title: CS23_E1S1, run18

description:
Library name: V2.5R2305180093
single nucleus RNA sequencing


title: CS23_E1S1, run17

status: Public on Mar 26 2026

type: SRA

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description:
Library name: V2.5R2305180092
single nucleus RNA sequencing

library_source: transcriptomic single cell

data_processing:
Gene count matrices were generated from FASTQ files by an in-house pipeline (BGI-Research, China).
The downstream analyses were performed using Scanpy package (V1.8.2).
Briefly, in the quality control step, cells with less than 1k genes, less than 2k counts, more than 10% mitochondrial genes, or more than 90 quantiles of total counts per library were filtered out from raw counts by scanpy.pp.filter_cells.
Genes that were captured in less than 3 cells were filtered out as well by scanpy.pp.filter_genes.
Assembly: GRCh38.p12
Supplementary files format and content: h5ad: raw counts, normalized counts and cell type annotation

molecule: polyA RNA

organism: Homo sapiens

source_name: embryo

extract_protocol:
Fresh frozen tissue were OCT embedded, and sagittal sections next to Stereo-seq section in five embryos (CS19E1, CS19E2, CS20E1, CS20E2 and CS23E1) were obtained for snRNA-seq.
Single-nucleus sequencing libraries were prepared with DNBelab C4 kits.

tag: tissue

value: embryo

tag: developmental stage

tag: Sex

value: Male


title: E21DCD371E, pVTA

city: La Jolla

first: Daniel

last: Munro

state: CA

address: 9500 Gilman Drive

department: Psychiatry

country: USA

institute: UC San Diego

description:
Library name: E21DCD371E
removed

library_source: transcriptomic

data_processing:
Expression levels were quantified directly from FASTQ files using kallisto v0.48. Transcript sequences from GRCr8 RefSeq were used as reference. Isoform-level counts were summed per gene to get gene expression counts.
Assembly: GRCr8
Supplementary files format and content: Log2-transformed read counts per gene per sample in BED format. Start/end coordinates indicate only the gene's TSS coordinate.

organism: Rattus norvegicus

source_name: Posterior ventral tegmental area

growth_protocol: Outbred laboratory rats

extract_protocol:
Unknown
Unknown

value: Posterior ventral tegmental area


title: E21DCD372A, pVTA

description: Library name: E21DCD372A


title: E21DCD3728, pVTA

description: Library name: E21DCD3728


title: E21DCD3725, pVTA

description:
Library name: E21DCD3725
Original label before genotype mismatch fix: E21DCD371E


title: CS23_E1S1, run16

description:
Library name: V2.5R2305180091
single nucleus RNA sequencing


title: CS23_E1S1, run13

description:
Library name: V2.5R2305180088
single nucleus RNA sequencing


title: CS23_E1S1, run14

description:
Library name: V2.5R2305180089
single nucleus RNA sequencing


title: E21DCD370F, pVTA

description: Library name: E21DCD370F


title: CS23_E1S1, run12

description:
Library name: V2.5R2305180087
single nucleus RNA sequencing


title: CS23_E1S1, run11

description:
Library name: V2.5R2305180086
single nucleus RNA sequencing


title: E21DCD370D, pVTA

description: Library name: E21DCD370D


title: CS23_E1S1, run9

description:
Library name: V2.5R2305180084
single nucleus RNA sequencing


title: CS23_E1S1, run10

description:
Library name: V2.5R2305180085
single nucleus RNA sequencing


title: E21DCD36EF, pVTA

description: Library name: E21DCD36EF


title: E21DCD3704, pVTA

description: Library name: E21DCD3704


title: E21DCD3703, pVTA

description: Library name: E21DCD3703


title: CS23_E1S1, run7

description:
Library name: V2.5R2305180082
single nucleus RNA sequencing


title: CS23_E1S1, run8

description:
Library name: V2.5R2305180083
single nucleus RNA sequencing


title: E21DCD36E1, pVTA

description: Library name: E21DCD36E1


title: E21DCD36E6, pVTA

description: Library name: E21DCD36E6


title: CS23_E1S1, run6

description:
Library name: V2.5R2305180081
single nucleus RNA sequencing


title: CS23_E1S1, run5

description:
Library name: V2.5R2305180080
single nucleus RNA sequencing


title: E21DCD36DF, pVTA

description: Library name: E21DCD36DF


title: E21DCD36DB, pVTA

description: Library name: E21DCD36DB


title: E21DCD36E0, pVTA

description: Library name: E21DCD36E0


title: CS23_E1S1, run15

description:
Library name: V2.5R2305180090
single nucleus RNA sequencing


title: E21DCD36D2, pVTA

description: Library name: E21DCD36D2


title: CS23_E1S1, run3

description:
Library name: V2.5R2305180078
single nucleus RNA sequencing


title: CS23_E1S1, run4

description:
Library name: V2.5R2305180079
single nucleus RNA sequencing


title: E21DCD36D7, pVTA

description: Library name: E21DCD36D7


title: E21DCD36AD, pVTA

description: Library name: E21DCD36AD


title: CS23_E1S1, run1

description:
Library name: V2.5R2305180076
single nucleus RNA sequencing


title: CS19_E1S3, run5

description:
Library name: V2.5R2305180040
single nucleus RNA sequencing

value: Female


title: E21DCD3706, pVTA

description: Library name: E21DCD3706


title: CS23_E1S1, run2

description:
Library name: V2.5R2305180077
single nucleus RNA sequencing


title: CS19_E1S3, run4

description:
Library name: V2.5R2305180039
single nucleus RNA sequencing


title: CS19_E1S3, run2

description:
Library name: V2.5R2305180037
single nucleus RNA sequencing


title: E21DCD36A2, pVTA

description: Library name: E21DCD36A2


title: E21DCD36BA, pVTA

description: Library name: E21DCD36BA


title: CS19_E1S3, run1

description:
Library name: V2.5R2305180036
single nucleus RNA sequencing


title: CS19_E1S3, run3

description:
Library name: V2.5R2305180038
single nucleus RNA sequencing


title: E21DCD367A, pVTA

description: Library name: E21DCD367A


title: E21DCD3678, pVTA

description: Library name: E21DCD3678


title: E21DCD3681, pVTA

description: Library name: E21DCD3681


title: CS19_E1S2, run5

description:
Library name: V2.5R2305180045
single nucleus RNA sequencing


title: CS19_E1S2, run4

description:
Library name: V2.5R2305180044
single nucleus RNA sequencing


title: CS19_E1S2, run3

description:
Library name: V2.5R2305180043
single nucleus RNA sequencing


title: E21DCD3672, pVTA

description: Library name: E21DCD3672


title: E21DCD366B, pVTA

description: Library name: E21DCD366B


title: E21DCD3671, pVTA

description: Library name: E21DCD3671


title: CS19_E1S2, run2

description:
Library name: V2.5R2305180042
single nucleus RNA sequencing


title: E21DCD3664, pVTA

description: Library name: E21DCD3664


title: E21DCD365F, pVTA

description: Library name: E21DCD365F


title: CS19_E1S2, run1

description:
Library name: V2.5R2305180041
single nucleus RNA sequencing


title: CS19_E1S1, run10

description:
Library name: V2.5R2305180029
single nucleus RNA sequencing


title: E21DCD365B, pVTA

description: Library name: E21DCD365B


title: CS19_E1S1, run7

description:
Library name: V2.5R2305180026
single nucleus RNA sequencing


title: CS19_E1S1, run5

description:
Library name: V2.5R2305180062
single nucleus RNA sequencing


title: E21DCD3656, pVTA

description: Library name: E21DCD3656


title: E21DCD3655, pVTA

description: Library name: E21DCD3655


title: CS19_E1S1, run6

description:
Library name: V2.5R2305180025
single nucleus RNA sequencing


title: E21DCD364A, pVTA

description: Library name: E21DCD364A


title: E21DCD367E, pVTA

description: Library name: E21DCD367E


title: E21DCD364D, pVTA

description: Library name: E21DCD364D


title: CS19_E1S1, run4

description:
Library name: V2.5R2305180061
single nucleus RNA sequencing


title: CS19_E1S1, run2

description:
Library name: V2.5R2305180059
single nucleus RNA sequencing


title: E21DCD3639, pVTA

description: Library name: E21DCD3639


title: E21DCD3644, pVTA

description: Library name: E21DCD3644


title: E21DCD362F, pVTA

description: Library name: E21DCD362F


title: CS19_E1S1, run3

description:
Library name: V2.5R2305180060
single nucleus RNA sequencing


title: CS19_E1S1, run8

description:
Library name: V2.5R2305180027
single nucleus RNA sequencing


title: E21DCD3640, pVTA

description: Library name: E21DCD3640


title: CS19_E1S1, run1

description:
Library name: V2.5R2305180058
single nucleus RNA sequencing


title: CS19_E1S1, run9

description:
Library name: V2.5R2305180028
single nucleus RNA sequencing


title: E21DCD362D, pVTA

description: Library name: E21DCD362D


title: E21DCD3635, pVTA

description: Library name: E21DCD3635


title: CS20_E2S4, run5

description:
Library name: V2.5R2305180056
single nucleus RNA sequencing


title: E21DCD3616, pVTA

description: Library name: E21DCD3616


title: sgHDAC2 3

city: Durham

first: Seth

last: Zimmerman

state: NC

address: 308 Research Dr.

institute: Duke University

description: Library name: Sample30

data_processing:
RNA-seq data was processed using the fastp toolkit to trim low-quality bases and sequencing adapters from the 3’ end of reads, then mapped to GRCh38 (downloaded from Ensembl, version 106) using the STAR RNA-seq alignment tool, and reads aligning to a single genomic location were summarized across genes.  For genes having an overlap of at least 10 reads, gene counts were normalized and differential expression was carried out using the DESeq2 Bioconductor package implemented for the R programming environment (R 4.3.0).  Consistent with the recommendation of the DESeq authors, independent filtering was utilized prior to calculating adjusted p-values and moderated log2 fold-changes were derived using the ashr package.
Assembly: GRch38
Supplementary files format and content: Transcript counts. Columns represent samples, rows represent genes.

molecule: total RNA

growth_protocol: RH4-flag cells were grown in RPMI+10% FBS.

extract_protocol:
For each sample, mRNA was isolated using RNeasy Plus Mini kits following the manufacturer’s instructions (Qiagen) from between 1 x 106 and 1 x 107 cells.  Extracted total RNA quality and concentration were assessed on Fragment Analyzer (Agilent Technologies) and Qubit 2.0 (Thermo Fisher Scientific), respectively.  All samples had an RQN > 7.
RNA-seq libraries were prepared using the commercially available KAPA Stranded mRNA-Seq Kit (Roche) using 500 ng of total RNA for each sample.  Illumina sequencing adapters were ligated to the output cDNA fragments and amplified to produce the final RNA-seq library with a dual-indexing approach for pooled library multiplex sequencing.

treatment_protocol: Cells were infected in a 6-well plate in 2 to 3 ml per well of RPMI media containing virus with of 8 µg/ml polybrene (Millipore Sigma) and spun 265 g for 1 hour.  After 4 to 6 hours at 37 °C, the cells were washed in 1x PBS and the media was replaced with RPMI supplemented with 10% FBS.  18 hours later, each infection was pooled into a 10 cm culture dish and selected withs or 2 µg/ml puromycin for at least 48 hours.

