title: Sample 16 cortex, Ash1lfl/fl, scRNA-seq

first: Stephanie

last: Bielas

state: Michigan

address: 3703 Med Sci II

data_processing:
Data was processd using Drop-seq Core Computational Protocol (v2.0.0) (McCarroll lab, Harvard Medical School)
Paired-end files merged into single BAM file per sample
Cell and molecular barcodes tagged
5' primer and 3' polyA sequences trimmed
STAR used as RNA aligner
Bead substitution and synthesis errors detected and corrected
Assembly: mm10
Supplementary files format and content: Digital expression matrix; gene expression measurements for each gene in each individual cell

source_name: Cortex

extract_protocol:
Embryonic cortices were dissected in Earle’s balanced salt solution (EBSS) and incubated with papain, 5.5 mM L-cysteine-HCL, 1.1 mM EDTA, and 100 mg/ml DNase I (all part of Papain Dissociation System. Worthington Biochemical Corporation, NJ, USA; cat: LK003153) in O2:CO2 equilibrated EBSS for 8 min at 37°C. Samples were titrated and centrifuged. Cells were resuspended with ovomucoid protease inhibitor and 50 mg/ml DNase I in O2:CO2 equilibrated EBSS and passed through a 70μm cell strainer (Becton Dickson, NJ, USA; cat: 08-771-2). Cells underwent centrifugation with an ovomucoid protease inhibitor gradient and then resuspended in N2/B27 media (all from Invitrogen, MA, USA. Neurobasal media cat: 21103-049; B27 supplement cat: 17504044; L-glutamine cat: 25030-081). Cells were counted before subsequent scRNA sequencing steps.
Single cell RNA sequencing was carried out using the Seq-Well platform (Gierahn et al, 2017). Briefly, functionalized Seq-Well arrays were loaded with mRNA Capture Beads (ChemeGenes, Wilmington, MA; cat: MACOSKO-2011-10). Cells were loaded on the arrays and incubated for 15 min. Functionalized membranes (custom ordered from Sterlitech, WA, USA) were sealed onto the arrays and incubated at 37°C for 45 min. Sealed arrays underwent incubations in lysis and hybridization buffers. Beads were removed from the arrays via centrifugation. Beads were incubated with Maxima Reverse Transcriptase (Thermo Fisher Scientific, MA, USA; cat: EPO0753) overnight, then treated with Exonuclease 1 (New England Biolabs, MA, USA; cat: M0293S). Transcriptome amplification was performed using the 2X KAPA Hifi Hotstart Readymix (Roche, Basel, Switzerland; cat: KK-2602). Products were purified with AMPure SPRI beads (Beckman Coulter, CA, USA; cat: A63881). Libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, CA, USA; cat: FC-131-1096) and libraries were sequenced on an Illumina NextSeq 2000 instrument. Digital gene expression matrices were generated from sequencing data using the Drop-seq Alignment protocol (Macosko et al, 2015). Reads were aligned to mm10 with STAR.

value: Cortex


title: Endoderm Ngn3Cre 27ss b2 017, scRNA-seq

status: Public on Jan 15 2025

type: SRA

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
Ngn3Cre_27ss_b2_017

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

molecule: total RNA

organism: Mus musculus

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.

tag: tissue

value: Endoderm

tag: strain

tag: genotype

value: Ngn3-Cre; Ai6

tag: time


title: Sample 15 cortex, Ash1lfl/fl, scRNA-seq

city: Ann Arbor

country: USA

institute: University of Michigan


title: caulineLeaf; treated; replicate 4

city: Chicago

first: Chang

last: Ye

state: Illinois

institute: University of Chicago

description: caulineLeaf; treated; replicate 4

library_source: transcriptomic

data_processing:
The code for sequencing processing and mutation calling has been packaged, and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: TAIR-10
Supplementary files format and content: TSV
Library strategy: BID-Seq

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: cauline

extract_protocol:
Total RNA isolation: total RNA was isolated according to TRIzol reagent manufacturer’s protocol, followed by isopropanol precipitation. PolyA+ RNA isolation: Dynabeads™ mRNA Purification Kit (Invitrogen™) was used for polyA+ RNA enrichment, from the purified total RNA.
With 10 ng synthetic RNA oligos carrying 0%, 20%, 40%, 60%, 80%, or 100% pseudouridine, 5′-phosphorylation were conducted with T4 polynucleotide kinase (PNK) (catalog no. EK0032, Thermo Fisher Scientific). To perform 3′-adapter ligation, 10 µl 5′-phosphorylated RNA fragments were incubated with 1.0 µl 20 µM RNA 3′ SR Adapter (5′App-NNNNN AGATCGGAAGAGCACACGTCT-3SpC3, with ATCACG as the inline barcode) at 70 °C for 2 mins and placed immediately on ice. Then, 2.5 µl 10× T4 RNA Ligase Reaction Buffer (catalog no. M0373L, NEB), 7.5 µl PEG8000 (50%), 1 µl SUPERase•In RNase Inhibitor and 2 µl T4 RNA Ligase 2 truncated KQ (catalog no. M0373L, NEB) were added to the RNA–adapter mixture48,49. The reaction was incubated at 25 °C for 2 h followed by 16 °C for 10 h. The reaction was further diluted to 47 µl with nuclease-free water, and the excessive adapters were removed with 2 µl 5′-deadenylase (catalog no. M0331S, NEB) at 30 °C for 30 min followed by adding 1 µl RecJf (catalog no. M0264L, NEB) for ssDNA digestion at 37 °C for 30 min. The 3′-end-ligated RNA was extracted by RNA Clean and Concentrator (Zymo Research) and eluted with 9.3 µl RNase-free water.  The purified RNA was incubated with 1.2 µl 10 µM 5′ SR Adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′) at 70 °C for 2 mins and placed immediately on ice. Then 2.5 µl 10× T4 RNA ligase reaction buffer, 1.0 µl 25 mM ATP, 10 µl PEG8000 (50%) and 1 µl T4 RNA Ligase 1 (high concentration, catalog no. M0437M, NEB) were added to the RNA–adapter mixture. The reaction was mixed well and incubated at 25 °C for 8 h, followed by RNA Clean and Concentrator (Zymo Research) purification, eluting with 10 µl RNase-free water.  A 1.5 µl aliquot of the purified RNA was saved for ‘Input’ library construction, 8.5 µl was subjected to BID-seq optimized bisulfite treatment, as the ‘Treated’ sample. The 8.5 µl RNA was mixed with 45 µl freshly prepared BID-seq BS reagent (2.4 M Na2SO3 and 0.36 M NaHSO3, prepared by dissolving 270 mg Na2SO3 and 34 mg NaHSO3 in 900 µl RNase-free water) and incubated at 70 °C for 3 h. Then, 75 µl RNase-free H2O, 270 µl RNA binding buffer (RNA Clean and Concentrator), and 400 µl ethanol were added to the reaction mixture, which was mixed well and loaded on a RNA Clean and Concentrator-5 column. After spinning and washing once with 200 µl RNA wash buffer (RNA Clean and Concentrator), 200 µl RNA Desulphonation Buffer (catalog no. R5001-3-40, Zymo Research) was added to the column and incubated at room temperature for 1 h. This was followed by spinning and washing twice with 700 µl RNA wash buffer (RNA Clean and Concentrator), followed by eluting RNA with 10.5 µl RNase-free water. Then the ‘Input’ was diluted to 10.5 µl with RNase-free water. Both ‘Input’ and ‘Treated’ samples were mixed with 1.0 µl 2.0 µM SR RT primer (5′-AGACGTGTGCTCTTCCGATCT -3′) at 65 °C for 2 min and moved immediately onto ice. To this was added 4 µl 5× SSIV Buffer, 2 µl 10 mM dNTP Solution Mix (NEB), 1 µl 100 mM dithiothreitol, 0.5 µl RNaseOUT Recombinant Ribonuclease Inhibitor (catalog no. 10777019, Thermo Scientific) and 1 µl SuperScript IV Reverse Transcriptase (SSIV, catalog no. 18090050, Thermo Scientific). The reaction was mixed well and incubated at 50 °C for 1 h, followed by adding 1 µl RNase H (catalog no. M0297L, NEB) and incubating at 37 °C for 20 min. The reaction mixture was heated at 70 °C for 5 min and then cDNA was purified using DNA Clean and Concentrator (Zymo Research). The eluted cDNAs (20 µl) were stored at –80 °C; 4 µl was used for each 15-cycle PCR amplification reaction, which was performed with the SR Primer for Illumina (NEB) and indexed primers (from NEBNext Multiplex Oligos for Illumina). All libraries were purified on a 3.5% low melting point agarose gel and sequenced on Illumina Nova-seq 6000 with single-end 100 bp read length.

value: cauline


title: HFF cells, SETDB1, HSV1, 6hpi, rep1

city: Freiburg

first: Florian

last: Full

address: Hermann-Herder-Str. 11

country: Germany

institute: institute of Virology, University Medical Center Freiburg

description: Library name: SETDB1_HSV1_6hpi_rep1

library_source: genomic

data_processing:
Sequence reads were mapping to hg38 by STAR or bowtie2
Assembly: hg38
Supplementary files format and content: counts files were generated by featurecounts or TEcounts and bigwig files were generated by deeptools
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

extract_protocol:
Cells were resuspended in Trizol (Invitrogen) and RNA extracted from Trizol.
RNA-sequencing libraries were constructed using commercial kits (New England Biolabs) total RNA-seq with rRNA depletion as indicated; CUT&RUN was performed according to the CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers V.3 protocol.

