title: s1_HCC1954_mC+_DMSO_B_MAG2 (ATAC-seq)

value: Monoculture

value: DMSO


title: gpSSCs-bulkRNAseq-ctrl-rep1

status: Public on Apr 24 2024

type: SRA

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

country: China

institute: Tongji University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 mouse genome using STAR (for RNA-seq) and Bowtie2 (for ATAC-seq).
For RNA-seq data, aligned reads with high quality were quantified by HTSeq. For ATAC-seq, reads mapped to mitochondrial DNA, with duplication or unknown identities were eliminated by Sambamba. Only unique reads were analyzed.
For RNA-seq data, counts per million reads (CPM) were calculated. For ATAC-seq, we performed peak calling using MACS2, summarized the read counts by bedtools and obtained the differential peaks by DESeq2.
For RNA-seq data, unique molecular identifiers (UMIs) were extracted from Read2. Raw gene counts were calculated by UMI number to get rmdup.count file. For ATAC-seq, motif enrichment was performed by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq data, we provided tab-delimited text files including raw count values for each sample. For ATAC-seq data, we provided tab-delimited text files and binary files including all peaks.

molecule: polyA RNA

organism: Mus musculus

source_name: growth plate

extract_protocol:
For scRNA-seq, td-Tomato+ cells were isolated from bone marrow and bone by flow cytometry. For RNA-seq and ATAC-seq, td-Tomato+ cells were isolated from growth plate or periosteum by flow cytometry, and 1000 of these cells were used for constructing RNA-seq library, while 3000~5000 of these cells were used for constructing ATAC-seq library.
RNA-seq libraries were constructed by a modified Smartseq2 method with UMI barcodes (Nature 533:487, 2016). ATAC-seq libraries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD502-01).

tag: cre line

value: Prx-Cre

tag: genotype

value: PrxCre; Z24fl/fl

tag: age


title: s6_HCC1954BM3_GFP+_NER_B_MAG16 (ATAC-seq)

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA mem.
For peak calling MACS2 was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using MACS2 using the CHIPS pipeline

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain

extract_protocol:
Transposed DNA fragments were obtained using OMNI-ATAC protocol from frozen cells in 10% DMSO
PCR amplification and purification were conducted and Qiagen cleanup kit was applied to obtain purified DNA of at least 10ng per sample.

tag: tissue

value: Brain

tag: cell line

tag: treatment 1

value: Coculture

tag: treatment 2

value: Neratinib


title: H20

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

library_source: other

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human genome hg19 by bismark.
Only uniquely mapped reads were kept for down-stream analyses.
Calling of mC was performed by scripts in bismark.
Assembly: hg19
Supplementary files format and content: bismark output cov files

molecule: other

source_name: Plasma separated from blood

extract_protocol:
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 1 ng cfDNA was used for library construction.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit.

tag: race

value: AA

tag: gender

value: Male

tag: group

value: HEA

value: Plasma separated from blood

tag: fraction

value: cfDNA


title: CB04-CMP_CMX-RNU-075

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

description: Cord Blood CMP RNAseq

data_processing:
Paired-end 150 bp sequencing was performed on the Illumina HiSeq 4000. Alignment (STAR) was performed to the human genome (hg19).
Data was normalized to fragments per kilobase of mappable length and million counts (FPKMs).
Assembly: hg19
Supplementary files format and content: GSE233478_FPKM_table.csv
Supplementary files format and content: FPKM table

molecule: total RNA

source_name: Umbillical Cord Blood

extract_protocol:
Tissues were disagregated in single cells suspensions and FACS-sorted for the indicated markers and profiled
Libraries were prepared with the Ovation RNA-seq system V2 kit (NuGEN)
KAPA DNA library amplification

value: Umbillical Cord Blood

tag: donor id

value: Newborn #04

tag: cell type

value: common myeloid progenitors (CD34+lin-CD38+CD45RA-CD123int)

value: birth

tag: treatment


title: ABM02-MEP_CMX-RNU-079a

description: Adult Bone Marrow MEP RNAseq

source_name: Adult Bone Marrow

value: Adult Bone Marrow

value: Adult #02


title: s6_HCC1954BM3_GFP+_NER_A_MAG15 (ATAC-seq)


title: pSSCs-bulkRNAseq-cko-rep2

source_name: periosteum


title: pSSCs-bulkRNAseq-cko-rep3


title: C50

value: Female

value: CRC


title: ABM01-CLP1_CMX-RNU-074a

description: Adult Bone Marrow CLP1 RNAseq

value: Adult #01

value: common lymphoid progenitors 1 (CD34+CD38+lin-CD10+CD45RA+CD24-)


title: H22


title: C48


title: s5_HCC1954BM3_GFP+_DMSO_B_MAG12 (ATAC-seq)

value: Brain

value: Coculture

value: DMSO


title: C49

value: White

value: Male


title: pSSCs-bulkRNAseq-ctrl-rep3

value: Prx-Cre

value: PrxCre; Z24fl/fl


title: s6_HCC1954BM3_mC+_NER_A_MAG13 (ATAC-seq)

source_name: Breast cancer

value: Breast cancer

value: Neratinib


title: ABM01-CDP_CMX-RNU-072a

description: Adult Bone Marrow CDP RNAseq

value: common dendritic progenitors (CD34+lin-CD38+CD45RA+CD10-CD123hi)


title: ABM01-GMP_CMX-RNU-070a

description: Adult Bone Marrow GMP RNAseq


title: C47

value: Plasma separated from blood

value: cfDNA


title: ABM01-LMPP_CMX-RNU-073a

description: Adult Bone Marrow LMPP RNAseq

value: Adult Bone Marrow

value: lymphoid-primed multipotent progenitors (CD34+lin-CD38+CD10-CDRA+CD123intCD115-CD62Lhi)


title: s5_HCC1954BM3_GFP+_DMSO_A_MAG11 (ATAC-seq)


title: pSSCs-bulkRNAseq-cko-rep1


title: C46

value: Female

value: CRC


title: ABM01-MEP_CMX-RNU-069a

description: Adult Bone Marrow MEP RNAseq

value: Adult #01


title: H19

value: AA

value: HEA


title: Prx1-cko-scRNAseq

source_name: bone marrow and bone


title: s1_HCC1954_mC+_DMSO_A_MAG1 (ATAC-seq)

value: Monoculture

value: DMSO


title: ABM01-MoP_CMX-RNU-071a

description: Adult Bone Marrow MoP RNAseq


title: C45


title: Prx1-ctrl-scRNAseq

value: PrxCre; Z24fl/+


title: AGM11-HPC_CMX-RNU-068

description: AGM HPC RNAseq

source_name: Aorta-gonad-mesonephros

value: Aorta-gonad-mesonephros

value: Embryo #11

value: hematopoietic progenitors (CD34+CD90- (CD43+CD45+))


title: C44


title: s6_HCC1954BM3_mC+_NER_B_MAG14 (ATAC-seq)

value: Breast cancer

value: Coculture

value: Neratinib


title: 453plusBM3_NER_2 (ATAC-seq)


title: ABM01-CMP_CMX-RNU-068a

description: Adult Bone Marrow CMP RNAseq

value: common myeloid progenitors (CD34+lin-CD38+CD45RA-CD123int)


title: 453plusBM3_NER_1 (ATAC-seq)


title: pSSCs-bulkRNAseq-ctrl-rep2

value: Prx-Cre

value: PrxCre; Z24fl/fl


title: C42

value: Male

value: Plasma separated from blood

value: cfDNA


title: Osx-Cre_scRNAseq

value: Osx-Cre

value: OsxCre; Z24fl/fl


title: AGM11-HSPC_CMX-RNU-067

description: AGM HSPC RNAseq

value: hematopoietic stem/progenitors cells (CD34+CD90+CD43+)


title: C43

value: AA

value: CRC


title: pSSCs-bulkRNAseq-ctrl-rep1


title: 453plusBM3_DMSO_1 (ATAC-seq)

value: DMSO


title: AGM11-endo_CMX-RNU-066

description: AGM endothelium RNAseq

value: Aorta-gonad-mesonephros

value: Embryo #11

value: endothelium (CD34+CD90+CD43-CD45-)


title: 453plusBM3_DMSO_2 (ATAC-seq)

value: Breast cancer

value: Coculture


title: s5_HCC1954BM3__mC+_DMSO_B_MAG10 (ATAC-seq)


title: ABM01-HSC_CMX-RNU-066a

description: Adult Bone Marrow HSC RNAseq

value: Adult Bone Marrow

value: Adult #01

value: hematopoietic stem cells (CD34+lin-CD38-CD45RA-CD90+)


title: C40

value: Male


title: C39

value: White

value: Female

value: Plasma separated from blood


title: 453_NER_2 (ATAC-seq)

value: Monoculture

value: Neratinib


title: Prx1-Cre-scRNAseq

value: Prx-Cre

value: PrxCre; Z24fl/fl


title: FL10-CLP2_CMX-RNU-065a

description: Fetal liver CLP2 RNAseq

source_name: Fetal liver

value: Fetal liver

value: Fetus #10

value: common lymphoid progenitors 2 (CD34+CD38+lin-CD10+CD45RA+CD24+)


title: FL10-CDP_CMX-RNU-063a

description: Fetal liver CDP RNAseq

value: common dendritic progenitors (CD34+lin-CD38+CD45RA+CD10-CD123hi)


title: 453_DMSO_2 (ATAC-seq)

value: Breast cancer

value: DMSO


title: AGM10-HPC_CMX-RNU-062

description: AGM HPC RNAseq

value: Aorta-gonad-mesonephros

value: Embryo #10

value: hematopoietic progenitors (CD34+CD90- (CD43+CD45+))


title: C38

value: Male

value: CRC

value: cfDNA


title: C37

value: White

value: Female

value: Plasma separated from blood


title: shRPL35A_01

type: RNA

city: Taiyuan

first: Liqin

last: Yan

address: Jiefang Road

institute: Shanxi Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip primeview human PathArrayTM.

scan_protocol: Affymetrix human GeneChip PrimeView and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing: The statistical significance of raw data was completed by a Welch t-test with Benjamini-Hochberg FDR.

label: 3’ IVT Biotin Label

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NCI-H1299 cells were cultured in 1640 medium containing 10% fetal bovine serum (FBS) in cell incubator with 5% CO2 at 37°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: NCI-H1299 cells in logarithmic growth phase were infected by adding 20 μL 1×108 TU/mL shCtrl or shRPL35A lentivirus, culturing in 1640 medium with 10% FBS in a 6-well dish with 2×105 cells per well.

value: infected with shRPL35A


title: shRPL35A_02


title: shRPL35A_03


title: 453_DMSO_1 (ATAC-seq)

value: Monoculture


title: shCtrl_02

value: infected with shCtrl


title: shCtrl_03


title: C41

value: AA


title: FL10-MoP_CMX-RNU-062a

description: Fetal liver MoP RNAseq

value: Fetal liver

value: Fetus #10


title: C36


title: Brdu-ip Pol32Δ experiment 3

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

data_processing:
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To calculate the genome-wide read coverage BEDTools and self-developed Perl programs was performed.
In order to calculate the average bias of each nucleosome, the reads of eSPAN at each nucleosome surrounding the 134 early DNA replication origins were counted separately and assigned to their determined nucleosome positions.
After normalization against the corresponding BrdU-IP-ssSeq, the average bias pattern of eSPAN was calculated by log2 (Watson strand reads/ Crick strand reads) at each nucleosome position. Similarly, log2 (Watson strand reads/ Crick strand reads) at each nucleosome position of each of the 134 early replication origins was used to analyze the bias pattern of eSPAN peaks at each origin.
Assembly: sacCer3
Supplementary files format and content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

organism: Saccharomyces cerevisiae

growth_protocol: All yeast strains used in this study were W303-1 background except the histone H3-tag switch strains (Cyc565 and cyc1276), which were S228C background. Mutagenesis was performed using the CRISPR/Cas9 plasmid pML104 or pML107 along with dsDNA donor, while gene deletion and TAP/myc-tag were knock-in using PCR-based methods.