tag: cell line

tag: cell type

value: rhabdomyosarcoma

tag: genotype


title: E21DCD360D, pVTA

description: Library name: E21DCD360D


title: CS20_E2S4, run4

description:
Library name: V2.5R2305180055
single nucleus RNA sequencing


title: E21DCD3600, pVTA

description: Library name: E21DCD3600


title: E21DCD3603, pVTA

description: Library name: E21DCD3603


title: sgHDAC2 2

description: Library name: Sample29


title: CS20_E2S4, run3

description:
Library name: V2.5R2305180054
single nucleus RNA sequencing


title: CS20_E2S4, run6

description:
Library name: V2.5R2305180057
single nucleus RNA sequencing


title: sgHDAC2 1

description: Library name: Sample28


title: CS20_E2S4, run1

description:
Library name: V2.5R2305180052
single nucleus RNA sequencing


title: 933000320187873, pVTA

description: Library name: 933000320187873


title: AA1DCD67CE, pVTA

description: Library name: AA1DCD67CE


title: sgWWTR1 3

description: Library name: Sample27


title: 933000320187870, pVTA

description: Library name: 933000320187870


title: CS20_E2S4, run2

description:
Library name: V2.5R2305180053
single nucleus RNA sequencing


title: 933000320187872, pVTA

description: Library name: 933000320187872


title: CS20_E2S3, run6

description:
Library name: V2.5R2305180035
single nucleus RNA sequencing


title: sgWWTR1 2

description: Library name: Sample26


title: sgWWTR1 1

description: Library name: Sample25


title: 933000320187463, pVTA

description: Library name: 933000320187463


title: CS20_E2S3, run5

description:
Library name: V2.5R2305180034
single nucleus RNA sequencing


title: 933000320049149, pVTA

description: Library name: 933000320049149


title: 933000320049126, pVTA

description: Library name: 933000320049126


title: 933000320187858, pVTA

description: Library name: 933000320187858


title: AA1DCD6806, pVTA

description: Library name: AA1DCD6806


title: sgTYMS 3

description: Library name: Sample24


title: sgTYMS 2

description: Library name: Sample23


title: CS20_E2S3, run3

description:
Library name: V2.5R2305180032
single nucleus RNA sequencing


title: 933000320049093, pVTA

description: Library name: 933000320049093


title: CS20_E2S3, run4

description:
Library name: V2.5R2305180033
single nucleus RNA sequencing


title: 933000320049084, pVTA

description: Library name: 933000320049084


title: CS20_E2S3, run2

description:
Library name: V2.5R2305180031
single nucleus RNA sequencing


title: 933000320187471, pVTA

description: Library name: 933000320187471


title: 933000320049082, pVTA

description: Library name: 933000320049082


title: CS20_E2S3, run1

description:
Library name: V2.5R2305180030
single nucleus RNA sequencing


title: sgINO80 3

description: Library name: Sample21


title: 933000320049096, pVTA

description: Library name: 933000320049096


title: 933000320049074, pVTA

description: Library name: 933000320049074


title: 933000320049075, pVTA

description: Library name: 933000320049075


title: CS20_E2S2, run6

description:
Library name: V2.5R2305180051
single nucleus RNA sequencing


title: CS20_E2S2, run5

description:
Library name: V2.5R2305180050
single nucleus RNA sequencing


title: sgMAML1 3

description: Library name: Sample18


title: 933000320049066, pVTA

description: Library name: 933000320049066


title: sgINO80 2

description: Library name: Sample20


title: 933000320049068, pVTA

description: Library name: 933000320049068


title: 933000320049067, pVTA

description: Library name: 933000320049067


title: sgTYMS 1

description: Library name: Sample22


title: 933000320049079, pVTA

description: Library name: 933000320049079


title: 933000320049086, pVTA

description: Library name: 933000320049086


title: 933000320049056, pVTA

description: Library name: 933000320049056


title: 933000320049070, pVTA

description: Library name: 933000320049070


title: CS20_E2S2, run4

description:
Library name: V2.5R2305180049
single nucleus RNA sequencing


title: 933000320049063, pVTA

description: Library name: 933000320049063


title: CS20_E2S2, run3

description:
Library name: V2.5R2305180048
single nucleus RNA sequencing


title: 933000320049047, pVTA

description: Library name: 933000320049047


title: sgMAML1 2

description: Library name: Sample17


title: 933000320049038, pVTA

description: Library name: 933000320049038


title: sgINO80 1

description: Library name: Sample19


title: CS20_E2S2, run2

description:
Library name: V2.5R2305180047
single nucleus RNA sequencing


title: sgMAML1 1

description: Library name: Sample16


title: 933000320049037, pVTA

description: Library name: 933000320049037


title: sgINO80D 3

description: Library name: Sample15


title: CS20_E2S2, run1

description:
Library name: V2.5R2305180046
single nucleus RNA sequencing


title: 933000320049036, pVTA

description: Library name: 933000320049036


title: sgINO80D 2

description: Library name: Sample14


title: 933000320048896, pVTA

description: Library name: 933000320048896


title: 933000320049029, pVTA

description: Library name: 933000320049029


title: sgINO80D 1

description: Library name: Sample13


title: 933000320048862, pVTA

description: Library name: 933000320048862


title: CS20_E2S1, run5

description:
Library name: V2.5R2305180023
single nucleus RNA sequencing


title: CS20_E2S1, run4

description:
Library name: V2.5R2305180022
single nucleus RNA sequencing


title: 933000320048876, pVTA

description: Library name: 933000320048876


title: 933000320048883, pVTA

description: Library name: 933000320048883


title: 933000320048893, pVTA

description: Library name: 933000320048893


title: CS20_E2S1, run2

description:
Library name: V2.5R2305180020
single nucleus RNA sequencing


title: 933000320048835, pVTA

description: Library name: 933000320048835


title: 933000320048860, pVTA

description: Library name: 933000320048860


title: 933000320048840, pVTA

description: Library name: 933000320048840


title: 933000320048831, pVTA

description: Library name: 933000320048831


title: CS20_E2S1, run3

description:
Library name: V2.5R2305180021
single nucleus RNA sequencing


title: CS20_E2S1, run6

description:
Library name: V2.5R2305180024
single nucleus RNA sequencing


title: 933000320048829, pVTA

description: Library name: 933000320048829


title: sgNCOA2 2

description: Library name: Sample11


title: CS20_E2S1, run1

description:
Library name: V2.5R2305180019
single nucleus RNA sequencing


title: sgNCOA1 2

description: Library name: Sample8


title: sgNCOA2 1

description: Library name: Sample10


title: 933000320048823, pVTA

description: Library name: 933000320048823


title: 933000320048711, pVTA

description: Library name: 933000320048711


title: sgNCOA2 3

description: Library name: Sample12


title: 933000320048725, pVTA

description: Library name: 933000320048725


title: Day10 Pralatrexate Repeat3

description:
Library name: Sample9
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3

library_source: genomic

data_processing:
Sequencing reads were de-multiplexed using fastx_barcode_splitter (v0.0.13) to identify inline barcodes and aligned to the reference library using bowtie (v1.0.0), allowing for 0 mismatches.  Sample sgRNA read counts were first normalized to total reads/sample.  sgRNA fold-change values were then calculated by comparing in vitro and in vivo sample sgRNA counts to their paired initial sample sgRNA count.  Gene target enrichment scores were then calculated by averaging the 5 sgRNA fold-change values within a sample.  Average sample enrichment fold-changes distributions were normalized by first zeroing each sample on the average enrichment of non-targeting control sgRNAs and then calculating a z-score.  To compare in vitro enrichment to in vivo enrichment, replicate sample z-scores were averaged and compared by T-test.  Resultant p-values were adjusted by calculating false discovery rates.
Supplementary files format and content: txt file contains raw sgRNA counts per sample
Library strategy: CRISPR Screen

molecule: genomic DNA

growth_protocol: RH4 Cells were grown in RPMI supplemented with 10% FBS

extract_protocol:
Genomic DNA was isolated using an ammonium acetate precipitation method.
The sgRNA sequences from each sample were PCR amplified using primers with Illumina adaptors and indexes for multiplexing as described.

treatment_protocol: Cells were treated with 1.5 nM pralatrexate or vehicle control and passaged at 4 day intervals for 10 days.

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion

tag: treatment

value: Kinome library + Pralatrexate


title: sgNCOA1 1

description: Library name: Sample7


title: 933000320048639, pVTA

description: Library name: 933000320048639


title: 933000320048856, pVTA

description: Library name: 933000320048856


title: sgNCOA1 3

description: Library name: Sample9


title: Day10 Pralatrexate Repeat2

description:
Library name: Sample8
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: 933000320048635, pVTA

description: Library name: 933000320048635


title: 933000320048356, pVTA

description:
Library name: 933000320048356
Original label before genotype mismatch fix: 933000320048575


title: sgFOXO1 3

description: Library name: Sample6


title: 933000320048574, pVTA

description: Library name: 933000320048574


title: sgFOXO1 2

description: Library name: Sample5


title: Day10 Control Repeat2

description:
Library name: Sample5
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3

value: Kinome library


title: Day10 Control Repeat3

description:
Library name: Sample6
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: 933000320048573, pVTA

description: Library name: 933000320048573


title: sgFOXO1 1

description: Library name: Sample4


title: 933000320048565, pVTA

description:
Library name: 933000320048565
Original label before genotype mismatch fix: 933000320048572


title: 933000320048567, pVTA

description: Library name: 933000320048567


title: 933000320048563, pVTA

description: Library name: 933000320048563


title: sg Non-targeting control 2

description: Library name: Sample2


title: sg Non-targeting control 1

description: Library name: Sample1


title: 933000320048557, pVTA

description: Library name: 933000320048557


title: 933000320048559, pVTA

description: Library name: 933000320048559


title: Supt6 KO mouse_4

city: Ghuangzhou

first: Yushuang

last: Sun

address: NO.2 Zhongshan Road

department: Institute of Precision Medicine

institute: The First Affiliated Hospital of Sun Yat-sen University

description: Library name: Sample 9

data_processing:
The raw data obtained from sequencing were filtered using SOAPnuke to remove. Software Version: 1.5.6
Firstly, HISAT anchors partial sequences of each read to the genome using global FM indexing; then, it utilizes local indexing of these alignment positions to align the remaining sequences of each read to extend the alignment region. Software Version: 2.2.1
Clean data was aligned to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression quantification was performed using RSEM (v1.3.1) software, and gene expression clustering heatmaps across different samples were generated using pheatmap (v1.0.8). DESeq2 (v1.4.5)  was employed for differential gene detection, with criteria set as Q value ≤ 0.05 or FDR ≤ 0.001.
Assembly: mm10
Supplementary files format and content: Text file includes raw counts for each sample

organism: Mus musculus

source_name: ear

growth_protocol: The mice were housed in an SPF environment.

extract_protocol:
RNA was isolated using Eastep® Super Total RNA Extraction Kit (Promega).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

treatment_protocol: Supt6 knockdown induced by tamoxifen injection

value: ear

value: Supt6 knockdown


title: 933000320048570, pVTA

description: Library name: 933000320048570


title: Supt6 KO mouse_3

description: Library name: Sample 8

value: Supt6 knockdown induced by tamoxifen injection


title: Day10 Pralatrexate Repeat1

description:
Library name: Sample7
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: Day10 Control Repeat1

description:
Library name: Sample4
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: 933000320048571, pVTA

description: Library name: 933000320048571


title: sg Non-targeting control 3

description: Library name: Sample3


title: 933000320048555, pVTA

description: Library name: 933000320048555


title: N41

city: Jinhua

first: Yi

last: Zhan

address: houshan Road 266

institute: Jinhua Maternal and Child Health Care Hospital

description:
Library name: SAMPLES 23
FPKM.N41

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: pbmcs

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

tag: disease

value: healthy

value: pbmcs


title: 933000320048556, pVTA

description: Library name: 933000320048556


title: 933000320048552, pVTA

description: Library name: 933000320048552


title: Supt6 KO mouse_2

description: Library name: Sample 7


title: 933000320048551, pVTA

description: Library name: 933000320048551


title: 933000320048554, pVTA

description: Library name: 933000320048554


title: 933000320048512, pVTA

description: Library name: 933000320048512


title: N37

description:
Library name: SAMPLES 22
FPKM.N37


title: 933000320048572, pVTA

description:
Library name: 933000320048572
Original label before genotype mismatch fix: 933000320048565


