title: TTchemSeq 15min recovery after h2o2 replicate 3 exp1

city: København

first: Lea

middle: Haarup

last: Gregersen

address: Blegdamsvej 3B,

department: ICMM

country: Denmark

institute: University of Copenhagen

description: Library name: TT1_H2O2_15min_recovery_r3

data_processing:
Raw fastq files for Read 1 were labelled with appropriate UMI reads using UMItools
adapter trimming with cutadapt (v4.5) within trim_galore (v0.6.10) and read length filtering > 19nt
samples were mapped with STAR75 (v2.7.11b) against a merged human-yeast genome assemblies (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Genome alignments BAM files were filtered for multimapped reads with samtools (v1.21) view function (-q 10)
UMI duplicates were then removed with UMItools dedup function. A yeast gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate yeast size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific and spike-in normalised BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/ yeast size-factor) with bin size of 25 nt (-bs 25)
Assembly: (Homo sapiens GRCh38 and Saccharomyces cerevisiae sacCer, Ensembl release 108)
Supplementary files format and content: bigwig forward and reverse strands

source_name: HEK293 Flp-in T-Rex

growth_protocol: Flp-InTM T-REx HEK293 cells (HEK293, R78007, ThermoFisher Scientific, human embryonic kidney epithelial, female origin) were cultured at 37C with 5% CO2 in high glucose DMEM (Biowest, Cat#L0104) supplemented with 10% v/v FBS (Gibco, Cat#10270106), 100 U/mL penicillin, 100 μg/mL streptomycin (Gibco, 10378016) 2 mM L-glutamine.

extract_protocol:
80% confluent cells RNA were labelled in vivo for 15 min with 4sU by adding it directly to the tissue culture media to a final concentration of 1 mM. Per samples 80-100 μg of total RNA resuspended in 100 μL RNAse-free H2O was complemented with 1 % (relative to total RNA concentration) of S. cerevisiae 4tU-labelled RNA spike-in. Total RNA was fragmented by adding 20 μL of freshly prepared 1 M NaOH per sample, thoroughly mixed and incubated for 40 min on ice to < 400 nt fragments. Resuspended and purified 4sU labelled RNA in RNAse-free water was biotinylated in 10 mM Tris-HCl pH = 7.4; 1 mM EDTA complemented with 0.5 mg/ μL MTSEA biotin-XX linker (Biotum, Cat# BT90066) for 30 min in the dark at room temperature. Biotinylated RNA was immediately purified by ROTI®Aqua-P/C/I extraction and isopropanol precipitation and resuspended in 50 μL RNAse-free water. and isolated with μMACS Streptavidin Kit (Miltenyi, Cat#130-074-101). A total of 100uL μMACS Streptavidin MicroBeads were added to denatured 4sU total RNA and incubated for 15 min at room temperature with agitation. Beads bound to 4sU biotinylated RNA were applied to magnetic μColumns and transferred to the magnetic field of the μMACS magnetic separator (Miltenyi).
Approx. 30 ng of purified 4sU biotinylated RNA was used to prepare libraries with NEBNext® Ultra™ II RNA library prep kit (NEB, Cat#E7760) according to manufacturer’s protocol (protocol 5 for fragmented RNA) with ligation of two barcodes of 8 nt and 11 nt UMIs (NEB, Cat#E7416).

treatment_protocol: Inhibitors treatments were carried out by direct addition to the cell culture media with the following concentration 100 μM DRB (Sigma, D1916) or/and 10 μM Olaparib (PARPi, MedchemExpress, Cat#HY-10162) or/and 10 μM TH5487 (OGG1i, MedchemExpress, Cat#HY-125276). Oxidative stress induction treatments were carried out for 15 min (or 30 min for EU-labelling) with direct addition of freshly prepare 1000x concentrate to cell culture media, fresh H2O2 (maximum 3 month old kept at 4CC) to final concentration of 1 mM H2O2 (Sigma, H1009) or freshly resuspended Menadione sodium bisulfite (MND, Sigma, M5750) in water to final concentration of 0.25 mM.

value: HEK293 Flp-in T-Rex


title: FJD-CAM-Spatial

status: Public on Jun 11 2026

type: SRA

city: London

first: Theodoros

last: Xenakis

address: 20 Guilford Street

country: United Kingdom

institute: UCL

description:
Library name: FJD-sp-CAM-gex
Control

library_source: transcriptomic

data_processing:
Spatial transcriptomics: Fast files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger multit".
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Homo sapiens

source_name: Chorioamniotic membranes

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell and nuclei transcriptomics: samples were freshly dissociated using custom protocol. Nuclei were isolated using 10X Genomics nuclei isolation kit according to manufacturers recommended protocol.
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell an nuclei transcriptomics: single cell or nuclei suspensions were prepared and processed using the Chromium Single Cell 5’ Reagent Kits v3.1

tag: tissue

value: Chorioamniotic membranes


title: FAM-PVBP-Spatial

description:
Library name: FAM-sp-AB-gex
Preeclamptic

source_name: Placenta

value: Placenta


title: HV_4_PBMC

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

country: USA

institute: NIAMS/NIH

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 or v6.0.2
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: PBMC

extract_protocol:
Skin biopsy from Degos disease patients and healthy volunteers were washed with PBS and digested enzymatically using whole skin dissociation kit (Miltenyi Biotec).  Following mechanical dissociation and filteration, cells were resuspended in 500 μL of complete RPMI-1640 with 10% FBS before sorting. Skin live cells were enriched by fluorescence-activated cell sorting (FACS) using Sytox green. PBMCs from blood were isolated according to desity centrifugation method. PBMCs and CSF samples were subjected to ACK lysis treatment to remove RBCs. Finally, single cell suspensions prepared from skin, PBMCs and CSF were counted and and cell concentration was adjusted in the range of 700-1200 cells/ul with the viability of > 70% before being used for single-cell RNA-sequencing.
Library construction was performed in accordance with 10X Genomics protocol (10X Chromium 5' v2 or 5'-HT kit).

value: PBMC


title: HV_3_PBMC

description: 10x Genomics


title: FAM-CAM-Spatial

description:
Library name: FAM-sp-CAM-gex
Preeclamptic


title: HV_2_PBMC

description: 10x Genomics


title: FEP-Myometrium-Spatial

description:
Library name: FEP-sp-CD-gex
Preeclamptic

source_name: Myometrium

value: Myometrium


title: FEP-PVBP-Spatial

description:
Library name: FEP-sp-AB-gex
Preeclamptic


title: HV_1_PBMC

description: 10x Genomics


title: HV_7_Skin

description: 10x Genomics

source_name: Skin

value: Skin


title: HV_6_Skin

description: 10x Genomics


title: FVT-Myometrium-Spatial

description:
Library name: FVT-sp-CD-gex
Control


title: FVT-PVBP-Spatial

description:
Library name: FVT-sp-AB-gex
Control


title: HV_4_Skin

description: 10x Genomics


title: HV_3_Skin

description: 10x Genomics


title: FFM-Myometrium-Spatial

description:
Library name: FFM-sp-CD-gex
Preeclamptic


title: FGS-PVBP-Spatial

description:
Library name: FGS-sp-AB-gex
Preeclamptic


title: Hif1a-WT6

city: Beijing

first: Ming

last: Hao

address: Shuangqing Rd.

country: China

institute: Tsinghua Univ

description: Library name: cKO8

data_processing:
NGS data were mapped to mouse genome by Hisat2, and transcripts were quantified by Salmon.
Assembly: mm10
Supplementary files format and content: .sf

organism: Mus musculus

source_name: ovarian follicle

extract_protocol:
LCM-RNA sequencing was performed according to the previously described Geo-seq protocol. Briefly, granulosa cells (GCs) from follicles of interest on the PEN membrane slides were separated using laser microdissection (Leica LMD7000) and collected into EP tubes. Samples were lysed in 4M GuSCN and precipitated in glycogen-containing 70% ethanol.
Extracted RNA were reverse transcripted , followed by amplification using  Smart2-seq protocol. cDNA libraries that passed quality control were used for Tn5-based NGS library construction.

value: ovarian follicle

tag: cell type

value: Granulosa cell

tag: genotype

value: Hif1a wild type


title: FFM-CAM-Spatial

description:
Library name: FFM-sp-CAM-gex
Preeclamptic


title: Hif1a-WT5

description: Library name: cKO7


title: FGS-CAM-Spatial

description:
Library name: FGS-sp-CAM-gex
Preeclamptic


title: Hif1a-WT4

description: Library name: cKO6


title: FVB-PVBP-Spatial

description:
Library name: FVB-sp-AB-gex
Control


title: FSH-Myometrium-Spatial

description:
Library name: FSH-sp-CD-gex
Preeclamptic


title: Hif1a-WT2

description: Library name: cKO4


title: Hif1a-WT1

description: Library name: cKO3


title: Hif1a-cKO1

description: Library name: cKO1

value: Hif1a knockdown


title: FLR-Myometrium-Spatial

description:
Library name: FLR-sp-CD-gex-2
Control


title: WT_Ctrl_3

status: Public on Jun 12 2026

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: Library name: WC3

library_source: genomic

data_processing:
Base-calling was performed using NextSeq Control Software 2.2.0.4 (RTA 2.4.11) and the BCL files were demultiplexed into fastq files using bcl2fast2 v2.20.0.422.
Bulk ATAC-seq data were preprocessed using the ATAC-seq Pipeline (v1.2.0) on Via Foundry (https://www.gcp.viafoundry.com/). Specifically, read quality filtering (phred >= 33) and adaptors trimming were performed using Trimmomatic v0.39, trimmed reads were then aligned to the mm10 mouse genome using Bowtie2 v2.3.5, and duplicated reads were marked and removed by Picard v2.18.27. BAM files were sorted and indexed using Samtools v1.3.
Data were further cleaned up by filtering out the reads that meet any of the following criteria using deepTools v3.5.6: (1) mapped to chrM (mitochondria), chr*_random, chrUn, and chrY (because cells are derived from female mice); (2) mapped to blacklist regions (https://github.com/Boyle-Lab/Blacklist); (3) with low mapping quality (MAPQ < 30); (4) fragment length < 50bp. Peak calling was then performed for all samples together using Genrich v0.6.1 (joint ATAC-seq mode). Peaks were then quantified using featureCounts v2.1.1 from the Subread package.
Assembly: mm10
Supplementary files format and content: Tab-separated values (.tsv) files include read counts for every peak (rows)  in every sample (columns)
Supplementary files format and content: BigWig (.bw) files contain the normalized, genome-wide chromatin accessibility signal (read depth) for each sample.

molecule: genomic DNA

source_name: in vitro; originally from spleen and dLN

extract_protocol:
6,000 cells were sorted by FACS into PBS buffer supplemented with 0.5% BSA.
For library preparation, cells were lysed and tagmented with 9.5uL lysis and transposition mix buffer (10mM TAPS-NaOH pH 8.5, 5mM MgCl2, 10% DMF, 0.02% digitonin) and 0.5uL Tn5 transposase (Diagenode) at 37 °C for 30 min. Tagmentation was terminated by the direct addition of 10 µL stop buffer (100 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.4% SDS, 40 µg/mL proteinase K), followed by incubation at 55 °C overnight. Subsequently, 5 µL of 25% Tween-20 was added directly to the reaction. Libraries were amplified by PCR for 16 cycles under the following conditions: 72 °C for 5 min; 98 °C for 3 min; followed by cycling at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min; with a final extension at 72 °C for 5 min. PCR products were purified using a two-step SPRI beads cleanup (1.5× followed by 0.6×). Library concentration was measured using the Qubit dsDNA HS Assay Kit (Invitrogen), and fragment size distribution was assessed using an Agilent FA5400 Fragment Analyzer. Final libraries were sequenced on an Illumina NextSeq™ 1000/2000 platform using a P2 XLEAP-SBS™ Reagent Kit (100 cycles; Cat. No. 20100987).

value: T cell

tag: treatment

value: control


title: FLR-CAM-Spatial

description:
Library name: FLR-sp-CAM-gex
Control


title: L-GCK-KO 3

city: Philadelphia

first: Patrick

last: Seale

state: PA

address: 3400 Civic Center Blvd.

