: non-mated


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell16

value: DSP

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: Treg_nontargeting_control_2

description: Library name: Treg_nontargeting_control_2

value: FOXP3-IRES-GFP, nontargeting gRNA RNP

value: Female


title: HeLa_DSP_FRISCR_IgG_cell5

description: FRISCR_DSP_editing.tsv.gz;FRISCR_DSP_TPM.tsv.gz

value: HeLa cell line

value: WT

value: rabbit IgG (CST, 2729S)


title: Patient2_Alveolar_Tconv

value: Tconv cells(CD4+)

value: severe SARS-CoV-2 pneumonia


title: CHRF_CUTRUN_KMT2A

description: Library name: CHRF_CUTRUN_KMT2A

value: leukemia

value: no treatment


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell15


title: Patient1_Alveolar_Treg

value: Treg cells (CD4+CD127lowCD25+)


title: OR_Mated_03

description: Library name: ORM3

value: Tesitis

value: gonadal cells

value: OR

value: mated


title: Patient1_Alveolar_Tconv


title: Treg_nontargeting_control_1

description: Library name: Treg_nontargeting_control_1

value: Spleen, Lymph Nodes

value: Treg

value: Male


title: OR_Mated_02

description: Library name: ORM2


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell14

value: DSP

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: CHRF_CUTRUN_MOZ

description: Library name: CHRF_CUTRUN_MOZ


title: OR_Mated_01

description: Library name: ORM1


title: MSKG5191_5day_scRNAseq_SNDX

description: Library name: MSKG5191_5day_scRNAseq_SNDX

value: spleen


title: mESCs, BRM014, RAD21, rep 2

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina - Chapel Hill

description:
Library name: BRM014, RAD21, rep 2
BRM014_RAD21.bw

data_processing:
Alignment: reads were either aligned to a combined mm10+hg38  genome with bowtie (v1.3.1) (parameters -v 2 -p 24 -S -m 1 -best -strata) or to both mm10 and hg38 separately with bowtie2 (v2.4.5)
PCR Duplicate Removal: duplicates were removed with samtools v1.17 fixmate -m followed by markdup -r -s
Peak Calling: peaks were called using MACS (v2.12) with parameters -f BED -g mm -q 0.01
Spike-in Normalization Factor: reads mapping to each genome (mouse and human) were counted. Normalization factor = (5/(# human reads / # mouse reads))*100
Coverage File Generation: bigwig files were generated using bedtools (v2.25.0) genomecov with parameters -bga -g mm10.chrom.sizes -scale (Normaliztion Factor) followed by ucsctools (v320) bedGraphToBigWig
Assembly: Mus musculus (mm10) and Homo sapiens (hg38) as well as a custom built bowtie index of Mus musculus (mm10) plus Homo sapiens (hg38)
Supplementary files format and content: For each ChIP sample, a BigWig coverage track of merged replicates is provided for viewing in a genome browser.

source_name: v6.5 mESC

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Kagey et al. 2010).

extract_protocol:
mESCs were crosslinked in 1% formaldehyde for 5 minutes before quenching with 2.5M glycine. After chromatin extraction, 5% of HEK293T chromatin was added to the mESC samples to be later used as a spike-in normalization. Crosslinked cells were lysed using Lysis Buffer 1 and Lysis Buffer 2 before washing and resuspension in Shearing Buffer. Sonication of nuclei was performed on a Covaris E220 with the following settings: Duty Factor 5, PIP/W 140, and 200 cycles per burst for 12 minutes. Chromatin fragments of 200-1000 base pairs were generated.
Sequencing libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems).

treatment_protocol: mESCs were untreatd or either treated with BRG1 targeting small molecule drugs (ACBI1 (1µM), BRM014 (10µ), or PFI-3 (30µM)) or DMSO.

tag: chip antibody

value: RAD21 (abcam, ab992)

value: v6.5 mESC


title: CHRF_CUTRUN_NUP98

description: Library name: CHRF_CUTRUN_NUP98


title: mESCs, BRM014, RAD21, rep 1

description:
Library name: BRM014, RAD21, rep 1
BRM014_RAD21.bw


title: CHRF_CUTRUN_IgG

description: Library name: CHRF_CUTRUN_IgG


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell12

value: HeLa cell line

value: WT


title: OR_Single_03

description: Library name: OR3

value: non-mated


title: mESCs, DMSO matched with BRM014, RAD21, rep 2

description:
Library name: DMSO matched with BRM014, RAD21, rep 2
DMSO-B_RAD21.bw

value: DMSO


title: 2100551_1

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA39473

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 28+90 or 28+51-base paired-end mode.
Raw sequencing data for the sample was converted to a matrix of expression using Space Ranger version: 1.3.0 (10X Genomics).
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.zip: zipped file of Space Ranger output folder "filtered_feature_bc_matrix"
Supplementary files format and content: raw_feature_bc_matrix.zip: zipped file of Space Ranger output folder "raw_feature_bc_matrix"
Supplementary files format and content: spatial.zip:  zipped file of Space Ranger output folder "spatial"
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
The gene expressions of human FFPE slide were detected by Visium CytAssist and 10x Visium Spatial Gene Expression Reagent Kits for FFPE.
RNA libraries were prepared by using 10x Visium spatial protocols.

