title: A2.2_0nM_IgG_rep1

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: Library name: S125332

data_processing:
CUT&RUN reads were processed using the nf-core/cutandrun pipeline (version 3.2.2) with the GRCh38.p14 primary assembly as reference and Gencode v46 annotation. In the pipeline, we set the peak caller to MACS2 with the broad peak setting for histone marks (H3K4me3, H3K27me3, H3K27ac) and narrow peak setting for all other samples. As a quality measure, we removed all peaks that overlapped regions that are known to cause high unspecific signal (ENCODE4 exclusion list ENCFF356LFX). To remove spurious signal, we defined consensus peak regions per antibody target as follows: keep only significant peaks (FDR < 0.01) in every replicate, create union of peak ranges, keep only ranges that overlap significant peaks from at least two replicates. For FLI1 we combined the genotype-specific consensus peak ranges (parental and A2.2 clone) into one consensus range set by taking the union. To quantify the CUT&RUN signal at consensus peaks, we counted the fragments that map to those regions using the bamsignals R package (v 1.34.0).
Assembly: GRCh38.p14
Supplementary files format and content: bigWig
Supplementary files format and content: MACS2 peak calling output, TSV
Supplementary files format and content: Consensus peaks, compressed archive of bigBed files
Supplementary files format and content: MACS2 peak calling output, compressed archive of TSV files
Supplementary files format and content: sample metadata, TSV
Library strategy: CUT&RUN

growth_protocol: The A673 EwS cell line derived from a primary tumor localized in muscle, was purchased from Cell Lines Service (CLS GmbH, 300454) and authenticated by short tandem repeat (STR) profiling at Microsynth. All cells were cultured in complete DMEM medium (Gibco, 31966-021) supplemented with 10% fetal calf serum (FCS, Gibco, A5256701) and 1% penicillin-streptomycin (PAN Biotech, P06-07100) at 37°C and 5% CO2. Cells were passaged at a 1:10 ratio every 3-4 days, or upon reaching confluency, using Accutase (PAN Biotech, P10-21100). Regular mycoplasma testing was performed using the MycoAlert Mycoplasma detection kit (Lonza, LT07-318).

extract_protocol:
The frozen cells were then subjected to the CUT&RUN protocol according to the manufacturer's instructions using the CUTANA CUT&RUN Kit (EpiCypher, 14-1048). H3K4me3 and IgG antibodies served as positive and negative controls, respectively. A K-MetStat panel was added to these samples for quality control. E. coli DNA (0.25 ng) was used as spike-in control for library normalization.
After purification, CUT&RUN DNA was quantified using a Qubit 1X dsDNA high sensitivity assay (Invitrogen, Q33230). A maximum of 5 ng DNA served as input for library preparation using CUTANA CUT&RUN Library Prep Kits with primer set 1 and 2 for multiplexing (EpiCypher, 14-1001 and 14-002). Of note, to avoid denaturing small fragments, end repair inactivation was performed at 50°C for 1 hour instead of 65°C for 30 minutes 94. The distribution of DNA fragment sizes was analyzed using High Sensitivity D1000 assay (Agilent, ScreenTape 5067-5548 and Reagents 5067-5585) in Agilent 4200 Tapestation. The molarity of each library was calculated and normalized to 5 nM. Libraries were pooled and sequenced using the NovaSeq 6000 platform (Illumina), generating 50-bp paired-end reads.

treatment_protocol: Cells were expanded into 10 cm dishes and pre-treated with dTAGV-1 ligand at concentrations ranging from 0 to 150 nM for 3 hours. Following treatment, cells were detached using accutase and subsequently frozen in aliquots of 650,000 cells per condition.

tag: dtag conc

tag: antibody target

value: IgG

tag: replicate

tag: flowcell


title: Peripheral blood CD14+ monocyte, Healthy Control, Rep8

status: Public on Apr 10 2025

type: SRA

city: Glasgow

first: Kieran

last: Woolcock

address: Sir Graeme Davies Building, 120 University Place

department: School of Infection & Immunity

country: United Kingdom

institute: University of Glasgow

description: Library name: HC_R28

library_source: transcriptomic

data_processing:
The fastQ files were quality control checked using FastQC (Andrews, GitHub, v0.11.7) and then aligned to the reference genome and transcriptome GRCh38 (release 102) using STAR (v2.6)
Assembly: GRCh38 (release 102)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Peripheral Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were separated from fresh human blood samples by density gradient centrifugation using Ficoll® Paque Plus (Sigma-Aldrich). To isolate CD14+ monocytes, the EasySep human CD14 positive selection kit II (StemCell Technologies) was used following manufacturer’s instructions.

extract_protocol:
Cells were lysed in RLT buffer (Qiagen) containing 1% beta-mercaptoethanol. RNA was extracted using the PureLinkTM RNA Mini Kit (Invitrogen), as per manufacturer’s instructions. Quality control was performed on the RNA samples using the high sensitivity RNA Analysis Kit (Agilent) on the 2100 Bioanalyzer Instrument (Agilent).
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s instructions. Quality control was performed on the RNA libraries using a high sensitivity DNA Chip (Agilent) on the 2100 Bioanalyzer Instrument (Agilent).

tag: tissue

value: Peripheral Blood

tag: subject status

value: Healthy Control

tag: cell type

value: Monocyte


title: A2.2_0nM_IgG_rep5

description: Library name: S154842

library_source: genomic

molecule: genomic DNA


title: A2.2_0nM_IgG_rep2

description: Library name: S134727


title: A2.2_0nM_IgG_rep4

description: Library name: S154841


title: A2.2_0nM_IgG_rep3

description: Library name: S134726


title: A2.2_0nM_H3K4me3_rep3

description: Library name: S154846


title: A2.2_0nM_H3K4me3_rep2

description: Library name: S154845


title: A2.2_0nM_H3K27me3_rep2

description: Library name: S134685


title: A2.2_0nM_H3K27me3_rep1

description: Library name: S134686


title: A2.2_0nM_H3K4me3_rep1

description: Library name: S125333


title: A2.2_0nM_H3K27ac_rep1

description: Library name: S154909


title: A2.2_0nM_H3K27ac_rep2

description: Library name: S154910


title: A2.2_150nM_FLI1_rep1

description: Library name: S154837


title: A2.2_150nM_FLI1_rep2

description: Library name: S154838


title: Pt6

city: London

first: Kristina

middle: Elizabeth Neergaard

last: Clark

state: England

address: Royal Free Hospital, Pond Street

institute: UCL

description:
Library name: TY42
10X genomics

library_source: transcriptomic single cell

data_processing:
FASTQ files were demultiplexed for each 10× library using the Cell Ranger (V.3.1.0) mkfastq function. Reads were mapped to the GRCh38 human genome
Assembly: GRCh38 human genome
Supplementary files format and content: Tab separated values files and matrix files

molecule: total RNA

source_name: Skin

extract_protocol:
The sample was dissociated using the Human Whole Skin Dissociation Kit (Miltenyi Biotech Inc) with Enzyme P, with overnight incubation as per manufacturers guidelines. The dissociated cells were stored in CryoStor CS10 (StemCell Technologies) at −80°C, then transferred to liquid nitrogen after 24 hours.
Thawing occurred just prior to 7-AAD staining (BioLegend 420404) and viable cell sorting by the SH800 Cell sorter (Sony Biotechnology). Viable cells in single-cell suspension were resuspended in 1% BSA in phosphate-buffered saline (PBS) at a concentration of 1000 cells/µL. A maximum of 20 000 cells were counted using the fluorescence cell counter LUNA-FX7 (Logos Biosystems) and loaded onto a single 10× lane and processed with the 10× Genomics Single Cell 3’ kit (V.3.1) following manufacturer user guide (CG000330). Only 3 samples did not reach this target, and about 17 000 cells were loaded. Sequencing was carried out by the Oxford Genomics Centre, using Illumina NovaSeq 6000 (V.1.5 chemistry, 28 bp/98 bp) and libraries were sequenced to a minimum of 50 000 reads/cell. Cells were analysed in 2 batches.

value: Skin

tag: disease

value: SSc

tag: batch


title: A2.2_50nM_FLI1_rep1

description: Library name: S154839


title: A2.2_15nM_FLI1_rep2

description: Library name: S154834


title: A2.2_5nM_FLI1_rep2

description: Library name: S154830


title: A2.2_5nM_FLI1_rep1

description: Library name: S154829


title: A2.2_15nM_FLI1_rep1

description: Library name: S154833


title: Pt1

description:
Library name: CLA8821A1
10X genomics


title: A2.2_1.5nM_FLI1_rep2

description: Library name: S154832


title: A2.2_0nM_FLI1_rep6

description: Library name: S154828


title: A2.2_1.5nM_FLI1_rep1

description: Library name: S154831


title: A2.2_0nM_FLI1_rep2

description: Library name: S125330


title: A2.2_0nM_FLI1_rep3

description: Library name: S134721


title: A2.2_0nM_FLI1_rep5

description: Library name: S154827


title: A2.2_0nM_FLI1_rep4

description: Library name: S134723


title: A673_0nM_IgG_rep3

description: Library name: S134728


title: A673_0nM_IgG_rep4

description: Library name: S154847


title: A673_0nM_H3K4me3_rep3

description: Library name: S154852


title: A673_0nM_IgG_rep5

description: Library name: S154848


title: A2.2_0nM_FLI1_rep1

description: Library name: S125331


title: A673_0nM_IgG_rep2

description: Library name: S134729


title: A673_0nM_IgG_rep1

description: Library name: S125328


title: A673_0nM_H3K4me3_rep2

description: Library name: S154851


title: A673_0nM_H3K4me3_rep1

description: Library name: S125329


title: A673_0nM_H3K27me3_rep2

description: Library name: S134701


title: A673_0nM_FLI1_rep6

description: Library name: S154844


title: A673_0nM_H3K27ac_rep2

description: Library name: S154916


title: A673_0nM_FLI1_rep5

description: Library name: S154843


title: A2.2_50nM_FLI1_rep2

description: Library name: S154840


title: A673_0nM_H3K27me3_rep1

description: Library name: S134702


title: A673_0nM_FLI1_rep3

description: Library name: S134725


title: A673_0nM_FLI1_rep2

description: Library name: S125326


title: A2.2_150nM_SLAM-seq_rep2

description: Library name: S131872

data_processing:
library strategy: SLAM-seq
SLAM-seq reads were processed using the nf-core/slamseq pipeline (version 1.0.0). The minimum number of T>C conversions in a read to call it a T>C read was set to 2. We used the count matrix of T>C reads (newly synthesized RNA) on the transcript level for downstream analysis.
Assembly: GRCh38.p14
Supplementary files format and content: Matrix of TC conversion containing read counts, TSV
Library strategy: SLAM-seq

growth_protocol: Approximately 4.5 million cells were seeded onto 10 cm dishes and grown to 80% confluency.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen, 74134) according to the manufacturer’s instructions. Total RNA was subjected to alkylation with 10 mM iodoacetamide (IAA, Sigma-Aldrich, I6125) for 15 minutes and RNA was re-purified by ethanol precipitation. The purified RNA was quantified using a Qubit RNA broad range assay (Invitrogen, Q10210).
400 ng of alkylated RNA were used as input for generating 3’-end mRNA sequencing libraries using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, 113.96) and PCR Add-on Kit for Illumina (Lexogen, 020). The distribution of RNA fragments was analyzed using High Sensitivity D1000 assay (Agilent, ScreenTape 5067-5548 and Reagents 5067-5585) in Agilent 4200 Tapestation. Libraries were pooled at 4 nM, and shallow sequencing was performed using MiSeq (Illumina) to estimate the required read counts per sample, aiming for conditions where more than 3% of reads contained ≥2 T>C conversions. Deep sequencing was performed on an Illumina NovaSeq SP flow cell, generating 150 bp single-end reads.

treatment_protocol: The next day, cells were pre-treated with dTAGV-1 ligand at concentrations ranging from 0 to 150 nM for 3 hours to establish an EF protein gradient. Subsequently, newly synthesized RNA was labeled with 1 mM 4-thiouridine (4SU, Biosynth, NT06186) for 100 minutes and cells were harvested by snap-freezing plates on dry ice.


