title: Patient 1686, intermediate-risk, no tumor progression

description: Library name: N1686


title: Patient 1207, high-risk, tumor progression

status: Public on Sep 15 2025

type: SRA

city: Saint Louis

first: Christopher

middle: A.

last: Maher

state: Missouri

address: Division of Oncology

country: USA

institute: Washington University School of Medicine in Saint Louis: Washington University in St Louis School of Medicine

description: Library name: N1207

library_source: genomic

data_processing:
Raw reads were trimmed using TrimmGalore (v0.6.10). To remove methylation bias and remove low-quality sequences, an additional 10 bp of the 5’ ends of each read was removed. Duplicated reads were removed to reduce PCR bias. Then, they were aligned to the human genome reference (hg38) using Bismark (v0.24.0), with methylation calls derived by comparing cytosines at converted (T) versus protected (C) positions.
Assembly: hg38
Supplementary files format and content: csv contains differentially methylated region data
Library strategy: EM-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: Prostate Cancer

extract_protocol:
Genomic DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) and quantified by Qubit 4.0 fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). Sample integrity and absence of degradation were verified via spike-in controls of Lambda DNA (Thermo Fisher Scientific, Waltham, MA, USA) and pUC19 plasmid (New England Biolabs, Ipswich, MA, USA).
EM-seq libraries were prepared by an enzymatic conversion approach2. Briefly, 50–100 ng of input DNA was treated with TET2 enzyme (New England Biolabs, Ipswich, MA, USA) to oxidize 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) to 5-carboxylcytosine. Oxidized residues were protected via glucosylation with β-glucosyltransferase (β-GT; New England Biolabs, Ipswich, MA, USA). Unmodified cytosines were deaminated to uracil using APOBEC3A (Zymo Research, Irvine, CA, USA), while glucosylated 5-carboxylcytosines remained intact. Converted DNA was purified using AMPure XP beads (Beckman Coulter, Brea, CA, USA), enzymatically fragmented to ~300 bp (Covaris S2 sonicator; Covaris, Woburn, MA, USA), and processed for library preparation using the Illumina DNA Prep Kit (Illumina, San Diego, CA, USA). Libraries underwent end repair, adapter ligation by IDT for Illumina UD Indexes (Integrated DNA Technologies, Coralville, IA, USA), and PCR amplification by KAPA HiFi HotStart ReadyMix (Roche, Basel, Switzerland). Library quality and size distribution were assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), followed by paired-end sequencing (2 × 150 bp) on an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

tag: tissue

value: Prostate Cancer

tag: clinical t_stage

tag: surgical t_stage

tag: gleason score1

tag: gleason score2

tag: gleason score

tag: recurrence

tag: psa recurrence

tag: death

tag: lymp nodes_mets

tag: tumor progression

tag: risk

value: high-risk


title: Patient 1167, low-risk, no tumor progression

description: Library name: N1167

value: low-risk


title: Patient 1158, intermediate-risk, tumor progression

description: Library name: N1158

value: intermediate-risk


title: Patient 1132, high-risk, tumor progression

description: Library name: N1132


title: Patient 1197, high-risk, tumor progression

description: Library name: N1197


title: Patient 1107, intermediate-risk, no tumor progression

description: Library name: N1107


title: Patient 1085, intermediate-risk, tumor progression

description: Library name: N1085


title: Patient 1049, intermediate-risk, tumor progression

description: Library name: N1049


title: Patient 1088, low-risk, no tumor progression

description: Library name: N1088


title: Patient 1034, intermediate-risk, tumor progression

description: Library name: N1034


title: Patient 1011, high-risk, tumor progression

description: Library name: N1011


title: Patient 1032, low-risk, no tumor progression

description: Library name: N1032


title: Patient 0987, intermediate-risk, tumor progression

description: Library name: N0987


title: Patient 0954, high-risk, tumor progression

description: Library name: N0954


title: Patient 0950, intermediate-risk, no tumor progression

description: Library name: N0950


title: Patient 0974, high-risk, no tumor progression

description: Library name: N0974


title: Patient 0924, intermediate-risk, tumor progression

description: Library name: N0924


title: Patient 0933, intermediate-risk, tumor progression

description: Library name: N0933


title: Patient 0913, intermediate-risk, tumor progression

description: Library name: N0913


title: Patient 0876, intermediate-risk, tumor progression

description: Library name: N0876


title: Patient 0843, intermediate-risk, tumor progression

description: Library name: N0843


title: Patient 0899, intermediate-risk, tumor progression

description: Library name: N0899


title: Patient 0810, intermediate-risk, tumor progression

description: Library name: N0810


title: Patient 0795, intermediate-risk, no tumor progression

description: Library name: N0795


title: Patient 0788, high-risk, tumor progression

description: Library name: N0788


title: Patient 0824, intermediate-risk, tumor progression

description: Library name: N0824


title: Patient 0771, high-risk, tumor progression

description: Library name: N0771


title: Patient 0715, intermediate-risk, no tumor progression

description: Library name: N0715


title: Patient 0704, intermediate-risk, no tumor progression

description: Library name: N0704


title: Patient 0723, intermediate-risk, no tumor progression

description: Library name: N0723


title: Patient 0676, high-risk, tumor progression

description: Library name: N0676


title: Patient 0671, intermediate-risk, tumor progression

description: Library name: N0671


title: Patient 0639, intermediate-risk, tumor progression

description: Library name: N0639


title: Patient 0641, high-risk, tumor progression

description: Library name: N0641


title: Patient 0630, intermediate-risk, tumor progression

description: Library name: N0630


title: Patient 0688, intermediate-risk, tumor progression

description: Library name: N0688


title: Patient 0609, intermediate-risk, tumor progression

description: Library name: N0609


title: Patient 0651, intermediate-risk, tumor progression

description: Library name: N0651


title: Patient 0604, intermediate-risk, tumor progression

description: Library name: N0604


title: Patient 0593, intermediate-risk, tumor progression

description: Library name: N0593


title: Patient 0964, intermediate-risk, tumor progression

description: Library name: N0964


title: Patient 0535, intermediate-risk, tumor progression

description: Library name: N0535


title: Patient 0468, low-risk, no tumor progression

description: Library name: N0468


title: Patient 0525, low-risk, no tumor progression

description: Library name: N0525


title: Patient 0467, intermediate-risk, tumor progression

description: Library name: N0467


title: Patient 0506, intermediate-risk, tumor progression

description: Library name: N0506


title: Patient 0457, intermediate-risk, tumor progression

description: Library name: N0457


title: Patient 0791, intermediate-risk, no tumor progression

description: Library name: N0791


title: Patient 0454, intermediate-risk, tumor progression

description: Library name: N0454


title: Patient 0446, low-risk, no tumor progression

description: Library name: N0446


title: Patient 0436, intermediate-risk, tumor progression

description: Library name: N0436


title: Patient 0429, low-risk, no tumor progression

description: Library name: N0429


title: Patient 0433, intermediate-risk, no tumor progression

description: Library name: N0433


title: Patient 0393, intermediate-risk, no tumor progression

description: Library name: N0393


title: Patient 0381, high-risk, no tumor progression

description: Library name: N0381


title: Patient 0361, intermediate-risk, no tumor progression

description: Library name: N0361


title: Patient 0366, high-risk, tumor progression

description: Library name: N0366


title: Patient 0357, high-risk, tumor progression

description: Library name: N0357


title: Patient 0313, low-risk, no tumor progression

description: Library name: N0313


title: Patient 0326, low-risk, no tumor progression

description: Library name: N0326


title: Patient 0306, intermediate-risk, no tumor progression

description: Library name: N0306


title: Patient 0321, intermediate-risk, tumor progression

description: Library name: N0321


title: Patient 0305, high-risk, tumor progression

description: Library name: N0305


title: Patient 0354, low-risk, no tumor progression

description: Library name: N0354


title: Patient 0323, high-risk, tumor progression

description: Library name: N0323


title: Patient 0555, intermediate-risk, no tumor progression

description: Library name: N0555


title: Patient 0171, intermediate-risk, no tumor progression

description: Library name: N0171


title: Patient 0257, low-risk, no tumor progression

description: Library name: N0257


title: Patient 0225, low-risk, no tumor progression

description: Library name: N0225


title: Patient 0486, intermediate-risk, tumor progression

description: Library name: N0486


title: Patient 0120, intermediate-risk, tumor progression

description: Library name: N0120


title: Patient 0164, intermediate-risk, no tumor progression

description: Library name: N0164


title: Patient 0099, low-risk, no tumor progression

description: Library name: N0099


title: Patient 0133, low-risk, no tumor progression

description: Library name: N0133


title: Patient 0096, intermediate-risk, tumor progression

description: Library name: N0096


title: Patient 0095, low-risk, no tumor progression

description: Library name: N0095


title: Patient 0079, low-risk, no tumor progression

description: Library name: N0079


title: Patient 0107, intermediate-risk, no tumor progression

description: Library name: N0107


title: Patient 0036, intermediate-risk, tumor progression

description: Library name: N0036


title: Patient 0062, intermediate-risk, no tumor progression

description: Library name: N0062


title: Patient 0009, low-risk, no tumor progression

description: Library name: N0009


title: Patient 0013, intermediate-risk, tumor progression

description: Library name: N0013


title: Patient 0031, low-risk, no tumor progression

description: Library name: N0031


title: Patient 0010, intermediate-risk, tumor progression

description: Library name: N0010


title: SUDHL6-NTCTRL, bio rep 6

city: St. Louis

first: George

middle: P.

last: Souroullas

state: MO

address: 660 S. Euclid Av

department: Medicine

institute: Washington University School of Medicine

description: Library name: Sample 21

library_source: transcriptomic

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
RNA-seq reads were then aligned and quantitated to the appropriate mouse or human genome with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights  function and were fitted using a Limma generalized linear model with additional unknown latent effects as determined by surrogate variable analysis (SVA).  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals
Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Assembly: Ensembl release 101 for human samples and mouse Ensembl GRCm39.113 for mouse samples
Supplementary files format and content: tab-delimited text file contains CPM and RPKM values for each sample

molecule: total RNA

source_name: B cell

growth_protocol: SUDHL6 cells were cultured in RPMI 1640 supplemented with 20% FBS and 1% Pen/Strep.  Mouse primary multipotent progenitors (MPPs) were harvested from bone marrow, sorted using FACS, and processed for RNA isolation right after.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Micro kit according to the manufacturer's instructions.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: B cell

tag: cell line

tag: cell type

value: DLBCL

tag: genotype

value: NTCTRL


title: Patient 0271, intermediate-risk, no tumor progression

description: Library name: N0271


title: C429, recurrence surgery sample

city: Helsinki

first: Anna

last: Vähärautio

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: C429_rOva
10x Genomics, v2 chemistry

library_source: transcriptomic single cell

data_processing:
The Cell Ranger v.6.0.1 pipeline (10x Genomics) was used for demultiplexing, alignment, barcode processing, and unique molecular identifier (UMI) quantification.
Assembly: GRCh38.d1.vd1

source_name: Ovary

extract_protocol:
Tumor specimens were incubated overnight in a mixture of collagenase and hyaluronidase (Department of Pathology, University of Turku) to obtain single-cell suspensions.
Library construction was performed according to the manufacturer's (10x Genomics) protocols for indicated assay chemistries (v2, v3, and v3.1).

