title: control fetus ZT0 rep2

description:
ZT_0_REP_1
CF.tsv


title: circadian disruption mother ZT12 rep2

status: Public on Jan 15 2025

type: SRA

city: Irvine

first: Kousha

last: Changizi Ashtiani

state: California

address: Institute for Genomics and Bioinformatics 243, Info & Computer Science Building 2

department: ICS

country: USA

institute: University of California, Irvine

description:
ZT_12_REP_1
P.tsv

library_source: transcriptomic

data_processing:
Reads aligned to mm10 assembly and RefSeq genes using TopHat release 2.1.1
Gene expression results (FPKM) obtained using Cufflinks release 2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Samples

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from the liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
RNA libraries for each group were prepared as described in the Illumina TruSeq mRNA stranded protocol.

tag: tissue

value: Liver

tag: maternal stress

value: circadian disruption

tag: developmental stage

value: mother

tag: time


title: control mother ZT18 rep2

description:
ZT_18_REP_1
C.tsv

value: control


title: control mother ZT12 rep1

description:
ZT_12_REP_0
C.tsv


title: control mother ZT6 rep3

description:
ZT_6_REP_2
C.tsv


title: control mother ZT6 rep2

description:
ZT_6_REP_1
C.tsv


title: control fetus ZT12 rep3

description:
ZT_12_REP_2
CF.tsv

value: fetus


title: control mother ZT0 rep2

description:
ZT_0_REP_1
C.tsv


title: control mother ZT18 rep1

description:
ZT_18_REP_0
C.tsv


title: offspring circadian disruption high-fat diet ZT18 rep3

description:
ZT_18_REP_2
OPH.tsv

value: offspring

tag: diet

value: high-fat diet


title: offspring circadian disruption high-fat diet ZT12 rep1

description:
ZT_12_REP_0
OPH.tsv


title: offspring circadian disruption high-fat diet ZT6 rep3

description:
ZT_6_REP_2
OPH.tsv


title: control mother ZT12 rep3

description:
ZT_12_REP_2
C.tsv


title: offspring circadian disruption high-fat diet ZT6 rep1

description:
ZT_6_REP_0
OPH.tsv


title: offspring circadian disruption high-fat diet ZT0 rep3

description:
ZT_0_REP_2
OPH.tsv


title: offspring circadian disruption high-fat diet ZT0 rep2

description:
ZT_0_REP_1
OPH.tsv


title: control mother ZT12 rep2

description:
ZT_12_REP_1
C.tsv


title: offspring control high-fat diet ZT12 rep3

description:
ZT_12_REP_2
OCH.tsv


title: offspring control high-fat diet ZT6 rep1

description:
ZT_6_REP_0
OCH.tsv


title: control mother ZT6 rep1

description:
ZT_6_REP_0
C.tsv


title: control mother ZT0 rep1

description:
ZT_0_REP_0
C.tsv


title: control mother ZT0 rep3

description:
ZT_0_REP_2
C.tsv


title: offspring circadian disruption low-fat diet ZT18 rep1

description:
ZT_18_REP_0
OPL.tsv

value: low-fat diet


title: offspring circadian disruption low-fat diet ZT12 rep3

description:
ZT_12_REP_2
OPL.tsv


title: offspring circadian disruption high-fat diet ZT18 rep2

description:
ZT_18_REP_1
OPH.tsv


title: offspring circadian disruption high-fat diet ZT18 rep1

description:
ZT_18_REP_0
OPH.tsv


title: offspring circadian disruption high-fat diet ZT0 rep1

description:
ZT_0_REP_0
OPH.tsv


title: offspring circadian disruption high-fat diet ZT12 rep3

description:
ZT_12_REP_2
OPH.tsv


title: offspring control high-fat diet ZT18 rep2

description:
ZT_18_REP_1
OCH.tsv


title: offspring circadian disruption low-fat diet ZT12 rep1

description:
ZT_12_REP_0
OPL.tsv


title: offspring control high-fat diet ZT12 rep2

description:
ZT_12_REP_1
OCH.tsv


title: offspring control high-fat diet ZT18 rep3

description:
ZT_18_REP_2
OCH.tsv


title: offspring control high-fat diet ZT18 rep1

description:
ZT_18_REP_0
OCH.tsv


title: offspring control high-fat diet ZT6 rep2

description:
ZT_6_REP_1
OCH.tsv


title: offspring circadian disruption high-fat diet ZT6 rep2

description:
ZT_6_REP_1
OPH.tsv


title: offspring control high-fat diet ZT12 rep1

description:
ZT_12_REP_0
OCH.tsv


title: offspring circadian disruption low-fat diet ZT0 rep1

description:
ZT_0_REP_0
OPL.tsv


title: offspring control low-fat diet ZT18 rep2

description:
ZT_18_REP_1
OCL.tsv


title: offspring control high-fat diet ZT0 rep3

description:
ZT_0_REP_2
OCH.tsv


title: offspring control high-fat diet ZT0 rep2

description:
ZT_0_REP_1
OCH.tsv


title: offspring control high-fat diet ZT0 rep1

description:
ZT_0_REP_0
OCH.tsv


title: offspring control low-fat diet ZT18 rep1

description:
ZT_18_REP_0
OCL.tsv


title: offspring circadian disruption high-fat diet ZT12 rep2

description:
ZT_12_REP_1
OPH.tsv


title: offspring circadian disruption low-fat diet ZT18 rep3

description:
ZT_18_REP_2
OPL.tsv


title: offspring control low-fat diet ZT12 rep1

description:
ZT_12_REP_0
OCL.tsv


title: offspring control low-fat diet ZT6 rep1

description:
ZT_6_REP_0
OCL.tsv


title: offspring circadian disruption low-fat diet ZT12 rep2

description:
ZT_12_REP_1
OPL.tsv


title: offspring circadian disruption low-fat diet ZT6 rep3

description:
ZT_6_REP_2
OPL.tsv


title: offspring circadian disruption low-fat diet ZT6 rep2

description:
ZT_6_REP_1
OPL.tsv


title: Astro_Glut1_KO_Background_5

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

country: Switzerland

institute: ETH Zürich

data_processing:
Adaptor trimmed with cutadapt (v 1.15), maximum error rate of 0.05 and a minimum length of 15
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Assembly: GRCm38
Supplementary files format and content: kallisto output (.h5 and .tsv files) (pseudoaligned read counts). Files are further tarballed and zipped
Library strategy: TRAP-seq

molecule: total RNA

source_name: Brain

growth_protocol: Mice are originally all from a C57BL/6J Background. More details about mouselines and KO models can be found in the metadata

extract_protocol:
RNeasy Plus Micro Kit
Illumina Smartseq2

treatment_protocol: Homecage

value: Brain

tag: sample processing

value: Background

tag: mouse genotype

tag: region

value: Cortex

tag: biological replicate

tag: animal id

tag: mouse type

value: GLUT1 flox/flox;GLAC +/wt

tag: Sex

value: male

tag: strain


title: offspring control high-fat diet ZT6 rep3

description:
ZT_6_REP_2
OCH.tsv


title: offspring circadian disruption low-fat diet ZT0 rep3

description:
ZT_0_REP_2
OPL.tsv


title: WT_Background_4

value: WT

value: GLAC +/wt


title: offspring circadian disruption low-fat diet ZT0 rep2

description:
ZT_0_REP_1
OPL.tsv


title: Astro_Glut1_KO_TRAP_3

value: TRAP


title: WT_TRAP_3


title: Astro_Glut1_KO_Background_3


title: offspring control low-fat diet ZT18 rep3

description:
ZT_18_REP_2
OCL.tsv


title: offspring control low-fat diet ZT12 rep3

description:
ZT_12_REP_2
OCL.tsv


title: offspring control low-fat diet ZT12 rep2

description:
ZT_12_REP_1
OCL.tsv


title: WT_Background_1


title: offspring circadian disruption low-fat diet ZT6 rep1

description:
ZT_6_REP_0
OPL.tsv


title: WT_TRAP_1


title: offspring control low-fat diet ZT6 rep3

description:
ZT_6_REP_2
OCL.tsv


title: Astro_Glut1_KO_Background_1


title: offspring circadian disruption low-fat diet ZT18 rep2

description:
ZT_18_REP_1
OPL.tsv


title: WTcal7

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

data_processing:
The raw files were aligned to mouse genome/GRCm38 using STAR-2.5.3.
Sequences located at transcripts were quantified by using RSEM-1.3.1.
Differentially expressed genes (DEG) analysis was performed using DESeq2-1.24.0.
Assembly: Mouse genome/GRCm38
Supplementary files format and content: tab-delimited text files containing read counts estimated by using RSEM

source_name: PyMT tumor

extract_protocol:
Lysis buffer
Libraries were prepared by Novogene (Sacramento, CA) using the NEBNext Ultra RNA Library Prep kit for Illumina (New England Biolabs, Ipswich, MA, catalog no. E7770).
Sequencing was performed by Novogene using the Illumina NovaSeq6000 System

value: PyMT tumor

tag: cell line

value: PyMT

tag: cell type

value: Epithenial cell

tag: treatment

value: Calcipotriol


title: WTcal6


title: offspring control low-fat diet ZT6 rep2

description:
ZT_6_REP_1
OCL.tsv

value: Liver

value: control


title: offspring control low-fat diet ZT0 rep3

description:
ZT_0_REP_2
OCL.tsv

value: offspring


title: WT3

value: Ethanol


title: offspring control low-fat diet ZT0 rep2

description:
ZT_0_REP_1
OCL.tsv

value: low-fat diet


title: Endoderm Ngn3GFP HZ 27ss b2 025, scRNA-seq

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_025

library_source: transcriptomic single cell

data_processing:
For the Smart-seq3xpress scRNA-seq data, initial quality control was executed with FastQC version 0.11.9 under default settings. Index, primer, and adaptor sequences were then trimmed from paired-end reads using Trimmomatic version 0.39 with default parameters. Alignment of trimmed reads to the Mus musculus Genome assembly GRCm38 (mm10) was accomplished using HISAT version 2.1.0.
Assembly: mm10
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

source_name: Endoderm

extract_protocol:
Endodermal and gut tissues from 9SS to 27SS, were enzymatically dissociated using 0.25% trypsin (Gibco, 25200-056) for roughly 4 minutes at 37°C. The reaction was halted by the addition of 0.4 volumes of fetal bovine serum (FBS). The resultant cell suspension was centrifuged at 1000 rpm for 5 minutes at 4°C, followed by supernatant removal. To prepare single-cell suspensions from endodermal and gut samples, cells were incubated with anti-EpCAM-APC antibody (Invitrogen, 17-5791-82, dilution 1:100) in FACS buffer (comprising HBSS buffer with 1% FBS) for 20 minutes at 4°C in darkness. Following incubation, cells were washed with FACS buffer and subjected to analysis and sorting using BD FACSAriaTM Fusion flow cytometers. Dead cells were excluded from the analysis through staining with 1 µg/mL DAPI (Macklin, D807022).
The Smart-seq3xpress libraries were prepared following Smart3-seq3xpress's protocols.