title: A2.2_50nM_SLAM-seq_rep2

description: Library name: S131870


title: A673_0nM_FLI1_rep1

description: Library name: S125327


title: A673_0nM_FLI1_rep4

description: Library name: S134724


title: A2.2_150nM_SLAM-seq_rep1

description: Library name: S131871


title: A2.2_50nM_SLAM-seq_rep1

description: Library name: S131869


title: A2.2_15nM_SLAM-seq_rep2

description: Library name: S131868


title: A2.2_1.5nM_SLAM-seq_rep2

description: Library name: S131862


title: A2.2_5nM_SLAM-seq_rep2

description: Library name: S131864


title: A2.2_1.5nM_SLAM-seq_rep1

description: Library name: S131861


title: A2.2_5nM_SLAM-seq_rep1

description: Library name: S131863


title: A2.2_0nM_SLAM-seq_rep1

description: Library name: S131859


title: A2.2_0nM_SLAM-seq_rep2

description: Library name: S131860


title: A673_0nM_H3K27ac_rep1

description: Library name: S154915


title: B3.1_21day_0nM_dTAG_7day_washout_rep2

description: Library name: VF_48

data_processing:
nf-core/rnaseq v3.14.0
Assembly: GRCh38.p14
Supplementary files format and content: bigWig
Supplementary files format and content: STAR/salmon merged transcript counts, TSV
Supplementary files format and content: STAR/salmon merged gene counts, TSV
Supplementary files format and content: sample metadata table, TSV

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74106), following the manufacturer's instructions, including on-column DNase digestion. Quality control was performed using a DeNovix DS-11 FX spectrophotometer.
Libraries were prepared using the QuantSeq 3’mRNA-Seq V2 Library Prep Kit FWD for Illumina (Lexogen, 113.96) and sequencing was performed on an Illumina NovaSeq SP flow cell, generating 100 bp single-end reads.

treatment_protocol: In one group of of samples, cells were not treated (ssc_experiment). In the other samples, to establish an EF protein gradient, EF-dTAG clones were treated with increasing concentrations of dTAGV-1 ligand (Bio-Techne, 7374). Serial dilutions were prepared from a 10 mM stock to obtain micromolar working stocks, which were further diluted 1000-fold to achieve final dTAGV-1 concentrations of 1.5 nM, 5 nM, 15 nM, 50 nM and 150 nM. Cells were treated with these concentrations for different time intervals as indicated in the text. DMSO was used as vehicle control. For ligand washout, cells were washed twice with DPBS (Gibco, 14190-094), detached using Accutase, and transferred to new culture flasks to allow full recovery of EF expression.

tag: days treated

tag: days washout

tag: sample group


title: B3.1_21day_1.5nM_dTAG_7day_washout_rep1

description: Library name: VF_49


title: B3.1_21day_50nM_dTAG_7day_washout_rep2

description: Library name: VF_58


title: B3.1_21day_0nM_dTAG_7day_washout_rep1

description: Library name: VF_47


title: B3.1_21day_150nM_dTAG_7day_washout_rep1

description: Library name: VF_59


title: B3.1_21day_15nM_dTAG_7day_washout_rep2

description: Library name: VF_56


title: B3.1_21day_5nM_dTAG_7day_washout_rep1

description: Library name: VF_51


title: B3.1_21day_150nM_dTAG_0day_washout_rep2

description: Library name: VF_46


title: B3.1_21day_150nM_dTAG_0day_washout_rep1

description: Library name: VF_45


title: B3.1_21day_5nM_dTAG_7day_washout_rep2

description: Library name: VF_52


title: B3.1_21day_50nM_dTAG_7day_washout_rep1

description: Library name: VF_57


title: B3.1_21day_50nM_dTAG_0day_washout_rep2

description: Library name: VF_44


title: B3.1_21day_5nM_dTAG_0day_washout_rep2

description: Library name: VF_38


title: B3.1_21day_15nM_dTAG_0day_washout_rep2

description: Library name: VF_42


title: B3.1_21day_15nM_dTAG_0day_washout_rep1

description: Library name: VF_41


title: B3.1_21day_1.5nM_dTAG_0day_washout_rep1

description: Library name: VF_35


title: B3.1_21day_150nM_dTAG_7day_washout_rep2

description: Library name: VF_60


title: A2.2_15nM_SLAM-seq_rep1

description: Library name: S131867


title: B3.1_21day_50nM_dTAG_0day_washout_rep1

description: Library name: VF_43


title: B3.1_21day_5nM_dTAG_0day_washout_rep1

description: Library name: VF_37


title: A2.2_28day_150nM_dTAG_7day_washout_rep2

description: Library name: LTC_134


title: A2.2_28day_50nM_dTAG_7day_washout_rep1

description: Library name: LTC_131


title: A2.2_28day_50nM_dTAG_7day_washout_rep2

description: Library name: LTC_132


title: B3.1_21day_15nM_dTAG_7day_washout_rep1

description: Library name: VF_55


title: B3.1_21day_1.5nM_dTAG_7day_washout_rep2

description: Library name: VF_50


title: A2.2_28day_5nM_dTAG_7day_washout_rep1

description: Library name: LTC_125


title: A2.2_28day_15nM_dTAG_7day_washout_rep1

description: Library name: LTC_129


title: A2.2_28day_1.5nM_dTAG_7day_washout_rep2

description: Library name: LTC_124


title: A2.2_28day_1.5nM_dTAG_7day_washout_rep1

description: Library name: LTC_123


title: A2.2_28day_5nM_dTAG_7day_washout_rep2

description: Library name: LTC_126


title: B3.1_21day_0nM_dTAG_0day_washout_rep2

description: Library name: VF_34


title: A2.2_28day_150nM_dTAG_0day_washout_rep1

description: Library name: LTC_69


title: B3.1_21day_1.5nM_dTAG_0day_washout_rep2

description: Library name: VF_36


title: A2.2_28day_0nM_dTAG_7day_washout_rep1

description: Library name: LTC_121


title: A2.2_28day_50nM_dTAG_0day_washout_rep1

description: Library name: LTC_67


title: B3.1_21day_0nM_dTAG_0day_washout_rep1

description: Library name: VF_33


title: A2.2_28day_50nM_dTAG_0day_washout_rep2

description: Library name: LTC_68


title: A2.2_28day_0nM_dTAG_7day_washout_rep2

description: Library name: LTC_122


title: A2.2_28day_150nM_dTAG_7day_washout_rep1

description: Library name: LTC_133


title: A2.2_28day_150nM_dTAG_0day_washout_rep2

description: Library name: LTC_70


title: A2.2_28day_5nM_dTAG_0day_washout_rep2

description: Library name: LTC_62


title: A2.2_28day_15nM_dTAG_0day_washout_rep1

description: Library name: LTC_65


title: A2.2_28day_0nM_dTAG_0day_washout_rep2

description: Library name: LTC_58


title: A2.2_28day_1.5nM_dTAG_0day_washout_rep2

description: Library name: LTC_60


title: A2.2_28day_1.5nM_dTAG_0day_washout_rep1

description: Library name: LTC_59


title: A2.2_28day_0nM_dTAG_0day_washout_rep1

description: Library name: LTC_57


title: A2.2_21day_50nM_dTAG_7day_washout_rep2

description: Library name: LTC_116


title: A2.2_21day_15nM_dTAG_7day_washout_rep1

description: Library name: LTC_113


title: A2.2_21day_50nM_dTAG_7day_washout_rep1

description: Library name: LTC_115


title: A2.2_21day_15nM_dTAG_7day_washout_rep2

description: Library name: LTC_114


title: A2.2_21day_150nM_dTAG_7day_washout_rep1

description: Library name: LTC_117


title: A2.2_28day_15nM_dTAG_7day_washout_rep2

description: Library name: LTC_130


title: A2.2_28day_15nM_dTAG_0day_washout_rep2

description: Library name: LTC_66


title: A2.2_28day_5nM_dTAG_0day_washout_rep1

description: Library name: LTC_61


title: A2.2_21day_5nM_dTAG_7day_washout_rep1

description: Library name: LTC_109


title: A2.2_21day_1.5nM_dTAG_7day_washout_rep1

description: Library name: LTC_107


title: A2.2_21day_1.5nM_dTAG_7day_washout_rep2

description: Library name: LTC_108


title: A2.2_21day_0nM_dTAG_7day_washout_rep1

description: Library name: LTC_105


title: A2.2_21day_5nM_dTAG_7day_washout_rep2

description: Library name: LTC_110


title: A2.2_21day_150nM_dTAG_7day_washout_rep2

description: Library name: LTC_118


title: A2.2_21day_0nM_dTAG_7day_washout_rep2

description: Library name: LTC_106


title: A2.2_21day_50nM_dTAG_0day_washout_rep2

description: Library name: LTC_52


title: A2.2_21day_150nM_dTAG_0day_washout_rep1

description: Library name: LTC_53


title: A2.2_21day_15nM_dTAG_0day_washout_rep1

description: Library name: LTC_49


title: A2.2_21day_150nM_dTAG_0day_washout_rep2

description: Library name: LTC_54


title: A2.2_21day_5nM_dTAG_0day_washout_rep2

description: Library name: LTC_46


title: A2.2_21day_50nM_dTAG_0day_washout_rep1

description: Library name: LTC_51


title: A2.2_21day_15nM_dTAG_0day_washout_rep2

description: Library name: LTC_50


title: A2.2_21day_1.5nM_dTAG_0day_washout_rep1

description: Library name: LTC_43


title: A2.2_21day_5nM_dTAG_0day_washout_rep1

description: Library name: LTC_45


title: A2.2_14day_150nM_dTAG_7day_washout_rep2

description: Library name: LTC_102


title: A2.2_21day_0nM_dTAG_0day_washout_rep1

description: Library name: LTC_41


title: A2.2_14day_150nM_dTAG_7day_washout_rep1

description: Library name: LTC_101


title: A2.2_21day_0nM_dTAG_0day_washout_rep2

description: Library name: LTC_42


title: A2.2_14day_50nM_dTAG_7day_washout_rep1

description: Library name: LTC_99


title: A2.2_14day_15nM_dTAG_7day_washout_rep2

description: Library name: LTC_98


title: A2.2_14day_5nM_dTAG_7day_washout_rep2

description: Library name: LTC_94


title: A2.2_21day_1.5nM_dTAG_0day_washout_rep2

description: Library name: LTC_44


title: A2.2_14day_15nM_dTAG_7day_washout_rep1

description: Library name: LTC_97


title: A2.2_14day_1.5nM_dTAG_7day_washout_rep2

description: Library name: LTC_92


title: A2.2_14day_0nM_dTAG_7day_washout_rep2

description: Library name: LTC_90


title: A2.2_14day_50nM_dTAG_7day_washout_rep2

description: Library name: LTC_100


title: A2.2_14day_0nM_dTAG_7day_washout_rep1

description: Library name: LTC_89


title: A2.2_14day_1.5nM_dTAG_7day_washout_rep1

description: Library name: LTC_91


title: A2.2_14day_150nM_dTAG_0day_washout_rep1

description: Library name: LTC_37


title: Multiome, murine lung tissue, ATAC5

city: New Haven

first: Pei-Chun

last: Cha

state: CT

address: 333 Cedar Street

country: USA

institute: Yale University

description:
Library name: sample5_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
scRANseq and scATACseq files were demultiplexed using Cellranger v7.1.0 and Cellranger ATAC v2.1.0, respectively.
Assembly: Mouse mm10
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger ATAC output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz

organism: Mus musculus

source_name: lung

extract_protocol:
Nuclei were isolated from human snap frozen lung tissue using the 10x genomics nuclei isolation kit, per manual (document number CG000505, revision A, May 2022). An aliquot of nuclei was stained with 0.4% trypan blue stain and DAPI and subsequently counted with the Thermo Fisher countess II FL. Samples with > 90% viability were used for downstream analysis.
Approximately 10,000 nuclei per sample were loaded onto chip J and processed with the Chromium X Series to create to create Gel Beads-in-emulsion (GEMs). The next steps were carried out according to the manufacturer’s user guide (CG000338, revision G, September 2024) [10], including post-GEM-RT Dynabead cleanup and Pre-Amplification. Each sample was then split into two portions: one for ATAC library construction and the other for cDNA amplification and gene expression library construction. DNA from the ATAC libraries (scATAC libraries) and cDNA from the gene expression libraries (scRNA libraries) were assessed at two time points using the Agilent Bioanalyzer High Sensitivity Chip to ensure quality. Six scATAC libraries and six scRNA libraries were sequenced on the Novaseq 6000 platform, using 2 × 100 bp paired-end sequencing configuration.

