title: Fibroblasts + therapy-induced secretome, repeat 2

first: Ksenia

middle: S

last: Anufrieva

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description: incubation with therapy-unduced secretome from fibroblasts

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: Fibroblasts

growth_protocol: All cells were cultivated at 37°C under humidified atmosphere with 5% CO2. SKOV3 cells and fibroblasts 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 SKOV3 cells and fibroblasts 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 all libraries (12 pM) 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For collection of conditional media (secretomes), the donor SKOV3 cells and fibroblasts achieved approximately 80% confluence were incubated with standard medium contained or not cisplatin (40 µM and 80µM, respectively). During this experiment, donor cells were incubated with cisplatin-containing medium for 7 h, then cells were washed with PBS three times and incubated in FBS-free medium for another 41 hours. The cisplatin concentration was selected so that death of donor cells was approximately 50-60% at the time of secretome collecting. This method provides a high level of apoptosis in cells and simultaneously enables to obtain a drug-free medium. Then recipient SKOV3 cells and fibroblasts were incubated for 3 days with their control or therapy-induced secretomes, after that total RNA was isolated.

value: Fibroblasts


title: Naive, RAP input, Rep1

status: Public on Apr 24 2024

type: SRA

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Helene Brion

department: Epigenetics and Cell Fate

country: France

institute: Université Paris Cité, CNRS

library_source: genomic

data_processing:
Reads were TM using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the human genome (hg38) using bowtie 2 (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5) with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
BigWig track files were generated with bamCoverage from deeptools (v3.5.0) using the following parameters: --normalizeUsing BPM --binSize 20 --smoothLength 40. normalizeUsing "BPM" --binSize 20 --smoothLength 40.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: RAP-seq

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
DNA was eluted by RNase H digestion, and crosslinking was reversed via proteinase K digestion at 65˚C for 1h. Finally, DNA was purified using the GeneJET Gel Extraction kit (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq ChIP Library Preparation Kit from Illumina.

tag: hesc status

value: Naive

tag: cell line

tag: cell type

value: human embryonic stem cell

tag: fraction

value: RAP input


title: Fibroblasts + therapy-induced secretome, repeat 1

city: Boston

state: MA

country: USA

library_source: transcriptomic

molecule: polyA RNA


title: ApcDHep GFP+ J15

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

institute: INSERM U1138

data_processing:
Illumina RTA 1.18.64 (Hiseq2500) and bcl2fastq Conversion Software v2.20 was used for basecalling and demultiplexing.
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie2 the -X  2000 parameter
Bam were reordered and PCR duplicates removed using samtools
BigWig were generated using bamCoverage command from deepTools with the following parameters : --binSize 10 --normalizeUsing RPKM --extendReads
Assembly: Mus_musculus mm9
Supplementary files format and content: BigWIG

organism: Mus musculus

source_name: mouse ApcDHep hepatocytes

extract_protocol: Transposition was performed on 50,000 hepatocytes with 4,5 L Tn5 and digitonin 0.1%

treatment_protocol: ATAC-seq profiles from hepatocytes isolated from  ApcDHep livers by perfusion with collagenase in three-month old mice injected  with Ad5-Cre-GFP and sorted with ARIA3

tag: cell types

value: mouse  hepatocytes

tag: strain

tag: treatment

value: Ad5-Cre-GFP 1,5x109 Vg


title: 168_KMT2D_KO rep2

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using cellranger v7.0.1.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

molecule: total RNA

source_name: primary breast tumor

growth_protocol: Primary tumors were induced by injecting cells into mammary fat pads of Balb/c mice.

extract_protocol:
Whole tumors were disrupted using micropestles and digested for 1h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium. Immediately before library preparation, dead cells and debris was removed using percoll purification (50%/40%/20% layers).
About 26,000 single cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s recommendations. The scRNAseq libraries were generated using Chromium Next GEM Single Cell 5' HT Kit v2 (10x Genomics).

tag: tissue

value: primary breast tumor

value: complete tumor suspensions

tag: genotype

value: MFP injection


title: 168_KMT2D_KO rep1

description: 10x Genomics


title: ApcDHep GFP+ J6


title: Naive, RAP input, Rep2


title: Fibroblasts + control secretome, repeat 2

description: incubation with control secretome from fibroblasts


title: run_2198_s_2_Exo1KOtreated_sequence.txt_ATGACAG

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 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

value: Exo1 KO


title: Primed, RAP input, Rep2

value: Primed


title: 168_KMT2C_KO rep2

description: 10x Genomics


title: Apcwt GFP-

source_name: mouse wt hepatocytes


title: PXGL, fastGRO-seq CRISPRi XIST Dox, Rep3

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the human genome (hg38) using bowtie 2 (version?) (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5)  with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
Read counts were quantified for each gene with htseq-count from htseq (v0.13.5) (Anders et al., 2015) using the following options:  --stranded reverse  -a 10 -t exon -i gene_id -m intersection-nonempty. The annotation file used: Homo_sapiens.GRCh38.90.gtf.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Library strategy: GRO-seq

extract_protocol:
RNA was extracted with TRIzol LS reagent (Invitrogen)
Libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit according to the manufacturer’s recommendation

value: PXGL

value: CRISPRi XIST Dox


title: 168_KMT2C_KO rep3

description: 10x Genomics


title: 168_WT_H3K4me1_rep2

data_processing:
Fastq data was processed using CoBRA pipeline (https://bitbucket.org/cfce/cobra/src/master/).
Steps include alignment using BWA mem, filtering for uniquely mapped read and sorting bam files.
Peaks were called using macs2 with default settings (-broad mode for H3K4me1 and H3K27me3)
Output bedgraph files were then used to generate bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: breast cancer

growth_protocol: DMEM, 10% FBS, 1x Pen/Strep, 1x Glutamin, 1x Non-essential amino acids, 5% CO2, 37C

extract_protocol:
Cells were fixed with 1% formaldehyd for 10 minutes. Then, cells were collected, nuclei were isolated and lysed and chromatin was sheared with an ultrasonicator (Covaris E220)
ChIPseq libraries were prepared using xGen DNA library prep reagents (IDT) on a Biomek i7 (Beckman Coulter) liquid handling platform from approximately 1ng of DNA with 14 cycles of PCR amplification according to manufacturer’s protocol.

value: breast cancer

value: cell line

value: WT

tag: chip antibody

value: H3K4me1 (abcam, ab8895)


title: Primed, RAP input, Rep1

value: human embryonic stem cell

value: RAP input


title: 168_KMT2C_KO rep1

description: 10x Genomics


title: SKOV3 + therapy-induced secretome, repeat 3

description: incubation with therapy-unduced secretome from SKOV3 cells

source_name: Ovarian adenocarcinoma

value: Ovarian adenocarcinoma


title: 168_WT rep2

description: 10x Genomics

value: primary breast tumor


title: SKOV3 + therapy-induced secretome, repeat 2


title: 168_WT rep3

description: 10x Genomics

value: complete tumor suspensions


title: PXGL, fastGRO-seq CRISPRi XIST Dox, Rep2


title: PXGL, fastGRO-seq CRISPRi XIST Dox, Rep1


title: PXGL, fastGRO-seq CRISPRi XIST UT, Rep2

value: CRISPRi XIST UT


title: PXGL, fastGRO-seq CRISPRi XIST UT, Rep3


title: 168_WT rep1

description: 10x Genomics

value: MFP injection


title: 67_KMT2D_KO_rep3

data_processing:
VIPER pipeline (https://github.com/hanfeisun/viper-rnaseq/blob/master/cfce/README_CFCE.md) was used for alignment, assembly and gene counting.
Assembly: mm9
Supplementary files format and content: csv files including raw counts for each gene and each sample

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
libraries were prepared from 100 ng RNA using Kapa mRNA HyperPrep (Roche) according to manufacturers protocol


title: SKOV3 + control secretome, repeat 2

description: incubation with control secretome from SKOV3 cells


title: 67_KMT2D_KO_rep2


title: PXGL, fastGRO-seq  CRISPRi XIST UT, Rep1


title: SKOV3 + control secretome, repeat 1


title: 67_KMT2D_KO_rep1


title: cancer cells from patient 11 incubated with ascites before chemotherapy

description: incubation with ascites before chemotherapy

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: High-grade serous ovarian cancer, stage IV

tag: patient

value: Patient 11; 76 years old; before neoadjuvant chemotherapy


title: cancer cells from patient 11 incubated with ascites after chemotherapy

description: incubation with ascites after chemotherapy

value: Patient 11; 76 years old; after neoadjuvant chemotherapy (3 courses)


title: 67_KMT2C_KO_rep3


title: Primed, H2AK119Ub, Rep2

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the human genome (hg38) using bowtie 2 (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5) with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
BigWig track files were generated with bamCoverage from deeptools (v3.5.0) using the following parameters: --normalizeUsing BPM --binSize 20 --smoothLength 40. normalizeUsing "BPM" --binSize 20 --smoothLength 40.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
Digested chromatin was treated with proteinase K and  eluted using phenol chloroform extraction as described in Skene et al.,2017.
High-throughput sequencing libraries were constructed using the TruSeq ChIP Library Preparation Kit according to the manufacturer’s recommendation. Paired-end sequencing was done on the Illumina NovaSeq 6000  with a read length of 100 bp.