value: cell line

tag: cell line

value: HFF

tag: cell type

value: HFF cells

value: WT

tag: treatment


title: caulineLeaf; treated; replicate 2

description: caulineLeaf; treated; replicate 2


title: HFF cells, SETDB1, HSV1, 6hpi, rep2

description: Library name: SETDB1_HSV1_6hpi_rep2


title: Endoderm Ngn3Cre 27ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_016


title: stem; treated; replicate 1

description: stem; treated; replicate 1

source_name: stem

value: stem


title: HFF cells, H3K9me3, Mock, rep2

description: Library name: H3K9me3_Mock_rep2

value: Mock


title: Sample 14 cortex, Ash1lfl/fl, scRNA-seq


title: Endoderm Ngn3Cre 27ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_021


title: HFF cells, SETDB1, Mock, rep2

description: Library name: SETDB1_Mock_rep2


title: caulineLeaf; treated; replicate 1

description: caulineLeaf; treated; replicate 1


title: Endoderm Ngn3Cre 27ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_013


title: Sample 12 cortex, Emx1CreERT2;Ash1lfl/fl, scRNA-seq


title: Sample 17 cortex, Emx1CreERT2;Ash1lfl/fl, scRNA-seq


title: Endoderm Ngn3Cre 27ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_018


title: macrophages, R1_1h_Mock

city: Würzburg

first: Alexander

last: Westermann

address: Josef-Schneider Straße 2

institute: HIRI

data_processing:
Base-calling with Illumina NextSeq RTA v3.10.30
FASTQ conversion with BCL Convert v4.0.3 (Illumina)
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a ACTGTCTCTTATACACATCT)
Read tagging based on mouse and Salmonella genomes via FastQ Screen (Wingett, 2018) v0.15.2 (parameters: --aligner bowtie2 --tag --subset 0)
Read assignment to either mouse or Salmonella via FastQ Screen (parameters: --filter '03' --subset 0 for mouse and  --filter '30' --subset 0 for Salmonella)
Alignment of Salmonella assigned reads to Salmonella reference genome using segemehl v0.2.0 with READemption (Förstner et al., 2014) v0.4.5 (parameters: align -l 12 -a 95 -R)
Calculation of Salmonella read counts via READemption (parameters: gene_quanti -o 10 --features "3UTR,5UTR,CDS,rRNA,sRNA,transcript,tRNA" -a)
Alignment of mouse assigned reads to mouse genome using STAR (Dobin et al., 2013) v2.7.2b with default parameters based on exons from RefSeq annotation version 109
Calculation of mouse read counts on exon level summarized for each gene (RefSeq annotation version 109 for GRCm39) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction)
Assembly: RefSeq GRCm39 (mouse), GCF_000210855.2 (Salmonella)
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

source_name: RAW264.7 (ATCC TIB-71)

growth_protocol: Raw macrophages were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.

extract_protocol:
Trizol
Total RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥5.0. DNA libraries suitable for sequencing were prepared from 500 ng of total RNA using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero™ Plus (Illumina) according to manufacturer’s instructions. After 14 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~330 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.
Dual RNA-seq

treatment_protocol: Infection was carried out following the protocol of (Schulte et al., 2011) with the indicated Salmonella Typhimurium (SL1344) strain in 6-well format. At the indicated time point post-infection, cells were harvested and sorted for invaded (GFP+) and non-infected (GFP-) host cells using a FACSAria III device (BD).

value: RAW264.7 (ATCC TIB-71)

value: macrophages

tag: infection condition

value: mock

tag: timepoint post_infection

value: 1 h

tag: biological replicate


title: Endoderm Ngn3Cre 27ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_014


title: silique; treated; replicate 6

description: silique; treated; replicate 6

source_name: silique

value: silique


title: HFF cells, SETDB1, Mock, rep1

description: Library name: SETDB1_Mock_rep1


title: Endoderm Ngn3Cre 27ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_012


title: Sample 11 cortex, Emx1CreERT2;Ash1lfl/fl, scRNA-seq


title: silique; treated; replicate 5

description: silique; treated; replicate 5


title: caulineLeaf; treated; replicate 3

description: caulineLeaf; treated; replicate 3


title: Endoderm Ngn3Cre 27ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_011


title: s011; 10 days

city: Bergamo

first: Susanna

last: Tomasoni

state: BG

address: Via Stezzano 87

department: Molecular Medicine

country: Italy

institute: Istituto di Ricerche Farmacologiche Mario Negri IRCCS

description:
Library name: s011
s011 in gene_count.txt

data_processing:
Sequence reads were trimed for adapter sequence with trimmomatic
Trimmed reads were aligned to GRCh38 with STAR
Gene count matrix was obtained with FeatureCounts
Assembly: GRCh38
Supplementary files format and content: raw gene count for each sample

extract_protocol:
Day 10 spheroids and day 24 organoids were harvested, homogenised and RNA was extracted using the PureLink RNA Mini Kit.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the RNA samples according to manufacturer’s instructions.

value: hIPSC differentiated towards ureteric bud-like cells

value: 10 days


title: Sample 10 cortex, Emx1CreERT2;Ash1lfl/fl, scRNA-seq

value: Cortex


title: Endoderm Ngn3Cre 27ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_010

value: Endoderm


title: sim1cre_HTO

city: Dallas

first: Baijie

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: 10x Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (version 6.0.0).
Assembly: mm10
Supplementary files format and content: Matrix table with UMI counts

molecule: protein

source_name: PVH

extract_protocol:
The snRNA-seq protocol was adapted from others’ (Gaublomme et al., 2019; Stoeckius et al., 2018).
Library was performed according to the manufacter's instructions.

value: PVH

value: Sim1cre;sun1GFP & Sim1-Cre; Sun-GFP; Otpfl/+ & Sim1cre; sun1GFP; Otpq153r

tag: age

value: 4 weeks old


title: s006; 24 days

description:
Library name: s006
s006 in gene_count.txt

value: 24 days


title: silique; treated; replicate 2

description: silique; treated; replicate 2


title: Endoderm Ngn3Cre 27ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_009

value: Ngn3-Cre; Ai6


title: MN9_T

city: Zürich

first: Enni

last: Markkanen

state: State...

address: Winterthurerstr. 260, TFA 00.31

department: Institute of Pharmacology and Toxicology, Vetsuisse Faculty Zurich

country: Switzerland

institute: University of Zurich

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Fastp (Version 0.20).
The read alignment was done with STAR.  As reference we used the Ensembl genome build Felis_catus_9.0 (Ensembl)  with the gene annotations downloaded on 2021-02-02 from Ensembl (release 102).
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: Felis_catus_9.0 (Ensembl) with gene model annotations of release 102 (2021-02-02)
Supplementary files format and content: tab-delimited txt-file including raw gene counts from Rsubreads

organism: Felis catus

source_name: Tumor

growth_protocol: patient-derived tissue

extract_protocol:
Covaris TruXtract FFPE RNA extraction, as described in Amini et al, 2017, doi: 10.1186/s12867-017-0099-7
RNA libraries were prepared for sequencing using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (TaKaRa)

treatment_protocol: FFPE

value: Tumor

tag: tissue source

value: feline patient-derived tissue


title: silique; treated; replicate 1

description: silique; treated; replicate 1


title: Endoderm Ngn3Cre 27ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_007


title: s002; 24 days

description:
Library name: s002
s002 in gene_count.txt

value: WT


title: sim1cre_GE

description: 10x Genomics


title: s001; 10 days

description:
Library name: s001
s001 in gene_count.txt


title: Endoderm Ngn3Cre 27ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_008


title: seedling; treated; replicate 7

description: seedling; treated; replicate 7

source_name: seedling

value: seedling


title: MN8_SM

source_name: Skeletal muscle

value: Skeletal muscle


title: MN8_T


title: MN8_CT

source_name: Connective tissue

value: Connective tissue


title: Endoderm Ngn3Cre 27ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_005


title: Endoderm Ngn3Cre 27ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_006


title: s012; 24 days

description:
Library name: s012
s012 in gene_count.txt


title: ACTN1_1788300_repAtx1_5.000000uM_E1_techrep1

city: Carlsbad

first: Sagar

last: Damle

state: CA

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

description: Library name: 205825

data_processing:
Reads were aligned to the specified genome (Ensembl build 96) using STAR
Gene counts were tabulated using salmon v0.7 using default parameters (pseudoalignment mode)
Assembly: mm10, hg39
Supplementary files format and content: tab-delimited default salmon output including raw counts for each sample

extract_protocol:
Total RNA was isolated using the PureLink Pro 96 Total RNA Purification Kit (Life Technologies, Carlsbad, CA)
Tag-Seq performed using lexogen 3' QuantSeq kit FWD


title: ACTN1_1788300_repAtx1_5.000000uM_E1_techrep2

description: Library name: 205792


title: seedling; treated; replicate 5

description: seedling; treated; replicate 5


title: silique; treated; replicate 4

description: silique; treated; replicate 4


title: caulineLeaf; treated; replicate 6

description: caulineLeaf; treated; replicate 6

value: cauline


title: s005; 10 days

description:
Library name: s005
s005 in gene_count.txt


title: MN7_T


title: Endoderm Ngn3Cre 27ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_003