value: lung

tag: cell line

value: mixed cells

tag: treatment

value: hyperoxia


title: Multiome, murine lung tissue, ATAC6

description:
Library name: sample6_ATAC
10x Genomics

value: cigarette smoke, hyperoxia


title: A2.2_14day_50nM_dTAG_0day_washout_rep2

description: Library name: LTC_36


title: A2.2_14day_15nM_dTAG_0day_washout_rep2

description: Library name: LTC_34


title: HFD+Abx-1

type: RNA

city: Suzhou

first: Songbing

last: He

address: No 188 Shizi street

country: China

institute: Department of General Surgery

description: Gene expression

hyb_protocol: The labelled circRNA was hybridised onto an Arraystar Mouse circRNA array (8 × 15 K, Arraystar) and incubated in an Agilent Hybridization Incubator (Agilent, Santa Clara, CA, USA) at 65°C for 17 h.

scan_protocol: The slides were scanned with an Agilent G2505C Scanner.

data_processing: Data were extracted using Agilent feature extraction software.Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.

source_name: intestine

label_protocol: The enriched circular RNA was amplified using random primers and transcribed into fluorescent circRNA.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.Circular RNA was enriched and obtained with the use of RNase R to total RNA.

value: Intestinal tumors


title: HFD-3

description: Gene expression


title: Multiome, murine lung tissue, ATAC4

description:
Library name: sample4_ATAC
10x Genomics

value: cigarette smoke, influenza infection


title: A2.2_14day_15nM_dTAG_0day_washout_rep1

description: Library name: LTC_33


title: HFD-2

description: Gene expression


title: HFD-1

description: Gene expression


title: HFD+Abx-2

description: Gene expression


title: Multiome, murine lung tissue, ATAC1

description:
Library name: sample1_ATAC
10x Genomics


title: A2.2_14day_5nM_dTAG_7day_washout_rep1

description: Library name: LTC_93


title: CTR-2

description: Gene expression


title: Multiome, murine lung tissue, ATAC3

description:
Library name: sample3_ATAC
10x Genomics

value: influenza infection


title: A2.2_14day_50nM_dTAG_0day_washout_rep1

description: Library name: LTC_35


title: Multiome, murine lung tissue, GEX6

description:
Library name: sample6_RNA
10x Genomics


title: Multiome, murine lung tissue, ATAC2

description:
Library name: sample2_ATAC
10x Genomics

value: cigarette smoke


title: A2.2_14day_5nM_dTAG_0day_washout_rep1

description: Library name: LTC_29


title: A2.2_14day_1.5nM_dTAG_0day_washout_rep1

description: Library name: LTC_27


title: A2.2_14day_5nM_dTAG_0day_washout_rep2

description: Library name: LTC_30


title: Multiome, murine lung tissue, GEX3

description:
Library name: sample3_RNA
10x Genomics


title: Multiome, murine lung tissue, GEX5

description:
Library name: sample5_RNA
10x Genomics


title: A2.2_14day_150nM_dTAG_0day_washout_rep2

description: Library name: LTC_38


title: HFD+Abx-3

description: Gene expression


title: CTR-1

description: Gene expression


title: A2.2_7day_150nM_dTAG_7day_washout_rep2

description: Library name: LTC_86


title: Multiome, murine lung tissue, GEX1

description:
Library name: sample1_RNA
10x Genomics


title: A2.2_14day_1.5nM_dTAG_0day_washout_rep2

description: Library name: LTC_28


title: A2.2_7day_150nM_dTAG_7day_washout_rep1

description: Library name: LTC_85


title: A2.2_7day_50nM_dTAG_7day_washout_rep1

description: Library name: LTC_83


title: Multiome, murine lung tissue, GEX4

description:
Library name: sample4_RNA
10x Genomics


title: YAP/TAZ fibroblast KD_doxycycline day 7_biological replicate 1 (scRNA-seq)

city: South San Francisco

first: David

last: Garfield

state: CA

address: 1 DNA Way

department: OMNI Bx

institute: Genentech

description:
Library name: SAM24429072
10x Genomics

data_processing:
This is the RNA portion of a multiome experiment. After sequencing, we aligned the fastq files to the mouse genome (GRCm38/mm10) and performed initial cell calling using CellRange-arc v2.0 from 10x. The resulting alignment files were then further processed with CellBender to adjust the per-cell counts for estimated ambient RNA. Data were then imported from the CellBender output into a count matrix using DropletUtils and were further analyzed using the scran.chan package in R.
Assembly: GRCm38/mm10
Supplementary files format and content: Raw count data  count data are given as .mtx files. Sample level (column) data for each processed cell can be found in metaData.txt. Gene level (row) data can be found in geneData.txt A barcode file is also provided.

growth_protocol: Alveolospheres were maintained in MTEC/Plus medium in a humidified condition with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Rneasy mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following manufacturer's protocol

treatment_protocol: All samples were treated with 3 ug/mL doxycycline, dissolved in DMSO, added directly to the cell culture media from day 7 until collection on day 14.

value: alveolar type 2 cells and PDGFRa+ lung  fibroblasts

tag: genotype

value: wildtype alveolar type 2 cells and PDGFRa-specific YAP/TAZ KD

value: 3ug/ml doxycycline at day 7 of culture


title: A2.2_7day_50nM_dTAG_7day_washout_rep2

description: Library name: LTC_84


title: A2.2_14day_0nM_dTAG_0day_washout_rep2

description: Library name: LTC_26


title: Control_doxycycline day 7_biological replicate 2 (scRNA-seq)

description:
Library name: SAM24429071
10x Genomics

value: wildtype


title: A2.2_7day_15nM_dTAG_7day_washout_rep1

description: Library name: LTC_81


title: A2.2_7day_5nM_dTAG_7day_washout_rep2

description: Library name: LTC_78


title: Multiome, murine lung tissue, GEX2

description:
Library name: sample2_RNA
10x Genomics


title: YAP/TAZ fibroblast KD_doxycycline day 7_biological replicate 2 (scRNA-seq)

description:
Library name: SAM24429073
10x Genomics


title: Control_doxycycline day 7_biological replicate 1 (scRNA-seq)

description:
Library name: SAM24429070
10x Genomics


title: YAP/TAZ fibroblast KD_doxycycline day 7_biological replicate 2 (scATAC-seq)

description: Library name: SAM24429073

data_processing:
This is the ATAC portion of a multiome experiment. After sequencing, we aligned the fastq files to the mouse genome (GRCm38/mm10) and performed initial cell calling using CellRange-arc v2.0 from 10x. Data were then imported from the CellBender output into ArchR for further QC and clustering.
Assembly: GRCm38/mm10
Supplementary files format and content: Raw count data  count data are given as .mtx files and in this case represents counts per peak. Sample level (column) data for each processed cell can be found in metaData.txt. Peak level (row) data can be found in geneData.txt A barcode file is also provided.

molecule: nuclear RNA


title: YAP/TAZ fibroblast KD_doxycycline day 7_biological replicate 1 (scATAC-seq)

description: Library name: SAM24429072


title: A2.2_7day_1.5nM_dTAG_7day_washout_rep2

description: Library name: LTC_76


title: Control_doxycycline day 7_biological replicate 2 (scATAC-seq)

description: Library name: SAM24429071


title: CTR-3

description: Gene expression


title: A2.2_7day_5nM_dTAG_7day_washout_rep1

description: Library name: LTC_77


title: myocardial tissues, T6

city: Jinan

first: Xiaohong

last: Wang

address: Wenhuaxi Road

institute: Qilu Hospital of Shandong University

description: Library name: Sample 9

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 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. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: myocardial tissues

growth_protocol: Take heart tissue from the ischemic area of mice

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ischemia reperfusion for 24 hours

value: myocardial tissues

value: STING-knockout

value: Ischemia reperfusion for 24 hours


title: A2.2_7day_150nM_dTAG_0day_washout_rep2

description: Library name: LTC_22


title: myocardial tissues, T3

description: Library name: Sample 6


title: myocardial tissues, T5

description: Library name: Sample 8


title: A2.2_7day_1.5nM_dTAG_7day_washout_rep1

description: Library name: LTC_75


title: A2.2_14day_0nM_dTAG_0day_washout_rep1

description: Library name: LTC_25


title: myocardial tissues, T2

description: Library name: Sample 5


title: myocardial tissues, T4

description: Library name: Sample 7


title: A2.2_7day_0nM_dTAG_7day_washout_rep2

description: Library name: LTC_74


title: A2.2_7day_0nM_dTAG_7day_washout_rep1

description: Library name: LTC_73


title: A2.2_7day_15nM_dTAG_0day_washout_rep2

description: Library name: LTC_18


title: myocardial tissues, N1

description: Library name: Sample 1

value: WT


title: A2.2_7day_150nM_dTAG_0day_washout_rep1

description: Library name: LTC_21


title: A2.2_7day_15nM_dTAG_7day_washout_rep2

description: Library name: LTC_82


title: A2.2_7day_15nM_dTAG_0day_washout_rep1

description: Library name: LTC_17


title: myocardial tissues, N3

description: Library name: Sample 3


title: A2.2_7day_50nM_dTAG_0day_washout_rep2

description: Library name: LTC_20


title: A2.2_7day_50nM_dTAG_0day_washout_rep1

description: Library name: LTC_19


title: A2.2_7day_5nM_dTAG_0day_washout_rep2

description: Library name: LTC_14


title: A2.2_7day_5nM_dTAG_0day_washout_rep1

description: Library name: LTC_13


title: Female, WT, unique identifier 782

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: 102

data_processing:
These files were then further processed with Seurat v5.1.  Low-quality nuclei were filtered out by subsetting the objects with the following criteria: nCount_RNA > 2,000; percent.mt < 2.0; and nFeature > 500. Gene expression was merged, normalized using LogNormalization, and underwent Harmony batch correction. Cell type assignment was generated in the internal dataset using the Azimuth package and the RunAzimuth function, and the ‘predicted.annotation.l3’ cell-type assignment was used for further analysis.
Assembly: mm10
Supplementary files format and content: barcodes with annotations barcodes.csv file
Supplementary files format and content: seurat.qs is the analyzed seurat object

source_name: kidney

extract_protocol:
Nuclei from that kidney were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (cOmplete™ ULTRA tab; Sigma-Aldrich) . The frozen kidney cubes were placed in a sterile petri dish with 1 ml of Nuclei EZ lysis buffer (plus protease and RNase inhibitors) and quickly minced.  The tissue was then homogenized with RNase-free, disposable pellet pestles and tubes (Fisher #12-141-368), and a hand held, Bel-Art™ Micro-Tube homogenizer (Wayne, NJ).  The homogenate was filtered through a 40 micron strainer (all strainers were purchase from pluriSelect Life Science).  The homogenate was moved to a sterile, RNase-free 15 ml tube with an additional 2 ml of Nuclei EZ lysis buffer (plus protease and RNase inhibitors).  After a 5 min incubation on ice, the homogenate was filtered through a 40 micron strainer.  The subsequent homogenate was centrifuged at 500 g for 5 min at 4°C.  The pellet was resuspending in DPBS buffer (plus 1% BSA, 1 ul/ml of SUPERaseIN and RNAsin), incubated on ice for 5 min and centrifuged again.  The pellet was resuspended in 0.5 ml of this DPBS+BSA and inhibitors, filtered through a 5 micron strainer, and nuclei immediately counted with a hemocytometer.
5000-10000 nuclei per sample were loaded in the Chromium Next GEM Chip G Single Cell Kit and the DNA libraries generated with the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1.