value: Ovary

tag: subject status

value: HGSC patient

tag: tissue type

value: recurrent tumor tissue


title: C218, recurrence surgery sample 2 (right ovary)

description:
Library name: C218_rOvaR
10x Genomics, v2 chemistry

tag: tissue


title: Patient 0039, low-risk, no tumor progression

description: Library name: N0039

tag: clinical t_stage


title: SUDHL6-NTCTRL, bio rep 4

description: Library name: Sample 19


title: SUDHL6-NTCTRL, bio rep 5

description: Library name: Sample 20


title: C218, recurrence surgery sample 1 (left ovary)

description:
Library name: C218_rOvaL
10x Genomics, v2 chemistry


title: C865, recurrence surgery sample

description:
Library name: C865_rAdnR
10x Genomics, v2 chemistry

source_name: Adnex (Right)

value: Adnex (Right)


title: SUDHL6-NTCTRL, bio rep 2

description: Library name: Sample 17


title: SUDHL6-NTCTRL, bio rep 1

description: Library name: Sample 16


title: Patient 0154, intermediate-risk, tumor progression

description: Library name: N0154

tag: surgical t_stage


title: SUDHL6-NTCTRL, bio rep 3

description: Library name: Sample 18


title: SUDHL6-ARID1A-ARID1B-double KO, bio rep 2

description: Library name: Sample 14

value: ARID1A-ARID1B DKO


title: SUDHL6-ARID1A-ARID1B-double KO, bio rep 3

description: Library name: Sample 15


title: SUDHL6-ARID1A-ARID1B-double KO, bio rep 1

description: Library name: Sample 13


title: SUDHL6-ARID1B-KO, bio rep 5

description: Library name: Sample 11


title: SUDHL6-ARID1B-KO, bio rep 4

description: Library name: Sample 10


title: Patient 0063, intermediate-risk, tumor progression

description: Library name: N0063

tag: gleason score1


title: SUDHL6-ARID1B-KO, bio rep 2

description: Library name: Sample 8


title: SUDHL6-ARID1B-KO, bio rep 3

description: Library name: Sample 9


title: Patient 0001, intermediate-risk, tumor progression

description: Library name: N0001

tag: gleason score2


title: SUDHL6-ARID1B-KO, bio rep 1

description: Library name: Sample 7


title: SUDHL6-ARID1A-KO, bio rep 1

description: Library name: Sample 1


title: SUDHL6-ARID1A-KO, bio rep 2

description: Library name: Sample 2


title: SUDHL6-ARID1A-KO, bio rep 6

description: Library name: Sample 6


title: SUDHL6-ARID1A-KO, bio rep 3

description: Library name: Sample 3


title: SUDHL6-ARID1A-KO, bio rep 4

description: Library name: Sample 4


title: SUDHL6-ARID1A-KO, bio rep 5

description: Library name: Sample 5


title: KYSE30-shNC-MYC

city: Beijing

first: Ji

last: Cong

address: No.17, Panjiayuan Nanli, South Huawei Road

country: China

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Sample 6

data_processing:
Raw reads were quality checked with FastQC v0.11.9 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg38) genome with Bowtie2 v2.5.0 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.6.
Peaks were called using SEACR 1.3 with the default setting. Visualization of detected peaks was performed using deeptools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: KYSE30 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
For CUT&Tag experiment, 100,000 cells were collected for CUT&Tag followed manuals (cat. #N259-YH01, Novoprotein Inc.) to get SMARCA5, H3K18la or MYC-enriched DNA.
DNA libraries were prepared through PCR using a commercial ATAC kit (cat. #N259-YH01, Novoprotein Inc.) according to the manufacture’s protocol. The sequencing libraries were qualified with Qubit 2.0 and Agilent 2100, and sequenced on an Illumina NovaSeq 6000 platform for each library.

value: esophageal squamous cell carcinoma

value: SMARCA5 wildtype

tag: antibody

value: MYC


title: KYSE30-shNC-SMARCA5

description: Library name: Sample 5


title: KYSE30-H3K18la

description: Library name: Sample 3

value: WT


title: KYSE30-sh1-SMARCA5

description: Library name: Sample 7

value: SMARCA5 knockdown


title: KYSE30-MYC

description: Library name: Sample 4


title: MCF10A cells, Control (DMSO)

city: Taichung

first: Wei-Chien

last: Huang

address: 9F, No.6, Hsueh-Shih Road

department: Graduate Institute of Cancer Biology

country: Taiwan

institute: China Medical University

description: Library name: Sample 1

data_processing:
Qubit@ 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

growth_protocol: MCF-10A breast epithelial cells were maitained in DME/F12 containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin (P/S) and incubated at 37°C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol:
Total RNA extracted from either parental or DEHP-treated MCF-10A cell lines was processed using TRIzol reagent.
Library generation was performed using the KAPA mRNA HyperPrep Kit, following the manufacturer’s instructions, with the inclusion of index codes for sample attribution.

treatment_protocol: Breast epithelial cells MCF-10A were treated with DEHP or control vehicle for 24 hrs.

value: breast epithelial cells

tag: treatment

value: DMSO

tag: time

value: 24 hrs


title: KYSE30-IgG

description: Library name: Sample 1

value: IgG


title: KYSE30-sh1-MYC

description: Library name: Sample 8


title: KYSE30-sh2

description: Library name: Sample 3

data_processing:
Raw reads were quality checked with FastQC v0.11.9 and trimmed to remove sequencing adaptors and low-quality reads using Trim Galore v0.6.7 with default parameters.
Trimmed sequence reads were mapped to the human (hg38) genome with Bowtie2 v2.5.0 using standard settings for paired reads. The .sam and .bam files were manipulate with samtools v1.6.
Peaks were called using macs2 2.2.7.1 with the default setting. Visualization of detected peaks was performed using deeptools 3.5.1.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
For ATAC-seq experiment, 50,000 KYSE30 cells were collected for ATAC-seq followed commercial manual ATAC kit (cat. #N248, Novoprotein Inc.).
DNA libraries were prepared through PCR using a commercial ATAC kit (cat. #N248, Novoprotein Inc.) according to the manufacture’s protocol. The sequencing libraries were qualified with Qubit 2.0 and Agilent 2100, and sequenced on an Illumina NovaSeq 6000 platform for each library.


title: MCF10A cells, DEHP (1 μM, 24h)

description: Library name: Sample 2

value: DEHP


title: KYSE30-sh1

description: Library name: Sample 2


title: KYSE30-SMARCA5

description: Library name: Sample 2


title: SUDHL6-ARID1B-KO, bio rep 6

description: Library name: Sample 12

value: B cell

value: DLBCL


title: pADamID-RPE_WT_MERB200_Dam_r18

city: Milano

first: Stefano

middle: Giustino

last: Manzo

state: MI

address: Via Celoria 26, Dipartimento Bioscienze, Torre A, Piano 4

department: Biosciences

country: Italy

institute: University of Milan

description:
Library name: pA-DamID_Sample_225
Merbarone_3_hours, RPE1, Dam, B

data_processing:
The full protocol is described in the corresponding manuscript. The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the human genome (hg38) using bwa mem 0.7.17. Reads overlapping GATC fragments were counted in 20 kb bins and normalized to 1 million reads, after which a log2-ratio was calculated of LaminB1 over the Dam control using custom R scripts.
Assembly: hg38
Supplementary files format and content: BigWig files of log2-normalized LaminB2 pA-DamID scores for 20 kb genomic bins.
Library strategy: DamID-Seq

source_name: retina

growth_protocol: Two different hTERT immortalized RPE1 cell lines were used in this study. An RPE1 cell line that expresses the SunTag system Two different hTERT immortalized RPE1 cell lines were used in this study. An RPE1 cell line that expresses the SunTag system system {Brueckner, 2020, 32080885; Tanenbaum, 2014, 25307933} was used to perform TOP1, TOP2A and TOP2B depletions and the mapping of heterochromatin components. This cell line was mantained in DMEM (Gibco), FBS 10% and penicillin- streptomycin 1%. A second RPE1 cell line expressing an inducible Cas9 {van den Berg, 2018, 30184135} was used for the generation of LBR knockout and all the other experiments. This cell line was mantained in DMEM:F12 (Gibco), FBS 10% and penicillin-streptomycin 1%. HCT116 were mantained in McCoy medium (Gibco) FBS10% and penicillin-streptomycin 1%. K562 cell lines were mantained in IMDM medium (Gibco), FBS10% and penicillin-streptomycin 1%. HCT116 and K562 TOP2B knockout cell lines were a kind gift from Vassilis Roukos. GM12878 were mantained in RPMI1640 medium (Gibco) FBS15% and penicillin-streptomycin 1%. All cells were routinely checked for Mycoplasma contamination.was used to perform TOP1, TOP2A and TOP2B depletions and the mapping of heterochromatin components. This cell line was mantained in DMEM (Gibco), FBS 10% and Pen strep 1%. A second RPE1 cell line expressing and inducible Cas9 (ref) was used for the generation of LBR knockout and all the other experiments. This cell line was mantained in DMEM:F12 (Gibco), FBS 10% and pen/strep 1%. HCT116 were mantained in McCoy medium (Gibco) FBS10% and pen-strep 1%. K562 cell lines were mantained in IMDM medium (Gibco), FBS10% and pen-strep 1%. HCT116 and K562 TOP2B knockout cell lines were a kind gift from Vassilis Roukos. All cells were routinely checked for Mycoplasma contamination.

extract_protocol:
LMNB2 pA-DamID maps were generated as previously described (van Shaik, 2022, 36050765). Briefly, one million of RPE1, HCT116 or K562 were collected by centrifugation (500 g, 3 min) and washed sequentially in ice-cold PBS and digitonin wash buffer (D-Wash) (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.02% digitonin, cOmplete Protease Inhibitor Cocktail). Cells were rotated for 2 hours at 4 °C in 200 μL D-Wash with 1:200 of: LMNB2 (Abcam, ab8983,), LMNB1 (Abcam, ab16048), LBR (Abcam, ab32535), H3K9me3 (Diagenode, C15410193), H3K9me2 (Active Motif, 39239) , H3K27me3 (Diagenode, C15410195), TOP2B (Novus Biological, NB100-40842), followed by a wash step with D-Wash. Following this step, cells were incubated with a solution of D-Wash buffer and Rabbit-anti-mouse IgG (1:200, Abcam, ab6709), followed by a wash step. This incubation was repeated with a 1:200 pA-Dam solution (equivalent to nearly 60 Dam units from NEB), followed by two wash steps. Dam activity was induced by incubation for 30 min at 37 °C in 100 μL D-Wash supplemented with the methyl donor SAM (30 µM) while gently shaking (500 rpm). Genomic DNA was isolated and processed similarly to DamID, except that the DpnII digestion was omitted, and 65-bp reads were sequenced. For every condition, another 1 million cells were processed in only D-Wash and, during Dam activation, incubated with 4 units of Dam enzyme (NEB, M0222L). We use Dam control samples to account for DNA accessibility and amplification biases.
Genomic DNA was isolated (Bioline, bio-52067) and ~ 500 ng were digested with DpnI (10 U, NEB, R0176L) in CutSmart Buffer 1X (8h 37°C, 20 min 80°C) in a total volume of 10 µL. A-tailing was performed by addition of 5 µL of the A-tailing mix (0.5 µL of Cutsmart buffer 10X, 0.25 µL Klenow 50 U/µL (NEB, M0212M), 0.05 µL dATP 100 mM, 4.2 µL H2O) and incubation 30 min at 37°C followed by 20 min at 75°C. Adapters were ligated by adding 15 µL of the ligation mix (3 µL T4 Ligase Buffer 10X, 0.5 µL T4 ligase (5 U/µL , Roche, 10799009001), 0.25 µl of x-Gene Stubby Adapter 50 mM (IDT), 11.25 µl H2O) and incubating samples 16h at 16°C and 10 min at 65°C. Finally, the Methyl Indexed PCR was performed by mixing 4 µL of ligated DNA with x-Gen Dual combinatorial Indexes (IDT) (125 nM final concentration) and MyTaq RedMix (Bioline, BIO-25048) in a final volume of 40 µL. The following PCR program was used: 1 X (1 min 94°C), 14 X (30 sec 94°C, 30 sec 58°C, 30 sec 72°C), 1X (2 min 72°C). Libraries were sequenced on Illumina platform Hiseq2500 with single end 65 bp reads.

value: retina


title: pADamID-RPE_WT_MERB200_Lmnb2_r18

description:
Library name: pA-DamID_Sample_226
Merbarone_3_hours, RPE1, Lmnb1, B


title: pADamID-RPE_WT_ICRF20_Lmnb2_r18

description:
Library name: pA-DamID_Sample_224
ICRF193_3_hours, RPE1, Lmnb1, B


title: KYSE30-shNC

description: Library name: Sample 1


title: pADamID-RPE_WT_ICRF20_Dam_r18

description:
Library name: pA-DamID_Sample_223
ICRF193_3_hours, RPE1, Dam, B


title: pADamID-RPE_WT_CT20_Lmnb2_r18

description:
Library name: pA-DamID_Sample_222
control_DMSO, RPE1, Lmnb1, B


title: pADamID-RPE_WT_CT20_Dam_r18

description:
Library name: pA-DamID_Sample_221
control_DMSO, RPE1, Dam, B


title: pADamID-RPE_WT_MERB200_Dam_r17

description:
Library name: pA-DamID_Sample_219
Merbarone_3_hours, RPE1, Dam


title: pADamID-RPE_WT_MERB200_Lmnb2_r17

description:
Library name: pA-DamID_Sample_220
Merbarone_3_hours, RPE1, Lmnb1


title: pADamID-RPE_WT_ICRF20_Lmnb2_r17

description:
Library name: pA-DamID_Sample_218
ICRF193_3_hours, RPE1, Lmnb1


title: pADamID-RPE_WT_CT20_Lmnb2_r17

description:
Library name: pA-DamID_Sample_216
control_DMSO, RPE1, Lmnb1


title: pADamID-RPE_WT_CT20_Dam_r17

description:
Library name: pA-DamID_Sample_215
control_DMSO, RPE1, Dam


title: pADamID-GM12878_ICRF10m_Dam_r2

description:
Library name: pA-DamID_Sample_213
ICRF193_10_minutes,GM12878, Dam, B

source_name: bone marrow

value: bone marrow

value: lymphoblastoid cell line


title: pADamID-GM12878_DMSO_Dam_r2

description:
Library name: pA-DamID_Sample_211
control_DMSO,GM12878, Dam, B


title: pADamID-GM12878_DMSO_Lmnb1_r2

description:
Library name: pA-DamID_Sample_212
control_DMSO,GM12878_Lmnb1, B


title: pADamID-GM12878_ICRF10m_Lmnb1_r1

description:
Library name: pA-DamID_Sample_210
ICRF193_10_minutes, GM12878, Lmnb1