title: seedling; treated; replicate 4

description: seedling; treated; replicate 4


title: ACTN1_1788297_repAtx1_5.000000uM_C1_techrep2

description: Library name: 205826


title: silique; treated; replicate 3

description: silique; treated; replicate 3

value: silique


title: MN7_SM


title: seedling; treated; replicate 3

description: seedling; treated; replicate 3


title: ACTN1_1788297_repAtx1_5.000000uM_C1_techrep1

description: Library name: 205781


title: Endoderm Ngn3Cre 27ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_002


title: seedling; treated; replicate 6

description: seedling; treated; replicate 6


title: seedling; treated; replicate 2

description: seedling; treated; replicate 2


title: MN6_SM


title: ACTN1_1744547_repAtx1_5.000000uM_A1_techrep2

description: Library name: 205844


title: MN6_CT


title: ACTN1_1788300_repAtx1_1.000000uM_E3_techrep1

description: Library name: 205849


title: flower; treated; replicate 7

description: flower; treated; replicate 7

source_name: flower

value: flower


title: Endoderm Ngn3Cre 24ss b2 155, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_155


title: MN6_T


title: flower; treated; replicate 6

description: flower; treated; replicate 6


title: seedling; treated; replicate 1

description: seedling; treated; replicate 1


title: Endoderm Ngn3Cre 27ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_001


title: Endoderm Ngn3Cre 24ss b2 154, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_154


title: Endoderm Ngn3Cre 24ss b2 153, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_153


title: ACTN1_1788300_repAtx1_1.000000uM_E3_techrep2

description: Library name: 205785


title: Endoderm Ngn3Cre 27ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_27ss_b2_004


title: MN5_T


title: MN6_AT

source_name: Adipose tissue

value: Adipose tissue


title: Endoderm Ngn3Cre 24ss b2 152, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_152


title: flower; treated; replicate 5

description: flower; treated; replicate 5


title: MN5_SM


title: flower; treated; replicate 4

description: flower; treated; replicate 4


title: Endoderm Ngn3Cre 24ss b2 151, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_151


title: MN5_AT


title: ACTN1_1744547_repAtx1_5.000000uM_A1_techrep1

description: Library name: 205751


title: Endoderm Ngn3Cre 24ss b2 150, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_150


title: flower; treated; replicate 3

description: flower; treated; replicate 3


title: MN34_T


title: flower; treated; replicate 2

description: flower; treated; replicate 2


title: ACTN1_1744547_repAtx1_1.000000uM_A3_techrep2

description: Library name: 205706


title: ACTN1_1744547_repAtx1_1.000000uM_A3_techrep1

description: Library name: 205852


title: Endoderm Ngn3Cre 24ss b2 149, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_149


title: MN33_T


title: flower; treated; replicate 1

description: flower; treated; replicate 1


title: ACTN1_1788300_repAtx1_0.200000uM_E5_techrep2

description: Library name: 205832


title: Endoderm Ngn3Cre 24ss b2 147, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_147


title: ACTN1_1788297_repAtx1_1.000000uM_C3_techrep1

description: Library name: 205814


title: root; input; replicate 2

description: root; input; replicate 2

source_name: root

value: root


title: ACTN1_1788300_repAtx1_0.200000uM_E5_techrep1

description: Library name: 205707


title: MN33_SM


title: ACTN1_1788297_repAtx1_0.200000uM_C5_techrep1

description: Library name: 205795


title: Endoderm Ngn3Cre 24ss b2 146, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_146

value: Endoderm


title: ACTN1_1788297_repAtx1_1.000000uM_C3_techrep2

description: Library name: 205834


title: root; input; replicate 1

description: root; input; replicate 1


title: shoot; input; replicate 2

description: shoot; input; replicate 2

source_name: shoot

value: shoot


title: Endoderm Ngn3Cre 24ss b2 145, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_145


title: MN32_T


title: shoot; input; replicate 1

description: shoot; input; replicate 1


title: ACTN1_1744547_repAtx1_0.200000uM_A5_techrep1

description: Library name: 205793


title: ACTN1_1788297_repAtx1_0.200000uM_C5_techrep2

description: Library name: 205778


title: Endoderm Ngn3Cre 24ss b2 144, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_144


title: MN32_SM


title: MN32_CT


title: seed; input; replicate 1

description: seed; input; replicate 1

source_name: seed

value: seed


title: MN34_SM


title: Endoderm Ngn3Cre 24ss b2 148, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_148


title: MN31_T


title: Endoderm Ngn3Cre 24ss b2 143, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_143


title: ACTN1_1744547_repAtx1_0.200000uM_A5_techrep2

description: Library name: 205719


title: ACTN1_UTC_repAtx1_10.000000uM_K23_techrep1

description: Library name: 205805

value: UTC


title: rosettaLeaf; input; replicate 1

description: rosettaLeaf; input; replicate 1

source_name: rosetta

value: rosetta


title: Endoderm Ngn3Cre 24ss b2 142, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_142

source_name: Endoderm

value: Ngn3-Cre; Ai6


title: ACTN1_UTC_repAtx1_5.000000uM_C23_techrep1

description: Library name: 205797


title: stem; input; replicate 2

description: stem; input; replicate 2

value: stem


title: MN31_CT

value: feline patient-derived tissue


title: Endoderm Ngn3Cre 24ss b2 141, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_141


title: Endoderm Ngn3Cre 24ss b2 140, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_140


title: ACTN1_UTC_repAtx1_10.000000uM_A23_techrep1

description: Library name: 205766


title: ACTN1_UTC_repAtx1_1.250000uM_G23_techrep1

description: Library name: 205858


title: MN31_AT


title: Endoderm Ngn3Cre 24ss b2 139, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_139


title: stem; input; replicate 1

description: stem; input; replicate 1


title: caulineLeaf; input; replicate 2

description: caulineLeaf; input; replicate 2

source_name: cauline


title: MN30_T

value: Tumor


title: Endoderm Ngn3Cre 24ss b2 138, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_138


title: MN30_SM


title: Endoderm Ngn3Cre 24ss b2 137, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_137


title: ACTN1_UTC_repAtx1_10.000000uM_E21_techrep1

description: Library name: 205848


title: caulineLeaf; input; replicate 1

description: caulineLeaf; input; replicate 1


title: MN30_CT


title: silique; input; replicate 1

description: silique; input; replicate 1


title: MN29_T


title: Endoderm Ngn3Cre 24ss b2 136, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_136


title: ACTN1_UTC_repAtx1_10.000000uM_M23_techrep1

description: Library name: 205701


title: MN29_SM


title: seedling; input; replicate 2

description: seedling; input; replicate 2

value: seedling


title: Endoderm Ngn3Cre 24ss b2 135, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_135


title: MN31_SM

value: Skeletal muscle


title: Endoderm Ngn3Cre 24ss b2 134, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_134


title: MN29_CT

value: Connective tissue


title: flower; input; replicate 1

description: flower; input; replicate 1


title: MN29_AT


title: Endoderm Ngn3Cre 24ss b2 132, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_132


title: silique; input; replicate 2

description: silique; input; replicate 2


title: ACTN1_UTC_repAtx1_10.000000uM_I21_techrep1

description: Library name: 205699


title: marginal zone lymphoma4

city: Rochester

first: Zhizhang

last: Yang

address: 200 1st ST SW

institute: Mayo Clinic

description:
Library name: Sample 4
patient 4

data_processing:
RNA library construction and RNA sequencing were performed by Mayo Genomic Core Facility
raw data collection and secondary analysis were done with CellRange
further analysis was perfomed using R packages of Seurat and CellChat
Supplementary files format and content: rds
Library strategy: CITE-seq

source_name: Spleen

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries
CITE was perfomed by incubating  cells with 35 TotalSeq™-C antibodies (1μg per Ab per sample) for 30 min at 4 °C.

value: Spleen

value: mononuclear cells

tag: batch


title: MN28_T


title: MN28_AT


title: Endoderm Ngn3Cre 24ss b2 130, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_130


title: marginal zone lymphoma3

description:
Library name: Sample 3
patient 3


title: ACTN1_UTC_repAtx1_2.500000uM_E23_techrep1

description: Library name: 205803


title: MN27_T


title: ACTN1_UTC_repAtx1_10.000000uM_K21_techrep1

description: Library name: 205744


title: marginal zone lymphoma2

description:
Library name: Sample 2
patient 2


title: Endoderm Ngn3Cre 24ss b2 129, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_129


title: seedling; input; replicate 1

description: seedling; input; replicate 1


title: MN27_AT


title: MN26_T


title: siSFPQ_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

description: expression profile in column siSFPQ_rep3

data_processing:
RNA-seq quality control performed with FastQC
Transcripts were aligned using the STAR package (v2.7.9a) and quantified using the “quantMode GeneCounts” function with ENSEMBL annotation and the human genome version GRCh38 as a reference.
Read counts generated by STAR were analyzed using the DESeq2 R package to detect differentially expressed genes (DEGs) with an adjusted P value (Adj.P) less than 0.05.
Assembly: human genome version GRCh38 with ENSEMBL annotation v104 GTF
Supplementary files format and content: tab delimited file with gene raw count for each sample

source_name: Bone

growth_protocol: U-2 OS cells (osteosarcoma, ATCC HTB-96) were cultured in low glucose Dulbecco’s modified Eagle’s (DMEM) medium (Euroclone) with 10% foetal bovine serum (Corning), 1% L- glutamine (Gibco), 1% penicillin/streptomycin (Gibco)

extract_protocol:
Total RNA was prepared using the Norgen Biotech RNA extraction Kit following manufacturer’s instructions.
Libraries were constructed with the Illumina TruSeq RNA kits. 150 base pair reads (pair ends).