treatment_protocol: ad libitum food and water

value: kidney

tag: Sex

value: female


title: 2838 Mcu CRISPR-KO cells clone 42 3

city: Philadelphia

first: J. Kevin

last: Foskett

state: PA

address: CRB Room 720, 415 Curie Blvd

department: Physiology

institute: University of Pennsylvania

description:
Library name: 2838sgMCU42_3
2838sgMCU42_4

data_processing:
sequenced by Novogene with a NovoSeq PE150 at ~20 M paired-end reads. Raw reads were processed with Salmon and DESeq2 before analysis.
Assembly: mm10
Supplementary files format and content: Gene TPM, .csv format

source_name: pancreatic tumor derived

growth_protocol: Cells were maintained in DMEM+10%FBS+ 1x Anti/Anti (Gibco) at 37 degrees C and 5% CO2 in a humidified incubator and passaged every 2-3 days. Mcu re-expressing cells and their isogenic Cre-KO pairs were also maintained in the presence of 2 μg/mL puromycin dihydrochloride.

extract_protocol:
RNA was isolated from untreated cells with a RNeasy Mini kit (Qiagen 74104) from 10-15-cm dishes.
provided by Novogene

treatment_protocol: Cells were not treated.

value: pancreatic tumor derived

value: Mcu CRISPR knockout

value: untreated


title: Male, WT, unqiue identifier 684

description: Library name: 100

value: male


title: A2.2_7day_1.5nM_dTAG_0day_washout_rep2

description: Library name: LTC_12


title: Control_doxycycline day 7_biological replicate 1 (scATAC-seq)

description: Library name: SAM24429070

value: lung


title: A2.2_7day_1.5nM_dTAG_0day_washout_rep1

description: Library name: LTC_11


title: 2838 Mcu CRISPR-KO cells clone 42 2

description:
Library name: 2838sgMCU42_2
2838sgMCU42_4


title: 2838 Mcu CRISPR-KO cells clone 42 1

description:
Library name: 2838sgMCU42_1
2838sgMCU42_4


title: A2.2_7day_0nM_dTAG_0day_washout_rep2

description: Library name: LTC_10


title: myocardial tissues, T1

description: Library name: Sample 4


title: 2838 Mcu CRISPR-KO cells clone 17 3

description:
Library name: 2838sgMCU17_3
2838sgMCU17_1


title: 2838 Mcu CRISPR-KO cells clone 17 1

description:
Library name: 2838sgMCU17_1
2838sgMCU17_1


title: A2.2_7day_0nM_dTAG_0day_washout_rep1

description: Library name: LTC_9


title: 2838 Mcu CRISPR-KO cells clone 17 2

description:
Library name: 2838sgMCU17_2
2838sgMCU17_1


title: myocardial tissues, N2

description: Library name: Sample 2


title: 2838 Mcu WT cells, empty vector expressing clone 22 2

description:
Library name: 2838WT22_2
2838WT22_2

value: Mcu wild type


title: B3.1_24h_50nM_dTAG_rep2

description: Library name: VF_30


title: 2838 Mcu WT cells, empty vector expressing clone 22 1

description:
Library name: 2838WT22_1
2838WT22_2


title: B3.1_24h_50nM_dTAG_rep1

description: Library name: VF_29


title: B3.1_24h_15nM_dTAG_rep2

description: Library name: VF_28


title: 2838 Mcu WT cells, empty vector expressing clone 22 3

description:
Library name: 2838WT22_3
2838WT22_2


title: 2838 Mcu WT cells, empty vector expressing clone 15 3

description:
Library name: 2838WT15_3
2838WT15_1


title: 2838 Mcu WT cells, empty vector expressing clone 15 2

description:
Library name: 2838WT15_2
2838WT15_1


title: B3.1_24h_5nM_dTAG_rep2

description: Library name: VF_24


title: B3.1_24h_5nM_dTAG_rep1

description: Library name: VF_23


title: 1151 Mcu Cre-KO cells, MCU re-expressing 3

description:
Library name: 1151_MCU3
1151_MCU3

value: Mcu reexpressing


title: 1151 Mcu Cre-KO cells, MCU re-expressing 1

description:
Library name: 1151_MCU1
1151_MCU1


title: B3.1_24h_1.5nM_dTAG_rep2

description: Library name: VF_22


title: 1151 Mcu Cre-KO cells, MCU re-expressing 2

description:
Library name: 1151_MCU2
1151_MCU2


title: B3.1_24h_1.5nM_dTAG_rep1

description: Library name: VF_21


title: 1151 Mcu Cre-KO cells, empty vector expressing 3

description:
Library name: 1151_EV3
1151_EV3

value: Mcu Cre knockout


title: B3.1_24h_0nM_dTAG_rep1

description: Library name: VF_19


title: B3.1_24h_0nM_dTAG_rep2

description: Library name: VF_20


title: 1151 Mcu Cre-KO cells, empty vector expressing 2

description:
Library name: 1151_EV2
1151_EV2


title: B3.1_24h_150nM_dTAG_rep2

description: Library name: VF_32


title: B3.1_24h_150nM_dTAG_rep1

description: Library name: VF_31


title: A2.2_24h_150nM_dTAG_rep2

description: Library name: VF_18


title: 1151 Mcu Cre-KO cells, empty vector expressing 1

description:
Library name: 1151_EV1
1151_EV1


title: A2.2_24h_150nM_dTAG_rep1

description: Library name: VF_17


title: A2.2_24h_50nM_dTAG_rep2

description: Library name: VF_16


title: A2.2_24h_50nM_dTAG_rep1

description: Library name: VF_15


title: Multiome, DRG neurons, wild-type5 GEX

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description:
Library name: P29461_1005
3' mRNA (v3.1 10x Genomics): Read1 contains cell barcode and UMI; Read2 contains transcript sequence

data_processing:
Pooled ATAC libraries were sequenced on Illumina sequencing platform NovaSeq 6000 system on one S1-100 (v1.5) flowcell with a custom read set-up of 50-8-24-49 bp and pooled gene expression libraries were sequenced on Illumina sequencing platform NovaSeq 6000 system on one lane of a S4-300 (v1.5) flowcell with a custom read set-up of 28-10-10-90 bp in National Genomics Infrastructure (SciLifeLab).
Raw sequencing data were de-multiplexed, converted into fastq format, and aligned to mouse reference mm10 using the CellRanger ARC (v.2.0) to generate aggregated gene-cell and fragment-cell matrices.
Assembly: mm10
Supplementary files format and content: CellRanger output files: aggregated_filtered_feature_bc_matrix.h5; aggregated_raw_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files: aggregated_atac_fragments.tsv.gz; aggregated_atac_fragments.tsv.gz.tbi
Supplementary files format and content: Analysis output files: rna_counts.tsv; celltype_peak_counts.tsv; metadata.tsv

source_name: DRG

extract_protocol:
Frozen DRG from 12 wild type mice (n=6 males, n=6 females, 8-10 weeks) were pooled and thawn on wet ice in 300 µl homogenization buffer (10mM Tris pH 8.0, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 0.1 mM DTT, 0.1 % Triton-X-100, 0.2 U/µl RNasin RNase inhibitor (Promega), 1x Protease inhibitor cocktail (Promega)). The tissue was motor grinded (20x 3s) and incubated on ice for 10 min followed by 20x douncing with pestle A and 20x pestle B and another 5 min incubation on ice. Cells were then filtered through a 100 µm, 50 µm and finally 30 µm cell strainer (BD falcon) and homogenization buffer was added to a final volume of 10 ml before centrifugation at 1500 xg, 10 min, 4°C. For debris removal a 25-29 % iodixanol (in 60mM Tris pH 8.0, 250 mM sucrose, 150 mM KCl, 30 mM MgCl2) gradient centrifugation was performed for 25 min at 13,500 xg, 4°C. The pellet was resuspended in blocking buffer I (1x PBS pH 7.4, 1 % BSA, 0.2 U/µl RNase inhibitor) and stained with anti-NeuN-PE antibody (Millipore, FCMAB317PE) at 1:250 dilution for 30 min on ice. Afterward the sample was centrifuged at 500 xg, 4°C for 5 min and resuspended in clean blocking buffer II (1X PBS pH 7.4, 2.5 % BSA, 0.2 U/µl RNase inhibitor) and DAPI was added to a final concentration of 0.1 µg/ ml. NeuN+/DAPI+ nuclei were sorted using fluorescence activated cell sorting (FACS, BD FACS Aria Fusion), centrifuged (500 xg, 5 min, 4°C) and resuspended in 1X diluted nuclei buffer (10X Genomics) and counted.
Multi-omics sequencing was performed using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit. In short, a targeted number of sorted nuclei (1,000-5,000) was treated with Tn5 transposase for 60 min at 37°C for DNA fragmentation and insertion of adaptor sequences into open chromatin of the nuclei. Nuclei suspension was the loaded onto Chromium Next GEM Chip J for single nuclei droplet generation using Chromium Controller. Reverse transcription, cDNA amplification and Gene expression and ATAC library construction were performed according to the user guide provided by manufacture

value: DRG

value: Neuron

value: wild-type

value: Naive


title: Multiome, DRG neurons, wild-type4 ATAC

description:
Library name: P29460_1004
ATAC: Read1 contains cell barcode and UMI; Read2 contains ATAC sequences


title: A2.2_24h_15nM_dTAG_rep2

description: Library name: VF_14


title: B3.1_24h_15nM_dTAG_rep1

description: Library name: VF_27


title: Multiome, DRG neurons, wild-type3 GEX

description:
Library name: P29461_1003
3' mRNA (v3.1 10x Genomics): Read1 contains cell barcode and UMI; Read2 contains transcript sequence


title: Multiome, DRG neurons, wild-type4 GEX

description:
Library name: P29461_1004
3' mRNA (v3.1 10x Genomics): Read1 contains cell barcode and UMI; Read2 contains transcript sequence


title: A2.2_24h_5nM_dTAG_rep2

description: Library name: VF_10


title: Multiome, DRG neurons, wild-type3 ATAC

description:
Library name: P29460_1003
ATAC: Read1 contains cell barcode and UMI; Read2 contains ATAC sequences


title: Multiome, DRG neurons, wild-type5 ATAC

description:
Library name: P29460_1005
ATAC: Read1 contains cell barcode and UMI; Read2 contains ATAC sequences


title: A2.2_24h_5nM_dTAG_rep1

description: Library name: VF_9


title: Multiome, DRG neurons, wild-type2 ATAC

description:
Library name: P29460_1002
ATAC: Read1 contains cell barcode and UMI; Read2 contains ATAC sequences


title: Multiome, DRG neurons, wild-type2 GEX

description:
Library name: P29461_1002
3' mRNA (v3.1 10x Genomics): Read1 contains cell barcode and UMI; Read2 contains transcript sequence


title: 2838 Mcu WT cells, empty vector expressing clone 15 1

description:
Library name: 2838WT15_1
2838WT15_1


title: A2.2_24h_1.5nM_dTAG_rep1

description: Library name: VF_7


title: Multiome, DRG neurons, wild-type1 ATAC

description:
Library name: P29460_1001
ATAC: Read1 contains cell barcode and UMI; Read2 contains ATAC sequences


title: A2.2_24h_0nM_dTAG_rep1

description: Library name: VF_5


title: A2.2_24h_1.5nM_dTAG_rep2

description: Library name: VF_8


title: Multiome, DRG neurons, wild-type1 GEX

description:
Library name: P29461_1001
3' mRNA (v3.1 10x Genomics): Read1 contains cell barcode and UMI; Read2 contains transcript sequence


title: A2.2_24h_0nM_dTAG_rep2

description: Library name: VF_6


title: B3.1_rep2

description: Library name: VF_68


title: A2.2_rep2

description: Library name: VF_64


title: B3.1_rep1

description: Library name: VF_67


title: PoolN_Collection4_embryo11

city: Munich

first: Maria-Elena

last: Torres-Padilla

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: PoolN_Collection4_embryo11
2x150bp reads

data_processing:
RNA-seq read pairs were aligned to the mouse reference genome using STAR (version 2.7.6a) with the Gencode annotation (vM20). ERCC spike-in sequences and annotations were included from the ThermoFisher repository. Additionally, human SUV39H1 and membrane-eGFP sequences were appended to the reference genome before alignment. STAR was run with the parameters --outFilterMultimapNmax 100 and --winAnchorMultimapNmax 100. Gene and transposable element (TE) counts were generated using TEcount, with parameters --mode multi --stranded no.
Assembly: GRCm38
Supplementary files format and content: RNAseq count table from TECount

source_name: Late 2-cell embryo

growth_protocol: Zygotes were collected at 18h post-hCG, microinjected and cultured in KSOM until 48h post-hCG (late 2-cell stage), and collected for RNA-sequencing.