value: Endoderm

tag: genotype


title: Endoderm Ngn3GFP HZ 27ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_023

tag: tissue


title: Endoderm Ngn3GFP HZ 27ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_020


title: Endoderm Ngn3GFP HZ 27ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_019


title: offspring control low-fat diet ZT0 rep1

description:
ZT_0_REP_0
OCL.tsv

tag: maternal stress


title: WT_Background_5

value: Brain

value: Background


title: Endoderm Ngn3GFP HZ 27ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_018


title: WT_TRAP_5

value: Cortex


title: Endoderm Ngn3GFP HZ 27ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_026


title: Astro_Glut1_KO_TRAP_5

value: GLUT1 flox/flox;GLAC +/wt

value: male


title: WT_TRAP_4

value: WT

value: GLAC +/wt


title: Endoderm Ngn3GFP HZ 27ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_015


title: Endoderm Ngn3GFP HZ 27ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_014


title: Endoderm Ngn3GFP HZ 27ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_011


title: Macrophages JQ1 Treatment Replicate 2

city: Aurora

first: Timothy

last: McKinsey

state: CO

department: Medicine

institute: University of Colorado Anschutz Medical Campus

description:
Library name: JQ1_2
p2_J7_S15

data_processing:
Analyses were performed using the mouse mm10_vM14_minusGm20388 genome.
RNA-seq datasets were aligned to the transcriptome using Tophat2 (version 2.0.11). Gene expression values were quantified using Cufflinks and Cuffnorm and differential expression was determined with Cuffdiff (version 2.2.0).
Significant RNA-seq genes (FDR < 0.05) with absolute log fold-change > 1 were uploaded to Metascape for process enrichment analysis using KEGG Pathway, GO Biological Processes, Reactome Gene Sets and CORUM.
Assembly: mm10
Supplementary files format and content: XLS file of differentially expressed genes

source_name: Heart

growth_protocol: For isolation of resident cardiac macrophages, ventricles were digested into single-cell suspensions and cells were purified using biotinylated anti-MerTK antibody and anti-biotin microbeads. Macrophages were isolated from 3 pooled hearts per condition.

extract_protocol:
Total RNA was prepared from MerTK+ macrophages using the Direct-zol RNA miniprep kit.
Complementary DNA libraries were prepared using the NEBNext Ultra Directional Library Preparation Kit following rRNA depletion using the NEB rRNA Depletion Kit. Sequencing libraries were submitted to the UC Denver Genomics and Microarray core facility for sequencing.

treatment_protocol: Wild-type C57BL/6 mice were treated with JQ1 (50 mg/kg) or vehicle control (50:50 DMSO:PEG-300) for 3 days.

value: Heart

value: Macrophages

value: Wild-type C57BL/6

value: JQ1 50mg/kg/day


title: Endoderm Ngn3GFP HZ 27ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_010


title: WT_Background_3


title: WT_Background_2


title: WT_TRAP_2

value: TRAP


title: Astro_Glut1_KO_TRAP_2


title: Astro_Glut1_KO_TRAP_1


title: Endoderm Ngn3GFP HZ 27ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_009


title: Endoderm Ngn3GFP HZ 27ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_008


title: Macrophages JQ1 Treatment Replicate 3

description:
Library name: JQ1_3
p2_J8_S16


title: WTcal5

value: PyMT tumor

value: PyMT

value: Epithenial cell

value: Calcipotriol


title: WT4

value: Ethanol


title: Macrophages Vehicle Treatment Replicate 2

description:
Library name: Vehicle_2
p2_C2_S11

value: Vehicle (50:50 DMSO:PEG-300)


title: Macrophages Vehicle Treatment Replicate 3

description:
Library name: Vehicle_3
p2_C3_S12


title: WTcal1


title: Astro_Glut1_KO_Background_2

value: Brain

value: Background


title: Endoderm Ngn3GFP HZ 27ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_006

value: Endoderm


title: Endoderm Ngn3GFP HZ 27ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_005


title: KO LMX1B 3

city: Riverside

first: Brendan

last: Gongol

state: Ca

address: 900 University Ave

institute: University of California, Riverside

description: Library name: LMX1B--_11_TGGTTGTT

data_processing:
RNA-seq analyses were performed using the systempipeR Bioconductor package. Reads were aligned to GRCm39 release 111 obtained from ensemble using hisat2.
Assembly: GRCm39
Supplementary files format and content: Excel files contain raw count values for each sample.
Supplementary files format and content: Excel files contain FPKM values for each sample.

source_name: Brain stem

extract_protocol:
Tissue samples were homogenized in TRIzol reagent from Life Technologies (cat # 10296-028) and RNA was isolated according to the manufacturer’s instructions.
RNA was prepared for sequencing using the NEXTflex™ Rapid Directional qRNA-Seq™ Library Prep Kit and sequenced using an Illumina HiSeq 2000.

value: Brain stem


title: WT1


title: Endoderm Ngn3GFP HZ 27ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_024


title: Endoderm Ngn3GFP HZ 27ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_022


title: KO LMX1B 2

description: Library name: LMX1B--_10_TGGCTCAG


title: Endoderm Ngn3GFP HZ 27ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_004


title: Endoderm Ngn3GFP HZ 27ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_003


title: Endoderm Ngn3GFP HZ 27ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_021


title: Endoderm Ngn3GFP HZ 27ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_017


title: Endoderm Ngn3GFP HZ 27ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_016


title: WT2


title: HT LMX1B 3

description: Library name: LMX1B+-_7_ACTTGATG


title: Endoderm Ngn3GFP HZ 27ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_013


title: HT LMX1B 2

description: Library name: LMX1B+-_6_TGACAGAC


title: Endoderm Ngn3GFP HZ 24ss b2 085, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_085


title: Endoderm Ngn3GFP HZ 27ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_001


title: Endoderm Ngn3GFP HZ 24ss b2 084, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_084


title: WT LMX1B 3

description: Library name: LMX1B++_4_CGATGTTT


title: Macrophages JQ1 Treatment Replicate 4

description:
Library name: JQ1_4
p2_J9_S17


title: WT LMX1B 2

description: Library name: LMX1B++_2_CGATGTTT


title: Endoderm Ngn3GFP HZ 24ss b2 083, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_083


title: Macrophages JQ1 Treatment Replicate 1

description:
Library name: JQ1_1
p2_J6_S14

value: JQ1 (50mg/kg/day)


title: Endoderm Ngn3GFP HZ 27ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_012


title: KO AMPK 3

description: Library name: flowcell538_lane1_pair1_GGTCGTGT

value: AMPK-/-


title: Endoderm Ngn3GFP HZ 24ss b2 081, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_081


title: WT LMX1B 1

description: Library name: LMX1B++_1_TAGAACAC


title: Macrophages Vehicle Treatment Replicate 4

description:
Library name: Vehicle_4
p2_C5_S13

value: Heart


title: Endoderm Ngn3GFP HZ 27ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_007


title: Macrophages Vehicle Treatment Replicate 1

description:
Library name: Vehicle_1
p2_C1_S10

value: Macrophages


title: Endoderm Ngn3GFP HZ 24ss b2 078, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_078


title: KO LMX1B 1

description: Library name: LMX1B--_9_TTGTTCCA


title: WT AMPK 2

description: Library name: flowcell538_lane1_pair1_TTGGTATG

value: AMPK+/+


title: Endoderm Ngn3GFP HZ 27ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_27ss_b2_002


title: Endoderm Ngn3GFP HZ 24ss b2 076, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_076


title: Endoderm Ngn3GFP HZ 24ss b2 074, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_074


title: iMEF, RNA-seq, rep2

city: Columbus

first: Mark

last: Parthun

state: Ohio

address: 1060 Carmack Rd.

department: Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
RNA-seq data was processed using the nf-core rnaseq pipeline version 3.13.12 with alignment by Star.
Assembly: mm10

source_name: iMEF

growth_protocol: Mouse embryonic fibroblasts were cultured at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle’s High Glucose Medium supplemented with 10% FBS, 1% glutamine, and 1% Penn-Strep and passaged approximately every 2-3 days.

extract_protocol:
RNA-seq was extracted from iMEFs using Total RNA purification plus kit from Norgen Biotek Corp. as previously described [Nagarajan et al. (2019), Aging Cell. https://doi.org/10.1111/acel.12992]
Libraries were prepared using the TruSeq RNA Sample Prep Kit.

value: iMEF

value: mouse embryonic fibroblast


title: Endoderm Ngn3GFP HZ 24ss b2 080, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_080


title: HT LMX1B 1

description: Library name: LMX1B+-_5_ACTTGATG


title: KO AMPK 2

description: Library name: flowcell538_lane1_pair1_TTGGAGGT


title: Endoderm Ngn3GFP HZ 24ss b2 082, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_082


title: Endoderm Ngn3GFP HZ 24ss b2 079, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_079


title: WT AMPK 3

description: Library name: flowcell538_lane1_pair1_CGATGTTT


title: KO AMPK 1

description: Library name: flowcell538_lane1_pair1_TTGTTCCA


title: Day 8 FLT3L

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description: 10X Genomics Chromium X

data_processing:
The raw sequencing files (FASTQ) for each of the four samples were initially assessed for read quality using the FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC(Ewels et al., 2016) programs. After quality control, the raw reads were aligned to the mouse genome (GRCm39) using Cell Ranger from 10x Genomics to identify the 10X cell barcodes and generate gene expression count matrix. Given that these samples were sequenced for gene expression as well as surface protein data, Cell Ranger was run with both the Gene Expression and Antibody Capture library_type options to generate the respective count matrices. The sample-specific count matrix files were imported into the Seurat package(Hao et al., 2024; Lun et al., 2016) in R for further processing and analysis. During quality control, cells with mitochondrial counts greater than 10%, cells that had less than 200 uniquely expressed genes or cells that had more than 7,500 uniquely expressed genes were filtered out to remove the dead cells, likely to be of poor-quality cells and potential doublets respectively. Each sample was normalized using the SCTransform algorithm(Choudhary and Satija, 2022; Hafemeister and Satija, 2019), after normalization all the four samples were integrated using the "IntegrateData" function in Seurat(Stuart et al., 2019).
Assembly: GRCm39
Supplementary files format and content: tsv
Supplementary files format and content: filtered barcode, features and matrix
Library strategy: CITE-seq

source_name: bone marrow

growth_protocol: 400ng/ml of FLT3L (BioXCell, cat# BE0342) in 3ml of RPMIc in a 6-well plate (Thermo Scientific™ BioLite™ Microwell Plates, cat #12-556-004) at 3e6 cells per well. RPMI complete media (RPMIc): RPMI (11875093, Gibco), 10% FBS (Sigma), 2 mmol/L of l-glutamine (25030081, Gibco), 1 mmol/L of sodium pyruvate (11360070, Gibco), 50 μmol/L of β-mercaptoethanol (M6250, Sigma), and 100 U/mL of Penicillin/Streptomycin (15140122, Gibco).