title: pADamID-GM12878_DMSO_Lmnb1_r1

description:
Library name: pA-DamID_Sample_208
control_DMSO,GM12878_Lmnb1


title: pADamID-GM12878_DMSO_Dam_r1

description:
Library name: pA-DamID_Sample_207
control_DMSO,GM12878, Dam


title: Patient 8 & 15 (SJ18 & SJ32) CD39+ CD8+ T cells GEX

city: Amsterdam

first: Austin

last: George

address: Plesmanlaan 121,

department: Division of Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: Sample_14_GEX
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting , TCR counting and aggregation were made using Cell Ranger v7.0.1
Assembly: hg38
Supplementary files format and content: comma separated values as gz files

source_name: Melanoma lymph node metastasis

extract_protocol:
Tumor digests were thawed, stained and sorted as described above. Five populations were sorted from live cells: tumor singlets (NGFR/CD146+); tumor:CD8+ T cell clusters (NGFR/CD146+, CD8+); APC:CD8+ T cell clusters (NGFR-, CD146-, CD11c+, CD8+), CD8+ T cell singlets (NGFR-, CD146-, CD11c-, CD8+) and APC singlets (NGFR-, CD146-, CD11c+, CD8-). For two patients, CD8+CD39+ T cells were sorted seperately from live cells. Singlets were pooled together during sort in a ratio of 1:1:1. If the number of clusters was low, they were kept as separate samples. If sufficient numbers of clusters were sorted (>40.000 clusters), they were hashtagged with TotalSeq-C0251 (T:Tumor clusters, 394661, Biolegend) or with TotalSeq-C0252 (T:APC clusters, 394663, Biolegend) and subsequently pooled 1:1. Both CD8+CD39+ samples were also hashtagged using the same antibodies and pooled 1:1. For hashtagging, sorted cells were washed once with 2% BSA in PBS and incubated with the hashtagging antibody for 30 min on ice. After hashtagging, cells were washed an additional two times with 0.04% BSA in PBS, after which they were pooled. Cells that did not need hashtagging were washed twice with 0.04% BSA in PBS, before proceeding to single-cell 5’ sequencing library preparation.
The Chromium Controller and Chromium X platform of 10X Genomics were used for single cell partitioning and barcoding. Each cell's transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5' Gene Expression (GEX), V(D)J and Feature Barcode (FB) Libraries were prepared according to the manufacturer's protocols (CG000330 and CG000331, 10X Genomics). All libraries were quantified and normalized on library QC data generated on the Bioanalyzer system according to manufacturer's protocols (G2938-90321 and G2938-90024, Agilent Technologies). Based on the expected target cell counts, a balanced library sub-pool of samples was compsed for SC5'GEX, V(D)J and FB libraries. Library sub-pools were quantified by qPCR, accodring to the KAPA Library Quantification Kit Illumina(R) Platforms protocol (KR0405, KAPA Biosystems). Based on qPCR results a final sequencing pool was composed. Paired end sequencing was performed on a NovaSeq 6000 Instrument (Illumina) using NovaSeq 6000 Reagent Kits v1.5 100 cycles (cat. no. 20028401, 20028319, 20028316 Illumina), using 28 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 90 cycles for Read 2.

value: Melanoma lymph node metastasis


title: SNU-886

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center

description:
Library name: Sample_Gudima-12
CVCL_5103

data_processing:
Illumina bcl2fastq conversion software used for basecalling.
reads were aligned using the STAR (2.5.2b) software.
raw read counts were obtained using htseq-count (HTSeq-0.6.1p12)
Assembly: GRCh38
Supplementary files format and content: excel file of raw read count values for each Sample

molecule: polyA RNA

source_name: Liver

extract_protocol:
Total RNA from parental (untransfected) SNU cell lines and Huh7 cells transfected with pT-HBV1.3 was isolated using TRI reagent according to the instructions of the manufacturer. Up to 1 µg of extracted total RNA was used further for generation of individual libraries.
RNA-seq (using poly(A) selection) was conducted on individual libraries generated using total RNA isolated from parental SNU cell lines or from transfected Huh7 cells on Illumina NovaSeq 6000 Sequencing System at the Genomics Core of the University of Kansas Medical Center (KUMC).  Library preparation used the TECAN Universal Plus stranded (fr-secondstrand) mRNA-Seq kit, and sequencing was conducted with 100-cycle paired-end reads. Each sample yielded between 33.8 and 42.8 million reads, with a median of 38.5 million reads. Quality assessment with the FastQC software (60) showed that all samples had an average Phred score above 30. Sequencing reads were trimmed with TrimGalore (61)  to remove low-quality and spurious sequences.

value: Liver

value: SNU

value: hepatocytes

value: SNU 886

tag: disease

value: Adult hepatocellular carcinoma

tag: Sex

value: Male


title: Huh-7 WT

description:
Library name: Sample_Gudima-13
CVCL_0336

value: Huh

value: Huh 7 WT


title: SNU-368

description:
Library name: Sample_Gudima-11
CVCL_3948

value: SNU 368


title: SNU-475

description:
Library name: Sample_Gudima-9
CVCL_0497

value: SNU 475


title: pADamID-GM12878_ICRF10m_Dam_r1

description:
Library name: pA-DamID_Sample_209
ICRF193_10_minutes,GM12878, Dam

value: WT


title: SNU-761

description:
Library name: Sample_Gudima-5
CVCL_5089

value: SNU 761


title: SNU-423

description:
Library name: Sample_Gudima-6
CVCL_0366

value: SNU 423


title: SNU-354

description:
Library name: Sample_Gudima-3
CVCL_3947

value: SNU 354


title: SNU-398

description:
Library name: Sample_Gudima-7
CVCL_0077

value: SNU 398


title: SNU-387

description:
Library name: Sample_Gudima-10
CVCL_0250

value: SNU 387

value: Female


title: Huh-7 transfected

description:
Library name: Sample_Gudima-1
CVCL_0336

value: Liver

value: Huh 7 transfected  with pT-HBV1.3


title: PB-TRIBE-STAMP_siNC-2

city: Shenzhen

first: Wei

last: Chen

state: Guangdong

address: 1088 Xueyuan Avenue, Shenzhen 518055,P.R. China

department: Department of Systems Biology

institute: Southern University of Science and Technology

description:
Library name: sample8
PB-TRIBE-STAMP-EDC4-knockdown_A2I_Editing_Score.csv
PB-TRIBE-STAMP-EDC4-knockdown_C2U_Editing_Score.csv

data_processing:
RNA-seq libraries were sequenced using a paired-end 150 bp strategy on the Illumina NovaSeq 6000 System (Haplox genomics center). Sequencing quality was assessed with FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences were removed using Cutadapt (v1.18) with parameters: -j 40 -m 20 -q 20. The reads were then filtered for those derived from repetitive elements using sequences from the UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgTables) and afterwards aligned to the hg38 reference genome with STAR (v2.7.9a). Uniquely mapped reads were quantified using featureCounts (v2.0.1) against Gencode annotations (v37, Ensembl 103) with the following parameters: -T 24 -s 2 -p -B -C -g gene_name -Q 30.
Assembly: hg38 reference genome
Supplementary files format and content: Editing score of genes; featureCounts of genes

extract_protocol:
For RNA-seq, total RNAs were extracted using TRlzol Reagent (Invitrogen, 15596026) according to the manufacturer’s protocol.
RNA-seq libraries were prepared using 500 ng of total RNA, 100 ng of cytosolic RNA, and 50 ng of sorted P-body RNA as input material, following the manufacturer’s protocol (YEASEN, 12309ES96).

value: Human embryonic kidney cells

tag: sample group

value: siNC

tag: batch


title: PB-TRIBE-STAMP_siNC-1

description:
Library name: sample7
PB-TRIBE-STAMP-EDC4-knockdown_A2I_Editing_Score.csv
PB-TRIBE-STAMP-EDC4-knockdown_C2U_Editing_Score.csv

tag: cell line


title: pADamID-RPE_WT_ICRF20_Dam_r17

description:
Library name: pA-DamID_Sample_217
ICRF193_3_hours, RPE1, Dam

value: retina

tag: cell type


title: SNU-449

description:
Library name: Sample_Gudima-4
CVCL_0454

value: SNU

value: hepatocytes

tag: genotype

value: SNU 449

value: Adult hepatocellular carcinoma

value: Male


title: PB-TRIBE-STAMP_siEDC4-2

description:
Library name: sample6
PB-TRIBE-STAMP-EDC4-knockdown_A2I_Editing_Score.csv
PB-TRIBE-STAMP-EDC4-knockdown_C2U_Editing_Score.csv


title: PB-TRIBE-STAMP_siEDC4-1

description:
Library name: sample5
PB-TRIBE-STAMP-EDC4-knockdown_A2I_Editing_Score.csv
PB-TRIBE-STAMP-EDC4-knockdown_C2U_Editing_Score.csv


title: PB-TRIBE-STAMP_Cytosol-2

description:
Library name: sample4
PB-TRIBE-STAMP-FAPS_A2I_Editing_Score.csv
PB-TRIBE-STAMP-FAPS_C2U_Editing_Score.csv
FAPS_counts.txt

molecule: cytoplasmic RNA

value: Cytosol


title: PB-TRIBE-STAMP_Sorted-Pbodies-2

description:
Library name: sample2
PB-TRIBE-STAMP-FAPS_A2I_Editing_Score.csv
PB-TRIBE-STAMP-FAPS_C2U_Editing_Score.csv
FAPS_counts.txt

value: Sorted-Pbodies


title: pADamID-GM12878_ICRF10m_Lmnb1_r2

description:
Library name: pA-DamID_Sample_214
ICRF193_10_minutes, GM12878, Lmnb1, B

value: bone marrow

value: lymphoblastoid cell line

value: WT


title: PB-TRIBE-STAMP_Sorted-Pbodies-1

description:
Library name: sample1
PB-TRIBE-STAMP-FAPS_A2I_Editing_Score.csv
PB-TRIBE-STAMP-FAPS_C2U_Editing_Score.csv
FAPS_counts.txt


title: TSCp_3

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

department: Research Program for Molecular Neurology

description: Library name: TSCp_3

data_processing:
The raw data was filtered with cutadapt (Martin, 2011) to remove adapter sequences, poly-A sequences, ambiguous (N) and low quality bases (Phred score < 25).
The miRNA reads were analyzed using miRDeep2 (Friedländer et al., 2012). The reads were mapped against the human genome (GRCh38) with the provided mapper.pl-script, and known miRNA’s were identified using miRBase (v22.1) (Kozomara et al., 2019).
DESeq2 (Love et al., 2014). was used for differential expression analysis of the detected miRNA’s.
Assembly: GRCh38
Supplementary files format and content: csv (DESeq2 results and read counts)

source_name: Human trophoblast cell line derived from primed H9 line

growth_protocol: Primed ESCp were cultured on wells coated with Matrigel (Corning) in E8 (Gibco) or E8 Flex (Gibco) medium. . Naive ESCn were cultured on mouse (ICR) inactivated embryonic fibroblasts (iMEF, Thermo A24903) in tt2iLGö Naïve Expansion medium (Stem Cell Technologies 05590). TSC were cultured in plates coated with 5 µg/ml Collagen-IV (Col-IV, Corning) in TSC medium (Basal DMEM/F12 + GlutaMax supplemented with 0.1 mM 2-mercaptoethanol (Gibco), 0.2% FBS (Gibco), 0.5% Penicillin-Streptomycin (Sigma-Aldrich P4333), 0.3% BSA (Sigma A7030-500G), 1% Insulin-Transferrin-Selenium-Ethanolamine (Gibco 51500056), 1.5 µg/ml L-ascorbic acid (Sigma A4544), 50 ng/ml EGF (Peprotech, AF-100-15-1MG), 2 µM CHIR99021 (Stemgent 04-0004-10), 0.5 µM A83-01 (Sigma SML0788-5MG), 1 µM SB431542 (Cayman Chemicals 13031) 0.8 mM Sodium Butyrate (Sigma B5887-1G) and 5 µM Y-27632 (Selleckchem S1049)). The medium was changed every other day. All cells were kept in an incubator at 37 °C and 5% CO2 and were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA including miRNA were extracted using miRNEasy Mini Kit (Qiagen 217004) from TSCn, TSCp, ESCn, ESCp, CT30 and bTS5 samples with three biological replicates each. Small RNA sequencing was performed at Novogen after the samples passed quality control.
Novogene small RNA library method. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing with SE50.