extract_protocol:
We performed eSPAN according to the protocol in our previous studies with some modifications. Briefly, yeast cells were synchronized with alpha-factor and released in YPD medium with BrdU (400ug/ml) following the standard protocol. The cells were digested with MNase (NEB, Cat# M0247S), after saving 1% for BrdU-IP, the rest of digested chromatin was subjected to ChIP against H3K4me3 (ab8580), H3K56ac, HA-Tag (BETHYL,Cat#12CA5), or T7-Tag (BETHYL,Cat#A190-117A), individually. Then DNA extracted from the ChIP products was end-repaired and ligated with adapters using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat#ND607).
After saving 1% for ChIP-seq analysis, the products was subjected to BrdU-IP as previous reported, and the products was amplified with NEBNext High-Fidelity 2X PCR Master Mix (NEB, Cat# M0541L) and indexing primers. The obtained libraries were sequenced using the paired-end method by Illumina nova 6000.
eSPAN


title: C35


title: AGM10-HSPC_CMX-RNU-061

description: AGM HSPC RNAseq

value: hematopoietic stem/progenitors cells (CD34+CD90+CD43+)


title: ehe PDX [NO_39_S10]

city: Milano

first: Stefano

last: Percio

address: VIa Amadeo 42

country: Italy

institute: Istituto Nazionale dei Tumori

data_processing:
Sequence reads were checked for quality using fastQC
Sequence reads mapping to GrCh38/hg38 and count extration were performed using STAR with default parameters
Assembly: hg38
Supplementary files format and content: tab-delimited text files include CPM values for each sample

source_name: PDX

growth_protocol: From 6 to 8 week-old female SCID mice were implanted into the right flank with the PDX. When xenografts were approximately 500 mm3 was explanted and frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from frozen EHE specimen and PDX with an RNeasy mini kit (Qiagen) in accordance with the manufacture's protocol.
cDNA libraries were synthesized from 200 ng total RNA with RNA Prep kit with Tagmentation (Illumina), following manufacturers’ instructions. Libraries were quantified by Qubit assay (Thermo Fisher Scientific Inc) and quality was assessed by the High Sensitivity kit on the 4200TapeStation (Agilent)

value: PDX

value: epithelioid hemangioendothelioma (EHE)

value: WT


title: C34


title: FL10-GMP_CMX-RNU-061a

description: Fetal liver GMP RNAseq


title: 453_NER_1 (ATAC-seq)

value: Breast cancer

value: Neratinib


title: AGM10-endo_CMX-RNU-060

description: AGM endothelium RNAseq

value: Aorta-gonad-mesonephros

value: Embryo #10

value: endothelium (CD34+CD90+CD43-CD45-)


title: SKOV3 SYNCRIP + Cisplatin (40 uM) 24 h, repeat 2

first: Ksenia

middle: S

last: Anufrieva

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description: Control cell line stably overexpressing SYNCRIP and treated with cisplatin (40 uM) for 24 h

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trimmomatic.
Trimmed RNAseq reads were mapped against Homo Sapiens GRCh38.13 genome annotation using STAR(v.2.5.2b). The gene read quantification was performed using HTSeq-count (v.0.6.0).
Differentially expressed genes were identified using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: processed data files format and content: tab-delimited tsv files include count values for every gene and every sample

source_name: Ovarian adenocarcinoma

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. SKOV3 cells were cultivated in DMEM medium containing 10% FBS (Gibco), 2 mM L-glutamine (Gibco) and 1% penicillin/streptomycin (Paneco). The culture medium was changed every 3-4 days. Cells were dissociated using Trypsin (Gibco).

extract_protocol:
Total RNA was isolated from cancer cells using RNeasy Mini Kit (Qiagen) followed by treatment with DNAse I (NEB). The reaction was purifed with PureLink RNA Mini Kit (ThermoFisher). RNA quality was checked by 2100 bioanalyzer (Agilent, USA). Enrichment of polyadenylated RNA and library preparation was performed with NEBNext Ultra II Directional RNA Library Prep Kit (NEB), according to the manufacturer’s protocol. The library underwent a final cleanup using the Agencourt AMPure XP system (Beckman Coulter) after which the libraries’ size distribution and quality were assessed using a high sensitivity DNA chip (Agilent Technologies). Libraries were subsequently quantified by Quant-iT DNA Assay Kit, High Sensitivity (ThermoFisher). Samples were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (300 Cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To establish overexpression cell lines, Phoenix-GP packaging cells (ATCC, CRL-3215) were co-transfected with pCDH-EF1-MCS-IRES-Puro, pCDH-SYNCRIP, or pCDH-SNU13 lentiviral vectors, and two packaging plasmids psPAX2 and pMD2.G (Addgene, 12260, 12259). Growth media were changed the following day and lentivirus-containing supernatants were harvested 72 h later. One day before transduction, SKOV3 cells were seeded on 25 cm2 cell culture flasks so they will be 30% confluent at the time of transduction. The next day, SKOV3 cells were incubated with viral supernatants for 24 h in the presence of 10 μg/ml polybrene (Sigma-Aldrich, TR-1003-G). Two days after infection, transduced cells were selected with 1 μg/ml puromycin (Sigma-Aldrich, P7255) for 4 days. Overexpression was validated with RT-PCR and western blot. SKOV3 cell lines stably overexpressing SYNCRIP or SNU13 and control SKOV3 cell line expressing empty vector pCDH were treated or untreated with cisplatin (40 uM) for 24 hours. RNA was isolated from samles.

value: Ovarian adenocarcinoma


title: Brdu-ip WT experiment 3


title: SKOV3 SYNCRIP + Cisplatin (40 uM) 24 h, repeat 1


title: shCtrl_01


title: FL10-CMP_CMX-RNU-059a

description: Fetal liver CMP RNAseq

value: common myeloid progenitors (CD34+lin-CD38+CD45RA-CD123int)


title: SKOV3 SYNCRIP, repeat 2

description: Cell line stably overexpressing SYNCRIP


title: C32

value: White

value: Female

value: CRC

value: Plasma separated from blood

value: cfDNA


title: FL10-MEP_CMX-RNU-060a

description: Fetal liver MEP RNAseq

value: Fetal liver

value: Fetus #10


title: Brdu-ip WT experiment 2


title: Brdu-ip Pol32aa experiment 1


title: C31

value: AA

value: Male


title: SKOV3 SYNCRIP, repeat 1

description: Cell line stably overexpressing SYNCRIP


title: Brdu-ip Pol1-2A2/Pol32Δ experiment 2


title: ehe patient [NO_44_S9]

source_name: clinical sample

value: clinical sample

value: epithelioid hemangioendothelioma (EHE)

value: WT


title: C30


title: FL10-HSC_CMX-RNU-056a

description: Fetal liver HSC RNAseq

value: hematopoietic stem cells (CD34+lin-CD38-CD45RA-CD90+)


title: SKOV3 SNU13 + Cisplatin (40 uM) 24 h, repeat 1

description: Control cell line stably overexpressing SNU13 and treated with cisplatin (40 uM) for 24 h


title: Brdu-ip Pol1-2A2 experiment 2


title: FPL06-HSPC_CMX-RNU-036

description: Placenta HSPC RNAseq

source_name: Placenta

value: Placenta

value: Embryo #06

value: hematopoietic stem/progenitors cells (CD34+CD90+CD43+)


title: C29


title: SKOV3 SNU13 + Cisplatin (40 uM) 24 h, repeat 2

value: Ovarian adenocarcinoma


title: Brdu-ip Pol32△270-309AA experiment 2


title: input Pol32Δ experiment 1


title: C33

value: White


title: C28


title: FPL06-HPC_CMX-RNU-037

description: Placenta HPC RNAseq

value: hematopoietic progenitors (CD34+CD90- (CD43+CD45+))


title: SKOV3 SNU13, repeat 1

description: Cell line stably overexpressing SNU13


title: FPL06-endo_CMX-RNU-035

description: Placenta endothelium RNAseq

value: endothelium (CD34+CD90+CD43-CD45-)


title: C26

value: CRC

value: Plasma separated from blood


title: SKOV3 SNU13, repeat 2

description: Cell line stably overexpressing SNU13


title: Brdu-ip Pol1-2A2/MCM2-3A experiment 1


title: SKOV3 pCDH + Cisplatin (40 uM) 24 h, repeat 1

description: Control cell line stably overexpressing empty vector and treated with cisplatin (40 uM) for 24 h


title: C25

value: Female

value: cfDNA


title: SKOV3 pCDH + Cisplatin (40 uM) 24 h, repeat 2


title: Sample_111

city: Rochester

first: Numrah

last: Fadra

state: MN

institute: Mayo clinic

data_processing:
Base calling was performed by the instrument computer using Illumina Real Time Analysis (RTA) software that is integrated with HiSeq Control Software (HCS) and provides a summary of quality statistics as per Illumina's acceptance criteria for sequencing. CASAVA 1.8.2 was used for de-multiplexing and conversion of base calls to paired-end FASTQ files
The MAP-Rseq (https://pubmed.ncbi.nlm.nih.gov/24972667/) pipeline was used to process the RNA sequencing reads, aligning them against human genome and transcriptome for reference build hg19 using Tophat2 (https://pubmed.ncbi.nlm.nih.gov/23618408/). Quality control of transcriptome sequencing data was done using RSEQC (https://pubmed.ncbi.nlm.nih.gov/22743226/).
Assembly: hg19
Supplementary files format and content: tab delimited gene counts file derived from HTSeq

source_name: blood

extract_protocol:
RNA from whole blood for all patients was extracted in a PAXgene Tube following manufacturer’s instructions (Qiagen).
The miRNeasy Mini kit from Qiagen was used for isolation of RNA and 101 base pair paired libraries were prepared using capture probes from the TruSeq®RNA Access Library Prep Kit (Illumina)
TruSeq® RNA Access

tag: Sex

value: female

value: blood


title: Sample_112


title: Brdu-ip Pol1-2A2/Pol32Δ experiment 1


title: Sample_110


title: SKOV3 pCDH, repeat 2

description: Control cell line stably overexpressing empty vector


title: C24

value: AA


title: Brdu-ip Pol32△270-309AA experiment 1


title: C23

value: Male


title: Sample_109


title: Brdu-ip WT experiment 1

value: WT


title: SKOV3 pCDH, repeat 1


title: SKOV3 transfected control fragment of mRNA GFP (89 b), repeat 3

description: cells transfected control fragment of mRNA GFP (89 b)

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trimmomatic.
Trimmed RNAseq reads were mapped against Homo Sapiens GRCh37.p13 genome annotation using STAR(v.2.5.2b). The gene read quantification was performed using HTSeq-count (v.0.6.0).
Differentially expressed genes were identified using the R package DESeq2.
Assembly: GRCh37
Supplementary files format and content: processed data files format and content: tab-delimited tsv files include count values for every gene and every sample

extract_protocol:
Total RNA was isolated from cancer cells using RNeasy Mini Kit (Qiagen) followed by treatment with DNAse I (NEB). The reaction was purifed with PureLink RNA Mini Kit (ThermoFisher). RNA quality was checked by 2100 bioanalyzer (Agilent, USA). Enrichment of polyadenylated RNA and library preparation was performed with NEBNext Ultra II Directional RNA Library Prep Kit (NEB), according to the manufacturer’s protocol. The library underwent a final cleanup using the Agencourt AMPure XP system (Beckman Coulter) after which the libraries’ size distribution and quality were assessed using a high sensitivity DNA chip (Agilent Technologies). Libraries were subsequently quantified by Quant-iT DNA Assay Kit, High Sensitivity (ThermoFisher). Samples were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro synthesis of U12 and U6atac small nuclear RNAs as well as a control fragment of GFP (89 bases) were performed as described previously (Stepanov et al., 2018). SKOV3 cells were transfected with in vitro synthesized snRNAs: U12, U6atac snRNAs, or a control GFP mRNA fragment (89 bases). SKOV3 cells treated with empty transfectant RNAiMax (Invitrogen) were taken as a contol.  The accumulation of synthetic RNAs into cells was confirmed by RT-PCR using specific primers. RNA was isolated from samles 48 h after transfection.