extract_protocol:
Samples were collected and stained with TotalSeq™-B Mouse Myeloid Cocktail, V1.0 (Biolegend, cat# 199904) separately after 8 days of culture. Stained samples were adjusted to a concentration of 1500 cells/μL and loaded onto a Chromium controller (10X Genomics) as per manufacturer protocol for GEM generation and barcoding.
Samples were prepared for sequencing using the 10X Genomics Single Cell NGS library prep platform in accordance with manufacturer’s instructions for capture of 20,000 cells per sample. Reverse transcription, cDNA amplification and sequencing libraries were generated using 10X Genomics Single Cell NGS NSQ2K kit - P4 100 cycle v3. Across samples, cells were sequenced to a target depth of 20,000 reads per cell.

treatment_protocol: 10ng/ml of ultra-purified Flagellin derived from S. typhimurium (InvivoGen, cat# tlrl-epstfla-5)

value: bone marrow


title: Endoderm Ngn3GFP HZ 24ss b2 075, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_075


title: genomic DNA isolated from whole blood [PROPGER368]

type: genomic

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on Illumina iScan scanner using iScan Control Software (ICS) with standard recommended Illumina scanner settings

data_processing:
R v3.6.3
Average Beta (non normalized) values for Illumina Infinium MethylationEPIC BeadChip probes.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood WB

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood samples using Puregene Blood kit (Qiagen) according to manufacturer’s instructions.

value: Blood WB

value: female

tag: phenotype

value: painful diabetic neuropathy


title: Endoderm Ngn3GFP HZ 24ss b2 068, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_068

tag: time


title: Endoderm Ngn3GFP HZ 24ss b2 077, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_077


title: Endoderm Ngn3GFP HZ 24ss b2 067, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_067


title: Endoderm Ngn3GFP HZ 24ss b2 073, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_073


title: genomic DNA isolated from whole blood [PROPGER342]

value: male

value: painles diabetic neuropathy


title: Day 8 FLT3L + FLA

description: 10X Genomics Chromium X


title: Endoderm Ngn3GFP HZ 24ss b2 072, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_072


title: iMEF, RNA-seq, rep1


title: Endoderm Ngn3GFP HZ 24ss b2 071, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_071


title: Endoderm Ngn3GFP HZ 24ss b2 070, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_070


title: genomic DNA isolated from whole blood [PROPGER379]


title: genomic DNA isolated from whole blood [PROPGER351]


title: genomic DNA isolated from whole blood [PROPGER318]


title: Endoderm Ngn3GFP HZ 24ss b2 069, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_069


title: Endoderm Ngn3GFP HZ 24ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_060


title: genomic DNA isolated from whole blood [PROPGER355]


title: WT AMPK 1

description: Library name: flowcell538_lane1_pair1_TAGAACAC


title: genomic DNA isolated from whole blood [PROPGER305]


title: Endoderm Ngn3GFP HZ 24ss b2 066, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_066


title: genomic DNA isolated from whole blood [PROPGER321]


title: iMEF, RNA-seq, rep3


title: Endoderm Ngn3GFP HZ 24ss b2 065, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_065


title: Endoderm Ngn3GFP HZ 24ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_059


title: Endoderm Ngn3GFP HZ 24ss b2 064, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_064


title: genomic DNA isolated from whole blood [PROPGER302]


title: genomic DNA isolated from whole blood [PROPGER314]


title: Endoderm Ngn3GFP HZ 24ss b2 063, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_063


title: Endoderm Ngn3GFP HZ 24ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_058


title: Endoderm Ngn3GFP HZ 24ss b2 062, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_062


title: Endoderm Ngn3GFP HZ 24ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_057


title: genomic DNA isolated from whole blood [PROPGER281]


title: genomic DNA isolated from whole blood [PROPGER278]


title: Endoderm Ngn3GFP HZ 24ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_056


title: Endoderm Ngn3GFP HZ 24ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_054


title: genomic DNA isolated from whole blood [PROPGER313]


title: genomic DNA isolated from whole blood [PROPGER275]


title: genomic DNA isolated from whole blood [PROPGER307]


title: genomic DNA isolated from whole blood [PROPGER293]


title: Endoderm Ngn3GFP HZ 24ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_055


title: genomic DNA isolated from whole blood [PROPGER274]


title: Endoderm Ngn3GFP HZ 24ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_061


title: Endoderm Ngn3GFP HZ 24ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_052


title: genomic DNA isolated from whole blood [PROPGER303]


title: genomic DNA isolated from whole blood [PROPGER270]


title: Endoderm Ngn3GFP HZ 24ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_051


title: genomic DNA isolated from whole blood [PROPGER268]


title: genomic DNA isolated from whole blood [PROPGER267]


title: genomic DNA isolated from whole blood [PROPGER263]


title: genomic DNA isolated from whole blood [PROPGER266]


title: Endoderm Ngn3GFP HZ 24ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_048


title: Endoderm Ngn3GFP HZ 24ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_049


title: Endoderm Ngn3GFP HZ 24ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_047


title: genomic DNA isolated from whole blood [PROPGER257]


title: genomic DNA isolated from whole blood [PROPGER255]


title: Endoderm Ngn3GFP HZ 24ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_045


title: genomic DNA isolated from whole blood [PROPGER246]


title: genomic DNA isolated from whole blood [PROPGER254]


title: genomic DNA isolated from whole blood [PROPGER245]


title: Endoderm Ngn3GFP HZ 24ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_043


title: Endoderm Ngn3GFP HZ 24ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_042


title: genomic DNA isolated from whole blood [PROPGER244]


title: Endoderm Ngn3GFP HZ 24ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_053


title: Endoderm Ngn3GFP HZ 24ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_040


title: Endoderm Ngn3GFP HZ 24ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_039


title: genomic DNA isolated from whole blood [PROPGER242]


title: genomic DNA isolated from whole blood [PROPGER243]


title: Endoderm Ngn3GFP HZ 24ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_041


title: Endoderm Ngn3GFP HZ 24ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_038


title: genomic DNA isolated from whole blood [PROPGER238]


title: genomic DNA isolated from whole blood [PROPGER226]


title: Endoderm Ngn3GFP HZ 24ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_050


title: genomic DNA isolated from whole blood [PROPGER227]


title: Endoderm Ngn3GFP HZ 24ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_035


title: genomic DNA isolated from whole blood [PROPGER221]


title: genomic DNA isolated from whole blood [PROPGER217]


title: Endoderm Ngn3GFP HZ 24ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_034


title: Endoderm Ngn3GFP HZ 24ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_036


title: genomic DNA isolated from whole blood [PROPGER213]


title: genomic DNA isolated from whole blood [PROPGER219]


title: genomic DNA isolated from whole blood [PROPGER209]


title: Endoderm Ngn3GFP HZ 24ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_044


title: genomic DNA isolated from whole blood [PROPGER208]


title: Endoderm Ngn3GFP HZ 24ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_030


title: Endoderm Ngn3GFP HZ 24ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_037


title: genomic DNA isolated from whole blood [PROPGER200]


title: Endoderm Ngn3GFP HZ 24ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_029


title: Endoderm Ngn3GFP HZ 24ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_028


title: Endoderm Ngn3GFP HZ 24ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_046


title: genomic DNA isolated from whole blood [PROPGER191]


title: genomic DNA isolated from whole blood [PROPGER202]


title: Endoderm Ngn3GFP HZ 24ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_031


title: genomic DNA isolated from whole blood [PROPGER188]


title: genomic DNA isolated from whole blood [PROPGER189]


title: Endoderm Ngn3GFP HZ 24ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_025


title: genomic DNA isolated from whole blood [PROPGER187]


title: Endoderm Ngn3GFP HZ 24ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_024


title: Endoderm Ngn3GFP HZ 24ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_026


title: Endoderm Ngn3GFP HZ 24ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_023


title: genomic DNA isolated from whole blood [PROPGER185]


title: Endoderm Ngn3GFP HZ 24ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_032


title: Endoderm Ngn3GFP HZ 24ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_033


title: genomic DNA isolated from whole blood [PROPGER180]


title: Endoderm Ngn3GFP HZ 24ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_022


title: Endoderm Ngn3GFP HZ 24ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_020


title: genomic DNA isolated from whole blood [PROPGER186]


title: genomic DNA isolated from whole blood [PROPGER178]


title: genomic DNA isolated from whole blood [PROPGER183]


title: Endoderm Ngn3GFP HZ 24ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_021


title: Endoderm Ngn3GFP HZ 24ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_019


title: genomic DNA isolated from whole blood [PROPGER175]


title: Endoderm Ngn3GFP HZ 24ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_018


title: genomic DNA isolated from whole blood [PROPGER174]


title: Endoderm Ngn3GFP HZ 24ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_017


title: genomic DNA isolated from whole blood [PROPGER172]


title: Endoderm Ngn3GFP HZ 24ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_027


title: genomic DNA isolated from whole blood [PROPGER170]


title: Endoderm Ngn3GFP HZ 24ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_016


title: genomic DNA isolated from whole blood [PROPGER168]


title: Endoderm Ngn3GFP HZ 24ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_015


title: Endoderm Ngn3GFP HZ 24ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_014


title: genomic DNA isolated from whole blood [PROPGER167]


title: genomic DNA isolated from whole blood [PROPGER166]


title: Endoderm Ngn3GFP HZ 24ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_013


title: Endoderm Ngn3GFP HZ 24ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_012


title: genomic DNA isolated from whole blood [PROPGER162]


title: genomic DNA isolated from whole blood [PROPGER163]


title: Endoderm Ngn3GFP HZ 24ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_009


title: genomic DNA isolated from whole blood [PROPGER156]