title: Supt6 KO mouse_1

description: Library name: Sample 6


title: Wild-type mouse_4

description: Library name: Sample 4

value: WT


title: N33

description:
Library name: SAMPLES 21
FPKM.N33


title: N30

description:
Library name: SAMPLES 20
FPKM.N30


title: Wild-type mouse_5

description: Library name: Sample 5


title: Wild-type mouse_3

description: Library name: Sample 3


title: unknown-PL3-8, PL

description:
Library name: unknown-PL3-8
removed_no_matching_genotype_sample

source_name: Prelimbic cortex

value: Prelimbic cortex


title: E21DCD36B0, PL

description:
Library name: E21DCD36B0
Original label before genotype mismatch fix: unknown-PL3-9


title: N29

description:
Library name: SAMPLES 19
FPKM.N29


title: 933000320048575, pVTA

description:
Library name: 933000320048575
Original label before genotype mismatch fix: 933000320048356


title: 933000320048422, pVTA

description: Library name: 933000320048422


title: unknown-PL3-7, PL

description:
Library name: unknown-PL3-7
removed_no_matching_genotype_sample


title: N26

description:
Library name: SAMPLES 18
FPKM.N26


title: unknown-PL3-6, PL

description:
Library name: unknown-PL3-6
removed_no_matching_genotype_sample


title: N25

description:
Library name: SAMPLES 17
FPKM.N25


title: Wild-type mouse_1

description: Library name: Sample 1


title: 933000320048351, pVTA

description: Library name: 933000320048351


title: Baseline Repeat 3

description:
Library name: Sample3
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: E21DCD37A1, PL

description:
Library name: E21DCD37A1
Original label before genotype mismatch fix: unknown-PL3-44


title: N23

description:
Library name: SAMPLES 15
FPKM.N23


title: Wild-type mouse_2

description: Library name: Sample 2


title: E21DCD37BB, PL

description:
Library name: E21DCD37BB
Original label before genotype mismatch fix: unknown-PL3-43


title: E21DCD37D8, PL

description:
Library name: E21DCD37D8
Original label before genotype mismatch fix: unknown-PL3-42


title: E21DCD377D, PL

description:
Library name: E21DCD377D
Original label before genotype mismatch fix: unknown-PL3-41


title: E21DCD3780, PL

description:
Library name: E21DCD3780
Original label before genotype mismatch fix: unknown-PL3-38


title: N24

description:
Library name: SAMPLES 16
FPKM.N24


title: N21

description:
Library name: SAMPLES 13
FPKM.N21


title: E21DCD3610, PL

description:
Library name: E21DCD3610
Original label before genotype mismatch fix: unknown-PL3-37


title: E21DCD37CD, PL

description:
Library name: E21DCD37CD
Original label before genotype mismatch fix: unknown-PL3-36


title: Baseline Repeat2

description:
Library name: Sample2
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: E21DCD363A, PL

description:
Library name: E21DCD363A
Original label before genotype mismatch fix: unknown-PL3-39


title: unknown-PL3-35, PL

description:
Library name: unknown-PL3-35
removed_no_matching_genotype_sample


title: K39

description:
Library name: SAMPLES 12
FPKM.K39

value: Kawasaki


title: unknown-PL3-34, PL

description:
Library name: unknown-PL3-34
removed_no_matching_genotype_sample


title: hiPSC, siLMNA mCh, rep4,  tech rep 2

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: siLMNA mCh rep4 tech rep 2

data_processing:
Cut&Run: Adapters were trimmed from fastq files using TrimGalore with default parameters (ver 0.6.4 using Cutadapt 4.2, (Krueger, 2023). The resulting reads were mapped to the hg38 assembly with bowtie2 (Langmead and Salzberg, 2012) with the parameters -X 2000 -N 1 --local --dovetail. Duplicates were marked using Picard MarkDuplicates (Broad Institute) and removed for downstream analysis. LADs were called using the Enriched Domain Detector (Lund et al., 2014) with parameters required_fraction_of_informative_bins=0.98, p_hat_CI_method=agresti_coull, log_ratio_bin_size=10, fdr=0.05, and gap parameter 4, using LMNB1 as the signal file and matched IgG file as background. Genome-wide LMNB1 signal was calculated for visualization and downstream analysis by counting reads detected in each 1kb or 10kb genomic bin using deeptools multiBigwigSummary (Ramirez et al., 2016), z-scores were calculated excluding any bin with no reads from any sample mapped, and then were smoothed using a rolling mean of the flanking 5 windows to each side.
RNAseq: Adapters were trimmed as described above in Cut&Tag analysis section. Reads were mapped to the hg38 genome with STAR v2.7.10a (Dobin et al., 2013) with the parameters --genomeSAindexNbases 14 --outFilterScoreMinOverLread 0.9 --outFilterMatchNmin 16 --outFilterMatchNoverLmax 0.05 --alignIntronMax 100000, with the additional parameter --peOverlapNbasesMin 5 for paired-end reads. Duplicates were marked with Picard as described above and excluded from count and differential expression analysis. Counts on exons of genes from the NCBI RefSeq Select hg38 annotation (Goldfarb et al., 2025)  were calculated using an in-house R script utilizing summarizeOverlaps from the GenomicRanges package (Lawrence et al., 2013).
Assembly: hg38
Supplementary files format and content: zscore bws: bigwig signal files containing zscores called in 10kb window and smoothed using a rolling mean of the flanking 5 windows to each side
Supplementary files format and content: RNA.counts.txt: number of reads mapped to exons of each gene from RNA-seq samples

source_name: NCardia

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS (16000044; Gibco), 1% Penicillin-Streptomycin (15140122; Gibco), and 2% B-27 (17504044; Gibco).

extract_protocol:
RNA was isolated from hiPSC-CMs 48 hours after treatment with either scramble control or LMNA siRNA (+mChery control) using TRIzol reagent, following manufacturer’s protocol (15596018, Invitrogen).
CUT&RUN was performed using ~150,000 hiPSC-CMs and LMNB1 antibody or control IgG antibody as described in Skene & Henikoff 2018.
RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich for poly-A tailed RNA molecules. RNA-seq library quality was analyzed by TapeStation (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).
CUT&RUN DNA concentrations were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for multiplex sequencing. Library quality was analyzed by TapeStation (Agilent Genomics) and quantified using qPCR (Kapa Biosystems).

treatment_protocol: On day 0, cells were treated with siRNAs, against either a non-targeting scramble control (D-001210-05-20; Horizon) or LMNA (SMARTPool, L-004978-00-0005; Horizon) at a concentration of 5nM using Lipofectamine RNAiMax (13778150; ThermoFisher) transfection reagent diluted in Opti-MEM (31985062; Gibco).  Cells were treated with either control mCherry AdV (1767; VectorBiolabs) or dominant-negative KASH AdV (VectorBiolabs) at a concentration of ~500 PFU/mL.

value: NCardia

value: hiPSC-cardiomyocyte

value: siLMNA + mCh


title: hiPSC, siLMNA mCh, rep2,  tech rep 2

description: Library name: siLMNA mCh rep2  tech rep 2


title: hiPSC, siLMNA mCh, rep1,  tech rep 2

description: Library name: siLMNA mCh rep1 tech rep 2


title: K43

description:
Library name: SAMPLES 11
FPKM.K43


title: hiPSC, siLMNA mCh, rep3,  tech rep 2

description: Library name: siLMNA mCh rep3 tech rep 2


title: unknown-PL3-3, PL

description:
Library name: unknown-PL3-3
removed_no_matching_genotype_sample


title: K50

description:
Library name: SAMPLES 9
FPKM.K50


title: K54

description:
Library name: SAMPLES 10
FPKM.K54


title: hiPSC, siScr mCh, rep3,  tech rep 2

description: Library name: siScr mCh rep3 tech rep 2

value: siScr + mCh


title: E21DCD37E1, PL

description:
Library name: E21DCD37E1
Original label before genotype mismatch fix: unknown-PL3-40


title: unknown-PL3-31, PL

description:
Library name: unknown-PL3-31
removed_no_matching_genotype_sample


title: unknown-PL3-33, PL

description:
Library name: unknown-PL3-33
removed_no_matching_genotype_sample


title: unknown-PL3-32, PL

description:
Library name: unknown-PL3-32
removed_no_matching_genotype_sample


title: Baseline Repeat1

description:
Library name: Sample1
Column Names for Processed file: sgRNA gene Baseline_1 Baseline_2 Baseline_3 Control_1 Control_2 Control_3 Prala_1 Prala_2 Prala_3


title: unknown-PL3-28, PL

description:
Library name: unknown-PL3-28
removed_no_matching_genotype_sample


title: unknown-PL3-4, PL

description:
Library name: unknown-PL3-4
removed_no_matching_genotype_sample


title: hiPSC, siScr mCh, rep1,  tech rep 2

description: Library name: siScr mCh rep1 tech rep 2


title: unknown-PL3-30, PL

description:
Library name: unknown-PL3-30
removed_no_matching_genotype_sample


title: K48

description:
Library name: SAMPLES 8
FPKM.K48


title: unknown-PL3-24, PL

description:
Library name: unknown-PL3-24
removed_no_matching_genotype_sample


title: unknown-PL3-29, PL

description:
Library name: unknown-PL3-29
removed_no_matching_genotype_sample


title: hiPSC, siScr mCh, rep2,  tech rep 2

description: Library name: siScr mCh rep2 tech rep 2


title: unknown-PL3-25, PL

description:
Library name: unknown-PL3-25
removed_no_matching_genotype_sample


title: E21DCD3708, PL

description:
Library name: E21DCD3708
Original label before genotype mismatch fix: unknown-PL3-5


title: unknown-PL3-26, PL

description:
Library name: unknown-PL3-26
removed_no_matching_genotype_sample


title: K41

description:
Library name: SAMPLES 7
FPKM.K41


title: K37

description:
Library name: SAMPLES 6
FPKM.K37


title: hiPSC, siLMNA mCh, rep3,  tech rep 1

description: Library name: siLMNA mCh rep3 tech rep 1


title: unknown-PL3-23, PL

description:
Library name: unknown-PL3-23
removed_no_matching_genotype_sample


title: hiPSC, siLMNA mCh, rep4,  tech rep 1

description: Library name: siLMNA mCh rep4 tech rep 1


title: K36

description:
Library name: SAMPLES 5
FPKM.K36


title: unknown-PL3-27, PL

description:
Library name: unknown-PL3-27
removed_no_matching_genotype_sample


title: K32

description:
Library name: SAMPLES 3
FPKM.K32


title: hiPSC, siLMNA mCh, rep2,  tech rep 1

description: Library name: siLMNA mCh rep2  tech rep 1


title: unknown-PL3-22, PL

description:
Library name: unknown-PL3-22
removed_no_matching_genotype_sample


title: unknown-PL3-20, PL

description:
Library name: unknown-PL3-20
removed_no_matching_genotype_sample


title: unknown-PL3-21, PL

description:
Library name: unknown-PL3-21
removed_no_matching_genotype_sample


title: hiPSC, siScr mCh, rep2,  tech rep 1

description: Library name: siScr mCh rep2 tech rep 1


title: unknown-PL3-2, PL

description:
Library name: unknown-PL3-2
removed_no_matching_genotype_sample


title: hiPSC, siLMNA mCh, rep1,  tech rep 1

description: Library name: siLMNA mCh rep1 tech rep 1


title: K33

description:
Library name: SAMPLES 4
FPKM.K33


title: hiPSC, siScr mCh, rep3,  tech rep 1

description: Library name: siScr mCh rep3 tech rep 1


title: unknown-PL3-19, PL

description:
Library name: unknown-PL3-19
removed_no_matching_genotype_sample


title: unknown-PL3-15, PL

description:
Library name: unknown-PL3-15
removed_no_matching_genotype_sample


title: unknown-PL3-18, PL

description:
Library name: unknown-PL3-18
removed_no_matching_genotype_sample


title: unknown-PL3-17, PL

description:
Library name: unknown-PL3-17
removed_no_matching_genotype_sample


title: unknown-PL3-16, PL

description:
Library name: unknown-PL3-16
removed_no_matching_genotype_sample


title: K30

description:
Library name: SAMPLES 2
FPKM.K30


title: N22

description:
Library name: SAMPLES 14
FPKM.N22


title: hiPSC, siScr mCh, rep1,  tech rep 1

description: Library name: siScr mCh rep1 tech rep 1


title: Blood, Control, RNA-seq, S146

city: Madrid

first: Ana I

last: Fernandez-Avila

state: Madrid

address: C/ Doctor Esquerdo, 46

department: Cardiology

country: Spain

institute: Hospital GU Gregorio Marañon

description:
Library name: Control9
column_name_in_FPKM_allSamples: Control9

data_processing:
Sequencing was conducted in four randomized batches. FASTQ files from sequencing were aligned to the reference genome (hg38) with and transcript quantification was conducted with Salmon
FPKM were extracted with DESeq2 in a generalized linear modeling, adjusting for age, sex, body surface area, and sequencing batch
Assembly: hg38
Supplementary files format and content: FPKM in a csv file, samples (columns) and genes (rows)