value: Primed

tag: antibody


title: cancer cells from patient 6 incubated with ascites after chemotherapy

value: High-grade serous ovarian cancer, stage IIIC

value: Patient 6; 49 years old; after neoadjuvant chemotherapy (3 courses)


title: Fibroblasts + control secretome, repeat 1

value: Fibroblasts


title: Primed, IgG, Rep2

value: IgG


title: Primed, H3K27me3, Rep2

value: human embryonic stem cell


title: 67_KMT2C_KO_rep1

value: breast cancer

value: cell line


title: SKOV3 + control secretome, repeat 3

value: Ovarian adenocarcinoma


title: 67_KMT2C_KO_rep2


title: 67_WT_rep3

value: WT


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

value: High-grade serous ovarian cancer, stage III

value: Patient 3; 68 years old; after neoadjuvant chemotherapy (4 courses), relapse after 4 months


title: Primed, IgG, Rep1


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

value: ovarian cancer ascites

value: Patient 3; 68 years old; before neoadjuvant chemotherapy


title: Primed, H3K4me3, Rep2


title: 67_WT_rep2


title: 168_KMT2D_KO_rep2


title: Primed, H2AK119Ub, Rep1


title: Primed, H3K27me3, Rep1


title: Primed, H3K4me3, Rep1


title: Primed, H3K9me3, Rep2


title: 168_KMT2D_KO_rep3


title: 168_KMT2D_KO_rep1


title: cancer cells from patient 6 incubated with ascites before chemotherapy

value: primary culture of ovarian cancer cells

value: Patient 6; 49 years old; before neoadjuvant chemotherapy


title: cancer cells from patient 7 after chemotherapy

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 all libraries (12 pM) 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: primary culture of ovarian cancer cells (passage 3)

value: High-grade serous ovarian cancer, stage IIIС

value: Patient 7; 17 years old; after neoadjuvant chemotherapy (4 courses)


title: 67_WT_rep1


title: cancer cells from patient 4 before chemotherapy

value: Patient 4; 50 years old; before neoadjuvant chemotherapy


title: 168_KMT2C_KO_rep3


title: PXGL, IgG, KO, Rep2

value: PXGL

value: KO


title: PXGL, H2AK119Ub, KO, Rep2

value: human embryonic stem cell


title: cancer cells from patient 2 after chemotherapy

value: primary culture of ovarian cancer cells (passage 2)

value: High-grade serous ovarian cancer, stage IV

value: Patient 2; 58 years old; after neoadjuvant chemotherapy (4 courses)


title: 168_KMT2C_KO_rep2

value: breast cancer

value: cell line


title: cancer cells from patient 8 after chemotherapy

value: Patient 8; 63 years old; after neoadjuvant chemotherapy (4 courses)


title: PXGL, H3K9me3, KO, Rep2


title: cancer cells from patient 2 before chemotherapy

value: ovarian cancer ascites

value: Patient 2; 58 years old; before neoadjuvant chemotherapy


title: cancer cells from patient 8 before chemotherapy

value: Patient 8; 63 years old; before neoadjuvant chemotherapy


title: 168_KMT2C_KO_rep1


title: PXGL, H3K27me3, KO, Rep2


title: cancer cells from patient 7 before chemotherapy

value: Patient 7; 17 years old; beforer neoadjuvant chemotherapy


title: Primed, H3K9me3, Rep1

value: Primed


title: 168_WT_rep3

value: WT


title: PXGL, H3K4me3, KO, Rep2


title: cancer cells from patient 4 after chemotherapy (relapse)

value: primary culture of ovarian cancer cells (passage 3)

value: High-grade serous ovarian cancer, stage III

value: Patient 4; 50 years old; after neoadjuvant chemotherapy (4 courses), relapse after 7 months


title: cancer cells from patient 6 after chemotherapy

value: Patient 6; 49 years old; after neoadjuvant chemotherapy (3 courses)


title: cancer cells from patient 6 before chemotherapy

value: primary culture of ovarian cancer cells (passage 4)

value: Patient 6; 49 years old; before neoadjuvant chemotherapy


title: PXGL, H3K27ac, KO, Rep2

value: PXGL

value: human embryonic stem cell

value: KO


title: cancer cells from patient 5 after chemotherapy

value: Patient 5; 57 years old; after neoadjuvant chemotherapy (6 courses)


title: cancer cells from patient 5 before chemotherapy

value: Patient 5; 57 years old; before neoadjuvant chemotherapy


title: cancer cells from patient 3 after chemotherapy (relapse)

value: ovarian cancer ascites

value: Patient 3; 68 years old; after neoadjuvant chemotherapy (4 courses), relapse after 4 months


title: PXGL, IgG, WT, Rep2

value: IgG


title: YiLi04_Mo_12H_CITE

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description: 10X Genomics_5v2_0

library_source: other

data_processing:
blc2fastq (v2.20.0.422) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Assembly: GRCm38 (mm10-3.0.0 from Cell Ranger)
Supplementary files format and content: sc_mouse_cd4_annotation.txt.gz meta data and annotation of 18,860 cells
Supplementary files format and content: sc_mouse_cd4_feature_barcodes.csv.gz barcodes used for processing of antibody capture counts
Supplementary files format and content: sc_mouse_cd4_umi.txt.gz UMI count data matrix for 18,860 cells

molecule: protein

source_name: Colon

extract_protocol:
Colonic T cells were sorted into 1.5 mL tubes containing 500 ul of 1:1 PBS to FBS with 1:100 Recombinant RNAse Inhibitor (Takara Bio 2313B). Following sorting, tubes were filled up to 1.4 mL with PBS and spun at 600xg for 10 minutes. Pellets were resuspended in 35 ul PBS supplemented with 0.04% w/v BSA (Invitrogen) and cells were processed according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit. HTO (CITE) cDNA was separated from PolyA cDNA through size selection with AMPure XP Purification reagent (Beckman Coulter, A63882)
All Libraries were prepared according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit.
scRNA-Seq, Cell Surface Protein library preparation

treatment_protocol: Colons were dissociated into single cell, and stained with dead cell discriminating dye, fluorophore-tagged FACS antibodies, and unique anti-mouse hashtag antibodies against beta2 microglobulin for individual mouse deconvolution. T cells from each mouse were FACS-sorted for scRNA-seq using the 10X genomics platform.

value: Colon

value: TCRb+CD4+ T cells


title: PXGL, H3K9me3, WT, Rep2

value: WT


title: YiLi04_Mo_12H_Gex

description: 10X Genomics_5v2_0


title: cancer cells from patient 3 before chemotherapy

value: primary culture of ovarian cancer cells (passage 3)

value: Patient 3; 68 years old; before neoadjuvant chemotherapy


title: PXGL, H2AK119Ub, WT, Rep2


title: PXGL, H3K27me3, WT, Rep2


title: RNA library from E18.5 Male Natural Fetal liver 4

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
summary_count_E18.5_Fetalliver.txt
Male-Natural-C6B

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: E18.5 Fetal Liver

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols.

treatment_protocol: E12.5 Placentas and fetuses, E18.5 placentas and fetal livers were collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

tag: gender

value: Male

tag: group

value: Natural

value: Fetal Liver

tag: age


title: RNA library from E18.5 Male Natural Fetal liver 5

description:
summary_count_E18.5_Fetalliver.txt
Male-Natural-C7B


title: ICM-rep3-RNA-seq

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

country: Germany

institute: University Medical Center Göttingen

data_processing:
Reads pairs were aligned to the human reference genome (GRCh37) and transcriptome (Gencode.v29) using STAR (v2.6.0c).
Quantification of unique quants was done with featureCounts. RUVs function of RUVseq was used to further normalize the counts, prior to differential gene expression estimation using DESeq2
Read coverage tracks (BigWig) were generated and normalized by scale factor using the bamCoverage function of deepTools2 (v3.5.1).
Assembly: GRCh37

extract_protocol:
IMR90s grown to near-confluence in a 15cm plate were directly lysed using Trizol (Invitrogen), total RNA was isolated using the DirectZol kit (Zymo).
Ribomaps Ltd according to Ivanov et al, 2018

value: human lung fibroblast


title: RNA library from E18.5 Male Natural Fetal liver 3

description:
summary_count_E18.5_Fetalliver.txt
Male-Natural-C5J


title: ICM-rep2-RNA-seq


title: RNA library from E18.5 Male Natural Fetal liver 1

description:
summary_count_E18.5_Fetalliver.txt
Male-Natural-C4E


title: PXGL, H3K4me3, WT, Rep2

value: PXGL


title: PXGL, H3K27ac, WT, Rep2

value: human embryonic stem cell


title: ICM-rep1-RNA-seq


title: RNA library from E18.5 Male IVF+TEBx Fetal liver 5

description:
summary_count_E18.5_Fetalliver.txt
Male-IVFTEBx-2026-1

value: IVF+TEBx


title: 168_WT_rep2

value: breast cancer

value: cell line


title: RNA library from E18.5 Male IVF+TEBx Fetal liver 4

description:
summary_count_E18.5_Fetalliver.txt
Male-IVFTEBx-2016-1


title: PXGL, IgG, KO, Rep1

value: KO


title: PXGL, H2AK119Ub, KO, Rep1


title: 168_WT_rep1


title: old-rep2-RNA-seq


title: RNA library from E18.5 Male IVF+TEBx Fetal liver 3

description:
summary_count_E18.5_Fetalliver.txt
Male-IVFTEBx-2002-1


title: old-rep1-RNA-seq


title: PXGL, H3K27me3, KO, Rep1


title: RNA library from E18.5 Male IVF+TEBx Fetal liver 2

description:
summary_count_E18.5_Fetalliver.txt
Male-IVFTEBx-1943-1


title: young-rep3-RNA-seq


title: old-rep3-RNA-seq


title: RNA library from E18.5 Male IVF Fetal liver 3

description:
summary_count_E18.5_Fetalliver.txt
Male-IVF-1943-2

value: IVF


title: RNA library from E18.5 Male IVF Fetal liver 4

description:
summary_count_E18.5_Fetalliver.txt
Male-IVF-B48C


title: RNA library from E18.5 Male IVF+TEBx Fetal liver 1

description:
summary_count_E18.5_Fetalliver.txt
Male-IVFTEBx-1893-2


title: young-rep2-RNA-seq


title: ICM-rep3-Ribo-seq

data_processing:
Reads pairs were aligned to the human reference genome (GRCh37) and transcriptome (Gencode.v29) using STAR (v2.6.0c).
Quantification of unique quants was done with featureCounts. RUVs function of RUVseq was used to further normalize the counts, prior to differential gene expression estimation using DESeq2
Read coverage tracks (BigWig) were generated and normalized by scale factor using the bamCoverage function of deepTools2 (v3.5.1).
Assembly: GRCh37
Library strategy: Ribo-seq