title: Endoderm Ngn3GFP HZ 24ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_011


title: genomic DNA isolated from whole blood [PROPGER153]


title: genomic DNA isolated from whole blood [PROPGER160]


title: Endoderm Ngn3GFP HZ 24ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_008


title: genomic DNA isolated from whole blood [PROPGER154]


title: genomic DNA isolated from whole blood [PROPGER155]


title: Endoderm Ngn3GFP HZ 24ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_005


title: Endoderm Ngn3GFP HZ 24ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_007


title: Endoderm Ngn3GFP HZ 24ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_006


title: genomic DNA isolated from whole blood [PROPGER152]


title: Endoderm Ngn3GFP HZ 24ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_010


title: Endoderm Ngn3GFP HZ 24ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_002


title: Endoderm Ngn3GFP HZ 24ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_003


title: genomic DNA isolated from whole blood [PROPGER149]


title: genomic DNA isolated from whole blood [PROPGER148]


title: Endoderm Ngn3GFP HZ 24ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_004


title: Endoderm Ngn3GFP HZ 24ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_24ss_b2_001


title: Endoderm Ngn3GFP HZ 21ss b2 149, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_149


title: genomic DNA isolated from whole blood [PROPGER145]


title: genomic DNA isolated from whole blood [PROPGER146]


title: genomic DNA isolated from whole blood [PROPGER143]


title: Endoderm Ngn3GFP HZ 21ss b2 148, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_148


title: genomic DNA isolated from whole blood [PROPGER142]


title: Endoderm Ngn3GFP HZ 21ss b2 146, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_146


title: Endoderm Ngn3GFP HZ 21ss b2 145, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_145


title: genomic DNA isolated from whole blood [PROPGER137]


title: genomic DNA isolated from whole blood [PROPGER141]


title: genomic DNA isolated from whole blood [PROPGER127]


title: Endoderm Ngn3GFP HZ 21ss b2 143, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_143


title: Endoderm Ngn3GFP HZ 21ss b2 142, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_142


title: Endoderm Ngn3GFP HZ 21ss b2 141, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_141


title: genomic DNA isolated from whole blood [PROPGER134]


title: genomic DNA isolated from whole blood [PROPGER150]


title: Endoderm Ngn3GFP HZ 21ss b2 144, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_144


title: Endoderm Ngn3GFP HZ 21ss b2 140, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_140


title: genomic DNA isolated from whole blood [PROPGER123]


title: genomic DNA isolated from whole blood [PROPGER147]


title: genomic DNA isolated from whole blood [PROPGER121]


title: genomic DNA isolated from whole blood [PROPGER110]


title: Endoderm Ngn3GFP HZ 21ss b2 147, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_147


title: genomic DNA isolated from whole blood [PROPGER119]


title: Endoderm Ngn3GFP HZ 21ss b2 138, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_138


title: genomic DNA isolated from whole blood [PROPGER117]


title: Endoderm Ngn3GFP HZ 21ss b2 139, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_139


title: Endoderm Ngn3GFP HZ 21ss b2 134, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_134


title: Endoderm Ngn3GFP HZ 21ss b2 136, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_136


title: Endoderm Ngn3GFP HZ 21ss b2 133, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_133


title: Endoderm Ngn3GFP HZ 21ss b2 137, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_137


title: Endoderm Ngn3GFP HZ 21ss b2 135, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_135


title: genomic DNA isolated from whole blood [PROPGER104]


title: genomic DNA isolated from whole blood [PROPGER124]


title: genomic DNA isolated from whole blood [PROPGER102]


title: Endoderm Ngn3GFP HZ 21ss b2 132, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_132


title: genomic DNA isolated from whole blood [PROPGER101]


title: genomic DNA isolated from whole blood [PROPGER103]


title: Endoderm Ngn3GFP HZ 21ss b2 131, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_131


title: Endoderm Ngn3GFP HZ 21ss b2 130, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_130


title: Endoderm Ngn3GFP HZ 21ss b2 129, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_129


title: genomic DNA isolated from whole blood [PROPGER100]


title: Endoderm Ngn3GFP HZ 21ss b2 128, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_128


title: genomic DNA isolated from whole blood [PROPGER099]


title: Endoderm Ngn3GFP HZ 21ss b2 127, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_127


title: Endoderm Ngn3GFP HZ 21ss b2 126, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_126


title: genomic DNA isolated from whole blood [PROPGER094]


title: Endoderm Ngn3GFP HZ 21ss b2 125, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_125


title: genomic DNA isolated from whole blood [PROPGER108]


title: Endoderm Ngn3GFP HZ 21ss b2 124, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_124


title: Endoderm Ngn3GFP HZ 21ss b2 123, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_123


title: genomic DNA isolated from whole blood [PROPGER093]


title: genomic DNA isolated from whole blood [PROPGER089]


title: genomic DNA isolated from whole blood [PROPGER092]


title: genomic DNA isolated from whole blood [PROPGER087]


title: genomic DNA isolated from whole blood [PROPGER107]


title: Endoderm Ngn3GFP HZ 21ss b2 120, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_120


title: Endoderm Ngn3GFP HZ 21ss b2 121, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_121


title: Endoderm Ngn3GFP HZ 21ss b2 122, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_122


title: genomic DNA isolated from whole blood [PROPGER078]


title: genomic DNA isolated from whole blood [PROPGER079]


title: genomic DNA isolated from whole blood [PROPGER083]


title: Endoderm Ngn3GFP HZ 21ss b2 118, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_118


title: genomic DNA isolated from whole blood [PROPGER096]


title: Endoderm Ngn3GFP HZ 21ss b2 117, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_117


title: genomic DNA isolated from whole blood [PROPGER068]


title: Endoderm Ngn3GFP HZ 21ss b2 116, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_116


title: genomic DNA isolated from whole blood [PROPGER072]


title: Endoderm Ngn3GFP HZ 21ss b2 113, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_113


title: Endoderm Ngn3GFP HZ 21ss b2 112, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_112


title: Endoderm Ngn3GFP HZ 21ss b2 115, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_115


title: genomic DNA isolated from whole blood [PROPGER070]


title: Endoderm Ngn3GFP HZ 21ss b2 108, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_108


title: genomic DNA isolated from whole blood [PROPGER054]


title: Endoderm Ngn3GFP HZ 21ss b2 114, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_114


title: genomic DNA isolated from whole blood [PROPGER064]


title: genomic DNA isolated from whole blood [PROPGER086]


title: genomic DNA isolated from whole blood [PROPGER053]


title: Endoderm Ngn3GFP HZ 21ss b2 111, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_111


title: genomic DNA isolated from whole blood [PROPGER067]


title: genomic DNA isolated from whole blood [PROPGER066]


title: genomic DNA isolated from whole blood [PROPGER063]


title: genomic DNA isolated from whole blood [PROPGER085]


title: Endoderm Ngn3GFP HZ 21ss b2 109, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_109


title: genomic DNA isolated from whole blood [PROPGER051]


title: genomic DNA isolated from whole blood [PROPGER048]


title: genomic DNA isolated from whole blood [PROPGER046]


title: Endoderm Ngn3GFP HZ 21ss b2 119, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_119


title: genomic DNA isolated from whole blood [PROPGER043]


title: Endoderm Ngn3GFP HZ 21ss b2 104, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_104


title: genomic DNA isolated from whole blood [PROPGER045]


title: Endoderm Ngn3GFP HZ 21ss b2 106, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_106


title: Endoderm Ngn3GFP HZ 21ss b2 105, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_105


title: Endoderm Ngn3GFP HZ 21ss b2 101, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_101


title: genomic DNA isolated from whole blood [PROPGER041]


title: Endoderm Ngn3GFP HZ 21ss b2 102, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_102


title: genomic DNA isolated from whole blood [PROPGER039]


title: Endoderm Ngn3GFP HZ 21ss b2 110, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_110


title: genomic DNA isolated from whole blood [PROPGER034]


title: Endoderm Ngn3GFP HZ 21ss b2 107, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_107


title: Endoderm Ngn3GFP HZ 21ss b2 100, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_100


title: genomic DNA isolated from whole blood [PROPGER031]


title: genomic DNA isolated from whole blood [PROPGER030]


title: Endoderm Ngn3GFP HZ 21ss b2 097, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_097


title: Endoderm Ngn3GFP HZ 21ss b2 099, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_099


title: genomic DNA isolated from whole blood [PROPGER029]


title: genomic DNA isolated from whole blood [PROPGER028]


title: Endoderm Ngn3GFP HZ 21ss b2 096, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_096


title: Endoderm Ngn3GFP HZ 21ss b2 095, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_095


title: genomic DNA isolated from whole blood [PROPGER024]


title: genomic DNA isolated from whole blood [PROPGER022]


title: Endoderm Ngn3GFP HZ 21ss b2 093, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_093


title: Endoderm Ngn3GFP HZ 21ss b2 103, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_103


title: Endoderm Ngn3GFP HZ 21ss b2 094, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_094


title: Endoderm Ngn3GFP HZ 21ss b2 092, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_092


title: genomic DNA isolated from whole blood [PROPGER021]


title: Endoderm Ngn3GFP HZ 21ss b2 089, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_089


title: genomic DNA isolated from whole blood [PROPGER019]


title: Endoderm Ngn3GFP HZ 21ss b2 091, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_091


title: genomic DNA isolated from whole blood [PROPGER014]


title: genomic DNA isolated from whole blood [PROPGER033]


title: Endoderm Ngn3GFP HZ 21ss b2 088, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_088


title: Endoderm Ngn3GFP HZ 21ss b2 090, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_090


title: genomic DNA isolated from whole blood [PROPGER016]


title: genomic DNA isolated from whole blood [PROPGER015]


title: genomic DNA isolated from whole blood [PROPGER009]


title: Endoderm Ngn3GFP HZ 21ss b2 098, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_098


title: Endoderm Ngn3GFP HZ 21ss b2 087, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_087


title: genomic DNA isolated from whole blood [PROPGER012]


title: genomic DNA isolated from whole blood [PROPGER018]


title: Endoderm Ngn3GFP HZ 21ss b2 084, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_084


title: Endoderm Ngn3GFP HZ 21ss b2 083, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_083


title: Endoderm Ngn3GFP HZ 21ss b2 082, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_082


title: Endoderm Ngn3GFP HZ 21ss b2 085, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_085


title: Endoderm Ngn3GFP HZ 21ss b2 078, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_078


title: genomic DNA isolated from whole blood [PROPENG219]


title: genomic DNA isolated from whole blood [PROPGER011]