value: Lung


title: mESCs, DMSO matched with BRM014, RAD21, rep 1

description:
Library name: DMSO matched with BRM014, RAD21, rep 1
DMSO-B_RAD21.bw


title: 24_2100577_1

description: Library name: GA38984


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell10


title: OR_Single_02

description: Library name: OR2

value: Tesitis

value: gonadal cells


title: mESCs, PFI-3, RAD21, rep 1

description:
Library name: PFI-3, RAD21, rep 1
PFI3_RAD21.bw


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell9


title: OR_Single_01

description: Library name: OR1

source_name: Testis

value: Testis

value: OR


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell13


title: BlaER_168h

description: Treatment: CEBPa Hours: 168

data_processing:
Raw reads were trimmed using the package Trimmomatic and the remaining sequences were mapped using Bismark
Reads were deduplicated, and CpG methylation calls were extracted using Bismark
The genome was split into 1Kb bins using the function makewindows from the bedtools package
DNA methylation signal was quantified by calculating the mean methylation on these 1Kb bin regions
Assembly: GRCh38
Supplementary files format and content: Methylation levels for CpGs passing the 5X coverage

source_name: B-ALL cell line

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

extract_protocol:
DNA was isolated using Bllood & Cell Culture DNA Mini Kit (QIAGEN).
Treatment to produce single-strand DNA (ssDNA). During the bisulfite conversion process, unmethylated cytosines were converted into uracils, while methylated cytosines remained unchanged. Following this, methylation sequencing adapters were ligated, and double-strand DNA synthesis was carried out. The library was considered ready after size selection and PCR amplification. Illumina sequencing was performed with a PE150 (read length).

treatment_protocol: BlaER cells were cultured with 100 nM 17-beta estradiol (E2) (Sigma Aldrich), human IL-3 (10 ng per ml) (PeproTech) and human M-CSF (10 ng per ml) (PeproTech) to activate C/EBPα during 7 days.

value: B-ALL cell line

value: BLaER cell line

value: iMac

value: CEBPa

tag: time


title: mESCs, PFI-3, RAD21, rep 2

description:
Library name: PFI-3, RAD21, rep 2
PFI3_RAD21.bw


title: mESCs, DMSO matched with PFI-3, RAD21, rep 2

description:
Library name: DMSO matched with PFI-3, RAD21, rep 2
DMSO-P_RAD21.bw


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell8

value: DSP

value: Anti-G3BP1 (Proteintech, 13057-2-AP)

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell7


title: BlaER_96h

description: Treatment: CEBPa Hours: 96

value: 96 hr


title: BlaER_24h

description: Treatment: CEBPa Hours: 24

value: B cell

value: 24 hr


title: Patient3_Alveolar_Treg

description: Sorted Tconv cells from BAL fluid obtained from a patient with severe SARS-CoV-2 pneumonia within 48 hours of intubation

value: Treg cells (CD4+CD127lowCD25+)

value: severe SARS-CoV-2 pneumonia


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell6

value: HeLa cell line

value: WT


title: mESCs, ACBI1, RAD21, rep 2

description:
Library name: ACBI1, RAD21, rep 2
ACBI1_RAD21.bw

value: RAD21 (abcam, ab992)

value: v6.5 mESC


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell5


title: 57

city: Boadilla del Monte

first: Andrea

middle: Escolar

last: Peña

state: Madrid

address: Urbanización Montepríncipe

institute: Universidad San Pablo CEU

data_processing:
## remove rRNAS contamination - PROGRAM: sortmerna - PARAMETERS: --num_alignments 1 -m 64000 -a 32 --paired_in -v --log  ##trimming adapters - PROGRAM: bbduk - PARAMETERS: tbo tpe mink=20 ktrim=r  #Pre-processing files - PROGRAM: cutadapt - PARAMETERS: -q 20,20 -m 20 -j 40  ## Alingment PROGRAM: bowtie2 - PARAMETERS: --very-sensitive -p 40   ## TRANSFORM TO BAM - PROGRAM: samtools - PARAMETERS: view -F 0xC -@ 40 -bS  ## SORT - PROGRAM: samtools - PARAMETERS: sort -n -@40  ## INDEX - PROGRAM: samtools - PARAMETERS: index  ## COUNT mRNAs - PROGRAM: HTSeq - PARAMETERS: -m intersection-nonempty -f bam -r pos -s no -t exon -i gene_id  Genome Build Assembly: Homo_sapiens.GRCh38.dna.primary_assembly.fa  GTF: Homo_sapiens.GRCh38.96.gtf
Supplementary files format and content: RNA-Seq normalized counts by DESeq2 (tsv)

source_name: serum

extract_protocol:
RNA was isolated with Rneasy Mini Kit (Qiagen) and the samples were treated with Dnase
New England BioLabs Next® Ultra II Directional RNA Library Prep Kit

value: serum

value: grade III-IV


title: BlaER_0h

first: José

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

institute: Josep Carreras Leukaemia Research Institute

description: Treatment: CEBPa Hours: 0

value: B-ALL cell line

value: BLaER cell line

value: 0 hr


title: mESCs, ACBI1, RAD21, rep 1

description:
Library name: ACBI1, RAD21, rep 1
ACBI1_RAD21.bw


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell11

value: DSP


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell3

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: mESCs, DMSO matched with ACBI1, RAD21, rep 2