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description:
Library name: Sample 6
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFGK3

data_processing:
The raw fastq files were first analyzed with FastQC (version 0.11.9) for quality control checks. The paired-end reads were mapped to the GRCm39.
Ensembl reference transcriptome for Mus musculus using kallisto (version 0.44.0).
The abundance.tsv files generated by kallisto were read into R (version 4.3.0) at the gene level using the tximport package (version 1.28.0).
Limma (version 3.56.2) was used for differential gene expression analysis.
Assembly: GRCm39
Supplementary files format and content: Raw counts as a comma-separated value file
Supplementary files format and content: Log2 counts per million expression with a trimmed-mean of M-values normalization as a comma-separated value file

source_name: Liver

extract_protocol:
RNA was purified from liver samples using the Qiagen RNeasy Mini Kit. 5 µg of RNA for each sample were given to Novogene for processing.
Library construction was performed by Novogene

value: Liver

value: Liver GCK knockout

value: High Carbohydrate Diet:overnight fasted & 6 hour refed


title: L-GCK-KO 2

description:
Library name: Sample 5
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFGK2


title: HV_5_Skin

description: 10x Genomics


title: FND-Myometrium-Spatial

description:
Library name: FND-sp-CD-gex
Preeclamptic


title: FFM-PVBP-Spatial

description:
Library name: FFM-sp-AB-gex
Preeclamptic


title: FGS-Myometrium-Spatial

description:
Library name: FGS-sp-CD-gex
Preeclamptic


title: HV_2_Skin

description: 10x Genomics


title: FND-CAM-Spatial

description:
Library name: FND-sp-CAM-gex
Preeclamptic


title: L-GCK-KO 1

description:
Library name: Sample 4
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFGK1


title: Control 3

description:
Library name: Sample 3
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFCon3

value: Control


title: FLJ-PVBP-Spatial-2

description:
Library name: FLJ-sp-AB-gex-2
Control


title: Control 2

description:
Library name: Sample 2
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFCon2


title: FLJ-PVBP-Spatial

description:
Library name: FLJ-sp-AB-gex
Control


title: Control 1

description:
Library name: Sample 1
Column name in AllSamples_RawCounts_GENENAME and AllSamples_Log2CP_TMM_GENENAME: RFCon1


title: FVB-CAM-Spatial

description:
Library name: FVB-sp-CAM-gex
Control


title: LJ-Myometrium-Spatial

description:
Library name: FLJ-sp-CD-gex
Control


title: CCT3-input

city: Nanjing

first: lingxiu

last: Tong

state: Jiangsu

address: Nanjing Medical University 101 Longmian Avenue, Jiangning District, Nanjing 211166, Jiangsu Province, P.R. China

institute: Nanjing Medical University

description:
Library name: sample4
CCT3_rep1_merge_peak_anno.txt

data_processing:
Illumina bcl2fastq v2.20 software was used for base calling and sample demultiplexing
Assembly: mm10
Supplementary files format and content: merge_peak_anno files containing aligned reads for all PABPC1 IP, CCT3 IP and Input samples (2 biological replicates each)

extract_protocol:
Cell pellets were resuspended in eCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with 1 mM PMSF, protease inhibitor cocktail and RNase inhibitor (Superase-in). Lysates were sonicated on ice and treated with RNase I to fragment RNA. Immunoprecipitation was performed using anti-PABPC1 antibody and anti-CCT3 antibody conjugated to protein G magnetic beads overnight at 4°C
eCLIP libraries were constructed following the standard enhanced crosslinking immunoprecipitation protocol. Briefly, RNA fragments bound to beads were dephosphorylated, ligated to 3' RNA adapters, reverse transcribed with barcoded primers, and PCR amplified. Input control libraries were prepared in parallel from the same cell lysates without immunoprecipitation

tag: cell line

value: mouse spermatocyte cells


title: Hif1a-cKO2

description: Library name: cKO2


title: LJ-CAM-Spatial

description:
Library name: FLJ-sp-CAM-gex
Control


title: CCT3

description:
Library name: sample3
CCT3_rep1_merge_peak_anno.txt


title: PABPC1-input

description:
Library name: sample2
PABPC1_rep1_merge_peak_anno.tsv


title: FVS-PVBP-Spatial

description:
Library name: FVS-sp-AB-gex
Preeclamptic


title: FVS-PVBP-Spatial-2

description:
Library name: FVS-sp-AB-gex-2
Preeclamptic


title: PABPC1

description:
Library name: sample1
PABPC1_rep1_merge_peak_anno.tsv


title: FVS-Myometrium-Spatial

description:
Library name: FVS-sp-CD-gex
Preeclamptic


title: Duodenum-Khk KO-4

city: Louisville

first: MING

last: SONG

state: KY

address: 505 S. Hancock St.

institute: University of Louisville

description:
Library name: CKRN230038674-1A
KO_DuovsWT_Duo_deg_all.xls

data_processing:
Hisat2 v2.0.5
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome [Mus Musculus(GRCm38/mm10)]  using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: Excel file include counts and FPKM values for each sample

source_name: Duodenum

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini Kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Duodenum


title: Duodenum-Khk KO-3

description:
Library name: CKRN230038673-1A
KO_DuovsWT_Duo_deg_all.xls


title: Duodenum-Khk KO-2

description:
Library name: CKRN230038672-1A
KO_DuovsWT_Duo_deg_all.xls


title: FRK-PVBP-Spatial-2

description:
Library name: FRK-sp-B-gex
Control


title: Duodenum-Khk KO-1

description:
Library name: CKRN230038671-1A
KO_DuovsWT_Duo_deg_all.xls


title: FRK-PVBP-Spatial

description:
Library name: FRK-sp-A-gex
Control


title: Duodenum-WT-4

description:
Library name: CKRN230038670-1A
KO_DuovsWT_Duo_deg_all.xls


title: FRK-Myometrium-Spatial

description:
Library name: FRK-sp-CD-gex
Control


title: Duodenum-WT-3

description:
Library name: CKRN230038669-1A
KO_DuovsWT_Duo_deg_all.xls


title: FRK-CAM-Spatial

description:
Library name: FRK-sp-CAM-gex
Control

value: Chorioamniotic membranes


title: Duodenum-WT-2

description:
Library name: CKRN230038668-1A
KO_DuovsWT_Duo_deg_all.xls


title: FRH-PVBP-Spatial-2

description:
Library name: FRH-sp-B-gex
Preeclamptic

value: Placenta


title: Duodenum-WT-1

description:
Library name: CKRN230038667-1A
KO_DuovsWT_Duo_deg_all.xls


title: Ileum-Khk KO-4

description:
Library name: CKRN220019532-1A
KO_ILvsWT_IL_deg_all.xls

source_name: Ileum

value: Ileum


title: FRH-PVBP-Spatial

description:
Library name: FRH-sp-A-gex
Preeclamptic


title: FRH-Myometrium-Spatial

description:
Library name: FRH-sp-CD-gex
Preeclamptic

value: Myometrium


title: Ileum-Khk KO-3

description:
Library name: CKRN220019531-1A
KO_ILvsWT_IL_deg_all.xls


title: Ileum-Khk KO-2

description:
Library name: CKRN220019530-1A
KO_ILvsWT_IL_deg_all.xls


title: FRH-CAM-Spatial

description:
Library name: FRH-sp-CAM-gex
Preeclamptic


title: FCM-PVBP-Spatial-2

description:
Library name: FCM-sp-B-gex
Preeclamptic


title: Ileum-Khk KO-1

description:
Library name: CKRN220019529-1A
KO_ILvsWT_IL_deg_all.xls


title: Ileum-WT-4

description:
Library name: CKRN220019528-1A
KO_ILvsWT_IL_deg_all.xls


title: FCM-PVBP-Spatial

description:
Library name: FCM-sp-A-gex
Preeclamptic


title: FCM-Myometrium-Spatial

description:
Library name: FCM-sp-CD-gex
Preeclamptic


title: Ileum-WT-3

description:
Library name: CKRN220019527-1A
KO_ILvsWT_IL_deg_all.xls


title: umbilical cord blood hematopoietic stem cells (CD34+) cells, 8-Me-PIQ rep2

city: Shanghai

first: Yu

last: Li

state: Shanghai

address: No.600 Yishan Road

department: Department of Obstetrics and Gynecology

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: sample2

data_processing:
The sequence reads were aligned to GRCm38/M25 using STAR (2.7.10a).
Uniquely mapped sequencing reads were assigned to Gencode M25 gene using featureCounts (v2.0.1)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files of ’gene_fpkm‘ include log2RPKM values for all Sample.

source_name: cord blood

growth_protocol: Cells were cultured in Stemline II Hematopoietic Stem Cell Expansion Medium (Sigma, S0912) supplemented with 100 ng/mL stem cell factor (SCF) (R&D Systems, #7466 - SC - 010/CF), 100 ng/mL thrombopoietin (TPO) (R&D Systems, #288 - TP - 200/CF), and 50 ng/mL Fms - like tyrosine kinase 3 ligand (Flt3L) (BioLegend, #710802) in the presence of 50 IU/mL penicillin and 50 μg/mL streptomycin.

extract_protocol:
Total RNA was isolated from  umbilical cord blood hematopoietic stem cells (CD34+) ex vivo cultured for 7 days treated with DMSO and 8-Me-PIQ using FastPure Cell/Tissue Total RNA Isolation Kit (Vazyme).
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then RNA was digested with RNase H. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. Each group was sequenced in replicates by Illumina NovaSeq 6000 with single end 150 bp read length.

treatment_protocol: PBS

value: cord blood

value: Primary cells

value: Hematopoietic Stem and Progenitor Cells (HSPCs)

value: ex vivo cultured for 7 days


title: Ileum-WT-2

description:
Library name: CKRN220019526-1A
KO_ILvsWT_IL_deg_all.xls


title: FCM-CAM-Spatial

description:
Library name: FCM-sp-CAM-gex
Preeclamptic


title: FVQ-PVBP-Spatial

description:
Library name: FVQ-sp-A-gex
Control


title: Ileum-WT-1

description:
Library name: CKRN220019525-1A
KO_ILvsWT_IL_deg_all.xls


title: FVQ-CAM-Spatial

description:
Library name: FVQ-sp-CAM-gex
Control


title: Jejunum-Khk KO-4

description:
Library name: CKRN220019524-1A
KO_JvsWT_J_deg_all.xls

source_name: Jejunum

value: Jejunum


title: FVS-CAM-Spatial

description:
Library name: FVS-sp-CAM-gex
Preeclamptic


title: FVQ-Myometrium-Spatial-2

description:
Library name: FVQ-sp-CD-gex-2
Control


title: FVQ-Myometrium-Spatial

description:
Library name: FVQ-sp-CD-gex
Control


title: Jejunum-Khk KO-3

description:
Library name: CKRN220019523-1A
KO_JvsWT_J_deg_all.xls


title: FMM-CAM

description:
Library name: FMM-sc-CAM-gex
Preeclamptic

data_processing:
Spatial transcriptomics: Fast files were processed using 10X Genomics' SpaceRanger v2.1.0. Fastq files were generated with `mkfastq`, and processed files with `count`.
Single cell Transcriptomics:Fastq files were processed using 10X Genomics CellRanger 3.1.0 with "cellranger multit".
Assembly: Spatial transcriptomics: 10X Genomics' genome build: GRCh38-2020-A. Single-cell transcriptomics: Pre-built human reference 3.0.0, GRCh38 (Ensembel release 93)
Supplementary files format and content: Spatial transcriptomics: Spaceranger count spatial directory. Paraphrased from https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/spatial-outputs: aligned_fiducials.jpg: shows which fiducial spots on the slide were detected by spaceranger; detected_tissue_image.jpg: shows the section of tissue detected by spaceranger; scalefactors_json.json: relative scales of user-supplied images; spatial_enrichment.csv: Moran's I values for each expressed feature; tissue_hires_image.png: high-resolution image of the tissue; tissue_lowres_image.png: low-resolution image of the tissue; tissue_positions.csv: table with information about each spot; barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz: gene expression matrix files.
Supplementary files format and content: Single-cell transcriptomics: CellRanger count output with the files accounting for filtered feature-barcode matrices for each GEM well in "gz" compressed format.