treatment_protocol: Primed ESCp were reset to naive ESCn using NaïveCult Induction kit (Stem Cell Technologies 05580) and further cultured on mouse (ICR) inactivated embryonic fibroblasts (iMEF, Thermo A24903) in tt2iLGö Naïve Expansion medium (Stem Cell Technologies 05590). For derivation of TSC from naive cells, 1 x 10^6 ESCn were passaged with Accutase for 3 min to achieve a single-cell suspension. Cells were seeded in TSC medium on 6 well plates coated with 5 µg/ml Col-IV. Medium was changed every other day, until the cells grew 80% confluent and were passaged 1:1 onto new Col-IV coated wells with 10 min TrypLE. The medium was changed every other day and once the cells were 80% confluent they were passaged on 1:3 ratio onto new Col-IV coated wells. For derivation of TSC from primed cells 4 x 10^5 ESCp or iPSC were passaged with TrypLE for 3 min to achieve a single-cell suspension. Cells were seeded on Matrigel coated wells with E8 medium supplemented with 10 µM Y-27632. After 24 hours, medium was changed to TSC-medium supplemented with 10 ng/ml BMP4 (Proteintech HZ-1045). Medium was changed daily, and on day 3 of differentiating cells were passaged 1:3 onto a new well with EDTA. After 5 days, BMP4 was cut from the cells, and the cells were continued to be cultured in TSC-medium. Medium was changed every other day and the cells were passaged with 10 min TrypLE on 1:3 ratio when the wells were growing 80% confluent.

value: TSC

tag: naive/primed

value: primed


title: Patient 8 & 15 (SJ18 & SJ32) CD39+ CD8+ T cells TCR

description:
Library name: Sample_14_TCR
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting , TCR counting and aggregation were made using Cell Ranger v7.0.1
Assembly: hg38
Supplementary files format and content: comma separated values as gz files
Library strategy: TCR-Seq

value: Melanoma lymph node metastasis


title: TSCp_2

description: Library name: TSCp_2


title: SNU-182

description:
Library name: Sample_Gudima-8
CVCL_0090

value: Liver

value: SNU 182


title: TSCn_3

description: Library name: TSCn_3

source_name: Human trophoblast cell line derived from naive H9 line

value: naive


title: TSCn_2

description: Library name: TSCn_2


title: H9p_1

description: Library name: H9p_1

source_name: Human primed H9 embryonic stem cell line

value: ESC


title: H9p_2

description: Library name: H9p_2


title: H9p_3

description: Library name: H9p_3


title: H9n_3

description: Library name: H9n_3

source_name: Human naive H9 embryonic stem cell line


title: H9n_2

description: Library name: H9n_2


title: SNU-739

description:
Library name: Sample_Gudima-2
CVCL_5088

value: SNU

value: SNU 739


title: CT30_3

description: Library name: CT30_3

source_name: First trimester derived human trophoblast cell line CT30


title: H9n_1

description: Library name: H9n_1


title: CT30_2

description: Library name: CT30_2


title: bTS5_3

description: Library name: bTS5_3

source_name: Blastocyst derived human trophoblast cell line bTS5


title: bTS5_2

description: Library name: bTS5_2


title: PB-TRIBE-STAMP_Cytosol-1

description:
Library name: sample3
PB-TRIBE-STAMP-FAPS_A2I_Editing_Score.csv
PB-TRIBE-STAMP-FAPS_C2U_Editing_Score.csv
FAPS_counts.txt

value: Human embryonic kidney cells


title: Sample_T1_032521_S8 (5 cell lines)

city: Baltimore

first: Tomoyo

last: Sawada

state: MD

address: 855 N Wolfe St

department: Molecular Neurogenetics

institute: Lieber Institute for Brain Development

description:
Library name: Sample_T1_032521_S8
Multiplexed sample containing: LIBD7c6 CA137 #109 (WT, day 48, barcode: TGTCTTTCCTGCCAG); LIBD7c6 CA137 #37 (WT, day 48, barcode: TAACGACCAGCCATA); LIBD7c6 CA137 #69 (Hetero, day 48, barcode: CTCCTCTGCAATTAC); LIBD7c6 CM130 #30 (Hetero, day 48, barcode: ATTGACCCGCGTTAG); LIBD7c6 CM130 #78 (WT, day 48, barcode: CAGTAGTCACGGTCA)

data_processing:
Fastq files were quality-checked using FastQC (ver. 0.11.3) and MultiQC101 (ver.1.12).
Raw sequencing data were preprocessed with Cell Ranger 7.2 (10x Genomics), in which reads were aligned to the hg38 human reference genome. The expression data was processed with Scanpy95 (ver. 1.9.3) in Python (ver. 3.11.3).
The columns 'hashtag ab', 'barcode seq' and 'index' contains the information for demultiplexing each sample
Assembly: hg38
Supplementary files format and content: .h5ad Anndata annotation file with single-cell expression data

source_name: Cerebral Organoid

growth_protocol: iPSCs were treated with 10 μM Y-27632 at 37°C overnight when they reached 50-60% confluency. Cells were then incubated with StemPro Accutase at 37°C for 7 min and dissociated into single cells. Dissociated iPSCs were plated on 96-well V-bottom plates at 9,000 cells/150 μL per well in StemFlex medium to make EB. The medium was supplemented with 30 μM Y-27632 for the first 24 h. Forty-eight hours later, the medium was gradually switched to DFN2 supplemented with 10 μM SB 431542 and 100 nM LDN-193189 (day 0). Organoids were fed every three days. On day 12, each EB was embedded in a droplet of Matrigel GFR and transferred to a 60-mm culture dish in DFN2 supplemented with 100 nM LDN-193189. The organoids were fed on day 14. On day 16, the medium was switched to differentiation medium consisting of 1:1 mixture of DMEM/F12 + GlutaMAX and Neurobasal supplemented with 0.5 × N-2 Supplement, 0.5 × NeuroCult SM1 without vitamin A, 0.5 × NEAA, 100 μM 2-ME, and 2.65 μg/ml Insulin (Thermo Fisher Scientific). Organoids were fed every three days and maintained with agitation in an incubator shaker (Eppendorf, New Brunswick S41i) at 80 r.p.m. On day 30, the medium was switched to neuronal medium as described above. From day 60, dibutyryl-cAMP and ascorbic acid were withdrawn from the medium and the organoids were fed every four days. CO was treated with 0.25 μM aphidicolin (Cayman Chemical) for 24 h before fixation

extract_protocol:
Cells from all five iPSC lines were pooled into one library per time point by cell hashing94 with TotalSeq-A Hashtag antibodies (BioLegend).
The libraries were generated with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10 × Genomics). We prepared three libraries (three technical replicates) from pooled cells for each time point. Libraries were sequenced on an Illumina NovaSeq 6000 (SP, 2×150 bp).

treatment_protocol: COs were differentiated from three WT and two SETD1A patient mutant lines from the LIBD7c6 prenatal iPSC line. Five organoids from each iPSC line on days 30 and 48 were dissociated into single cells with the Papain dissociation system (Worthington Biochemical).

tag: sample type

value: Cerebral Organoid day 48 multiplexed samples

value: Cerebral Organoid

tag: hashtag ab

tag: barcode seq

value: TGTCTTTCCTGCCAG; TAACGACCAGCCATA; CTCCTCTGCAATTAC; ATTGACCCGCGTTAG; CAGTAGTCACGGTCA

tag: technical replicate

value: WT; WT; Hetero; Hetero; WT

tag: day

tag: index


title: Sample_T3_032521_S5 (5 cell lines)

description:
Library name: Sample_T3_032521_S5
Multiplexed sample containing: LIBD7c6 CA137 #109 (WT, day 48, barcode: TGTCTTTCCTGCCAG); LIBD7c6 CA137 #37 (WT, day 48, barcode: TAACGACCAGCCATA); LIBD7c6 CA137 #69 (Hetero, day 48, barcode: CTCCTCTGCAATTAC); LIBD7c6 CM130 #30 (Hetero, day 48, barcode: ATTGACCCGCGTTAG); LIBD7c6 CM130 #78 (WT, day 48, barcode: CAGTAGTCACGGTCA)

tag: tissue


title: Sample_T3_030721_S10 (5 cell lines)

description:
Library name: Sample_T3_030721_S10
Multiplexed sample containing: LIBD7c6 CA137 #109 (WT, day 30, barcode: TGTCTTTCCTGCCAG); LIBD7c6 CA137 #37 (WT, day 30, barcode: TAACGACCAGCCATA); LIBD7c6 CA137 #69 (Hetero, day 30, barcode: CTCCTCTGCAATTAC); LIBD7c6 CM130 #30 (Hetero, day 30, barcode: ATTGACCCGCGTTAG); LIBD7c6 CM130 #78 (WT, day 30, barcode: CAGTAGTCACGGTCA)

value: Cerebral Organoid day 30 multiplexed samples


title: Sample_T2_030721_S9 (5 cell lines)

description:
Library name: Sample_T2_030721_S9
Multiplexed sample containing: LIBD7c6 CA137 #109 (WT, day 30, barcode: TGTCTTTCCTGCCAG); LIBD7c6 CA137 #37 (WT, day 30, barcode: TAACGACCAGCCATA); LIBD7c6 CA137 #69 (Hetero, day 30, barcode: CTCCTCTGCAATTAC); LIBD7c6 CM130 #30 (Hetero, day 30, barcode: ATTGACCCGCGTTAG); LIBD7c6 CM130 #78 (WT, day 30, barcode: CAGTAGTCACGGTCA)


title: LIBD7c6_CA137_52_Neuron_4wks

description:
Library name: 14_S14
Column name in raw_counts.tsv: LIBD7c6_CA137_52_Neuron_4wks

data_processing:
Fastq files were quality-checked using FastQC (ver. 0.11.3) and MultiQC101 (ver.1.12).
The reads were aligned to the human genome version hg38.p12 using HISAT2102 (ver. 2.2.1). For count quantification, we used featureCounts algorithm103 (ver. 2.0.1), using the options of the paired end (option -P), ignoring chimeric reads (option -C), stranded alignment on the reverse strand (option -s 2) and considering only primary alignments (option --primary)
Assembly: hg38.p12
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: iPSC-derived Neurons

growth_protocol: Two iPSC lines from postmortem dura-derived fibroblasts of two neurotypical individuals (LIBD2c1 and LIBD7c6)44 were maintained on a tissue culture plate coated with Cultrex Reduced Growth Factor Basement Membrane Matrix (R&D Systems) in StemFlex medium (Thermo Fisher Scientific)

extract_protocol:
Total RNA was extracted from NPCs and four-week-old neurons derived from iPSCs using TRIzol Reagent and a Direct-zol RNA MiniPrep kit, following the manufacturer’s instructions.
Libraries were prepared using a TruSeq Stranded Total RNA with RiboZero Human/Mouse/Rat Library Prep Kit (Illumina) and sequenced on NovaSeq6000 with a read length of 150-bp paired-end by Psomagen

treatment_protocol: To generate isogenic SETD1A mutant lines, an oligonucleotide (sgRNA) targeting around the splice acceptor of intron 15 in SETD1A was designed and cloned into U6-gRNA:CMV-CAS9-2A-tGFP vector by MilliporeSigma. Single-strand oligonucleotide (ssODN) carrying SETD1A c.4582-2delAG>- mutation and PAM blocking mutation (Supplementary Fig. 1a) was also designed by MilliporeSigma

value: iPSC-derived Neurons

value: Neurons

tag: iPSc clone

value: mut

tag: passage


title: LIBD7c6_CA137_43_Neuron_4wks

description:
Library name: 13_S13
Column name in raw_counts.tsv: LIBD7c6_CA137_43_Neuron_4wks


title: LIBD2c1_CM130_51_Neuron_4wks

description:
Library name: 11_S11
Column name in raw_counts.tsv: LIBD2c1_CM130_51_Neuron_4wks


title: LIBD2c1_CM130_11_Neuron_4wks

description:
Library name: 10_S10
Column name in raw_counts.tsv: LIBD2c1_CM130_11_Neuron_4wks


title: TSCp_1

description: Library name: TSCp_1

value: TSC

value: WT

value: primed


title: LIBD7c6_CM130_30_Neuron_4wks

description:
Library name: LIBD7c6_CM130_30_Neuron_4wks
Column name in raw_counts.tsv: LIBD7c6_CM130_30_Neuron_4wks


title: LIBD7c6_CA137_69_Neuron_4wks

description:
Library name: LIBD7c6_CA137_69_Neuron_4wks
Column name in raw_counts.tsv: LIBD7c6_CA137_69_Neuron_4wks


title: TSCn_1

description: Library name: TSCn_1


title: LIBD7c6_CA137_37_Neuron_4wks

description:
Library name: 12_S12
Column name in raw_counts.tsv: LIBD7c6_CA137_37_Neuron_4wks

value: wt


title: LIBD2c1_CM130_9_Neuron_4wks

description:
Library name: 9_S9
Column name in raw_counts.tsv: LIBD2c1_CM130_9_Neuron_4wks


title: LIBD7c6_CM130_78_Neuron_4wks

description:
Library name: LIBD7c6_CM130_78_Neuron_4wks
Column name in raw_counts.tsv: LIBD7c6_CM130_78_Neuron_4wks


title: LIBD7c6_CA137_109_Neuron_4wks

description:
Library name: LIBD7c6_CA137_109_Neuron_4wks
Column name in raw_counts.tsv: LIBD7c6_CA137_109_Neuron_4wks


title: LIBD2c1_CA137_11_Neuron_4wks

description:
Library name: 8_S8
Column name in raw_counts.tsv: LIBD2c1_CA137_11_Neuron_4wks