treatment_protocol: Specific siRNA for SFPQ were transfected using RNAi-MAX Lipofectamine (Invitrogen) at 30 nM final concetration, according to the manufacturer’s suggestions.

value: Bone

value: Osteosarcoma Cell Line

value: Polyploid

value: siRNA targeting SFPQ gene


title: Endoderm Ngn3Cre 24ss b2 128, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_128

value: Endoderm


title: ACTN1_UTC_repAtx1_10.000000uM_C21_techrep1

description: Library name: 205760


title: MN26_AT

value: Adipose tissue


title: Endoderm Ngn3Cre 24ss b2 127, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_127


title: marignal zone lymphoma1

description:
Library name: Sample 1
patient 1


title: OA6

city: x

first: Lunhao

last: Bai

address: x

institute: x

description: Library name: OA6

data_processing:
Real-Time Analysis (version 3.4.4) and bcl2fastq (version 2.19 ).
Assembly: GRCh38
Supplementary files format and content: processed data.xlsx

source_name: Cartilage tissue of knee joint

extract_protocol:
RNA was extracted by using TRIzol (Ambion/Invitrogen，USA) reagent.  200 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina®  following manufacturer's protocols.

value: Cartilage tissue of knee joint


title: Endoderm Ngn3Cre 24ss b2 126, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_126


title: Endoderm Ngn3Cre 24ss b2 131, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_131


title: flower; input; replicate 2

description: flower; input; replicate 2

value: flower


title: siSFPQ_rep2

description: expression profile in column siSFPQ_rep2


title: Endoderm Ngn3Cre 24ss b2 133, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_133

value: Ngn3-Cre; Ai6


title: OA5

description: Library name: OA5


title: siSFPQ_rep1

description: expression profile in column siSFPQ_rep1


title: OA4

description: Library name: OA4


title: MN25_T


title: siCTRL_rep3

description: expression profile in column siCTRL_rep3

value: control siRNA


title: MN24_T

value: feline patient-derived tissue


title: Endoderm Ngn3Cre 24ss b2 124, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_124


title: OA3

description: Library name: OA3


title: Endoderm Ngn3Cre 24ss b2 123, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_123


title: siCTRL_rep1

description: expression profile in column siCTRL_rep1


title: siCTRL_rep2

description: expression profile in column siCTRL_rep2


title: Endoderm Ngn3Cre 24ss b2 125, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_125


title: MN23_T

value: Tumor


title: MN24_SM


title: OA1

description: Library name: OA1


title: Wild-type ChIP-seq data

city: New York

first: Fei

last: Li

state: New York

address: 24 Waverly Pl

department: Department of Biology

institute: New York University

description: Library name: Wild-type ChIP-seq data

data_processing:
ChIP-seq reads were aligned to RefSeq ASM294v3 assembly GCF_000002945.2 using Bowtie2 version 2.4.4.
Samtools version 1.20 was used to remove PCR duplicates, merge, sort, and index aligned files.
BigWig files for genome coverage were generated using deepTools version 3.5.0 with a bin size of 10. Reads were normalized to reads per kilobase per million (RPKM).
Log 2-fold change between mutant and control was calculated using deepTools version 3.5.0 with a bin size of 10. Reads were normalized to reads per kilobase per million (RPKM).
Assembly: ASM294v3/GCF_000002945.2
Supplementary files format and content: BigWig

organism: Schizosaccharomyces pombe

source_name: Wild-type

growth_protocol: Cells were grown to log phase in rich medium at 30°C

extract_protocol:
Log phase yeast cells were treated with 1% formaldehyde to generate DNA-protein crosslinking. Immunoprecipitation was performed using an anti-GFP antibody. Precipitated DNA was suspended TE buffer.
Libraries were prepared following the instructions of the Illumina TruSeq ChIP sample prep kit.

value: Wild-type

value: h- ade6+::cnp1-GFP leu1-32 ura4-D18

tag: antibody

value: GFP (Abcam, ab290)


title: MN23_SM

value: Skeletal muscle


title: Endoderm Ngn3Cre 24ss b2 120, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_120


title: MN23_AT


title: Endoderm Ngn3Cre 24ss b2 122, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_122


title: Endoderm Ngn3Cre 24ss b2 121, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_121


title: NC6

description: Library name: NC6


title: NC5

description: Library name: NC5


title: EOC042_WES

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

description:
Library name: EOC042_WES
Whole exome-seq S042T

data_processing:
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Assembly: hg19
Supplementary files format and content: Excel file include TPM (Transcripts Per Million) normalized expression values for samples
Library strategy: Whole exome-seq (WES)

source_name: ovarian tumor

extract_protocol:
Tumor DNA and RNA were extracted from tumor tissues using ALLPrep DNA/RNA mini kit
Whole transcriptome sequencing was performed using the library constructed with 500 ng genomic RNA from each sample. The library construct was performed using a Truseq RNA sample preparation v2 kit (Illumina, USA). Whole-exome sequencing was carried out using 200 ng genomic DNA per sample, which was sheared using Covaris S220 (Covaris, MA, USA). A paired-end sequencing library was constructed using SureSelect XT Human All Exon v5 and a SureSelect XT reagent kit, HSQ (Agilent Technologies, Santa Clara, CA, USA)

value: ovarian tumor


title: MN22_T

source_name: Tumor


title: Endoderm Ngn3Cre 24ss b2 119, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_119


title: NC4

description: Library name: NC4


title: EOC041_WES

description:
Library name: EOC041_WES
Whole exome-seq S041T


title: EOC040_WES

description:
Library name: EOC040_WES
Whole exome-seq S040T


title: Endoderm Ngn3Cre 24ss b2 118, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_118


title: NC3

description: Library name: NC3


title: Endoderm Ngn3Cre 24ss b2 117, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_117


title: MN22_CT

value: Connective tissue


title: OA2

description: Library name: OA2


title: MN21_T


title: NC2

description: Library name: NC2


title: EOC038_WES

description:
Library name: EOC038_WES
Whole exome-seq S038T


title: EOC039_WES

description:
Library name: EOC039_WES
Whole exome-seq S039T


title: Endoderm Ngn3Cre 24ss b2 116, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_116


title: NC1

description: Library name: NC1


title: Endoderm Ngn3Cre 24ss b2 115, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_115


title: MN21_CT


title: MN20_T


title: EOC037_WES

description:
Library name: EOC037_WES
Whole exome-seq S037T


title: Dbp7 mutant ChIP-seq data

description: Library name: Dbp7 mutant ChIP-seq data

source_name: Mutatnt

value: Mutatnt

value: h+ dbp7Delta::Kan Cnp1-GFP ade6-M210 ura4-D18 leu1-32 his3D


title: MN22_SM

source_name: Skeletal muscle


title: MN20_SM


title: MN19_T


title: EOC036_WES

description:
Library name: EOC036_WES
Whole exome-seq S036T


title: Endoderm Ngn3Cre 24ss b2 113, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_113


title: Endoderm Ngn3Cre 24ss b2 112, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_112


title: MN19_SM


title: EOC035_WES

description:
Library name: EOC035_WES
Whole exome-seq S035T


title: Endoderm Ngn3Cre 24ss b2 114, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_114


title: EOC034_WES

description:
Library name: EOC034_WES
Whole exome-seq S034T


title: Endoderm Ngn3Cre 24ss b2 111, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_111


title: EOC033_WES

description:
Library name: EOC033_WES
Whole exome-seq S033T


title: Endoderm Ngn3Cre 24ss b2 110, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_110


title: MN18_SM


title: MN18_T


title: MN19_AT


title: EOC031_WES

description:
Library name: EOC031_WES
Whole exome-seq S031T


title: Endoderm Ngn3Cre 24ss b2 108, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_108


title: EOC030_WES

description:
Library name: EOC030_WES
Whole exome-seq S030T


title: EOC029_WES

description:
Library name: EOC029_WES
Whole exome-seq S029T


title: Endoderm Ngn3Cre 24ss b2 109, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_109


title: MN18_AT


title: Endoderm Ngn3Cre 24ss b2 107, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_107


title: MN17_T


title: Endoderm Ngn3Cre 24ss b2 106, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_106


title: MN17_CT

source_name: Connective tissue


title: EOC028_WES

description:
Library name: EOC028_WES
Whole exome-seq S028T


title: Endoderm Ngn3Cre 24ss b2 105, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_105


title: EOC027_WES

description:
Library name: EOC027_WES
Whole exome-seq S027T


title: MN17_AT


title: Endoderm Ngn3Cre 24ss b2 104, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_104


title: MN16_T


title: EOC026_WES

description:
Library name: EOC026_WES
Whole exome-seq S026T


title: Endoderm Ngn3Cre 24ss b2 103, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_103


title: EOC024_WES

description:
Library name: EOC024_WES
Whole exome-seq S024T


title: EOC032_WES

description:
Library name: EOC032_WES
Whole exome-seq S032T


title: Endoderm Ngn3Cre 24ss b2 102, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_102


title: EOC025_WES

description:
Library name: EOC025_WES
Whole exome-seq S025T


title: MN15_T


title: MN16_AT


title: Endoderm Ngn3Cre 24ss b2 101, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_101


title: MN15_AT


title: MN14_T


title: Endoderm Ngn3Cre 24ss b2 100, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_100


title: EOC023_WES

description:
Library name: EOC023_WES
Whole exome-seq S023T


title: EOC021_WES

description:
Library name: EOC021_WES
Whole exome-seq S021T


title: Endoderm Ngn3Cre 24ss b2 099, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_099