source_name: whole blood

extract_protocol:
Tempus collection tube_Tempus RNA isolation kit
TruSeq Stranded Total RNA Library Prep Globin Kit , following guide

value: whole blood

value: Male

tag: sample group

value: Control

tag: batch


title: Blood, Control, RNA-seq, S145

description:
Library name: Control7
column_name_in_FPKM_allSamples: Control7

value: Female


title: REI_POWR353

type: genomic

city: Atlanta

first: Alicia

middle: K

last: Smith

state: GA

address: 101 Woodruff Circle NE

institute: Emory University

hyb_protocol: Bisulfite conveted DNA was fragmented and hybridized according to MethylationEPICv2 (Illumina) standard protocol

scan_protocol: Array was imaged with HiScan and standard Illumina settings

data_processing:
Enmix package
*processed value definition: Average betas

label: Cy3, Cy5

source_name: Blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from blood using QiaQuick (Qiagen) kit using standard protocol

value: Blood

tag: subject group

value: Excluded


title: unknown-PL3-13, PL

description:
Library name: unknown-PL3-13
removed_no_matching_genotype_sample


title: unknown-PL3-1, PL

description:
Library name: unknown-PL3-1
removed_no_matching_genotype_sample


title: N47

description:
Library name: SAMPLES 24
FPKM.N47


title: Blood, Control, RNA-seq, S144

description:
Library name: Control6
column_name_in_FPKM_allSamples: Control6


title: Blood, Control, RNA-seq, S143

description:
Library name: Control5
column_name_in_FPKM_allSamples: Control5


title: E21DCD37BF, PL

description: Library name: E21DCD37BF


title: Blood, Control, RNA-seq, S142

description:
Library name: Control4
column_name_in_FPKM_allSamples: Control4


title: E21DCD37B9, PL

description: Library name: E21DCD37B9


title: Blood, Control, RNA-seq, S140

description:
Library name: Control31
column_name_in_FPKM_allSamples: Control31


title: REI_POWR196


title: REI_POWR405


title: REI_POWR233


title: Blood, Control, RNA-seq, S138

description:
Library name: Control3
column_name_in_FPKM_allSamples: Control3


title: E21DCD3766, PL

description: Library name: E21DCD3766


title: REI_POWR366


title: Blood, Control, RNA-seq, S137

description:
Library name: Control29
column_name_in_FPKM_allSamples: Control29


title: REI_POWR209


title: Blood, Control, RNA-seq, S135

description:
Library name: Control27
column_name_in_FPKM_allSamples: Control27


title: REI_POWR385


title: REI_POWR1012


title: K29

description:
Library name: SAMPLES 1
FPKM.K29


title: E21DCD37DE, PL

description: Library name: E21DCD37DE


title: E21DCD3781, PL

description: Library name: E21DCD3781


title: E21DCD3790, PL

description: Library name: E21DCD3790


title: Blood, Control, RNA-seq, S141

description:
Library name: Control32
column_name_in_FPKM_allSamples: Control32


title: unknown-PL3-14, PL

description:
Library name: unknown-PL3-14
removed_no_matching_genotype_sample


title: E21DCD37ED, PL

description: Library name: E21DCD37ED


title: unknown-PL3-12, PL

description:
Library name: unknown-PL3-12
removed_no_matching_genotype_sample


title: Blood, Control, RNA-seq, S139

description:
Library name: Control30
column_name_in_FPKM_allSamples: Control30


title: REI_POWR1005


title: E21DCD37EF, PL

description: Library name: E21DCD37EF


title: E21DCD37F1, PL

description: Library name: E21DCD37F1


title: unknown-PL3-11, PL

description:
Library name: unknown-PL3-11
removed_no_matching_genotype_sample


title: unknown-PL3-10, PL

description:
Library name: unknown-PL3-10
removed_no_matching_genotype_sample


title: E21DCD37BE, PL

description: Library name: E21DCD37BE


title: E21DCD375F, PL

description: Library name: E21DCD375F


title: E21DCD375C, PL

description: Library name: E21DCD375C


title: E21DCD37B2, PL

description: Library name: E21DCD37B2


title: E21DCD375A, PL

description: Library name: E21DCD375A


title: E21DCD3753, PL

description: Library name: E21DCD3753


title: REI_POWR234


title: E21DCD3737, PL

description: Library name: E21DCD3737


title: E21DCD3739, PL

description: Library name: E21DCD3739


title: Blood, Control, RNA-seq, S136

description:
Library name: Control28
column_name_in_FPKM_allSamples: Control28


title: E21DCD3728, PL

description: Library name: E21DCD3728


title: REI_POWR615

value: Infertile


title: E21DCD3745, PL

description: Library name: E21DCD3745


title: REI_POWR782


title: REI_POWR594


title: E21DCD372A, PL

description: Library name: E21DCD372A


title: E21DCD370D, PL

description: Library name: E21DCD370D


title: Blood, Control, RNA-seq, S134

description:
Library name: Control26
column_name_in_FPKM_allSamples: Control26


title: Blood, Control, RNA-seq, S133

description:
Library name: Control25
column_name_in_FPKM_allSamples: Control25


title: E21DCD36EF, PL

description: Library name: E21DCD36EF


title: REI_POWR522


title: Blood, Control, RNA-seq, S131

description:
Library name: Control23
column_name_in_FPKM_allSamples: Control23


title: REI_POWR607


title: E21DCD371E, PL

description: Library name: E21DCD371E


title: Blood, Control, RNA-seq, S132

description:
Library name: Control24
column_name_in_FPKM_allSamples: Control24


title: E21DCD3725, PL

description: Library name: E21DCD3725


title: E21DCD3704, PL

description: Library name: E21DCD3704


title: E21DCD36D7, PL

description: Library name: E21DCD36D7


title: Blood, Control, RNA-seq, S130

description:
Library name: Control21
column_name_in_FPKM_allSamples: Control21


title: REI_POWR593


title: E21DCD36E6, PL

description: Library name: E21DCD36E6


title: E21DCD36E1, PL

description: Library name: E21DCD36E1


title: REI_POWR804


title: Blood, Control, RNA-seq, S129

description:
Library name: Control20
column_name_in_FPKM_allSamples: Control20


title: E21DCD36DB, PL

description: Library name: E21DCD36DB


title: E21DCD36D2, PL

description: Library name: E21DCD36D2


title: E21DCD367A, PL

description: Library name: E21DCD367A


title: E21DCD36A2, PL

description: Library name: E21DCD36A2


title: Blood, Control, RNA-seq, S127

description:
Library name: Control19
column_name_in_FPKM_allSamples: Control19


title: E21DCD368C, PL

description: Library name: E21DCD368C


title: REI_POWR272


title: Blood, Control, RNA-seq, S126

description:
Library name: Control18
column_name_in_FPKM_allSamples: Control18


title: REI_POWR806


title: REI_POWR636


title: E21DCD3678, PL

description: Library name: E21DCD3678


title: E21DCD366B, PL

description: Library name: E21DCD366B


title: E21DCD36DF, PL

description: Library name: E21DCD36DF


title: REI_POWR572


title: E21DCD3672, PL

description: Library name: E21DCD3672


title: Blood, Control, RNA-seq, S124

description:
Library name: Control16
column_name_in_FPKM_allSamples: Control16


title: E21DCD3664, PL

description: Library name: E21DCD3664


title: E21DCD365B, PL

description: Library name: E21DCD365B


title: E21DCD3656, PL

description: Library name: E21DCD3656


title: Blood, Control, RNA-seq, S125

description:
Library name: Control17
column_name_in_FPKM_allSamples: Control17


title: Blood, Control, RNA-seq, S123

description:
Library name: Control15
column_name_in_FPKM_allSamples: Control15


title: REI_POWR687


title: REI_POWR1216


title: E21DCD3655, PL

description: Library name: E21DCD3655


title: Blood, Control, RNA-seq, S128

description:
Library name: Control2
column_name_in_FPKM_allSamples: Control2


title: E21DCD3644, PL

description: Library name: E21DCD3644


title: E21DCD36BA, PL

description: Library name: E21DCD36BA


title: E21DCD3640, PL

description: Library name: E21DCD3640


title: REI_POWR1234


title: Blood, Control, RNA-seq, S122

description:
Library name: Control14
column_name_in_FPKM_allSamples: Control14


title: E21DCD362F, PL

description: Library name: E21DCD362F


title: REI_POWR664


title: E21DCD3639, PL

description: Library name: E21DCD3639


title: Blood, Control, RNA-seq, S121

description:
Library name: Control13
column_name_in_FPKM_allSamples: Control13


title: REI_POWR613


title: Blood, Control, RNA-seq, S120

description:
Library name: Control12
column_name_in_FPKM_allSamples: Control12


title: E21DCD3671, PL

description: Library name: E21DCD3671


title: REI_POWR739


title: E21DCD3603, PL

description: Library name: E21DCD3603


title: E21DCD3600, PL

description: Library name: E21DCD3600


title: Blood, Control, RNA-seq, S119

description:
Library name: Control11
column_name_in_FPKM_allSamples: Control11


title: 933000320187873, PL

description: Library name: 933000320187873


title: E21DCD360D, PL

description: Library name: E21DCD360D


title: 933000320187870, PL

description: Library name: 933000320187870


title: REI_POWR614


title: Blood, Control, RNA-seq, S118

description:
Library name: Control10
column_name_in_FPKM_allSamples: Control10


title: Blood, Control, RNA-seq, S117

description:
Library name: Control1
column_name_in_FPKM_allSamples: Control1


title: REI_POWR484


title: 933000320187869, PL

description:
Library name: 933000320187869
removed


title: 933000320187858, PL

description: Library name: 933000320187858


title: Blood, HTPII,  S116

description:
Library name: 8A-454
column_name_in_FPKM_allSamples: 8A-454

value: HTP


title: 933000320187471, PL

description: Library name: 933000320187471


title: Blood, HTP_II, RNA-seq, S115

description:
Library name: 8A-010
column_name_in_FPKM_allSamples: 8A-010


title: 933000320187463, PL

description: Library name: 933000320187463


title: 933000320187462, PL

description: Library name: 933000320187462


title: Blood, HTP_II, RNA-seq, S114

description:
Library name: 8A-008
column_name_in_FPKM_allSamples: 8A-008


title: REI_POWR1224


title: E21DCD362D, PL

description: Library name: E21DCD362D


title: REI_POWR807


title: 933000320049126, PL

description: Library name: 933000320049126


title: REI_POWR577


title: 933000320049096, PL

description: Library name: 933000320049096


title: Blood, HTP_II, RNA-seq, S113

description:
Library name: 8A-007
column_name_in_FPKM_allSamples: 8A-007


title: 933000320049149, PL

description: Library name: 933000320049149


title: 933000320187872, PL

description: Library name: 933000320187872


title: 933000320049093, PL

description: Library name: 933000320049093


title: Blood, HTP_II, RNA-seq, S112

description:
Library name: 8A-004
column_name_in_FPKM_allSamples: 8A-004


title: REI_POWR1020


title: REI_POWR551


title: 933000320049084, PL

description: Library name: 933000320049084


title: Blood, HTP_II, RNA-seq, S111

description:
Library name: 8A-003
column_name_in_FPKM_allSamples: 8A-003


title: Blood, HTP_II, RNA-seq, S110

description:
Library name: 8A-002
column_name_in_FPKM_allSamples: 8A-002


title: 933000320049079, PL

description: Library name: 933000320049079


title: REI_POWR552


title: 933000320049080, PL

description: Library name: 933000320049080


title: 933000320049075, PL

description: Library name: 933000320049075


title: 933000320049074, PL

description: Library name: 933000320049074


title: 933000320049070, PL

description: Library name: 933000320049070


title: Blood, HTP_II, RNA-seq, S109

description:
Library name: 8A-001
column_name_in_FPKM_allSamples: 8A-001


title: 933000320049068, PL

description: Library name: 933000320049068