title: LIBD2c1_CM130_24_Neuron_4wks

description:
Library name: LIBD2c1_CM130_24_Neuron_4wks
Column name in raw_counts.tsv: LIBD2c1_CM130_24_Neuron_4wks


title: LIBD7c6_CA137_52_NPC

description:
Library name: 7_S7
Column name in raw_counts.tsv: LIBD7c6_CA137_52_NPC

source_name: iPSC-derived Neural Progenitor Cells

value: iPSC-derived Neural Progenitor Cells

value: NPCs


title: LIBD7c6_CA137_43_NPC

description:
Library name: 6_S6
Column name in raw_counts.tsv: LIBD7c6_CA137_43_NPC


title: LIBD2c1_CM130_11_NPC

description:
Library name: 3_S3
Column name in raw_counts.tsv: LIBD2c1_CM130_11_NPC


title: CT30_1

description: Library name: CT30_1


title: bTS5_1

description: Library name: bTS5_1


title: Sample_T2_032521_S6 (5 cell lines)

description:
Library name: Sample_T2_032521_S6
Multiplexed sample containing: LIBD7c6 CA137 #109 (WT, day 48, barcode: TGTCTTTCCTGCCAG); LIBD7c6 CA137 #37 (WT, day 48, barcode: TAACGACCAGCCATA); LIBD7c6 CA137 #69 (Hetero, day 48, barcode: CTCCTCTGCAATTAC); LIBD7c6 CM130 #30 (Hetero, day 48, barcode: ATTGACCCGCGTTAG); LIBD7c6 CM130 #78 (WT, day 48, barcode: CAGTAGTCACGGTCA)


title: LIBD7c6_CM130_30_NPC

description:
Library name: LIBD7c6_CM130_30_NPC
Column name in raw_counts.tsv: LIBD7c6_CM130_30_NPC


title: LIBD2c1_CM130_51_NPC

description:
Library name: 4_S4
Column name in raw_counts.tsv: LIBD2c1_CM130_51_NPC


title: LIBD7c6_CA137_69_NPC

description:
Library name: LIBD7c6_CA137_69_NPC
Column name in raw_counts.tsv: LIBD7c6_CA137_69_NPC


title: LIBD7c6_CA137_37_NPC

description:
Library name: 5_S5
Column name in raw_counts.tsv: LIBD7c6_CA137_37_NPC


title: LIBD2c1_CM130_9_NPC

description:
Library name: 2_S2
Column name in raw_counts.tsv: LIBD2c1_CM130_9_NPC


title: Sample_T1_030721_S7 (5 cell lines)

description:
Library name: Sample_T1_030721_S7
Multiplexed sample containing: LIBD7c6 CA137 #109 (WT, day 30, barcode: TGTCTTTCCTGCCAG); LIBD7c6 CA137 #37 (WT, day 30, barcode: TAACGACCAGCCATA); LIBD7c6 CA137 #69 (Hetero, day 30, barcode: CTCCTCTGCAATTAC); LIBD7c6 CM130 #30 (Hetero, day 30, barcode: ATTGACCCGCGTTAG); LIBD7c6 CM130 #78 (WT, day 30, barcode: CAGTAGTCACGGTCA)


title: LIBD7c6_CA137_109_NPC

description:
Library name: LIBD7c6_CA137_109_NPC
Column name in raw_counts.tsv: LIBD7c6_CA137_109_NPC


title: LIBD2c1_CA137_11_NPC

description:
Library name: 1_S1
Column name in raw_counts.tsv: LIBD2c1_CA137_11_NPC


title: LIBD7c6_CM130_78_NPC

description:
Library name: LIBD7c6_CM130_78_NPC
Column name in raw_counts.tsv: LIBD7c6_CM130_78_NPC


title: LIBD2c1_CM130_24_NPC

description:
Library name: LIBD2c1_CM130_24_NPC
Column name in raw_counts.tsv: LIBD2c1_CM130_24_NPC


title: SW1417_M_2

city: London

first: Daniel

middle: Martinez

last: Martinez

state: London

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Medical Research Council

description:
Library name: Sample 22
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv

data_processing:
HiSeq Control Software 2.2.58, RTA 2.11.3 and bcl2fastq2_2.20.0 were used for raw reads quality control and treatment
Raw sequences were quality filtered and trimmed with trimmomatic (v.0.39)
The resulting reads were mapped to the human reference transcriptome from ensembl database.
Quantification of samples was made via salmon (v 1.5.0) with mapping validation and gcbias options activated
Assembly: GRCh38.p13, version 103
Supplementary files format and content: tab-separated file of raw reads from Salmon mapping
Supplementary files format and content: tab-separated file of normalised reads done in deseq2 in R

source_name: Colon

growth_protocol: HCT116, LoVo, DLD-1 and SW948 cells were plated in 6 wells plates with complete medium

extract_protocol:
Samples were prepared using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
RNA-seq libraries were prepared using Illumina Stranded mRNA Prep kit and protocols

treatment_protocol: 10 mM of 2-MiCit was used as a treatment, or vehicle (water) for control condition

value: Colon

value: epithelial

value: wild-type

tag: treatment

value: Micit


title: SW1417_M_4

description:
Library name: Sample 24
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SW1417_M_3

description:
Library name: Sample 23
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SW1417_M_1

description:
Library name: Sample 21
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SW1417_C_4

description:
Library name: Sample 20
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv

value: control


title: SW1417_C_3

description:
Library name: Sample 19
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SW1417_C_1

description:
Library name: Sample 17
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SW1417_C_2

description:
Library name: Sample 18
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_M_3

description:
Library name: Sample 15
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_M_4

description:
Library name: Sample 16
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_M_2

description:
Library name: Sample 14
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_M_1

description:
Library name: Sample 13
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_C_4

description:
Library name: Sample 12
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_C_1

description:
Library name: Sample 9
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: SK-CO-1_C_3

description:
Library name: Sample 11
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_M_3

description:
Library name: Sample 7
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_M_4

description:
Library name: Sample 8
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_M_1

description:
Library name: Sample 5
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_M_2

description:
Library name: Sample 6
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_C_3

description:
Library name: Sample 3
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_C_4

description:
Library name: Sample 4
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_C_1

description:
Library name: Sample 1
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: HT29_C_2

description:
Library name: Sample 2
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: D28_eGFPneg_rep2

city: Guangzhou

first: Xiufeng

last: Zhong

address: 54 xianlie Rd

department: Zhongshan Ophthalmic Center

institute: Sun Yat-sen University

description: Library name: Sample 2

data_processing:
RNA-seq were performed as previously described [14, 26]. D60 ROs and GFP+ and GFP- cells pooled at D28, D55, D118 and D170 were collected in TRIzol reagent (Invitrogen) and stored at -80°C until they were submitted to Gene Denovo Biotechnology Co. (Guangzhou, China) for RNA extraction, library preparation, sequencing and data analyses. Total RNA was extracted via a TRIzol reagent kit (Invitrogen). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Oligo (dT) beads were used to isolate the poly mRNA from the total RNA. The enriched mRNA was fragmented and reverse transcribed into cDNA via random primers. After synthesis of the second strand, the cDNA was purified, end-repaired and ligated to Illumina sequencing adapters. The ligation products were size selected via agarose gel electrophoresis, amplified via PCR, and sequenced via the Illumina NovaSeq 6000 platform. The raw data was processed via the fastp tool (version 0.18.0) and short-read alignment tool Bowtie2 (version 2.2.8) to obtain clean reads. Paired-end clean reads were mapped to the reference genome via HISAT2. 2.4. The mapped reads of each sample were assembled via StringTie (version 1.3.1). For each transcription region, the fragment per kilobase of transcript per million mapped reads (FPKM) value was calculated to quantify the expression levels of each gene via RSEM.
Assembly: Ensembl_release94
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: hiPSCs derived retinal organoids

growth_protocol: Two hiPSC lines, BC1-hiPSC (Chou et al., 2011) and BC1-VSX2eGFP-hiPSC (Zheng et al., 2020) were used in this study. All hiPSCs had normal karyotype and were confirmed contamination free. The cells were maintained on Matrigel (Corning) coated plates with mTeSR1 medium (Stem Cell Technologies), and passage every 4-6 days at 80% confluences.

extract_protocol:
The differentiation of hiPSCs into retinal organoids (ROs) was according to published protocols (Li et al., 2019; Li et al., 2018; Luo et al., 2018; Zhong et al., 2014). Briefly, on day 0 (D0) of differentiation, hiPSCs were dissociated to induce embryonic bodies (EBs) formation. EBs were gradually transitioned into neural induction medium (NIM) containing DMEM/F12 (1:1) (GIBCO), 1% N2 supplement (GIBCO), 1% minimum essential media-non essential amino acids (NEAAs, GIBCO), 2 mg/ml heparin (Sigma-Aldrich). On D4 to D6, EBs were seeded onto Matrigel-coated dishes containing NIM, and then switched to retinal differentiation medium (RDM) containing DMEM/F12 (12: 5) supplemented with 2% B27 (without vitamin A, GIBCO), 1% NEAAs and 1% antibiotic-antimycotic (GIBCO) on D16. Since the fourth week of differentiation, optic vesicles (OVs) were gradually formed and morphologically identifiable. OVs were lifted up and cultured in suspension with RDM. The medium was supplemented with 10% fetal bovine serum (FBS, Natocor), 100 mM Taurine (Sigma-Aldrich) and 2 mM GlutaMAX (GIBCO) on D42. Since D90, the medium was supplemented with 1% N2 instead of B27 (without vitamin A). 3D ROs collected at D28, D55, D118, and D170 were dissociated into single cells by Papain Dissociation System (Worthington Biochemical) according to the manufacture’ instructions. Cell suspension was centrifuged at 400g for 10 minutes (Allegrax-15R, Beckman Coulter), and cell pellets were resuspended in sorting buffer (PBS containing 1 mM EDTA (GIBCO), 2% [vol/vol] FBS). Cells were sorted at 4℃ by FACSAriafusion (Becton Dickinson). eGFP positive and eGFP negative cells were separately collected in collecting buffer (medium plus 50% [vol/vol] FBS). FSC-A and FSC-H were examined for all cells to obtain live single eGFP positive cells. ROs derived from  parental hiPSCs were used to determine gate for sorting.Total RNA were extracted using Trizol reagent kit (Invitrogen). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen), end repaired, Abaseadded, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: hiPSCs derived retinal organoids

value: day post induction:Day 28

value: eGFP negative retinal cells derived from VSX2-eGFP reporter hiPSCs

value: Introducing the enhanced green fluorescence protein sequence at the reading frame terminator of exon 5 of VSX2

value: flow sorted eGFP negative cells at 28 days post neural retina induction


title: Patient 15 (SJ32) APC,tumor, and CD8+ T cell singlets TCR

description:
Library name: Sample_13_TCR
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting , TCR counting and aggregation using Cell Ranger v7.0.1
Assembly: hg38
Supplementary files format and content: comma separated values as gz files
Library strategy: scTCR-seq

extract_protocol:
Melanoma lymph node metastases tumor digests were thawed, stained with appropriate antibodies and populations of interest were isolated using FACS. Five populations were sorted from live cells: tumor singlets (NGFR/CD146+); tumor:CD8+ T cell clusters (NGFR/CD146+, CD8+); APC:CD8+ T cell clusters (NGFR-, CD146-, CD11c+, CD8+), CD8+ T cell singlets (NGFR-, CD146-, CD11c-, CD8+) and APC singlets (NGFR-, CD146-, CD11c+, CD8-). Singlets were pooled together during sort in a ratio of 1:1:1. If the amount of clusters was low, they were kept as separate samples. If sufficient numbers of cluster were sorted (>40.000), they were hashtagged with TotalSeq-C0251 (T:Tumor clusters, 394661, Biolegend) or with TotalSeq-C0252 (T:APC clusters, 394663, Biolegend) and subsequently pooled 1:1. For hashtagging, sorted cells were washed once with 2% BSA in PBS and incuated with the hashtagging antibody for 30min on ice. After hashtagging, cells were washed an additional two times with 0.04% BSA in PBS, after which they were pooled. Cells that did not need hashtagging were washed twice with 0.04% BSA in PBS, before proceeding to single cell 5' sequencing library prep.
The Chromium Controller and Chromium X platfor of 10X Genomics were used for single cell partitioning and barcoding. Each cell's transcriptome was barcoded during reverse transcription, pooled cDNA was amplified and Single Cell 5' Gene Expression (GEX), V(D)J and Feature Barcode (FB) Libraries were prepared according to the manufacturer's protocols (CG000330 and CG000331, 10X Genomics). All libraries were quantified and normalized on library QC data generated on the Bioanalyzer system according to manufacturer's protocols (G2938-90321 and G2938-90024, Agilent Technologies). Based on the expected target cell counts, a balanced library sub-pool of samples was compsed for SC5'GEX, V(D)J and FB libraries. Library sub-pools were quantified by qPCR, accodring to the KAPA Library Quantification Kit Illumina(R) Platforms protocol (KR0405, KAPA Biosystems). Based on qPCR results a final sequencing pool was composed. Paired end sequencing was performed on a NovaSeq 6000 Instrument (Illumina) using NovaSeq 6000 Reagent Kits v1.5 100 cycles (cat. no. 20028401, 20028319, 20028316 Illumina), using 28 cycles for Read 1, 10 cycles for Read i7, 10 cycles for Read i5 and 90 cycles for Read 2.