title: EOC022_WES

description:
Library name: EOC022_WES
Whole exome-seq S022T


title: MN14_CT


title: Endoderm Ngn3Cre 24ss b2 098, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_098


title: EOC020_WES

description:
Library name: EOC020_WES
Whole exome-seq S020T


title: Hu1205_day29

city: Duarte

first: Guihua

last: Sun

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

description: 10x genomics

data_processing:
cellranger-5.0.0
fastq
filtered_feature_bc_matrix
Seurat v5.0
Assembly: hg38_gencode_release35
Supplementary files format and content: csv, filtered_feature_bc_matrix

source_name: pancreas

extract_protocol:
Chromium
Single Cell 3' v3

value: pancreas

value: islets

value: primary cells

value: wild type

value: in vitro culture for 29 day


title: Day_6_8_10_rep1

first: Michigan

middle: CDB

last: Bioinformatics

state: MI

address: 109 Zina Pitcher Pl

department: Cell & Developmental Biology

data_processing:
BCL Convert Conversion Software v4 (Illumina)
(4830-KJ) samples were run through Cell Ranger v7.0.1 count against reference GRCh38-2020-A. (9704-BC) samples were run through Cell Ranger v7.1.0 multi against reference GRCh38-2020-A; config_9704_CellRanger_Multi.csv supplied to recreate the hd5 files; (11288-BC) samples were run through Cell Ranger v7.1.0 multi against reference GRCh38-2020-A; config_11288_CellRanger_Multi.csv supplied to recreate the hd5 files
Assembly: GRCh38-2020-A
Supplementary files format and content: hd5 files from cellranger count or multi (see 10x website for format)
Supplementary files format and content: config_9704_CellRanger_Multi.csv and config_11288_CellRanger_Multi.csv are the configuration files for cellranger multi for the 9704 and 11288 sample fastqs
Supplementary files format and content: h5ad files are the count matrices after cellranger filtering and our own QC steps as anndata python matrices
Supplementary files format and content: csv files contain the intermediate/final results from our analysis pipeline, specifically the "map2human" maps our micropattern data onto Tyser et al. cell references.

growth_protocol: Human pluripotent stem cells were grown in defined pluripotency maintenance media mTeSR1 at low density with 0.1% ROCK inhibitor in an incubator at 37C and 5% CO2

extract_protocol:
Samples (9704-BC, 11288-BC) for single-cell RNA sequencing were harvested with the 10x Flex fixation kit based on the manufacturer’s manual. Samples (4830-KJ) were collected using accutase and resuspended in ice cold PBS. Cells were barcoded using the 10x Genomics Chromium system (part numbers 1000268, 1000120, 1000215). For quality control cDNA was quantified by Qubit High Sensitivity DNA assay and Agilent TapeStation
For all samples, the University of Michigan Advanced Genomics Core performed library preparation.

treatment_protocol: To differentiate cells for 2D gastruloids by micropatterning, cells were pre-incubated for 24 hours in mTeSR before adding the 50ng/ml BMP4 treatment by a full medium change. Full media changes with 50ng/ml BMP4 were performed every 24 hours.

value: human embryonic stem cells

value: 50ng/ml BMP4


title: MN13_SM

value: feline patient-derived tissue


title: Endoderm Ngn3Cre 24ss b2 097, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_097

value: Endoderm

value: Ngn3-Cre; Ai6


title: Hu1205_day1

description: 10x genomics

value: in vitro culture for 1 day


title: EOC019_WES

description:
Library name: EOC019_WES
Whole exome-seq S019T


title: MN13_CT


title: Blood sample from 038

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

description:
cell_metadata_blood.txt
counts_matrix_blood.txt
filtered_feature_bc_matrix_barcodes.tsv.gz
filtered_feature_bc_matrix_features.tsv.gz
filtered_feature_bc_matrix_matrix.mtx.gz
raw_feature_bc_matrix_barcodes.tsv.gz
raw_feature_bc_matrix_features.tsv.gz
raw_feature_bc_matrix_matrix.mtx.gz

data_processing:
10X Genomics Cell Ranger (v6.0.1) (PMID: 28091601) was used to process the fastq files to cell and gene count tables using unique molecule identifiers (UMIs) aligning to GRCh38 (compiled by 10X Genomics as 2020-A).
Downstream quality control and analysis utilized the Seurat pipeline (PMID: 34062119). Cell Ranger-filtered data was further processed by removing genes identified in fewer than 10 cells. Cell barcodes were removed if they had greater than 50,000 UMIs, greater than 7,000 genes, greater than 20% of UMIs from mitochondria or fewer than 200 genes. Cell doublets were identified and removed using the scDblFinder R package (PMID: 35814628).
The primary and CTC-enriched blood samples were further processed independently. The gene counts were normalized using Seurat where counts are divided by each cell’s total counts and multiplied by 10,000 followed by natural-log transformation. The top 2,000 most variable genes were scaled with total UMI and percentage mitochondria regressed out.
Assembly: GRCh38 (compiled by 10X Genomics as 2020-A)
Supplementary files format and content: For primary tumor and blood samples, text files containing filtered UMIs by gene by cell (counts_matrix_primary.txt and counts_matrix_blood.txt, respectively) and metadata for each cell (cell_metadata_primary.txt and cell_metadata_blood.txt, respectively)
Supplementary files format and content: Aggregated (without normalization) Cell Ranger files are supplied as raw (raw_feature_bc_*) and Cell Ranger filtered (filtered_feature_bc_*) for all samples including some that are not in the final, filtered dataset. The file aggregation.csv corresponds to the order of these samples.

source_name: Peripheral Blood

extract_protocol:
Tumor tissue was thawed at 37°C and gently dissociated using an optimized Collagenase-IV/DNaseI/RPMI digestion protocol. Tumor-digest suspensions were strained through a 70µm filter membrane & washed, then treated using the ErythroClear™ Red Blood Cell Depletion Kit followed by DAPI-exclusion FACS.
3' end 10x Genomics library prep

value: Peripheral Blood

tag: sample

value: sample 038


title: EOC018_WES

description:
Library name: EOC018_WES
Whole exome-seq S018T

value: ovarian tumor


title: Endoderm Ngn3Cre 24ss b2 095, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_095


title: Blood sample from 012

value: sample 012


title: MN13_AT

source_name: Adipose tissue

value: Adipose tissue


title: EOC017_WES

description:
Library name: EOC017_WES
Whole exome-seq S017T


title: Endoderm Ngn3Cre 24ss b2 094, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_094


title: EOC015_WES

description:
Library name: EOC015_WES
Whole exome-seq S015T


title: MN12_T

value: Tumor


title: MN13_T


title: Blood sample from 006

value: sample 006


title: Endoderm Ngn3Cre 24ss b2 092, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_092


title: Blood sample from 009

value: sample 009


title: MN12_AT


title: Blood sample from 005

value: sample 005


title: MN12_SM

value: Skeletal muscle


title: EOC013_WES

description:
Library name: EOC013_WES
Whole exome-seq S013T


title: MN11_T


title: Endoderm Ngn3Cre 24ss b2 090, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_090


title: Blood sample from 002

value: sample 002


title: Endoderm Ngn3Cre 24ss b2 093, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_093


title: MN11_SM


title: EOC014_WES

description:
Library name: EOC014_WES
Whole exome-seq S014T


title: EOC012_WES

description:
Library name: EOC012_WES
Whole exome-seq S012T


title: Blood sample from 001

value: sample 001


title: Blood sample from 010

value: sample 010


title: Endoderm Ngn3Cre 24ss b2 088, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_088


title: MN10_T

value: feline patient-derived tissue


title: Primary tumor sample 066

description:
cell_metadata_primary.txt
counts_matrix_primary.txt
filtered_feature_bc_matrix_barcodes.tsv.gz
filtered_feature_bc_matrix_features.tsv.gz
filtered_feature_bc_matrix_matrix.mtx.gz
raw_feature_bc_matrix_barcodes.tsv.gz
raw_feature_bc_matrix_features.tsv.gz
raw_feature_bc_matrix_matrix.mtx.gz

source_name: Ewing Sarcoma primary tumor

value: Ewing Sarcoma primary tumor

value: Ewing sarcoma

value: sample 066


title: MN10_SM


title: EOC016_WES

description:
Library name: EOC016_WES
Whole exome-seq S016T


title: EOC010_WES

description:
Library name: EOC010_WES
Whole exome-seq S010T


title: Endoderm Ngn3Cre 24ss b2 087, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_087

value: Endoderm

value: Ngn3-Cre; Ai6


title: Primary tumor sample 061

value: sample 061


title: Endoderm Ngn3Cre 24ss b2 091, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_091


title: Endoderm Ngn3Cre 24ss b2 086, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_086


title: shoot; replicate 3; treated

description: shoot; replicate 3; treated

data_processing:
The code for sequencing processing and mutation calling has been packaged, and all the analysis can be achieved by running one line of code. The source code is publicly available on GitHub (https://github.com/y9c/pseudoU-BIDseq).
Assembly: Gmax_508_v4.0
Supplementary files format and content: TSV
Library strategy: BID-Seq

organism: Glycine max

source_name: shoot

value: shoot


title: EOC008_WES

description:
Library name: EOC008_WES
Whole exome-seq S008T

value: ovarian tumor


title: EOC009_WES

description:
Library name: EOC009_WES
Whole exome-seq S009T


title: Primary tumor sample 038

value: sample 038


title: shoot; replicate 2; treated

description: shoot; replicate 2; treated


title: Endoderm Ngn3Cre 24ss b2 084, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_084