title: Brdu-ip Pol1-2A2 experiment 1


title: C27


title: C22


title: Sample_107


title: Brdu-ip H3-HA/T7 Pol32Δ experiment 2


title: Brdu-ip Pol1-2A2/MCM2-3A/Pol32Δ experiment 1


title: C21


title: Brdu-ip H3-HA/T7 Pol32Δ experiment 1


title: Sample_108


title: Sample_106


title: SKOV3 transfected control fragment of mRNA GFP (89 b), repeat 1


title: C20


title: Sample_105


title: SKOV3 transfected U6atac snRNA, repeat 3

description: cells transfected U6atac snRNA


title: C19


title: Brdu-ip H3-HA/T7 WT experiment 1


title: Sample_104


title: Pol32Δ H3K4me3 eSPAN noHU experiment 2


title: SKOV3 transfected U6atac snRNA, repeat 2

description: cells transfected U6atac snRNA


title: Sample_103


title: TET1KO c42KO2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: M1-BTAG TET1(-/-) KO#2, expansion culture c42 BMP2(+) BT(+) AG(+)

data_processing:
Paired-end reads were processed with Trim_Galore! V0.6.3 and mapped on the GRCh38.p12 genome using Bismark v0.22.1 and Bowtie2 v2.3.4.1 with the “-X 2000” option.  BAM files were, then, processed with deduplicate_bismark script to remove PCR duplicates, and bismark_methylation_extractor to count methyl- and unmehyl-Cytosine per at CpG or CpA sequences.
Assembly: GRCh38.p12
Supplementary files format and content: bismark report file
Library strategy: EM-seq

source_name: 585B1(XY) BTAG868 TET1KO_2

extract_protocol:
Gemomic DNA extraction was integrated in "library construction protocol" process.
EM-seq libraries were generated as described previously (Gyobu-Motani, 2023).
EM-seq, (Vaisvila, 2021)

value: differentiated hPGCLC

tag: transgene

value: TFAP2C-EGFP, BLIMP1-tdTomato knock-in

value: TET1 knockout

tag: time point

value: culture day 42

value: Expansion culture with BMP signalling


title: SKOV3 transfected U6atac snRNA, repeat 1

description: cells transfected U6atac snRNA

value: Ovarian adenocarcinoma


title: M1-BTAG c42 TET1 WT

description: M1-BTAG (585B1-868), expansion culture c42 BMP2(+) BT(+) AG(+)


title: SKOV3 transfected control fragment of mRNA GFP (89 b), repeat 2


title: SKOV3 transfected U12 snRNA, repeat 3

description: cells transfected U12 snRNA


title: WT H3K4me3 eSPAN noHU experiment 1


title: TET1KO c12KO2

description: M1-BTAG TET1(-/-) KO#2, expansion culture c12 BMP2(+) BT(+) AG(+)

value: culture day 12


title: Pol32aa H3K4me3 eSPAN experiment 2


title: Sample_101


title: Pol32aa H3K4me3 eSPAN experiment 1


title: TET1KO c12KO1

description: M1-BTAG TET1(-/-) KO#1, expansion culture c12 BMP2(+) BT(+) AG(+)

source_name: 585B1(XY) BTAG868 TET1KO_1


title: SKOV3 transfected U12 snRNA, repeat 1

description: cells transfected U12 snRNA


title: Sample_100


title: SKOV3 transfected U12 snRNA, repeat 2

description: cells transfected U12 snRNA


title: Sample_99


title: Sample_102


title: Pol32Δ H3K4me3 eSPAN experiment 3


title: M1-BTAG c12 TET1 WT

description: M1-BTAG (585B1-868), expansion culture c12 BMP2(+) BT(+) AG(+)


title: Sample_98


title: SKOV3 control, repeat 2

description: Control cells, treated with empty transfectant


title: Pol32Δ H3K4me3 eSPAN noHU experiment 1


title: F1-AGVT c127AGVT

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c127 BMP2(+) AG(+) VT(+)

source_name: NCLCN(XX) AGVT261

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: culture day 127


title: F1-AGVT c86AGVT

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c86 BMP2(+) AG(+) VT(+)

value: culture day 86


title: Brdu-ip Pol32Δ experiment 2


title: SKOV3 control, repeat 3


title: WT H3K4me3 eSPAN experiment 3


title: Sample_97


title: TET1KO c42KO1

description: M1-BTAG TET1(-/-) KO#1, expansion culture c42 BMP2(+) BT(+) AG(+)


title: SKOV3 control, repeat 1


title: Sample_96


title: F1-AGVT c72AGVT

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c72 BMP2(+) AG(+) VT(+)

value: culture day 72


title: Sample_95


title: cancer cells from patient 1 incubated with ascites after chemotherapy, repeat 3

description: incubation with ascites after chemotherapy

data_processing:
RNA-seq reads were trimmed for quality, paired reads were cropped using Trim Galore.
Trimmed RNAseq reads were quantified against Homo Sapiens GRCh38.12 genome annotation at the transcript level using Salmon (v.0.12.0). Results were aggregated to gene level using the R package tximport.
Differentially expressed genes were identified using the R package DESeq2.
Assembly: GRCh38
Supplementary files format and content: processed data files format and content: tab-delimited tsv files include TPM values for every gene and every sample

source_name: ovarian cancer ascites

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. Primary cultures of ovarian cancer cells were cultivated in RPMI medium containing 10% FBS (Gibco), 2 mM L-glutamine (ICN Biomedicals Inc) and 1% penicillin/streptomycin (Paneco). The culture medium was changed every 3-4 days. Cells were dissociated using Trypsin (ThermoFisher).

extract_protocol:
Total RNA was isolated from primary cultures of cancer cells using RNeasy Mini Kit (Qiagen). DNase treatment was carried out with TURBO DNA-free kit (Thermo Fisher Scientific, Waltham, MA, USA), in volumes of 50 µl. RNA cleanup was performed with the Agencourt RNA Clean XP kit (Beckman Coulter). The concentration and quality of the total RNA were checked by the Quant-it RiboGreen RNA assay (ThermoFisher) and the RNA 6000 Pico chip (Agilent Technologies), respectively. Enrichment of polyadenylated RNA and library preparation was performed with NEBNext Ultra II Directional RNA Library Prep Kit (NEB), according to the manufacturer’s protocol. The library underwent a final cleanup using the Agencourt AMPure XP system (Beckman Coulter) after which the libraries’ size distribution and quality were assessed using a high sensitivity DNA chip (Agilent Technologies). Libraries were subsequently quantified by Quant-iT DNA Assay Kit, High Sensitivity (ThermoFisher). Finally, equimolar quantities of libraries (12 pM) for samples Sh74-Sh75 and Sh103-Sh106 were sequenced by a high throughput run on the Illumina HiSeq 2500 using 2 × 100 bp paired-end reads and a 5% Phix spike-in control. Samples P1-3 and R1-3 were sequenced on NextSeq 500 System (Illumina, USA) with NextSeq 500/550 High Output Kit v2.5 (75 Cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary cultures of ovarian cancer cells isolated from paired ascitic fluids from 7 patients before and after chemotherapy. Total RNA was isolated from early passages of cancer cells.

value: ovarian cancer ascites

value: primary culture of ovarian cancer cells

tag: disease

value: Ovarian small cell carcinoma, stage IIIC

tag: patient

value: Patient 1; 45 years old; after neoadjuvant chemotherapy (3 courses)


title: Brdu-ip Mcm2-3A experiment 2

tag: genotype


title: F1-AGVT c72AG

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c72 BMP2(+) AG(+) VT(-)


title: Sample_94

value: female

tag: tissue

value: blood


title: cancer cells from patient 1 incubated with ascites before chemotherapy, repeat 3

description: incubation with ascites before chemotherapy

value: Patient 1; 45 years old; before neoadjuvant chemotherapy


title: F1-AGVT hPGCLC_2

description: F1-AGVT (NCLCN-261), hPGCLC day6, replicate 2

tag: cell line

value: human PGCLC

value: WT

value: culture day 0


title: Brdu-ip Pol32Δ experiment 1


title: Sample_93


title: cancer cells from patient 1 incubated with ascites after chemotherapy, repeat 2


title: Sample_92


title: Brdu-ip Mcm2-3A experiment 1


title: F1-AGVT hPGCLC_1

description: F1-AGVT (NCLCN-261), hPGCLC day6, replicate 1


title: Brdu-ip Mcm2-3A/Pol32Δ experiment 1


title: cancer cells from patient 1 incubated with ascites before chemotherapy, repeat 2


title: F1-AGVT iPSC

description: F1-AGVT (NCLCN-261), iPSC day6

value: human iPSC


title: Pol1-2A2/Pol32Δ H3K56ac eSPAN experiment 2


title: cancer cells from patient 1 incubated with ascites before chemotherapy, repeat 1


title: Sample_90


title: cancer cells from patient 1 incubated with ascites after chemotherapy, repeat 1


title: Pol1-2A2 H3K56ac eSPAN experiment 2


title: M1-AGDT c122 AGDT

description: M1-AGDT (585B1-7453) expansion culture c122 BMP2(+) AG(+) DT(+)

value: differentiated hPGCLC

value: TFAP2C-EGFP, DAZL-tdTomato knock-in

value: culture day 122

value: Expansion culture with BMP signalling


title: Brdu-ip Mcm2-3A/Pol32Δ experiment 2


title: Pol1-2A2/Pol32Δ H3K56ac eSPAN experiment 1


title: Sample_89


title: M1-AGDT c82_2 AG

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(-) replicate 2

value: culture day 82


title: P07

source_name: Plasma separated from blood

value: White

tag: age

value: Female

value: PDAC

value: Plasma separated from blood

value: cfDNA


title: Pol1-2A2 H3K56ac eSPAN experiment 1


title: P06


title: Sample_88

value: female


title: Sample_87

value: blood


title: P08


title: M1-AGDT c32 AG

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(+) AG(+) DT(-)

value: culture day 32


title: Mcm2-3A/Pol32Δ H3K56ac eSPAN experiment 2


title: Sample_91


title: M1-AGDT c82_1 AG

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(-) replicate 1


title: M1-AGDT c82 AGDT

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(+)


title: Mcm2-3A/Pol32Δ H3K56ac eSPAN experiment 1


title: P04


title: M1-AGDT c32_2 AG no BMP2

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(-) AG(+) DT(-) replicate 2

value: Expansion culture without BMP signalling


title: P03

value: AA

value: Male


title: Sample_86


title: Sample_85


title: NCLCN AGVT c117

description: NCLCN AGVT hPGCLC BMP2-driven differentiation c117

library_source: transcriptomic single cell

data_processing:
Read data generated from samples labeled with Cell Multiplexing Oligo were processed with cellranger v6.0.1 with “multi” option.
Assembly: GRCh38.p12

source_name: NCLCN AGVT

extract_protocol:
RNA extraction was integrated in "library construction protocol" process.
Whole-cell suspensions harvested from the expansion culture were pelleted and were subjected to Cell Multiplexing Oligo labeling.  Alternatively, samples for analysis were cryopreserved as follows: whole-cell suspensions harvested from the expansion culture were pelleted and were resuspended in Cell Banker Type 1 Plus for cryopreservation at −80˚C.  For Cell Multiplexing Oligo labeling, after thawing in the water bath at 37℃ if needed, collected cells were resuspended in Cell Multiplexing Oligo solution and were incubated for 5 minutes at room temperature.  After the incubation, cells were washed with 1% BSA (SIGMA, A1519)-PBS (−) and were collected by centrifugation at 200g for 10 minutes.  Collected cells were resuspended in 1% BSA-PBS (−) containing anti-TRA-1-85 antibody (BD Bioscience, 563302, 1:20) and placed on ice for 30 minutes in the dark.  Then, the cells were washed with PBS once and were resuspended in 1% BSA-PBS (−) containing 3 μM DRAQ7 (abcam, ab109202).  To isolate live human cells, TRA-1-85 (+) DRAQ7(−) cells were sorted into DMEM/F12 (GIBCO, 10565-018) + 1% BSA by FACS Aria III.  Sorted cells were subjected to the subsequent library construction using 10X Genomics Single Cell 3’ Kit v. 3.1, followed by sequencing on an Illumina NovaSeq 6000 platform.  All steps were performed in accordance with the manufacturer's instructions.
scRNAseq(10X Genomics Single Cell 3’ Kit v. 3.1)

value: NCLCN AGVT

value: human iPSC

value: WT


title: Pol32Δ H3K56ac eSPAN experiment 2


title: P02


title: Mcm2-3A H3K56ac eSPAN experiment 1


title: Mcm2-3A H3K56ac eSPAN experiment 2


title: Pol32Δ H3K56ac eSPAN experiment 1


title: P01


title: Sample_82


title: NCLCN AGVT c56

description: NCLCN AGVT hPGCLC BMP2-driven differentiation c56


title: WT H3K56ac eSPAN experiment 1


title: H18

value: HEA


title: M1-AGDT c32_1 AG no BMP2

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(-) AG(+) DT(-) replicate 1

value: differentiated hPGCLC

value: TFAP2C-EGFP, DAZL-tdTomato knock-in


title: H3-T7 Pol32Δ eSPAN experiment 2


title: Sample_80


title: H16

value: White


title: Sample_79


title: Sample_81


title: 585B1 BTAG TET1 KO#1

description: 585B1 BTAG TET1 KO#1 hPGCLC BMP2-driven differentiation c18

source_name: 585B1 BTAG

value: 585B1 BTAG

value: TET1 KO#1

value: Expansion culture with BMP signalling


title: NCLCN AGVT c11

description: NCLCN AGVT hPGCLC BMP2-driven differentiation c11


title: 585B1 BTAG TET1 KO#2

description: 585B1 BTAG TET1 KO#2 hPGCLC BMP2-driven differentiation c18

value: TET1 KO#2


title: H3-T7 Pol32Δ eSPAN experiment 1


title: H17

value: Plasma separated from blood

value: cfDNA


title: NCLCN AGVT c86

description: NCLCN AGVT hPGCLC BMP2-driven differentiation c86


title: H15

value: Asian


title: H3-HA Pol32Δ eSPAN experiment 2


title: H14

value: Female


title: Sample_78

value: female

value: blood


title: 585B1 BTAG WT

description: 585B1 BTAG WT hPGCLC BMP2-driven differentiation c18


title: Sample_76


title: H3-HA Pol32Δ eSPAN experiment 1


title: Sample_77


title: Sample_83


title: Sample_84


title: H3-T7 WT eSPAN experiment 1


title: H12


title: PGPC14 WT- EV RNAseq

city: Toronto

first: Lina

last: Antounians

state: Ontario

address: 686 Bay St

country: Canada

institute: The Hospital for Sick Children

data_processing:
Raw sequencing data was processed into count data using the open source web-based platform galaxy.org MiRDeep2 tool as previously, mapping reads to hg38 human genome annotation and mature and precursor miRNA sequences from miRbase database. To generate a counts table for differential gene expression, miRNA counts for same mature miRNA from different precursor origin were averaged. Differential expression analysis was performed using DESeq2 package in R. Quality of samples was analyzed using principal component analysis (PCA) in DESeq2 package and pheatmap function was used to display variance between samples and replicates.
Assembly: hg38

source_name: PGPC14 WT- EV

extract_protocol:
For whole cell samples (PGPC14WT, HCA), 1µg was provided The Centre for Applied Genomics, Hospital for Sick Children, Toronto. For ADEV samples, all isolates were provided for bioanalyzer and sequencing.
Sequencing libraries were made using the Small RNA library preparation kit NEBNext (NEB) Small RNA library prep set according to the manufacturer’s instructions. Sequencing was performed using Illumina NovaSeq SP flowcell for single end 50bp length reads, aiming for 40M reads per transcript. Library preparation and sequencing were done at TCAG.