title: Jejunum-Khk KO-2

description:
Library name: CKRN220019522-1A
KO_JvsWT_J_deg_all.xls


title: HV_5_PBMC

description: 10x Genomics

value: PBMC


title: FMM-PBMCs

description:
Library name: FMM-sc-E-gex
Preeclamptic

source_name: PBMCs

value: PBMCs


title: FAM-Myometrium-Spatial

description:
Library name: FAM-sp-CD-gex
Preeclamptic


title: Jejunum-Khk KO-1

description:
Library name: CKRN220019521-1A
KO_JvsWT_J_deg_all.xls


title: FMM-Myometrium

description:
Library name: FMM-sc-CD-gex
Preeclamptic


title: FEP-CAM-Spatial

description:
Library name: FEP-sp-CAM-gex
Preeclamptic


title: HV_8_Skin

description: 10x Genomics

value: Skin


title: FMM-PVBP

description:
Library name: FMM-sc-AB-gex
Preeclamptic


title: Jejunum-WT-4

description:
Library name: CKRN220019520-1A
KO_JvsWT_J_deg_all.xls


title: Jejunum-WT-3

description:
Library name: CKRN220019519-1A
KO_JvsWT_J_deg_all.xls


title: FJJ-CAM

description:
Library name: FJJ-sc-CAM-gex
Control


title: Jejunum-WT-2

description:
Library name: CKRN220019518-1A
KO_JvsWT_J_deg_all.xls


title: FVT-CAM-Spatial

description:
Library name: FVT-sp-CAM-gex
Control


title: FJJ-PBMCs

description:
Library name: FJJ-sc-E-gex
Control


title: Jejunum-WT-1

description:
Library name: CKRN220019517-1A
KO_JvsWT_J_deg_all.xls


title: FJJ-Myometrium

description:
Library name: FJJ-sc-CD-gex
Control


title: Liver-Khk KO-4

description:
Library name: CKRN220019516-1A
KO_LvsWT_L_deg_all.xls

value: Liver


title: FJJ-PVBP

description:
Library name: FJJ-sc-AB-gex
Control


title: HV_1_Skin

description: 10x Genomics


title: Liver-Khk KO-3

description:
Library name: CKRN220019515-1A
KO_LvsWT_L_deg_all.xls


title: Liver-Khk KO-2

description:
Library name: CKRN220019514-1A
KO_LvsWT_L_deg_all.xls


title: FSH-PVBP

description:
Library name: FSH-sc-AB-gex
Preeclamptic


title: FSH-PBMCs

description:
Library name: FSH-sc-E-gex
Preeclamptic


title: Liver-Khk KO-1

description:
Library name: CKRN220019513-1A
KO_LvsWT_L_deg_all.xls


title: FSH-Myometrium

description:
Library name: FSH-sc-CD-gex
Preeclamptic


title: Liver-WT-4

description:
Library name: CKRN220019512-1A
KO_LvsWT_L_deg_all.xls


title: Liver-WT-3

description:
Library name: CKRN220019511-1A
KO_LvsWT_L_deg_all.xls


title: FNS-PBMCs

description:
Library name: FNS-sc-E-gex
Control


title: Liver-WT-2

description:
Library name: CKRN220019510-1A
KO_LvsWT_L_deg_all.xls


title: FNS-Myometrium

description:
Library name: FNS-sc-CD-gex
Control


title: FNS-CAM

description:
Library name: FNS-sc-CAM-gex
Control


title: ELCAP 4H8 untreated replicate 3

description: Library name: 4H8-Unt-3

data_processing:
reads were mapped with STAR (–-alignEndsType Extend5pOfRead1 --clip3pAdapterSeq GATCGTCGGACT) against a human genome assembly merged with drosophila melanogaster genome assembly (GRCh38, Ensembl release 108 and BDGP6, Ensembl release 46)
Genome alignment BAM files were deduplicated using UMItools dedup function and subsequently filtered with samtools view function for low quality mapped reads (-q 10,)
For HEK parental samples complemented with Drosophila spike-in, a Drosophila gene-level count matrix was generated with Subread (v2.0.6) featureCounts76 and used to calculate drosophila spike-in size-factors with DEseq277 (v1.42.0) “estimateSizeFactors” function. Strand specific, spike-in normalised (for HEK parental cells) or RPKM (for RPB3-FLAG cells)
single-nucleotide BigWig files were generated from strand-specific bam files using Deeptools78 (v3.5.5) bamCoverage function (--scaleFactor = 1/size-factor or --normalizeUsing RPKM ) with bin size of 1 nt (-bs 1).
Assembly: GRCh38, Ensembl release 108 and BDGP6, Ensembl release 46
Supplementary files format and content: bigwig for forward and reverse strands

molecule: nuclear RNA

growth_protocol: For RNAPII IPs from the RPB3-FLAG expressing cell line 4x15cm plates of cells were induced with 100 ng/mL doxycycline for 16 hours and grown to 80-90% confluency. For RNAPII IPs with 4H8 and 8WG16 antibodies for ELCAP-seq, triplicates of 2x15cm and 6x15cm plates HEK293 parental cells were used. Drosophila spike-ins were used. For this Drosophila S2 cells were grown at 27oC in Schneider’s medium (Gibco, Cat#21720024) complemented with heat inactivated 10% v/v FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
Normalised parental HEK293 chromatin fractions were spiked-in with 10% protein/protein of Drosophila S2 chromatin extract and added to ab-conjugated magnetic Dynabeads for 3 hours at 4oC with agitation. The beads were washed 4 times with ELCAP wash buffer (10 mM Tris-HCl pH = 7.5; 250 mM NaCl; 0.5% (v/v) NP-40; 0.5 mM EDTA; fresh protease inhibitor; protease Inhibitors cocktail and fresh phosphatase inhibitors). Short RNA fragments trapped by RNAPII complexes were extracted with the Quick-RNA MicroPrep kit (Zymo, Cat#R1050) according to the manufacture’s instruction for short RNA extraction (17-200 nt). Briefly, RNPAII bound beads were incubated for 5 min at RT in extraction buffer (per 100 μL sample; 100 μL of supplied Zymo RNA lysis Buffer, 100 μL of IP wash buffer,100 μL ethanol). RNA was isolated using kit supplied Zymo-Spin™ IC columns following the manufacturer’s instructions.
Library were prepared using 5 ul of short RNAs with NEBNext® Small RNA library preparation kit (NEB, Cat# E7300) according to the manufacturer’s protocol with the only modification being inclusion of a UMI containing adapter; the initial ligation was carried with the custom ligation adapter ‘5'-App-NNNNNNAGATCGGAAGAGCACACGTCT-3' (IDT) with the same ligation conditions as manufacturer’s protocol. Libraries were amplified with 8 cycles of PCR and the whole library was separated by size with Novex™ TBE Gels, 10% (Invitrogen, ThermoFischer Scientific, Cat# EC62752BOX), stained with 1/50.000 SYBRTMgold (Invitrogen, ThermoFischer Scientific, Cat# S11494) and fragment size ranging from 147 nt to 190 nt were excised from the gel and purified according to NEBNext® Small RNA library preparation kit protocol.

treatment_protocol: In all cases oxidative stress was induced by treatment with 1 mM H2O2 for 15 min. And for some samples let to recovery for indicated times after media change.

value: HEK293 Flp-in T-Rex


title: C&R_Rh30_SIX4_BI1347-24hr_rep2

first: Susu

last: Zhang

address: 360 Longwood Ave, LC6102

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Library name: C_R_Rh30_SIX4_BI1347-24hr_rep2

data_processing:
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9). Raw FASTQ data were trimmed using Trimmomatic-v0.38 and paired end reads were aligned to human hg38 genome using Bowtie2 (v2.3.5) in very sensitive local mode --dovetail --phred33 -I 0 -X 2000 -N 1 --very-sensitive). Peaks were called using MAXS2 (v2.1.4) with a threshold of q<0.01 and peak were annotated to the nearest TSS using HOMER. Differential analysis was performed using DiffBind and DESeq2. Significantly changed peaks were defined by a 1.5-fold change threshold and FDR<0.05. Bigwig files were normalized and generated using Deeptools. Heatmaps were created by Deeptools using the normalized bigwig files.
Assembly: hg38
Supplementary files format and content: Bigwig file
Library strategy: CUT&Run

growth_protocol: Rh30 is cultured in DMEN containing 10% FBS, 1% L-Glutamin, and 1% P.S.

extract_protocol:
CUT&RUN+NEB DNA clean up
NEB Next Ultra II library prep kit

treatment_protocol: DMSO or BI1347 were added to cell after adhering.

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: C&R_Rh30_TADA2B_DMSO_rep2

description: Library name: C_R_Rh30_TADA2B_DMSO_rep2


title: Liver-WT-1

description:
Library name: CKRN220019509-1A
KO_LvsWT_L_deg_all.xls


title: FNS-PVBP

description:
Library name: FNS-sc-AB-gex
Control


title: Hif1a-WT3

description: Library name: cKO5

value: ovarian follicle

value: Granulosa cell

value: Hif1a wild type


title: FVB-Myometrium-Spatial

description:
Library name: FVB-sp-CD-gex
Control


title: FYI-PBMCs

description:
Library name: FYI-sc-E-gex
Control


title: CCSP_KP

city: Rochester

first: Cheng

state: MN

address: 200 1st street SW

institute: Mayo Clinic

description:
Library name: CCSP_KP
10X Genomics

data_processing:
Sequencing output was demultiplexed and aligned to the mouse reference genome GR. Cm38 using Cell Ranger (10x Genomics, v7.1.0). Alignment output from Cell Ranger is in the form of gene-barcode matrix.
Assembly: GRCm38
Supplementary files format and content: gene-barcode matrix in h5 format

source_name: LUAD tumor

extract_protocol:
Individual tumors were microdissected from moribund KP (KrasG12D; Trp53 fl/fl) and KP-Gain (KrasG12D; Trp53 fl/fl; Rosa26 Prkci/Prkci; Col1a1 Ect2/Ect2) animals infected with either Ad-SPC-Cre or Ad-CCSP-Cre via intratracheal administration (n = 5 tumors/animal; 2-3 animals/genotype). Microdissected tumors were dissociated using the Lung Dissociation Kit (Miltenyi Biotech, 130-095-927) according to the manufacturer’s instructions. Dissociated cells were filtered using 70-μm and 30-μm strainers. CD31+ and TER-119+ cells were further removed using the EasySep Mouse Biotin Positive Selection Kit II (StemCell Technologies, 17665), followed by removal of dead cells using the EasySep Dead Cell Removal (Annexin V) Kit (StemCell Technologies, 17899).
scRNA-seq was performed on purified suspensions of epithelial and immune cells using the Chromium Next GEM Automated Single Cell 3' Library & Gel Bead Kit v3.1 (10X Genomics, 1000147) according to the manufacturer’s instructions. Briefly, cell number and viability were determined using 0.2% (w/v) Trypan Blue staining. 10,000 cells were then loaded onto the Chromium Connect for an automated process of GEM generation, post GEM-RT cleanup, cDNA amplification, and 3' gene expression library construction. Single-cell libraries were then sequenced on the Illumina NovaSeq S4 by the Mayo Clinic Genome Analysis Core.