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


title: Endoderm Ngn3Cre 24ss b2 096, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_096


title: Primary tumor sample 010


title: shoot; replicate 1; treated

description: shoot; replicate 1; treated


title: EOC005_WES

description:
Library name: EOC005_WES
Whole exome-seq S005T


title: Endoderm Ngn3Cre 24ss b2 083, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_083


title: Endoderm Ngn3Cre 24ss b2 089, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_089


title: shoot; replicate 2; input

description: shoot; replicate 2; input


title: EOC011_WES

description:
Library name: EOC011_WES
Whole exome-seq S011T


title: Primary tumor sample 005


title: EOC003_WES

description:
Library name: EOC003_WES
Whole exome-seq S003T


title: EOC004_WES

description:
Library name: EOC004_WES
Whole exome-seq S004T


title: shoot; replicate 1; input

description: shoot; replicate 1; input


title: Primary tumor sample 001


title: Endoderm Ngn3Cre 24ss b2 082, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_082


title: Endoderm Ngn3Cre 24ss b2 081, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_081


title: MN10_AT

value: Adipose tissue


title: EOC002_WES

description:
Library name: EOC002_WES
Whole exome-seq S002T


title: Primary tumor sample 051

value: sample 051


title: Endoderm Ngn3Cre 24ss b2 080, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_080


title: EOC001_WES

description:
Library name: EOC001_WES
Whole exome-seq S001T


title: Sample_6

city: Davis

first: Rachisan Gabriel

middle: Djiake

last: Tihagam

address: 919 Drake Drive,, 113

department: BMG

institute: University of virginia

data_processing:
The Galaxy platform Galaxy version 23.0.rc1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (Galaxy Version 23.0.rc1) with the parameters:  ILLUMINACLIP:/TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:15 MINLEN:35 LEADING:3 TRAILING:3
Trimmed sequence reads were mapped to GRCh38/hg38 whole genome using HISAT2 (Galaxy Tool version 23.0.rc1)
Gene expression counts were quantified from the mapped reads using featureCounts (Galaxy Tool version 23. 0.rc1)
Assembly: Human
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Breast

extract_protocol:
Total RNA was isolated using Rneasy Mini Kit.
RNA-seq libraries were prepared by Beijing Novogene.

value: Breast

value: Normal breast epithelial cell line


title: Endoderm Ngn3Cre 24ss b2 085, scRNA-seq

city: Beijing

first: Cheng-ran

institute: Peking University

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_085

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.


title: Sample 413

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description: Glioblastoma, IDH wildtype

data_processing:
The Salmon (v 0.12.0) index was generated using the GRCh38 human genome (GENCODE 43/Ensembl 109) with --type quasi -k 31
Transcript quantification was performed using Salmon (v 0.12.0) with --validateMapping
Transcript quantifications were converted to gene-level counts in R using the tximport (v 1.32.0)
Assembly: Human GRCh38/hg38
Supplementary files format and content: tab-delimited text file with Gene ID and transcript per million (TPM) for all the samples

source_name: Brain tumor

extract_protocol:
FFPE-tumor samples were deparaffined using Deparaffinization Solution (Qiagen) and total RNA was extracted using the RNeasy DSP FFPE kit (Qiagen). The concentration was assessed using the Qubit RNA Assay kit (Thermo Fisher) and the RNA quality was quantified by measuring the DV200 value, using the RNA ScreenTape Assay (Agilent, Santa Clara, CA, USA) in the Agilent 4200 TapeStation System. Only samples with a DV200 value of ≥ 31.6 were sequenced.
The starting amount of total RNA was 100 ng for preparing the sequencing library using the Illumina RNA Prep with Enrichment (L) Tagmentation and Illumina Exome panel – Enrichment Oligos Only (Illumina) following manufacturer's recommendations.

value: Brain tumor


title: Sample 410

description: Glioblastoma, IDH wildtype


title: EOC006_WES

description:
Library name: EOC006_WES
Whole exome-seq S006T


title: Sample_5


title: Endoderm Ngn3Cre 24ss b2 079, scRNA-seq

last: Xu

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

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_079


title: Sample_4


title: EOC042_RNAseq

description:
Library name: EOC042_RNAseq
RNA-seq S042T

data_processing:
An RNA sequencing library was prepared by cDNA amplification, end-repair, 3’ end adenylation, adapter ligation, and amplification. Library quality and quantity were measured using the Bioanalyzer and Qubit.
Sequencing of the RNA library was carried out using the 100-bp paired-end mode of the TruSeq Rapid PE Cluster Kit and the TruSeq Rapid SBS Kit (Illumina).
Reads from the FASTQ files were mapped to the hg19 human reference genome, using STAR alignment tool. Raw read counts mapped to genes were measured using the BAM format file by RSEM.
Assembly: hg19
Supplementary files format and content: Excel file include TPM (Transcripts Per Million) normalized expression values for samples


title: Sample 238

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 078, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_078


title: Endoderm Ngn3Cre 24ss b2 077, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_077


title: Sample 233

description: Glioblastoma, IDH wildtype


title: Sample_2


title: EOC040_RNAseq

description:
Library name: EOC040_RNAseq
RNA-seq S040T


title: Endoderm Ngn3Cre 24ss b2 076, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_076


title: Sample 197

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 2


title: EOC039_RNAseq

description:
Library name: EOC039_RNAseq
RNA-seq S039T


title: Sample_1


title: Endoderm Ngn3Cre 24ss b2 075, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_075


title: Sample 183

description: Glioblastoma, IDH wildtype


title: K109067


title: EOC038_RNAseq

description:
Library name: EOC038_RNAseq
RNA-seq S038T


title: Endoderm Ngn3Cre 24ss b2 074, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_074


title: Sample 151

description: Astrocytoma, IDH-mutant, grade 2


title: EOC037_RNAseq

description:
Library name: EOC037_RNAseq
RNA-seq S037T


title: EOC036_RNAseq

description:
Library name: EOC036_RNAseq
RNA-seq S036T


title: K108875


title: Endoderm Ngn3Cre 24ss b2 072, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_072


title: K107975


title: EOC041_RNAseq

description:
Library name: EOC041_RNAseq
RNA-seq S041T


title: Sample_3


title: Sample 136

description: Glioblastoma, IDH wildtype


title: K108617


title: Endoderm Ngn3Cre 24ss b2 071, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_071


title: EOC034_RNAseq

description:
Library name: EOC034_RNAseq
RNA-seq S034T


title: Sample 120

description: Glioblastoma, IDH wildtype


title: Sample 337

description: Astrocytoma, IDH-mutant, grade 2


title: K107908


title: Endoderm Ngn3Cre 24ss b2 070, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_070


title: Sample 98

description: Glioblastoma, IDH wildtype


title: EOC035_RNAseq

description:
Library name: EOC035_RNAseq
RNA-seq S035T


title: EOC033_RNAseq

description:
Library name: EOC033_RNAseq
RNA-seq S033T


title: K107799


title: Endoderm Ngn3Cre 24ss b2 069, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_069


title: Sample 88

description: Glioblastoma, IDH wildtype


title: EOC032_RNAseq

description:
Library name: EOC032_RNAseq
RNA-seq S032T


title: K106473


title: Sample 84

description: Glioblastoma, IDH wildtype


title: EOC031_RNAseq

description:
Library name: EOC031_RNAseq
RNA-seq S031T


title: Endoderm Ngn3Cre 24ss b2 073, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_073


title: Endoderm Ngn3Cre 24ss b2 067, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_067


title: Sample 133

description: Glioblastoma, IDH wildtype


title: EOC030_RNAseq

description:
Library name: EOC030_RNAseq
RNA-seq S030T


title: K106165


title: Sample 83

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 3


title: Sample 75

description: Glioblastoma, IDH wildtype


title: EOC029_RNAseq

description:
Library name: EOC029_RNAseq
RNA-seq S029T


title: K105392


title: Endoderm Ngn3Cre 24ss b2 065, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_065


title: K105440


title: Sample 343


title: EOC028_RNAseq

description:
Library name: EOC028_RNAseq
RNA-seq S028T


title: Endoderm Ngn3Cre 24ss b2 066, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_066


title: Endoderm Ngn3Cre 24ss b2 064, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_064


title: EOC027_RNAseq

description:
Library name: EOC027_RNAseq
RNA-seq S027T


title: Sample 330

description: Glioblastoma, IDH wildtype


title: EOC025_RNAseq

description:
Library name: EOC025_RNAseq
RNA-seq S025T


title: K105166


title: Endoderm Ngn3Cre 24ss b2 068, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_068


title: Endoderm Ngn3Cre 24ss b2 062, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_062


title: Sample 278

description: Glioblastoma, IDH wildtype


title: EOC024_RNAseq

description:
Library name: EOC024_RNAseq
RNA-seq S024T


title: KTB39, TRIM37 rep1

value: Immortalized normal breast epithelial cell line

value: Infected with TRIM37_OE virus


title: Sample 272

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 061, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_061


title: EOC022_RNAseq

description:
Library name: EOC022_RNAseq
RNA-seq S022T


title: KTB39, Control rep2

value: Empty


title: EOC021_RNAseq

description:
Library name: EOC021_RNAseq
RNA-seq S021T


title: Sample 256

description: Glioblastoma, IDH wildtype


title: KTB39, Control rep1


title: Endoderm Ngn3Cre 24ss b2 060, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_060