value: Astrocyte EVs


title: HCA RNAseq

source_name: HCA

value: Astrocytes


title: H11

value: Male


title: Sample_74


title: H3-HA WT eSPAN experiment 1

value: WT


title: PGPC14WT RNAseq


title: H10

value: HEA


title: Sample_72


title: Pol32△270-309AA H3K4me3 eSPAN experiment 2


title: Sample_73


title: Donor7-TAK981-3

city: Cambridge

first: Min Young

last: Lee

address: 40 Landsdowne St

institute: Takeda Pharmaceutical Company Limited

data_processing:
Read quality were performed for all samples by using FastQC. PE 150 were applied to sequence the samples, ie a pair-end 150 bp sequence.However, the length of DNA segment may be less than 150 bp during library preparation, in results of adapter sequences in the raw reads. Skewer (v0.2.2) software was used to remove the adapter sequence of raw data(Fastq) and the reads whose length is longer than 75bp were selected after adapters were removed. Then the selected reads, named as Clean reads, were used for downstream analysis.
The alignment analysis can basically be divided into two steps: 1)genemeGenerate Build an index; 2) Sequence alignment. In this project, clean reads of each samplewere align to reference genome by using STAR software with default parameters.
Expression estimation of gene and transcript was performed by using RSEM with setting --estimate-rspd parameter to estimate the distribution of thestarting position of the sequencing sequence (RSPD) and other parameters were defalut. Then edgeR (v3.8.5) package in R were used to perform TMM (trimmed mean of M values) and CPM (count per million) normalization for the the gene expression.
Raw read counts of gene expression were applied to estimate the diff eretiation between pair samples or groups by using edgeR package in R.
a setof signifi cantly up-regulated or down-regulated genes was used as input to test the signifi cance ofgene enrichment
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: Count of each sample

extract_protocol: second generation sequencing was performed according to Illumina's standard protocol

treatment_protocol: RNA sequencing of human monocyte-derived macrophages treated with control (DMSO) and 1 uM TAK-981 for 24 h, with 2 donors in 3 biological replicates

value: human monocyte-derived macrophages

tag: treatment time

value: 24 hours


title: H09

tag: race

value: White


title: Donor7-TAK981-2


title: Pol1-2A2/Pol32Δ H3K4me3 eSPAN experiment 2


title: HCA-EV RNAseq

source_name: HCA-EV


title: H13

tag: gender


title: H08

tag: group


title: Donor7-TAK981-1


title: Pol1-2A2 H3K4me3 eSPAN experiment 2


title: H07

tag: fraction


title: Sample_71


title: Pol1-2A2/Pol32Δ H3K4me3 eSPAN experiment 1


title: Sample_70


title: Donor7-DMSO-3

value: DMSO


title: H06


title: Sample_75


title: Donor7-DMSO-2


title: Sample_68


title: H05

value: AA


title: Sample_69


title: Pol32△270-309AA H3K4me3 eSPAN experiment 1


title: H04


title: Mcm2-3A/Pol32Δ H3K4me3 eSPAN experiment 1


title: Donor4-TAK981-3


title: Mcm2-3A/Pol32Δ H3K4me3 eSPAN experiment 2


title: Mcm2-3A H3K4me3 eSPAN experiment 2


title: H03


title: Sample_66


title: Sample_67


title: H02


title: Donor4-TAK981-2


title: Sample_65


title: Mcm2-3A H3K4me3 eSPAN experiment 1


title: Pol32Δ H3K4me3 eSPAN experiment 2


title: H01


title: C18

value: CRC


title: Sample_64


title: Pol1-2A2 H3K4me3 eSPAN experiment 1


title: Pol32Δ H3K4me3 eSPAN experiment 1


title: Donor4-DMSO-3


title: Donor4-DMSO-2


title: Donor7-DMSO-1


title: Sample_63


title: C17

value: Plasma separated from blood


title: Donor4-DMSO-1


title: Sample_62


title: WT H3K4me3 eSPAN experiment 2


title: WT H3K4me3 eSPAN experiment 1


title: Sample_61


title: C16

value: cfDNA


title: C15

value: Asian


title: MDA-MB-231_TEPA24_rep3

city: Bologna

first: Daniele

last: Mercatelli

address: Via Irnerio 45

department: Pharmacy and Biotechnology

institute: University of Bologna

data_processing:
QC with Fastqc
alignment of the reads with hisat 2
Counting reads to genomic features with featureCounts using Homo_sapiens.GRCh38.103.gtf as reference. Command: featureCounts -T 7 -p -s 2 -t exon -g gene_name -a Homo_sapiens.GRCh38.103.gtf
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Epithelial human breast cancer cell line

growth_protocol: The MDA-MB-231 human triple-negative breast cancer cell line was plated at 5x10^6 cells/T75 flask in DMEM media supplemented with 10% FBS.

extract_protocol:
Cells were washed with PBS, and then lysed using the Qiagen RNA Extraction Kit. The RNA purity and concentration was then assessed using the Nanodrop.
Quality control and library preparation were carried out by Ramaciotti Centre for Genomics (UNSW, Australia). Paired-end 100 bp sequencing was performed on the Illumina NovaSeq 6000 using TruSeq stranded mRNA for a total of 1.6B reads.

treatment_protocol: Treatment with copper chelator occurred for 24h (MDA-MB-231 TEPA 8mM, DIPG007 TEPA 4mM, DIPG010 TEPA 8mM).

value: Epithelial human breast cancer

value: Treated with TEPA (24 hours)


title: C14

value: Female


title: MDA-MB-231_TEPA24_rep2


title: WT Mnase repeat 3

data_processing:
Sequence reads were mapped back to the yeast reference genome (sacCer3) using Bowtie2 software. Only consistent pair-end reads were chosen for further analysis.
The sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To obtain the nucleosome occupancy, DNA fragments from 120 to 170 bp in size determined by the paired-reads were firstly selected for calculation. The length of DNA fragments were then adjusted to half of the nucleosome size (74bp) to increase the signal-to-noise ratio. Finally, the count of adjusted DNA fragments covering each base pair in the genome were used to calculate the nucleosome occupancy.
To identify BrdU-IP-ssSeq peaks, the sequence reads of both Watson and Crick strands were merged and used to call peaks using SICER software with false discovery rate (FDR) cut-off 0.01.
Assembly: sacCer3
Supplementary files format and content: bigwig files were generated for Watson and Crick strand, scores represent the normalization reads density.

source_name: WT

growth_protocol: To synchronize cells at G1, alpha factor was added at cell density OD600=0.4-0.5 to achieve a final concentration of five µg/mL for yeast strains. After three hours arrest at 25°C, the cells were released to fresh YPD medium with or without 200 mM HU. For the histone H3 Recombination-induced Tag Exchange (RITE) experiments, yeast cells were grown overnight in YPD in the presence of hygromycin B (200 μg/mL, Invitrogen). The cells were then diluted 1:10 into two fresh YPD flask (one with, the other without hygromycin B) and incubated for 32 hours (G0 state). The cells were centrifuged by 3000 rpm for 10 minutes. The cells cultured with hygromycin B were transferred to another flask containing depleted medium without hygromycin B. Recombination was induced by the addition of 1 μM β-estradiol (E-8875, Sigma-Aldrich) and the cells were cultured for additional 16 hours. Subsequently, these cells were diluted 1:25 in fresh YPD media containing 200 mM HU and 400ul/ml BrdU. After incubation at 25 C for 90 minutes, samples were collected for ChIP and eSPAN.

extract_protocol:
All ChIP and eSPAN assays were performed as described previously except that Mnase digestion was used for chromatin fragmentation in order to map nucleosomes. Briefly, the samples were incubated with 1% fresh-made formaldehyde at 25 °C for 20 min, and then quenched with 0.125M glycine for five min.  The cells wer harvested and lysed with glass beads in ChIP lysis buffer (50 mM HEPES, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% sodium deoxycholate). The resulting cell and chromatin pellet was washed with NP buffer (1.6 M sorbitol, 2 mM CaCl2, 5mM MgCl, 50 mM NaCl, 14 mM β-mercaptoethanol, 10 mM Tris-HCl (pH 7.4), 0.075% NP-40, 5 mM spermidine).  Proper amounts of Mnase was added to ensure that majority of chromatin are mono- and di-nucleosomes with incubation at 37 °C for 20 min . The reacation was terminated by adding 5ul 0.5M EDTA. Further, ¼ volume 5X ChIP lysis buffer was added into dilute thedigested chromatin. The lysates was incubated in ice for 30 minutes. After clarification of lysates by centrifugation, soluble chromatin (mainly mononucleosomes) was immunoprecipitated with a specific antibody including anti-H3K4me3 antibody (ab8580), anti-H3K56ac antibody (6), anti-HA antibody (12CA5) or anti-T7 (A190-117A BETHYL)). ChIP DNA was recovered using Chelex-100. The ChIP or total DNA was denatured at 100°C for five min and was immediately transferred to ice bath for five minutes.  The DNA was diluted at least ten times with BrdU IP solution (PBS, 0.0625% Triton X-100(v/v), 6.7 g/mL Escherichia. coli tRNA, 0.67 ul/mL BrdU antibody (BD Bioscience)).  After the samples were incubated at 4°C for two hour, 20 uL protein G beads (GE Healthcare) were added.  After incubation at 4°C for another hour, the protein G beads was washed extensively. DNA were eluted using 100 uL 1XTE buffer plus 1% SDS and incubation at 65 °C for 15 min. Eluted DNA was purified using a Qiagen Mini-elute kit.
We used the ssDNA library preparation kit to prepare library (Cat no. 10096 Swift Bioscience). The ssDNA libraries were sequenced using the paired-end method by different sequencing platform over the years including Illumina NextSeq 500, Hi-seq 2000 or 2500 machine at Mayo Clinic or Columbia University.

value: synchronized yeast cells


title: WT Mnase repeat 2


title: Sample_60

value: female

value: blood


title: MDA-MB-231_TEPA24_rep1


title: C13


title: WT Mnase repeat 1

value: WT


title: Sample_57


title: WT input repeat 2


title: MDA-MB-231_TEPA8_rep3

value: Treated with TEPA (8 hours)


title: Donor4-TAK981-1

value: human monocyte-derived macrophages


title: WT input repeat 1


title: Sample_56


title: C10


title: Sample_55


title: MDA-MB-231_TEPA8_rep1


title: MDA-MB-231_CTRL_rep3

value: Untreated


title: WT H3K56ac eSPAN repeat 3


title: C09

value: White


title: WT H3K56ac eSPAN repeat 2


title: Sample_54


title: Sample_59


title: C08


title: C07


title: WT H3K56ac eSPAN repeat 1


title: MDA-MB-231_CTRL_rep1


title: Sample_53


title: WT H3K56ac ChIP-ssSeq repeat 2


title: Sample_58


title: C06

value: Male


title: C12


title: MDA-MB-231_TEPA8_rep2


title: WT H3K56ac ChIP-ssSeq repeat 1


title: C05


title: WT H3K4me3 eSPAN repeat 3


title: Sample_50


title: C04

value: AA


title: WT H3K4me3 eSPAN repeat 2


title: Sample_48


title: MDA-MB-231_CTRL_rep2


title: C11

value: CRC


title: iMGL_TREM2-192_48h_20uM_rep3

city: Beerse

last: Vandermeulen

address: Turnhoutseweg 30

department: Neuroscience

country: Belgium

institute: Johnson & Johnson

description: Off-target analysis of APOE and TREM2 ASOs in iPSC derived microglia

hyb_protocol: Biotin-labeled target samples were hybridized to the Clariom™ GO Screen containing probes for 19,409 protein-coding genes.

scan_protocol: Target hybridization was processed on the GeneTitan® Instrument according to manufacturer’s instructions provided for Expression Array Plates (P/N 952361). Images were analyzed using the GeneChip® Command Console Software (GCC) (ThermoFisher).

data_processing:
Microarray data were processed using the statistical computing R-program package limma (Version 3.42.0) and Bioconductor tools.
The gene expression values were normalized using Robust Multi-array Average (RMA). Individual probes were grouped into gene-specific probe sets based on Entrez Gene using the metadata package goscreenhuhsentrezg (version 25.0.0)

label: biotin

source_name: iPSC derived microglia

label_protocol: Amplification and labelling of total RNA were performed using the GeneChip® PICO Reagent Kit following the manufacturer’s protocol (ThermoFisher 2016, P/N 902790).