title: PXGL, H3K4me3, KO, Rep1


title: PXGL, IgG, WT, Rep1

value: IgG


title: young-rep1-RNA-seq


title: PXGL, H2AK119Ub, WT, Rep1


title: PXGL, H3K9me3, KO, Rep1


title: PXGL, H3K27ac, KO, Rep1


title: PXGL, H3K9me3, WT, Rep1


title: RNA library from E18.5 Male IVF Fetal liver 2

description:
summary_count_E18.5_Fetalliver.txt
Male-IVF-1902-3


title: ICM-rep1-Ribo-seq


title: RNA library from E18.5 Female Natural Fetal liver 3

description:
summary_count_E18.5_Fetalliver.txt
Female-Natural-C6A

value: Female


title: RNA library from E18.5 Female Natural Fetal liver 1

description:
summary_count_E18.5_Fetalliver.txt
Female-Natural-C1F


title: PXGL, H3K27me3, WT, Rep1


title: old-rep3-Ribo-seq


title: PXGL, H3K27ac, WT, Rep1


title: PXGL, H3K4me3, WT, Rep1


title: ICM-rep2-Ribo-seq


title: RNA library from E18.5 Female IVF+TEBx Fetal liver 5

description:
summary_count_E18.5_Fetalliver.txt
Female-IVFTEBx-B48A


title: old-rep2-Ribo-seq


title: old-rep1-Ribo-seq


title: PXGL, IgG, CRISPRi XIST Dox, Rep3

value: CRISPRi XIST Dox


title: young-rep3-Ribo-seq


title: RNA library from E18.5 Female IVF+TEBx Fetal liver 4

description:
summary_count_E18.5_Fetalliver.txt
Female-IVFTEBx-2006-1


title: PXGL, H2AK119Ub, CRISPRi XIST Dox, Rep3


title: young-rep2-Ribo-seq


title: PXGL, H3K9me3, CRISPRi XIST Dox, Rep3


title: RNA library from E18.5 Female IVF+TEBx Fetal liver 3

description:
summary_count_E18.5_Fetalliver.txt
Female-IVFTEBx-1991-1


title: young-rep1-Ribo-seq


title: PXGL, H3K27me3, CRISPRi XIST Dox, Rep3


title: RNA library from E18.5 Male IVF Fetal liver 1

description:
summary_count_E18.5_Fetalliver.txt
Male-IVF-1900-2


title: RNA library from E18.5 Female IVF+TEBx Fetal liver 1

description:
summary_count_E18.5_Fetalliver.txt
Female-IVFTEBx-1902-2


title: PXGL, H3K4me3, CRISPRi XIST Dox, Rep3


title: PXGL, H3K27ac, CRISPRi XIST Dox, Rep3


title: RNA library from E18.5 Female IVF Fetal liver 5

description:
summary_count_E18.5_Fetalliver.txt
Female-IVF-2064-2


title: RNA library from E18.5 Female IVF Fetal liver 4

description:
summary_count_E18.5_Fetalliver.txt
Female-IVF-2028-1


title: PXGL, IgG, CRISPRi XIST Dox, Rep2


title: RNA library from E18.5 Female IVF Fetal liver 3

description:
summary_count_E18.5_Fetalliver.txt
Female-IVF-1950-1


title: Offspring of control diet-fed dam, repeat 2

city: Clayton

first: Francine

middle: Coelho

last: Marques

address: 25 Rainforest Walk

department: School of Biological Sciences

country: Australia

institute: Monash University

data_processing:
Cell ranger version 3.1.0
Assembly: mm10
Supplementary files format and content: 3 processed files generated by cell ranger, barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz are provided.

source_name: Heart

extract_protocol:
Hearts were excised and continiousy perfused with enzymatic buffer solution containing 2 mg/mL collagenase IV (LS004188, Worthington Biochem) and 1 mg/mL dispase II (04942078001, Roche). Single cell suspension were then stained with antibodies and with Sytox™ Green (S34860, Invitrogen) and Vybrant™ DyeCycle™ (V10273, Invitrogen) and verapamil and sorted for live, metabolically active and nucleated cells using FACSAria™ III cell sorter (B.D.)
Libraries were prepared using according to the 10x Genomics chemistry 3` v2 kit and sequenced in an Illumina HiSeq instrument. Analysis was performed using 10X Genomics pipeline.

value: Heart

value: Offspring of control diet-fed dam


title: PXGL, H2AK119Ub, CRISPRi XIST Dox, Rep2


title: Offspring of high fibre intake dam, repeat 2

value: Offspring of high fibre intake dam


title: Offspring of high fibre intake dam, repeat 1


title: RNA library from E18.5 Female IVF Fetal liver 2

description:
summary_count_E18.5_Fetalliver.txt
Female-IVF-1948-2


title: PXGL, H3K9me3, CRISPRi XIST Dox, Rep2


title: RNA library from E18.5 Female IVF Fetal liver 1

description:
summary_count_E18.5_Fetalliver.txt
Female-IVF-1914-1


title: PXGL, H3K27me3, CRISPRi XIST Dox, Rep2


title: RNA library from E18.5 Male Natural Placenta 5

description:
summary_count_E18.5_Placenta.txt
Male-Natural-C7B

source_name: E18.5 Placenta

value: Male

value: Placenta


title: Cell Line, JW23

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

data_processing:
library strategy: Whole Exome Sequencing
Quality Trimming via Trimmomatic 0.33
Read alignment via Illumina Dragen
Somatic Variant calling via Illumina Dragen
Sample variant comparison via Illumina Dragen
Assembly: GRCm39
Supplementary files format and content: Count Quantification via Stringtie 1.3.4d
Supplementary files format and content: Somatic Variant calling via Illumina Dragen

source_name: Cell Line

growth_protocol: All cell lines were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM, Gibco, Life Technologies) with 10% fetal bovine serum (FBS, Gibco), 200U/mL of Penicillin/Streptomycin (Gibco); Cells were incubated at 37°C with 5% CO2 under humidified conditions.

extract_protocol:
Genomic DNA of each JW cell line was extracted utilizing the QIAamp DNA Mini Kit (Qiagen, 51304) for whole exome sequencing
Genomic DNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA). Enrichment probes were designed against the region of interest and synthesized through SureSelectXT Mouse All Exon Kit (Agilent, Santa Clara, CA, USA). Library preparation was performed according to the manufacturer’s guidelines.

value: Cell Line


title: PXGL, H3K4me3, CRISPRi XIST Dox, Rep2


title: RNA library from E18.5 Male Natural Placenta 4

description:
summary_count_E18.5_Placenta.txt
Male-Natural-C6B

value: Natural


title: RNA library from E18.5 Female IVF+TEBx Fetal liver 2

description:
summary_count_E18.5_Fetalliver.txt
Female-IVFTEBx-1951-3

value: Fetal Liver


title: Cell Line, JW18


title: PXGL, H3K27ac, CRISPRi XIST Dox, Rep2

value: PXGL

value: human embryonic stem cell


title: RNA library from E18.5 Male Natural Placenta 2

description:
summary_count_E18.5_Placenta.txt
Male-Natural-C5HS11


title: Offspring of control diet-fed dam, repeat 1


title: RNA library from E18.5 Male Natural Placenta 3

description:
summary_count_E18.5_Placenta.txt
Male-Natural-C5HS17


title: HMGB2_KD_rep2_RNA-seq

data_processing:
Reads pairs were aligned to the human reference genome (GRCh37) and transcriptome (Gencode.v29) using STAR (v2.6.0c).
Quantification of unique quants was done with featureCounts. RUVs function of RUVseq was used to further normalize the counts, prior to differential gene expression estimation using DESeq2
Read coverage tracks (BigWig) were generated and normalized by scale factor using the bamCoverage function of deepTools2 (v3.5.1).
Assembly: GRCh37
Supplementary files format and content: allDE_RUVs_deseq2

extract_protocol:
IMR90s grown to near-confluence in a 15cm plate were directly lysed using Trizol (Invitrogen), total RNA was isolated using the DirectZol kit (Zymo).
Standard poly(A)+ selection and library preparation with the TruSeq kit (Illumina).

value: human lung fibroblast

value: HMGB2 knockdown


title: PXGL, H2AK119Ub, CRISPRi XIST Dox, Rep1


title: RNA library from E18.5 Male Natural Placenta 1

description:
summary_count_E18.5_Placenta.txt
Male-Natural-C4E


title: HMGB2_KD_rep1_RNA-seq


title: WT_rep2_RNA-seq

value: wild type


title: RNA library from E18.5 Male IVF+TEBx Placenta 4

description:
summary_count_E18.5_Placenta.txt
Male-IVFTEBx-2026

value: IVF+TEBx


title: PXGL, H3K9me3, CRISPRi XIST Dox, Rep1


title: PXGL, H3K27me3, CRISPRi XIST Dox, Rep1


title: WT_rep1_RNA-seq


title: RNA library from E18.5 Male IVF+TEBx Placenta 2

description:
summary_count_E18.5_Placenta.txt
Male-IVFTEBx-1943


title: PXGL, H3K4me3, CRISPRi XIST Dox, Rep1


title: PXGL, H3K27ac, CRISPRi XIST Dox, Rep1


title: RNA library from E18.5 Male IVF+TEBx Placenta 3

description:
summary_count_E18.5_Placenta.txt
Male-IVFTEBx-2002


title: PBMC-RA_FPKM

city: Taipei

first: Yi-Lin

last: Chiu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Department of Biochemistry, College of Biomedical Sciences

country: Taiwan

institute: National Defense Medical University

data_processing:
Salmon (v0.91)
The resulting sequencing data in fastq format was processed and generated by GENEWIZ®. Transcript abundance for each sample was estimated through the use of Salmon (v0.91), which quasi-mapped the sequencing reads using the 31bp k-mer index of the GRCh38 human reference transcript (GENCODE v41)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: PBMC

growth_protocol: PBMC were cultured in RPMI 1640 medium, supplemented with 10% Fetal Bovine Serum and 1% penicillin/streptomycin

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent/RNeasy Mini Kit (Qiagen) kits.
Library preparation for sequencing involves a detailed, multi-step process. It starts with the isolation of poly(A) mRNA, which can be done using a Poly(A) mRNA Magnetic Isolation Module or an rRNA removal Kit. Next, the mRNA is fragmented and primed using First Strand Synthesis Reaction Buffer and Random Primers. This is followed by the synthesis of the first strand cDNA using ProtoScript II Reverse Transcriptase, and then the synthesis of the second-strand cDNA using a Second Strand Synthesis Enzyme Mix. The double-stranded cDNA undergoes end preparation and adaptor ligation, involving purification, treatment with End Prep Enzyme Mix for end repair and dA-tailing, and T-A ligation for adaptor addition. Size selection is then performed using beads to recover fragments around 400 bp. This is followed by PCR amplification using P5 and P7 primers, and the purification of PCR products. Finally, the PCR products are validated and quantified using Qsep100 (Bioptic, Taiwan, China) and a Qubit3.0 Fluorometer (Invitrogen, USA).