description:
Library name: DMSO matched with ACBI1, RAD21, rep 2
DMSO-A_RAD21.bw

value: DMSO


title: 55


title: 53


title: mESCs, DMSO matched with ACBI1, RAD21, rep 1

description:
Library name: DMSO matched with ACBI1, RAD21, rep 1
DMSO-A_RAD21.bw


title: SplenocyteTreg_RREM-seq_2ng_05

description: Library name: Sample 44

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: standard bedGraph files generated by the Bismark pipeline
Supplementary files format and content: standard bigwig files generated using the bedGraphToBigWig function from kentUtils
Library strategy: EM-seq

source_name: Splenic Tconv cells from 18-20 week-old healthy mice

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. For WGEM-seq libraries, gDNA was first fragmented to a size of 240–290-bp using the Covaris E220 sonicator and then enzymatically converted with TET2 and APOBEC (New England Biolabs) per the manufacturer’s instructions. For WGBS libraries, gDNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Additional restriction enzyme digestion step was included for RRBS and RREM-seq libraries, in which gDNA was fragmented with MspI (New England Biolabs) and then size-selected for 100- to 250-bp fragments using solid-phase reversible immobilization beads (MagBio Genomics). CG-enriched gDNA was then bisulfite converted for RRBS libraries and enzymatically converted for RREMseq libraries. Random priming, adaptor ligation, PCR product clean-up, and final library amplification were performed using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs) for WGEM-seq libraries and the Pico Methyl-Seq Library Prep Kit (Zymo Research) was used for WGBS, RRBS, and RREM-seq libraries. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and four pooled libraries per run were sequenced on an Illumina NextSeq 2000 instrument using the 200 cycles NextSeq 2000 P3 reagent kit (whole-genome libraries) or the 100 cycles NextSeq 2000 P2 reagent kit (reduced representation libraries).

value: Treg cells (CD4+CD25+Foxp3-YFP+)


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell1

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: SplenocyteTreg_RREM-seq_2ng_04

description: Library name: Sample 43


title: HeLa_FA_FRISCR_IgG_cell15

description: FRISCR_FA_editing.tsv.gz;FRISCR_FA_TPM.tsv.gz

value: rabbit IgG (CST, 2729S)


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell2


title: 59

value: grade IV


title: Treg_Smarcc1_RNP_edited_2

description: Library name: Treg_Smarcc1_RNP_edited_2

value: Spleen, Lymph Nodes

value: Treg

value: FOXP3-IRES-GFP, Smarcc1 targeting gRNA RNP

value: Female


title: 39


title: 50


title: mESCs, DMSO matched with PFI-3, RAD21, rep 1

description:
Library name: DMSO matched with PFI-3, RAD21, rep 1
DMSO-P_RAD21.bw

value: RAD21 (abcam, ab992)

value: v6.5 mESC


title: 32

value: serum


title: SplenocyteTreg_RREM-seq_2ng_03

description: Library name: Sample 42


title: HeLa_DSP_FRISCR_Anti-G3BP1_cell4

description: FRISCR_DSP_editing.tsv.gz;FRISCR_DSP_TPM.tsv.gz

value: HeLa cell line

value: WT


title: 2


title: HeLa_FA_FRISCR_IgG_cell13


title: HeLa_FA_FRISCR_IgG_cell12


title: SplenocyteTreg_RREM-seq_25ng_04

description: Library name: Sample 40


title: SplenocyteTreg_RREM-seq_25ng_05

description: Library name: Sample 41


title: 14


title: SplenocyteTreg_RRBS_25ng_05

description: Library name: Sample 38

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary files format and content: standard bedGraph files generated by the Bismark pipeline
Supplementary files format and content: standard bigwig files generated using the bedGraphToBigWig function from kentUtils


title: 1

value: grade III


title: HeLa_FA_FRISCR_IgG_cell11

data_processing:
Reads mapping to abundant RNA types were discarded using BWA-MEM (v0.7.17), retaining unmapped reads for further analysis. The processed reads were aligned to the human genome (hg38) via a two-round mapping strategy designed to capture more mismatches for RNA editing candidates, sequentially utilizing HISAT2 (v2.2.1) and BWA-MEM, with GENCODE (v40) as the transcriptome guide. Unique mapped reads with up to 0.04 mismatches per fragment relative to read length were selected using pysam (v0.22.1) (https://github.com/pysam-developers/pysam) for subsequent analysis. PCR duplicates were removed using Picard (v3.1.1) (https://github.com/broadinstitute/picard).
All usable reads spanning exon-exon junctions were segmented using the GATK (v4.5.0.0) SplitNCigarReads command. Base quality scores were recalibrated using two rounds of GATK BaseRecalibrator and ApplyBQSR commands. RNA variants were identified from BAM files of usable reads via the GATK HaplotypeCaller command. RNA single nucleotide variants were selected using the GATK SelectVariants command. Single nucleotide polymorphisms (SNPs) from dbSNP (v151), the 1000 Genomes Project, and the University of Washington Exome Sequencing Project were removed in SNVs. Raw counts were quantified using Subread featureCounts (v2.0.1) and normalized to transcripts per million (TPM) as gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM for each single cell
Supplementary files format and content: tab-delimited text including RNA editing data for each single cell
Library strategy: FRISCR_MAPIT-seq