growth_protocol: The iPSC lines used in the cellular assays were obtained from the EBiSC consortium (https://ebisc.org) (Suppl Table 2). The human iPSC lines BIONi010-C (parental; CVCL_1E68) was used to evaluate the off target effects of the ASOs in vitro.  Human iPSC-derived microglia (iMGL) were differentiated using a method described by Cowley lab (Wilgenburg, B. van, Browne, C., Vowles, J. & Cowley, S. A. Efficient, Long Term Production of Monocyte-Derived Macrophages from Human Pluripotent Stem Cells under Partly-Defined and Fully-Defined Conditions. PLoS One 8, e71098 (2013)/Haenseler, W. et al. A Highly Efficient Human Pluripotent Stem Cell Microglia Model Displays a Neuronal-Co-culture-Specific Expression Profile and Inflammatory Response. Stem Cell Reports 8, 1727–1742 (2017)). Briefly, iPSCs were dissociated with TrypLE select (ThermoFisher, 12563011) into single cell suspension and embryoid bodies (EBs) were produced in AggreWell800 (Stem Cell Technologies, 34811) in mTeSR medium (Stemcell Technologgies, 85850) supplemented with 50 ng/ml BMP-4 (Invitrogen, PHC9534), 50 ng/ml VEGF (PeproTech, 100-20) and 20 ng/ml SCF (Miltenyi, 130-096-693). The medium was refreshed daily by 75% for 3 consecutive days. Next, EBs were transferred to factory plates to create precursor factories by placing 10-20 EBs per well in X-VIVO 15 medium (Lonza, BE02-060F) containing 100 U/ml Penicillin and 100 µg/ml Streptomycin (ThermoFisher, 15140-122), 2 mM Glutamax supplement, 0.05 mM 2-mercaptoethanol (ThermoFisher, 31350-010), 0.1 µg/ml M-CSF (ThermoFisher, PHC9501) and 0.025 µg/ml IL-3 (ThermoFisher, PHC0031). The factories were cultured for 6-8 weeks (with weekly 50% medium change) before the cells were harvested for final differentiation into microglia. Microglia precursors were harvested for no more than once a week. At harvest, microglia precursors were plated at a density of 15,000 cells/well in non-coated 96-well µclear plates (Greiner, 655090) and cultured in advanced DMEM/F12 medium (ThermoFisher, 12634-010) containing 100 U/ml Penicillin and 100 µg/ml Streptomycin, 2 mM Glutamax supplement, 0.05 mM 2-mercaptoethanol, 10 ng/ml GM-CSF (ThermoFisher, PHC2015) and 100 ng/ml IL-34 (Peprotech, 200-34) for maximally 14 days (with 50 % medium change every 2-3 days).

extract_protocol: Total cellular RNA was isolated using the RNeasy96 kit (Qiagen, 74182) according to manufacturer’s protocol. Briefly, cells were lysed with RLT buffer at RT and an equal volume of 70% (v/v) ethanol was added. The mixture was pipetted 5 times and transferred to columns in which the RNA was bound to the filter by a vacuum system (Qiagen). The RNA was washed sequentially with the RW1 and RPE buffers provided in the kit. After the final RPE washing step, a centrifugation was applied to make sure any residual buffer was eliminated (6 min at 5,600 x g at room temperature (RT). The RNA was then eluted with RNase-free water by centrifugation at 5,600 x g at RT for 4 min. The RNA concentration was determined by spectroscopy using a Nanodrop (ThermoFisher, ND-8000).

treatment_protocol: ASOs were added directly into the medium of the microglia on DIV7. ASOs were incubated for 24 and 48hours. Medium was removed and cells were lysed in 150uL RLT buffer (Qiagen, 74182).

tag: aso

tag: treatment time (h)

tag: dose (microm)


title: iMGL_TREM2-192_48h_20uM_rep2


title: WT H3K4me3 ChIP-ssSeq repeat 1

tag: cell type


title: C02

value: Plasma separated from blood


title: iMGL_TREM2-192_48h_20uM_rep1


title: WT H3K4me3 ChIP-ssSeq repeat 2


title: C01

value: cfDNA


title: Sample_52

tag: Sex


title: C03


title: Sample_49


title: Sample_47


title: Sample_46


title: WT BrdU-IP-ssSeq repeat 1


title: Sample_51


title: iMGL_TREM2-171_48h_20uM_rep3


title: c42_TET1-KO#1_rep1 (MS397_109)

description: M1-BTAG TET1(-/-) KO#1, expansion culture c42 BMP2(+) BT(+) AG(+) replicate 1

data_processing:
All reads were processed with cutadapt v1.18 for trimming adaptor and poly-A, then mapped onto GRCh38.p12 transcript references using Tophat v2.1.1.
Resulting BAM files were processed with HTseq v0.9.1 to calculate read counts per gene.
Read counts per gene were divided by total read counts in all chromosomal genes to estimate RPM values for genes.
Resulting BAM files were separately processed with SNPsplit v0.3.2 to split into alleles. Resulting bam files were processed with Htseq v0.9.1 to calculate read counts per gene.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample

extract_protocol:
Total RNA was extracted from cells by NucleoSpin RNA XS (MACHEREY-NAGEL, U0902A) according to the manufacturer’s instructions.
1 ng of extracted RNA was used for the reverse transcription and the cDNA amplification described in the previous report (Nakamura, 2015). Sequencing libraries were generated from amplified cDNA as described previously (Murase, 2020).
SC3-seq (Nakamura, 2015)

tag: transgene

value: TFAP2C-EGFP, BLIMP1-tdTomato knock-in

value: differentiated hPGCLC

tag: time

value: culture day 42

tag: treatment

value: Expansion culture with BMP signalling


title: WT BrdU-IP-ssSeq repeat 2

value: synchronized yeast cells

tag: genotype


title: WT H3K4me3 eSPAN repeat 1


title: iMGL_TREM2-171_48h_20uM_rep2


title: iMGL_TREM2-171_48h_20uM_rep1


title: iMGL_APOE13_48h_20uM_rep2


title: rtt106Δ mcm2-3a H3K4me3 ChIP-ssSeq

source_name: rtt106Δ mcm2-3a

value: rtt106{delta} mcm2-3a


title: Sample_44

value: female

tag: tissue

value: blood


title: c42_TET1-WT_rep1 (MS397_108)

description: M1-BTAG (585B1-868), expansion culture c42 BMP2(+) BT(+) AG(+) replicate 1

tag: cell line

value: WT


title: iMGL_APOE13_48h_20uM_rep3


title: Sample_42


title: c32_TET1-KO#2_rep1 (MS397_106)

description: M1-BTAG TET1(-/-) KO#2, expansion culture c32 BMP2(+) BT(+) AG(+) replicate 1

value: culture day 32


title: rtt106Δ mcm2-3a H3K4me3 eSPAN


title: Sample_43


title: c32_TET1-KO#1_rep2 (MS397_105)

description: M1-BTAG TET1(-/-) KO#1, expansion culture c32 BMP2(+) BT(+) AG(+) replicate 2


title: c32_TET1-KO#1_rep1 (MS397_104)

description: M1-BTAG TET1(-/-) KO#1, expansion culture c32 BMP2(+) BT(+) AG(+) replicate 1


title: rtt106Δ mcm2-3a BrdU-IP-ssSeq


title: iMGL_APOE1_48h_20uM_rep3


title: Sample_41


title: Sample_39


title: P05

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human genome hg19 by bismark.
Only uniquely mapped reads were kept for down-stream analyses.
Calling of mC was performed by scripts in bismark.
Assembly: hg19
Supplementary files format and content: bismark output cov files

extract_protocol:
Plasma were separated from blood,then cfDNA were extracted from plasma using zymo research Quick-cfRNA Serum & Plasma, 1 ng cfDNA was used for library construction.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit.

tag: age

value: PDAC


title: c32_TET1-WT_rep1 (MS397_102)

description: M1-BTAG (585B1-868), expansion culture c32 BMP2(+) BT(+) AG(+) replicate 1


title: Sample_40


title: iMGL_APOE1_48h_20uM_rep2


title: iMGL_APOE13_48h_20uM_rep1


title: c32_TET1-WT_rep2 (MS397_103)

description: M1-BTAG (585B1-868), expansion culture c32 BMP2(+) BT(+) AG(+) replicate 2


title: c32_TET1-KO#2_rep2 (MS397_107)

description: M1-BTAG TET1(-/-) KO#2, expansion culture c32 BMP2(+) BT(+) AG(+) replicate 2


title: rtt106Δ H3K4me3 ChIP-ssSeq


title: c12_TET1-KO#2_rep2 (MS337_020)

description: M1-BTAG TET1(-/-) KO#2, expansion culture c12 BMP2(+) BT(+) AG(+) replicate 2

value: culture day 12


title: rtt106Δ dpb3Δ H3K4me3 ChIP-ssSeq

source_name: rtt106Δ dpb3Δ

value: rtt106{delta} dpb3{delta}


title: Sample_37


title: rtt106Δ dpb3Δ H3K4me3 eSPAN


title: iMGL_Scrambled_48h_20uM_rep2

value: Scrambled


title: iMGL_Scrambled_48h_20uM_rep3


title: c12_TET1-WT_rep2 (MS337_017)

description: M1-BTAG (585B1-868), expansion culture c12 BMP2(+) BT(+) AG(+) replicate 2


title: rtt106Δ H3K4me3 eSPAN


title: c12_TET1-KO#2_rep1 (MS337_016)

description: M1-BTAG TET1(-/-) KO#2, expansion culture c12 BMP2(+) BT(+) AG(+) replicate 1


title: iMGL_APOE1_48h_20uM_rep1


title: Sample_34


title: iMGL_Scrambled_48h_20uM_rep1


title: Sample_36


title: c12_TET1-WT_rep1 (MS337_013)

description: M1-BTAG (585B1-868), expansion culture c12 BMP2(+) BT(+) AG(+) replicate 1


title: c12_TET1-KO#1_rep2 (MS337_019)

description: M1-BTAG TET1(-/-) KO#1, expansion culture c12 BMP2(+) BT(+) AG(+) replicate 2


title: rtt106Δ BrdU-IP-ssSeq


title: Sample_38


title: mcm2-3a Mnase repeat 3


title: Sample_33


title: mcm2-3a Mnase repeat 2


title: Sample_35


title: hPGCLC_TET1-KO#1_rep2 (MS337_012)

description: M1-BTAG TET1(-/-) KO#1, hPGCLC day6 replicate 2

value: human PGCLC

value: culture day 0


title: iMGL_TREM2-192_48h_1.25uM_rep3


title: Sample_32


title: iMGL_TREM2-192_48h_1.25uM_rep2


title: rtt106Δ dpb3Δ BrdU-IP-ssSeq


title: iMGL_TREM2-192_48h_1.25uM_rep1


title: hPGCLC_TET1-KO#2_rep2 (MS337_073)

description: M1-BTAG TET1(-/-) KO#2, hPGCLC day6 replicate 2


title: Sample_30


title: mcm2-3a input


title: Sample_29


title: hPGCLC_TET1-WT_rep2 (MS337_010)

description: M1-BTAG (585B1-868), hPGCLC day6 replicate 2


title: Sample_31


title: mcm2-3a H3K56ac eSPAN repeat 2


title: mcm2-3a H3K56acChIP-ssSeq


title: mcm2-3a H3K56ac eSPAN repeat 1


title: hPGCLC_TET1-KO#2_rep1 (MS337_009)

description: M1-BTAG TET1(-/-) KO#2, hPGCLC day6 replicate 1


title: Sample_28


title: iMGL_TREM2-171_48h_1.25uM_rep2

description: Off-target analysis of APOE and TREM2 ASOs in iPSC derived microglia


title: iMGL_APOE13_48h_1.25uM_rep3


title: hPGCLC_TET1-KO#1_rep1 (MS337_008)

description: M1-BTAG TET1(-/-) KO#1, hPGCLC day6 replicate 1


title: iMGL_APOE13_48h_1.25uM_rep2


title: mcm2-3a H3K4me3 eSPAN repeat 2


title: iMGL_TREM2-171_48h_1.25uM_rep1


title: hPGCLC_TET1-WT_rep1 (MS337_006)

description: M1-BTAG (585B1-868), hPGCLC day6 replicate 1


title: Sample_26


title: Sample_27


title: iMGL_APOE13_48h_1.25uM_rep1


title: iMeLC_TET1-KO#2_rep2 (MS386_105)

description: M1-BTAG TET1(-/-) KO#2, iMeLC replicate 2

value: human iMeLC


title: Sample_25


title: mcm2-3a H3K4me3 ChIP-ssSeq


title: mcm2-3a dpb3Δ Mnase repeat 3

source_name: mcm2-3a dpb3Δ

value: mcm2-3a dpb3{delta}


title: Sample_24

source_name: blood


title: iMeLC_TET1-KO#1_rep2 (MS386_103)