title: 933000320049086, PL

description: Library name: 933000320049086


title: 933000320049066, PL

description: Library name: 933000320049066


title: REI_POWR567


title: REI_POWR348


title: Blood, HTP_II, RNA-seq, S108

description:
Library name: 7A-009
column_name_in_FPKM_allSamples: 7A-009


title: REI_POWR410


title: 933000320049082, PL

description: Library name: 933000320049082


title: Blood, HTP_II, RNA-seq, S107

description:
Library name: 7A-008
column_name_in_FPKM_allSamples: 7A-008


title: REI_POWR826


title: 933000320049047, PL

description: Library name: 933000320049047


title: 933000320049038, PL

description: Library name: 933000320049038


title: 933000320049063, PL

description: Library name: 933000320049063


title: 933000320049067, PL

description: Library name: 933000320049067


title: REI_POWR207


title: 933000320049056, PL

description: Library name: 933000320049056


title: 933000320049036, PL

description: Library name: 933000320049036


title: 933000320048896, PL

description: Library name: 933000320048896


title: 933000320049029, PL

description: Library name: 933000320049029


title: Blood, HTP_II, RNA-seq, S104

description:
Library name: 7A-005
column_name_in_FPKM_allSamples: 7A-005


title: Blood, HTP_II, RNA-seq, S105

description:
Library name: 7A-006
column_name_in_FPKM_allSamples: 7A-006


title: REI_POWR443


title: Blood, HTP_II, RNA-seq, S103

description:
Library name: 7A-002
column_name_in_FPKM_allSamples: 7A-002


title: Blood, HTP_II, RNA-seq, S102

description:
Library name: 5A-015
column_name_in_FPKM_allSamples: 5A-015


title: 933000320049037, PL

description: Library name: 933000320049037


title: REI_POWR190


title: 933000320048876, PL

description: Library name: 933000320048876


title: 933000320048893, PL

description: Library name: 933000320048893


title: 933000320048883, PL

description: Library name: 933000320048883


title: REI_POWR1017


title: 933000320048862, PL

description: Library name: 933000320048862


title: REI_POWR846


title: REI_POWR462


title: REI_POWR241


title: 933000320048856, PL

description: Library name: 933000320048856


title: 933000320048860, PL

description: Library name: 933000320048860


title: 933000320048840, PL

description: Library name: 933000320048840


title: Blood, HTP_II, RNA-seq, S99

description:
Library name: 5A-012c
column_name_in_FPKM_allSamples: 5A-012c


title: 933000320048867, PL

description: Library name: 933000320048867


title: Blood, HTP_II, RNA-seq, S100

description:
Library name: 5A-013
column_name_in_FPKM_allSamples: 5A-013


title: REI_POWR350


title: 933000320048835, PL

description: Library name: 933000320048835


title: Blood, HTP_II, RNA-seq, S101

description:
Library name: 5A-014
column_name_in_FPKM_allSamples: 5A-014


title: REI_POWR398


title: 933000320048831, PL

description: Library name: 933000320048831


title: 933000320048826, PL

description: Library name: 933000320048826


title: 933000320048823, PL

description: Library name: 933000320048823


title: Blood, HTP_II, RNA-seq, S97

description:
Library name: 5A-010
column_name_in_FPKM_allSamples: 5A-010


title: REI_POWR328


title: REI_POWR315


title: 933000320048725, PL

description: Library name: 933000320048725


title: Blood, HTP_II, RNA-seq, S96

description:
Library name: 5A-009
column_name_in_FPKM_allSamples: 5A-009


title: 933000320048639, PL

description: Library name: 933000320048639


title: Blood, HTP_II, RNA-seq, S95

description:
Library name: 5A-008
column_name_in_FPKM_allSamples: 5A-008


title: REI_POWR318


title: 933000320048574, PL

description: Library name: 933000320048574


title: 933000320048829, PL

description: Library name: 933000320048829


title: REI_POWR337


title: Blood, HTP_II, RNA-seq, S94

description:
Library name: 1A-103
column_name_in_FPKM_allSamples: 1A-103


title: 933000320048635, PL

description: Library name: 933000320048635


title: 933000320048573, PL

description: Library name: 933000320048573


title: Blood, HTP_II, RNA-seq, S93

description:
Library name: 1A-102
column_name_in_FPKM_allSamples: 1A-102


title: REI_POWR639


title: Blood, HTP_II, RNA-seq, S98

description:
Library name: 5A-011
column_name_in_FPKM_allSamples: 5A-011


title: 933000320048570, PL

description: Library name: 933000320048570


title: 933000320048571, PL

description: Library name: 933000320048571


title: 933000320048572, PL

description: Library name: 933000320048572


title: Blood, HTP_II, RNA-seq, S106

description:
Library name: 7A-007
column_name_in_FPKM_allSamples: 7A-007


title: REI_POWR438


title: Blood, HTP_II, RNA-seq, S91

description:
Library name: 1A-100
column_name_in_FPKM_allSamples: 1A-100


title: 933000320048565, PL

description: Library name: 933000320048565


title: 933000320048563, PL

description: Library name: 933000320048563


title: REI_POWR139


title: 933000320048559, PL

description: Library name: 933000320048559


title: Blood, HTP_II, RNA-seq, S92

description:
Library name: 1A-101
column_name_in_FPKM_allSamples: 1A-101


title: REI_POWR331


title: REI_POWR436


title: 933000320048711, PL

description: Library name: 933000320048711


title: 933000320048557, PL

description: Library name: 933000320048557


title: 933000320048575, PL

description: Library name: 933000320048575


title: 933000320048567, PL

description: Library name: 933000320048567


title: 933000320048555, PL

description: Library name: 933000320048555


title: 933000320048556, PL

description: Library name: 933000320048556


title: Blood, HTP_II, RNA-seq, S89

description:
Library name: 1A-098
column_name_in_FPKM_allSamples: 1A-098


title: 933000320048554, PL

description: Library name: 933000320048554


title: 933000320048512, PL

description: Library name: 933000320048512


title: Blood, HTP_II, RNA-seq, S88

description:
Library name: 1A-097
column_name_in_FPKM_allSamples: 1A-097


title: REI_POWR224


title: REI_POWR311


title: 933000320048551, PL

description: Library name: 933000320048551


title: 933000320048422, PL

description: Library name: 933000320048422


title: Blood, HTP_II, RNA-seq, S90

description:
Library name: 1A-099
column_name_in_FPKM_allSamples: 1A-099


title: Blood, HTP_II, RNA-seq, S87

description:
Library name: 1A-096
column_name_in_FPKM_allSamples: 1A-096


title: REI_POWR330


title: 933000320048356, PL

description: Library name: 933000320048356


title: Blood, HTP_II, RNA-seq, S86

description:
Library name: 1A-095
column_name_in_FPKM_allSamples: 1A-095


title: Blood, HTP_II, RNA-seq, S85

description:
Library name: 1A-094
column_name_in_FPKM_allSamples: 1A-094


title: 933000320048418, PL

description: Library name: 933000320048418


title: Blood, HTP_II, RNA-seq, S84

description:
Library name: 1A-093
column_name_in_FPKM_allSamples: 1A-093


title: 933000320048351, PL

description: Library name: 933000320048351


title: Mon7_19_CD34_RNAseq

city: Perugia

first: Cristina

last: Mecucci

address: Piazzale Menghini n.9

department: Department of Medicine, Hematology and Bone Marrow Transplantation Unit

country: Italy

institute: University of Perugia

description: Library name: Mon7_19_CD34_RNAseq

data_processing:
Sequenced reads were trimmed for adaptor sequences using cutadapt
Reads were aligned against hg19 build of the human genome using STAR
Counts were generated using STAR
DESeq2 was used for differential expression analysis
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts generated for each Sample

source_name: Sorted CD34+ Bone Marrow cells

extract_protocol:
RNA were extracted from bone marrow cells of patients using All Prep DNA/RNA Mini Kit (Qiagen). Libraries were prepared from 500ng of RNA using Oligo-dT and standard Illumina TruSeq® Stranded mRNA Library Prep kit following manufacturer’s instructions (Illumina San Diego, CA).
RNA-seq libraries were sequenced on Illumina system using manufacturer’s recommended protocol for 150 bp stranded paired-end read runs (Illumina San Diego, CA).

value: Sorted CD34+ Bone Marrow cells

tag: cytogenetics

tag: age

tag: mutations

value: Not found

value: AML


title: Blood, HTP_II, RNA-seq, S83

description:
Library name: 1A-092
column_name_in_FPKM_allSamples: 1A-092


title: REI_POWR120


title: REI_POWR174


title: REI_POWR399


title: CTL_8_RNAseq

description: Library name: CTL_8_RNAseq

source_name: Unsorted Bone Marrow cells

value: Unsorted Bone Marrow cells

value: Healthy


title: CTL_7_RNAseq

description: Library name: CTL_7_RNAseq


title: Blood, HTP_II, RNA-seq, S82

description:
Library name: 1A-091
column_name_in_FPKM_allSamples: 1A-091


title: REI_POWR189


title: Blood, HTP_II, RNA-seq, S81

description:
Library name: 1A-090
column_name_in_FPKM_allSamples: 1A-090


title: REI_POWR537


title: CTL_9_RNAseq

description: Library name: CTL_9_RNAseq


title: CTL_5_RNAseq

description: Library name: CTL_5_RNAseq


title: nkMN_10_RNAseq

description: Library name: nkMN_10_RNAseq


title: CTL_6_RNAseq

description: Library name: CTL_6_RNAseq


title: Blood, HTP_II, RNA-seq, S80

description:
Library name: 1A-088
column_name_in_FPKM_allSamples: 1A-088


title: CTL_4_RNAseq

description: Library name: CTL_4_RNAseq


title: REI_POWR1028


title: Blood, HTP_II, RNA-seq, S79

description:
Library name: 1A-087
column_name_in_FPKM_allSamples: 1A-087


title: REI_POWR280


title: Blood, HTP_II, RNA-seq, S78

description:
Library name: 1A-086
column_name_in_FPKM_allSamples: 1A-086


title: nkMN_8_RNAseq

description: Library name: nkMN_8_RNAseq

value: MDS


title: nkMN_7_RNAseq

description: Library name: nkMN_7_RNAseq


title: nkMN_6_RNAseq

description: Library name: nkMN_6_RNAseq


title: nkMN_5_RNAseq

description: Library name: nkMN_5_RNAseq


title: nkMN_4_RNAseq

description: Library name: nkMN_4_RNAseq

value: Not available


title: nkMN_2_RNAseq

description: Library name: nkMN_2_RNAseq


title: nkMN_3_RNAseq

description: Library name: nkMN_3_RNAseq


title: REI_POWR418

value: Fertile


title: nkMN_1_RNAseq

description: Library name: nkMN_1_RNAseq


title: Blood, HTP_II, RNA-seq, S77

description:
Library name: 1A-085
column_name_in_FPKM_allSamples: 1A-085


title: nkMN_17_CD34_RNAseq

description: Library name: nkMN_17_CD34_RNAseq

value: FLT3 ITD+


title: Blood, HTP_II, RNA-seq, S76

description:
Library name: 1A-084
column_name_in_FPKM_allSamples: 1A-084

value: whole blood


title: REI_POWR584


title: Mon7_17_RNAseq

description: Library name: Mon7_17_RNAseq


title: Mon7_18_RNAseq

description: Library name: Mon7_18_RNAseq


title: Blood, HTP_II, RNA-seq, S75

description:
Library name: 1A-083
column_name_in_FPKM_allSamples: 1A-083


title: REI_POWR633


title: 933000320048552, PL

description: Library name: 933000320048552

value: Prelimbic cortex


title: Blood, HTP_II, RNA-seq, S74

description:
Library name: 1A-082c
column_name_in_FPKM_allSamples: 1A-082c


title: Mon7_16_RNAseq

description: Library name: Mon7_16_RNAseq


title: REI_POWR644


title: Blood, HTP_II, RNA-seq, S73

description:
Library name: 1A-081c
column_name_in_FPKM_allSamples: 1A-081c

value: Male


title: REI_POWR367

value: Female


title: Mon7_12_RNAseq

description: Library name: Mon7_12_RNAseq


title: Mon7_14_RNAseq

description: Library name: Mon7_14_RNAseq

value: 60% of monosomy 7 (FISH)