title: 54

value: grade II


title: HeLa_FA_FRISCR_IgG_cell10


title: SplenocyteTreg_RRBS_25ng_04

description: Library name: Sample 37


title: 52


title: HeLa_FA_FRISCR_IgG_cell14


title: SplenocyteTreg_RREM-seq_25ng_03

description: Library name: Sample 39


title: HeLa_FA_FRISCR_IgG_cell9


title: SplenocyteTreg_RRBS_25ng_03

description: Library name: Sample 36


title: 46


title: HeLa_FA_FRISCR_IgG_cell8


title: SplenocyteTreg_WGEM-seq_2ng_05

description: Library name: Sample 35


title: 45


title: 43


title: HeLa_FA_FRISCR_IgG_cell5


title: SplenocyteTreg_WGEM-seq_2ng_04

description: Library name: Sample 34


title: HeLa_FA_FRISCR_IgG_cell7


title: SplenocyteTreg_WGEM-seq_2ng_03

description: Library name: Sample 33


title: 37


title: HeLa_FA_FRISCR_IgG_cell3


title: 25


title: SplenocyteTreg_WGEM-seq_2ng_02

description: Library name: Sample 32


title: 23


title: SplenocyteTreg_WGEM-seq_2ng_01

description: Library name: Sample 31


title: 22


title: HeLa_FA_FRISCR_IgG_cell4


title: SplenocyteTreg_WGEM-seq_25ng_03

description: Library name: Sample 28


title: SplenocyteTreg_WGEM-seq_25ng_04

description: Library name: Sample 29


title: HeLa_FA_FRISCR_Anti-G3BP1_cell16

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: HeLa_FA_FRISCR_IgG_cell1


title: SplenocyteTreg_WGBS_25ng_05

description: Library name: Sample 27


title: HeLa_FA_FRISCR_IgG_cell2


title: T4 Cas9-SOC1 3'UTR bio rep 5

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: BSAS_T4_Cas9-SOC1_3UTR_bio_rep_5
Bisulfite amplicon sequencing (BSAS)

data_processing:
Raw reads were trimmed for adapters and mapped to all the amplicons pooled together for sequencing using methylpy (https://github.com/yupenghe/methylpy)
Assembly: Custom genome containing amplicon sequences
Supplementary files format and content: allC tsv files containing methylation results produced from methylpy

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:
Genomic DNA was extracted using DNA Extraction Buffer followed by isopropanol precipitation.
DNA  was treated with RNAse A, recovered with phenol chloroform isolation then treated with sodium bisulfite using the EZ DNA methylation kit (Zymo Research). PCR-amplified amplicons were gel-purified and pooled in equimolar ratios. The Illumina Nextera DNA Flex kit (https://doi.org/10.1101/779215) was used to prepare the library. Single-end Illumina sequencing of 300 bp with an Illumina MiSeq.

value: Inflorescence

value: other


title: HeLa_FA_FRISCR_IgG_cell6

first: Yangming

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

source_name: HeLa cell line

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: SplenocyteTreg_WGEM-seq_25ng_05

description: Library name: Sample 30

value: Treg cells (CD4+CD25+Foxp3-YFP+)


title: HeLa_FA_FRISCR_Anti-G3BP1_cell14


title: T4 Cas9-SOC1 3'UTR bio rep 4

description:
Library name: BSAS_T4_Cas9-SOC1_3UTR_bio_rep_4
Bisulfite amplicon sequencing (BSAS)


title: T4 Cas9-SOC1 3'UTR bio rep 3

description:
Library name: BSAS_T4_Cas9-SOC1_3UTR_bio_rep_3
Bisulfite amplicon sequencing (BSAS)


title: 31


title: SplenocyteTreg_WGBS_25ng_04

description: Library name: Sample 26


title: HeLa_FA_FRISCR_Anti-G3BP1_cell13


title: T4 Cas9-SOC1 3'UTR bio rep 6

description:
Library name: BSAS_T4_Cas9-SOC1_3UTR_bio_rep_6
Bisulfite amplicon sequencing (BSAS)


title: T4 Cas9-SOC1 3'UTR bio rep 2

description:
Library name: BSAS_T4_Cas9-SOC1_3UTR_bio_rep_2
Bisulfite amplicon sequencing (BSAS)


title: RT112 shE6#2_3

city: Tsukuba

first: Takashi

last: Matsuzaka

state: Ibaraki

address: 1-1-1 Tennodai

department: Internal Medicine

institute: University of Tsukuba

description: Library name: PR1381_09A7373_H1

data_processing:
CLC Genomics Workbench
Assembly: NCBI
Supplementary files format and content: tab-delimited taxt file includes raw counts for each sample

growth_protocol: Total RNA was extracted from RT112 cell lines stably expressing shControl (shCtrl, n=3), shELOVL6#1 (shE6#1, n=3), or shELOVL6#2 (shE6#1, n=3) that were cultured in E-MEM supplemented with 5% FBS for 48 hours.

extract_protocol:
Total RNA was extracted using Sepasol-RNA I Super G (Nacalai Tesque, Kyoto, Japan) according to the manufacturer’s instructions. 2.0 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded mRNA Sasmple Prep Kit according to the manufacturer’s instructions.