description: M1-BTAG TET1(-/-) KO#1, iMeLC replicate 2

value: TFAP2C-EGFP, BLIMP1-tdTomato knock-in


title: iMeLC_TET1-WT_rep2 (MS386_101)

description: M1-BTAG (585B1-868), iMeLC replicate 2


title: Sample_23


title: mcm2-3a dpb3Δ Mnase repeat 2


title: iMGL_APOE1_48h_1.25uM_rep3


title: iMGL_APOE1_48h_1.25uM_rep1


title: iMGL_APOE1_48h_1.25uM_rep2


title: iMeLC_TET1-KO#2_rep1 (MS386_104)

description: M1-BTAG TET1(-/-) KO#2, iMeLC replicate 1


title: mcm2-3a H3K4me3 eSPAN repeat 1


title: iMGL_TREM2-171_48h_1.25uM_rep3


title: Sample_22


title: iMGL_Scrambled_48h_1.25uM_rep2


title: iMeLC_TET1-KO#1_rep1 (MS386_102)

description: M1-BTAG TET1(-/-) KO#1, iMeLC replicate 1


title: iMGL_Scrambled_48h_1.25uM_rep3


title: Sample_21


title: mcm2-3a dpb3Δ input


title: iMeLC_TET1-WT_rep1 (MS386_100)

description: M1-BTAG (585B1-868), iMeLC replicate 1


title: Sample_20


title: mcm2-3a dpb3Δ H3K56acChIP-ssSeq


title: iMGL_Scrambled_48h_1.25uM_rep1


title: iPSC_TET1-KO#2_rep2 (MS386_099)

description: M1-BTAG TET1(-/-) KO#2, iPSC replicate 2

value: human iPSC


title: iMGL_Untreated_48h_rep18

value: Untreated


title: Sample_19


title: Sample_18


title: iPSC_TET1-WT_rep2 (MS386_095)

description: M1-BTAG (585B1-868), iPSC replicate 2


title: iPSC_TET1-KO#1_rep2 (MS386_097)

description: M1-BTAG TET1(-/-) KO#1, iPSC replicate 2


title: mcm2-3a dpb3Δ H3K4me3 eSPAN repeat 2

value: synchronized yeast cells


title: iMGL_Untreated_48h_rep16


title: mcm2-3a dpb3Δ Mnase repeat 1


title: Sample_17


title: iMGL_Untreated_48h_rep15


title: mcm2-3a dpb3Δ H3K4me3 ChIP-ssSeq


title: iPSC_TET1-KO#1_rep1 (MS386_096)

description: M1-BTAG TET1(-/-) KO#1, iPSC replicate 1


title: Sample_15


title: iPSC_TET1-WT_rep1 (MS386_094)

description: M1-BTAG (585B1-868), iPSC replicate 1


title: mcm2-3a BrdU-IP-ssSeq


title: iPSC_TET1-KO#2_rep1 (MS386_098)

description: M1-BTAG TET1(-/-) KO#2, iPSC replicate 1


title: Sample_14


title: iMGL_Untreated_48h_rep13


title: mcm2-3a dpb3Δ H3K56ac eSPAN


title: mcm2-3a dpb3Δ BrdU-IP-ssSeq


title: iMGL_Untreated_48h_rep12


title: M1-AGDT_c122_AGDT,rep2 (MS356_044)

description: M1-AGDT (585B1-7453) expansion culture c112 BMP2(+) AG(+) DT(+) replicate 2

source_name: 585B1 AGDT

value: TFAP2C-EGFP, DAZL-tdTomato knock-in

value: differentiated hPGCLC

value: culture day 122

value: Expansion culture with BMP signalling


title: iMGL_Untreated_48h_rep14


title: dpb3Δ Mnase repeat 3


title: mcm2-3a dpb3Δ H3K4me3 eSPAN repeat 1


title: iMGL_Untreated_48h_rep11


title: iMGL_Untreated_48h_rep17


title: Sample_13

value: female

value: blood


title: Sample_45


title: Sample_12


title: M1-AGDT_c112_AGDT,rep1 (MS356_043)

description: M1-AGDT (585B1-7453) expansion culture c112 BMP2(+) AG(+) DT(+) replicate 1

value: WT

value: culture day 112


title: Sample_16


title: M1-AGDT_c102_AGDT,rep2 (MS356_042)

description: M1-AGDT (585B1-7453) expansion culture c102 BMP2(+) AG(+) DT(+) replicate 2

value: culture day 102


title: dpb3Δ Mnase repeat 2


title: dpb3Δ Mnase repeat 1


title: iMGL_Untreated_48h_rep10


title: iMGL_Untreated_48h_rep8


title: Sample_11


title: M1-AGDT_c102_AGDT,rep1 (MS356_041)

description: M1-AGDT (585B1-7453) expansion culture c102 BMP2(+) AG(+) DT(+) replicate 1


title: iMGL_Untreated_48h_rep9


title: M1-AGDT_c92_AGDT,rep2 (MS356_040)

description: M1-AGDT (585B1-7453) expansion culture c92 BMP2(+) AG(+) DT(+) replicate 2

value: culture day 92


title: dpb3Δ input


title: dpb3Δ H3K56ac eSPAN repeat 2


title: Sample_10


title: Sample_9


title: dpb3Δ H3K56ac eSPAN repeat 1


title: Sample_7


title: M1-AGDT_c92_AGDT,rep1 (MS356_039)

description: M1-AGDT (585B1-7453) expansion culture c92 BMP2(+) AG(+) DT(+) replicate 1


title: dpb3Δ H3K56ac ChIP-ssSeq


title: iMGL_Untreated_48h_rep7

description: Off-target analysis of APOE and TREM2 ASOs in iPSC derived microglia


title: M1-AGDT_c82_AGDT,rep2 (MS356_038)

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(+) replicate 2

value: culture day 82


title: dpb3Δ H3K4me3 eSPAN repeat 2


title: M1-AGDT_c82_AG,rep2 (MS356_037)

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(-) replicate 2


title: Sample_8


title: dpb3Δ H3K4me3 eSPAN repeat 1


title: Sample_6


title: M1-AGDT_c82_AGDT,rep1 (MS356_036)

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(+) replicate 1


title: Sample_5


title: iMGL_Untreated_48h_rep6


title: iMGL_Untreated_48h_rep5


title: iMGL_Untreated_48h_rep3


title: M1-AGDT_c82_AG,rep1 (MS356_035)

description: M1-AGDT (585B1-7453) expansion culture c82 BMP2(+) AG(+) DT(-) replicate 1


title: M1-AGDT_c62_AG,rep2 (MS356_029)

description: M1-AGDT (585B1-7453) expansion culture c62 BMP2(+) AG(+) DT(-) replicate 2

value: culture day 62


title: iMGL_Untreated_48h_rep4


title: Sample_4


title: Sample_3


title: dpb3Δ BrdU-IP-ssSeq


title: cac1Δ mcm2-3a H3K4me3 eSAPN

source_name: cac1Δ mcm2-3a

value: cac1{delta} mcm2-3a


title: iMGL_Untreated_48h_rep2


title: M1-AGDT_c62_AG,rep1 (MS337_071)

description: M1-AGDT (585B1-7453) expansion culture c62 BMP2(+) AG(+) DT(-) replicate 1


title: M1-AGDT_c42_AG,rep2 (MS337_066)

description: M1-AGDT (585B1-7453) expansion culture c42 BMP2(+) AG(+) DT(-) replicate 2

value: culture day 42


title: cac1Δ mcm2-3a H3K56ac eSAPN


title: Sample_1


title: Sample_2


title: iMGL_TREM2-192_24h_20uM_rep2


title: M1-AGDT_c42_AG_noBMP2 (MS337_065)

description: M1-AGDT (585B1-7453) expansion culture c42 BMP2(-) AG(+) DT(-)

value: Expansion culture without BMP signalling


title: cac1Δ mcm2-3a BrdU-IP-ssSeq


title: iMGL_TREM2-192_24h_20uM_rep3


title: AGM06-HPC_CMX-RNU-034

description: AGM HPC RNAseq

data_processing:
Paired-end 150 bp sequencing was performed on the Illumina HiSeq 4000. Alignment (STAR) was performed to the human genome (hg19).
Data was normalized to fragments per kilobase of mappable length and million counts (FPKMs).
Assembly: hg19
Supplementary files format and content: GSE233478_FPKM_table.csv
Supplementary files format and content: FPKM table

source_name: Aorta-gonad-mesonephros

extract_protocol:
Tissues were disagregated in single cells suspensions and FACS-sorted for the indicated markers and profiled
Libraries were prepared with the Ovation RNA-seq system V2 kit (NuGEN)
KAPA DNA library amplification

value: Aorta-gonad-mesonephros

tag: donor id

value: Embryo #06

value: hematopoietic progenitors (CD34+CD90- (CD43+CD45+))


title: M1-AGDT_c42_AG,rep1 (MS337_064)

description: M1-AGDT (585B1-7453) expansion culture c42 BMP2(+) AG(+) DT(-) replicate 1

value: TFAP2C-EGFP, DAZL-tdTomato knock-in

value: differentiated hPGCLC


title: cac1Δ input repeat 2

value: synchronized yeast cells


title: dpb3Δ H3K4me3 ChIP-ssSeq


title: AGM06-HSPC_CMX-RNU-033

description: AGM HSPC RNAseq

value: hematopoietic stem/progenitors cells (CD34+CD90+CD43+)


title: M1-AGDT_c32_AG,rep2 (MS337_034)

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(+) AG(+) DT(-) replicate 2

value: culture day 32

value: Expansion culture with BMP signalling


title: c12_TET1-KO#1_rep1 (MS337_015)

description: M1-BTAG TET1(-/-) KO#1, expansion culture c12 BMP2(+) BT(+) AG(+) replicate 1

value: TFAP2C-EGFP, BLIMP1-tdTomato knock-in

value: culture day 12


title: AGM06-endo_CMX-RNU-032

description: AGM endothelium RNAseq

value: endothelium (CD34+CD90+CD43-CD45-)


title: cac1Δ input repeat 1


title: iMGL_Untreated_48h_rep1

value: Untreated


title: iMGL_TREM2-192_24h_20uM_rep1


title: M1-AGDT_c32_AG_noBMP2,rep2 (MS337_033)

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(-) AG(+) DT(-) replicate 2

value: WT


title: cac1Δ H3K56ac eSAPN repeat 2


title: iMGL_TREM2-171_24h_20uM_rep3


title: iMGL_TREM2-171_24h_20uM_rep2


title: M1-AGDT_c32_AG,rep1 (MS337_032)

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(+) AG(+) DT(-) replicate 1


title: cac1Δ H3K56ac eSAPN repeat 1


title: mcm2-3a Mnase repeat 1


title: iMGL_TREM2-171_24h_20uM_rep1


title: FL11-HSC_CMX-RNU-201

description: Fetal liver HSC RNAseq

source_name: Fetal liver

value: Fetal liver

value: Fetus #11

value: hematopoietic stem cells (CD34+lin-CD38-CD45RA-CD90+)


title: M1-AGDT_c32_AG_noBMP2,rep1 (MS337_031)

description: M1-AGDT (585B1-7453) expansion culture c32 BMP2(-) AG(+) DT(-) replicate 1

value: Expansion culture without BMP signalling


title: cac1Δ H3K56ac ChIP-ssSeq repeat 2


title: M1-AGDT_c22_AG,rep2 (MS337_030)

description: M1-AGDT (585B1-7453) expansion culture c22 BMP2(+) AG(+) DT(-) replicate 2

value: culture day 22


title: cac1Δ H3K56ac ChIP-ssSeq repeat 1


title: iMGL_APOE13_24h_20uM_rep3


title: M1-AGDT_c22_AG_noBMP2,rep2 (MS337_029)

description: M1-AGDT (585B1-7453) expansion culture c22 BMP2(-) AG(+) DT(-) replicate 2


title: cac1Δ H3K4me3 eSAPN repeat 2


title: iMGL_APOE13_24h_20uM_rep2

description: Off-target analysis of APOE and TREM2 ASOs in iPSC derived microglia


title: CB04-HSC_CMX-RNU-072

description: Cort Blood HSC RNAseq

source_name: Umbillical Cord Blood

value: Umbillical Cord Blood

value: Newborn #04

value: birth


title: M1-AGDT_c22_AG,rep1 (MS337_028)

description: M1-AGDT (585B1-7453) expansion culture c22 BMP2(+) AG(+) DT(-) replicate 1

value: TFAP2C-EGFP, DAZL-tdTomato knock-in

value: differentiated hPGCLC


title: cac1Δ H3K4me3 eSAPN repeat 1

value: synchronized yeast cells


title: iMGL_APOE13_24h_20uM_rep1


title: iMGL_APOE1_24h_20uM_rep3


title: cac1Δ H3K4me3 ChIP-ssSeq repeat 2


title: cac1Δ H3K4me3 ChIP-ssSeq repeat 1


title: M1-AGDT_c12_AG,rep2 (MS337_026)

description: M1-AGDT (585B1-7453) expansion culture c12 BMP2(+) AG(+) DT(-) replicate 2

value: Expansion culture with BMP signalling


title: cac1Δ dpb3Δ H3K4me3 eSAPN

source_name: cac1Δ dpb3Δ

value: cac1{delta} dpb3{delta}


title: Patients No10-pre

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

institute: Kanazawa University

hyb_protocol: Biotin-labeled cDNA was suspended in 220 ul of hybridization cocktail (NuGen) and 200 ul was used for hybridization to the Affymetrix Human 133 Plus 2.0 microarray chip containing 54,675 probes.GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After stringent washing, the microarray chips were stained with streptavidin-phycoerythrin and probe hybridization was determined using a GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. If the detection call contained 'Absent', the probe set was removed from analysis.