title: K105180


title: Endoderm Ngn3Cre 24ss b2 059, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_059


title: EOC020_RNAseq

description:
Library name: EOC020_RNAseq
RNA-seq S020T


title: Sample 218

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 058, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_058


title: Sample 205

description: Glioblastoma, IDH wildtype


title: KTB51, TRIM37 rep1


title: KTB51, TRIM37 rep2


title: Endoderm Ngn3Cre 24ss b2 063, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_063


title: EOC019_RNAseq

description:
Library name: EOC019_RNAseq
RNA-seq S019T


title: Sample 328

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 2


title: Sample 203

description: Glioblastoma, IDH wildtype


title: KTB39, TRIM37 rep2


title: EOC018_RNAseq

description:
Library name: EOC018_RNAseq
RNA-seq S018T


title: KTB51, Control rep2


title: Sample 198

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 057, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_057


title: EOC017_RNAseq

description:
Library name: EOC017_RNAseq
RNA-seq S017T


title: Endoderm Ngn3Cre 24ss b2 056, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_056


title: Sample 192

description: Glioblastoma, IDH wildtype


title: EOC016_RNAseq

description:
Library name: EOC016_RNAseq
RNA-seq S016T


title: KTB51, rs57141087 rep2

value: Transfected with rs57141087 ssODNs


title: Sample 190

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 054, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_054


title: Endoderm Ngn3Cre 24ss b2 055, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_055


title: EOC015_RNAseq

description:
Library name: EOC015_RNAseq
RNA-seq S015T


title: Sample 141

description: Glioblastoma, IDH wildtype


title: EOC014_RNAseq

description:
Library name: EOC014_RNAseq
RNA-seq S014T


title: Sample 132

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 052, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_052


title: MMS-CY-2

first: yu

last: Wang

state: Beijing

address: 22 South Zhongguancun Street, Haidian District

department: Peking University School and Hospital of Stomatology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm38
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Human periodontal ligament stem cell

growth_protocol: PDLSCs were maintained in a-MEM with 10% fetal bovine serum (FBS) with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: Lipopolysaccharide stimulation was added into the culture medium, then MMS and MMS-CY were added into the medium.

value: Human periodontal ligament stem cell

value: MMS-CY


title: MMS-CY-1


title: Endoderm Ngn3Cre 24ss b2 051, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_051

value: Endoderm


title: EOC012_RNAseq

description:
Library name: EOC012_RNAseq
RNA-seq S012T


title: MMS-2

value: MMS


title: EOC011_RNAseq

description:
Library name: EOC011_RNAseq
RNA-seq S011T


title: Sample 465

description: Astrocytoma, IDH-mutant, grade 2


title: Endoderm Ngn3Cre 24ss b2 050, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_050

value: Ngn3-Cre; Ai6


title: EOC013_RNAseq

description:
Library name: EOC013_RNAseq
RNA-seq S013T


title: MMS-1


title: Endoderm Ngn3Cre 24ss b2 049, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_049


title: Endoderm Ngn3Cre 24ss b2 053, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_053


title: KTB51, Control rep1


title: EOC010_RNAseq

description:
Library name: EOC010_RNAseq
RNA-seq S010T


title: Sample 453

description: Astrocytoma, IDH-mutant, grade 3


title: Sample 430

description: Supratentorial ependymoma, NOS


title: Sample 104

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 048, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_048


title: EOC008_RNAseq

description:
Library name: EOC008_RNAseq
RNA-seq S008T


title: KTB51, rs57141087 rep1


title: Endoderm Ngn3Cre 24ss b2 046, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_046


title: EOC007_RNAseq

description:
Library name: EOC007_RNAseq
RNA-seq S007T


title: Endoderm Ngn3Cre 24ss b2 047, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_047


title: Endoderm Ngn3Cre 24ss b2 045, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_045


title: Sample 316

description: Glioblastoma, IDH wildtype


title: Sample 313

description: Glioblastoma, IDH wildtype


title: EOC006_RNAseq

description:
Library name: EOC006_RNAseq
RNA-seq S006T


title: EOC005_RNAseq

description:
Library name: EOC005_RNAseq
RNA-seq S005T


title: Endoderm Ngn3Cre 24ss b2 044, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_044


title: Sample 306

description: Glioblastoma, IDH wildtype


title: EOC004_RNAseq

description:
Library name: EOC004_RNAseq
RNA-seq S004T


title: Sample 279

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 042, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_042


title: Hu1193D14 [RNA-Seq]

description: Single end bulk RNA-seq

data_processing:
Real-Time Analysis (RTA) v3.4.4 software was used for base calling and Illumina BCL
Convert v3.9.3 to convert base call (BCL) files into FASTQ files
Subread package (release 2.0.6) was used for allignment
featureCounts was used for gene counts
DEseq2
Assembly: human hg38 genome
Supplementary files format and content: Hu1181_1192_1193 gene_TPM.xlsx
Supplementary files format and content: Hu1181_1192_1193 raw gene count.xlsx

growth_protocol: In vitro culture

extract_protocol:
Trozol
KAPA mRNA HyperPrep kit Ribo-minus RNAseq

treatment_protocol: RNA extraction at different days

value: pancreas

value: islets

value: primary cells

value: wild type

value: in vitro culture for 14 day


title: Sample 276

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 041, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_041


title: Sample 225

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 040, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_040


title: Hu1193D21 [RNA-Seq]

description: Single end bulk RNA-seq

value: in vitro culture for 21 day


title: Endoderm Ngn3Cre 24ss b2 039, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_039


title: Sample 216

description: Supratentorial ependymoma, NOS


title: Sample 209

description: Glioblastoma, IDH wildtype


title: Hu1193D1 [RNA-Seq]

description: Single end bulk RNA-seq

value: in vitro culture for 1 day


title: EOC009_RNAseq

description:
Library name: EOC009_RNAseq
RNA-seq S009T

value: ovarian tumor


title: Sample 428

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Endoderm Ngn3Cre 24ss b2 038, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_038


title: Sample 193

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 037, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_037


title: Sample 152

description: Glioblastoma, IDH wildtype


title: Hu1192D28 [RNA-Seq]

description: Single end bulk RNA-seq

value: in vitro culture for 28 day


title: Hu1192D21 [RNA-Seq]

description: Single end bulk RNA-seq


title: Endoderm Ngn3Cre 24ss b2 036, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_036


title: Hu1192D14 [RNA-Seq]

description: Single end bulk RNA-seq


title: Endoderm Ngn3Cre 24ss b2 043, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_043


title: Endoderm Ngn3Cre 24ss b2 035, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_035


title: Hu1192D7 [RNA-Seq]

description: Single end bulk RNA-seq

value: in vitro culture for 7 day


title: Endoderm Ngn3Cre 24ss b2 034, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_034


title: Hu1193D7 [RNA-Seq]

description: Single end bulk RNA-seq


title: Hu1192D1 [RNA-Seq]

description: Single end bulk RNA-seq


title: Sample 448


title: Hu1181D28 [RNA-Seq]

description: Single end bulk RNA-seq


title: Sample 461

description: Glioblastoma, IDH wildtype


title: Sample 445

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 033, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_033


title: Endoderm Ngn3Cre 24ss b2 032, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_032


title: Hu1181D21 [RNA-Seq]

description: Single end bulk RNA-seq


title: Sample 443

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 031, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_031


title: Hu1181D7 [RNA-Seq]

description: Single end bulk RNA-seq


title: Sample 444

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 029, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_029


title: Endoderm Ngn3Cre 24ss b2 030, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_030


title: Hu1181D14 [RNA-Seq]

description: Single end bulk RNA-seq


title: Hu1193D21

description: small RNA high throughput sequencing,raw fastq, processed read count and count per million reads

data_processing:
Basecalls performed using CASAVA version 1.8
cutadapt to remove three nucletide from 5' end
miRge2
DEseq2
Assembly: hg38
Supplementary files format and content: Hu1181-1192-1193 islet culture miRNA count and RPM.xlsx

extract_protocol:
trizol
Modified illumina v1.5 protocol, 3 random nucleotide added to the end of the 5' adaptor
small RNA sequencing


title: Endoderm Ngn3Cre 24ss b2 028, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_028


title: Sample 117

description: Glioblastoma, IDH wildtype


title: Sample 417

description: Glioblastoma, IDH wildtype


title: Hu1193D14


title: Endoderm Ngn3Cre 24ss b2 026, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_026


title: Sample 426

description: Glioblastoma, IDH wildtype


title: Hu1181D1 [RNA-Seq]

description: Single end bulk RNA-seq


title: Endoderm Ngn3Cre 24ss b2 025, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_025


title: Sample 415

description: Glioblastoma, IDH wildtype


title: Sample 144

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 027, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_027


title: Hu1193D7


title: Sample 411

description: Glioblastoma, IDH wildtype


title: Hu1193D1


title: Sample 414

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 023, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_023


title: Endoderm Ngn3Cre 24ss b2 024, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_024


title: Sample 360

description: Glioblastoma, IDH wildtype


title: Hu1192D21


title: Hu1192D28


title: Sample 442

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 021, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_021


title: Sample 327

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 3


title: Hu1192D7


title: Endoderm Ngn3Cre 24ss b2 022, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_022


title: Sample 344

description: Glioblastoma, IDH wildtype


title: Hu1192D14


title: Hu1192D1


title: Endoderm Ngn3Cre 24ss b2 020, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_020