title: Mon7_13_RNAseq

description: Library name: Mon7_13_RNAseq


title: REI_POWR554

value: Blood


title: REI_POWR393

value: Infertile


title: Mon7_10_RNAseq

description: Library name: Mon7_10_RNAseq


title: Blood, HTP_II, RNA-seq, S71

description:
Library name: 1A-079
column_name_in_FPKM_allSamples: 1A-079

value: HTP


title: Mon7_9_RNAseq

description: Library name: Mon7_9_RNAseq


title: Blood, HTP_II, RNA-seq, S70

description:
Library name: 1A-078
column_name_in_FPKM_allSamples: 1A-078


title: Mon7_6_RNAseq

description: Library name: Mon7_6_RNAseq


title: Mon7_7_RNAseq

description: Library name: Mon7_7_RNAseq


title: REI_POWR1229


title: REI_POWR746


title: Mon7_5_RNAseq

description: Library name: Mon7_5_RNAseq

value: not found


title: REI_POWR574


title: Mon7_4_RNAseq

description: Library name: Mon7_4_RNAseq


title: Mon7_15_RNAseq

description: Library name: Mon7_15_RNAseq

value: Not found


title: Blood, HTP_II, RNA-seq, S68

description:
Library name: 1A-076
column_name_in_FPKM_allSamples: 1A-076


title: Mon7_8_RNAseq

description: Library name: Mon7_8_RNAseq


title: REI_POWR545


title: DNMT1_KO_h3k36me3_in_rep__chip_seq

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description:
Library name: DNMT1_KO_h3k36me3_in_rep__chip_seq
DNMT1_KO_h3k36me3_rep_2_chip_seq.bigWig

data_processing:
Fastq files were quality checked using FastQC (v0.11.4) and reads trimmed using TrimGalore (v0.4.1). Reads were then mapped to the genome (hg38) using bowtie2 (v2.3.1 with settings: -N 1 -L 20 --no-unal) (Langmead & Salzberg, 2012) for paired end data. Low mapping quality reads or fragments were removed using samtools (v1.6 with settings -bq 10). Duplicate reads were removed using sambamba markdup (v0.5.9, for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 ChIP-seq) or using UMI tools dedup function (v1.0.0 and setting: --paired, DNMT3A/B and H3K36me2 ChIP-seq). The number of reads pre- and post- alignment as well as the reads after deduplication and low mapping was then extracted and counted. Bed counts for 10 kb genomic windows and domains were generated from the bam files using bedtools coverage (seetings: -counts, v2.27.1). For paired-end data, the BAM file was first converted to a BED file of fragment locations using BEDtools bamtobed function. Coverage counts were scaled to counts per 10 million based on total number of mapped reads per sample and divided by the input read count to obtain a normalised read count. An offset of 0.5 was added to all windows prior to scaling and input normalisation to prevent intervals with zero reads in the input sample generating a normalised count of infinity. Regions where coverage was 0 in all samples were removed from the analysis. BigWig files for visualisation in the genome browser were generated, by calculating counts per million mapped reads using bamCoverage from deeptools (v3.2.0). Normalisation over inputs and means between replicas were then performed using bigwigCompare ratio and mean respectively. For a summary of ChIP-seq alignment statistics, see Supplementary Tables 4-9.
Assembly: hg38
Supplementary files format and content: Processed data files are bigWig files generated by normalisation over input as described under data processing.

source_name: HCT116 DNMT1 KO

growth_protocol: HCT116 and DNMT1 KO cells were gifts from B. Vogelstein (Rhee et al., 2000). Cells were cultured in McCoy’s 5A (Gibco) supplemented with 10% Fetal Calf Serum (Life Technologies) and penicillin–streptomycin antibiotics at 140 and 400 μg/ml, respectively at 37°C with 5% CO2. Cell lines were routinely tested for mycoplasma contamination. DNMT1 KO genotype was confirmed by western blot and sequencing.

extract_protocol:
ChIP-seq was performed as previously described (Masalmeh et al., 2021; Taglini et al., 2024). For T7-DNMT3B and T7-DNMT3A ChIP-seq experiments, 1×107 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS for 8 min at room temperature. Crosslinked cells were lysed for 10 min on ice in 50 μl of lysis buffer (50 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 1% SDS) freshly supplemented with proteinase inhibitor (Sigma-Aldrich). IP dilution buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 1 mM EDTA, 0.1% Triton X-100) freshly supplemented with proteinase inhibitor, DTT and PMSF was added to the samples to reach a final volume of 500 μl. Chromatin was fragmented using Benzonase (Pchelintsev et al, 2016): samples were sonicated on ice with Soniprep 150 twice for 30 s to break up nuclei; then 200 U of Benzonase Nuclease (Sigma) and MgCl2 (final concentration 2.5 mM) were added and samples were incubated on ice for 15 min. The reaction was blocked by adding 10 μl of 0.5 M EDTA pH 8. Following centrifugation for 30 min at 18,407 g at 4 °C, supernatants were collected and supplemented with Triton X-100 (final concentration 1%) and 5% input aliquots were retained for later use. Protein A Dynabeads (Invitrogen) previously coupled with 10 μl of T7-Tag antibody per 1×107 cells in blocking solution (1x PBS, 0.5% BSA) were added and the samples incubated overnight under rotation at 4 °C. Beads were then washed for 10 min at 4 °C with the following buffers: IP dilution buffer 1% Triton X-100 (20 mM Tris-HCl pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), buffer A (50mM HEPES pH 7.9, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B (20 mM Tris pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), TE buffer (1mM EDTA pH 8, 10 mM Tris pH 8). Chromatin was eluted by incubating the beads in extraction buffer (0.1 M NaHCO3, 1% SDS) for 15 min at 37 °C. To reverse the cross-linking Tris-HCl pH 6.8 and NaCl were added to final concentrations of 130 mM and 300 mM respectively, and immunoprecipitations were incubated at 65 °C overnight. Samples were then incubated at 37 °C for 1 h after addition of 2 μl of RNase Cocktail Enzyme Mix (Ambion). Then 40 μg of Proteinase K (Roche) were added, followed by 2 h incubation at 55 °C. Input material was similarly de-crosslinked. Samples were purified with the MinElute PCR purification kit (QIAGEN). For ChIP-Rx-seq of ectopic T7-DNMT3B and T7-DNMT3A 20 μg of Spike-in chromatin (ActiveMotif 53083) was added to each sample after sonication. 2 μl of spike-in antibody per sample (ActiveMotif 61686) was also added in a ratio 1:5 versus the T7 antibody. A similar protocol was used for H3K4me3, H3K9me3, H3K27me3 and H3K36me3 ChIP-seq experiments, except: 0.5×107 cells were harvested and crosslinked with 1% methanol-free formaldehyde in PBS for 5 min at room temperature. For H3K36me3 ChIP-Rx-seq crosslinked Drosophila S2 cells were spiked into samples before sonication at a ratio of 20:1 human to Drosophila cells. Following nuclei rupture by sonication on ice with Soniprep 150, chromatin was fragmented using Bioruptor Plus sonicator (Diagenode) for 40 cycles (30 s on/30 s off on high setting at 4 °C). 2 μl /1×106 cells of the following antibodies were used for immunoprecipitations: H3K4me3 (EpiCypher 13-00041), H3K9me3 (Active Motif 39161), H3K27me3 (Cell Signaling Technology C36B11) and H3K36me3 (Abcam ab9050).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB) barcode adapters according to the manufacturer instructions. were used. Specifically, Illumina Index Primers Set 1 (E7335) for H3K36me3, and Unique Dual Index UMI Adaptors DNA Set 1 (E7395) for the other libraries. For histone modifications ChIP-seq, adapter-ligated DNA was size selected for an insert size of 150 bp using Agencourt AMPure XP beads. Libraries were quantified using the Qubit dsDNA HS or BR assay kit and assessed for size and quality using the Agilent Bioanalyser. H3K36me3 ChIP-Rx-seq libraries were sequenced using the NextSeq 500/550 high-output version 2.5 kit (75 bp single end reads). The other ChIP-seq libraries were sequenced using the NextSeq 2000 P3 (50 bp paired end reads). Libraries were combined into equimolar pools to run within individual flow cells. Sequencing was performed at the Edinburgh Clinical Research Facility.

value: HCT116 DNMT1 KO

value: colorectal cancer cell line

value: DNMT1 KO

tag: chip antibody

value: none (input)


title: hrtRz_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: Sample 2

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm39 (Ensembl release 109) with STAR 2.7.11a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Alignments were filtered to remove: duplicates with Picard 3.1.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm39
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Heart

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 250ng of total RNA was used as input for Watchmaker mRNA Library Prep Kit following manufacture’s protocol (Watchmaker Genomics). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

treatment_protocol: Immunoprecipitation and purification of ribosome-associated RNA was performed as described previously (Sanz et al., 2009) with modifications. 7 days after induction of myocardial infarction by coronary ligation, hearts of Cdh5-CreERT2;Rpl22tm1.1Psam mice (EC-RiboTag) were perfused through the right ventricle with cold HBSS containing 100 µg/ml cyclohexamide and dissected before snap freezing in liquid nitrogen. Tissues were homogenized in polysome buffer (50 mM Tris-HCl pH 7.4, 100 mM KCl, 12 mM MgCl2, cOmplete ULTRA (Roche), 1% NP-40, 1 mM DTT, 200 U/ml SUPERasein (Thermo Fisher Scientific), 100 µg/ml cyclohexamide, 1 mg/ml heparin) with Pestle (ARgos) and clarified by centrifugation at 20,000 × g for 10 min at 4 °C. Before immunoprecipitation, 5% of supernatants were kept as input and the remaining supernatants were mixed with anti-HA-tag Magnetic Beads (MBL) and rotated for 8 hours at 4 °C. Magnetic beads were washed three times for 5 min in high salt buffer (50 mM Tris-HCl pH 7.4, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 100 µg/ml cyclohexamide). Qiagen RLT buffer was added to magnetic beads, and total RNA was isolated by RNeasy Micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. There are three biological replicates.