source_name: Liver

label_protocol: Aliquots of total RNA (50 ng) isolated from biopsied liver tissues were subjected to amplification using the Ovation Pico WTA System V2 3302-12 (AS ONE, Japan) according to the manufacturer’s instructions. Approximately 10 μg of cDNA was amplified from 50 ng of total RNA, and 5 μg of cDNA was used for fragmentation and biotin labeling using the FL-Ovation cDNA Biotin Module V2 (NuGen) according to the manufacturer’s instructions.

extract_protocol: RNA was extracted with the RNAqueousTM-Micro Total RNA Isolation Kit AM1931 (Thermo Fisher Scientific K.K., Yokohama, Japan) according to the manufacturer's instructions.

value: Liver biopsied tissue

tag: disease state

value: metabolic dysfunction-associated steatohepatitis (MASH)

tag: condition

value: before L-carnitine


title: M1-AGDT_c12_AG,rep1 (MS337_024)

description: M1-AGDT (585B1-7453) expansion culture c12 BMP2(+) AG(+) DT(-) replicate 1

value: WT

value: culture day 12


title: cac1Δ dpb3Δ mcm2-3a H3K4me3 eSAPN

source_name: cac1Δ dpb3Δ mcm2-3a

value: cac1{delta} dpb3{delta} mcm2-3a


title: M1-AGDT_c12_AG_noBMP2,rep1 (MS337_023)

description: M1-AGDT (585B1-7453) expansion culture c12 BMP2(-) AG(+) DT(-) replicate 1


title: M1-AGDT_c22_AG_noBMP2,rep1 (MS337_027)

description: M1-AGDT (585B1-7453) expansion culture c22 BMP2(-) AG(+) DT(-) replicate 1


title: iMGL_APOE1_24h_20uM_rep2


title: Patients No8-after

value: after L-carnitine


title: Patients No10-after


title: M1-AGDT_hPGCLC (MS337_022)

description: M1-AGDT (585B1-7453) d6hPGCLC AG(+) replicate 2

value: human PGCLC

value: culture day 0


title: Patients No8-pre


title: iMGL_Scrambled_24h_20uM_rep3

value: Scrambled


title: cac1Δ dpb3Δ mcm2-3a BrdU-IP-ssSeq


title: iMGL_APOE1_24h_20uM_rep1


title: M1-AGDT_c12_AG_noBMP2,rep2 (MS337_025)

description: M1-AGDT (585B1-7453) expansion culture c12 BMP2(-) AG(+) DT(-) replicate 2

value: Expansion culture without BMP signalling


title: Patients No4-after


title: cac1Δ dpb3Δ H3K56ac eSAPN


title: M1-AGDT_hPGCLC (MS337_021)

description: M1-AGDT (585B1-7453) d6hPGCLC AG(+) replicate 1


title: iMGL_Scrambled_24h_20uM_rep2


title: mouse,kidney,snRNA,imq_2,rep3

city: Oxford

first: Rui

last: Qi

state: Oxford

address: Old Road Campus

country: United Kingdom

institute: University of Oxford

description:
MM04032_library1.rds
instrument model used to produce the reads: DNBSEQ-T10

data_processing:
BGI's  iDrop_scRNA_Common_V2.3 pipeline
Assembly: mm10
Supplementary files format and content: .rds file: Seurat object includes raw counts for each library

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
To isolate single nuclei, kidney tissues were placed in a Dounce homogenizer with  Homogenization Buffer. After incubation, tissues were homogenized with loose pestles and then with tight pestles. After filter and centrifuge, the pellet was resuspended in blocking buffer and centrifuged for twice, and then the pellet was resuspended using cell resuspension buffer (MGI) at concentration of 1000 nuclei/µL for further library preparation. snRNA-seq libraries were prepared using DNBelab C Series Single-Cell Library Prep Set (MGI, #1000021082). Droplets were generated from a single nuclei suspension, followed by emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries.
After cDNA interruption, amplification and double-selection, libraries were subjected to Agilent 2100 quality inspection. Finally, the double-selection libraries were constructed into libraries suitable for the MGI DNBSEQ-Tx sequencing platform through circularization steps and were sequenced to collect data (50 bp for read 1 and 100 bp for read 2).

value: Kidney

value: imq


title: Patients No2-after


title: iMGL_Scrambled_24h_20uM_rep1


title: F1-AGVT_c107_VT (MS356_057)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c107 BMP2(+) AG(+) VT(+)

source_name: NCLCN AGVT

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: differentiated hPGCLC

value: culture day 107


title: cac1Δ dpb3Δ BrdU-IP-ssSeq

value: synchronized yeast cells

value: cac1{delta} dpb3{delta}


title: Patients No4-pre

value: Liver biopsied tissue

value: metabolic dysfunction-associated steatohepatitis (MASH)


title: Patients No2-pre

value: before L-carnitine


title: iMGL_TREM2-192_24h_1.25uM_rep3


title: iMGL_TREM2-192_24h_1.25uM_rep2


title: cac1Δ dpb3Δ mcm2-3a H3K56ac eSAPN


title: iMGL_TREM2-192_24h_1.25uM_rep1


title: mouse,kidney,snRNA,imq_2,rep2


title: Patients No1-after


title: Patients No1-pre


title: iMGL_TREM2-171_24h_1.25uM_rep3


title: F1-AGVT_c118_AGVT (MS356_070)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c118 BMP2(+) AG(+) VT(+)

value: WT

value: culture day 118

value: Expansion culture with BMP signalling


title: mouse,kidney,snRNA,imq_2,rep1


title: iMGL_TREM2-171_24h_1.25uM_rep2


title: cac1Δ BrdU-IP-ssSeq repeat 2


title: F1-AGVT_c117_AGVT (MS356_058)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c117 BMP2(+) AG(+) VT(+)

value: culture day 117


title: mouse,kidney,snRNA,imq_1,rep3

description:
MM04030_library1.rds
instrument model used to produce the reads: DNBSEQ-T10


title: cac1Δ BrdU-IP-ssSeq repeat 1


title: mouse,kidney,snRNA,imq_1,rep2


title: F1-AGVT_c108_AGVT (MS356_069)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c108 BMP2(+) AG(+) VT(+)

value: culture day 108


title: asf1Δ mcm2-3a H3K4me3 eSPAN

source_name: asf1Δ mcm2-3a

value: asf1{delta} mcm2-3a


title: iMGL_APOE13_24h_1.25uM_rep3


title: asf1Δ mcm2-3a H3K4me3 ChIP-ssSeq


title: F1-AGVT_c107_AGVT (MS356_056)


title: iMGL_TREM2-171_24h_1.25uM_rep1


title: mouse,kidney,snRNA,imq_1,rep1


title: mouse,kidney,snRNA,control_3,rep3

description:
control_library3.rds
instrument model used to produce the reads: DNBSEQ-T10

value: control


title: asf1Δ mcm2-3a BrdU-IP-ssSeq


title: F1-AGVT_c96_AGVT (MS356_055)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c96 BMP2(+) AG(+) VT(+)

value: culture day 96


title: iMGL_APOE13_24h_1.25uM_rep2

description: Off-target analysis of APOE and TREM2 ASOs in iPSC derived microglia


title: iMGL_APOE13_24h_1.25uM_rep1


title: mouse,kidney,snRNA,control_3,rep2

value: Kidney


title: asf1Δ H3K4me3 eSAPN repeat 2


title: F1-AGVT_c87_AGVT (MS356_067)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c87 BMP2(+) AG(+) VT(+)

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: culture day 87


title: asf1Δ H3K4me3 eSAPN repeat 1


title: mouse,kidney,snRNA,control_2,rep3

description:
control_library2.rds
instrument model used to produce the reads: DNBSEQ-T10


title: iMGL_APOE1_24h_1.25uM_rep3


title: F1-AGVT_c86_AGVT (MS356_054)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c86 BMP2(+) AG(+) VT(+)

value: differentiated hPGCLC

value: culture day 86


title: mouse,kidney,snRNA,control_3,rep1


title: F1-AGVT_c67_AGVT (MS356_065)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c67 BMP2(+) AG(+) VT(+)

value: culture day 67


title: mouse,kidney,snRNA,control_2,rep2


title: iMGL_APOE1_24h_1.25uM_rep1


title: asf1Δ H3K4me3 ChIP-ssSeq repeat 1

value: synchronized yeast cells


title: mouse,kidney,snRNA,control_2,rep1


title: F1-AGVT_c97_AGVT (MS356_068)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c97 BMP2(+) AG(+) VT(+)

value: culture day 97


title: asf1Δ input


title: iMGL_Scrambled_24h_1.25uM_rep2

value: Scrambled


title: asf1Δ dpb3Δ H3K4me3 eSPAN

source_name: asf1Δ dpb3Δ

value: asf1{delta} dpb3{delta}


title: F1-AGVT_c86_AG (MS356_053)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c86 BMP2(+) AG(+)

value: WT


title: iMGL_APOE1_24h_1.25uM_rep2

source_name: iPSC derived microglia


title: iMGL_Scrambled_24h_1.25uM_rep3


title: mouse,kidney,snRNA,control_1,rep3

description:
control_library1.rds
instrument model used to produce the reads: DNBSEQ-T10


title: iMGL_Scrambled_24h_1.25uM_rep1


title: asf1Δ dpb3Δ H3K4me3 ChIP-ssSeq


title: F1-AGVT_c44_AG (MS356_049)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c44 BMP2(+) AG(+)

value: culture day 44

value: Expansion culture with BMP signalling


title: mouse,kidney,snRNA,control_1,rep2_part1


title: asf1Δ dpb3Δ BrdU-IP-ssSeq


title: asf1Δ H3K4me3 ChIP-ssSeq repeat 2


title: F1-AGVT_c35_AG (MS356_062)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c35 BMP2(+) AG(+)

value: culture day 35


title: iMGL_Untreated_24h_rep15

value: Untreated


title: asf1Δ BrdU-IP-ssSeq repeat 2


title: iMGL_Untreated_24h_rep14


title: F1-AGVT_c24_AG (MS356_061)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c24 BMP2(+) AG(+)

value: culture day 24


title: iMGL_Untreated_24h_rep13


title: asf1Δ BrdU-IP-ssSeq repeat 1


title: GSK_PolII

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

data_processing:
All reads were mapped to unique genomic regions of mm10 using Bowtie2. PCR duplicates were removed manually. Bedtools genome coverage function was used to generate bedgraph files for further analysis. To compare changes in ChIP-seq signals, libraries were normalized by random picking to obtain the same numbers of reads. Normalized reads were used to generate bedgraph files for comparison in IGV. MACS2 was used to call peaks using default parameters with p value cutoff at 0.001. Differential peaks were found using the edgeR R package at p < 0.05, with changes over 20% up/down.
Enhancers were defined by merging H3K4me1 and H3K4me2 peaks in both conditions but excluding H3K4me3 peaks and TSS ± 2.5kb. Differential enhancers were found using the edgeR R package based on H3K27ac ChIP-seq signals with a p value cutoff at 0.05 and more than 3-fold changes in either condition. K-means clustering of enhancer heatmaps was done using Cluster3 on center ± 3 bins signals of H3K4me1 heatmaps, all heatmaps were plotted in this same order on center ± 1kb.
For deriving heatmaps of ChIP-seq signals, anchors plus flanking regions were binned equally to get a blank matrix (anchors × bins). To compare between samples, reads from the same antibody analysis were normalized by random pick. Normalized read pairs were mapped to each genomic bin with the bedtools intersect function to obtain read counts in each bin for the whole matrix. To normalize for sequencing depth, values in the matrix were divided by library sizes in millions to obtain reads per million per covered bin (RPMPCG or RPM), which was then visualized with Java TreeView to derive heatmaps. Average profiles of the ChIP-seq data were calculated and plotted using mean values of bins at the same distances from specific anchors. K-means clustering of ChIP-seq heatmaps was done using Cluster3 on center ± 3 bins signals of appropriate heatmaps. K-means clustering of promoter heatmaps was done using Cluster3 on TSSs ± 3 bins signals of H3K27ac heatmaps, all heatmaps were plotted in this same order on TSSs ± 1kb.
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: peak files

source_name: CD8+ T cell ChIP

growth_protocol: CD8+ T cells isolated from the spleens of OT1 mice were stimulated with plate-bound anti-CD3 (2μg/ml) and soluble anti-CD28 (2μg/ml) with the addition of 20 ng/mL IL-2 at a density of 1 million/ml for 48 h. Activated CD8+ T cells were expanded with IL2 in fresh medium for 3 days.