treatment_protocol: Intratracheal administration of Ad-SPC-Cre and Ad-CCSP-Cre in KP and KP-Gain animals

value: LUAD tumor

value: KP

value: Ad-CCSP-Cre


title: CCSP_KP_Gain

description:
Library name: CCSP_KP_Gain
10X Genomics

value: KP-Gain


title: SPC_KP_Gain

description:
Library name: SPC_KP_Gain
10X Genomics

value: Ad-SPC-Cre


title: FYI-Myometrium

description:
Library name: FYI-sc-CD-gex
Control

value: Myometrium


title: SPC_KP

description:
Library name: SPC_KP
10X Genomics


title: FLR-PVBP-Spatial

description:
Library name: FLR-sp-AB-gex
Control

value: Placenta


title: FYI-CAM

description:
Library name: FYI-sc-CAM-gex
Control

value: Chorioamniotic membranes


title: FYI-PVBP

description:
Library name: FYI-sc-AB-gex
Control


title: TotalSeq-B Hashtag Library Rep3; Samples mLN: WT3, FLStar3, cKO3, RedcKO3/ CoLP: WT3, FLStar3, cKO3, RedcKO3

first: Grozdan

last: Cvijetic

state: Maryland

address: 30 Convent Dr, Building 30, Room 332

institute: NIH/NIDCR

description:
Library name: CSP-Lib9
10x Genomics
Lib9_raw_feature_bc_matrix.h5
Lib9_sample_demultiplexing_info.csv

data_processing:
Single-cell sequencing data were processed using Cell Ranger (v7.1.0, 10x Genomics) for quality control and demultiplexing. Reads were aligned to the mouse genome (mm10, GRCm38) gene expression was quantified using "STARsolo" (version 2.7.10a). Hashtag oligonucleotide (HTOs) were quantified using "STARsolo" and used to assign genotypes, conditions and tissues. Each sample represents an independent biological replicate.
Assembly: Mouse mm10
Supplementary files format and content: Multiplexed raw expression matrices in Cell Ranger’s hdf5 format and per-libray HTO demultiplexing information.

source_name: mesenteric lymph node (mLN), colon lamina propria (CoLP)

extract_protocol:
Cells derived from mLN or CoLP of Control WT (Notch2fl/fl), Control Re-derived Notch2cKO (Notch2fl/fl CD11cCre+), dysbiotic WT (Notch2fl/fl CD11cCre-) and dysbiotic Notch2cKO (Notch2fl/fl CD11cCre+) mice were individually multiplexed by labeling each cell suspension with a unique Hashtag (HTO) antibody. Per biological replicate, ~37K mLN and ~3K CoLP sort-purified CD26+CD11c+MHCII+ dendritic cells, pooled across all genotypes and conditions, were loaded onto a 10x Genomics Chromium Single Cell Controller.
Single cell capture, cDNA and library preparations were performed with the Single Cell 3' v4 Reagent Kit (10x Genomics) according to manufacturer's instructions. GEX and HTO sequencing libraries were loaded on an Illumina NovaSeq 6000 with high output cycle kits and sequenced paired-end using the following read configuration:150-10-10-150 (R1-I1-I2-R2). R2 contains the 15bp HTO barcode sequence.

value: Lin-CD26+CD11c+MHCII+ dendritic cells

value: Control WT (Notch2fl/fl), Control Re-derived Notch2cKO (Notch2fl/fl CD11cCre+), dysbiotic WT (Notch2fl/fl CD11cCre-) and dysbiotic Notch2cKO (Notch2fl/fl CD11cCre+).

tag: condition

value: Eubiosis and Dysbiosis

tag: age

value: 7-12 weeks old


title: FJD-CAM

description:
Library name: FJD-sc-CAM-gex
Control


title: TotalSeq-B Hashtag Library Rep2; Samples mLN: WT2, FLStar2, cKO2, RedcKO2/ CoLP: WT2, FLStar2, cKO2, RedcKO2

description:
Library name: CSP-Lib8
10x Genomics
Lib8_raw_feature_bc_matrix.h5
Lib8_sample_demultiplexing_info.csv

value: mesenteric lymph node (mLN), colon lamina propria (CoLP)


title: Multiplexed GEX Library Rep3; Samples mLN: WT3, FLStar3, cKO3, RedcKO3/ CoLP: WT3, FLStar3, cKO3, RedcKO3

description:
Library name: GEX-Lib9
10x Genomics
Lib9_raw_feature_bc_matrix.h5
Lib9_sample_demultiplexing_info.csv


title: FJD-PVBP

description:
Library name: FJD-sc-AB-gex
Control


title: FAM-CAM

description:
Library name: FAM-sc-CAM-gex
Preeclamptic


title: Multiplexed GEX Library Rep2; Samples mLN: WT2, FLStar2, cKO2, RedcKO2/ CoLP: WT2, FLStar2, cKO2, RedcKO2

description:
Library name: GEX-Lib8
10x Genomics
Lib8_raw_feature_bc_matrix.h5
Lib8_sample_demultiplexing_info.csv


title: FAM-PBMCs

description:
Library name: FAM-sc-E-gex
Preeclamptic

value: PBMCs


title: Pnvp Mutant EC enriched P8 rep

city: Montréal

first: Gael

middle: Louis Max

last: Cagnone

state: QC

address: 3175 Chemin de la Côte-Sainte-Catherine

department: The Montreal single-cell Academy

country: Canada

institute: CHU Sainte Justine

description:
Library name: PnvpMut_rep
10X Genomics

data_processing:
Libraries were sequenced  on Illumina NovaSeq6000 S4 , followed by de-multiplexing and mapping to the mouse genome (Mus_musculus:GRCm38) using CellRanger (pipeline cellranger-6.1.1) (10x Genomics). Count matrices were analyzed using Seurat V5. Following quality control and dimensionality reduction , endothelial cells were then analyzed separately. Briefly, ECs from the 4 four datasets (CTL PNVP = 2179 cells, CTL BRAIN = 5331 cells, mutant PNVP = 3044 cells, mutant BRAIN = 6551 cells) were merged together, normalised using SCTranform (vars.to.regress = c("nFeature_RNA", "percent.mt")) then dimensionality reduction was performed using runUMAP based on the first 20 PCs from PCA analysis on 3000 variable genes (SCT assay). Clustering was then performed on UMAP first and second dimensions (dims=1:2, reduction = “umap”) at a resolution of 1.2, followed by differential marker expression analysis between clusters based on normalised RNA count (RNA assay). Normalised RNA counts were then scaled (vars.to.regress = c("nFeature_RNA", "percent.mt")) for data visualization. Clusters were finally annotated based on known endothelial subtype marker genes.
Assembly: Mus_musculus:GRCm38
Supplementary files format and content: h5 files (filtered_feature_bc_matrix.h5)
Supplementary files format and content: Seurat object containing ECs from 2 replicates (brain_pnvp_ct_mut_integration_ref_rep1_Rep2_ref93.Seurat_object.rds)

source_name: Pnvp

extract_protocol:
The cell suspension was washed with a FACS buffer (PBS containing 1% FBS and 0.2% EDTA). Cells were stained for 30 minutes at room temperature with PE anti-mouse CD140b Antibody (Biolegend, 136006); APC-conjugated anti-mouse CD31 antibody (BD Biosciences, 551262) and FITC-conjugated anti-mouse CD45 antibody (BioLegend, 103108) in Fc block solution (5 µg/mL CD16/CD32 Fc Block, eBioscience, 16-0161-82). After washing, cells were stained with Live/Dead Fixable Aqua Dead Cell Stain (ThermoFisher Scientific, L34957) for 20 minutes at room temperature. Stained cells were washed and resuspended in PBS. The gating strategy was defined using unstained and single-stained controls. Dead cells and doublets were excluded, and endothelial cells (CD45⁻ CD31⁺) were sorted using a BD FACS Aria Fusion. Cells were resuspended in PBS containing 0.04% BSA. Cells from WT PNVP/brain and mutant PNVP/brain sample were then subjected to single-cell RNAseq aiming at a yield of 5 000 cells per condition.
Four libraries (CTL PNVP, CTL BRAIN, mutant PNVP, mutant BRAIN) were generated using the Chromium  Single Cell 3’ Reagent Kits v3.1 (10x Genomics; Pleasanton, CA, USA).

value: Pnvp

value: Endothelial enriched


title: FAM-Myometrium

description:
Library name: FAM-sc-CD-gex
Preeclamptic


title: Brain Mutant EC enriched P8 rep

description:
Library name: BrainMut_rep
10X Genomics

source_name: Brain

value: Brain


title: FAM-PVBP

description:
Library name: FAM-sc-AB-gex
Preeclamptic


title: Brain Control EC enriched P8 rep

description:
Library name: BrainCT_rep
10X Genomics


title: FEP-CAM

description:
Library name: FEP-sc-CAM-gex
Preeclamptic

source_name: Chorioamniotic membranes


title: FEP-PBMCs

description:
Library name: FEP-sc-E-gex
Preeclamptic


title: FEP-Myometrium

description:
Library name: FEP-sc-CD-gex
Preeclamptic


title: 08280028-1-KA-KD-2

city: HEFEI

first: Zhiyu

last: Xi

address: 1 Tianehu Road

department: Neurosurgery

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

description: Library name: KD fed mice 2

data_processing:
The data generated from Illumina platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology. Raw data of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads. FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: brain

extract_protocol:
Total RNA was extracted from the brain using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.

value: brain

value: KD


title: FEP-PVBP

description:
Library name: FEP-sc-AB-gex
Preeclamptic

source_name: Placenta


title: 08280028-1-KA-KD-1

description: Library name: KD fed mice 1


title: FRK-CAM

description:
Library name: FRK-sn-CAM-gex
Control


title: FGS-CAM

description:
Library name: FGS-sn-CAM-gex
Preeclamptic


title: 08280028-1-KA-2

description: Library name: CD fed mice 2

value: CD


title: ELCAP 4H8 h2o2 treated replicate 2

description: Library name: 4H8-Treated-2

source_name: HEK293 Flp-in T-Rex

value: HEK293 Flp-in T-Rex


title: WT_EB_1_ATAC

first: HeungSun

last: Kwon

address: 50 South Drive Building 50

department: NIDDK

institute: NIH

description: EB, WT, replicate 1

data_processing:
Paired-end raw fastq reads were trimmed using cutadapt (v4.4)
Preprocessed reads were aligned to the mouse genome Gencode M18 using Bowtie2 (v2.5.1)
Uniquely mapped, properly paired, non-supplementary, non-mitochondrial alignments were retained using samtools view command with options “-F 2048 -f 2 -q 20” piped with “grep -v chrM”.
Duplicated reads were cleaned using picard MarkDuplicates (v2.27.5) with “REMOVE_DUPLICATES=true”.
Peaks were called using MACS2 (v2.2.7.1) with the settings “-f BAMPE --keep-dup all -g 2.3e9” at default cutoffs.
Browser track files were generated using the deepTools bamCoverage with “--minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300”.
Assembly: mm10 (Gencode M18)
Supplementary files format and content: bigwig

growth_protocol: ESC were maintained and differentiated as described, with modifications (Carotta et al. 2004). Undifferentiated ESC were cultured on 0.1% gelatin-coated plates in EmbryoMax DMEM (MilliporeSigma, SLM-220-M supplemented with 10% fetal bovine serum (MilliporeSigma), 2-β-mercaptoethanol (MilliporeSigma, ES-007-E), GlutaMax, penicillin/streptomycin, non-essential amino acids, and ESGRO-2i (MilliporeSigma, cat# SF016-200. To generate EB, cultures were adjusted to 1 × 10^5 cells/ml and incubated in EB medium (STEMCELL TECH, Aggrewell EB formation medium) for 3 to 5 days in Aggrewell plates (STEMCELL TECH, 34421). After 4 days, EB were pooled and grown in suspension in non-adherent plates, with media changed daily. EB were collected on days 3 and 5.

extract_protocol:
Genomic DNA was extracted by QIAquick PCR purification kit (Quiagen 28104).
ATAC-seq was performed with the ATAC-Seq Kit (Active Motif, 53150), according to manufacturer’s protocol.

treatment_protocol: gRNAs targeting Ldb1 were cloned into the CRISPR-Cas9 and gRNA expression vector pSpCas9(BB)-2A-GFP (PX458) (Addgene, cat #48138). ES cells were transfected with Mouse ES Cell Nucleofector® Kit (Lonza, cat # VPH-1001) according to the manufacturer’s instructions. Fluorescent cells were sorted 48 hours later and plated at limiting dilution to isolate single clones harboring the LDB1 gene knockout.