value: Melanoma lymph node metastasis


title: D28_eGFPneg_rep1

description: Library name: Sample 1


title: Patient 15 (SJ32) CD8+ T cell:APC clusters TCR

description:
Library name: Sample_12_TCR
10X Genomics


title: Patient 15 (SJ32) CD8+ T cell:tumor cell clusters TCR

description:
Library name: Sample_11_TCR
10X Genomics


title: Patient 15 (SJ32) CD8+ T cell:tumor cell clusters GEX

description:
Library name: Sample_11_GEX
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting , TCR counting and aggregation using Cell Ranger v7.0.1
Assembly: hg38
Supplementary files format and content: comma separated values as gz files


title: Patient 9 (SJ20) CD8+ T cell:APC clusters TCR

description:
Library name: Sample_9_TCR
10X Genomics


title: Patient 9 (SJ20) APC,tumor, and CD8+ T cell singlets GEX

description:
Library name: Sample_10_GEX
10X Genomics


title: Patient 9 (SJ20) CD8+ T cell:APC clusters GEX

description:
Library name: Sample_9_GEX
10X Genomics


title: Patient 9 (SJ20) CD8+ T cell:tumor cell clusters TCR

description:
Library name: Sample_8_TCR
10X Genomics


title: Patient 9 (SJ20) CD8+ T cell:tumor cell clusters GEX

description:
Library name: Sample_8_GEX
10X Genomics


title: Patient 8  (SJ18)  APC,tumor, and CD8+ T cell singlets TCR

description:
Library name: Sample_7_TCR
10X Genomics


title: Patient 8 (SJ18) CD8+ T cell:tumor cell, CD8+ T cell:APC clusters TCR

description:
Library name: Sample_6_TCR
10X Genomics


title: SK-CO-1_C_2

description:
Library name: Sample 10
raw_counts_deseq2_Novaseq.csv
norm_counts_deseq2_Novaseq.csv


title: Patient 2 (SJ2) APC,tumor, and CD8+ T cell singlets TCR

description:
Library name: Sample_5_TCR
10X Genomics


title: Patient 8 (SJ18) CD8+ T cell:tumor cell, CD8+ T cell:APC clusters GEX

description:
Library name: Sample_6_GEX
10X Genomics


title: Patient 2 (SJ2) APC,tumor, and CD8+ T cell singlets GEX

description:
Library name: Sample_5_GEX
10X Genomics


title: Patient 2 (SJ2) CD8+ T cell:tumor cell, CD8+ T cell:APC clusters TCR

description:
Library name: Sample_4_TCR
10X Genomics


title: Patient 1 (AKB460) APC,tumor, and CD8+ T cell singlets TCR

description:
Library name: Sample_3_TCR
10X Genomics


title: Patient 2 (SJ2) CD8+ T cell:tumor cell, CD8+ T cell:APC clusters GEX

description:
Library name: Sample_4_GEX
10X Genomics


title: Patient 1 (AKB460) CD8+ T cell:tumor cell clusters TCR

description:
Library name: Sample_1_TCR
10X Genomics


title: Patient 1 (AKB460) CD8+ T cell:APC clusters GEX

description:
Library name: Sample_2_GEX
10X Genomics


title: Patient 1 (AKB460) APC,tumor, and CD8+ T cell singlets GEX

description:
Library name: Sample_3_GEX
10X Genomics


title: Patient 15 (SJ32) CD8+ T cell:APC clusters GEX

description:
Library name: Sample_12_GEX
10X Genomics


title: Patient 15 (SJ32) APC,tumor, and CD8+ T cell singlets GEX

description:
Library name: Samepl_13_GEX
10X Genomics


title: Patient 1 (AKB460) CD8+ T cell:APC clusters TCR

description:
Library name: Sample_2_TCR
10X Genomics


title: Patient32

city: Shanghai

first: Changrui

last: Yang

address: 160 Pu Jian Rd

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: 32

data_processing:
fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads. STAR software (v2.7.9a) was used to align the high-quality clean reads to the human reference genome (hg38). featureCounts software (v2.0) was used to get the raw gene level mRNA read counts as the mRNA expression profile. DESeq2 software (v1.30.1) was used to normalize and calculate the fold change and Pvalue between two groups.
Assembly: hg38
Supplementary files format and content: comma-separated values, containing the raw counts of genes for all samples.

source_name: Bladder Urothelial Carcinoma, male, 57

extract_protocol:
total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample preparation kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument with 151 bp paired end reads.

value: Tumor tissue

value: primary cells

tag: histologic type_of_tumor

value: Bladder Urothelial Carcinoma

tag: Sex

value: male

tag: age


title: Patient33

description: Library name: 33

source_name: High-grade serous ovarian cancer, female, 62

value: High-grade serous ovarian cancer

value: female


title: Patient 1 (AKB460) CD8+ T cell:tumor cell clusters GEX

description:
Library name: Sample_1_GEX
10X Genomics


title: Patient31

description: Library name: 31

source_name: Bladder Urothelial Carcinoma, female, 61


title: Patient 9 (SJ20) APC,tumor, and CD8+ T cell singlets TCR

description:
Library name: Sample_10_TCR
10X Genomics


title: Patient29

description: Library name: 29

source_name: High-grade serous ovarian cancer, female, 58


title: Patient30

description: Library name: 30

source_name: High-grade serous ovarian cancer, female, 60


title: Patient27

description: Library name: 27

source_name: Pulmonary neuroendocrine tumor, male, 79

value: Pulmonary neuroendocrine tumor


title: Patient26

description: Library name: 26

source_name: High-grade serous ovarian cancer, female, 56


title: Patient28

description: Library name: 28

source_name: High-grade serous ovarian cancer, female, 72


title: Patient 8  (SJ18)  APC,tumor, and CD8+ T cell singlets GEX

description:
Library name: Sample_7_GEX
10X Genomics

source_name: Melanoma lymph node metastasis


title: Patient25

description: Library name: 25

source_name: Lung adenocarcinoma, female, 67

value: Lung adenocarcinoma


title: Patient22

description: Library name: 22

source_name: High-grade serous ovarian cancer, female, 55


title: Patient21

description: Library name: 21

source_name: Bladder Urothelial Carcinoma, male, 72


title: Patient23

description: Library name: 23

source_name: High-grade serous ovarian cancer, female, 51


title: Patient19

description: Library name: 19

source_name: High-grade serous ovarian cancer, female, 75


title: Patient15

description: Library name: 15

source_name: Lung adenocarcinoma, female, 70


title: Patient18

description: Library name: 18

source_name: High-grade serous ovarian cancer, female, 78


title: Patient16

description: Library name: 16


title: Patient13

description: Library name: 13

source_name: Endometrioid carcinoma, female, 60

value: Endometrioid carcinoma


title: Patient14

description: Library name: 14

source_name: Malignant mesothelioma, female, 60

value: Malignant mesothelioma


title: Patient12

description: Library name: 12

source_name: High-grade serous ovarian cancer, female, 53


title: Patient10

description: Library name: 10

source_name: High-grade serous ovarian cancer, female, 69


title: Patient9

description: Library name: 9

source_name: High-grade serous ovarian cancer, female, 73


title: Patient8

description: Library name: 8

source_name: High-grade serous ovarian cancer, female, 68


title: Patient7

description: Library name: 7

source_name: High-grade serous ovarian cancer, female, 70


title: Patient6

description: Library name: 6

source_name: Lung squamous cell carcinoma, male, 76

value: Lung squamous cell carcinoma


title: Patient5

description: Library name: 5

source_name: Lung adenocarcinoma, female, 78


title: Patient11

description: Library name: 11

source_name: Endometrioid carcinoma, female, 52


title: Patient4

description: Library name: 4

source_name: High-grade serous ovarian cancer, female, 57


title: Patient1

description: Library name: 1

source_name: High-grade serous ovarian cancer, female, 47


title: Patient2

description: Library name: 2

source_name: High-grade serous ovarian cancer, female, 50


title: Day 6 TSCp

description: Day 6 mid-differentiation sample from primed H9 cells

data_processing:
Sample de-multiplexing, alignment, filtering, and UMI counting was performed with 10x Genomics Cell Ranger pipeline.
The reads were mapped to the human reference genome (GRCh38.98).
The filtered counts were analyzed with Seurat.
Assembly: GRCh38.98
Supplementary files format and content: single cell read count matrix (mtx), cell barcode (tsv), gene names (tsv)

source_name: cell line

growth_protocol: Primed ESC and iPSC were cultured on wells coated with Matrigel (Corning) in E8 (Gibco) or E8 Flex (Gibco) medium. . Naive ESC were cultured on mouse (ICR) inactivated embryonic fibroblasts (iMEF, Thermo A24903) in tt2iLGö Naïve Expansion medium (Stem Cell Technologies 05590). TSC were cultured in plates coated with 5 µg/ml Collagen-IV (Col-IV, Corning) in TSC medium (Basal DMEM/F12 + GlutaMax supplemented with 0.1 mM 2-mercaptoethanol (Gibco), 0.2% FBS (Gibco), 0.5% Penicillin-Streptomycin (Sigma-Aldrich P4333), 0.3% BSA (Sigma A7030-500G), 1% Insulin-Transferrin-Selenium-Ethanolamine (Gibco 51500056), 1.5 µg/ml L-ascorbic acid (Sigma A4544), 50 ng/ml EGF (Peprotech, AF-100-15-1MG), 2 µM CHIR99021 (Stemgent 04-0004-10), 0.5 µM A83-01 (Sigma SML0788-5MG), 1 µM SB431542 (Cayman Chemicals 13031) 0.8 mM Sodium Butyrate (Sigma B5887-1G) and 5 µM Y-27632 (Selleckchem S1049)). The medium was changed every other day. All cells were kept in an incubator at 37 °C and 5% CO2 and were routinely tested for mycoplasma contamination.

extract_protocol:
Cells were dissociated with Accutase at 37 °C for 5 (ESC samples) or 10 min (TSC samples), resuspended in PBS + 0.04% BSA on ice and passed through a Flowmi tip strainer (Fisher Scientific) to yield a single-cell suspension. The quality of the samples was assessed using a Luna cell counter (Logos Biosystems). Single cell RNA sequencing (scRNA-seq) was performed using the 10x Genomics Chromium Single Cell 3’RNA-seq platform at Institute of Molecular Medicine Finland (FIMM).
10x Genomics Chromium Single Cell 3’RNAseq platform using the Chromium Next GEM Single Cell 3' Gene Expression (version 3.1 chemistry)

treatment_protocol: ESCp were reverted to ESCn using NaïveCult Induction kit (Stem Cell Technologies 05580) and further cultured on mouse (ICR) inactivated embryonic fibroblasts (iMEF, Thermo A24903) in tt2iLGö Naïve Expansion medium (Stem Cell Technologies 05590). For derivation of TSC from naive cells, 1 x 106 ESCn were passaged with Accutase for 3 min to achieve a single-cell suspension. Cells were seeded in TSC medium on 6 well plates coated with 5 µg/ml Col-IV. Medium was changed every other day, until the cells grew 80% confluent and were passaged 1:1 onto new Col-IV coated wells with 10 min TrypLE. The cells started proliferating faster after the initial passaging. The medium was changed every other day and once the cells were 80% confluent they were passaged on 1:3 ratio onto new Col-IV coated wells. For derivation of TSC from primed cells 4 x 105 ESCp or iPSC were passaged with TrypLE for 3 min to achieve a single-cell suspension. Cells were seeded on Matrigel coated wells with E8 medium supplemented with 10 µM Y-27632. After 24 hours, medium was changed to TSC-medium supplemented with 10 ng/ml BMP4 (Proteintech HZ-1045). Medium was changed daily, and on day 3 of differentiating cells were passaged 1:3 onto a new well with EDTA. After 5 days, BMP4 was cut from the cells, and the cells were continued to be cultured in TSC-medium. Medium was changed every other day and the cells were passaged with 10 min TrypLE on 1:3 ratio when the wells were growing 80% confluent.