extract_protocol:
In vitro cultured CD8+ T cells were fixed in 1% formaldehyde (Thermo Fisher Scientific, 28908) for 10 min at RT on a shaker, followed by quenching in 125 mM glycine. Next, cells were washed twice with ice-cold PBS and lysed in sonication buffer (50 mM HEPES pH7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS and protease inhibitor), then sonicated to obtain DNA fragments mostly between 300-800 bp. Subsequent procedures were performed following the Epigenetics Protocols Database PROT-11 (https://www.epigenome-noe.net/researchtools/protocols.php.html). The following antibodies were used for immunoprecipitation: anti-LSD1 (Abcam, ab17721), anti-H3K4me1 (Abcam, ab8895), anti-H3K4me2 (EMD Millipore, 07-030), anti-H3K4me3 (Active Motif, 39060), anti-H3K27ac (Active Motif, 39034), anti-Pol II (Santa Cruz Biotechnology, sc-56767) and rabbit normal IgG (Proteintech, 30000-0-AP).
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-01) according to the manufacturer’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at Novaseq 6000 (Illumina) to generate 150 bp paired-end reads or at DNBSEQ-T7 (MGI Tech) to generate 100 bp paired-end reads.

treatment_protocol: 0.5 μM GSK2879552 (GSK) or vehicle control was added to CD8+ T cells during in vitro activation and expansion.

value: Spleen

tag: antibody

value: PolII (SantaCruz, cat#sc-56767)


title: iMGL_Untreated_24h_rep12


title: F1-AGVT_c65_AG (MS356_051)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c65 BMP2(+) AG(+)

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: culture day 65


title: GSK_H3K27ac

value: H3K27ac (Active Motif, cat#39034)


title: PH7

city: Xi’an

first: wang

middle: gui

last: hu

address: No.157#, The West 5th Road

department: The Second Affiliated Hospital

institute: Xi'an Jiaotong University

description: Portal hypertension combined with hypersplenism (PHcH)

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencelow-quality sequence using CLC genomic benchvork(parameter-Quality limit 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork(parameters-mismath cost 2insertion cost 3 deletion cost 3length fraction: 0.8 similarity fraction. 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: nm10
Supplementary files format and content: tab-delinited text fle includes rav counts for each Sample
Supplementary files format and content: 'tab-delimited text fles include RPKM values foreach Sample

source_name: Spleen

growth_protocol: Spleen macrophages are sorted by CD11b+magnetic beads

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 2ug of total RNA was used for the construction of sequnencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: macrophage


title: mouse,kidney,snRNA,control_1,rep2_part2

value: Kidney

value: control


title: F1-AGVT_c12_AG (MS356_060)

description: F1-AGVT (NCLCN-261), d8hPGCLC, expansion culture c12 BMP2(+) AG(+)

value: differentiated hPGCLC

value: culture day 12


title: PH5

value: Portal hypertension combined with hypersplenism (PHcH)


title: F1-AGVT_c11_AG (MS356_045)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c11 BMP2(+) AG(+)

value: WT

value: culture day 11


title: iMGL_Untreated_24h_rep11


title: mouse,kidney,snRNA,control_1,rep1


title: GSK_Input2


title: iMGL_Untreated_24h_rep9


title: iMGL_Untreated_24h_rep10


title: iMGL_Untreated_24h_rep8


title: PH3


title: veh_PolII


title: F1-AGVT_hPGCLC,rep2 (MS356_059)

description: F1-AGVT (NCLCN-261), hPGCLC day6, replicate 2

value: human PGCLC

value: culture day 0


title: veh_H3K27ac


title: F1-AGVT_c21_AG (MS356_046)

description: F1-AGVT (NCLCN-261), d6hPGCLC, expansion culture c21 BMP2(+) AG(+)

value: culture day 21

value: Expansion culture with BMP signalling


title: iMGL_Untreated_24h_rep7

description: Off-target analysis of APOE and TREM2 ASOs in iPSC derived microglia

value: Untreated


title: PH1

value: Spleen


title: veh_H3K4me3

value: H3K4me3 (Active Motif, cat#39060)


title: Schwann Cells, NF2-KO, Passage 7, Replicate 2

city: Heidelberg

first: Aurelio

middle: A

last: Teleman

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center (DKFZ)

data_processing:
Adapters were trimmed with cutadapt
Reads were aligned to a FASTA file containing sequences of all the sgRNAs in the library using bowtie2
Reads per sgRNA were counted using custom software ("count_features") available at https://github.com/aurelioteleman/Teleman-Lab
Assembly: N/A
Supplementary files format and content: tab-delimited file containing raw read counts for all samples as well as read counts normalized to library size

source_name: Schwannoma

extract_protocol:
genomic DNA was extracted using the QIAamp DNA Blood Maxi kit (#51192, Qiagen)
A total of 140 PCR reactions were performed using 1μg of genomic or plasmid library DNA, Q5 Hot Start HF polymerase (#M0493L, NEB), and primers harboring the Illumina TruSeq adapter sequences. PCR products were purified using DNA Clean and Concentrator TM-100 (#C1016-50, Zymo Research) and MagSi-NGSprep Plus beads (#SL-MDKT-01500, Steinbrenner). Sample concentrations were measured using Qubit HS DNA Assay (#Q32851, Thermo Fisher). Library amplicon size was verified using DNA High Sensitivity Assay on a BioAnalyzer 2100 (Agilent) and then sequenced on a NextSeq (Illumina) by 75bp single-end sequencing and addition of 25% PhiX control v3 (Illumina).

value: Schwannoma

value: Schwann Cells


title: GSK_H3K4me3


title: F1-AGVT_iPSC (MS356_047)

description: F1-AGVT (NCLCN-261), iPSC day6

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: human iPSC


title: Nor7

description: Spleen-injury

value: macrophage

value: Spleen-injury


title: veh_Input2


title: PH4


title: iMGL_Untreated_24h_rep5


title: Nor6

description: Spleen-injury


title: Schwann Cells, NF2-KO, Passage 7, Replicate 1


title: Nor4

description: Spleen-injury


title: Schwann Cells, NF2-KO, Passage 0


title: FABP4-/-_3

city: Nan ning

first: Hao

last: Xing

address: zhongshan Street

institute: Guangxi Key Laboratory of Immunology and Metabolism for Liver Diseases, Nanning

data_processing:
Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: :TRAILING:20,SLIDINGWINDOW:4:15 MINLEN:52, to remove trailing sequences below a phred quality score of 20 and to achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software.  Adapter removal and read trimming were performed using Trimmomatic.  Sequencing reads were trimmed from the end (base quality less than Q20) and filtered by length (less than 52).
Assembly: mm10
Supplementary files format and content: Normalized expression matrix.txt

organism: Mus

source_name: liver

extract_protocol:
Total RNA was extracted from the flash-frozen liver tissues of FABP4-/- and their littermate ASH mice using TRIzol reagent.
The quality of the RNA samples was evaluated with a NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and Agilent’s bioanalyzer. Sequencing libraries were generated by reverse transcription-polymerase chain reaction (RT-PCR) amplification and sequenced on a HiSeq 2500 sequencing system (RIBOBIO, Guangzhou, China).

value: liver

value: FABP4 knock out

value: 8 weeks Lieber-Decarli ethanol liquid diet, plus single ethanol binge.


title: PH2

value: Portal hypertension combined with hypersplenism (PHcH)


title: F1-AGVT_hPGCLC,rep1 (MS356_048)

description: F1-AGVT (NCLCN-261), hPGCLC day6, replicate 1

value: human PGCLC

value: WT


title: FABP4-/-_2


title: Nor3

description: Spleen-injury


title: Schwann Cells, NF2-WT, Passage 7, Replicate 2


title: CD4 T-cells, uninfected, day 0, 509238

city: Edinburgh

first: Elisabeth

middle: Margaretha Diana Louise

last: van der Heijden

state: Midlothian

address: Easter Bush Campus

department: Division of Immunology

institute: The Roslin Institute, The University of Edinburgh

data_processing:
Quality control using FastQC (v 0.11.9 - default parameters)
Trimming using TrimGalore (v 0.6.4) (--illumina --length 35 --paired)
Pseudoalignment using kallisto (v 0.46.1 - default parameters - 10 bootstraps)
Import of transcript-level abundances into R using tximport (v 1.24.0)
Differential expression analysis using DESeq2 (v 1.36.0)
Assembly: bosTau 9 (ARS-UCD1.2) and PiroplasmDB T. parva Muguga (GCA_000165365.1)
Supplementary files format and content: Comma-separated values files with raw counts of Bos taurus genes for each sample
Supplementary files format and content: Comma-separated values files with raw counts of Theileria parva genes for each sample

organism: Bos taurus

source_name: CD4 T-cells

growth_protocol: Cells were maintained in RPMI-1640 medium supplemented with 10% FBS, 50mM beta-mercaptoethanol and 1X penicillin-streptomycin, in a humidified incubator at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen). 500ng of total RNA was use for library preparation.
The NEBNEXT Ultra II Directional RNA Library Prep kit was used with the Poly-A mRNA magnetic isolation module for library construction.

treatment_protocol: Cells were infected with saturating levels of fresh T. parva Muguga sporozoites.

value: CD4 T-cells

value: day 0

value: uninfected


title: FABP4-/-_1


title: Schwann Cells, NF2-WT, Passage 7, Replicate 1


title: iMGL_Untreated_24h_rep3

value: Untreated


title: iMGL_Untreated_24h_rep6


title: iMGL_Untreated_24h_rep2


title: Nor2

description: Spleen-injury

value: Spleen


title: WT_3


title: iMGL_Untreated_24h_rep1


title: WT_2


title: Schwann Cells, NF2-WT, Passage 0

value: Schwannoma


title: CD4 T-cells, uninfected, day 0, 709247


title: Nor1

description: Spleen-injury


title: Schwann Cells, NF2-KO + Cas9

data_processing:
Data were processed on the Galaxy server
Adapters were trimmed with "Trim Galore !"
Reads were aligned to UCSC hg38
Reads per sgRNA were counted using custom software ("count_features") available at https://github.com/aurelioteleman/Teleman-Lab
Assembly: hg38
Supplementary files format and content: tab-delimited file containing raw read counts for all samples as well as read counts normalized to library size

extract_protocol:
Total RNA was isolated using an RNeasy kit from Qiagen
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Schwann Cells

value: NF2-KO + Cas9


title: CD4 T-cells, uninfected, day 0, 000066


title: iMGL_Untreated_24h_rep4


title: s_4_withindex_sequence.txt_ATCGAGC.fq

city: Boston

first: Abigael

last: Cheruiyot

address: 1 Joslin Place

institute: Joslin Diabetes Center

data_processing:
A custom Perl script was used to determine the read counts for each sgRNA and map the sgRNAs to their gene IDs in the reference GeCKOv2 library
Supplementary files format and content: Raw read counts for each sgRNAs is provided in GeCKOV2 library B read counts.xls with multiple tabs for different samples

source_name: Uterus; Cervix

growth_protocol: HeLa cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Genomic DNA was extracted using PureLink Genomic DNA kit (ThermoFisher Scientific, K182001)
Two PCR reactions were used to prepare samples for Illumina Next-Gen sequencing. The first PCR was used to amplify sgRNA inserts in the cells, and the second PCR was used to add Illumina sequencing tags as well as index tags for sample identification. To improve the complexity of the library required for deep sequencing, a mixture of 5 forward primers with staggered nucleotides immediately upstream of the sgRNA sequences was used in the second PCR.
Survival screen after genome-wide KO of genes that may be important for survival under HU treatment, but not needed when Exo1 is also depleted

treatment_protocol: Exo1-KO cell lines were generated by transfection of  HeLa with pCRSIPRv2-sgRNA-expressing constructs with sgRNAs targeting human Exo1. Twenty-four hours after transfection, cells were selected withpuromycin(1.5μg/ml) for 2days. Single cells were grown in 96-well plates for amplification. Individual clones were verified bywestern blotto detect the depletion of Exo1. To carry out the screen, HeLa-Cas9 cells were infected with lentiviruses expressing the GeCKOv2 library (containing two sub-libraries) at a multiplicity of infection (MOI) of 0.3 with a 500x coverage of the library, selected 2 days post infection, and then cultured for 10 days. Cells were then treated with 4 mM HU for 24 hours and recovered in fresh DMEM medium for 3 days.

value: Uterus; Cervix

value: HeLa

value: epithelial cell


title: CD4 T-cells, uninfected, day 0, 609232


title: Schwann Cells, NF2-WT + Cas9

value: NF2-WT + Cas9


title: WT_1

value: liver


title: CD4 T-cells, uninfected, day 0, 309236


title: Schwann Cells, NF2-KO


title: s_4_withindex_sequence.txt_TGAGGTT.fq

value: untreated