value: bladder cancer

value: ELOVL6 knockdown #2


title: HeLa_FA_FRISCR_Anti-G3BP1_cell12


title: RT112 shE6#2_2

description: Library name: PR1381_08A7272_H1


title: SplenocyteTreg_WGBS_25ng_03

description: Library name: Sample 25


title: HeLa_FA_FRISCR_Anti-G3BP1_cell15


title: HeLa_FA_FRISCR_Anti-G3BP1_cell11


title: T4 Cas9-4xBS bio rep 6

description:
Library name: BSAS_T4_Cas9-4xBS_bio_rep_6
Bisulfite amplicon sequencing (BSAS)


title: SplenocyteTreg_WGBS_25ng_02

description: Library name: Sample 24


title: T4 Cas9-SOC1 3'UTR bio rep 1

description:
Library name: BSAS_T4_Cas9-SOC1_3UTR_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: HeLa_FA_FRISCR_Anti-G3BP1_cell10


title: RT112 shE6#2_1

description: Library name: PR1381_07A7171_H1


title: RT112 shE6#1_3

description: Library name: PR1381_06A7070_H1

value: ELOVL6 knockdown #1


title: SplenocyteTconv_RREM-seq_2ng_05

description: Library name: Sample 22

source_name: Splenic Treg cells from 18-20 week-old healthy mice

value: Tconv cells (CD4+Foxp3YFP-)


title: SplenocyteTconv_RREM-seq_2ng_04

description: Library name: Sample 21


title: HeLa_FA_FRISCR_Anti-G3BP1_cell8


title: RT112 shE6#1_1

description: Library name: PR1381_04A6868_H1


title: Whole Blood, A06_99

description: Gene expression data from human whole blood

data_processing: rma

source_name: Whole Blood

extract_protocol: RNA from whole blood was extracted using the PAXgene blood RNA isolation kit.

value: Whole Blood

tag: age

tag: surgery

value: CABG

value: Male


title: SplenocyteTconv_RREM-seq_25ng_04

description: Library name: Sample 18


title: SplenocyteTconv_RREM-seq_25ng_05

description: Library name: Sample 19


title: T4 Cas9-4xBS bio rep 2

description:
Library name: BSAS_T4_Cas9-4xBS_bio_rep_2
Bisulfite amplicon sequencing (BSAS)


title: T4 Cas9-4xBS bio rep 3

description:
Library name: BSAS_T4_Cas9-4xBS_bio_rep_3
Bisulfite amplicon sequencing (BSAS)


title: SplenocyteTreg_WGBS_25ng_01

description: Library name: Sample 23


title: HeLa_FA_FRISCR_Anti-G3BP1_cell7

extract_protocol:
mRNA was isolated with Oligo d(T) Magnetic Beads (NEB, S1419S) and directly subjected to Smart-seq2 protocol.
RNA-seq library was generated according to the Smart-seq2 protocol.


title: RT112 shCtrl_3

description: Library name: PR1381_03A6767_H1

value: control


title: RT112 shCtrl_2

description: Library name: PR1381_02A6666_H1


title: T4 Cas9-4xBS bio rep 5

description:
Library name: BSAS_T4_Cas9-4xBS_bio_rep_5
Bisulfite amplicon sequencing (BSAS)


title: T4 Cas9-4xBS bio rep 1

description:
Library name: BSAS_T4_Cas9-4xBS_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: HeLa_FA_FRISCR_Anti-G3BP1_cell6

value: HeLa cell line


title: SplenocyteTconv_RRBS_25ng_04

description: Library name: Sample 15


title: SplenocyteTconv_RREM-seq_2ng_03

description: Library name: Sample 20


title: T4 Cas9-1xBS bio rep 6

description:
Library name: BSAS_T4_Cas9-1xBS_bio_rep_6
Bisulfite amplicon sequencing (BSAS)


title: RT112 shCtrl_1

description: Library name: PR1381_01A6565_H1


title: HeLa_FA_FRISCR_Anti-G3BP1_cell9

value: WT


title: T4 Cas9-1xBS bio rep 5

description:
Library name: BSAS_T4_Cas9-1xBS_bio_rep_5
Bisulfite amplicon sequencing (BSAS)


title: SplenocyteTconv_RREM-seq_25ng_03

description: Library name: Sample 17


title: HeLa_FA_FRISCR_Anti-G3BP1_cell4

description: FRISCR_FA_editing.tsv.gz;FRISCR_FA_TPM.tsv.gz


title: HeLa_FA_FRISCR_Anti-G3BP1_cell3


title: MSKG5191_scRNAseq_PF

description:
Library name: MSKG5191_scRNAseq_PF
MSKG5191_scRNAseq_PF

data_processing:
WGS data were mapped to mm10 mouse genome reference. Tumor/pseudo-control matched variant calling was performed, with the normal sample from a different mouse used as pseudo-control. An ensemble strategy with optimized filtering (SNVs/Indels called by at least 2 callers) was employed to identify potential somatic coding mutations (SNVs/indels) using multiple callers, including Mutect2 (v4.1.2.0), SomaticSniper (v1.0.5.0), VarScan2 (v2.4.3), MuSE (v1.0rc), and Strelka2 (v2.9.10). To exclude mouse germline SNPs, variants observed in either mouse dbsnp142 from NCBI or mouse EVA SNP databases from the European Variation Archive (EVA) at the European Bioinformatics Institute (EBI) were excluded. Variant annotation was performed using Annovar17.
ATAC-seq data were mapped to hg38 human genome reference with BWA mem (0.7.17-r1188), then converted to BAM format and deduplicated with fq2bam (v3.0.0.6). Uniquely mapped properly paired reads were extracted with samtools (v1.2) and fragments were extracted with bedtools (v2.24.0).
Single-cell RNA-seq data were aligned and quantified using the Cell Ranger (v7.0.1) pipeline (http://www.10xgenomics.com) against the human genome GRCh38 (refdata-gex-GRCh38-2020-A).
Assembly: For WGS: mm10.  For ATAC-seq/scRNAseq: hg38
Supplementary files format and content: Tsv for WGS. BigWig for ATAC-seq. Tsv.gz and Mtx.gz for scRNAseq