treatment_protocol: The cells were treated with cilostazol,Ginkgo Biloba Extract and resveratrol, with an appropriate vehicle control and were incubated for 24 hours at standard culture conditions

value: PBMC


title: RNA library from E18.5 Male IVF+TEBx Placenta 1

description:
summary_count_E18.5_Placenta.txt
Male-IVFTEBx-1893


title: PXGL, IgG, CRISPRi XIST UT, Rep3

value: CRISPRi XIST UT

value: IgG


title: RNA library from E18.5 Male IVF Placenta 5

description:
summary_count_E18.5_Placenta.txt
Male-IVF-B48C

value: IVF


title: PBMC-GBE_FPKM


title: PXGL, H2AK119Ub, CRISPRi XIST UT, Rep3


title: RNA library from E18.5 Male IVF Placenta 4

description:
summary_count_E18.5_Placenta.txt
Male-IVF-2028


title: PXGL, H3K9me3, CRISPRi XIST UT, Rep3


title: PBMC-GBE


title: PXGL, IgG, CRISPRi XIST Dox, Rep1

value: CRISPRi XIST Dox


title: Cell Line, JW16


title: RNA library from E18.5 Male IVF Placenta 3

description:
summary_count_E18.5_Placenta.txt
Male-IVF-1943


title: PBMC-CTRL_FPKM


title: PXGL, H3K27me3, CRISPRi XIST UT, Rep3


title: RNA library from E18.5 Male IVF Placenta 2

description:
summary_count_E18.5_Placenta.txt
Male-IVF-1902


title: PBMC-CTRL


title: PXGL, H3K4me3, CRISPRi XIST UT, Rep3


title: PBMC-CILO_FPKM


title: PXGL, H3K27ac, CRISPRi XIST UT, Rep3


title: RNA library from E18.5 Female Natural Placenta 5

description:
summary_count_E18.5_Placenta.txt
Female-Natural-C7A

value: Female


title: PBMC-RA


title: PXGL, IgG, CRISPRi XIST UT, Rep2


title: RNA library from E18.5 Female Natural Placenta 3

description:
summary_count_E18.5_Placenta.txt
Female-Natural-C6A


title: PXGL, MeD, Rep3

data_processing:
Raw fastq files were subjected to Illumina adaptor trimming
Reads were filtered based on LpnPI restriction site occurrence between 13-17 bp from either 5' or 3' end of the read.
Reads that passed the filter were mapped to hg38 using bowtie2.
Genome-wide individual LpnPI site scores were used to generate read count scores for the following annotated regions: transcription start sites (TSS, 1 kb before and 1 kb after), CpG-islands and gene bodies (1kb after TSS till TES). Gene and CpG-island annotations were downloaded from ENSEMBL (www.ensembl.org).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each sample
Library strategy: MeD-seq

extract_protocol:
DNA was purified using phenol-chlorofom extraction protocol.
Briefly,90 ng from naïve hESCs were digested with LpnPI (New England Biolabs) generating 32 bp fragments around the fully methylated recognition site containing a CpG. These short DNA fragments were further processed using the ThruPlex DNA–seq 96D kit (Rubicon Genomics Ann Arbor). Stem-loop adapters were blunt-end ligated to repaired input DNA and amplified to include dual indexed barcodes using a high-fidelity polymerase to generate an indexed Illumina NGS library. The amplified end product was purified on a Pippin HT system with 3% agarose gel cassettes (Sage Science).


title: RNA library from E18.5 Female Natural Placenta 4

description:
summary_count_E18.5_Placenta.txt
Female-Natural-C6C


title: PXGL, MeD, Rep2


title: PXGL, H3K9me3, CRISPRi XIST UT, Rep2


title: PXGL, H2AK119Ub, CRISPRi XIST UT, Rep2


title: RNA library from E18.5 Female Natural Placenta 1

description:
summary_count_E18.5_Placenta.txt
Female-Natural-C1F


title: PXGL, H3K27me3, CRISPRi XIST UT, Rep2


title: RNA library from E18.5 Female Natural Placenta 2

description:
summary_count_E18.5_Placenta.txt
Female-Natural-C2G


title: PXGL, MeD, Rep1


title: PXGL, H3K4me3, CRISPRi XIST UT, Rep2


title: ICM2-scRNA-seq

data_processing:
Libraries that passed QC criteria were paired-end sequenced to at least 250mil reads per library. The downstream analysis was performed by Active Motif.
Assembly: GRCh38

extract_protocol:
In brief proliferating, ICM-treated and senescent IMR90s (8x105 cells/condition) were grown at 80% confluency, harvested with trypsin and froze at -80oC.
Single cell RNA-seq was performed using the 10X Genomics kit in collaboration with Active Motif.


title: Senescent2-scRNA-seq


title: PXGL, H3K27ac, CRISPRi XIST UT, Rep2


title: RNA library from E18.5 Female IVF+TEBx Placenta 5

description:
summary_count_E18.5_Placenta.txt
Female-IVFTEBx-B48A


title: RNA library from E18.5 Female IVF+TEBx Placenta 6

description:
summary_count_E18.5_Placenta.txt
Female-IVFTEBx-1910


title: RNA library from E18.5 Male IVF Placenta 1

description:
summary_count_E18.5_Placenta.txt
Male-IVF-1900

value: Male


title: PXGL, IgG, CRISPRi XIST UT, Rep1


title: MetaICM_rep2_factory_seq


title: PXGL, H2AK119Ub, CRISPRi XIST UT, Rep1


title: RNA library from E18.5 Female IVF+TEBx Placenta 4

description:
summary_count_E18.5_Placenta.txt
Female-IVFTEBx-2006

value: Placenta


title: RNA library from E18.5 Female IVF+TEBx Placenta 3

description:
summary_count_E18.5_Placenta.txt
Female-IVFTEBx-1991


title: PBMC-CILO


title: MetaICM_rep1_factory_seq


title: PXGL, H3K9me3, CRISPRi XIST UT, Rep1


title: RNA library from E18.5 Female IVF+TEBx Placenta 2

description:
summary_count_E18.5_Placenta.txt
Female-IVFTEBx-1951


title: ICM_6days_rep2_factory_seq


title: RNA library from E18.5 Female IVF+TEBx Placenta 1

description:
summary_count_E18.5_Placenta.txt
Female-IVFTEBx-1902


title: PXGL, H3K27me3, CRISPRi XIST UT, Rep1


title: ICM_6days_rep1_factory_seq


title: ICM_3days_rep2_factory_seq


title: PXGL, H3K27ac, CRISPRi XIST UT, Rep1


title: PXGL, H3K4me3, CRISPRi XIST UT, Rep1


title: ICM_3days_rep1_factory_seq


title: RNA library from E18.5 Female IVF Placenta 3

description:
summary_count_E18.5_Placenta.txt
Female-IVF-1950


title: PXGL, ATAC, Rep2

data_processing:
ATAC-seq raw data was processed using the atacseq pipeline (v1.2.1) (https://github.com/nf-core/atacseq/) from nf-core using the default parameters
Adapter trimming using Trim Galore
Reads were aligned using BWA aligner
Duplicates were marked by picard
bigWig tracks were generated by BEDTools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
DNA was extracted using the MinElute PCR purification kit (QIAGEN).
Transposed DNA were pre-amplified for 5 cycles. The required number of additional cycles for each sample was determined by qPCR as described (Buenrostro et al., 2015). After the final amplification, double-sided bead purification was performed with AMPure XP beads.

value: Primed


title: young_rep2_factory_seq


title: Young1-scRNA-seq


title: young_rep1_factory_seq


title: PXGL, ATAC, Rep3


title: RNA library from E12.5 Male Natural Whole Fetus 5

description:
summary_count_E12.5_WholeFetus.txt
Male-Natural-1611-3

source_name: E12.5 Whole Fetus

value: Natural

value: Whole Fetus


title: RNA library from E18.5 Female IVF Placenta 1

description:
summary_count_E18.5_Placenta.txt
Female-IVF-1914


title: I79ICMrep2-RNA-seq


title: PXGL, ATAC, Rep1


title: I79ICMrep1-RNA-seq


title: RNA library from E12.5 Male Natural Whole Fetus 4

description:
summary_count_E12.5_WholeFetus.txt
Male-Natural-1611-13


title: EHE-siNeg-5

city: Milano

first: Stefano

last: Percio

address: VIa Amadeo 42

country: Italy

institute: Istituto Nazionale dei Tumori

description: control

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: EHE

growth_protocol: EHE cells were seeded in 6 well-plates at 120.000 cells/well in DMEM/F-12 10% FBS medium, so that they were 60-70% confluent at the time of transfection.

extract_protocol:
Cells were lysed with QIAzol Lysis Reagent and RNA was extracted using QIAGEN miRNeasy kit according to manufacturer instructions.
RNA stranded libraries were generated starting from 500ng total RNA and mRNA was selected with poly-T oligo attached magnetic beads using Illumina® Stranded mRNA Prep, Ligation protocol. Libraries were quantified and quality checked on an Agilent 4200 TapeStation system (High Sensitivity D1000), and then sequenced on an Illumina NovaSeq platform with paired-end reads 150bp long.

treatment_protocol: EHE cells were transfected with 33 nM GDF-15 siRNA or negative control siRNA using Lipofectamine RNAiMAX as transfecting agent (resuspended in 500 uL of free-serum medium). After 24 h of siRNA exposure, the cell culture medium was removed and cells were maintained in a fresh complete medium for an additional 48 h.