value: cell line

tag: cell line

value: TSC

tag: differentiation day

value: day 6

value: WT

value: primed


title: Day 3 TSCp

description: Day 3 mid-differentiation sample from primed H9 cells

tag: cell type

value: day 3

tag: genotype


title: Patient3

description: Library name: 3

source_name: High-grade serous ovarian cancer, female, 54

value: Tumor tissue


title: Patient24

description: Library name: 24

source_name: Lung adenocarcinoma, male, 74

value: primary cells


title: Day 3 TSCn

description: Day 3 mid-differentiation sample from naive H9 cells

tag: naive/primed

value: naive


title: TSCp

description: Human trophoblast cell line derived from primes H9 cells

value: TSC p3


title: Patient20

description: Library name: 20

source_name: Lung adenocarcinoma, male, 78

value: male


title: TSCn

description: Human trophoblast cell line derived from naive H9 cells


title: ESCp

description: Human primed H9 embryonic stem cell line

value: ESC

value: day0 (ESC)


title: Patient17

description: Library name: 17

source_name: Endometrioid carcinoma, female, 39

value: female


title: TSCWT

description: Human trophoblast cell line derived from HEL24.4 iPSC line


title: TSCKO

description: Human trophoblast cell line derived from HEL24.4 iPSC line with homozygous ELF5 knockout


title: ESCn

description: Human naive H9 embryonic stem cell line


title: CT30

description: First trimester derived human trophoblast cell line CT30


title: Tri-TCE-368

source_name: Tumor tissue

growth_protocol: Ovarian cancer cell line (SKOV3) was purchased from the American Type Culture Collection. Cells were maintained in RPMI 1640 (Life Technologies) supplemented with 10% fetal bovine serum (Gibco), d-glutamine (2 mM), penicillin (100 U/ml), and streptomycin (100 μg/ml).

treatment_protocol: Each reconstituted NOG mouse received a subcutaneous injection of 1x10^6 cancer cells (SKOV3 cell line) in 200 μL of PBS/Matrigel mixture into the right flank. Mice then were treated with 5 mg/kg of control IgG, BiTEs or Tri-TCEs twice post-inoculation. At termination (28 days after injection), tumor tissue was harvested for analysis.

value: human ovarian adenocarcinoma cell line

value: Tri-TCE


title: bTS5

description: Blastocyst derived human trophoblast cell line bTS5


title: Tri-TCE-926


title: Tri-TCE-367


title: Tri-TCE-378


title: Tri-TCE-347


title: Tri-TCE-363


title: BiTE-928

value: BiTE


title: Tri-TCE-352


title: Tri-TCE-346


title: BiTE-389


title: BiTE-379


title: BiTE-376


title: Tri-TCE-362


title: BiTE-358


title: BiTE-353


title: BiTE-391


title: BiTE-348


title: control-390

value: control IgG


title: Day 6 TSCn

description: Day 6 mid-differentiation sample from naive H9 cells

value: cell line

value: TSC


title: control-349


title: control-343


title: control-361


title: control-384


title: control-360


title: control-642


title: Low-CDC-sensitive-3

city: Epalinges

first: Hilma

last: van der Horst

address: Chemin des Boveresses 155

department: Oncology

country: Switzerland

institute: Univeresity of Lausanne

data_processing:
Sequence reads were trimmed and filtered using fastp v.023.1 with the following params "--cut_window_size 5", "--cut_mean_quality 15", and "--length_required 35"
Alignment and quantification to the GRCh38 reference genome using ENSEMBL release 110 gene annotations was performed using STAR v2.7.8a with default parameters
Assembly: GRCh38
Supplementary files format and content: Raw counts stored in TSV format file with the following columns: 1) gene_ids, 2) unstranded counts, 3) stranded counts, 4) reverse stranded counts

source_name: DLBCL patient sample

growth_protocol: U2932 cell lines were cultured in cultured in RPMI-1640 (Invitrogen, Carlsbad, CA, USA), supplemented with 10% fetal bovine serum (Invitrogen) and 1% penicillin-streptomycin (Life Technologies, Carlsbad, CA, USA), at 37°C and 5% CO2). Cell suspensions from lymph node biopsies derived from DLBCL patients were isolated by mechanical disruption and cryopreserved in liquid nitrogen until further use. Upon thawing, cells were metabolically activated by 24-hour incubation with soluble human recombinant MEGACD40L® Protein.

extract_protocol:
Total RNA was isolated using the RNeasy micro – or mini kit (Qiagen) from cell pellets of the U2932 cell lines or of the FACS-isolated B-cells (CD19+CD3-) from DLBCL patient samples. RNA quality and quantity was assessed using the High Sensitivity RNA ScreenTape Analysis (Agilent), and RNA integrity numbers (RIN) of >8.5 were obtained for all samples.
A KAPA mRNA hyperPrep kit was used for mRNA library construction. The libraries were sequenced with paired-end reads on a NovaSeq-6000.
Bulk RNA-seq

treatment_protocol: U2932 cells treated once (U2932-Tr) or repeatedly (U2932-R) were treated with CDC-inducing antibody DuoHexaBody-CD37 (10µg/mL) in the presence of pooled normal human serum (NHS) as source of complement proteins for 45 minutes, after which the cells were washed.

value: DLBCL patient sample

tag: phenotype

value: Low-CDC-sensitive


title: control-345


title: High-CDC-sensitive-4

value: High-CDC-sensitive


title: Low-CDC-sensitive-1


title: Low-CDC-sensitive-2


title: High-CDC-sensitive-2


title: High-CDC-sensitive-3


title: High-CDC-sensitive-5


title: High-CDC-sensitive-1


title: U2932-R-3

value: B-cell lymphoma cell line

value: CDC repeatedly


title: U2932-R-1


title: U2932-R-4


title: U2932-Tr-2

value: CDC 1x


title: U2932-Tr-4


title: U2932-Tr-1


title: U2932-WT-2

value: control


title: U2932-WT-3


title: illumina_HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd-1

description:
illumina_HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd_A2I_Editing_score.txt
illumina_HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd_C2U_Editing_score.txt

data_processing:
Data processing for short-read RNA-seq: mRNA-seq libraries were sequenced using a paired-end 150 bp strategy on the Illumina NovaSeq 6000 System (Haplox genomics center). Sequencing quality was assessed with FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter sequences were removed using Cutadapt (v1.18) with parameters: -j 40 -m 20 -q 20. The reads were then filtered for those derived from repetitive elements using sequences from the UCSC Genome Browser (https://genome.ucsc.edu/cgi-bin/hgTables) and afterwards aligned to the hg38 reference genome with STAR (v2.7.9a). Uniquely mapped reads were quantified using featureCounts (v2.0.1) against Gencode annotations (v37, Ensembl 103) with the following parameters: -T 24 -s 2 -p -B -C -g gene_name -Q 30.
RNA editing analysis for short-read mRNA-seq: After aligning reads to the genome, BAM files were further processed using SAILOR (v1.2.0) to identify C-to-U and A-to-I edit sites across the hg38 reference genome. In brief, known SNPs (dbSNP, v155) and potential artifacts were filtered. Candidate edit sites were identified based on the number of C-to-U or A-to-I conversions. Edit sites with confidence value larger than 0.65 were retained. The retained edit sites were further filtered based on the coverage (coverage ≥ 10) and mutation frequency (frequency < 0.95). Subsequently, sites annotated within the 5' UTR, CDS, or 3' UTR were extracted for further analysis. The reads containing the high-confidence edit sites were extracted using biostar214299 (https://www.biostars.org/p/214299/).
Assembly: hg38 reference genome
Supplementary files format and content: Translation efficiency of genes; Editing score of genes; Poly(A)-tail length of genes; TPM of genes

extract_protocol:
For mRNA-seq and ONT long-read sequencing, total RNAs were extracted using TRlzol Reagent (Invitrogen, 15596026) according to the manufacturer’s protocol. For scRNA-seq, single cells were sorted into each well of 96-well plates containing 3 µL lysis buffer (0.3 µL 1% Triton X-100 (Sigma Aldrich, T9284), 0.05 µL 10 µM Oligo dT primer, 0.2 µL 10 mM dNTPs mix (Thermo Scientific, R0191), 0.03 µL 40 U/µL RNase inhibitor (Takara, 2313A), 0.4 µL 50% PEG8000 (Sigma Aldrich, 89510) and 2.02 µL ddH2O).
500 ng total RNA was used as input material for the mRNA-seq library construction (YEASEN, 12309ES96) following the manufacturer’s protocol. Sequencing library was generated using 500 ng-2 µg total RNA was as input for ONT long-read sequencing library construction (ONT, SQK-PCS109). Single-cell RNA sequencing libraries were generated using the Smart-seq3xpress protocol.

value: Human colon cancer cells


title: U2932-WT-1


title: U2932-WT-4


title: illumina_HCT116_induced_APOBEC1-ADAR2dd-2


title: HEK293T_WT_total-1

value: Human embryonic kidney cells


title: illumina_HCT116_induced_APOBEC1-ADAR2dd-1


title: HEK293T_WT_polysome-1


title: HEK293T_LSM14A-TRIBE-ID_Rapa60min-2

description: HEK293T_LSM14A-TRIBE-ID_Rapa60min_Editing_score.txt


title: HEK293T_WT_polysome-2


title: HEK293T_LSM14A-TRIBE-ID_Rapa30min-2

description: HEK293T_LSM14A-TRIBE-ID_Rapa30min_Editing_score.txt


title: HEK293T_WT_total-2


title: HEK293T_LSM14A-TRIBE-ID_Rapa15min-1

description: HEK293T_LSM14A-TRIBE-ID_Rapa15min_Editing_score.txt


title: illumina_HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd-2


title: HEK293T_LSM14A-TRIBE-ID_Rapa60min-1


title: HEK293T_LSM14A-TRIBE-ID_Rapa120min-2

description: HEK293T_LSM14A-TRIBE-ID_Rapa120min_Editing_score.txt


title: HEK293T_LSM14A-TRIBE-ID_Rapa0min-2


title: HEK293T_LSM14A-TRIBE-ID_Rapa0min-1


title: U2932-R-2


title: U2932-Tr-3


title: HEK293T_LSM14A-TRIBE-ID_Rapa30min-1


title: HEK293T_induced_APOBEC1-DDX6_LSM14A-ADAR2dd-2

description:
HEK293T_induced_APOBEC1-DDX6_LSM14A-ADAR2dd_A2I_Editing_score.txt
HEK293T_induced_APOBEC1-DDX6_LSM14A-ADAR2dd_C2U_Editing_score.txt


title: HEK293T_induced_APOBEC1-DDX6_LSM14A-ADAR2dd-1


title: HEK293T_induced_APOBEC1_ADAR2dd-control-1


title: HEK293T_DDX6-STAMP-ID-Rapa30min-2

description: HEK293T_DDX6-STAMP-ID-Rapa30min_Editing_score.txt


title: HEK293T_induced_APOBEC1_ADAR2dd-control-2


title: HEK293T_DDX6-STAMP-ID-Rapa30min-1


title: HEK293T_DDX6-STAMP-ID-Rapa15min-2

description: HEK293T_DDX6-STAMP-ID-Rapa15min_Editing_score.txt


title: HEK293T_DDX6-STAMP-ID-Rapa0min-1

description: HEK293T_DDX6-STAMP-ID-Rapa120min_Editing_score.txt


title: HEK293T_DDX6-STAMP-ID-Rapa120min-1


title: HEK293T_DDX6-STAMP-ID-Rapa15min-1


title: HEK293T_DDX6-STAMP-ID-Rapa120min-2


title: HEK293T_DDX6-STAMP-ID-Rapa0min-2


title: HEK293T_LSM14A-TRIBE-ID_Rapa15min-2


title: HCT116_uninduced_APOBEC1-DDX6-3


title: HCT116_WT_total-2


title: HCT116_uninduced_APOBEC1-control-1


title: HEK293T_DDX6-KO_polysome-2


title: HCT116_uninduced_APOBEC1_ADAR2dd-control-2


title: HCT116_uninduced_ADAR2dd-control-2


title: HCT116_uninduced_APOBEC1-DDX6-1


title: HEK293T_DDX6-KO_total-2


title: HEK293T_LSM14A-TRIBE-ID_Rapa120min-1


title: HCT116_uninduced_APOBEC1-control-3


title: HCT116_WT_polysome-2


title: HEK293T_DDX6-KO_total-1


title: HCT116_WT_polysome-1


title: HCT116_WT_total-1


title: HCT116_uninduced_ADAR2dd-control-1


title: HCT116_induced_PATL1-ADAR2dd-2

description: HCT116_induced_PATL1-ADAR2dd_Editing_score.txt


title: HEK293T_DDX6-KO_polysome-1


title: HCT116_induced_LSM14A-APOBEC1-1

description: HCT116_induced_LSM14A-APOBEC1_Editing_score.txt


title: HCT116_induced_LSM14A-APOBEC1-2


title: HCT116_induced_PATL1-ADAR2dd-1


title: HCT116_uninduced_APOBEC1-control-2


title: HCT116_induced_PATL1-APOBEC1-1

description: HCT116_induced_PATL1-APOBEC1_Editing_score.txt


title: HCT116_induced_LSM14A-ADAR2dd-1

description: HCT116_induced_LSM14A-ADAR2dd_Editing_score.txt


title: HCT116_induced_EDC4-APOBEC1-2

description: HCT116_induced_EDC4-APOBEC1_Editing_score.txt


title: HCT116_induced_EDC4-APOBEC1-1


title: HCT116_uninduced_APOBEC1-DDX6-2


title: HCT116_induced_EDC3-APOBEC1-2

description: HCT116_induced_EDC3-APOBEC1_Editing_score.txt


title: HCT116_induced_EDC3-ADAR2dd-2

description: HCT116_induced_EDC3-ADAR2dd_Editing_score.txt


title: HCT116_induced_EDC3-APOBEC1-1


title: HCT116_induced_EDC3-ADAR2dd-1


title: HCT116_induced_PATL1-APOBEC1-2


title: HCT116_induced_DDX6-APOBEC1-2

description: HCT116_induced_DDX6-APOBEC1_Editing_score.txt


title: HCT116_induced_DCP2-APOBEC1-2

description: HCT116_induced_DCP2-APOBEC1_Editing_score.txt


title: HCT116_induced_DDX6-ADAR2dd-1

description: HCT116_induced_DDX6-ADAR2dd_Editing_score.txt


title: HCT116_induced_DDX6-ADAR2dd-2


title: HCT116_induced_CNOT1-R-APOBEC1-1

description: HCT116_induced_CNOT10-APOBEC1_Editing_score.txt


title: HCT116_induced_DDX6-APOBEC1-1


title: HCT116_induced_LSM14A-ADAR2dd-2


title: HCT116_induced_APOBEC-DCP2-1

description: HCT116_induced_APOBEC-DCP2_Editing_score.txt


title: HCT116_induced_DCP2-APOBEC1-1


title: HCT116_induced_APOBEC1-PATL1-2

description: HCT116_induced_APOBEC1-PATL1_Editing_score.txt


title: HCT116_induced_CNOT10-APOBEC1-1

description: HCT116_induced_CNOT1-R-APOBEC1_Editing_score.txt


title: HCT116_induced_APOBEC-EDC3-1

description: HCT116_induced_APOBEC-EDC3_Editing_score.txt


title: HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd-1

description:
HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd_A2I_Editing_score.txt
HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd_C2U_Editing_score.txt