extract_protocol:
Single embryos were used for single embryo RNA-seq (Smart-seq+5'), for more information see methods of accompanying paper.
An adapted version of Smart-seq2 (called Smart-seq+5') enabling to capture both the 5' transcript information in addition to internal fragment. See methods of the accompanying paper for more information.
Smart-seq+5'

treatment_protocol: Embryos were microinjected with either membrane-eGFP mRNA alone (Control) or together with mRNAs encoding candidate proteins from the respective pools (Pool J: Suv39h1, Hp1a, Hp1g; Pool M: H1.2, H1.4, H1.5, macroH2A.1; Pool I: Lsd1, Kdm7a, Kdm7c; Pool N: Ehmt1, Ehmt2, Setdb1, Setdb2). For each batch, embryos were collected in aliquots of the same lysis buffer.

value: Late 2-cell embryo

value: (C57BL/6J x CBA) x DBA/2J

tag: mrna injected

value: PoolN (1200 ng/μL Ehmt1, 1200 ng/μL Ehmt2, 1200 ng/μL Setdb1, 700 ng/μL Setdb2)


title: PoolN_Collection4_embryo13

description:
Library name: PoolN_Collection4_embryo13
2x150bp reads


title: PoolN_Collection4_embryo12

description:
Library name: PoolN_Collection4_embryo12
2x150bp reads


title: PoolN_Collection4_embryo10

description:
Library name: PoolN_Collection4_embryo10
2x150bp reads


title: A2.2_rep1

description: Library name: VF_63


title: A673_bulk_rep2

description: Library name: VF_70


title: PoolN_Collection4_embryo9

description:
Library name: PoolN_Collection4_embryo9
2x150bp reads


title: PoolN_Collection4_embryo8

description:
Library name: PoolN_Collection4_embryo8
2x150bp reads


title: A2.2_24h_15nM_dTAG_rep1

description: Library name: VF_13

tag: dtag conc


title: PoolI_Collection4_embryo14

description:
Library name: PoolI_Collection4_embryo14
2x150bp reads

value: PoolI (800 ng/μL Lsd1, 800 ng/μL Kdm7a, 1000 ng/μL Kdm7c)


title: A673_clone7_rep2

description: Library name: VF_84


title: PoolI_Collection4_embryo12

description:
Library name: PoolI_Collection4_embryo12
2x150bp reads


title: PoolI_Collection4_embryo13

description:
Library name: PoolI_Collection4_embryo13
2x150bp reads


title: A673_clone6_rep2

description: Library name: VF_82


title: PoolI_Collection4_embryo10

description:
Library name: PoolI_Collection4_embryo10
2x150bp reads


title: PoolI_Collection4_embryo11

description:
Library name: PoolI_Collection4_embryo11
2x150bp reads


title: A673_clone6_rep1

description: Library name: VF_81


title: A673_clone5_rep2

description: Library name: VF_80


title: PoolI_Collection4_embryo8

description:
Library name: PoolI_Collection4_embryo8
2x150bp reads


title: mGFP_Control_Collection4_embryo12

description:
Library name: mGFP_Control_Collection4_embryo12
2x150bp reads

value: Control (100 ng/μL mGFP)


title: PoolI_Collection4_embryo9

description:
Library name: PoolI_Collection4_embryo9
2x150bp reads


title: A673_clone5_rep1

description: Library name: VF_79


title: A673_clone4_rep1

description: Library name: VF_77


title: A673_clone4_rep2

description: Library name: VF_78


title: A673_clone3_rep2

description: Library name: VF_76


title: mGFP_Control_Collection4_embryo11

description:
Library name: mGFP_Control_Collection4_embryo11
2x150bp reads


title: mGFP_Control_Collection4_embryo9

description:
Library name: mGFP_Control_Collection4_embryo9
2x150bp reads


title: A673_clone3_rep1

description: Library name: VF_75


title: A673_clone2_rep2

description: Library name: VF_74


title: mGFP_Control_Collection4_embryo10

description:
Library name: mGFP_Control_Collection4_embryo10
2x150bp reads


title: mGFP_Control_Collection4_embryo8

description:
Library name: mGFP_Control_Collection4_embryo8
2x150bp reads


title: A673_bulk_rep1

description: Library name: VF_69


title: A673_clone1_rep2

description: Library name: VF_72


title: A673_clone2_rep1

description: Library name: VF_73


title: PoolN_Collection3_embryo6

description:
Library name: PoolN_Collection3_embryo6
2x150bp reads


title: A673_clone7_rep1

description: Library name: VF_83


title: PoolN_Collection3_embryo5

description:
Library name: PoolN_Collection3_embryo5
2x150bp reads


title: A673_clone1_rep1

description: Library name: VF_71


title: PoolN_Collection3_embryo3

description:
Library name: PoolN_Collection3_embryo3
2x150bp reads


title: PoolN_Collection3_embryo4

description:
Library name: PoolN_Collection3_embryo4
2x150bp reads


title: GL0000267_CD45pos

first: Patrick

middle: Watson

last: Mellors

state: Pennsylvania

address: 3400 Civic Center Drive SCTR 8th Floor

description: Library name: EEM_scRNA_205

data_processing:
To generate H5 files, transcripts were mapped to the GRCh38 human reference genome and feature-barcode matrices were generated using Cell Ranger count v7.0.1 from 10X Genomics.
Assembly: GRCh38
Supplementary files format and content: raw*.H5: Cellranger RAW count files
Supplementary files format and content: filtered*.H5: Cellranger RAW count files
Supplementary files format and content: RDS:Processed data as a Seurat object 1) clad_normal_cd45pos.rds integrated, filtered/QC object with reference annotated CD45 positive cells from 4 CLAD and 3 NC patients 2) clad_normal_cd45neg.rds  integrated, filtered/QC object with reference annotated CD45 negative cells from 4 CLAD and 3 NC patients 3) gvhd_normal_cd45pos.rds integrated, filtered/QC object with reference annotated CD45 positive cells from 3 GVHD and 3 NC patients 4) gvhd_normal_cd45neg.rds integrated, filtered/QC object with reference annotated CD45 negative cells from 3 GVHD and 3 NC patients

source_name: distal lung

extract_protocol:
Peripheral samples: 2cm deep from the pleura, airway or vessel visible structures >2mm removed.
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two or one biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on Novaseq 6000 with 2 × 100 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

tag: disease state

value: Normal

tag: cell enrichment

value: distal lung

tag: library platform

tag: suspension type

value: cell


title: GL0000267_CD45neg

description: Library name: EEM_scRNA_206

tag: tissue


title: GL0000171_CD45pos

description: Library name: EEM_scRNA_074


title: GL0000189_CD45neg

description: Library name: EEM_scRNA_079


title: PoolN_Collection3_embryo2

description:
Library name: PoolN_Collection3_embryo2
2x150bp reads


title: GL0000171_CD45neg

description: Library name: EEM_scRNA_073


title: GL0000189_CD45pos

description: Library name: EEM_scRNA_080


title: PoolN_Collection3_embryo1

description:
Library name: PoolN_Collection3_embryo1
2x150bp reads


title: PoolI_Collection3_embryo7

description:
Library name: PoolI_Collection3_embryo7
2x150bp reads


title: R710000715_CD45neg

description: Library name: EEM_scRNA_247

value: CLAD BOS


title: PoolI_Collection3_embryo6

description:
Library name: PoolI_Collection3_embryo6
2x150bp reads


title: R710000705_CD45neg

description: Library name: EEM_scRNA_234


title: PoolI_Collection3_embryo4

description:
Library name: PoolI_Collection3_embryo4
2x150bp reads


title: R710000715_CD45pos

description: Library name: EEM_scRNA_248


title: PoolI_Collection3_embryo3

description:
Library name: PoolI_Collection3_embryo3
2x150bp reads


title: PoolI_Collection3_embryo5

description:
Library name: PoolI_Collection3_embryo5
2x150bp reads


title: PoolI_Collection3_embryo2

description:
Library name: PoolI_Collection3_embryo2
2x150bp reads


title: R710000705_CD45pos

description: Library name: EEM_scRNA_235


title: R710000652_CD45pos

description: Library name: EEM_scRNA_134


title: R710000652_CD45neg_1

description: Library name: EEM_scRNA_132


title: mGFP_Control_Collection3_embryo7

description:
Library name: mGFP_Control_Collection3_embryo7
2x150bp reads


title: R710000652_CD45neg_2

description: Library name: EEM_scRNA_133


title: PoolN_Collection3_embryo7

description:
Library name: PoolN_Collection3_embryo7
2x150bp reads


title: mGFP_Control_Collection3_embryo6

description:
Library name: mGFP_Control_Collection3_embryo6
2x150bp reads


title: R710000625_CD45pos

description: Library name: EEM_scRNA_090


title: R710000738_CD45neg

description: Library name: EEM_scRNA_304

value: cGVHD BOS


title: R710000738_CD45pos

description: Library name: EEM_scRNA_303


title: mGFP_Control_Collection3_embryo4

description:
Library name: mGFP_Control_Collection3_embryo4
2x150bp reads


title: mGFP_Control_Collection3_embryo2

description:
Library name: mGFP_Control_Collection3_embryo2
2x150bp reads


title: mGFP_Control_Collection3_embryo3

description:
Library name: mGFP_Control_Collection3_embryo3
2x150bp reads


title: R710000595_CD45pos

description: Library name: EEM_scRNA_061


title: R710000755_CD45pos

description: Library name: EEM_scRNA_318


title: R710000755_CD45neg

description: Library name: EEM_scRNA_317


title: PoolM_Collection2_embryo16

description: 2x150bp reads

extract_protocol:
Single embryos were used for single embryo RNA-seq (Smart-seq+5), for more information see methods of accompanying paper.
An adapted version of Smart-seq2 (called Smart-seq+5') enabling to capture both the 5' transcript information in addition to internal fragment. See methods of the accompanying paper for more information.

value: PoolM (100 ng/μL mGFP, 200 ng/μL H1.2, 200 ng/μL H1.5, 200 ng/μL H1.5, 400 ng/μL macroH2A.1)


title: mGFP_Control_Collection3_embryo1

description:
Library name: mGFP_Control_Collection3_embryo1
2x150bp reads


title: PoolI_Collection3_embryo1

description:
Library name: PoolI_Collection3_embryo1
2x150bp reads


title: PoolM_Collection2_embryo15

description: 2x150bp reads


title: R710000595_CD45neg

description: Library name: EEM_scRNA_060


title: PoolM_Collection2_embryo12

description: 2x150bp reads


title: PoolM_Collection2_embryo14

description: 2x150bp reads


title: PortalFibroblast, Donor2, Rep2

city: Chicago

first: Salman

last: Khetani

address: 851 S Morgan Street

department: Biomedical Engineering

institute: University of Illinois at Chicago

description: Library name: PF_D2_2

data_processing:
Data was alined using the BioJupies online interface using the standard parameters and the raw counts were derived
The edgeR package in R was then utilized to normalize the data
Assembly: Homo sapiens reference genome GRCh38 (hg38)
Supplementary files format and content: Processed data is provided as a txt file

source_name: Liver

growth_protocol: Both PFs and HSCs were grown in DMEM media containing 10% FBS prior to lysing

extract_protocol:
Strand-specific RNA-Seq libraries were prepared using a TruSEQ mRNA-SEQ library protocol (illinuma provided). Library quality and quantity was assessed using Agilent bio-analyzer and libraries were sequenced using an Illumina NovaSEQ6000.
RNA-Sequencing

value: Liver

tag: cell type

value: Portal Fibroblast


title: PortalFibroblast, Donor2, Rep1

description: Library name: PF_D2_1


title: PortalFibroblast, Donor1, Rep2

description: Library name: PF_D1_2


title: PoolM_Collection2_embryo13

description: 2x150bp reads


title: mGFP_Control_Collection3_embryo5

description:
Library name: mGFP_Control_Collection3_embryo5
2x150bp reads


title: PoolM_Collection2_embryo11

description: 2x150bp reads


title: R710000625_CD45neg

description: Library name: EEM_scRNA_089


title: PortalFibroblast, Donor1, Rep1

description: Library name: PF_D1_1


title: HepaticStellateCells, Donor2, Rep2

description: Library name: HSC_D2_2

value: Hepatic Stellate Cell


title: PoolM_Collection2_embryo10

description: 2x150bp reads


title: HepaticStellateCells, Donor2, Rep1

description: Library name: HSC_D2_1


title: PoolJ_Collection2_embryo16

description: 2x150bp reads

value: PoolJ (100 ng/μL mGFP, 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g)


title: PoolM_Collection2_embryo9

description: 2x150bp reads


title: 3D_iN_D21_Rep_1

city: Lund

first: Petter

last: Storm

state: Select...