value: EHE

value: treated with negative siRNA


title: EHE-siNeg-6

description: control


title: RNA library from E12.5 Male Natural Whole Fetus 3

description:
summary_count_E12.5_WholeFetus.txt
Male-Natural-1611-12


title: I10old_rep2-RNA-seq

value: human lung fibroblast


title: EHE-siNeg-4

description: control


title: RNA library from E12.5 Male Natural Whole Fetus 2

description:
summary_count_E12.5_WholeFetus.txt
Male-Natural-1563-9


title: EHE-siNeg-1

description: control


title: RNA library from E18.5 Female IVF Placenta 4

description:
summary_count_E18.5_Placenta.txt
Female-IVF-2028


title: I10young_rep2-RNA-seq


title: RNA library from E12.5 Male Natural Whole Fetus 1

description:
summary_count_E12.5_WholeFetus.txt
Male-Natural-1563-8


title: EHE-siGDF-15-4

description: treated

value: treated with siRNA for GDF-15


title: RNA library from E12.5 Male IVF+TEBx Whole Fetus 5

description:
summary_count_E12.5_WholeFetus.txt
Male-IVFTEBx-1604-3


title: RNA library from E18.5 Female IVF Placenta 2

description:
summary_count_E18.5_Placenta.txt
Female-IVF-1948


title: I10young_rep1-RNA-seq


title: RNA library from E12.5 Male IVF+TEBx Whole Fetus 4

description:
summary_count_E12.5_WholeFetus.txt
Male-IVFTEBx-1604-2


title: RNA library from E12.5 Male IVF+TEBx Whole Fetus 3

description:
summary_count_E12.5_WholeFetus.txt
Male-IVFTEBx-1544-6


title: EHE-siGDF-15-1

description: treated


title: I79old_rep1-RNA-seq


title: RNA library from E12.5 Male IVF+TEBx Whole Fetus 2

description:
summary_count_E12.5_WholeFetus.txt
Male-IVFTEBx-1544-4


title: I79young_rep2-RNA-seq


title: SR5

city: Qingdao

first: Xiaomeng

last: Chen

address: No. 17, Shandong Road

country: China

institute: Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences

data_processing:
HISAT v2.2.1, StringTie v2.2.0
The high-quality Clean Data was obtained by filtering out low-quality reads, which included removing reads with an N content exceeding 10% and reads with more than 50% of bases having a quality value (Q) of ≤10.
The HISAT2 software was used to perform rapid and accurate alignment of Clean Reads to the reference genome (version information: Homo_sapiens.GRCh38_release95.genome.fa), obtaining the location information of the reads on the reference genome. Subsequently.
The Mapped Reads were assembled into transcripts using the StringTie program. A maximum flow algorithm was employed, and the data was normalized using FPKM (Fragments Per Kilobase of transcript per Million fragments mapped), which serves as a measure of gene expression levels.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Blood

extract_protocol:
Total RNA from each sample was extracted from venous blood using the TRIzol reagent (Life Technologies, California, USA) following the manufacturer's instructions.
Specific rRNA probes were used to remove rRNA from the total RNA. The remaining RNA was randomly fragmented by adding Fragmentation Buffer. Using RNA as a template, random primers were used to synthesize the first strand of cDNA. Subsequently, the RNA chain was degraded using RNase H, and the second strand of cDNA was synthesized using dNTPs as a source. The double-stranded cDNA was then purified, and end repair, A-tailing, and sequencing adapter ligation were performed. Fragment size selection was carried out using AMPure XP beads. The cDNA's second strand containing uracil (U) was degraded using USER enzyme, and the cDNA library was finally enriched through PCR.

value: Blood

value: sinus rhythm maintenance


title: RNA library from E12.5 Male IVF+TEBx Whole Fetus 1

description:
summary_count_E12.5_WholeFetus.txt
Male-IVFTEBx-1544-1

value: IVF+TEBx


title: I79young_rep1-RNA-seq


title: I10old_rep1-RNA-seq


title: RNA library from E12.5 Male IVF Whole Fetus 4

description:
summary_count_E12.5_WholeFetus.txt
Male-IVF-1596-1


title: ABM04-CLP2_CMX-RNU-286

city: Los Angeles

first: Vincenzo

last: Calvanese

address: 615 Charles E Young Dr S

institute: UCLA

description: Adult Bone Marrow CLP2 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: Adult Bone Marrow

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: Adult Bone Marrow

tag: donor id

value: Adult #04

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


title: ABM04-CLP1_CMX-RNU-285

description: Adult Bone Marrow CLP1 RNAseq

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


title: RNA library from E12.5 Male IVF Whole Fetus 2

description:
summary_count_E12.5_WholeFetus.txt
Male-IVF-1542-1

value: IVF


title: SR2


title: RNA library from E12.5 Male IVF Whole Fetus 3

description:
summary_count_E12.5_WholeFetus.txt
Male-IVF-1544-2

value: Male


title: SR3


title: ABM04-LMPP_CMX-RNU-284

description: Adult Bone Marrow LMPP RNAseq

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


title: EHE-siGDF-15-3

description: treated


title: I79old_rep2-RNA-seq


title: SR1


title: AF5

value: AF recurrence


title: RNA library from E12.5 Male IVF Whole Fetus 1

description:
summary_count_E12.5_WholeFetus.txt
Male-IVF-1520-2


title: RNA library from E12.5 Female Natural Whole Fetus 5

description:
summary_count_E12.5_WholeFetus.txt
Female-Natural-1611-2

value: Female

value: Natural


title: ABM04-MoP_CMX-RNU-282

description: Adult Bone Marrow MoP RNAseq


title: RNA library from E12.5 Female Natural Whole Fetus 4

description:
summary_count_E12.5_WholeFetus.txt
Female-Natural-1611-14

value: Whole Fetus


title: AF4


title: EHE-siGDF-15-2

description: treated

value: EHE


title: ABM04-GMP_CMX-RNU-281

description: Adult Bone Marrow GMP RNAseq


title: SR4


title: RNA library from E12.5 Female Natural Whole Fetus 3

description:
summary_count_E12.5_WholeFetus.txt
Female-Natural-1563-4


title: ABM04-CMP_CMX-RNU-279

description: Adult Bone Marrow CMP RNAseq

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


title: AF3


title: neural tube organoids, 66 hrs post Day 2, N2B27+SAG, sorted for GFP+, biol rep 3

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
RNA-seq reads were trimmed using trimgalore v0.5.0
Ffiltered to remove abundant sequences using bowtie2 v2.3.4.1
Aligned to the Genome using star v2.6.0c
Summarized per gene with featureCounts (subread v1.6.2)
Assembly: GRCm38 genome (Ensembl release 94)
Supplementary files format and content: Tab delimited file of per gene read counts

source_name: neural tube organoid

growth_protocol: R1 mouse embryonic stem cells of FoxA2-Venus genotype were embedded in Matrigel and differentiaed into neural tube organoids via clonal growth in N2B27 medium with antibiotics at 37C, 5% CO2.

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNAseq libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol:
Two days after differentation, the medium was replaced with N2B27 or N2B27+250 µM all-trans retinoic acid.
Neural tube organoids were extracted from the Matrigel with Cell Recovery solution at 66 hrs post Day 2, FACS sorted for high or low fluorescence signal with a GFP filter set, and processed for RNA extraction.

value: neural tube organoid

value: mouse embryonic stem cell

value: 3D neuroepithelial differentiation in Matrigel


title: RNA library from E12.5 Female Natural Whole Fetus 2

description:
summary_count_E12.5_WholeFetus.txt
Female-Natural-1563-3


title: ABM04-HSC_CMX-RNU-277

description: Adult Bone Marrow HSC RNAseq

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


title: AF1

value: Blood


title: RNA library from E12.5 Female Natural Whole Fetus 1

description:
summary_count_E12.5_WholeFetus.txt
Female-Natural-1563-2


title: neural tube organoids, 66 hrs post Day 2, N2B27+SAG, sorted for GFP+, biol rep 2


title: 3D_SER_1_3

city: Utrecht

first: Jorke

last: Kamstra

state: Non United States Or Canada

address: PO Box 80177

department: Faculty of Veterinary Medicine

country: Netherlands

institute: Utrecht University

data_processing:
Raw fastq files were adapter trimmed using trim_galore (v0.4.5, Babraham in-stitute, UK) under standard parameters.
STAR aligner (v2.5.4 b) was used to align and map sequences to the homo sapiens genome (GRCh38_v102;  https:// www.ensembl.org).
Generated BAM files were loaded to SeqMonk sequence analysis tool (v1.41, Babraham institute, UK) and mRNAs were quantified using the built-in mRNA seq pipeline.
Normalization of the read counts and differential expression was conducted using the Deseq2 method.
Assembly: GRCh38_v102
Supplementary files format and content: The processed data files is an excel file containing raw read counts and log2 normalized (RPM) data

source_name: bone marrow

growth_protocol: hMSCs were plated in 24 (2D) and 96ULA (3D) well plates for RNA-seq analysis.

extract_protocol:
Total RNA was isolated and purified using the NucleoSpin® RNA extraction kit (Macherey-Nagel, Germany) from one confluent well of a 24 well plate (2D) or 10−20 spheroids pooled together (3D).
Library preparation and analysis was performed on the Novaseq using 150bp paired end se-quencing.

treatment_protocol: Cells were exposed to vehicle control (DMSO), positive control (0.1 µM rosiglitazone), or test chemicals (citalopram at 1-10 µM, sertraline at 0.1-1 µM). 3 independent experiments were performed for both 2D and 3D, with one extra control for 3D.

value: bone marrow

value: mesenchymal stem cell

value: hMSC-BM

tag: Sex

value: male

value: adipogenic differentiation


title: neural tube organoids, 66 hrs post Day 2, N2B27+SAG, sorted for GFP+, biol rep 1

tag: cell line


title: CB06-CLP2_CMX-RNU-266

description: Cord Blood CLP2 RNAseq

source_name: Umbillical Cord Blood

value: Umbillical Cord Blood

value: Newborn #06

tag: cell type

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

value: birth


title: ABM04-CDP_CMX-RNU-283

description: Adult Bone Marrow CDP RNAseq

value: Adult Bone Marrow

value: Adult #04

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


title: RNA library from E12.5 Female IVF+TEBx Whole Fetus 5

description:
summary_count_E12.5_WholeFetus.txt
Female-IVFTEBx-1888-3

value: Female

value: IVF+TEBx

value: Whole Fetus


title: 3D_SER_1_2


title: RNA library from E12.5 Female IVF+TEBx Whole Fetus 4

description:
summary_count_E12.5_WholeFetus.txt
Female-IVFTEBx-1598-2


title: CB06-CDP_CMX-RNU-264

description: Cord Blood CDP RNAseq


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, sorted for GFP+, biol rep 3

value: neural tube organoid

value: mouse embryonic stem cell

value: 3D neuroepithelial differentiation in Matrigel


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, sorted for GFP+, biol rep 2


title: CB06-MoP_CMX-RNU-263

description: Cord Blood MoP RNAseq


title: RNA library from E12.5 Female IVF+TEBx Whole Fetus 3

description:
summary_count_E12.5_WholeFetus.txt
Female-IVFTEBx-1574-3


title: 3D_SER_0.1_3

value: bone marrow

value: mesenchymal stem cell


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, sorted for GFP+, biol rep 1


title: RNA library from E12.5 Female IVF+TEBx Whole Fetus 2

description:
summary_count_E12.5_WholeFetus.txt
Female-IVFTEBx-1574-2


title: AF2

value: Blood

value: AF recurrence


title: CB06-GMP_CMX-RNU-262

description: Cord Blood GMP RNAseq

value: Umbillical Cord Blood


title: 3D_SER_0.1_2

value: hMSC-BM

value: male

value: adipogenic differentiation


title: CB06-MEP_CMX-RNU-261

description: Cord Blood MEP RNAseq

value: Newborn #06

value: birth


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, sorted for GFP-, biol rep 3


title: RNA library from E12.5 Female IVF+TEBx Whole Fetus 1

description:
summary_count_E12.5_WholeFetus.txt
Female-IVFTEBx-1574-1


title: 3D_SER_0.1_1


title: RNA library from E12.5 Female IVF Whole Fetus 6

description:
summary_count_E12.5_WholeFetus.txt
Female-IVF-1596-2

value: IVF


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, sorted for GFP-, biol rep 2


title: CB06-CLP1_CMX-RNU-265

description: Cord Blood CLP1 RNAseq

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


title: CB06-CMP_CMX-RNU-260

description: Cord Blood CMP RNAseq

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


title: neural tube organoids, 66 hrs post Day 2, N2B27+RA, sorted for GFP-, biol rep 1


title: 3D_CIT_10_3


title: 3D_CIT_10_2


title: FL12-CLP1_CMX-RNU-217

description: Fetal liver CLP1 RNAseq

source_name: Fetal liver

value: Fetal liver

value: Fetus #12


title: RNA library from E12.5 Female IVF Whole Fetus 4

description:
summary_count_E12.5_WholeFetus.txt
Female-IVF-1597-2

value: Female

value: Whole Fetus


title: slc7a5 IEC-KO, rep2

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: 10x Genomics

data_processing:
Raw fastq files were processed for gene counts with Illumina cellranger (version 2.1.1).
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: intestinal enriched crypts

growth_protocol: All mice were maintained in accordance with the NIH animal facility guidelines for laboratory animal research.