value: Heart


title: DNMT1_KO_h3k36me3_chip_rep_2_chip_seq

description:
Library name: DNMT1_KO_h3k36me3_chip_rep_2_chip_seq
DNMT1_KO_h3k36me3_rep_2_chip_seq.bigWig

value: H3K36me3 (Abcam ab9050)


title: Blood, HTP_II, RNA-seq, S67

description:
Library name: 1A-075
column_name_in_FPKM_allSamples: 1A-075


title: Blood, HTP_II, RNA-seq, S66

description:
Library name: 1A-074
column_name_in_FPKM_allSamples: 1A-074


title: DNMT1_KO_h3k36me3_chip_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k36me3_chip_rep_1_chip_seq
DNMT1_KO_h3k36me3_rep_1_chip_seq.bigWig


title: Mon7_11_RNAseq

description: Library name: Mon7_11_RNAseq

value: Unsorted Bone Marrow cells

value: Not available

value: MDS


title: hrtRz_3

description: Library name: Sample 3


title: hrtRz_1

description: Library name: Sample 1


title: REI_POWR618

value: Fertile


title: DNMT1_KO_h3k36me3_in_rep_1_chip_seq

description:
Library name: DNMT1_KO_h3k36me3_in_rep_1_chip_seq
DNMT1_KO_h3k36me3_rep_1_chip_seq.bigWig


title: Blood, HTP_II, RNA-seq, S65

description:
Library name: 1A-073
column_name_in_FPKM_allSamples: 1A-073

value: whole blood

value: Female


title: Blood, HTP_II, RNA-seq, S69

description:
Library name: 1A-077
column_name_in_FPKM_allSamples: 1A-077


title: REI_POWR1231

value: Blood


title: REI_POWR1240


title: DNMT1 KO WGBS

description:
Library name: DNMT1_KO_WGBS
HCT116 with knocked out DNMT1

data_processing:
Fastq files were quality checked using FastQC (v0.11.4) and reads trimmed with TrimGalore (v0.4.1) using default settings. Reads were then mapped to a bisulfite converted genome (hg38) and duplicates were removed using bismark (v 0.18.1) with bowtie2 (v2.3.1) for paired end data (settings: -N0 -L20) (Krueger & Andrews, 2011; Langmead & Salzberg, 2012) before PCR duplicates were identified and removed using Bismark’s deduplicate_bismark command. Aligned BAM files were processed to report coverage and the number of methylated reads for each CpG observed. Forward and reverse strands were combined using Bismark’s methylation extractor and bismark2bedgraph modules with custom Python and AWK scripts. Processed WGBS files were assessed for conversion efficiency based on the proportion of methylated reads mapping to the phage-λ genome spike-in (>99.5% in all cases). For summary of WGBS alignment statistics, see Supplementary Table 1.
Assembly: hg38
Supplementary files format and content: Processed coverage values for each CpG observed in sample (.cov files). CpG position and total coverage (T) and methylated coverage (M) combining both strands. Columns = chr, start, end, T, M. Positions are 0-based, ie BED format.
Supplementary files format and content: bigWig files for each sample also supplied for CpGs. Only windows with coverage >= 10 in that sample are in each file.

extract_protocol:
DNA was extracted from cell pellets snap-frozen in dry ice with ethanol. Cells pellets were resuspended in Genomic Lysis Buffer (300mM NaCl, 1% SDS, 20mM EDTA). The lysis mixture was syringed up and down using a 21G needle before being incubated at 55°C overnight with proteinase K. RNA was removed by incubation with RNase A/T1 Cocktail (Ambion) at 37 °C for 1 h, in between two phenol–chloroform extraction steps. DNA was quantified by Nanodrop 8000 spectrophotometer or Qubit fluorometer (Invitrogen) and purity was assessed using the Agilent 2100 BioAnalyzer.
DNA (100ng) was bisulphite converted using the EZ DNA Methylation-Lightning kit, according to the manufacturer’s instructions. Libraries were generated using the TruSeq DNA Methylation kit, according to the manufacturer’s instructions. Sequencing was performed at the Edinburgh Clinical Research Facility. Libraries were sequenced using the Illumina NextSeq 500/550 High-Output v2 (150 cycles) (#FC-404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002) over 1 flow cell.


title: Blood, HTP_II, RNA-seq, S64

description:
Library name: 1A-072
column_name_in_FPKM_allSamples: 1A-072

value: Male


title: Blood, HTP_II, RNA-seq, S72

description:
Library name: 1A-080
column_name_in_FPKM_allSamples: 1A-080

value: HTP


title: REI_POWR694


title: nri1Δ/Δ nri2Δ/Δ Rep3

city: Hyderabad

first: Amartya

last: Sanyal

state: Telangana

address: Jawahar Nagar, Kapra Mandal, Medchal District

department: Biological Sciences

country: India

institute: BITS Pilani Hyderabad Campus

description: Library name: S12

data_processing:
Raw FASTQ files were checked for their quality using FastQC v0.12.1. The reads were trimmed using Trimmomatic v0.39 and mapped to Candida albicans SC5314, Assembly 22 (A22) reference genome (downloaded from Candida Genome Database) using HISAT2 v2.2.1 with default parameters. For alignment, a modified FASTA file containing DNA sequences of one set (haplotype A) of homologous chromosomes (Ca22chr1A-7A, chrRA) and chrM from the phased, diploid C. albicans SC5314 A22 genome assembly was used. The resultant BAM files and the GFF annotation file (downloaded from Candida Genome Database) were used to generate the counts matrix using featureCounts v2.0.6. Each sample was sequenced across 4 Illumina lanes for this study. The transcript-specific raw counts generated in the counts matrix for the four lanes were merged for each sample before processing for differential gene expression analysis using DESeq2.
Assembly: Candida albicans SC5314, Assembly 22 (A22)
Supplementary files format and content: csv file includes raw counts for each sample

organism: Candida albicans

extract_protocol:
Manual RNA isolation using guanidinium thiocyanate-phenol-chloroform extraction
Illumina Truseq stranded total RNA library prep kit according to manufacturer's instructions

value: Yeast


title: REI_POWR559


title: HCT116_WGBS

description:
Library name: HCT116_WGBS
HCT116 cells

value: WT


title: nri2Δ/Δ Rep3

description: Library name: S11


title: Blood, HTP_II, RNA-seq, S62

description:
Library name: 1A-070
column_name_in_FPKM_allSamples: 1A-070


title: REI_POWR729


title: Blood, HTP_II, RNA-seq, S63

description:
Library name: 1A-071
column_name_in_FPKM_allSamples: 1A-071


title: Wild type control Rep3

description: Library name: S9

value: Wild type


title: nri1Δ/Δ Rep3

description: Library name: S10


title: nri1Δ/Δ nri2Δ/Δ Rep2

description: Library name: S8


title: nri2Δ/Δ Rep2

description: Library name: S7


title: REI_POWR1213


title: Blood, HTP_II, RNA-seq, S60

description:
Library name: 1A-068
column_name_in_FPKM_allSamples: 1A-068


title: REI_POWR424


title: Blood, HTP_II, RNA-seq, S61

description:
Library name: 1A-069
column_name_in_FPKM_allSamples: 1A-069


title: Blood, HTP_II, RNA-seq, S58

description:
Library name: 1A-066
column_name_in_FPKM_allSamples: 1A-066


title: REI_POWR1232


title: nri1Δ/Δ Rep1

description: Library name: S2


title: Wild type control Rep2

description: Library name: S5


title: Blood, HTP_II, RNA-seq, S59

description:
Library name: 1A-067
column_name_in_FPKM_allSamples: 1A-067


title: nri2Δ/Δ Rep1

description: Library name: S3


title: nri1Δ/Δ nri2Δ/Δ Rep1

description: Library name: S4


title: REI_POWR672


title: Wild type control Rep1

description: Library name: S1


title: Monocyte-derived macrophages from Donor ND410b, IFNg trained, harvested on Day 11, rep2

first: Aoife

last: O'Farrell

state: PA

address: 415 Curie Blvd

description:
Library name: A_IFN_D11_rep2
Counts_Matrix_MergedPeaks_D6vD11.csv
A36

data_processing:
Sequences were aligned to hg38 with Bowtie2 and cleaned using ATACseqQC. PCR duplicates were removed with Picard. Peaks were called using MACS2 with FDR cutoff of 0.05. To improve accuracy of peak calling, we input replicate-merged samples flitered to fragment size less than 300 base pairs. We then generated one nonredundant peak list filtered to peaks present in at least two samples, and generated a full counts matrix for all samples (not filtered by fragment size, and separated by replicates) for further analysis.
Assembly: hg38
Supplementary files format and content: Counts_Matrix_MergedPeaks_D6 : Counts matrix for reads within peaks for 3 donors shown in Figure 2 of manuscript
Supplementary files format and content: Counts_Matrix_MergedPeaks_D6vD11.csv : counts matrix for read within peaks for Donor ND410b sequenced six or eleven days after training, for data shown in Figure 4 of manuscript.
Supplementary files format and content: Counts_Matrix_MergedPeaks_DonorND607b.csv : counts matrix for reads within peaks for Donor ND607b, sequenced after training with a wider panel of stimuli, for data shown in Sup Fig  5 of manuscript.
Supplementary files format and content: Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv : counts matrix for reads within peaks for Donor ND500b, inclusive of samples after training with TGFb, for data shown in Sup Fig 5 of manuscript.

source_name: monocyte-derived macrophage

growth_protocol: Primary human monocytes were collected from the apheresis product of healthy donors, and cultured for six or eleven days in RPMI + 10% FBS + 1% PenStrep, at which point they differentiate into monocyte-derived macrophages.B95

extract_protocol:
100,000 cells were collected per replicate and lysed in buffer containing 10% NP-40, 10% Tween-20, and 1% digitonin for 3 minutes on ice, then transposed with Tn5 for 30 minutes at 37˚C. Transposed DNA was then isolated with a Zymo DNA Clean and Concentrator kit.
Libraries were amplified by PCR with custom ATACseq primers, purified by double-sided AMPure XP magnetic bead selection, and quantified by BioAnalyzer High Sensitivity chips.

treatment_protocol: Cells were stimulated ("trained") for the first 24 hours of culture with one of the following stimuli: beta-glucan (5ug/mL), MDP (1ug/mL), IFNg (50ng/mL), CpG (100ng/mL), PolyIC (10ug/mL), TGFb (2ng/mL), or oxLDL (10ug/mL). Untrained control cells received no stimulation at this time. After 24 hours, stimuli were washed out with PBS, then cells were rested in culture with no stimulation. On day 6 or day 11, cells were harvested for ATACseq. Cells were collected from four donors total: Donor ND410b (60F), Donor ND650 (25F), Donor ND500b (30F), and Donor ND607b (28F).

tag: individual

value: Donor ND410b

value: IFNg trained, harvested on Day 11

value: monocyte-derived macrophage


title: Blood, HTP_II, RNA-seq, S57

description:
Library name: 1A-065
column_name_in_FPKM_allSamples: 1A-065


title: Monocyte-derived macrophages from Donor ND410b, IFNg trained, harvested on Day 11, rep1

description:
Library name: A_IFN_D11_rep1
Counts_Matrix_MergedPeaks_D6vD11.csv
A33


title: Monocyte-derived macrophages from Donor ND410b, MDP trained, harvested on Day 11, rep2

description:
Library name: A_MDP_D11_rep2
Counts_Matrix_MergedPeaks_D6vD11.csv
A37

value: MDP trained, harvested on Day 11


title: REI_POWR1238


title: Blood, HTP_II, RNA-seq, S56

description:
Library name: 1A-064
column_name_in_FPKM_allSamples: 1A-064


title: REI_POWR787


title: nri1Δ/Δ Rep2

description: Library name: S6


title: REI_POWR549


title: Blood, HTP_II, RNA-seq, S55

description:
Library name: 1A-063
column_name_in_FPKM_allSamples: 1A-063


title: REI_POWR145


title: Monocyte-derived macrophages from Donor ND410b, Untrained, harvested on Day 11, rep2

description:
Library name: A_NT_D11_rep2
Counts_Matrix_MergedPeaks_D6vD11.csv
A30

value: Untrained, harvested on Day 11


title: Monocyte-derived macrophages from Donor ND410b, B-Glucan trained, harvested on Day 11, rep1

description:
Library name: A_BG_D11_rep1
Counts_Matrix_MergedPeaks_D6vD11.csv
A35

value: B-Glucan trained, harvested on Day 11


title: Blood, HTP_II, RNA-seq, S54

description:
Library name: 1A-062
column_name_in_FPKM_allSamples: 1A-062


title: REI_POWR683


title: Monocyte-derived macrophages from Donor ND410b, Untrained, harvested on Day 11, rep1

description:
Library name: A_NT_D11_rep1
Counts_Matrix_MergedPeaks_D6vD11.csv
A27


title: Monocyte-derived macrophages from Donor ND607b, PolyIC trained, rep2

description:
Library name: D_PolyIC_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A14