address: Sölvegatan 19, BMC A11

institute: Lund University

description: Library name: KL004_Sphere_D21_Rep_1

data_processing:
Raw base calls were demultiplexed and converted into sample specific fastq files using default parameters of the bcl2fastq program (v 2.20, Illumina). Trimmed reads (TrimGalore, 0.6.1) were aligned to the human genome version GRCh38 (Ensembl release 99) using STAR (58) (v2.7.3) and quantified using Salmon (59) (v0.14.0).
Assembly: GRCh38 (Ensembl release 99)
Supplementary files format and content: TPM values from Salmon

source_name: 3D iN

growth_protocol: hDFs were cultured on uncoated T175 flasks in fibroblast medium (DMEM, 10% fetal bovine serum, 1% penicillin-streptomycin) at 37 °C and 5% CO2. All media was changed every 2-3 days. Upon reaching a 90% confluency the cells were split with 0.05% trypsin in DPBS and further expanded, frozen down or replated for reprogramming experiments. Fibroblasts re-plated for reprogramming in 2D were seeded onto poly-ornithine, laminin, and fibronectin-coated plates at a density of 25.000 cells per cm2 according to our previous study

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen)
cDNA libraries were prepared using the Illumina TruSeq library preparation kit and sequenced with 2 x 150 bp paired end reads on an Illumina NextSeq 2000 using the P3 flow cell (~37M reads per sample).

treatment_protocol: For iN reprogramming a polycistronic vector containing Ascl1, Brn2 and shREST was used at an MOI of 20. For iDAN reprogramming 8 vectors were used (Ascl1, Nurr1, Lmx1A, Lmx1B, FoxA2, Otx2 and shREST) at an MOI of 5 per construct.

value: 3D iN

tag: time

value: day 21


title: PoolJ_Collection2_embryo14

description: 2x150bp reads

value: Late 2-cell embryo


title: PoolJ_Collection2_embryo15

description: 2x150bp reads

value: (C57BL/6J x CBA) x DBA/2J


title: PoolJ_Collection2_embryo10

description: 2x150bp reads


title: PoolJ_Collection2_embryo13

description: 2x150bp reads


title: HepaticStellateCells, Donor1, Rep1

description: Library name: HSC_D1_1


title: 3D_iN_D21_Rep_3

description: Library name: KL004_Sphere_D21_Rep_3


title: 3D_iN_D7_Rep_1

description: Library name: KL004_Sphere_D7_Rep_1

value: day 7


title: PoolJ_Collection2_embryo12

description: 2x150bp reads


title: 3D_iN_D21_Rep_2

description: Library name: KL004_Sphere_D21_Rep_2


title: PoolJ_Collection2_embryo11

description: 2x150bp reads


title: PoolJ_Collection2_embryo9

description: 2x150bp reads


title: 3D_iN_D7_Rep_3

description: Library name: KL004_Sphere_D7_Rep_3


title: HepaticStellateCells, Donor1, Rep2

description: Library name: HSC_D1_2


title: mGFP_Control_Collection2_embryo12

description: 2x150bp reads


title: 2D_iDAN_D21_Rep_1

description: Library name: iDANs_2D_C11_day28_1_S1

source_name: iDAN

value: iDAN

value: day 28


title: 3D_iN_D7_Rep_2

description: Library name: KL004_Sphere_D7_Rep_2


title: 3D_iDAN_D7_Rep_3

description: Library name: iDANoids_C11_day7_3_S24

source_name: 3D iDAN

value: 3D iDAN


title: mGFP_Control_Collection2_embryo9

description: 2x150bp reads

value: Control (100 ng/μL mGFP)


title: mGFP_Control_Collection2_embryo16

description: 2x150bp reads


title: 3D_iN_48_hr_Rep_1

description: Library name: KL004_Sphere_48_hr_Rep_1

value: day 2


title: 2D_iDAN_D21_Rep_3

description: Library name: iDANs_2D_C11_day28_3_S3


title: mGFP_Control_Collection2_embryo14

description: 2x150bp reads


title: mGFP_Control_Collection2_embryo15

description: 2x150bp reads


title: 3D_iN_48_hr_Rep_3

description: Library name: KL004_Sphere_48_hr_Rep_3


title: mGFP_Control_Collection2_embryo13

description: 2x150bp reads


title: mGFP_Control_Collection2_embryo11

description: 2x150bp reads


title: PoolM_Collection1_embryo7

description: 2x150bp reads


title: 3D_iDAN_D50_Rep_3

description: Library name: iDANoids_C11_day50_3_S30

value: day 50


title: PoolM_Collection1_embryo6

description: 2x150bp reads


title: mGFP_Control_Collection2_embryo10

description: 2x150bp reads


title: B6-CX3Cre-pos-Mut-3-Cup-6w-MG

city: Cleveland

first: Nagendra

middle: Kumar

last: Rai

state: Ohio

address: 9620 Carnegie Ave N Bldg, Cleveland, OH 44106

department: Neuroscience

institute: Cleveland Clinic Lerner College of Medicine

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.
A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF v.1.1-p2. The mgi GO list was used to cluster the set of genes based on their biological processes and determine their statistical significance.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Flow sorted CD45intCD11b+ microglia from brain

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Ultra-low input library preparation kit, according to the manufacturer’s instructions.

treatment_protocol: TMX-induced WT and Dicer1 KO animals, adult Cx3cr1creERT2 mouse brain microglia (CD45int/Cd11b+) were flow-sorted and processed for RNA sequencing (RNA-seq).

value: Cx3cr1 Cre+

value: Demyelination, Tmx treatment at the start


title: PoolM_Collection1_embryo5

description: 2x150bp reads

value: PoolM (100 ng/μL mGFP, 200 ng/μL H1.2, 200 ng/μL H1.5, 200 ng/μL H1.5, 400 ng/μL macroH2A.1)


title: wing disc_yw_L3_35hr_B

city: Marseille

first: Cédric

last: Maurange

address: Parc Scientifique de Luminy

department: Developmental Biology Institute of Marseille (IBDM)

country: France

institute: CNRS

description: Library name: 35 hr_B

data_processing:
RNA-seq reads were aligned to the fly genome (dm6) using STAR 2.7.10a_alpha_220207 software (Dobin et al., 2013) and the Ensembl Drosophila genome assembly BDGP6.32. Then, aligned reads were quantified in each sample using the featureCounts software (Liao et al., 2014) to give a count text file.
Assembly: dm6
Supplementary files format and content: RNAseq_WT_time_course_normalized_genes_counts_filtered.csv

organism: Drosophila melanogaster

source_name: wing imaginal disc

extract_protocol:
RNA was extracted with the Qiagen RNeasy Micro kit (Qiagen, #74004).
Total RNA-Seq libraries were generated from 200 ng or less of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: wing imaginal disc

value: yw


title: 3D_iDAN_D7_Rep_1

description: Library name: iDANoids_C11_day7_1_S22


title: 3D_iN_48_hr_Rep_2

description: Library name: KL004_Sphere_48_hr_Rep_2


title: PoolM_Collection1_embryo8

description: 2x150bp reads


title: 3D_iDAN_D50_Rep_1

description: Library name: iDANoids_C11_day50_1_S28


title: 2D_iDAN_D21_Rep_2

description: Library name: iDANs_2D_C11_day28_2_S2


title: B4-CX3Cre-pos-Mut-1-Cup-6w-MG

value: Flow sorted CD45intCD11b+ microglia from brain


title: A5-CX3Cre-neg-Ctr-2-Cup-6w-MG

value: Cx3cr1 Cre-


title: 3D_iDAN_D28_Rep_2

description: Library name: iDANoids_C11_day28_2_S26


title: 3D_iDAN_D7_Rep_2

description: Library name: iDANoids_C11_day7_2_S23


title: PoolM_Collection1_embryo4

description: 2x150bp reads


title: B3-CX3Cre-pos-Mut-3-MG

value: Naïve, Tmx treatment at the start


title: 3D_iDAN_D28_Rep_3

description: Library name: iDANoids_C11_day28_3_S27


title: 3D_iDAN_D28_Rep_1

description: Library name: iDANoids_C11_day28_1_S25


title: A4-CX3Cre-neg-Ctr-1-Cup-6w-MG


title: PoolM_Collection1_embryo1

description: 2x150bp reads

value: Late 2-cell embryo


title: B1-CX3Cre-pos-Mut-1-MG


title: PoolM_Collection1_embryo3

description: 2x150bp reads

value: (C57BL/6J x CBA) x DBA/2J


title: B5-CX3Cre-pos-Mut-2-Cup-6w-MG


title: wing disc_yw_L3_35hr_A

description: Library name: 35 hr_A


title: B2-CX3Cre-pos-Mut-2-MG


title: A3-CX3Cre-neg-Ctr-3-MG


title: 3D_iDAN_D50_Rep_2

description: Library name: iDANoids_C11_day50_2_S29


title: PoolJ_Collection1_embryo7

description: 2x150bp reads

value: PoolJ (100 ng/μL mGFP, 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g)


title: B-Rem-Cx3-Mut2-Microglia

value: Remyelination, Tmx treatment at the peak (5w Cup)


title: A6-CX3Cre-neg-Ctr-3-Cup-6w-MG


title: A1-CX3Cre-neg-Ctr-1-MG


title: PoolJ_Collection1_embryo6

description: 2x150bp reads


title: A2-CX3Cre-neg-Ctr-2-MG


title: PoolJ_Collection1_embryo8

description: 2x150bp reads


title: hFB_Rep_1

description: Library name: hFB_C11_1_S19

source_name: Fibroblast

value: Fibroblast


title: hFB_Rep_2

description: Library name: hFB_C11_2_S20


title: H/R-exposed HK2 cells with NAT10 silencing，M+KD3（IP）

city: hefei

first: jia nan

last: wang

address: 81 Meishan Road

institute: Anhui medical university

description:
Library name: M+KD3.IP
M+KD3.IP

data_processing:
Libraries were qualified using Agilent 2100 bioanalyzer and then subjected to 150-bp paired_x005f_x005f_x005F_x0002_end sequencing on an Illumina NovaSeq 6000 sequencer, and were controlled by Q30.  After 30 adaptor-trimming and removing low quality reads using cutadapt software (v1.9.3), clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4).
Paired-end reads were harvested and were quality controlled by Q30, FastQC, and FastQ Screen. After 3’adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome by STAR software. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Binding sites on RNAs (peaks) were identified by MACS software.
Differentially binding sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.GO and Pathway enrichment analysis were performed by the differentially binding mRNA coding genes.
Assembly: hg19
Supplementary files format and content: some tabular files which contains information about called peaks and differential genes expression analysis
Supplementary files format and content: tab-delimited text files include different transcript for each group

source_name: Human kidney tubular epithelial cell line

growth_protocol: HK2 were cultured in 5% FBS-containing HyClone™DMEM/F12 medium in 95% air and 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from cells using the Magzol Reagent (Magen, China)according to the manufacturer's protocol, The quantity and integrity of RNA yield was assessed by using the K5500(Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately. m6A antibody immunoprecipitation RNA was quality control with Qubit(Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA).
mRNA was enriched from total RNA using the DynabeadsTM mRNA Purification Kit (Invitrogen) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq, China). RNA was randomly fragmented into 100–200 nt fragments using RNA fragmentation reagents, and protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4 °C for 4 h to obtain immunoprecipitated RNA fragments. Both the input and ac4C IP samples were prepared for the next-generation sequencing.RNA libraries for IP and input samples were then generated with the NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: HK2 cells were induced with hypoxia/reoxygenation after knockdown of NAT10 by siRNA.