extract_protocol: 4 8-weeks-old mice were used for isolation of intestinal epithelial cells, the intestine was cut into 2-5 mm segments and incubated in phosphate-buffered saline (PBS) containing 20 mM EDTA for 30 min on ice on a rocker. Epithelial cells were released by vigorous shaking or pipetting and passed through a 70 um strainer to collect enriched crypts,  which were then washed with cold PBS containing 0.1% bovine serum albumin (BSA). The enriched intestinal crypts as isolated above were washed twice in PBS, centrifuged at 300 g for 3 min, and the epithelial cells were dissociated with TrypLE express (Invitrogen) for 1 min at 37 °C. The dissociated single cells were stained with an EpCAM (Thermo Fisher Scientific), CD45(Thermo Fisher Scientific), and propidium iodide (Thermo Fisher Scientific). The EpCAM+ CD45- live cells were sorted by flow cytometry and cell number was counted. The estimated ideal number of cells were used for scRNA-seq according to the manufacturer’s instructions (10x Genomics kit, chromium single cell 3’ reagent kits V2).

value: intestinal enriched crypts

value: slc7a5 IEC-KO


title: 3D_SER_1_1

value: bone marrow

value: mesenchymal stem cell


title: 3D_CIT_10_1


title: RNA library from E12.5 Female IVF Whole Fetus 3

description:
summary_count_E12.5_WholeFetus.txt
Female-IVF-1576-1


title: FL12-CDP_CMX-RNU-216

description: Fetal liver CDP RNAseq

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


title: 3D_CIT_1_3

value: hMSC-BM


title: slc7a5 IEC-KO, rep1

description: 10x Genomics


title: slc7a5 fl/fl, rep2

description: 10x Genomics

value: slc7a5 fl/fl


title: FL12-GMP_CMX-RNU-214

description: Fetal liver GMP RNAseq


title: RNA library from E12.5 Female IVF Whole Fetus 2

description:
summary_count_E12.5_WholeFetus.txt
Female-IVF-1544-3


title: slc7a5 fl/fl, rep1

description: 10x Genomics


title: RNA library from E12.5 Male Natural Placenta 5

description:
summary_count_E12.5_Placenta.txt
Male-Natural-C2I

source_name: E12.5 Placenta

value: Male

value: Natural

value: Placenta


title: 3D_CIT_1_2

value: male

value: adipogenic differentiation


title: 3D_CIT_1_1


title: SK-MEL5-wt-SOX10, ChIP

city: Charlestown

first: Mariko

middle: Sidi

last: Takahashi

state: Massachusetts

address: 149 13th Street, Charlestown Navy Yard

department: Cancer Center

institute: MGH

data_processing:
Reads were aligned to hg19 using bwa (Li and Durbin, 2009). Aligned reads were then filtered to exclude PCR duplicates.
Assembly: hg19
Supplementary files format and content: Aligned reads were extended to 200 bp to approximate fragment sizes. Density maps were generated by counting the number of fragments overlapping each position using igvtools, and normalized to 10 million reads.

source_name: skin

extract_protocol:
Chromatin from formaldehyde-fixed cells (2-5 x 10^6 cells per epitope) was fragmented to a size range of 200 - 700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with the indicated antibodies and Protein G-Dynabeads (Life Technologies). Immunoprecipitated DNA was extracted with AMP Pure beads(Beckman Coulter) after crosslink reversal, RNAse A and Proteinase K treatment.
ChIP DNA samples were used to generate Illumina sequencing libraries following standard protocols.

value: skin

value: melanoma


title: CB06-HSC_CMX-RNU-258

description: Cord Blood HSC RNAseq

value: Umbillical Cord Blood

value: Newborn #06

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

value: birth


title: 3D_ROSI3


title: FL12-MEP_CMX-RNU-213

description: Fetal liver MEP RNAseq

value: Fetal liver

value: Fetus #12


title: RNA library from E12.5 Female IVF Whole Fetus 5

description:
summary_count_E12.5_WholeFetus.txt
Female-IVF-42A

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

value: Female

value: IVF

value: Whole Fetus


title: SK-MEL5-wt-H3K27ac-201, ChIP


title: RNA library from E12.5 Male Natural Placenta 3

description:
summary_count_E12.5_Placenta.txt
Male-Natural-C2B


title: FL12-HSC_CMX-RNU-210

description: Fetal liver HSC RNAseq


title: RNA library from E12.5 Male Natural Placenta 2

description:
summary_count_E12.5_Placenta.txt
Male-Natural-C1HN


title: F2-AGVT c82_AGVT (MS462_012)

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: F2-AGVT (1390G3-526), expansion culture c82 BMP2(+) AG(+)VT(+)

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.  Data for male samples were mapped onto genome with chrY. Data for female samples were mapped onto genome without chrY. Data for female samples were also mapped onto genome with chrY to detect chrY genes as shown in extended figure 5a.
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.
For the estimation of allelic expression level, read data for F1-AGVT samples were mapped onto GRCh38.p12 genome with haplotype SNP locations masked, which was used for phasing EMseq data. Resulting BAM file were split by allele using SNPsplit with default setting and F1-AGVT allelic SNPs. Separated BAM files were processed with HTseq to calculate read count per gene. Read counts per gene were divided by total read count, which was estimated from the count without phasing, to estimate RPM values.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample
Library strategy: SC3-seq (Nakamura, 2015)

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).

tag: transgene

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

value: differentiated hPGCLC

value: WT

tag: time

value: culture day 82

value: Expansion culture with BMP signalling


title: 3D_ROSI1

value: bone marrow

value: mesenchymal stem cell

value: hMSC-BM

value: male

value: adipogenic differentiation


title: FL11-CLP2_CMX-RNU-209

description: Fetal liver CLP2 RNAseq

value: Fetus #11

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


title: F2-AGVT c68_AGVT (MS462_011)

description: F2-AGVT (1390G3-526), expansion culture c68 BMP2(+) AG(+)VT(+)

value: culture day 68


title: RNA library from E12.5 Male Natural Placenta 1

description:
summary_count_E12.5_Placenta.txt
Male-Natural-C1GO

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols.

value: Male

value: Natural

value: Placenta


title: FL11-CLP1_CMX-RNU-208

description: Fetal liver CLP1 RNAseq

value: Fetal liver

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


title: 3D_Control4


title: FL11-CDP_CMX-RNU-207

description: Fetal liver CDP RNAseq

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


title: RNA library from E12.5 Male IVF+TEBx Placenta 5

description:
summary_count_E12.5_Placenta.txt
Male-IVFTEBx-8A

value: IVF+TEBx


title: M2 c72 (MS462_010)

description: 1383D6, expansion culture c72 EpCAM(+) ITGA6(+)

value: differentiated hPGCLC

value: WT

value: culture day 72


title: RNA library from E12.5 Female IVF Whole Fetus 1

description:
summary_count_E12.5_WholeFetus.txt
Female-IVF-1520-1

value: Female

value: IVF

value: Whole Fetus


title: RNA library from E12.5 Male IVF+TEBx Placenta 4

description:
summary_count_E12.5_Placenta.txt
Male-IVFTEBx-3B


title: FL11-MoP_CMX-RNU-206

description: Fetal liver MoP RNAseq


title: FL11-GMP_CMX-RNU-205

description: Fetal liver GMP RNAseq


title: M1-AGVT c82_AGVT (MS462_006)

description: M1-AGVT (585B1-75), expansion culture c82 BMP2(+) AG(+)VT(+)

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

value: culture day 82

value: Expansion culture with BMP signalling


title: RNA library from E12.5 Male IVF+TEBx Placenta 3

description:
summary_count_E12.5_Placenta.txt
Male-IVFTEBx-1707-1


title: 3D_ROSI2

value: bone marrow

value: mesenchymal stem cell

value: hMSC-BM

value: male

value: adipogenic differentiation


title: 3D_Control1


title: M1-AGVT c62_AGVT (MS462_002)

description: M1-AGVT (585B1-75), expansion culture c62 BMP2(+) AG(+)VT(+)

value: culture day 62


title: 2D_ROSI3


title: RNA library from E12.5 Male IVF+TEBx Placenta 2

description:
summary_count_E12.5_Placenta.txt
Male-IVFTEBx-1604-1

value: Male

value: Placenta


title: FL11-MEP_CMX-RNU-204

description: Fetal liver MEP RNAseq

value: Fetal liver

value: Fetus #11


title: RNA library from E12.5 Male IVF+TEBx Placenta 1

description:
summary_count_E12.5_Placenta.txt
Male-IVFTEBx-13D

value: IVF+TEBx


title: FL11-CMP_CMX-RNU-203

description: Fetal liver CMP RNAseq

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


title: coHCC_NER_2 (RNA-seq)