growth_protocol: For conditional knock in mouse cells transplanted into CD45.1 recipients, FACS was used to isolate CD45.2+ spleen cells after staining with CD45.2-FITC antibody.  For conditional knock in mice with spontaneous leukemia, unfractionated spleen cells were used. Spleen from an independent mouse with the same parents was used as a control. [WGS] 0.5-1 million MSKG5191 (NUP98::NSD1) PDX cells were transplanted via tail vein injection into NSG mice.  Spleens were harvested and human leukemic cells were isolated using the human/mouse chimera kit (StemCell Technologies).  Two spleens per sample were combined for scRNAseq, and spleen from three mice were processed as independent replicates for ATAC-seq.

extract_protocol:
DNA for WGS was isolated using the Qiagen AllPrep kit.  For ATAC-seq, 50,000 human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 5 days and washed once in cold PBS before proceeding with cell lysis, nuclei extraction, tagmentation and library preparation as described in PMID 24097267.  Lysis and transposition were adjusted according to the Omni-ATAC protocol (PMID 28846090).  For scRNAseq, leukemic cells were human leukemic cells were isolated from the spleens of PDX-bearing mice treated for 4 weeks, washed three times in PBS + 0.04% BSA, and counted.  The volume of cells to load to have a desired recovery target of 8,000-10,000 cells was calculated and cells were loaded on Chromium Next GEM Chip K (10X Genomics).  Samples were processed using the 10X Genomics 5' kit (v2).
Mouse genomic libraries were generated using the SureSelectXT kit specific for the Illumina HiSeq instrument (G9611B, Agilent Technologies).  ATAC-seq libraries were prepared as described in PMID 24097267 with double-sided bead purification.  Single cell RNA-seq libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v2 (10X Genomics) according to manufacturer's protocols.

treatment_protocol: After the percentage of human leukemia cells in the peripheral blood reached ~30%, treatment was started.  Mice were treated for 5-days (ATAC-seq) or 4 weeks (scRNAseq) with vehicle, 3 mg/kg PF9363 (QD, IP), 75 mg/kg SNDX-5613 (BID, PO), or combination.

value: spleen

value: leukemia


title: RT112 shE6#1_2

description: Library name: PR1381_05A6969_H1


title: MSKG5191_scRNAseq_Combo

description:
Library name: MSKG5191_scRNAseq_Combo
MSKG5191_scRNAseq_Combo


title: SplenocyteTconv_RRBS_25ng_05

description: Library name: Sample 16


title: HeLa_FA_FRISCR_Anti-G3BP1_cell2

value: Anti-G3BP1 (Proteintech, 13057-2-AP)


title: SplenocyteTconv_RRBS_25ng_03

description: Library name: Sample 14


title: SplenocyteTconv_WGEM-seq_2ng_05

description: Library name: Sample 13


title: T4 Cas9-4xBS bio rep 4

description:
Library name: BSAS_T4_Cas9-4xBS_bio_rep_4
Bisulfite amplicon sequencing (BSAS)

value: Inflorescence


title: T4 Cas9-1xBS bio rep 4

description:
Library name: BSAS_T4_Cas9-1xBS_bio_rep_4
Bisulfite amplicon sequencing (BSAS)

value: other


title: SplenocyteTconv_WGEM-seq_2ng_04

description: Library name: Sample 12


title: HeLa_FA_FRISCR_Anti-G3BP1_cell1

value: guinea pig anti-rabbit (Antibodies Online, catalog no. ABIN101961)


title: HeLa_FA_FRISCR_Anti-G3BP1_cell5


title: MSKG5191_scRNAseq_vehicle

description:
Library name: MSKG5191_scRNAseq_vehicle
MSKG5191_scRNAseq_vehicle

value: vehicle


title: T4 Cas9-1xBS bio rep 2

description:
Library name: BSAS_T4_Cas9-1xBS_bio_rep_2
Bisulfite amplicon sequencing (BSAS)


title: MSKG5191_scRNAseq_SNDX

description:
Library name: MSKG5191_scRNAseq_SNDX
MSKG5191_scRNAseq_SNDX


title: Oligo-dT_DSP_HEK293T_Anti-G3BP1_rep2

data_processing:
Reads mapping to abundant RNA types were discarded using BWA-MEM (v0.7.17), retaining unmapped reads for further analysis. The processed reads were aligned to the human genome (hg38) via a two-round mapping strategy designed to capture more mismatches for RNA editing candidates, sequentially utilizing HISAT2 (v2.2.1) and BWA-MEM, with GENCODE (v40) as the transcriptome guide. Unique mapped reads with up to 0.04 mismatches per fragment relative to read length were selected using pysam (v0.22.1) (https://github.com/pysam-developers/pysam) for subsequent analysis. PCR duplicates were removed using Picard (v3.1.1) (https://github.com/broadinstitute/picard).
All usable reads spanning exon-exon junctions were segmented using the GATK (v4.5.0.0) SplitNCigarReads command. Base quality scores were recalibrated using two rounds of GATK BaseRecalibrator and ApplyBQSR commands. RNA variants were identified from BAM files of usable reads via the GATK HaplotypeCaller command. RNA single nucleotide variants were selected using the GATK SelectVariants command. Single nucleotide polymorphisms (SNPs) from dbSNP (v151), the 1000 Genomes Project, and the University of Washington Exome Sequencing Project were removed in SNVs. Raw counts were quantified using Subread featureCounts (v2.0.1) and normalized to transcripts per million (TPM) as gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM
Supplementary files format and content: tab-delimited text including RNA editing data