title: B-Rem-Cx3-Ctr1-Microglia


title: B-Rem-Cx3-Mut1-Microglia


title: hFB_Rep_3

description: Library name: hFB_C11_3_S21


title: B-Rem-Cx3-Ctr2-Microglia


title: PoolJ_Collection1_embryo5

description: 2x150bp reads


title: B2-Mglia

value: Remyelination, Tmx treatment at the start


title: B-Rem-Cx3-Ctr3-Microglia


title: PoolM_Collection1_embryo2

description: 2x150bp reads


title: A2-Mglia


title: H/R-exposed HK2 cells with NAT10 silencing，M+KD2（IP）

description:
Library name: M+KD2.IP
M+KD2.IP

value: Human kidney tubular epithelial cell line


title: PoolJ_Collection1_embryo4

description: 2x150bp reads


title: B1-Mglia


title: B3-Mglia


title: A1-Mglia


title: PoolJ_Collection1_embryo3

description: 2x150bp reads


title: A3-Mglia


title: H/R-exposed HK2 cells with NAT10 silencing，M+KD2（Input）

description:
Library name: M+KD2.Input
M+KD2.Input


title: H/R-exposed HK2 cells with NAT10 silencing，M+KD1（IP）

description:
Library name: M+KD1.IP
M+KD1.IP


title: B-Rem-Cx3-Mut3-Microglia


title: PoolJ_Collection1_embryo1

description: 2x150bp reads


title: Naïve_gfi1cko_RNA_day30_biol rep3

first: Oluwagbemiga

last: Ojo

state: Alabama

department: Radiation Oncology

institute: University of Alabama, at Birmingham

data_processing:
Quality and adapter trimming-TrimGalore v0.6.10
Alignment- STAR v.2.7.11a
Generation of count matrix-HTSeq v2.0.5
Assembly: mm10
Supplementary files format and content: delimited text files includes counts for each sample

source_name: Spleen

extract_protocol:
Single cell suspension was prepared from spleens of day 30 LCMV clone 13 infected mice or from uninfected mice for naive samples. GP33+ antigen specific CD8+ T cell subsets were FACS sorted into TRIzol LS reagent and RNA was puried according to manufacturer's instructions.
RNA-seq library preparation was performed by sequencing company

value: Spleen

value: day 0

value: Naive CD8+ T cell

value: Gfi1 Knockout

tag: infection

value: Uninfected


title: mGFP_Control_Collection1_embryo8

description: 2x150bp reads

value: Control (100 ng/μL mGFP)


title: H/R-exposed HK2 cells with NAT10 silencing，M+KD1（Input）

description:
Library name: M+KD1.Input
M+KD1.Input


title: Naïve_gfi1cko_RNA_day30_biol rep4


title: Naïve_gfi1cko_RNA_day30_biol rep2


title: H/R-exposed HK2 cells with NAT10 silencing，M+KD3（Input）

description:
Library name: M+KD3.Input
M+KD3.Input


title: Naïve_gfi1cko_RNA_day30_biol rep1


title: mGFP_Control_Collection1_embryo7

description: 2x150bp reads


title: Transitional_gfi1cko_RNA_day30_biol rep4

value: day 30

value: Ly108+CX3CR1+ GP33+ CD8+ T cell

value: LCMV clone 13


title: H/R-exposed HK2 cells，M3（Input）

description:
Library name: M3.Input
M3.Input

value: H/R-exposed HK2 cells


title: H/R-exposed HK2 cells，M3（IP）

description:
Library name: M3.IP
M3.IP


title: Transitional_gfi1cko_RNA_day30_biol rep2


title: mGFP_Control_Collection1_embryo6

description: 2x150bp reads

value: Late 2-cell embryo


title: H/R-exposed HK2 cells，M2（IP）

description:
Library name: M2.IP
M2.IP


title: Progenitor_gfi1cko_RNA_day30_biol rep4

value: Ly108+CX3CR1- GP33+ CD8+ T cell


title: PoolJ_Collection1_embryo2

description: 2x150bp reads

value: (C57BL/6J x CBA) x DBA/2J

value: PoolJ (100 ng/μL mGFP, 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g)


title: Transitional_gfi1cko_RNA_day30_biol rep1


title: Progenitor_gfi1cko_RNA_day30_biol rep3


title: H/R-exposed HK2 cells，M2（Input）

description:
Library name: M2.Input
M2.Input


title: Progenitor_gfi1cko_RNA_day30_biol rep2


title: mGFP_Control_Collection1_embryo5

description: 2x150bp reads


title: H/R-exposed HK2 cells，M1（IP）

description:
Library name: M1.IP
M1.IP


title: Naïve_wildtype_RNA_day30_biol rep4

value: Wildtype


title: mGFP_Control_Collection1_embryo4

description: 2x150bp reads


title: Progenitor_gfi1cko_RNA_day30_biol rep1


title: Naïve_wildtype_RNA_day30_biol rep3


title: H/R-exposed HK2 cells，M1（Input）

description:
Library name: M1.Input
M1.Input


title: Naïve_wildtype_RNA_day30_biol rep1


title: Transitional_gfi1cko_RNA_day30_biol rep3


title: Naïve_wildtype_RNA_day30_biol rep2


title: Terminally_exhausted_wildtype_RNA_day30_biol rep4

value: Ly108-CX3CR1- GP33+ CD8+ T cell


title: HEK293T KS FtoG replicate 3

city: Berlin

first: Alexandre

middle: P

last: Magalhaes

address: Ihnestrasse 63-73

institute: Max Planck Institute for Molecular Genetics

description: Library name: sample15_HEK293T_KS_FtoG_R3

data_processing:
Trimming with cutadapt default parameters
Align and count with STAR using hg38 human reference genome
Assembly: hg38
Supplementary files format and content: raw count matrix from STAR

growth_protocol: HEK293T (ATCC #CRL-3216) cell line were cultured in DMEM GlutaMAX (Gibco, 31966047) supplemented with 10% FBS (VWR, Cat#: 89510-186) and 1% Pen/Strep (Gibco, Cat#: 15140-122).

extract_protocol:
Total RNA was isolated from HEK293T cells 24h after transfection using RNEasy mini kit with in-column DNAse digestion (Qiagen). Reverse transcription was performed from 1µg of RNA with RevertAid First Strand cDNA synthesis kit (Thermo Scientific, K1622)
RNA sequencing libraries were prepared KAPA HyperPrep Kit with RiboErase (Roche, KK8562) and sequenced in 100bp paired-end mode with Illumina NovaSeq2 for 55-65M fragments per sample.

value: human embryonic kidney (HEK) 293 cell line

value: KS FtoG


title: HEK293T KS replicate 3

description: Library name: sample14_HEK293T_KS_R3

value: KS


title: mGFP_Control_Collection1_embryo1

description: 2x150bp reads


title: Terminally_exhausted_wildtype_RNA_day30_biol rep2

value: Spleen


title: HEK293T WT replicate 3

description: Library name: sample13_HEK293T_WT_R3

value: WT


title: Terminally_exhausted_wildtype_RNA_day30_biol rep3


title: Terminally_exhausted_wildtype_RNA_day30_biol rep1


title: H3K4me3_PoolI_2C_rep2

data_processing:
Paired-end reads were trimmed using Cutadapt (version 3.4). After trimming, the reads were aligned to the mouse reference genome (GRCm38) using Bowtie2 (version 2.3.5). Reads were then filtered based on mapping quality scores using Samtools (version 1.3). Read pairs were imported into R (version 4.1.2) using the readGAlignmentPairs function from the GenomicAlignment package (version 1.30), where they were filtered for unique fragments. Fragments aligning to the mitochondrial genome or small scaffolds were excluded from the analysis. The fragments were counted in 100-kb genomic bins, normalized by the total fragment counts, and scaled to a million. For detailed information, see the methods of the accompanying paper.
Assembly: GRCm38
Supplementary files format and content: Normalized read counts per 100-kb bins for each replicate
Supplementary files format and content: Average normalized read counts per 100-kb bins from replicates
Library strategy: CUT&Tag

growth_protocol: Zygotes were collected at 18h post-hCG, microinjected and cultured in KSOM until 48h post-hCG (late 2-cell stage), and collected for CUT&Tag.

extract_protocol:
Low-input CUT&Tag: For more information, see the methods in the accompanying paper. Briefly, late 2-cell embryos with intact zona pellucida were collected 48h post-hCG. They were permeabilized using a Triton-X buffer and incubated overnight at 4 °C with a primary antibody against H3K4me3. After this, the embryos were incubated at room temperature for 30 minutes with a secondary antibody. Next, the pA-Tn5 adaptor complex was added, and the mixture was incubated for 1 hour at room temperature. Tagmentation was then performed for 1 hour at 37 °C in a MgCl₂ buffer. DNA was extracted by incubating the samples for 1 hour at 58 °C in a 0.1% SDS buffer. SDS was neutralized with Triton-X, and the PCR reaction was conducted directly on the sample. Following 18 cycles of PCR amplification with NEBNext High-Fidelity 2X PCR Master Mix, the PCR product was purified and size-selected using AMPure XP.
See methods of the accompanying paper for more information.

treatment_protocol: Embryos were microinjected with either membrane-eGFP mRNA alone (Control) or together with mRNAs encoding candidate proteins (Pool J: Suv39h1, Hp1a, Hp1g ; Pool I: Kdm7a, Kdm7c, Lsd1).

tag: antibody

value: EpiCypher, 13-0041; 1:100 dilution

tag: pcr cycles

value: PoolI (100 ng/μL mGFP, 800 ng/μL Lsd1, 800 ng/μL Kdm7a, 1000 ng/μL Kdm7c)


title: HEK293T EGFP replicate 3

description: Library name: sample12_HEK293T_EGFP_R3

value: EGFP


title: Transitional_wildtype_RNA_day30_biol rep1

value: day 30

value: Ly108+CX3CR1+ GP33+ CD8+ T cell


title: HEK293T untransfected replicate 3

description: Library name: sample11_HEK293T_untr_R3

value: untransfected


title: Transitional_wildtype_RNA_day30_biol rep4

value: LCMV clone 13


title: H3K4me3_PoolJ_2C_rep2

value: Late 2-cell embryo


title: Transitional_wildtype_RNA_day30_biol rep2


title: Transitional_wildtype_RNA_day30_biol rep3


title: mGFP_Control_Collection1_embryo3

description: 2x150bp reads

value: (C57BL/6J x CBA) x DBA/2J

value: Control (100 ng/μL mGFP)


title: H3K4me3_mGFP_Control_2C_rep2


title: Effector_wildtype_RNA_day30_biol rep2

value: Ly108-CX3CR1+ GP33+ CD8+ T cell

value: Wildtype


title: H3K4me3_PoolJ_2C_rep1

value: PoolJ (100 ng/μL mGFP, 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g)


title: HEK293T KS replicate 2

description: Library name: sample09_HEK293T_KS_R2

value: human embryonic kidney (HEK) 293 cell line


title: Effector_wildtype_RNA_day30_biol rep3


title: H3K4me3_PoolI_2C_rep1


title: HEK293T KS FtoG replicate 2

description: Library name: sample10_HEK293T_KS_FtoG_R2

value: KS FtoG


title: Effector_wildtype_RNA_day30_biol rep1

value: Spleen


title: H3K4me3_mGFP_Control_2C_rep1


title: HEK293T EGFP replicate 2

description: Library name: sample07_HEK293T_EGFP_R2


title: mGFP_Control_Collection1_embryo2

description: 2x150bp reads


title: Progenitor_wildtype_RNA_day30_biol rep3

value: Ly108+CX3CR1- GP33+ CD8+ T cell


title: Progenitor_wildtype_RNA_day30_biol rep2


title: HEK293T WT replicate 2

description: Library name: sample08_HEK293T_WT_R2

value: WT


title: Progenitor_wildtype_RNA_day30_biol rep4


title: H3K9me3_PoolJ_2C_rep3

data_processing:
Paired-end reads were trimmed using Cutadapt (version 3.4). After trimming, the reads were aligned to the mouse reference genome (GRCm38) using Bowtie2 (version 2.3.5). Reads were then filtered based on mapping quality scores using Samtools (version 1.3). Read pairs were imported into R (version 4.1.2) using the readGAlignmentPairs function from the GenomicAlignment package (version 1.30), where they were filtered for unique fragments. Fragments aligning to the mitochondrial genome or small scaffolds were excluded from the analysis. The fragments were counted in 100-kb genomic bins, normalized by the total fragment counts, and scaled to a million. For detailed information, see the methods of the accompanying paper.
Assembly: GRCm38
Supplementary files format and content: Normalized read counts per 100-kb bins for each replicate
Supplementary files format and content: Average normalized read counts per 100-kb bins from replicates
Library strategy: CUT&RUN

growth_protocol: Zygotes were collected at 18h post-hCG, microinjected, and cultured in KSOM until 48h post-hCG (late 2-cell stage) and collected for CUT&RUN.