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018). Fastq files were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Genes with 0 counts across all samples were filtered out.
Assembly: hg19
Supplementary files format and content: csv file of FPKM table

source_name: Breast cancer

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The total RNA was measured by Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol.
The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500

value: Breast cancer

tag: treatment 1

value: Coculture

tag: treatment 2

value: Neratinib


title: 2D_ROSI2

tag: tissue

tag: treatment


title: FPL14-HPC_CMX-RNU-130

description: Placenta HPC RNAseq

source_name: Placenta

value: Embryo #14

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


title: 2D_ROSI1

value: bone marrow


title: coHCC_DMSO_2 (RNA-seq)

value: DMSO


title: RNA library from E12.5 Male IVF Placenta 5

description:
summary_count_E12.5_Placenta.txt
Male-IVF-1780-2

value: IVF


title: 3D_Control3

value: mesenchymal stem cell

value: hMSC-BM

value: male


title: coHCC_NER_1 (RNA-seq)


title: M2 c76 (MS462_009)

description: 1383D6, expansion culture c76 EpCAM(+) ITGA6(+)

value: differentiated hPGCLC

tag: genotype

value: WT

value: culture day 76

value: Expansion culture with BMP signalling


title: RNA library from E12.5 Male IVF Placenta 4

description:
summary_count_E12.5_Placenta.txt
Male-IVF-1598-1

value: Male

value: Placenta


title: 2D_Control3

value: adipogenic differentiation


title: FPL14-HSPC_CMX-RNU-129

description: Placenta HSPC RNAseq

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


title: RNA library from E12.5 Male IVF Placenta 3

description:
summary_count_E12.5_Placenta.txt
Male-IVF-13A


title: FL12-CMP_CMX-RNU-212

description: Fetal liver CMP RNAseq

value: Fetal liver

value: Fetus #12

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


title: 3D_Control2

value: bone marrow


title: 2D_Control2


title: coBM3_NER_2 (RNA-seq)

source_name: Brain

value: Brain

value: Coculture

value: Neratinib


title: RNA library from E12.5 Male IVF Placenta 2

description:
summary_count_E12.5_Placenta.txt
Male-IVF-12A

value: IVF


title: 2D_Control1

value: mesenchymal stem cell

value: hMSC-BM

value: male


title: AGM14-HPC_CMX-RNU-127

description: AGM HPC RNAseq

source_name: Aorta-gonad-mesonephros

value: Aorta-gonad-mesonephros

value: Embryo #14

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


title: RNA library from E12.5 Male IVF Placenta 1

description:
summary_count_E12.5_Placenta.txt
Male-IVF-11A

value: Male

value: Placenta


title: coBM3_NER_1 (RNA-seq)


title: AGM14-HSPC_CMX-RNU-126

description: AGM HSPC RNAseq

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


title: ICM_6days_GEO2459

data_processing:
Micro-C reads were aligned to the reference genome GRCh38 using bwa mem (v0.7.17) with “-SP5M”
Invalid data, including PCR duplicates and read pairs mapping to the same restriction fragment, were removed using MarkDuplicates function in Picard tools (v2.20.7)
Micro-C contact matrices were produced using Dovetail Genomics pipeline (https://micro-c.readthedocs.io/en/latest/fastq_to_bam.html
Assembly: GRCh38
Library strategy: Micro-C

extract_protocol:
Micro-C was performed on 0.5-1 million cells from each sample using the Micro-C v1.0 kit in collaboration with Dovetail Genomics according to the manufacturer’s instructions.
Dovetail Genomics Micro-C v1.0 kit

value: human lung fibroblast

tag: assay

value: Micro-C


title: AGM14-endo_CMX-RNU-125

description: AGM endothelium RNAseq

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


title: coBM3_DMSO_2 (RNA-seq)

value: DMSO


title: RNA library from E12.5 Female Natural Placenta 4

description:
summary_count_E12.5_Placenta.txt
Female-Natural-C4JO

value: Female

value: Natural


title: RNA library from E12.5 Female Natural Placenta 3

description:
summary_count_E12.5_Placenta.txt
Female-Natural-C4H


title: YS13-HPC_CMX-RNU-124

description: Yolk Sac HPC RNAseq

source_name: Yolk Sac

value: Yolk Sac

value: Embryo #13


title: young_GEO2457


title: 10x_042_JiCh02_TCR

description: 10X Genomics_5v2_0

data_processing:
blc2fastq (v2.20.0.422) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
vdj (Cell Ranger 3.1.0) was used to generate the clonotype information per cell
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Assembly: GRCh38-alts-ensembl-2.0.0 from Cell Ranger
Assembly: GRCh37 (hg19-3.0.0 from Cell Ranger)
Supplementary files format and content: sc_human_tcells_annotation.txt.gz meta data and annotation of 15,411 cells
Supplementary files format and content: sc_human_tcells_feature_barcodes.csv.gz barcodes used for processing of antibody capture counts
Supplementary files format and content: sc_human_tcells_umi.txt.gz UMI count data matrix for 15,411 cells

source_name: Colon

extract_protocol:
Colonic T cells were sorted into 1.5 mL tubes containing 500 ul of 1:1 PBS to FBS with 1:100 Recombinant RNAse Inhibitor (Takara Bio 2313B). Following sorting, tubes were filled up to 1.4 mL with PBS and spun at 600xg for 10 minutes. Pellets were resuspended in 35 ul PBS supplemented with 0.04% w/v BSA (Invitrogen) and cells were processed according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit. TCR (VDJ) sequences enriched according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit. HTO (CITE) cDNA was separated from PolyA cDNA through size selection with AMPure XP Purification reagent (Beckman Coulter, A63882)
All Libraries were prepared according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index) with Feature Barcoding kit.
scRNA-Seq, V(D)J library preparation and Cell Surface Protein library preparation

treatment_protocol: Colons were dissociated into single cell, and stained with dead cell discriminating dye, fluorophore-tagged FACS antibodies, anti-CD4 and anti-CD8a hashtag anitbodies, and unique anti-human hashtag antibodies against beta2 microglobulin for donor deconvolution. T cells from each donor were FACS-sorted for scRNA-seq using the 10X genomics platform. Experiments were performed in 6 batches.

value: Colon

value: CD45+CD3+ T cells


title: coHCC_DMSO_1 (RNA-seq)

value: Breast cancer

value: Coculture


title: monoHCC_NER_2 (RNA-seq)

value: Monoculture

value: Neratinib


title: FPL14-endo_CMX-RNU-128

description: Placenta endothelium RNAseq

value: Embryo #14


title: coBM3_DMSO_1 (RNA-seq)

value: Brain


title: 10x_042_JiCh02_Gex

description: 10X Genomics_5v2_0


title: RNA library from E12.5 Female Natural Placenta 1

description:
summary_count_E12.5_Placenta.txt
Female-Natural-C1GN

value: Placenta


title: RNA library from E12.5 Female Natural Placenta 2

description:
summary_count_E12.5_Placenta.txt
Female-Natural-C3J


title: YS13-HSPC_CMX-RNU-123

description: Yolk Sac HSPC RNAseq

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


title: 10x_042_JiCh02_CITE

description: 10X Genomics_5v2_0


title: RNA library from E12.5 Female IVF+TEBx Placenta 3

description:
summary_count_E12.5_Placenta.txt
Female-IVFTEBx-1574-1

value: IVF+TEBx


title: YS13-endo_CMX-RNU-122

description: Yolk Sac endothelium RNAseq

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


title: monoHCC_NER_1 (RNA-seq)


title: FPL13-HPC_CMX-RNU-118

description: Placenta HPC RNAseq

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


title: monoHCC_DMSO_2 (RNA-seq)

value: DMSO


title: 10x_035_JiCh_TCR

description: 10X Genomics_5v2_0


title: monoHCC_DMSO_1 (RNA-seq)


title: FPL13-HSPC_CMX-RNU-117

description: Placenta HSPC RNAseq


title: 10x_035_JiCh_Gex

description: 10X Genomics_5v2_0


title: RNA library from E12.5 Female IVF+TEBx Placenta 1

description:
summary_count_E12.5_Placenta.txt
Female-IVFTEBx-10A

value: Female


title: RNA library from E12.5 Female IVF+TEBx Placenta 2

description:
summary_count_E12.5_Placenta.txt
Female-IVFTEBx-11B


title: FPL13-endo_CMX-RNU-116

description: Placenta endothelium RNAseq


title: RNA library from E12.5 Female IVF Placenta 5

description:
summary_count_E12.5_Placenta.txt
Female-IVF-B16A

value: IVF


title: monoBM3_NER_2 (RNA-seq)


title: AGM13-HPC_CMX-RNU-115

description: AGM HPC RNAseq

value: Aorta-gonad-mesonephros

value: Embryo #13


title: monoBM3_DMSO_2 (RNA-seq)


title: 017_10x_048_JiCh03_B_CITE

description: 10X Genomics_5v2_0

value: Colon

value: CD45+CD3+ T cells


title: 10x_035_JiCh_CITE

description: 10X Genomics_5v2_0


title: monoBM3_NER_1 (RNA-seq)


title: RNA library from E12.5 Female IVF Placenta 3

description:
summary_count_E12.5_Placenta.txt
Female-IVF-1780-1


title: monoBM3_DMSO_1 (RNA-seq)


title: AGM13-HSPC_CMX-RNU-114

description: AGM HSPC RNAseq


title: 453BM3_NER_2 (RNA-seq)

value: Breast cancer

value: Coculture


title: 016_10x_048_JiCh03_N_CITE

description: 10X Genomics_5v2_0


title: RNA library from E12.5 Female IVF Placenta 4

description:
summary_count_E12.5_Placenta.txt
Female-IVF-7A


title: YS10-HPC_CMX-RNU-109

description: Yolk Sac HPC RNAseq

value: Yolk Sac

value: Embryo #10


title: 453BM3_NER_1 (RNA-seq)

value: Neratinib


title: AGM13-endo_CMX-RNU-113

description: AGM endothelium RNAseq


title: 015_10x_048_JiCh03_C_CITE

description: 10X Genomics_5v2_0


title: 013_10x_048_JiCh03_B_TCR

description: 10X Genomics_5v2_0


title: RNA library from E12.5 Female IVF Placenta 1

description:
summary_count_E12.5_Placenta.txt
Female-IVF-1520-1

value: Placenta


title: 014_10x_048_JiCh03_A_CITE

description: 10X Genomics_5v2_0


title: YS10-endo_CMX-RNU-107

description: Yolk Sac endothelium RNAseq


title: 453BM3_DMSO_1 (RNA-seq)


title: B5

city: Oxford

first: Sandy

last: Chu

address: Wellcome Trust Centre for Human Genetics, Roosevelt Drive

country: United Kingdom

institute: University of Oxford

data_processing:
Mapping with Hisat2
Sorting with samtools
Assembly: GRCm38

source_name: 16 weeks old cmGch1 KO hearts

extract_protocol: total RNA was harvested using Rneasy mini kit (Qiagen). 100ng of total RNA was used for the construction of sequencing libraries.