source_name: HEK293T cell line

extract_protocol:
For large samples, total RNA was extracted following the standard TRIzol protocol (Invitrogen) for bulk RNA library construction. For small samples, mRNA was isolated with Oligo d(T)25 Magnetic Beads (NEB, S1419S) and directly subjected to Smart-seq2 protocol, as detailed in Plate-based scMAPIT-seq.
RNA-seq library was generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604) or Smart-seq2 protocol.

value: HEK293T cell line

value: DSP

tag: inhouseid


title: SplenocyteTconv_WGEM-seq_2ng_03

description: Library name: Sample 11


title: MSKG5191_ATACseq_Combo_rep3

description:
Library name: MSKG5191_ATACseq_Combo_rep3
MSKG5191_ATACseq_Combo_rep3

tag: tissue


title: Oligo-dT_DSP_HEK293T_Anti-G3BP1_rep1


title: T4 Cas9-1xBS bio rep 3

description:
Library name: BSAS_T4_Cas9-1xBS_bio_rep_3
Bisulfite amplicon sequencing (BSAS)


title: T4 Cas9-1xBS bio rep 1

description:
Library name: BSAS_T4_Cas9-1xBS_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: MSKG5191_ATACseq_Combo_rep2

description:
Library name: MSKG5191_ATACseq_Combo_rep2
MSKG5191_ATACseq_Combo_rep2


title: T4 Cas9-0xBS bio rep 6

description:
Library name: BSAS_T4_Cas9-0xBS_bio_rep_6
Bisulfite amplicon sequencing (BSAS)


title: Oligo-dT_DSP_HEK293T_IgG_rep2

value: rabbit IgG (CST, 2729S)


title: SplenocyteTconv_WGEM-seq_2ng_02

description: Library name: Sample 10

value: Tconv cells (CD4+Foxp3YFP-)


title: SplenocyteTconv_WGEM-seq_2ng_01

description: Library name: Sample 9


title: T4 Cas9-0xBS bio rep 5

description:
Library name: BSAS_T4_Cas9-0xBS_bio_rep_5
Bisulfite amplicon sequencing (BSAS)


title: Oligo-dT_DSP_HEK293T_IgG_rep1


title: MSKG5191_ATACseq_Combo_rep1

description:
Library name: MSKG5191_ATACseq_Combo_rep1
MSKG5191_ATACseq_Combo_rep1


title: MSKG5191_ATACseq_PF_rep3

description:
Library name: MSKG5191_ATACseq_PF_rep3
MSKG5191_ATACseq_PF_rep3


title: T4 Cas9-0xBS bio rep 4

description:
Library name: BSAS_T4_Cas9-0xBS_bio_rep_4
Bisulfite amplicon sequencing (BSAS)


title: DSP_HeLa_Anti-G3BP1_rep2


title: SplenocyteTconv_WGEM-seq_25ng_05

description: Library name: Sample 8


title: SplenocyteTconv_WGEM-seq_25ng_03

description: Library name: Sample 6


title: MSKG5191_ATACseq_PF_rep2

description:
Library name: MSKG5191_ATACseq_PF_rep2
MSKG5191_ATACseq_PF_rep2


title: SplenocyteTconv_WGEM-seq_25ng_04

description: Library name: Sample 7


title: MSKG5191_ATACseq_PF_rep1

description:
Library name: MSKG5191_ATACseq_PF_rep1
MSKG5191_ATACseq_PF_rep1


title: DSP_HeLa_Anti-YTHDF2_rep2

value: Anti-YTHDF2 (Proteintech, 24744-1-AP)


title: MSKG5191_ATACseq_SNDX_rep3

description:
Library name: MSKG5191_ATACseq_SNDX_rep3
MSKG5191_ATACseq_SNDX_rep3


title: SplenocyteTconv_WGBS_25ng_04

description: Library name: Sample 4


title: T4 Cas9-0xBS bio rep 3

description:
Library name: BSAS_T4_Cas9-0xBS_bio_rep_3
Bisulfite amplicon sequencing (BSAS)


title: T4 Cas9-0xBS bio rep 1

description:
Library name: BSAS_T4_Cas9-0xBS_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: SplenocyteTconv_WGBS_25ng_05

description: Library name: Sample 5


title: MSKG5191_ATACseq_SNDX_rep2

description:
Library name: MSKG5191_ATACseq_SNDX_rep2
MSKG5191_ATACseq_SNDX_rep2


title: DSP_HeLa_Anti-G3BP1_rep1


title: MSKG5191_ATACseq_SNDX_rep1

description:
Library name: MSKG5191_ATACseq_SNDX_rep1
MSKG5191_ATACseq_SNDX_rep1


title: DSP_HeLa_IgG_rep2


title: SplenocyteTconv_WGBS_25ng_02

description: Library name: Sample 2


title: T1 Cas9-SOC1 3'UTR bio rep 1

description:
Library name: BSAS_T1_Cas9-SOC1_3_UTR_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: SplenocyteTconv_WGBS_25ng_03