extract_protocol:
Low-input CUT&RUN was performed as described in detail in the methods section of the accompanying paper. Late 2-cell stage embryos (48 hours post-hCG) with intact zona pellucida were washed in a buffer containing 0.5 mM spermidine, 0.1% BSA, and 1× protease inhibitor cocktail. They were then transferred to an antibody buffer (anti-H3K9me3 antibody diluted 1:100 in wash buffer containing Triton-X and EDTA) and incubated overnight at 4 °C. After washing, the embryos were incubated with pAG-MNase (diluted 1:20 or 1:200) for 1 hour at room temperature. The embryos were washed again and transferred to a calcium buffer for 30 minutes or 2 hours at 4 °C for targeted chromatin digestion. The reaction was stopped with an EGTA-STOP buffer, followed by a 30-minute incubation at 37 °C to release chromatin fragments. The supernatant was collected, and DNA was extracted using the QIAquick kit. Illumina library preparation was carried out with 15 or 18 PCR cycles.
See methods of the accompanying paper for more information.

treatment_protocol: Embryos were microinjected with mRNAs encoding candidate protein(s). GFP-injected embryos were processed together with Suv39h1-injected embryos, whereas membrane-GFP (mGFP) injected embryos were processed with Pool J (Suv39h1, Hp1a, Hp1g).

value: Millipore, 17-625

tag: dilution of_pag-mnase

value: 1:20 dilution

tag: incubation in_calcium_buffer

value: 2 h

value: PoolJ (100 ng/μL membrane-GFP, 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g)


title: HEK293T untransfected replicate 2

description: Library name: sample06_HEK293T_untr_R2

tag: cell line

value: untransfected


title: Progenitor_wildtype_RNA_day30_biol rep1

value: day 30

tag: genotype

value: LCMV clone 13


title: H3K9me3_PoolJ_2C_rep2

value: Late 2-cell embryo

value: (C57BL/6J x CBA) x DBA/2J

value: Abcam, ab8898

value: 1:200 dilution

value: 30 min


title: DMSO_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_DMSO_DBA_Lamin_Zygote.bedgraph
DMSO_DBA_Lamin_Zygote_LAD_coordinates.bed

data_processing:
Samples were sequenced using Illumina HiSeq4000 or HiSeq2500 platforms in 150 bp PE mode but only read1 was used for downstream analysis. For pre-processing of reads, first 6 random bases were discarded using trimmomatic (version 0.39). Subsequently, the reads were demultiplexed according to DamID indexes using fastx barcode splitter and the additional 15 bp of adaptors were trimmed using trimmomatic. The pre-processed reads starting with GATC were then mapped to the mm10 using bowtie2 (version 2.5.1) with default parameters. Reads aligning to the genome with quality score below 30 were discarded using samtools (version 1.17). Duplicates were removed using picard (version 3.0.0) to finally obtain unique GATC reads.
The computation of OE (Observed/Expected) values were performed in 100-kb genomic bins. To distinguish LAD domains from inter-LADs, a two-state hidden Markov model (HMM) was applied to non-zero OE mean values.
Assembly: mm10
Supplementary files format and content: Dam-LaminB1 observed over expected (OE) values calculated in 100-kb genomic bins provided in bedgraph files and LAD domain coordinates are provided in bed files.
Supplementary files format and content: Mean OE and LAD coordinates files are available on Rep 1 samples.
Library strategy: DamID-seq

source_name: Zygote

growth_protocol: Zygotes were collected from the oviduct and cumulus cells were removed upon brief incubation in M2 media containing hyaluronidase. Zygotes were placed in drops of KSOM and cultured at 37 ºC with 5% CO2.

extract_protocol:
Zona pellucida was removed by treatment with 0.5% pronase in M2 at 37 °C. Polar bodies were separated from the embryos by gentle pipetting after trypsin treatment and discarded. For each replicate, a pool of 10-20 blastomeres (10 to 20 zygotes or 5 to 10 2-cell embryos) were collected in 2 μL DamID buffer (10 mM TRIS acetate pH 7.5, 10 mM magnesium acetate, 50 mM potassium acetate) and stored at -80 °C until downstream processing.
Approximately 300 ng of PCR purified DNA was end-repaired using an End-It DNA End-Repair Kit. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Between steps, the DNA was purified with Agencourt AMPure XP beads with a 1.8 x bead volume and a 1.0 x bead volume after the ligation reaction. After adapter ligation, DNA was PCR amplified with Illumina primers for 8 cycles.

treatment_protocol: For DamID, early zygotes (18 h post hCG) were isolated and injected with 250 ng/μL Tir1, 50 ng/μL membrane-eGFP and 10 ng/μL AID-Dam-LaminB1 along with mRNA encoding candidate protein(s) and cultured in auxin (500μM)-containing medium. For mapping LADs in zygotic stage, auxin was removed from 22 h and late zygotes were collected at 28–30 h post hCG. For DamID in late 2-cell stage, auxin was washed out from 42 to 48-50 h post hCG and embryos were cultured in KSOM. The mRNA concentration of candidate proteins was decided based on size of the ORF to ensure roughly equimolar expression. For EZH2 inhibition experiment in zygote, embryos were treated with 0.01% DMSO (as control) or 5 μΜ GSK343 (Selleckchem, #S7164) from 18 h to 28 h post hCG.

value: Zygote

value: (C57BL/6J xCBA) x DBA/2J

tag: treatment

value: DMSO


title: GSK343_DBA_Lamin_Zygote_rep1

description:
Low-input LaminB1 DamID
OE_mean_GSK343_DBA_Lamin_Zygote.bedgraph
GSK343_DBA_Lamin_Zygote_LAD_coordinates.bed

tag: mrna injected


title: DMSO_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: DMSO_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: Suv39h1_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

source_name: 2-cell embryo

value: 2-cell embryo

value: 600 ng/μL Suv39h1


title: HEK293T KS replicate 1

description: Library name: sample04_HEK293T_KS_R1

value: human embryonic kidney (HEK) 293 cell line

value: KS


title: Suv39h1_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Suv39h1_DBA_Lamin_TwoCell.bedgraph
Suv39h1_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: Suv39h1_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: H3K9me3_mGFP_Control_2C_rep4

value: Millipore, 17-625

value: 1:20 dilution

value: 2 h

value: Control (100 ng/μL membrane-GFP)


title: HEK293T WT replicate 1

description: Library name: sample03_HEK293T_WT_R1

value: WT


title: H3K9me3_mGFP_Control_2C_rep2

value: Late 2-cell embryo


title: Setdb2_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 700 ng/μL Setdb2


title: Setdb2_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID


title: HEK293T EGFP replicate 1

description: Library name: sample02_HEK293T_EGFP_R1

value: EGFP


title: GSK343_DBA_Lamin_Zygote_rep2

description: Low-input LaminB1 DamID


title: GSK343_DBA_Lamin_Zygote_rep3

description: Low-input LaminB1 DamID


title: Setdb2_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Setdb2_DBA_Lamin_TwoCell.bedgraph
Setdb2_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: H3K9me3_mGFP_Control_2C_rep1

value: (C57BL/6J x CBA) x DBA/2J

value: Abcam, ab8898


title: Setdb1_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID

value: 1200 ng/μL Setdb1


title: HEK293T untransfected replicate 1

description: Library name: sample01_HEK293T_untr_R1

value: untransfected


title: Setdb1_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: (C57BL/6J xCBA) x DBA/2J


title: Setdb1_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Setdb1_DBA_Lamin_TwoCell.bedgraph
Setdb1_DBA_Lamin_TwoCell_LAD_coordinates.bed

value: 2-cell embryo


title: H3K9me3_Suv39h1_2C_rep3

value: 1:200 dilution

value: 30 min

value: Suv39h1 (250 ng/μL GFP, 600 ng/μL Suv39h1)


title: HEK293T KS FtoG replicate 1

description: Library name: sample05_HEK293T_KS_FtoG_R1

value: human embryonic kidney (HEK) 293 cell line

value: KS FtoG


title: H3K9me3_PoolJ_2C_rep1

value: 1:20 dilution

value: 2 h

value: PoolJ (100 ng/μL membrane-GFP, 600 ng/μL Suv39h1, 300 ng/μL Hp1a, 300 ng/μL Hp1g)


title: AK12

city: AUBURN

first: Amit

last: Mitra

state: AL

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

institute: AUBURN UNIVERSITY

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene counts in Samples

source_name: ALL

extract_protocol:
High quality RNA was isolated using QIAshredder columns and RNAeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 (poly A enrichment).
RNA sequencing was performed on Illumina’s NovaSeq 6000 platform (150 bp paired-end) at >20 million reads per sample.

value: ALL

value: lymphoblast cell line


title: H3K9me3_Suv39h1_2C_rep2

value: Late 2-cell embryo


title: Lsd1_DBA_Lamin_TwoCell_rep4

description: Low-input LaminB1 DamID

value: 800 ng/μL Lsd1


title: AK11


title: Lsd1_DBA_Lamin_TwoCell_rep3

description: Low-input LaminB1 DamID


title: K562_treated_with_Triptolide_RNAPIIS5P_CUTnTAG_rep2_(20240408_WW1112_240329)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag targeting RNAPIIS5P in K562 in Triptolide replicate 2

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We combined replicates and used bedtools 2.30.0 "genomecov" to make a raw count hg19 track which is the number of fragments aligned at each position (Supplementary file .hg19.raw_counts.bw)
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

tag: group

value: Cell Signaling Technology, 13523S


title: H3K9me3_GFP_Control_2C_rep2

value: (C57BL/6J x CBA) x DBA/2J

value: Abcam, ab8898

value: Control (250 ng/μL GFP)


title: H3K9me3_mGFP_Control_2C_rep3

value: Control (100 ng/μL membrane-GFP)


title: H3K9me3_Suv39h1_2C_rep1

value: 1:200 dilution


title: K562_treated_with_ActinomycinD_RNAPIIS5P_CUTnTAG_rep2_(20240408_WW1120_240329)

description: CUT&Tag targeting RNAPIIS5P in K562 in ActinomycinD replicate 2


title: Lsd1_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 2-cell embryo

value: (C57BL/6J xCBA) x DBA/2J


title: AK9


title: AK7


title: AK8


title: K562_treated_with_DMSO_RNAPIIS5P_CUTnTAG_rep2_(20240408_WW1107_240329)

description: CUT&Tag targeting RNAPIIS5P in K562 in DMSO replicate 2


title: Lsd1_DBA_Lamin_TwoCell_rep1

description:
Low-input LaminB1 DamID
OE_mean_Lsd1_DBA_Lamin_TwoCell.bedgraph
Lsd1_DBA_Lamin_TwoCell_LAD_coordinates.bed


title: AK6


title: Kdm7c_DBA_Lamin_TwoCell_rep2

description: Low-input LaminB1 DamID

value: 1000 ng/μL Kdm7c