value: cmGch1 KO

value: 16 weeks old


title: YS12-HPC_CMX-RNU-103

description: Yolk Sac HPC RNAseq

value: Embryo #12


title: YS10-HSPC_CMX-RNU-108

description: Yolk Sac HSPC RNAseq

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


title: 453_NER_2 (RNA-seq)

first: Kornelia

last: Polyak

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

value: Monoculture


title: B4


title: 011_10x_048_JiCh03_C_TCR

description: 10X Genomics_5v2_0


title: YS12-HSPC_CMX-RNU-102

description: Yolk Sac HSPC RNAseq


title: 453_NER_1 (RNA-seq)


title: 012_10x_048_JiCh03_N_TCR

description: 10X Genomics_5v2_0


title: B6


title: 453BM3_DMSO_2 (RNA-seq)

value: DMSO


title: 009_10x_048_JiCh03_B_Gex

description: 10X Genomics_5v2_0


title: 453_DMSO_1 (RNA-seq)


title: 008_10x_048_JiCh03_N_Gex

description: 10X Genomics_5v2_0


title: 010_10x_048_JiCh03_A_TCR

description: 10X Genomics_5v2_0


title: B2


title: B3


title: RNA library from E12.5 Female IVF Placenta 2

description:
summary_count_E12.5_Placenta.txt
Female-IVF-1597-1

value: Female

value: IVF


title: 453_DMSO_2 (RNA-seq)


title: B1


title: A6

source_name: 16 weeks old WT heart

value: WT


title: FPL12-endo_CMX-RNU-095

description: Placenta endothelium RNAseq

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


title: FPL12-HPC_CMX-RNU-097

description: Placenta HPC RNAseq

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


title: 453BM3_DMSO_mC_723 (RNA-seq)

description:
Date of collection: 723
453_Cuff_Gene_Counts2.csv

value: Breast cancer


title: A5


title: 007_10x_048_JiCh03_C_Gex

description: 10X Genomics_5v2_0

value: Colon

value: CD45+CD3+ T cells


title: 453BM3_DMSO_mC_729 (RNA-seq)

description:
Date of collection: 729
453_Cuff_Gene_Counts2.csv

value: Coculture


title: 453BM3_DMSO_DP_729 (RNA-seq)


title: FPL12-HSPC_CMX-RNU-096

description: Placenta HSPC RNAseq


title: AGM12-HPC_CMX-RNU-094

description: AGM HPC RNAseq

value: Aorta-gonad-mesonephros


title: 453BM3_DMSO_DP_723 (RNA-seq)


title: P14

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

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: White

value: PDAC

value: Plasma separated from blood

tag: fraction

value: cfDNA


title: P16

value: AA

tag: gender


title: YS12-endo_CMX-RNU-101

description: Yolk Sac endothelium RNAseq

value: Yolk Sac

value: Embryo #12


title: 453_NER_mC_729 (RNA-seq)

city: Boston

value: Monoculture

value: Neratinib


title: A4

value: WT

value: 16 weeks old


title: A1


title: AGM12-HSPC_CMX-RNU-093

description: AGM HSPC RNAseq

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


title: 453_NER_mC_723 (RNA-seq)

value: Breast cancer


title: AGM12-endo_CMX-RNU-092

description: AGM endothelium RNAseq

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


title: P15

value: Female

tag: group


title: 006_10x_048_JiCh03_A_Gex

city: San Diego

first: Pandurangan

last: Vijayanand

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: 10X Genomics_5v2_0

value: Colon

value: CD45+CD3+ T cells


title: A2


title: CB05-CLP1_CMX-RNU-090

description: Cord Blood CLP1 RNAseq

value: Umbillical Cord Blood

value: Newborn #05

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

tag: age

value: birth


title: P12

value: White

value: Male

value: PDAC

value: Plasma separated from blood

value: cfDNA


title: CB05-MoP_CMX-RNU-088

description: Cord Blood MoP RNAseq

tag: donor id


title: 453_DMSO_mC_729 (RNA-seq)

value: Monoculture

value: DMSO


title: P13


title: gpSSCs-bulkATACseq-cko-rep2

city: Shanghai

first: Dandan

last: Cao

address: 1239 Siping Road, Yangpu District

institute: Tongji University

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.

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

value: PrxCre; Z24fl/fl


title: CB05-GMP_CMX-RNU-087

description: Cord Blood GMP RNAseq


title: A3

value: WT

value: 16 weeks old


title: BM3_NER_GFP_729 (RNA-seq)

value: Brain

tag: cell line

value: Neratinib


title: CB05-MEP_CMX-RNU-086

description: Cord Blood MEP RNAseq

value: Umbillical Cord Blood

tag: cell type


title: gpSSCs-bulkATACseq-cko-rep3


title: CB05-CMP_CMX-RNU-085

description: Cord Blood CMP RNAseq

value: Newborn #05

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


title: gpSSCs-bulkATACseq-cko-rep1


title: gpSSCs-bulkATACseq-ctrl-rep3


title: BM3_NER_GFP_723 (RNA-seq)


title: H33

value: HEA


title: gpSSCs-bulkATACseq-ctrl-rep2


title: H34

value: AA

value: Female


title: BM3_DMSO_GFP_729 (RNA-seq)


title: gpSSCs-bulkATACseq-ctrl-rep1


title: BM3_DMSO_GFP_723 (RNA-seq)


title: ABM02-CLP2_CMX-RNU-085a

description: Adult Bone Marrow CLP2 RNAseq

source_name: Adult Bone Marrow

value: Adult Bone Marrow

value: Adult #02

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


title: 453_DMSO_mC_723 (RNA-seq)

value: Breast cancer

value: Monoculture


title: 453BM3_NER_mC_729 (RNA-seq)

value: Coculture


title: ABM02-LMPP_CMX-RNU-083a

description: Adult Bone Marrow LMPP RNAseq

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


title: P11

value: Male

value: PDAC

value: Plasma separated from blood

value: cfDNA


title: H31

value: White


title: CB05-HSC_CMX-RNU-082

description: Cort Blood HSC RNAseq

value: Umbillical Cord Blood

value: Newborn #05

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

value: birth


title: ABM02-CLP1_CMX-RNU-084a

description: Adult Bone Marrow CLP1 RNAseq

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


title: pSSCs-bulkATACseq-cko-rep3

source_name: periosteum

value: Prx-Cre

value: PrxCre; Z24fl/fl


title: pSSCs-bulkATACseq-cko-rep2


title: 453BM3_NER_mC_723 (RNA-seq)

value: Brain

value: Neratinib


title: ABM02-CDP_CMX-RNU-082a

description: Adult Bone Marrow CDP RNAseq

value: Adult Bone Marrow

value: Adult #02

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


title: H32

value: AA

value: Female

value: HEA


title: H30

value: Male

value: Plasma separated from blood

value: cfDNA


title: P09

value: PDAC


title: 453BM3_NER_DP_729 (RNA-seq)

value: Coculture


title: P10

value: White


title: CB04-CLP2_CMX-RNU-081

description: Cord Blood CLP2 RNAseq

source_name: Umbillical Cord Blood

value: Umbillical Cord Blood

value: Newborn #04

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

value: birth


title: pSSCs-bulkATACseq-cko-rep1

value: Prx-Cre

value: PrxCre; Z24fl/fl


title: 453BM3_NER_DP_723 (RNA-seq)

value: Brain

value: Neratinib


title: H29

value: AA


title: pSSCs-bulkATACseq-ctrl-rep3


title: s5_HCC1954BM3_mC+_DMSO_A_MAG9 (ATAC-seq)

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

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.

value: Breast cancer

value: DMSO


title: H28

value: Male

value: HEA


title: pSSCs-bulkATACseq-ctrl-rep2


title: CB04-CLP1_CMX-RNU-080

description: Cord Blood CLP1 RNAseq

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


title: H27

value: Plasma separated from blood

value: cfDNA


title: pSSCs-bulkATACseq-ctrl-rep1


title: s4_BM3_GFP+_NER_B_MAG8 (ATAC-seq)

value: Monoculture


title: ABM02-GMP_CMX-RNU-080a

description: Adult Bone Marrow GMP RNAseq

value: Adult Bone Marrow

value: Adult #02


title: H26

value: Female


title: gpSSCs-bulkRNAseq-cko-rep3


title: s4_BM3_GFP+_NER_A_MAG7 (ATAC-seq)


title: H25


title: SKOV3 + therapy-induced secretome, repeat 1

first: Ksenia

last: Anufrieva

address: 60 Fenwood Rd

institute: Brigham and Women's Hospital

description: incubation with therapy-unduced secretome from SKOV3 cells

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 adenocarcinoma

extract_protocol:
Total RNA was isolated from SKOV3 cells and fibroblasts 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 all libraries (12 pM) 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ovarian adenocarcinoma


title: s3_BM3_GFP+_DMSO_B_MAG6 (ATAC-seq)


title: H24


title: s3_BM3_GFP+_DMSO_A_MAG5 (ATAC-seq)


title: ABM02-CMP_CMX-RNU-078a

description: Adult Bone Marrow CMP RNAseq

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


title: gpSSCs-bulkRNAseq-cko-rep2

value: Prx-Cre

value: PrxCre; Z24fl/fl


title: gpSSCs-bulkRNAseq-cko-rep1


title: CB04-MoP_CMX-RNU-078

description: Cord Blood MoP RNAseq

value: Umbillical Cord Blood

value: Newborn #04

value: birth


title: s2_HCC1954_mC+_NER_B_MAG4 (ATAC-seq)

value: Breast cancer

value: Neratinib


title: H23

value: AA

value: HEA


title: CB04-GMP_CMX-RNU-077

description: Cord Blood GMP RNAseq


title: ABM02-MoP_CMX-RNU-081a

description: Adult Bone Marrow MoP RNAseq


title: s2_HCC1954_mC+_NER_A_MAG3 (ATAC-seq)


title: gpSSCs-bulkRNAseq-ctrl-rep3


title: gpSSCs-bulkRNAseq-ctrl-rep2


title: CB04-MEP_CMX-RNU-076

description: Cord Blood MEP RNAseq


title: H21

value: White

value: Plasma separated from blood


title: ABM02-HSC_CMX-RNU-076a

description: Adult Bone Marrow HSC RNAseq

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