value: mEB


title: LDB1KO_ESC_2_ATAC

description: ESC, LDB1KO, replicate 2

value: mESC


title: 08280028-1-KA-1

description: Library name: CD fed mice 1


title: FCM-CAM

description:
Library name: FCM-sn-CAM-gex
Preeclamptic


title: LDB1KO_ESC_1_ATAC

description: ESC, LDB1KO, replicate 1


title: FRH-CAM

description:
Library name: FRH-sn-CAM-gex
Preeclamptic


title: SW1 CRISPR KO library tumor

city: Hershey

first: Vladimir

last: Spiegelman

address: 500 University Drive Hershey, Pennsylvania

department: Pediatrics

institute: Penn State University

description:
Library name: Sample 2
Columns names in SW1_CRISPR_KO_screen_counts.xlsx: SW1 CRISPR KO library tumor

data_processing:
5’ adapters (TTGTGGAAAGGACGAAACACCG) were trimmed from the reads
For bioinformatic analysis, Galaxy platform was used. sgRNA counts performed using MAGeCK algorithm.
Assembly: Custom sgRNA library was used. The library file is included as a supplementary file on the series record.
Supplementary files format and content: xls file include raw counts for each sample
Library strategy: CRISPR Screen

source_name: cell line

growth_protocol: SW1 cells were maintained in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin in the humidified incubator at 37°C, 5% CO2.

extract_protocol:
DNA was isolated using the DNeasy Blood & Tissue Kit (Qiagen, 69504).
gDNA equivalent of 500x library coverage was amplified using Hifi high fidelity polymerase (Stellar Scientific, RAD HF1100), and primers synthesized in IDT according to previously described sequences (DOI: 10.1038/nprot.2017.016). Each PCR reaction contained 500 ng gDNA, 0.5 μL HiFi high fidelity polymerase, 10 μL of 5x buffer, 2 μL of forward and reverse primers and molecular biology grade water up to 50 μL. A total of 8000 ng was amplified for each sample. PCR conditions were as follows: 1 min at 95 °C, followed by 15 sec at 95 °C, 15 sec at 65 °C, 30 sec at 72 °C repeated for 25 cycles and finally 5 min at 72 °C. Finally, PCR products were purified with Agencourt AMPure XP SPRI beads according to the manufacturer’s instructions (Beckman Coulter, A63880). Product purity was evaluated using Agilent 2100 BioAnalyzer and DNA 1000 Kit (Agilent Technologies, 5067-1504), and concentration was measured with Qubit™ 1X dsDNA HS Assay (Qubit, Q33230). Lastly, the qualified RNA-seq libraries are sequenced using Illumina NovaSeq6000, to get on average 1.5 million, single-end 61 bp reads to achieve >500X coverage.

value: cell line

value: melanoma cell line

tag: batch


title: SW1 CRISPR KO library metastasis

description:
Library name: Sample 3
Columns names in SW1_CRISPR_KO_screen_counts.xlsx: SW1 CRISPR KO  library metastasis


title: FLJ-CAM

description:
Library name: FLJ-sn-CAM-gex
Control

value: Chorioamniotic membranes


title: FLJ-PBMCs-repeat

description:
Library name: FLJ-sc-E-gex-reprep
Control


title: dCas9KRAB_Clone4_H3K36me3

first: James

middle: A.

last: Cain

address: Guy's Hospital, Great Maze Pond

department: Infectious Diseases

institute: King's College London

description: Library name: dCas9-KRAB Clone 4, H3K36me3

data_processing:
CUT&RUN fastq files were processed using the pipeline summarised in Figure 2.2. Adapters were trimmed from fastq reads using trim-galore. Fastq files were aligned using bowtie2 (Langmead and Salzberg, 2012) to a N-Masked mouse genome (mm39). The N-Masked genome file was generated using SNPSplit (Krueger and Andrews, 2016) that required B6/CAST SNP information (.vcf) and the mm39 fasta genome sequence file. Once aligned, the aligned reads are then split into B6 (maternal) and CAST (paternal) read files for processing into .bigWigs using deeptools (Ramírez et al., 2014). Reads upstream and downstream of Mcts2 were counted using featureCounts with a custom .saf file from the aligned and split .bam file. RPKM normalisation was performed on aligned reads mapping to chr2 to alleviate normalisation artefacts derived from other chromosomes.
Assembly: mm39
Supplementary files format and content: .bigWig files showing RPKM normalisation. bigWig files also provided for split alleles post-SNPsplit processing, either RPKM normalised to the whole genome or specificallly at chromosome 2.
Library strategy: CUT&Run

growth_protocol: Hybrid C57BL/6 / CAST/EiJ mouse NSCs were extracted from the subventricular zone and expanded as previously described (Ferrón et al., 2007). NSCs were cultured in N2B27 media + Fgf2 + Egf : DMEM/F12 [Gibco, 11320033]: Neurobasal [Gibco, 21103049] at a 1:1 ratio, N2 1X final [Millipore, SCM012], B27 0.5x final [Gibco, 17504- 044], L-Glutamine 1x final [Gibco, 25030-024] and 2-mercaptoethanol 0.1mM [Gibco, 31350-010]. FGF2 [Peprotech, 100-18B] and EGF [Peprotech, 315-09] were reconstituted at in PBS + 0.1% BSA and 1µl of each growth factor was added per 10ml of N2B27 media to a final concentration of 10ng/ml. Cell culture plates were coated with 1/100th diluted GeltrexTM LDEV-Free Reduced Growth Factor Basement Membrane Matrix [Gibco, A1413201] in DMEM-F12 media prior to NSC plating. Cells were detached using Accutase [Millipore, SCR005] and passaged every 2-3 days when reaching 80% confluency. Cells being recovered from liquid nitrogen storage were cultured for one day in N2B27 + Fgf2 + Egf + RevitaCellTM Supplement 1X [ThermoFisher, A2644501].

extract_protocol:
CUT&RUN was performed on freshly detached NSCs following the protocol detailed in(Janssens and Henikoff, 2019) with some modifications detailed here. Activation buffer and Concanavalin A beads were purchased from Cell Signalling Technologies [#93569]. Digitonin concentration utilised was at 5% across all buffers and MNase digestion time was at 30mins on ice unless otherwise stated. Recovery of DNA fragments using each method was confirmed using Qubit dsDNA HS Assay [Invitrogen, Q32851]. 10ng of this DNA was utilised for generation of CUT&RUN libraries.
Libraries were generated using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® [E7645S] and index using NEBNext® Mtiplex Oligos for Illumina® (Index Primers Set 1) [E7335S]. 1µl of 3µM of NEBNext Adaptor was utilised to reduce adaptor dimers. Sera-Mag select beads [Cytiva, 29343052] were used for DNA clean-up and size selection. DNA Library size was measured using Agilent High Sensitivity D1000 ScreenTape [Agilent, 5067- 5585].

value: Neural Stem Cells

value: dCas9:KRAB, gRNA integrant


title: dCas9KRAB_Clone4_H3K4me3

description: Library name: dCas9-KRAB Clone 4, H3K4me3


title: dCas9KRAB_Clone3_H3K36me3

description: Library name: dCas9-KRAB Clone 3, H3K36me3


title: FLJ-PVBP-repeat

description:
Library name: FLJ-sc-AB-gex-reprep
Control

extract_protocol:
For spatial transcriptomics: Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat. For single-cell and nuclei transcriptomics: samples were freshly dissociated using custom protocol. Nuclei were isolated using 10X Genomics nuclei isolation kit according to manufacturers recommended protocol.
For spatial transcriptomics: Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction. For single-cell an nuclei transcriptomics: single cell or nuclei suspensions were prepared and processed using the Chromium Single Cell 5’ Reagent Kits v3.1

value: Placenta


title: FVB-Myometrium-repeat

description:
Library name: FVB-sc-CD-gex-reprep
Control

source_name: Myometrium

value: Myometrium


title: dCas9KRAB_Clone3_H3K4me3

description: Library name: dCas9-KRAB Clone 3, H3K4me3


title: dCas9KRAB_Clone2_H3K36me3

description: Library name: dCas9-KRAB Clone 2, H3K36me3


title: FGS-Myometrium-repeat

description:
Library name: FGS-sc-CD-gex-reprep
Preeclamptic


title: FVT-PBMCs

description:
Library name: FVT-sc-E-gex
Control

value: PBMCs


title: dCas9KRAB_Clone1_H3K4me3

description: Library name: dCas9-KRAB Clone 1, H3K4me3


title: FVT-Myometrium

description:
Library name: FVT-sc-CD-gex
Control


title: dPA_CloneF6_H3K36me3

description: Library name: dPA Clone F6, H3K36me3

value: deltaH13d poly(A)+/-


title: FFM-Myometrium

description:
Library name: FFM-sc-CD-gex
Preeclamptic


title: dPA_CloneA3_H3K4me3

description: Library name: dPA Clone A3, H3K4me3


title: FFM-PVBP

description:
Library name: FFM-sc-AB-gex
Preeclamptic


title: FGS-PBMCs

description:
Library name: FGS-sc-E-Sc-gex
Preeclamptic


title: FGS-Myometrium

description:
Library name: FGS-sc-CD-gex
Preeclamptic


title: E4/4_M_D4F_3

city: Minneapolis

first: Ling

email: lil@umn.edu, linglilab@umn.edu

address: 2001 6th Street SE Rm 4-208

department: Department of Experimental and Clinical Pharmacology

institute: University of Minnesota

description: Library name: 18739

data_processing:
Raw sequencing reads were evaluated and trimmed using Trimmomatic.
Trimmed reads were mapped to the mouse reference genome GRCm38 using HISAT2.
RNA-seq raw counts for each gene were extracted using FeatureCounts.
Assembly: GRCm38
Supplementary files format and content: xlsx file includes raw counts for each sample.

extract_protocol:
Total RNA was extracted from tissue homogenate using the Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio Rad 7326830) according to the manufacturer’s instructions.
Library preparation was performed using a TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: Sex

value: male


title: FGS-PVBP2

first: Theodoros

address: 20 Guilford Street

institute: UCL

description:
Library name: FGS-sc-AB2-gex-2
Preeclamptic


title: E4/4_M_D4F_2

description: Library name: 18646


title: FGS-PVBP

description:
Library name: FGS-sc-AB2-gex-1
Preeclamptic


title: E4/4_M_D4F_1

description: Library name: 18643


title: FVB-CAM

description:
Library name: FVB-sc-CAM-gex
Control


title: E4/4_F_D4F_4

description: Library name: 18688

value: female


title: FVQ-CAM

description:
Library name: FVQ-sn-CAM-gex
Control


title: FVB-PBMCs

description:
Library name: FVB-sc-E-gex
Control


title: FLJ-Myometrium2-repeat

description:
Library name: FLJ-sc-CD-gex-2-reprep
Control


title: FLJ-Myometrium-repeat

description:
Library name: FLJ-sc-CD-gex-reprep
Control


title: E4/4_F_D4F_3

description: Library name: 18662

value: brain


title: dCas9KRAB_Clone2_H3K4me3

description: Library name: dCas9-KRAB Clone 2, H3K4me3

value: Brain


title: FVT-CAM

description:
Library name: FVT-sc-CAM-gex
Control


title: E4/4_F_D4F_2

description: Library name: 18650


title: FVB-PVBP

description:
Library name: FVB-sc-AB-gex
Control


title: FVT-PVBP

description:
Library name: FVT-sc-AB-gex
Control


title: E4/4_F_D4F_1

description: Library name: 18648


title: FLR-CAM

description:
Library name: FLR-sc-CAM-gex
Control


title: E4/4_M_PBS_4

description: Library name: 18789

value: PBS


title: dPA_CloneA3_H3K36me3

description: Library name: dPA Clone A3, H3K36me3


title: WT_H3K36me3

description: Library name: WT, H3K36me3, Control

value: WT


title: FFM-CAM

description:
Library name: FFM-sc-CAM-gex
Preeclamptic


title: E4/4_M_PBS_3

description: Library name: 18660


title: FLR-PBMCs

description:
Library name: FLR-sc-E-gex
Control


title: FLR-Myometrium

description:
Library name: FLR-sc-CD-gex
Control


title: FLR-PVBP

description:
Library name: FLR-sc-AB-gex
Control


title: E4/4_M_PBS_2

description: Library name: 18645


title: E4/4_M_PBS_1

description: Library name: 18644


title: 12mo_female_high6

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description: Library name: 12month.884

data_processing:
Reads were aligned to the rn7 reference genome with STAR version 2.6
Read counts for annotated genes were obtained with Rsubread version 2.14
Normalized counts were obtained with DESq2 version 1.42
Assembly: rn7
Supplementary files format and content: DESeq2 normalized counts in tab delimited file