description: Library name: Sample 3


title: DSP_HeLa_IgG_rep1


title: Fixation_MEOH_HEK293T_Anti-G3BP1_rep2

description: HEK293T_fixative_editing.tsv.gz;HEK293T_fixative_TPM.tsv.gz

value: methanol


title: T1 Cas9-4xBS bio rep 2

description:
Library name: BSAS_T1_Cas9-4xBS_bio_rep_2
Bisulfite amplicon sequencing (BSAS)


title: Fixation_MEOH_HEK293T_Anti-G3BP1_rep1


title: SplenocyteTconv_RREM-seq_2ng_02

description: Splenic Tconv cells from 18-20 week-old healthy mice

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: RREM-seq


title: MSKG5191_ATACseq_vehicle_rep1

description:
Library name: MSKG5191_ATACseq_vehicle_rep1
MSKG5191_ATACseq_vehicle_rep1


title: T1 Cas9-SOC1 3'UTR bio rep 2

description:
Library name: BSAS_T1_Cas9-SOC1_3_UTR_bio_rep_2
Bisulfite amplicon sequencing (BSAS)


title: SplenocyteTconv_WGBS_25ng_01

description: Library name: Sample 1


title: MSKG5191_ATACseq_vehicle_rep2

description:
Library name: MSKG5191_ATACseq_vehicle_rep2
MSKG5191_ATACseq_vehicle_rep2


title: T1 Cas9-4xBS bio rep 1

description:
Library name: BSAS_T1_Cas9-4xBS_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: Fixation_MEOH_HEK293T_IgG_rep1


title: T4 Cas9-0xBS bio rep 2

description:
Library name: BSAS_T4_Cas9-0xBS_bio_rep_2
Bisulfite amplicon sequencing (BSAS)


title: DSP_HeLa_Anti-YTHDF2_rep1


title: Fixation_MEOH_HEK293T_IgG_rep2


title: SplenocyteTconv_RREM-seq_2ng_01


title: T1 Cas9-1xBS bio rep 1

description:
Library name: BSAS_T1_Cas9-1xBS_bio_rep_1
Bisulfite amplicon sequencing (BSAS)


title: T84 IFNLR KO cells at low density, replicate 3

city: Gainesville

first: Yagmur

last: Keser

state: Florida

address: 1200 Newell Dr.

department: Molecular Genetics and Microbiology (MGM)

institute: University of Florida

description: sample 18

data_processing:
Novogene Illumina PE150 sequencing was used.
Assembly: GRCh38 - hg38
Supplementary files format and content: tap deliminated 'gene_count.txt' file includes raw counts for each sample

growth_protocol: Wild type (WT) T84 as well as T84 reporter and knock-out (KO) cells were cultured in a 50:50 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM) and F12 supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and 100 μg/mL streptomycin. All cells were cultured on collagen coated surfaces, and were kept in a constant humid atmosphere at 37°C, 5% CO2 and 21% oxygen.

extract_protocol:
RNA was isolated using the RNAeasy RNA extraction kit. ≥ 200 ng of total RNA was used to generate sequencing library.
RNA libraries were prepared for RNA-sequencing by Novogene.

treatment_protocol: For high cell density, 2.2x10^5 cells/cm2 were seeded. One-day post-seeding, medium was exchanged with fresh medium, and two days post-seeding, cells were harvested for sequencing. For low cell density, 2.7x10^4 cells/cm2 were seeded. One-day post-seeding cell were harvested for sequencing.

value: intestinal epithelial cells

value: IFNLR KO

value: low density


title: SplenocyteTconv_RREM-seq_25ng_02

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. For WGEM-seq libraries, gDNA was first fragmented to a size of 240–290-bp using the Covaris E220 sonicator and then enzymatically converted with TET2 and APOBEC (New England Biolabs) per the manufacturer’s instructions. For WGBS libraries, gDNA was bisulfite converted with the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Additional restriction enzyme digestion step was included for RRBS and RREM-seq libraries, in which gDNA was fragmented with MspI (New England Biolabs) and then size-selected for 100- to 250-bp fragments using solid-phase reversible immobilization beads (MagBio Genomics). CG-enriched gDNA was then bisulfite converted for RRBS libraries and enzymatically converted for RREMseq libraries. Random priming, adaptor ligation, PCR product clean-up, and final library amplification were performed using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs) for WGEM-seq libraries and the Pico Methyl-Seq Library Prep Kit (Zymo Research) was used for WGBS, RRBS, and RREM-seq libraries. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and four pooled libraries per run were sequenced on an Illumina NextSeq 2000 instrument using the 200 cycles NextSeq 2000 P3 reagent kit (whole-genome libraries) or the 100 cycles NextSeq 2000 P2 reagent kit (reduced representation libraries).
EM-seq (whole-genome and reduced representation) and Bisulfite-seq (whole-genome and reduced representation)


title: MSKG5191_ATACseq_vehicle_rep3

description:
Library name: MSKG5191_ATACseq_vehicle_rep3
MSKG5191_ATACseq_vehicle_rep3


title: T84 IFNLR KO cells at low density, replicate 2

description: sample 17


title: SplenocyteTconv_RREM-seq_25ng_01


title: T1 Cas9-0xBS bio rep 2

description:
Library name: BSAS_T1_Cas9-0xBS_bio_rep_2
Bisulfite amplicon sequencing (BSAS)