title: genomic DNA isolated from whole blood [PROPGER007]


title: genomic DNA isolated from whole blood [PROPGER008]


title: genomic DNA isolated from whole blood [PROPGER013]


title: Endoderm Ngn3GFP HZ 21ss b2 081, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_081


title: genomic DNA isolated from whole blood [PROPENG221]


title: genomic DNA isolated from whole blood [PROPENG223]


title: Endoderm Ngn3GFP HZ 21ss b2 080, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_080


title: Endoderm Ngn3GFP HZ 21ss b2 086, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_086


title: Endoderm Ngn3GFP HZ 21ss b2 079, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_079


title: Endoderm Ngn3GFP HZ 21ss b2 076, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_076


title: genomic DNA isolated from whole blood [PROPENG212]


title: Endoderm Ngn3GFP HZ 21ss b2 074, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_074


title: genomic DNA isolated from whole blood [PROPENG211]


title: Endoderm Ngn3GFP HZ 21ss b2 077, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_077


title: genomic DNA isolated from whole blood [PROPENG208]


title: genomic DNA isolated from whole blood [PROPENG207]


title: Endoderm Ngn3GFP HZ 21ss b2 071, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_071


title: Endoderm Ngn3GFP HZ 21ss b2 070, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_070


title: genomic DNA isolated from whole blood [PROPENG216]


title: genomic DNA isolated from whole blood [PROPENG215]


title: genomic DNA isolated from whole blood [PROPENG213]


title: Endoderm Ngn3GFP HZ 21ss b2 075, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_075


title: genomic DNA isolated from whole blood [PROPENG209]


title: Endoderm Ngn3GFP HZ 21ss b2 072, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_072


title: Endoderm Ngn3GFP HZ 21ss b2 069, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_069


title: Endoderm Ngn3GFP HZ 21ss b2 073, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_073


title: genomic DNA isolated from whole blood [PROPENG205]


title: genomic DNA isolated from whole blood [PROPENG202]


title: genomic DNA isolated from whole blood [PROPENG198]


title: Endoderm Ngn3GFP HZ 21ss b2 068, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_068


title: Endoderm Ngn3GFP HZ 21ss b2 065, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_065


title: Endoderm Ngn3GFP HZ 21ss b2 063, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_063


title: genomic DNA isolated from whole blood [PROPENG201]


title: genomic DNA isolated from whole blood [PROPENG203]


title: genomic DNA isolated from whole blood [PROPENG199]


title: Endoderm Ngn3GFP HZ 21ss b2 066, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_066


title: genomic DNA isolated from whole blood [PROPENG192]


title: Endoderm Ngn3GFP HZ 21ss b2 067, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_067


title: Endoderm Ngn3GFP HZ 21ss b2 062, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_062


title: Endoderm Ngn3GFP HZ 21ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_058


title: Endoderm Ngn3GFP HZ 21ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_061


title: Endoderm Ngn3GFP HZ 21ss b2 064, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_064


title: Endoderm Ngn3GFP HZ 21ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_057


title: genomic DNA isolated from whole blood [PROPENG183]


title: Endoderm Ngn3GFP HZ 21ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_059


title: Endoderm Ngn3GFP HZ 21ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_056


title: Endoderm Ngn3GFP HZ 21ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_055


title: genomic DNA isolated from whole blood [PROPENG182]


title: genomic DNA isolated from whole blood [PROPENG191]


title: genomic DNA isolated from whole blood [PROPENG184]


title: genomic DNA isolated from whole blood [PROPENG186]


title: genomic DNA isolated from whole blood [PROPENG185]


title: Endoderm Ngn3GFP HZ 21ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_053


title: genomic DNA isolated from whole blood [PROPENG175]


title: Endoderm Ngn3GFP HZ 21ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_052


title: Endoderm Ngn3GFP HZ 21ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_051


title: genomic DNA isolated from whole blood [PROPENG169]


title: genomic DNA isolated from whole blood [PROPENG189]


title: genomic DNA isolated from whole blood [PROPENG167]


title: genomic DNA isolated from whole blood [PROPENG188]


title: Endoderm Ngn3GFP HZ 21ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_060


title: Endoderm Ngn3GFP HZ 21ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_049


title: Endoderm Ngn3GFP HZ 21ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_050


title: genomic DNA isolated from whole blood [PROPENG160]


title: genomic DNA isolated from whole blood [PROPENG165]


title: Endoderm Ngn3GFP HZ 21ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_048


title: genomic DNA isolated from whole blood [PROPENG159]


title: Endoderm Ngn3GFP HZ 21ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_047


title: genomic DNA isolated from whole blood [PROPENG155]


title: genomic DNA isolated from whole blood [PROPENG156]


title: Endoderm Ngn3GFP HZ 21ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_054


title: genomic DNA isolated from whole blood [PROPENG153]


title: Endoderm Ngn3GFP HZ 21ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_045


title: Endoderm Ngn3GFP HZ 21ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_046


title: Endoderm Ngn3GFP HZ 21ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_044


title: genomic DNA isolated from whole blood [PROPENG178]


title: genomic DNA isolated from whole blood [PROPENG152]


title: genomic DNA isolated from whole blood [PROPENG151]


title: Endoderm Ngn3GFP HZ 21ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_042


title: genomic DNA isolated from whole blood [PROPENG176]


title: Endoderm Ngn3GFP HZ 21ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_041


title: genomic DNA isolated from whole blood [PROPENG147]


title: genomic DNA isolated from whole blood [PROPENG146]


title: genomic DNA isolated from whole blood [PROPENG143]


title: Endoderm Ngn3GFP HZ 21ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_039


title: genomic DNA isolated from whole blood [PROPENG142]


title: genomic DNA isolated from whole blood [PROPENG141]


title: Endoderm Ngn3GFP HZ 21ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_037


title: Endoderm Ngn3GFP HZ 21ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_036


title: genomic DNA isolated from whole blood [PROPENG136]


title: Endoderm Ngn3GFP HZ 21ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_035


title: genomic DNA isolated from whole blood [PROPENG130]


title: Endoderm Ngn3GFP HZ 21ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_038


title: Endoderm Ngn3GFP HZ 21ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_034


title: Endoderm Ngn3GFP HZ 21ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_043


title: genomic DNA isolated from whole blood [PROPENG125]


title: Endoderm Ngn3GFP HZ 21ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_033


title: Endoderm Ngn3GFP HZ 21ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_032


title: genomic DNA isolated from whole blood [PROPENG124]


title: Endoderm Ngn3GFP HZ 21ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_030


title: genomic DNA isolated from whole blood [PROPENG128]


title: Endoderm Ngn3GFP HZ 21ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_031


title: genomic DNA isolated from whole blood [PROPENG118]


title: Endoderm Ngn3GFP HZ 21ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_027


title: genomic DNA isolated from whole blood [PROPENG122]


title: Endoderm Ngn3GFP HZ 21ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_028


title: Endoderm Ngn3GFP HZ 21ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_026


title: Endoderm Ngn3GFP HZ 21ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_029


title: genomic DNA isolated from whole blood [PROPENG115]


title: Endoderm Ngn3GFP HZ 21ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_040


title: genomic DNA isolated from whole blood [PROPENG111]


title: Endoderm Ngn3GFP HZ 21ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_025


title: genomic DNA isolated from whole blood [PROPENG105]


title: Endoderm Ngn3GFP HZ 21ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_024


title: genomic DNA isolated from whole blood [PROPENG108]


title: genomic DNA isolated from whole blood [PROPENG102]


title: Endoderm Ngn3GFP HZ 21ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_022


title: genomic DNA isolated from whole blood [PROPENG126]


title: genomic DNA isolated from whole blood [PROPENG101]


title: Endoderm Ngn3GFP HZ 21ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_023


title: genomic DNA isolated from whole blood [PROPENG104]


title: Endoderm Ngn3GFP HZ 21ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_021


title: genomic DNA isolated from whole blood [PROPENG099]


title: Endoderm Ngn3GFP HZ 21ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_020


title: genomic DNA isolated from whole blood [PROPENG117]


title: Endoderm Ngn3GFP HZ 21ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_019


title: genomic DNA isolated from whole blood [PROPENG096]


title: Endoderm Ngn3GFP HZ 21ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_018


title: genomic DNA isolated from whole blood [PROPENG095]


title: genomic DNA isolated from whole blood [PROPENG097]


title: Endoderm Ngn3GFP HZ 21ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_016


title: genomic DNA isolated from whole blood [PROPENG093]


title: Endoderm Ngn3GFP HZ 21ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_015


title: Endoderm Ngn3GFP HZ 21ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_014


title: Endoderm Ngn3GFP HZ 21ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_012


title: Endoderm Ngn3GFP HZ 21ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_013


title: genomic DNA isolated from whole blood [PROPENG087]


title: Endoderm Ngn3GFP HZ 21ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_011


title: genomic DNA isolated from whole blood [PROPENG085]


title: Endoderm Ngn3GFP HZ 21ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_010


title: genomic DNA isolated from whole blood [PROPENG084]


title: genomic DNA isolated from whole blood [PROPENG079]


title: Endoderm Ngn3GFP HZ 21ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_009


title: genomic DNA isolated from whole blood [PROPENG078]


title: Endoderm Ngn3GFP HZ 21ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_007


title: genomic DNA isolated from whole blood [PROPENG083]


title: Endoderm Ngn3GFP HZ 21ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_008


title: Endoderm Ngn3GFP HZ 21ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_006


title: Endoderm Ngn3GFP HZ 21ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_017


title: Endoderm Ngn3GFP HZ 21ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_003


title: genomic DNA isolated from whole blood [PROPENG069]


title: genomic DNA isolated from whole blood [PROPENG076]


title: Endoderm Ngn3GFP HZ 21ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_002


title: genomic DNA isolated from whole blood [PROPENG089]


title: Endoderm Ngn3GFP HZ 21ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_005


title: Endoderm Ngn3GFP HZ 18ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_061


title: Endoderm Ngn3GFP HZ 21ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_004


title: genomic DNA isolated from whole blood [PROPENG054]


title: genomic DNA isolated from whole blood [PROPENG070]


title: Endoderm Ngn3GFP HZ 21ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_21ss_b2_001


title: genomic DNA isolated from whole blood [PROPENG094]


title: genomic DNA isolated from whole blood [PROPENG072]


title: genomic DNA isolated from whole blood [PROPENG060]


title: genomic DNA isolated from whole blood [PROPENG091]


title: genomic DNA isolated from whole blood [PROPENG056]


title: Endoderm Ngn3GFP HZ 18ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_060


title: genomic DNA isolated from whole blood [PROPENG053]