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNAeasy Kit (Qiagen)
Illumina TruSeq Stranded mRNA

value: heart

value: cART


title: FND-CAM

description:
Library name: FND-sc-CAM-gex
Preeclamptic


title: 12mo_female_high5

description: Library name: 12month.875


title: E4/4_F_PBS_4

description: Library name: 18689


title: 12mo_female_high3

description: Library name: 12month.851


title: FND-PBMCs

description:
Library name: FND-sc-E-gex
Preeclamptic


title: 12mo_female_high4

description: Library name: 12month.864


title: E4/4_F_PBS_3

description: Library name: 18665


title: FND-Myometrium

description:
Library name: FND-sc-CD-gex
Preeclamptic


title: 12mo_female_high1

description: Library name: 12month.845


title: E4/4_F_PBS_2

description: Library name: 18649


title: 12mo_female_low5

description: Library name: 12month.816


title: FND-PVBP

description:
Library name: FND-sc-AB-gex
Preeclamptic


title: E4/4_F_PBS_1

description: Library name: 18647


title: 12mo_female_low4

description: Library name: 12month.807


title: FVS-CAM

description:
Library name: FVS-sc-CAM-gex
Preeclamptic


title: 12mo_female_low3

description: Library name: 12month.800


title: E3/3_M_D4F_4

description: Library name: 19037


title: 12mo_female_low2

description: Library name: 12month.792


title: FVS-PBMCs

description:
Library name: FVS-sc-E-gex
Preeclamptic


title: E3/3_M_D4F_3

description: Library name: 19024


title: 12mo_female_low1

description: Library name: 12month.789


title: 12mo_female_ctrl5

description: Library name: 12month.745


title: FVS-Myometrium

description:
Library name: FVS-sc-CD-gex
Preeclamptic


title: 12mo_female_ctrl6

description: Library name: 12month.754


title: E3/3_M_D4F_2

description: Library name: 19022


title: FVS-PVBP

description:
Library name: FVS-sc-AB-gex
Preeclamptic


title: 12mo_female_low6

description: Library name: 12month.830


title: E3/3_M_D4F_1

description: Library name: 19021


title: 12mo_female_ctrl3

description: Library name: 12month.726


title: 12mo_female_ctrl2

description: Library name: 12month.721


title: FVB-Myometrium

description:
Library name: FVB-sc-CD-gex
Control


title: FRK-PBMCs

description:
Library name: FRK-sc-E-gex
Control


title: 12mo_female_ctrl1

description: Library name: 12month.712


title: E3/3_F_D4F_4

description: Library name: 19045


title: FRK-Myometrium

description:
Library name: FRK-sc-CD-gex
Control


title: 12mo_male_high6

description: Library name: 12month.598


title: 12mo_male_high5

description: Library name: 12month.587


title: E3/3_F_D4F_3

description: Library name: 19042


title: 12mo_male_high4

description: Library name: 12month.580


title: 12mo_male_high3

description: Library name: 12month.576


title: E3/3_F_D4F_2

description: Library name: 19028


title: FRK-PVBP2

description:
Library name: FRK-sc-AB-gex-2
Control


title: 12mo_male_high2

description: Library name: 12month.565


title: FRK-PVBP

description:
Library name: FRK-sc-AB-gex-1
Control


title: 12mo_male_high1

description: Library name: 12month.552


title: E3/3_F_D4F_1

description: Library name: 19005


title: 12mo_male_low6

description: Library name: 12month.539


title: FRH-PBMCs-reprep

description:
Library name: FRH-sc-E-gex-reprep
Preeclamptic


title: 12mo_male_low5

description: Library name: 12month.531


title: E3/3_M_PBS_4

description: Library name: 19072


title: 12mo_male_low4

description: Library name: 12month.498


title: 12mo_male_low3

description: Library name: 12month.492


title: FRH-PBMCs

description:
Library name: FRH-sc-E-gex
Preeclamptic


title: TotalSeq-B Hashtag Library Rep1; Samples mLN: WT1, FLStar1, cKO1, RedcKO1/ CoLP: WT1, FLStar1, cKO1, RedcKO1

description:
Library name: CSP-Lib7
10x Genomics
Lib7_raw_feature_bc_matrix.h5
Lib7_sample_demultiplexing_info.csv

value: mesenteric lymph node (mLN), colon lamina propria (CoLP)

value: Lin-CD26+CD11c+MHCII+ dendritic cells

value: Control WT (Notch2fl/fl), Control Re-derived Notch2cKO (Notch2fl/fl CD11cCre+), dysbiotic WT (Notch2fl/fl CD11cCre-) and dysbiotic Notch2cKO (Notch2fl/fl CD11cCre+).

value: Eubiosis and Dysbiosis

value: 7-12 weeks old


title: FJD-PBMCs

description:
Library name: FJD-sc-E-gex
Control


title: FJD-Myometrium

description:
Library name: FJD-sc-CD-gex
Control


title: E3/3_M_PBS_3

description: Library name: 19071


title: FRH-Myometrium

description:
Library name: FRH-sc-CD-gex
Preeclamptic


title: 12mo_female_high2

description: Library name: 12month.849


title: Multiplexed GEX Library Rep1; Samples mLN: WT1, FLStar1, cKO1, RedcKO1/ CoLP: WT1, FLStar1, cKO1, RedcKO1

description:
Library name: GEX-Lib7
10x Genomics
Lib7_raw_feature_bc_matrix.h5
Lib7_sample_demultiplexing_info.csv


title: 12mo_male_low2

description: Library name: 12month.490


title: 12mo_male_low1

description: Library name: 12month.478


title: Pnvp Control EC enriched P8 rep

description:
Library name: PnvpCT_rep
10X Genomics

value: Pnvp

value: Endothelial enriched


title: E3/3_M_PBS_2

description: Library name: 19061


title: FRH-PVBP2

description:
Library name: FRH-sc-AB-gex-2
Preeclamptic

value: Placenta


title: 08280028-1-KA-KD-3

description: Library name: KD fed mice 3

value: KD


title: 12mo_male_ctrl6

description: Library name: 12month.442

value: male


title: 12mo_male_ctrl5

description: Library name: 12month.439


title: E3/3_M_PBS_1

description: Library name: 19002


title: E3/3_F_PBS_4

description: Library name: 19074

value: female


title: 12mo_male_ctrl4

description: Library name: 12month.432


title: FRH-PVBP

description:
Library name: FRH-sc-AB-gex-1
Preeclamptic


title: 12mo_male_ctrl3

description: Library name: 12month.429


title: 12mo_male_ctrl2

description: Library name: 12month.422


title: 08280028-1-KA-3

description: Library name: CD fed mice 3

value: brain

value: CD


title: E3/3_F_PBS_3

description: Library name: 19073

value: PBS


title: 12mo_male_ctrl1

description: Library name: 12month.402


title: FCM-PBMCs

description:
Library name: FCM-sc-E-gex
Preeclamptic

value: PBMCs


title: RNAseq_Rh30_DMSO_repeat_B

description:
Library name: RNAseq_Rh30_DMSO_repeat_B
RNAseq_Rh30_BI1347_vs_DMSO_repeat_raw_counts.txt

data_processing:
FastQC was used to evaluate read quality on raw RNA-seq reads. Reads were aligned to the human genome (hg38) using STAR (v2.7.2b) (Dobin et al., 2013). Transcript-level quantifications were calculated using RSEM (v1.3.1) (Li et al. 2011). Gene counts from STAR were then used to quantify differentially expressed genes between the experimental and control conditions using the R Bioconductor package DESeq2 (Anders, et al., 2010) using the approximate posterior estimation for GLM coefficients (apeglm) method for effect size. Normalized expression values for individual samples were obtained from RSEM log2 TPM values with the RSEM log2(TPM+1) values used for GSEA and producing RNA-seq heat map plots.
Assembly: hg38

extract_protocol:
Trizol
Novogene library prep pipeline

value: Rhabdomyosarcoma

value: PAX3::FOXO1 fusion


title: FCM-Myometrium

description:
Library name: FCM-sc-CD-gex
Preeclamptic

value: Myometrium


title: interim_female_high5

description: Library name: Interim.1623

value: heart

value: cART


title: interim_female_high6

description: Library name: Interim.1624


title: E3/3_F_PBS_2

description: Library name: 19007


title: SW1 CRISPR KO library cells

description:
Library name: Sample 1
Columns names in SW1_CRISPR_KO_screen_counts.xlsx: SW1 CRISPR KO library cells

value: cell line

value: melanoma cell line


title: interim_female_high4

description: Library name: Interim.1620


title: FCM-PVBP2

description:
Library name: FCM-sc-AB-gex-2
Preeclamptic


title: interim_female_high3

description: Library name: Interim.1618


title: E3/3_F_PBS_1

description: Library name: 19006


title: PM_rep6

first: Hye Kyung

last: Lee

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

description: Library name: Sample 5

data_processing:
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and subsequently aligned to the reference genome mm10 and hg19 applying STAR RNA-seq aligner (version 2.7.11b), Samtools (version 1.9) and Picard (version 2.9.2). Htseq (version 0.9.1) was applied to calculate raw read counts.
Assembly: mm10
Supplementary files format and content: raw read counts from RNA-seq samples

source_name: Hippocampus

growth_protocol: Pregnant mice were randomly divided and intranasally administered the PM on days 9, 12, and 15 of pregnancy. The mice delivered pups on day 21 of pregnancy. Hippocampal tissues were collected from the pups at 14–18 weeks of age.

extract_protocol:
Total RNA was extracted from frozen hippocampus tissue of mice using the PureLink RNA Mini kit according to the manufacturer’s instructions (Thermo Fisher Scientific). The concentration and quality of RNA were assessed by an Agilent Bioanalyzer 2100 (Agilent Technologies, CA). Ribosomal RNA was removed from 1 ug of total RNAs with more than RIN value 8.0 and cDNA was synthesized using SuperScript III (Invitrogen). Libraries for sequencing were prepared according to the manufacturer’s instructions with NEBNext Ultra II RNA Library Prep Kit (New England Biolabs, NEB#E7775) and 100bp paired-end sequencing was done with a NovaSeq 6000 instrument (Illumina).
Libraries for sequencing were prepared using standard New England Biolabs's protocols.