title: HCT116_induced_APOBEC1-LSM14A-1

description: HCT116_induced_APOBEC1-LSM14A_Editing_score.txt


title: HCT116_induced_APOBEC1-DDX6_LSM14A-ADAR2dd-2


title: HCT116_induced_APOBEC1-PATL1-1


title: HCT116_induced_APOBEC1-control-3

description: HCT116_induced_APOBEC1-DDX6_Editing_score.txt


title: HCT116_induced_APOBEC1-control-2


title: HCT116_induced_APOBEC1-DDX6-1


title: HCT116_induced_APOBEC1-EDC4-1

description: HCT116_induced_APOBEC1-EDC4_Editing_score.txt


title: HCT116_induced_APOBEC1-DDX6-3


title: HCT116_induced_APOBEC1-control-1


title: HCT116_induced_APOBEC1-CNOT10-1

description: HCT116_induced_APOBEC1-CNOT10_Editing_score.txt


title: HCT116_induced_APOBEC1-4E-T-2

description: HCT116_induced_APOBEC1-4E-T_Editing_score.txt


title: HCT116_induced_APOBEC1_ADAR2dd-control-1


title: HCT116_induced_ADAR2dd-PATL1-2

description: HCT116_induced_ADAR2dd-PATL1_Editing_score.txt


title: HCT116_induced_APOBEC1-4E-T-1


title: HCT116_induced_ADAR2dd-LSM14A-2

description: HCT116_induced_ADAR2dd-LSM14A_Editing_score.txt


title: HCT116_induced_ADAR2dd-LSM14A-1


title: HCT116_induced_APOBEC1_ADAR2dd-control-2


title: HCT116_induced_APOBEC1-DDX6-2


title: HCT116_induced_ADAR2dd-DDX6-2

description: HCT116_induced_ADAR2dd-DDX6_Editing_score.txt


title: HCT116_uninduced_APOBEC1_ADAR2dd-control-1


title: HCT116_induced_ADAR2dd-DDX6-1


title: HCT116_induced_ADAR2dd-4E-T-2

description: HCT116_induced_ADAR2dd-4E-T_Editing_score.txt


title: HCT116_induced_ADAR2dd-control-1

description: HCT116_induced_LSM14A-ADAR2dd_Editing_score.txt


title: HCT116_induced_ADAR2dd-PATL1-1


title: HCT116_induced_ADAR2dd-EDC3-2

description: HCT116_induced_ADAR2dd-EDC3_Editing_score.txt


title: HCT116_induced_ADAR2dd-control-2


title: HCT116_induced_ADAR2dd-EDC3-1


title: HCT116_induced_4E-T-APOBEC1-1

description: HCT116_induced_4E-T-APOBEC1_Editing_score.txt


title: HCT116_induced_4E-T-APOBEC1-2


title: HCT116_induced_4E-T-ADAR2dd-2

description: HCT116_induced_4E-T-ADAR2dd_Editing_score.txt


title: HCT116_induced_4E-T-ADAR2dd-1


title: HCT116_DDX6-KO_total-1


title: HCT116_DDX6-KO_total-2


title: HCT116_DDX6-KO_polysome-2


title: HCT116_DDX6-KO_polysome-1


title: HCT116_induced_ADAR2dd-4E-T-1


title: ctrl_6-SS3_6-SS3-H9

data_processing:
Sequencing reads were preprocessed and mapped to hg38 assembly. PCR duplicates were removed using Picard MarkDuplicates (v2.27.4, https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard) with the option REMOVE_DUPLICATES=true. FeatureCounts (v2.0.1) was used to quantify uniquely mapped reads with parameters: -p -B -C -g gene_name -Q 30. Cells with > 7,000?detected genes and > 150,000 deduplicated reads were included in downstream analysis. Genes with < 10 mapped reads across all cells were excluded. Feature counts for each cell were normalized using the NormalizeData function from Seurat (v5.0.3), with the LogNormalize method and a scale factor of 10,000.
Assembly: hg38 reference genome
Supplementary files format and content: Expression value for quality control-processed single cells

extract_protocol: For the single-cell RNA sequencing, single cells were sorted into each well of 96-well plates containing 3 µL lysis buffer (0.3 µL 1% Triton X-100 (Sigma Aldrich, T9284), 0.05 µL 10 µM Oligo dT primer, 0.2 µL 10 mM dNTPs mix (Thermo Scientific, R0191), 0.03 µL 40 U/µL RNase inhibitor (Takara, 2313A), 0.4 µL 50% PEG8000 (Sigma Aldrich, 89510) and 2.02 µL ddH2O). Single-cell RNA sequencing libraries were generated using the Smart-seq3xpress protocol.


title: ctrl_6-SS3_6-SS3-H7


title: ctrl_6-SS3_6-SS3-H6


title: ctrl_6-SS3_6-SS3-H4


title: ctrl_6-SS3_6-SS3-H3


title: ctrl_6-SS3_6-SS3-H10


title: ctrl_6-SS3_6-SS3-H11


title: ctrl_6-SS3_6-SS3-H2


title: TRIBEID_6-SS3_6-SS3-G9


title: TRIBEID_6-SS3_6-SS3-G7


title: TRIBEID_6-SS3_6-SS3-G8


title: TRIBEID_6-SS3_6-SS3-G4


title: TRIBEID_6-SS3_6-SS3-G5


title: ctrl_6-SS3_6-SS3-H8


title: TRIBEID_6-SS3_6-SS3-F5


title: TRIBEID_6-SS3_6-SS3-F10


title: TRIBEID_6-SS3_6-SS3-F2


title: TRIBEID_6-SS3_6-SS3-F3


title: TRIBEID_6-SS3_6-SS3-G11


title: TRIBEID_6-SS3_6-SS3-F7


title: TRIBEID_6-SS3_6-SS3-G2


title: TRIBEID_6-SS3_6-SS3-F6


title: TRIBEID_6-SS3_6-SS3-G12


title: TRIBEID_6-SS3_6-SS3-F1


title: TRIBEID_6-SS3_6-SS3-E6


title: TRIBEID_6-SS3_6-SS3-E7


title: TRIBEID_6-SS3_6-SS3-E2


title: TRIBEID_6-SS3_6-SS3-E4


title: ctrl_6-SS3_6-SS3-H5


title: TRIBEID_6-SS3_6-SS3-E10


title: TRIBEID_6-SS3_6-SS3-F9


title: TRIBEID_6-SS3_6-SS3-D6


title: TRIBEID_6-SS3_6-SS3-D7


title: TRIBEID_6-SS3_6-SS3-D5


title: TRIBEID_6-SS3_6-SS3-G1


title: TRIBEID_6-SS3_6-SS3-D4


title: TRIBEID_6-SS3_6-SS3-G3


title: TRIBEID_6-SS3_6-SS3-D3


title: TRIBEID_6-SS3_6-SS3-D1


title: TRIBEID_6-SS3_6-SS3-C6


title: TRIBEID_6-SS3_6-SS3-C5


title: TRIBEID_6-SS3_6-SS3-C8


title: TRIBEID_6-SS3_6-SS3-D11


title: TRIBEID_6-SS3_6-SS3-C11


title: TRIBEID_6-SS3_6-SS3-C12


title: TRIBEID_6-SS3_6-SS3-C3


title: TRIBEID_6-SS3_6-SS3-C10


title: TRIBEID_6-SS3_6-SS3-B7


title: TRIBEID_6-SS3_6-SS3-C7


title: TRIBEID_6-SS3_6-SS3-B9


title: TRIBEID_6-SS3_6-SS3-E11


title: TRIBEID_6-SS3_6-SS3-D12


title: TRIBEID_6-SS3_6-SS3-D8


title: TRIBEID_6-SS3_6-SS3-E3


title: TRIBEID_6-SS3_6-SS3-B8


title: TRIBEID_6-SS3_6-SS3-B6


title: TRIBEID_6-SS3_6-SS3-B11


title: TRIBEID_6-SS3_6-SS3-A9


title: TRIBEID_6-SS3_6-SS3-B3


title: TRIBEID_6-SS3_6-SS3-A4


title: TRIBEID_6-SS3_6-SS3-A8


title: TRIBEID_6-SS3_6-SS3-B12


title: TRIBEID_6-SS3_6-SS3-B10


title: TRIBEID_6-SS3_6-SS3-C2


title: TRIBEID_6-SS3_6-SS3-A3


title: TRIBEID_6-SS3_6-SS3-A10


title: TRIBEID_6-SS3_6-SS3-C4


title: TRIBEID_6-SS3_6-SS3-A11


title: TRIBEID_6-SS3_6-SS3-D10


title: TRIBEID_6-SS3_6-SS3-A12


title: TRIBEID_6-SS3_6-SS3-C1


title: ctrl_5-SS3_5-SS3-H7


title: ctrl_5-SS3_5-SS3-H5


title: ctrl_5-SS3_5-SS3-H8


title: ctrl_5-SS3_5-SS3-H9


title: ctrl_5-SS3_5-SS3-H4


title: ctrl_5-SS3_5-SS3-H3


title: ctrl_5-SS3_5-SS3-H2


title: ctrl_5-SS3_5-SS3-H6


title: ctrl_5-SS3_5-SS3-H1


title: ctrl_5-SS3_5-SS3-H12


title: ctrl_5-SS3_5-SS3-H11


title: ctrl_5-SS3_5-SS3-H10


title: TRIBEID_5-SS3_5-SS3-G7


title: TRIBEID_5-SS3_5-SS3-G8


title: TRIBEID_5-SS3_5-SS3-G6


title: TRIBEID_5-SS3_5-SS3-G5


title: TRIBEID_5-SS3_5-SS3-G3


title: TRIBEID_5-SS3_5-SS3-G2


title: TRIBEID_5-SS3_5-SS3-G11


title: TRIBEID_5-SS3_5-SS3-F9


title: TRIBEID_5-SS3_5-SS3-G10


title: TRIBEID_5-SS3_5-SS3-F6


title: TRIBEID_5-SS3_5-SS3-G12


title: TRIBEID_5-SS3_5-SS3-F5


title: TRIBEID_5-SS3_5-SS3-F10


title: TRIBEID_5-SS3_5-SS3-F11


title: TRIBEID_5-SS3_5-SS3-F12


title: TRIBEID_5-SS3_5-SS3-F2


title: TRIBEID_5-SS3_5-SS3-E8


title: TRIBEID_5-SS3_5-SS3-E9


title: TRIBEID_5-SS3_5-SS3-E6


title: TRIBEID_5-SS3_5-SS3-E4


title: TRIBEID_5-SS3_5-SS3-F3


title: TRIBEID_5-SS3_5-SS3-E7


title: TRIBEID_5-SS3_5-SS3-E10


title: TRIBEID_5-SS3_5-SS3-D9


title: TRIBEID_5-SS3_5-SS3-E12


title: TRIBEID_5-SS3_5-SS3-E11


title: TRIBEID_5-SS3_5-SS3-D7


title: TRIBEID_5-SS3_5-SS3-D5


title: TRIBEID_5-SS3_5-SS3-D6


title: TRIBEID_5-SS3_5-SS3-D4


title: TRIBEID_5-SS3_5-SS3-D2


title: TRIBEID_5-SS3_5-SS3-D3


title: TRIBEID_5-SS3_5-SS3-D1


title: TRIBEID_5-SS3_5-SS3-F4


title: TRIBEID_5-SS3_5-SS3-D12


title: TRIBEID_5-SS3_5-SS3-C7