title: Endoderm Ngn3GFP HZ 18ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_059


title: genomic DNA isolated from whole blood [PROPENG052]


title: Endoderm Ngn3GFP HZ 18ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_058


title: genomic DNA isolated from whole blood [PROPENG043]


title: Endoderm Ngn3GFP HZ 18ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_057


title: Endoderm Ngn3GFP HZ 18ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_056


title: genomic DNA isolated from whole blood [PROPENG030]


title: genomic DNA isolated from whole blood [PROPENG037]


title: Endoderm Ngn3GFP HZ 18ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_055


title: Endoderm Ngn3GFP HZ 18ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_054


title: genomic DNA isolated from whole blood [PROPENG025]


title: Endoderm Ngn3GFP HZ 18ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_053


title: genomic DNA isolated from whole blood [PROPENG020]


title: Endoderm Ngn3GFP HZ 18ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_052


title: genomic DNA isolated from whole blood [PROPENG019]


title: genomic DNA isolated from whole blood [PROPENG014]


title: Endoderm Ngn3GFP HZ 18ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_051


title: genomic DNA isolated from whole blood [PROPENG004]


title: Endoderm Ngn3GFP HZ 18ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_049


title: Endoderm Ngn3GFP HZ 18ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_048


title: genomic DNA isolated from whole blood [12509181]

value: control


title: genomic DNA isolated from whole blood [12509151]


title: Endoderm Ngn3GFP HZ 18ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_047


title: genomic DNA isolated from whole blood [12509161]


title: Endoderm Ngn3GFP HZ 18ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_045


title: Endoderm Ngn3GFP HZ 18ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_044


title: genomic DNA isolated from whole blood [12509112]


title: Endoderm Ngn3GFP HZ 18ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_046


title: genomic DNA isolated from whole blood [PROPENG040]


title: Endoderm Ngn3GFP HZ 18ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_043


title: Endoderm Ngn3GFP HZ 18ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_042


title: genomic DNA isolated from whole blood [12509111]


title: genomic DNA isolated from whole blood [12509101]


title: genomic DNA isolated from whole blood [12509091]


title: Endoderm Ngn3GFP HZ 18ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_041


title: genomic DNA isolated from whole blood [12509071]


title: Endoderm Ngn3GFP HZ 18ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_040


title: genomic DNA isolated from whole blood [12509191]


title: genomic DNA isolated from whole blood [12509061]


title: Endoderm Ngn3GFP HZ 18ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_038


title: Endoderm Ngn3GFP HZ 18ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_039


title: genomic DNA isolated from whole blood [12509051]


title: Endoderm Ngn3GFP HZ 18ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_050


title: genomic DNA isolated from whole blood [12509031]


title: genomic DNA isolated from whole blood [12509022]


title: genomic DNA isolated from whole blood [12509021]


title: Endoderm Ngn3GFP HZ 18ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_036


title: Endoderm Ngn3GFP HZ 18ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_035


title: genomic DNA isolated from whole blood [12509011]


title: genomic DNA isolated from whole blood [12509131]


title: genomic DNA isolated from whole blood [12509002]


title: Endoderm Ngn3GFP HZ 18ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_033


title: Endoderm Ngn3GFP HZ 18ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_032


title: genomic DNA isolated from whole blood [12509001]


title: genomic DNA isolated from whole blood [12500571]


title: Endoderm Ngn3GFP HZ 18ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_031


title: genomic DNA isolated from whole blood [12500511]


title: Endoderm Ngn3GFP HZ 18ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_030


title: genomic DNA isolated from whole blood [12500471]


title: genomic DNA isolated from whole blood [12500501]


title: Endoderm Ngn3GFP HZ 18ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_029


title: Endoderm Ngn3GFP HZ 18ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_027


title: genomic DNA isolated from whole blood [12500451]


title: Endoderm Ngn3GFP HZ 18ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_026


title: genomic DNA isolated from whole blood [12500401]


title: genomic DNA isolated from whole blood [12500331]


title: Endoderm Ngn3GFP HZ 18ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_024


title: Endoderm Ngn3GFP HZ 18ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_025


title: genomic DNA isolated from whole blood [12500301]


title: Endoderm Ngn3GFP HZ 18ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_037


title: Endoderm Ngn3GFP HZ 18ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_022


title: genomic DNA isolated from whole blood [12500271]


title: genomic DNA isolated from whole blood [12500262]


title: Endoderm Ngn3GFP HZ 18ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_021


title: Endoderm Ngn3GFP HZ 18ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_020


title: genomic DNA isolated from whole blood [12500241]


title: Endoderm Ngn3GFP HZ 18ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_019


title: genomic DNA isolated from whole blood [12500261]


title: Endoderm Ngn3GFP HZ 18ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_023


title: genomic DNA isolated from whole blood [12500221]


title: Endoderm Ngn3GFP HZ 18ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_018


title: genomic DNA isolated from whole blood [12500141]


title: Endoderm Ngn3GFP HZ 18ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_017


title: Endoderm Ngn3GFP HZ 18ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_028


title: genomic DNA isolated from whole blood [12500131]


title: Endoderm Ngn3GFP HZ 18ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_015


title: Endoderm Ngn3GFP HZ 18ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_014


title: genomic DNA isolated from whole blood [12500121]


title: genomic DNA isolated from whole blood [12500101]


title: genomic DNA isolated from whole blood [12500391]


title: Endoderm Ngn3GFP HZ 18ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_013


title: genomic DNA isolated from whole blood [12500081]


title: Endoderm Ngn3GFP HZ 18ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_012


title: Endoderm Ngn3GFP HZ 18ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_011


title: Endoderm Ngn3GFP HZ 18ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_034


title: genomic DNA isolated from whole blood [12500052]


title: genomic DNA isolated from whole blood [12500051]


title: Endoderm Ngn3GFP HZ 18ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_009


title: genomic DNA isolated from whole blood [12500032]


title: genomic DNA isolated from whole blood [12500031]


title: Endoderm Ngn3GFP HZ 18ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_008


title: genomic DNA isolated from whole blood [2100615]


title: Endoderm Ngn3GFP HZ 18ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_007


title: Endoderm Ngn3GFP HZ 18ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_006


title: Endoderm Ngn3GFP HZ 18ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_005


title: genomic DNA isolated from whole blood [2100610]


title: Endoderm Ngn3GFP HZ 18ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_004


title: Endoderm Ngn3GFP HZ 18ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_016


title: Endoderm Ngn3GFP HZ 18ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_003


title: genomic DNA isolated from whole blood [2100575]


title: Endoderm Ngn3GFP HZ 18ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_002


title: genomic DNA isolated from whole blood [2100548]


title: Endoderm Ngn3GFP HZ 18ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_001


title: genomic DNA isolated from whole blood [2100533]


title: genomic DNA isolated from whole blood [12500082]


title: Endoderm Ngn3GFP HZ 15ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_15ss_b2_005


title: genomic DNA isolated from whole blood [2100523]


title: genomic DNA isolated from whole blood [12500061]


title: Endoderm Ngn3GFP HZ 18ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_18ss_b2_010


title: genomic DNA isolated from whole blood [2100504]


title: Endoderm Ngn3GFP HZ 15ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_15ss_b2_003


title: genomic DNA isolated from whole blood [2100499]


title: genomic DNA isolated from whole blood [2100497]


title: genomic DNA isolated from whole blood [2100465]


title: Endoderm Ngn3GFP HZ 15ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_15ss_b2_002


title: Endoderm Ngn3GFP HM 27ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_27ss_b2_004


title: genomic DNA isolated from whole blood [2100453]


title: Endoderm Ngn3GFP HM 27ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_27ss_b2_002


title: genomic DNA isolated from whole blood [2100459]


title: genomic DNA isolated from whole blood [2100612]


title: Endoderm Ngn3GFP HM 27ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_27ss_b2_001


title: Endoderm Ngn3GFP HM 27ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_27ss_b2_003


title: genomic DNA isolated from whole blood [2100433]


title: genomic DNA isolated from whole blood [2100423]


title: Endoderm Ngn3GFP HM 24ss b2 080, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_080


title: Endoderm Ngn3GFP HM 24ss b2 079, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_079


title: genomic DNA isolated from whole blood [2100401]


title: Endoderm Ngn3GFP HM 24ss b2 078, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_078


title: genomic DNA isolated from whole blood [2100410]


title: Endoderm Ngn3GFP HZ 15ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_15ss_b2_004


title: Endoderm Ngn3GFP HM 24ss b2 076, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_076


title: Endoderm Ngn3GFP HM 24ss b2 077, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_077


title: genomic DNA isolated from whole blood [2100385]


title: Endoderm Ngn3GFP HM 24ss b2 075, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_075


title: genomic DNA isolated from whole blood [2100380]


title: genomic DNA isolated from whole blood [2100358]


title: Endoderm Ngn3GFP HM 24ss b2 074, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_074


title: Endoderm Ngn3GFP HM 24ss b2 073, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_073


title: genomic DNA isolated from whole blood [2100330]


title: Endoderm Ngn3GFP HM 24ss b2 072, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_072


title: genomic DNA isolated from whole blood [2100332]


title: Endoderm Ngn3GFP HM 24ss b2 071, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_071


title: genomic DNA isolated from whole blood [2100448]


title: Endoderm Ngn3GFP HZ 15ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HZ_15ss_b2_001


title: genomic DNA isolated from whole blood [2100323]


title: Endoderm Ngn3GFP HM 24ss b2 070, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_070


title: genomic DNA isolated from whole blood [2100312]


title: genomic DNA isolated from whole blood [2100307]


title: genomic DNA isolated from whole blood [2100295]


title: Endoderm Ngn3GFP HM 24ss b2 068, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_068


title: Endoderm Ngn3GFP HM 24ss b2 069, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_069


title: Endoderm Ngn3GFP HM 24ss b2 067, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_067


title: genomic DNA isolated from whole blood [2100284]


title: genomic DNA isolated from whole blood [2100285]


title: genomic DNA isolated from whole blood [2100263]


title: Endoderm Ngn3GFP HM 24ss b2 066, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_066


title: genomic DNA isolated from whole blood [2100394]


title: Endoderm Ngn3GFP HM 24ss b2 064, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_064


title: Endoderm Ngn3GFP HM 24ss b2 065, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_065


title: Endoderm Ngn3GFP HM 24ss b2 062, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_062


title: genomic DNA isolated from whole blood [2100231]


title: genomic DNA isolated from whole blood [2100229]


title: genomic DNA isolated from whole blood [2100242]


title: Endoderm Ngn3GFP HM 24ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_060


title: genomic DNA isolated from whole blood [2100232]


title: Endoderm Ngn3GFP HM 24ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_061