treatment_protocol: particulate matter (PM) (200ug/kg)

value: Hippocampus

value: particulate matter (PM) (200ug/kg)


title: interim_female_high2

description: Library name: Interim.1616


title: FCM-PVBP

last: Xenakis

description:
Library name: FCM-sc-AB-gex-1
Preeclamptic

value: Placenta


title: interim_male_high6

description: Library name: Interim.1612


title: 12mo_female_ctrl4

description: Library name: 12month.741


title: interim_male_high5

description: Library name: Interim.1611


title: interim_female_high1

description: Library name: Interim.1613


title: FVQ-PBMCs

description:
Library name: FVQ-sc-E-gex
Control


title: interim_male_high4

description: Library name: Interim.1608


title: PM_rep5

description: Library name: Sample 4


title: FVQ-Myometrium

description:
Library name: FVQ-sc-CD-gex
Control


title: interim_male_high3

description: Library name: Interim.1606


title: PM_rep4

description: Library name: Sample 3


title: FVQ-PVBP2

description:
Library name: FVQ-sc-AB-gex-2
Control


title: interim_female_low6

description: Library name: Interim.1524


title: Vehicle_rep5

description: Library name: Sample 2

value: normal saline (Veh)


title: dCas9KRAB_Clone1_H3K36me3

description: Library name: dCas9-KRAB Clone 1, H3K36me3

value: Brain

value: Neural Stem Cells

value: dCas9:KRAB, gRNA integrant


title: interim_male_high2

description: Library name: Interim.1604

value: male


title: interim_female_low3

description: Library name: Interim.1518

value: female


title: interim_male_high1

description: Library name: Interim.1601


title: sample6, LE biol rep3

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Library name: Sample6

data_processing:
Raw sequencing data were demultiplexed and mapped to the reference genome GRCh38-20 using Cell Ranger (v. 6.1.2; 10X Genomics). Filtered datasets (HDF5 files) from Cell Ranger for each of the paired patient samples representing lymphedema-affected and unaffected limbs were uploaded into the browser-based bioinformatic platform ICARUS (Interactive single Cell RNA-seq Analysis with R shiny Using Seurat) version 3.0 84-86. Low-quality cells were filtered out according to the expressed gene number, number of unique molecular identifiers (UMIs), and ribosomal percentage. Cells with a maximum of 20% mitochondrial genes were included, and high-confidence doublets were removed with DoubletFinder. Log-normalized data underwent linear dimensional reduction through principal component analysis (PCA) with Seurat v5, followed by integration with Harmony 87,88. The top 2,000 variable genes were used for PCA. The first 15 principal components were used for Louvain cell clustering (resolution 0.3) and uniform manifold approximation and projection (UMAP) dimensional reduction. Regression was performed to correct for common confounding factors, including cell cycle phase, gene number, UMI count, percent ribosomal genes, and percent mitochondrial genes. Cell populations in Seurat cluster types were identified with manual verification of cluster-specific upregulated gene expression using CellMarker 2.0 89.
Assembly: GRCh38-203
Supplementary files format and content: feature barcode maxtrix files in h5 format

source_name: Human skin cells

extract_protocol:
The skin was dissociated using the Whole Skin Dissociation Kit (Miltenyi Biotec, cat# 130-101-540) following the manufacturer's protocol. After removing red blood cells, the cells were resuspended in PBS with 2% FCS and stained with a viability dye. Live cells were then sorted and resuspended in PBS with 0.04% BSA.
Single cell suspensions were stained with Trypan blue and the Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, cells were loaded onto Chromium Next GEM Chip G (10X Genomics PN 1000120) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 8-17,000 cells proceeded using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics PN 1000268) according to the manufacturer’s protocol. cDNA amplification included 11 cycles and 70-128 ng of the material was used to prepare sequencing libraries with 10-12 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S4 Reagent Kit (200 cycles) (Illumina). An average of 22 thousand paired reads was generated per cell.

value: Human skin cells

value: Lymphedema affected


title: Sal-6

first: Ming

last: Hao

address: Shuangqing Rd.

institute: Tsinghua Univ

description:
Library name: S6
Transcriptom of granulosa cell collected via laser micro dissection

data_processing:
Transcriptom were quantified using Salmon (PMID: 28263959).
Assembly: GRCm38
Supplementary files format and content: Quantified gene expression data using Salmon.

source_name: ovary

extract_protocol:
LCM collected GC were lysised in 50 µl 4M GuSCN at 42 ℃ for 15 min. Lysis were added with 771 µl 80% EtOH with 20 µg glycogen, and incubated in -80 ℃ for 2h, and centrifuged at 12000g, 4℃ for 20 min.
library were constructed as GEO-Seq protocol (PMID: 28207000).

value: ovary

tag: strain

value: Granulosa cell

value: WT

value: intraperitoneal injected with Saline for 3 consecutive days


title: Vehicle_rep4

description: Library name: Sample 1


title: Sal-5

description:
Library name: S5
Transcriptom of granulosa cell collected via laser micro dissection


title: interim_male_low6

description: Library name: Interim.1512

value: heart

value: cART


title: interim_female_low2

description: Library name: Interim.1517


title: sample5, Normal biol rep3

description: Library name: Sample5

value: control


title: interim_male_low5

description: Library name: Interim.1510


title: interim_female_low1

description: Library name: Interim.1515


title: Sal-4

description:
Library name: S4
Transcriptom of granulosa cell collected via laser micro dissection


title: interim_male_low4

description: Library name: Interim.1507


title: sample3, Normal, biol rep2

description: Library name: Sample3


title: interim_male_low2

description: Library name: Interim.1505


title: Sal-3

description:
Library name: S3
Transcriptom of granulosa cell collected via laser micro dissection


title: interim_male_low1

description: Library name: Interim.1503


title: Sal-2

description:
Library name: S2
Transcriptom of granulosa cell collected via laser micro dissection


title: sample2, LE, biol rep1

description: Library name: Sample2


title: interim_male_low3

description: Library name: Interim.1506


title: sample1, Normal, biol rep1

description: Library name: Sample1


title: Sal-1

description:
Library name: S1
Transcriptom of granulosa cell collected via laser micro dissection


title: interim_female_ctrl4

description: Library name: Interim.1419


title: interim_female_ctrl3

description: Library name: Interim.1418


title: N-CM-B2

city: Matsumoto

first: Shin

last: Kadota

address: 3-1-1 Asahi

department: Regenerative Science and Medicine

country: Japan

institute: Shinshu University

description: Library name: Sample 13

data_processing:
RNA-seq reads were trimmed using Trimmomatic (v0.39).
All samples were mapped to the hg38 human genome using STAR (v2.7.11b), and a gene count matrix was generated using featureCounts (v2.0.6).
Raw counts were normalized with transcripts per million (TPM) normalization.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw gene-level read counts
Supplementary files format and content: csv file includes TPM values for each Sample

source_name: Cardiomyocytes

growth_protocol: Undifferentiated hiPSCs were cultured as a monolayer in Essential 8 medium (Thermo Fisher Scientific, Waltham, MA, USA) on Matrigel (Corning, NY, USA) -coated plates. For differentiation, 1 μM CHIR99021 was added to the culture. On the following day (Day 0), the medium was replaced with a cardiac differentiation medium consisting of RPMI 1640 supplemented with B27 minus insulin (Thermo Fisher Scientific). Activin A (100 ng/mL; R&D Systems, Minneapolis, MN, USA) was added to the medium on Day 0, followed by 5 ng/mL BMP4 (R&D Systems) and 1 μM CHIR99021 (Sigma-Aldrich, St. Louis, MO, USA) on Day 1, and 1 μM XAV939 (Sigma-Aldrich) on Day 3. On Day 5, the medium was changed to cardiac differentiation medium without any additional supplements. On Day 7, the medium was switched to RPMI 1640 with B27 supplement (Thermo Fisher Scientific). From Day 9 to Day 11, cardiomyocyte purification was conducted using glucose- and glutamine-free DMEM medium (Gibco, A14430-01) supplemented with 4 mM lactate. On Day 11, the media was changed to RPMI 1640 with B27 supplement. The medium was changed every 2-3 days until Day 19. On Day 19, both non-expanded and expanded CMs, with or without additional treatment with BCH001, were subjected to heat shock at 43 °C for 30 min. After the heat shock, the medium was replaced with RPMI 1640 supplemented with B27, 100 ng/mL insulin-like growth factor 1 (IGF-1), 200 nM cyclosporin A, and 5 μM Y-27632. On Day 20, the cells were dissociated using Trypsin-EDTA at 37 °C for 15 min, resuspended in CELLBANKER 1 Plus reagent (Takara Bio, Shiga, Japan, CB023), and transferred into cryovials. The cryovials were placed in a controlled-rate freezing container (CoolCell, Corning) and stored at -80 °C. On the following day, they were transferred to a -150 °C freezer for long-term storage.

extract_protocol:
RNA was extracted from frozen cells using the NucleoSpin RNA Kit (Takara Bio).
Library preparation was carried out using the Nextera DNA Library Preparation Kit, followed by sequencing on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA).

treatment_protocol: On Day 12 of differentiation, cells were dissociated with Trypsin-EDTA at 37 °C for 15 min and then replated onto Matrigel-coated dishes at a density of 8 × 104 cells/cm2 in RPMI 1640 medium supplemented with B27, 2 μM CHIR99021, 5 μM Y-27632 and 10% KnockOut Serum Replacement (Thermo Fisher Scientific). From Day 13 onward, the medium was replaced with RPMI 1640 supplemented with B27 and containing 2 μM CHIR99021 and was refreshed every two days. On Day 18, CHIR99021 was replaced with 2 μM Wnt-C59 (S7037, Selleck chemicals, Houston, TX, USA). For generating E-CM-B or E-CM-R, cells were treated with either 10 μM BCH001 (S8977, Selleck chemicals) or 1 μM RG7834 (T12719, TargetMol Chemicals, Boston, MA, USA), respectively, from Day 12 to Day 20.

value: Cardiomyocytes

value: human induced pluripotent stem cell-derived cardiomyocytes

value: Venus-Akaluc Knocked-in


title: NAC-4

description:
Library name: N4
Transcriptom of granulosa cell collected via laser micro dissection

value: intraperitoneal injected with 150 mg/kg N-acetyl-l-cysteine for 3 consecutive days


title: interim_female_ctrl2

description: Library name: Interim.1417


title: N-CM-B1

description: Library name: Sample 12


title: interim_male_ctrl6

description: Library name: Interim.1410


title: NAC-3

description:
Library name: N3
Transcriptom of granulosa cell collected via laser micro dissection


title: interim_male_ctrl5

description: Library name: Interim.1408


title: interim_male_ctrl4

description: Library name: Interim.1407


title: E-CM-R1

description: Library name: Sample 10

value: expanded with RG7834


title: NAC-1

description:
Library name: N1
Transcriptom of granulosa cell collected via laser micro dissection


title: Old-GSTA4-rep4

city: Cambridge

first: Yuancheng Ryan

last: Lu

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: Library name: Old-GSTA4-4

data_processing:
Paired-end human and mouse reads were mapped to the canonical chromosomes of the GRCh38/hg38 or GRCm38/mm10 genome genomes, respectively, with STAR (v 2.7.1a) using a genome index created using Ensembl 96 gene models (with sjdbOverhang=100). Gene counts were obtained for all genes using featureCounts (v1.6.2) and the same GTF file as for STAR and options "-p -s 1".
Assembly: mm10
Supplementary files format and content: csv; gene feature counts table

source_name: RPE

extract_protocol:
Total RNA was extracted following the TRIzol Reagent User Guide (Thermo Fisher Scientific). Glycogen (1 μl of 10 mg ml−1 solution) was added to the supernatant to increase RNA recovery. RNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was determined using TapeStation (Agilent Technologies).
RNA library preparations, sequencing reactions were conducted at Genewiz. A SMART-Seq v4 Ultra Low Input Kit for Sequencing was used for full-length cDNA synthesis and amplification (Clontech), and Illumina Nextera XT library was used for sequencing library preparation. In brief, cDNA was fragmented and adaptors were added using Transposase, followed by limited-cycle PCR to enrich and add an index to the cDNA fragments. The final library was assessed by a Qubit 2.0 Fluorometer and an Agilent TapeStation.

value: RPE


title: interim_male_ctrl3

description: Library name: Interim.1406

value: male


title: term_female_high6

description: Library name: Terminal.1322

value: female


title: interim_male_ctrl1

description: Library name: Interim.1402


title: E-CM-B2

description: Library name: Sample 8

value: expanded  with BCH001


title: term_female_high5

description: Library name: Terminal.1321


title: Old-GSTA4-rep3

description: Library name: Old-GSTA4-3


title: term_female_high4

description: Library name: Terminal.1317


title: E-CM-B1

description: Library name: Sample 7


title: Old-GSTA4-rep2

description: Library name: Old-GSTA4-2


title: term_female_high2

description: Library name: Terminal.1314


title: term_female_high1

description: Library name: Terminal.1313


title: E-CM3

description: Library name: Sample 6

value: expanded


title: term_male_high6

description: Library name: Terminal.1310


title: Old-GSTA4-rep1

description: Library name: Old-GSTA4-1


title: E-CM2

description: Library name: Sample 5


title: term_male_high4

description: Library name: Terminal.1305


title: term_male_high3

description: Library name: Terminal.1304


title: Old-GFP-rep2

description: Library name: Old-GFP-3


title: term_male_high2

description: Library name: Terminal.1302


title: N-CM3

description: Library name: Sample 3


title: term_male_high1

description: Library name: Terminal.1301


title: Old-GFP-rep1

description: Library name: Old-GFP-1


title: term_female_low6

description: Library name: Terminal.1224


title: N-CM2

description: Library name: Sample 2


title: sample4, LE biol rep2

description: Library name: Sample4

value: Human skin cells

value: Lymphedema affected


title: term_female_low5

description: Library name: Terminal.1223


title: term_female_low4

description: Library name: Terminal.1222


title: N-CM1

description: Library name: Sample 1


title: 24-months-OSKonoff-rep4

description: Library name: 42-24m-OSKonoff-e

source_name: Ear Fibroblasts

extract_protocol:
Total RNA was extracted following the TRIzol Reagent User Guide (Thermo Fisher Scientific). Glycogen (1 μl of 10 mg ml−1 solution) was added to the supernatant to increase RNA recovery. RNA was quantified using a Qubit 2.0 Fluorometer (Life Technologies), and RNA integrity was determined using TapeStation (Agilent Technologies).
The RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (New England Biolabs, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 3.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

value: Ear Fibroblasts


title: 24-months-OSKonoff-rep3

description: Library name: 41-24m-OSKonoff-d


title: term_female_low3

description: Library name: Terminal.1216


title: term_female_low2

description: Library name: Terminal.1215


title: term_female_low1

description: Library name: Terminal.1214


title: HBMVEC, Oligomeric amyloid beta, 12hr, 4

city: Daegu

first: Do-Geun

last: Kim

address: Cheomdan-ro 61

department: Dementia Research Group

country: South Korea

institute: Korea Brain Research Institute

description:
Library name: Ab_12h_4
HBMVEC treated with oligomeric Abeta (1 uM) for 12 hours

data_processing:
Raw reads were quality-checked and adapter-trimmed using Trimmomatic v0.38.
Reads were aligned to the human reference genome (GRCh38, Ensembl release 102) using HISAT2 v2.1.0.
Gene-level counts were obtained using StringTie v2.1.3b.
Assembly: Human genome GRCh38 (Ensembl release 102).
Supplementary files format and content: Tab-delimited text file including gene-level read counts, FPKM, and TPM values for each sample.