value: Donor ND607b

value: PolyIC trained


title: REI_POWR472

value: Fertile


title: Blood, HTP_II, RNA-seq, S53

description:
Library name: 1A-061
column_name_in_FPKM_allSamples: 1A-061

value: whole blood


title: Monocyte-derived macrophages from Donor ND410b, MDP trained, harvested on Day 11, rep1

description:
Library name: A_MDP_D11_rep1
Counts_Matrix_MergedPeaks_D6vD11.csv
A34


title: Monocyte-derived macrophages from Donor ND607b, CpG trained, rep2

description:
Library name: D_CpG_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A7

value: CpG trained


title: Monocyte-derived macrophages from Donor ND607b, PolyIC trained, rep1

description:
Library name: D_PolyIC_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A6


title: Blood, HTP_II, RNA-seq, S52

description:
Library name: 1A-060
column_name_in_FPKM_allSamples: 1A-060


title: Monocyte-derived macrophages from Donor ND410b, B-Glucan trained, harvested on Day 11, rep2

description:
Library name: A_BG_D11_rep2
Counts_Matrix_MergedPeaks_D6vD11.csv
A38


title: Blood, HTP_II, RNA-seq, S51

description:
Library name: 1A-059
column_name_in_FPKM_allSamples: 1A-059

value: Female


title: REI_POWR1239

value: Blood


title: Monocyte-derived macrophages from Donor ND607b, CpG trained, rep1

description:
Library name: D_CpG_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A3


title: Monocyte-derived macrophages from Donor ND607b, oxLDL trained, rep1

description:
Library name: D_oxLDL_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A4

value: oxLDL trained


title: Monocyte-derived macrophages from Donor ND607b, oxLDL trained, rep2

description:
Library name: D_oxLDL_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A5


title: REI_POWR471


title: REI_POWR1233


title: Blood, HTP_II, RNA-seq, S50

description:
Library name: 1A-058
column_name_in_FPKM_allSamples: 1A-058

value: Male

value: HTP


title: Monocyte-derived macrophages from Donor ND607b, IFNg trained, rep2

description:
Library name: D_IFN_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A11

value: IFNg trained


title: Monocyte-derived macrophages from Donor ND607b, MDP trained, rep1

description:
Library name: D_MDP_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A2

value: MDP trained


title: Monocyte-derived macrophages from Donor ND607b, IFNg trained, rep1

description:
Library name: D_IFN_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A9


title: Blood, HTP_II, RNA-seq, S49

description:
Library name: 1A-057
column_name_in_FPKM_allSamples: 1A-057


title: Monocyte-derived macrophages from Donor ND607b, MDP trained, rep2

description:
Library name: D_MDP_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A8


title: REI_POWR476


title: Blood, HTP_II, RNA-seq, S48

description:
Library name: 1A-056
column_name_in_FPKM_allSamples: 1A-056


title: Blood, HTP_II, RNA-seq, S47

description:
Library name: 1A-055
column_name_in_FPKM_allSamples: 1A-055


title: REI_POWR536


title: Monocyte-derived macrophages from Donor ND607b, B-Glucan trained, rep2

description:
Library name: D_BG_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A12

value: B-Glucan trained


title: Monocyte-derived macrophages from Donor ND607b, Untrained, rep2

description:
Library name: D_NT_D6_rep2
Counts_Matrix_MergedPeaks_DonorND607b.csv
A13

value: Untrained

value: monocyte-derived macrophage


title: Monocyte-derived macrophages from Donor ND607b, B-Glucan trained, rep1

description:
Library name: D_BG_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A1


title: REI_POWR758


title: REI_POWR582


title: Monocyte-derived macrophages from Donor ND500b, TGFb trained, rep1

description:
Library name: C_TGFb_D6_rep1
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A49

value: Donor ND500b

value: TGFb trained


title: Monocyte-derived macrophages from Donor ND500b, TGFb trained, rep2

description:
Library name: C_TGFb_D6_rep2
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A50


title: Blood, HTP_II, RNA-seq, S46

description:
Library name: 1A-054
column_name_in_FPKM_allSamples: 1A-054


title: Monocyte-derived macrophages from Donor ND500b, IFNg trained, rep2

description:
Library name: C_IFN_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A48


title: REI_POWR1207


title: Monocyte-derived macrophages from Donor ND500b, B-Glucan trained, rep2

description:
Library name: C_BG_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A47


title: Monocyte-derived macrophages from Donor ND500b, IFNg trained, rep1

description:
Library name: C_IFN_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A42


title: Monocyte-derived macrophages from Donor ND500b, MDP trained, rep1

description:
Library name: C_MDP_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A43


title: Blood, HTP_II, RNA-seq, S45

description:
Library name: 1A-053
column_name_in_FPKM_allSamples: 1A-053


title: REI_POWR1013


title: Monocyte-derived macrophages from Donor ND500b, Untrained, rep2

description:
Library name: C_NT_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A44


title: Monocyte-derived macrophages from Donor ND500b, MDP trained, rep2

description:
Library name: C_MDP_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A46


title: Monocyte-derived macrophages from Donor ND650, IFNg trained, rep2

description:
Library name: B_IFN_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
A24

value: Donor ND650


title: REI_POWR326


title: Monocyte-derived macrophages from Donor ND500b, B-Glucan trained, rep1

description:
Library name: C_BG_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A45


title: Monocyte-derived macrophages from Donor ND500b, Untrained, rep1

description:
Library name: C_NT_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_DonorND500b_TGFb.csv
A41


title: Blood, HTP_II, RNA-seq, S42

description:
Library name: 1A-050
column_name_in_FPKM_allSamples: 1A-050


title: Monocyte-derived macrophages from Donor ND607b, Untrained, rep1

description:
Library name: D_NT_D6_rep1
Counts_Matrix_MergedPeaks_DonorND607b.csv
A10

value: Donor ND607b


title: Blood, HTP_II, RNA-seq, S43

description:
Library name: 1A-051
column_name_in_FPKM_allSamples: 1A-051


title: Monocyte-derived macrophages from Donor ND650, MDP trained, rep1

description:
Library name: B_MDP_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
A17


title: Monocyte-derived macrophages from Donor ND650, MDP trained, rep2

description:
Library name: B_MDP_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
A19


title: REI_POWR287

value: Fertile


title: REI_POWR324


title: Blood, HTP_II, RNA-seq, S44

description:
Library name: 1A-052
column_name_in_FPKM_allSamples: 1A-052

value: whole blood


title: Monocyte-derived macrophages from Donor ND650, B-Glucan trained, rep2

description:
Library name: B_BG_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
A21


title: REI_POWR383


title: Monocyte-derived macrophages from Donor ND650, B-Glucan trained, rep1

description:
Library name: B_BG_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
A18


title: Monocyte-derived macrophages from Donor ND650, Untrained, rep2

description:
Library name: B_NT_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
A23


title: Blood, HTP_II, RNA-seq, S41

description:
Library name: 1A-049
column_name_in_FPKM_allSamples: 1A-049


title: REI_POWR106


title: Monocyte-derived macrophages from Donor ND410b, IFNg trained, rep2

description:
Library name: A_IFN_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A6

value: Donor ND410b


title: Blood, HTP_II, RNA-seq, S38

description:
Library name: 1A-046
column_name_in_FPKM_allSamples: 1A-046

value: Female


title: Monocyte-derived macrophages from Donor ND650, Untrained, rep1

description:
Library name: B_NT_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
A20


title: Blood, HTP_II, RNA-seq, S40

description:
Library name: 1A-048
column_name_in_FPKM_allSamples: 1A-048


title: Blood, HTP_II, RNA-seq, S37

description:
Library name: 1A-045
column_name_in_FPKM_allSamples: 1A-045


title: Blood, HTP_II, RNA-seq, S35

description:
Library name: 1A-043
column_name_in_FPKM_allSamples: 1A-043


title: Blood, HTP_II, RNA-seq, S36

description:
Library name: 1A-044
column_name_in_FPKM_allSamples: 1A-044


title: Monocyte-derived macrophages from Donor ND410b, IFNg trained, rep1

description:
Library name: A_IFN_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A1


title: Monocyte-derived macrophages from Donor ND650, IFNg trained, rep1

description:
Library name: B_IFN_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
A22


title: REI_POWR302

value: Blood


title: REI_POWR187


title: REI_POWR397


title: REI_POWR185


title: Monocyte-derived macrophages from Donor ND410b, B-Glucan trained, rep1

description:
Library name: A_BG_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A3


title: Monocyte-derived macrophages from Donor ND410b, Untrained, rep1

description:
Library name: A_NT_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A5


title: Monocyte-derived macrophages from Donor ND410b, B-Glucan trained, rep2

description:
Library name: A_BG_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A8


title: Monocyte-derived macrophages from Donor ND410b, MDP trained, rep1

description:
Library name: A_MDP_D6_rep1
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A2


title: Monocyte-derived macrophages from Donor ND410b, Untrained, rep2

description:
Library name: A_NT_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A7


title: Monocyte-derived macrophages from Donor ND410b, MDP trained, rep2

description:
Library name: A_MDP_D6_rep2
Counts_Matrix_MergedPeaks_D6.csv
Counts_Matrix_MergedPeaks_D6vD11.csv
A4


title: REI_POWR229


title: Blood, HTP_II, RNA-seq, S34

description:
Library name: 1A-042
column_name_in_FPKM_allSamples: 1A-042


title: Blood, HTP_II, RNA-seq, S33

description:
Library name: 1A-041
column_name_in_FPKM_allSamples: 1A-041


title: Hepatic multicellular organoid_rep4

city: Milano

first: Arianna

last: Vallerga

address: via Mario Negri 2

department: Experimental Oncology

institute: Mario Negri Institute for Pharmacological Research

description:
Library name: Sample_4
Single-cell RNA-seq of hypoimmunogenic iPSC-derived hepatic multicellular organoid (biological replicate 4).

data_processing:
Raw BCL files were demultiplexed using Illumina BCL Convert with default settings and lane merging enabled.
FASTQ files were processed with Cell Ranger (v9.0.1) using default parameters.
Reads were aligned to the GRCh38 reference genome and filtered feature–barcode matrices were generated for each sample.
Assembly: GRCh38
Supplementary files format and content: Processed data files are HDF5 files containing filtered gene expression feature–barcode matrices generated by Cell Ranger.

source_name: Hepatic multicellular organoid

growth_protocol: The organoids were maintained for 16 days with medium changes every other day. The medium was half Hepatocyte Growth Medium and half Endothelial Cell Growth Medium-2 supplemented with 20 ng/mL hepatocyte growth factor, 10 ng/mL oncostatin M, 100 nM dexamethasone, 1 µM A83-01 and 50 ng/mL VEGF-165.

extract_protocol:
Organoids were dissociated using 800 U/ml collagenase type IV in Trypsin-EDTA 0.25% for 30 minutes on an orbital shaker in a cell incubator.
Single-cell suspensions were loaded onto the 10x Genomics Chromium X platform and libraries were generated using the Chromium GEM-X Single Cell 3′ v4 kit according to the manufacturer’s protocol.

value: Hepatic multicellular organoid

value: 19L HYPO iPSC - derived Hepatic multicellular organoid


title: Hepatic multicellular organoid_rep3

description:
Library name: Sample_3
Single-cell RNA-seq of hypoimmunogenic iPSC-derived hepatic multicellular organoid (biological replicate 3).


title: Hepatic multicellular organoid_rep2

description:
Library name: Sample_2
Single-cell RNA-seq of hypoimmunogenic iPSC-derived hepatic multicellular organoid (biological replicate 2).


title: Hepatic multicellular organoid_rep1

description:
Library name: Sample_1
Single-cell RNA-seq of hypoimmunogenic iPSC-derived hepatic multicellular organoid (biological replicate 1).


title: Blood, HTP_II, RNA-seq, S32

description:
Library name: 1A-040
column_name_in_FPKM_allSamples: 1A-040

value: Male

value: HTP


title: REI_POWR178


title: Blood, HTP_II, RNA-seq, S31

description:
Library name: 1A-039
column_name_in_FPKM_allSamples: 1A-039