title: Endoderm Ngn3GFP HM 24ss b2 063, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_063


title: genomic DNA isolated from whole blood [2100224]


title: genomic DNA isolated from whole blood [2100222]


title: Endoderm Ngn3GFP HM 24ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_059


title: genomic DNA isolated from whole blood [2100209]


title: Endoderm Ngn3GFP HM 24ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_055


title: genomic DNA isolated from whole blood [2100203]


title: Endoderm Ngn3GFP HM 24ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_058


title: Endoderm Ngn3GFP HM 24ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_054


title: UR.14785.DLB.88

city: Royal Oak

first: Stewart

middle: F

last: Graham

state: Michigan

address: 3811 West 13 Mile Road, Suite 415

department: OBGYN

institute: Corewell Health - Research Institute

description: DLB analysis

hyb_protocol: Illumina Infinium MethylationEPIC BeadChip array

scan_protocol: Illumina iScan

data_processing: We performed array data preprocessing and normalization to reduce technical variation. Subsequent analyses were conducted using the normalized data. Beta values were preprocessed using preprocessNoob function from R package minfi v1.48.0 with the default parameters. Noob preprocessing method performs background and dye bias correction 16. Probes with infinite methylation values or detection p-values higher than 0.01 (P> 0.01) were marked as missing. Probes with missing values in more than 50% of samples, as well as probes on sex chromosomes, and common (minor allele frequency >0.05) single nucleotide polymorphisms (SNPs) were removed. Missing probe methylation values were imputed using impute.knn function from R package impute v1.76.0 with 5 nearest neighbors. Probes with a standard deviation less than 0.01 were considered invariant and were removed from further analysis.

label: Cy3, Cy5

extract_protocol: Genomic DNA was extracted from lyophilized and milled brain tissue using the QIAamp DNA Mini Kit (Qiagen  Hilden  Germany)

tag: condition

value: DLB

tag: age

value: M

tag: pmdelay

tag: row

tag: col


title: Endoderm Ngn3GFP HM 24ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_057

value: Endoderm


title: Endoderm Ngn3GFP HM 24ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_053


title: UR.14784.DLB.87

description: DLB analysis

label_protocol: Illumina Infinium MethylationEPIC BeadChip array


title: genomic DNA isolated from whole blood [2100182]


title: Endoderm Ngn3GFP HM 24ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_056


title: genomic DNA isolated from whole blood [2100159]


title: Meiotic cells, day 15, scATACseq, rep2

city: Boston

first: Merrick

middle: Pierson

last: Smela

address: 3 Blackfan Circle

institute: Harvard University

description: Library name: Meiosis_F3_ATAC

library_source: genomic single cell

data_processing:
10X CellRanger ARC (version 2.0.2)
Assembly: GRCh38
Supplementary files format and content: .h5mu files (gene counts and ATAC peaks) output from 10X CellRanger ARC

growth_protocol: A constitutive expression vector for the anti-apoptotic factor BCL2, as well as doxycycline-inducible expression vectors for meiosis-promoting factors (HOXB5, BOLL, and MEIOC), were integrated into three lines of human iPSCs (F2 female, F3 female, and PGP1 male) using PiggyBac transposase. The iPSCs were seeded at 50,000 cells/cm2 on Matrigel-coated plates in mTeSR1 supplemented with 5 µM GSK3484862, 1 µg/mL doxycycline, and 10 µM Y-27632. For 6-well plates, 1.5 mL of medium was used per well. After one day, the medium was replaced with APEL2 containing 5 µM GSK3484862 and 1 µg/mL doxycycline. A 50% media change was performed every 2 days, and GSK3484862 was withdrawn starting on day 7. Cells were harvested on day 15 and cryopreserved in CryoStor CS10 prior to sequencing. One sample was sequenced for each of the three iPSC lines.

extract_protocol:
10X Genomics Chromium Nuclei Isolation Kit
10X Genomics Chromium Multiome ATAC + 3' RNA-seq Library Prep

value: hiPSC-derived meiotic cells

value: meiosis differentiation, day 15


title: UR.14783.DLB.83

description: DLB analysis

value: F


title: Meiotic cells, day 15, scATACseq, rep1

description: Library name: Meiosis_F2_ATAC


title: UR.14782.DLB.55

description: DLB analysis


title: Meiotic cells, day 15, scRNAseq, rep3

description: Library name: Meiosis_PGP1_RNA

molecule: nuclear RNA


title: Meiotic cells, day 15, scRNAseq, rep2

description: Library name: Meiosis_F3_RNA


title: Meiotic cells, day 15, scRNAseq, rep1

description: Library name: Meiosis_F2_RNA


title: Endoderm Ngn3GFP HM 24ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_052


title: Endoderm Ngn3GFP HM 24ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_050


title: breast cells, E50K, Biological rep1 CUT&Tag

city: Atlanta

first: Jennifer

middle: Marie

last: Spangle

state: Georgia

address: 1365C Clifton Rd NE

institute: Emory University

description: Library name: Sample 3

library_source: genomic

data_processing:
fastq files were processed by first trimming adapter sequences with Trim Galore!
Fastq files were aligned to the GRCh38 human genome using Bowtie2
Files were then converted to BAM files, and reads sorted using Samtools
Duplicate reads were marked using PicardTools
Bigwig files were then generated using bamCoverage and reads aligned to the human genome counted with Samtools
Assembly: GrCh38
Supplementary files format and content: the processed files are .bw that contain peaks
Library strategy: CUT&Tag

source_name: HMEC DD

growth_protocol: HMEC DD cells were maintained at 37C and 5% CO2 in DMEM/F12 media supplemented with 0.6% FBS, 0.01 µg/ml EGF, 10 µg/ml insulin, 0.025 µg/ml hydrocortisone, 1 ng/ml cholera toxin, 2.5 µg/ml Amphotericin B, and 1% Penicillin-Streptomycin

extract_protocol:
cells were processed and CUT&Tag library was prepared by EpiCypher CUTANA CUT&Tag), using 1 ug H3K27me3 antibody
librry was prepared using EpiCypher CUTANA CUT&Tag kit

value: HMEC DD

value: Human mammary epithelial cells

value: no treatment


title: UR.14780.DLB.53

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_049


title: breast cells, WT, Biological rep2 CUT&Tag

description: Library name: Sample 2

value: WT


title: breast cells, E50K, Biological rep2 CUT&Tag

description: Library name: Sample 4


title: Meiotic cells, day 15, scATACseq, rep3

description: Library name: Meiosis_PGP1_ATAC


title: Endoderm Ngn3GFP HM 24ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_048


title: UR.14779.DLB.52

description: DLB analysis


title: breast cells, E50K, Biological rep2

description: Library name: Sample 5

data_processing:
checked for quality using FastQC and FastQ screen
trimmed using Trim Galore
aligned to hg38 with Bowtie2
files that had an alignment rate of higher than 80% were used
Mitochondrial reads, duplicates, non-unique alignment reads, and black-listed reads were removed using Samtools, PicardTools
.bam files were then indexed and imported into RStudio for peak calling using the ChrAccR package and MACS2
Assembly: GrCh38
Supplementary files format and content: the processed files are .bw that contain peaks

extract_protocol:
Cells were counted and 50,000 cells were washed with cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water), and permeabilized with ATAC-seq lysis buffer (RSB supplemented with 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin). For the transposition step, cells were resuspended in 44 µl of transposition mix (25 µl 2× TD buffer, 2.5 µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, and 0.5 µl 10% Tween-20) and incubated at 37 °C for 40 min in a thermomixer with shaking at 1,000 RPM.
The DNA fragments were cleaned up with the DNA Clean & Concentrator kit (Zymo Research, D4014) and PCR amplified for 8-12 cycles with Illumina Nextera adaptors using Kapa SYBR® FAST (Roche, 07959427001). The number of PCR cycles was determined based on monitoring for a change in fluorescence of 100,000 or a ΔRn of 0.1, after which PCR was stopped and the samples removed. After amplification, a second cleanup with 1.8x Ampure XP beads (Aline biosciences, Cat. C-1003-50) was performed and library eluted in 10mM Tris-HCl. Fragment size distribution and concentration were evaluated via Bioanalyzer High Sensitivity DNA kit (Agilent, 5067-4626), and libraries were sequenced to a target depth of at least 75 million paired-end reads per sample (Novogene).


title: Endoderm Ngn3GFP HM 24ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_047


title: UR.14778.DLB.51

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_046


title: breast cells, E50K, Biological rep1

description: Library name: Sample 4


title: breast cells, WT, Biological rep3

description: Library name: Sample 3


title: breast cells, WT, Biological rep2

description: Library name: Sample 2


title: UR.14777.DLB.50

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_051


title: breast cells, WT, Biological rep1

description: Library name: Sample1


title: UR.14781.DLB.54

description: DLB analysis


title: TSC_3_rep1

city: Amsterdam

first: Remco

last: Keijser

address: Meibergdreef 9

department: Reproductive Biology Laboratory

country: Netherlands

institute: Amsterdam UMC

data_processing:
Reads were quality-trimmed and adapters were removed using Trim Galore (v0.6.6).
The processed reads were analyzed to obtain transcript-level abundance estimates in transcripts per million using Salmon (v1.9.0).
Transcript-level abundance values were summarized to gene-level counts using the tximport package (v1.32.0).
Downstream gene-level analyses were performed with the EdgeR package (v4.2.1).
All statistical calculations were performed in the R programming language (v4.2.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes TMM normalised counts for each sample (log2-transformed with an offset value of 1.0)
Supplementary files format and content: Tab-delimited text file includes FPKM calculated counts from TMM normalized data for each sample

source_name: Trophoblast

growth_protocol: Mesenchymal stem cells were isolated from a term umbilical cord, and transduced with the OSKM reprogramming factors. Seven days post-transduction, reprogramming intermediates were transited into human TSC medium to induce TSC conversion, with or without supplementation of A-485, BMP4 or EPZ-6438 for 1-3 days. Transcriptome sequencing was performed to assess the similarity between the generated iTSCs and TSCs derived from first-trimester placental tissue. The dataset contains 1-3 experimental replicates of each iTSC condition, 3 TSC lines, and TSCs differentiated into extravillous trophoblast for reference.

extract_protocol:
Cells were washed in PBS and lysed directly in the culture plate using RLT Plus Buffer (from the RNeasy Plus Mini Kit (QIAGEN, 74136)) with 1% 2-mercaptoethanol. Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, 74136) according to the manufacturer’s protocol.
Total RNA libraries were prepared using the mRNA Capture KAPA HyperPrep Kit (Roche, 0000162206), after which 150 bp paired-end sequencing was performed on an Illumina NovaSeq X Plus system.