source_name: primary HBMVEC

growth_protocol: Primary human brain microvascular endothelial cells (HBMVECs) were cultured in complete classic media with 2% culture boost and 1% penicillin-streptomycin on attachment factor-coated plates at 37°C and 5% CO2 for 2–3 days.

extract_protocol:
After treatment, cells were washed with PBS and total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA concentration and integrity were assessed using Quant-IT RiboGreen and TapeStation RNA ScreenTape. Only samples with RIN > 7.0 were used.
0.5 μg of total RNA per sample was used to construct libraries with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). rRNA was removed using the Ribo-Zero kit, mRNA was fragmented, and cDNA was synthesized with SuperScript II and random primers. Libraries were PCR-enriched, quantified, and quality-checked before sequencing.

treatment_protocol: HBMVECs were treated with Amyloid beta oligomer for 1, 4 or 12 hours.

value: primary HBMVEC

value: brain microvascular endothelial cells

value: WT

value: Oligomeric amyloid beta (1 uM)


title: term_male_low6

description: Library name: Terminal.1212

value: heart

value: cART


title: 24-months-OSKonoff-rep2

description: Library name: 39-24m-OSKonoff-b


title: HBMVEC, Oligomeric amyloid beta, 12hr, 3

description:
Library name: Ab_12h_3
HBMVEC treated with oligomeric Abeta (1 uM) for 12 hours


title: term_male_low5

description: Library name: Terminal.1211


title: E-CM-B3

description: Library name: Sample 9

value: Cardiomyocytes

value: human induced pluripotent stem cell-derived cardiomyocytes

value: Venus-Akaluc Knocked-in


title: 24-months-OSKonoff-rep1

description: Library name: 38-24m-OSKonoff-a


title: term_male_low4

description: Library name: Terminal.1210


title: term_male_low3

description: Library name: Terminal.1204


title: 3-months-OSKonoff-rep4

description: Library name: 32-3m-OSKonoff-E


title: term_male_low2

description: Library name: Terminal.1203


title: HBMVEC, Oligomeric amyloid beta, 12hr, 1

description:
Library name: Ab_12h_1
HBMVEC treated with oligomeric Abeta (1 uM) for 12 hours


title: 3-months-OSKonoff-rep3

description: Library name: 31-3m-OSKonoff-C


title: term_female_ctrl5

description: Library name: Terminal.1121


title: HBMVEC, Oligomeric amyloid beta, 4hr, 4

description:
Library name: Ab_4h_4
HBMVEC treated with oligomeric Abeta (1 uM) for 4 hours


title: term_female_ctrl4

description: Library name: Terminal.1119


title: HBMVEC, Oligomeric amyloid beta, 4hr, 3

description:
Library name: Ab_4h_3
HBMVEC treated with oligomeric Abeta (1 uM) for 4 hours


title: 3-months-OSKonoff-rep2

description: Library name: 30-3m-OSKonoff-b2


title: term_female_ctrl2

description: Library name: Terminal.1115


title: 3-months-OSKonoff-rep1

description: Library name: 29-3m-OSKonoff-b1


title: term_female_ctrl1

description: Library name: Terminal.1113


title: HBMVEC, Oligomeric amyloid beta, 4hr, 2

description:
Library name: Ab_4h_2
HBMVEC treated with oligomeric Abeta (1 uM) for 4 hours


title: 24-months-OSK-rep4

description: Library name: 28-24m-OSK-e


title: term_male_ctrl6

description: Library name: Terminal.1109


title: HBMVEC, Oligomeric amyloid beta, 4hr, 1

description:
Library name: Ab_4h_1
HBMVEC treated with oligomeric Abeta (1 uM) for 4 hours


title: term_male_ctrl5

description: Library name: Terminal.1107


title: term_male_ctrl3

description: Library name: Terminal.1103


title: HBMVEC, Oligomeric amyloid beta, 1hr, 4

description:
Library name: Ab_1h_4
HBMVEC treated with oligomeric Abeta (1 uM) for 1 hour


title: term_male_ctrl2

description: Library name: Terminal.1102


title: term_male_ctrl1

description: Library name: Terminal.1101


title: HBMVEC, Oligomeric amyloid beta, 1hr, 3

description:
Library name: Ab_1h_3
HBMVEC treated with oligomeric Abeta (1 uM) for 1 hour


title: HEK293_Polysome_RMS_three_rep_combined

city: Copenhagen

first: Anders

last: Lund

address: Ole Maaløes Vej 5, Floor 4, Lund Group

department: Biotechnology Research and Innovation Centre (BRIC)

institute: Univeristy of Copenhagen

description:
Library name: HEK293_control
Ion540 kit

data_processing:
Data were analysed as previously reported (Birkedal et al. 2015; Krogh et al. 2016).
Reads per sequencing barcode de-multiplexed using a python script, Adaptor trimming using Cutadapt v. 1.2.1, Mapping to rRNA reference sequence using Bowtie2 v. 2.1.0
Counting of 5' and 3' read ends and calculation of RiboMeth-seq scores performed using RMS analysis python script.
The RiboMeth‑seq (RMS) score represents the fraction of molecules methylated at each nucleotide position and is calculated by comparing the number of read‑end counts at the queried position to those at six flanking positions on either side.
Assembly: Human 18S and 28S rRNA sequences, based on Human ribosomal DNA complete repeating unit (gi|555853|gb|U13369.1|HSU13369 and gi|555853|gb|U13369.1|HSU13369), corrected according to high-depth sequecing coverage as defined previously in Krogh, N. and Jannson, M. et al. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic acids research 44, 7884–7895 (2016).
Supplementary files format and content: Microsoft Excel files containing 5' and 3' read counts and the calculated RMS score at each nucleotide position the 18S and 28S rRNA sequences for each of three replicate RMS libraries. 2´-O-methylated rRNA psoritons (Nm), mean RMS score and SD for each rRNA position are also given.

molecule: cytoplasmic RNA

growth_protocol: HEK293 cells were maintained in DMEM (Gibco, 31966-047), cells were passaged approx. 2 times a week using Trypsin-EDTA (0.25%) (Gibco, 25200056). H9 human embryonic stem cell (hESC) lines (female) were maintained on plates coated with Matrigel (Corning Life Sciences, #354277) in mTeSR Plus medium (Stem Cell Technologies,#100-0276). The culture medium was changed every other day. Cells were passaged every three days using 1X TrypLE Select (Life Technologies,#12563-011)  reaching 80-90% confluence in a medium supplemented with Rock inhibitor (Y-27632) (LC laboratories, #Y-5301) at a final concentration of 10µM. For cryopreservation, cells were frozen in a solution 50% mTeSR Plus medium, 40% FBS 10% DMSO.

extract_protocol:
Following ER and cytosolic chemical fractionation, total RNA isolation was performed using QIAZOL (Qiagen) and chloroform following the manufacturer’s protocol.
RiboMeth‑seq library construction and sequencing were performed essentially as previously described (Birkedal et al. 2015; Krogh et al. 2016), except that libraries were pooled after 3′‑adapter ligation containing sample‑specific barcodes. Triplicate libraries were generated for each cell line or condition. A total of 1.5–4 µg of total RNA was used as input per library. RNA was partially degraded by alkaline hydrolysis at denaturing temperatures, and 20–40‑nucleotide fragments were purified on 10% TBE–urea polyacrylamide gels. 3′ adapters were ligated using a system based on a modified Arabidopsis tRNA ligase that joins 2′,3′‑cyclic phosphate and 5′‑phosphate termini. After 3′‑adapter ligation with distinct barcodes for each sample, barcoded RNA fragments were pooled, and 5′‑adapter ligation was performed similarly using the modified Arabidopsis tRNA ligase. The resulting libraries were processed on the Ion Chef system and sequenced using the Ion 540™ Kit‑Chef (Ion Torrent, A30011) and Ion 540™ Chip Kit (Ion Torrent, A27766).

treatment_protocol: H9 cells were differentiated into neural progenitor cells (NPCs) using the STEMdiff™ SMADi Neural Induction Medium (STEMCELL Technologies, #08581), following the monolayer protocol according to the manufacturer’s instructions. Briefly, H9 cells were plated on Matrigel-coated plates at a density of 2 × 10⁶ cells/cm² in neural induction medium supplemented with 10 µM ROCK inhibitor. The medium was changed daily, and the cells were passaged after 7 days. Following two additional passages (over the course of two weeks) in neural induction medium, the cells were transitioned to STEMdiff™ Neural Progenitor Medium (STEMCELL Technologies, #05833) for expansion, cryopreservation, or further differentiation. H9-derived NPCs were further differentiated into forebrain neurons following the manufacturer’s instructions. First, NPCs were plated at a density of 125,000 cells/cm² on Matrigel-coated plates in STEMdiff™ Forebrain Neuron Differentiation Medium (STEMCELL Technologies, #08600) for one week with daily medium changes. The cells were then dissociated using Accutase (STEMCELL Technologies, #07920) and replated at a density of 4-6 × 10⁴ cells/cm² in STEMdiff™ Forebrain Neuron Maturation Medium (STEMCELL Technologies, #08605) on plates coated with poly-L-ornithine (Sigma-Aldrich, #P3655; 15 µg/mL in PBS) and laminin (Sigma-Aldrich, #L2020; 5 µg/mL in DMEM/F-12). The medium was changed every other day, and the neurons were matured in culture for 22 days.

value: Human embryonic kidney


title: 24-months-OSK-rep1

description: Library name: 24-24m-OSK-a


title: term_male_low1

description: Library name: Terminal.1202

value: male


title: Neuron_fractionation_RMS_three_rep_combined

description:
Library name: Neuron_fractionation
Ion540 kit

source_name: H9-derived Neurons

value: H9-derived Neurons

value: Neuron

value: Neural differentiation


title: HBMVEC, Oligomeric amyloid beta, 1hr, 2

description:
Library name: Ab_1h_2
HBMVEC treated with oligomeric Abeta (1 uM) for 1 hour


title: term_female_ctrl3

description: Library name: Terminal.1116

value: female


title: NPC_fractionation_RMS_three_rep_combined

description:
Library name: NPC_fractionation
Ion540 kit

source_name: H9-derived NPC

value: H9-derived NPC

value: Neural Progenitor

value: Neural induction


title: 3-months-OSK-rep4

description: Library name: 18-3m-OSK-E

value: Ear Fibroblasts


title: HEK293_fractionation_RMS_three_rep_combined

description:
Library name: HEK293_fractionation
Ion540 kit

value: WT