value: Trophoblast

value: MALE


title: Endoderm Ngn3GFP HM 24ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_045


title: TSC_2_rep1

treatment_protocol: Mesenchymal stem cells were isolated from a term umbilical cord, and transduced with the OSKM reprogramming factors. Seven days post-transduction, reprogramming intermediates were transited into human TSC medium to induce TSC conversion, with or without supplementation of A-485, BMP4 or EPZ-6438 for 1-3 days. Transcriptome sequencing was performed to assess the similarity between the generated iTSCs and TSCs derived from first-trimester placental tissue. The dataset contains 1-3 experimental replicates of each iTSC condition, 3 TSC lines, and TSCs differentiated into extravillous trophoblast for reference.


title: TSC_1_rep3


title: Endoderm Ngn3GFP HM 24ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_044


title: iTSC_EPZ_rep3

value: FEMALE


title: breast cells, WT, Biological rep1 CUT&Tag

description: Library name: Sample1


title: breast cells, E50K, Biological rep3

description: Library name: Sample 6


title: Endoderm Ngn3GFP HM 24ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_042


title: iTSC_BMP4_rep3


title: iTSC_rep3

value: iTSC


title: UR.14774.DLB.47

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_043


title: Endoderm Ngn3GFP HM 24ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_041


title: iTSC_A-485_rep3


title: TSC_1_rep2


title: iTSC_EPZ_rep2


title: UR.14773.DLB.46

description: DLB analysis


title: UR.14771.DLB.32

description: DLB analysis


title: iTSC_BMP4_rep2


title: Endoderm Ngn3GFP HM 24ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_040


title: TSC_1_EVT_medium_rep2


title: iTSC_A-485_rep2


title: UR.14776.DLB.49

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_039


title: UR.14775.DLB.48

description: DLB analysis


title: iTSC_rep2


title: UR.14741.B16.Control

description: DLB analysis

value: Control


title: UR.14740.B15.Control

description: DLB analysis


title: TSC_1_EVT_medium_rep1


title: TSC_1_rep1


title: Endoderm Ngn3GFP HM 24ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_038


title: iTSC_BMP4_rep1


title: Endoderm Ngn3GFP HM 24ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_037


title: UR.14739.B14.Control

description: DLB analysis


title: UR.14738.B13.Control

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_036


title: iTSC_A-485_rep1


title: ctrl_P30007_1017_cs0

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.10a) was used to index the human genome (Homo sapiens, GRCh38) obtained from Ensembl and then map the fastq files.
featureCounts (v2.0.6) was used to count mapped reads in annotated exons using gene annotations from Ensembl (Homo_sapiens.GRCh38.101.gtf).
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Tab delimited text file that contains Ensembl gene IDs and the gene raw counts, one column for each sample.

source_name: vaginal biopsy

extract_protocol:
Qiagen RNeasy mini kit.
Illumina stranded mRNA ligation protocol.

value: vaginal biopsy


title: iTSC_rep1


title: UR.14772.DLB.40

description: DLB analysis


title: UR.14737.B12.Control

description: DLB analysis


title: ctrl_P30007_1010_cs0


title: ctrl_P30007_1009_cs0


title: Endoderm Ngn3GFP HM 24ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_034


title: Endoderm Ngn3GFP HM 24ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_035


title: iTSC_EPZ_rep1


title: ctrl_P30007_1007_cs0


title: UR.14735.B10.Control

description: DLB analysis


title: ctrl_P30007_1006_cs0


title: ctrl_P30007_1014_cs0


title: ctrl_P30007_1004_cs0


title: Endoderm Ngn3GFP HM 24ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_031


title: Endoderm Ngn3GFP HM 24ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_033


title: Endoderm Ngn3GFP HM 24ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_032


title: ctrl_P30007_1031_cs0


title: UR.14733.B8.Control

description: DLB analysis


title: UR.14734.B9.Control

description: DLB analysis


title: ctrl_P30007_1003_cs0


title: ctrl_P30007_1005_cs0


title: Endoderm Ngn3GFP HM 24ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_030


title: Endoderm Ngn3GFP HM 24ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_029


title: ctrl_P31315_1035_cs0


title: UR.14731.B6.Control

description: DLB analysis


title: UR.14732.B7.Control

description: DLB analysis


title: ctrl_P31315_1034_cs0


title: ctrl_P31315_1018_cs0


title: ctrl_P31315_1024_cs0


title: ctrl_P31315_1032_cs0


title: UR.14729.B4.Control

description: DLB analysis


title: ctrl_P31315_1026_cs0


title: Endoderm Ngn3GFP HM 24ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_026


title: ctrl_P31315_1020_cs0


title: neg_P30007_1024_cs0


title: UR.14736.B11.Control

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_028


title: Endoderm Ngn3GFP HM 24ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_027


title: Endoderm Ngn3GFP HM 24ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_024


title: ctrl_P31315_1013_cs0


title: neg_P31315_1015_cs0


title: UR.14726.B1.Control

description: DLB analysis


title: neg_P31315_1004_cs1


title: neg_P30007_1002_cs1


title: neg_P31315_1022_cs0


title: UR.14728.B3.Control

description: DLB analysis


title: Endoderm Ngn3GFP HM 24ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_025


title: Endoderm Ngn3GFP HM 24ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_023


title: neg_P31315_1012_cs0


title: neg_P31315_1003_cs0


title: MSC 135 3D

city: Berlin

last: Rosowski

address: Gusav-Meyer-Allee 25

country: Germany

institute: TU Berlin

data_processing:
RAW data were demultiplexed and processed on the Galaxy Project Platorm, using the FASTQ Groomer tool to convert the output data into Sanger sequencing data. Fragments were then mapped against the human genome (hg38) to detect splice junctons between exons by HISAT2. Mapped reads were processed by the FeatureCount tool. The Galaxy Community. [The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update,; Nucleic Acids Research, Volume 52, Issue W1, 5 July 2024, Pages W83–W94, https://doi.org/10.1093/nar/gkae410; https://usegalaxy.org/]
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts and GeneID for each sample

growth_protocol: Mesenchymal stromal cells were isolated from femoral heads and propagated in standard culture conditions (DMEM; 10%FCS; 1% Penicillin–Streptomycin).

extract_protocol:
whole RNA was isolated by the Nucleo Spin RNA Kit (Macherey & Nagel)
for samples from Donor 125 and 135: The indexed cDNA library was generated using the TruSeq Stranded mRNA LT Sample Prep Kit 24 (Illumina), according to the TruSeq Stranded mRNA Sample PreparaCon Protocol LS (Illumina). The inital quantity of total RNA was 800 ng for bone marrow stromal cells for samples from donor 351 and 355: Total RNA samples were quantified using a Qubit Fluorometer, and RNA integrity was checked on a TapeStation (Agilent). Double-indexed stranded mRNA-Seq libraries were prepared using the ILMN Stranded mRNA Library Prep Kit (Illumina, #20040534), starting from 500 ng of input material according to the manufacturer’s instructions.
for samples from donor 125 and 135: Libraries were quality checked by qPCR and equimolarly pooled based concentration measurements (nanodrop). The sequencing was performed on the Illumina MiSeq System. for sampls from donor 351 and 355: Libraries were equimolarly pooled based on Qubit concentration measurements and TapeStation size distributions. The loading concentration of the pool was determined using a qPCR assay (Roche, #7960573001). Libraries were then sequenced on the Illumina NovaSeq X Plus platform using PE100 sequencing mode, with a target of 50 million reads per library.

treatment_protocol: For 3D culture, ceramic scaffolds were seeded with mesenchymal stromal cells and cultured for seven days in standard culture conditions. As a control, the same biological donors were kept in a 2D monolayer culture (DMEM; 10%FCS; 1% Penicillin–Streptomycin).

value: bone marrow

value: primary cells

value: mesencymal stromal cells

value: wild type


title: as_P30007_1033_cs0


title: UR.14730.B5.Control

description: DLB analysis


title: as_P30007_1032_cs0


title: MSC 125 3D


title: as_P30007_1001_cs0


title: Endoderm Ngn3GFP HM 24ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_022

value: Endoderm


title: Endoderm Ngn3GFP HM 24ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_021


title: Endoderm Ngn3GFP HM 24ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_020


title: UR.14727.B2.Control

description: DLB analysis


title: MSC 135 ML

value: monolayer


title: neg_P31315_1021_cs2


title: as_P31315_1033_cs1


title: as_P31315_1029_cs0


title: as_P30007_1008_cs1


title: as_P31315_1028_cs1


title: pos_P30007_1029_cs2


title: MB2-24h-W+FR (H) RIR111

city: Valencia

first: jaume

middle: f

last: martinez-garcia

state: Valencia

address: CPI, Edifici 8E, Campus UPV, Carrer Enginyer Fausto Elio s/n

department: Development and Hormonal Action in Plants

country: Spain

institute: IBMCP, CSIC

description: MB2-24h-W+FR (H)

data_processing:
RNA-seq reads were mapped against Arabidopsis thaliana (TAIR10) reference genome with STAR/2.5.3a (ENCODE parameters)
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was Arabidopsis_thaliana.TAIR10.36
Assembly: TAIR10
Supplementary files format and content: Raw counts (tsv)

organism: Arabidopsis thaliana

source_name: floral bud

growth_protocol: Plants were grown on soil under long day (LD, 16 h light + 8 h dark) photoperiods in which white light (W) was generated by horizontal fluorescent tubes that provided  a PAR of ~100 µmol m-2 s-1, R:FR of ~3.0) until they flower

extract_protocol: Total RNA was extracted from the floral buds of a minimum of 4 inflorescences with the Maxwell 16 LEV simplyRNA Tissue Kit (Promega).

treatment_protocol: W treatment refer to long day (LD, 16 h light + 8 h dark) photoperiods provided by horizontal fluorescent tubes (W of a PAR of ~100 µmol m-2 s-1, R:FR of ~3.0). Simulated shade or W+FR treatments refer to LD photoperiods in with W was supplemented with far red light (FR) (W+FR, PAR of ~100 µmol m-2 s-1, R:FR of ~0.05-0.06) provided by LEDs.

value: floral bud

value: MB2 (pAP1:AP1-GR in ap1 cal background)

value: 24h white + far red light


title: Endoderm Ngn3GFP HM 24ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3GFP_HM_24ss_b2_019


title: MSC 125 ML


title: pos_P30007_1030_cs0