title: Sample 300

description: Glioblastoma, IDH wildtype


title: Sample 372

description: Astrocytoma, IDH-mutant, grade 2


title: Hu1181D28


title: Endoderm Ngn3Cre 24ss b2 019, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_019


title: Endoderm Ngn3Cre 24ss b2 018, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_018


title: Sample 367

description: Glioblastoma, IDH wildtype


title: Hu1181D21


title: Endoderm Ngn3Cre 24ss b2 017, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_017


title: Sample 366

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 016, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_016


title: Sample 365

description: Ganglioglioma


title: Hu1181D14


title: Hu1181D7


title: Endoderm Ngn3Cre 24ss b2 015, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_015


title: Hu1181D1


title: Endoderm Ngn3Cre 24ss b2 014, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_014


title: Sample 364

description: Glioblastoma, IDH wildtype


title: P45

city: beijing

first: Guanglong

last: Dong

state: None Selected

address: fuxin road

institute: Department of General Surgery, The First Medical Center, Chinese PLA General Hospital

description:
P45
processed data file.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: processed data file.xlsx

source_name: colorectal cancer (CRC) specimen

extract_protocol:
CRC tissue was taken out, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer (CRC) specimen

tag: msi status

value: MSS

tag: Sex

value: female

tag: bmi

tag: differentiation

value: high

tag: location

value: ascending colon

tag: t

tag: n

tag: m

tag: predictive score

tag: risk

value: Low


title: Sample 361

description: Glioblastoma, IDH wildtype

tag: tissue


title: Sample 362

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 013, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_013

value: Endoderm

tag: strain

tag: genotype

value: Ngn3-Cre; Ai6

tag: time


title: P44

description:
P44
processed data file.xlsx

tag: age

value: male

value: medium

value: sigmoid colon

value: High


title: High glucose-3

city: Indianapolis

first: Padmanabhan

middle: P

last: Pattabiraman

state: IN

address: Department of Ophthalmology, Room number 402, 1160 West Michigan Street

department: Ophthalmology

institute: Indiana University Purdue University Indianapolis

data_processing:
The sequence data were mapped to the human reference genome hg38 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Assembly: human reference genome hg38
Supplementary files format and content: excel file includeing raw counts, log2 fold change, p-values and FDR

source_name: Primary Human Trabecular Meshwork Cells

extract_protocol:
Post treatment HTM cells were collected using RIPA and RNA was extracted and purified using Direct-zol RNA kit (Zymo Research, #R2050S) following manufacturer's protocol.
KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries.

value: Primary Human Trabecular Meshwork Cells

tag: treatment

value: 30 mM (high glucose)


title: Sample 351

description: Astrocytoma, IDH-mutant, grade 3

value: Brain tumor


title: Endoderm Ngn3Cre 24ss b2 012, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_012


title: High glucose-2


title: Control-2

value: 5 mM (control/normal glucose)


title: Sample 320

description: Glioblastoma, IDH wildtype


title: P43

description:
P43
processed data file.xlsx

value: MSI


title: P42

description:
P42
processed data file.xlsx

value: colorectal cancer (CRC) specimen

value: cecum


title: High glucose-1


title: Endoderm Ngn3Cre 24ss b2 010, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_010


title: Control-1


title: P41

description:
P41
processed data file.xlsx

value: MSS

value: female

value: low

value: rectum


title: Endoderm Ngn3Cre 24ss b2 009, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_009

value: Endoderm


title: Sample 293

description: Glioblastoma, IDH wildtype


title: WT-IgG

city: Gainesville

first: Jonathan

last: Licht

state: Florida

address: 2033 Mowry Road

department: UF Health Cancer Center

institute: University of Florida

data_processing:
Trimming and quality control were performed on raw fastq files using Trimmomatic (v0.36) and FastQC (v0.11.4).
The input reads were aligned to the genome using Bowtie (v2.4.5).
Peak detection was performed using SEACR (v1.3) with the following options: mode=relaxed, normalization=True.
Assembly: GRCh38
Supplementary files format and content: bed files generated by SEACR
Library strategy: CUT&RUN

source_name: TKO

growth_protocol: Cells were plated at a density of 0.2x10^6 cells/mL and harvest at 70-80% confluence

extract_protocol:
Cell lines were cross-linked with 0.8% formaldehyde and quenched with 0.125 mol/L glycine. Extracted chromatin was sonicated and immunoprecipitated with overnight at −4°C with the indicated antibody. Precipitated chromatin was washed and incubated in Tagmentation buffer containing Tagment enzyme and DNA was purified after reverse cross-linking
Purified DNA samples were amplified for the library with index primers using the KAPA HiFi HotStart Kit

tag: cell line

value: TKO

tag: cell type

value: plasma cell

tag: chip antibody

value: IgG

tag: biological replicates


title: Endoderm Ngn3Cre 24ss b2 008, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_008

value: Ngn3-Cre; Ai6


title: Endoderm Ngn3Cre 24ss b2 007, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_007


title: WT-H3K4me3


title: Control-3


title: Sample 287

description: Glioblastoma, IDH wildtype


title: P40

description:
P40
processed data file.xlsx

tag: msi status

tag: Sex

tag: bmi

tag: differentiation

value: medium

value: Low


title: Sample 286

description: Glioblastoma, IDH wildtype


title: WT-H3K27me3-Rep1


title: Sample 228

description: Glioblastoma, IDH wildtype


title: P36

description:
P36
processed data file.xlsx

value: male

tag: location

value: ascending colon

tag: t

tag: n

tag: m

value: High


title: Sample 138

description: Glioblastoma, IDH wildtype

tag: tissue

value: Brain tumor


title: P38

description:
P38
processed data file.xlsx

value: colorectal cancer (CRC) specimen

value: MSI

tag: predictive score

tag: risk


title: Endoderm Ngn3Cre 24ss b2 006, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_006

tag: strain

tag: genotype

tag: time


title: Sample 299

description: Glioblastoma, IDH wildtype


title: TKO-IgG

tag: cell line

tag: cell type


title: Endoderm Ngn3Cre 24ss b2 004, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_004


title: Sample 322

description: Pilocytic astrocytoma


title: TKO-H3K4me3

tag: chip antibody

tag: biological replicates


title: Endoderm Ngn3Cre 24ss b2 005, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_005


title: WT-H3K27me3-Rep2


title: P35

description:
P35
processed data file.xlsx

tag: msi status

value: MSS

tag: age

tag: Sex

value: descending colon


title: Endoderm Ngn3Cre 24ss b2 003, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_003


title: P37

description:
P37
processed data file.xlsx

value: female

tag: bmi

tag: differentiation

tag: location

value: sigmoid colon


title: Sample 294

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 24ss b2 002, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_002

value: Endoderm


title: P34

description:
P34
processed data file.xlsx

tag: t

tag: n

tag: m


title: Sample 280

description: Glioblastoma, IDH wildtype

tag: tissue


title: TKO-H3K27me3-Rep1

value: TKO


title: P39

description:
P39
processed data file.xlsx

value: high

tag: predictive score

tag: risk


title: P33

description:
P33
processed data file.xlsx

value: low


title: F1295A-IgG

value: plasma cell

tag: genotype

value: IgG


title: Sample 274

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 106, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_106

tag: strain

value: Ngn3-Cre; Ai6

tag: time


title: Sample 232

description: Astrocytoma, IDH-mutant, grade 2


title: F1295A-H3K4me3

tag: cell line

tag: cell type

tag: chip antibody


title: Endoderm Ngn3Cre 24ss b2 011, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_011


title: Sample 219

description: Glioblastoma, IDH wildtype


title: P31

description:
P31
processed data file.xlsx

tag: msi status

tag: age

value: male

value: medium

value: Low


title: Endoderm Ngn3Cre 21ss b2 105, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_105


title: Sample 171

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Endoderm Ngn3Cre 21ss b2 104, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_104


title: F1295A-H3K27me3-Rep1

tag: biological replicates


title: Sample 161

description: Glioblastoma, IDH wildtype


title: D1240A-IgG


title: Endoderm Ngn3Cre 21ss b2 103, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_103


title: P29

description:
P29
processed data file.xlsx

value: colorectal cancer (CRC) specimen

tag: Sex

tag: bmi

tag: differentiation

value: rectum


title: Endoderm Ngn3Cre 21ss b2 102, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_102


title: P30

description:
P30
processed data file.xlsx

value: MSI

tag: location

value: ascending colon

tag: t

tag: n

value: High


title: Sample 160

description: Glioblastoma, IDH wildtype

tag: tissue


title: TKO-H3K27me3-Rep2


title: D1240A-H3K4me3


title: Sample 159

description: Glioblastoma, IDH wildtype


title: P27

description:
P27
processed data file.xlsx

value: MSS

value: female

tag: m

tag: predictive score

tag: risk


title: Endoderm Ngn3Cre 24ss b2 001, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_24ss_b2_001

value: Endoderm

tag: strain

tag: genotype

tag: time


title: P32

description:
P32
processed data file.xlsx


title: D1240A-H3K27me3-Rep2

tag: cell line

value: TKO

tag: cell type

tag: chip antibody


title: P26

description:
P26
processed data file.xlsx

tag: msi status

tag: age

value: descending colon


title: Sample 157

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 099, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_099


title: F1295A-H3K27me3-Rep2

value: plasma cell

tag: biological replicates


title: P25

description:
P25
processed data file.xlsx

tag: Sex

tag: bmi

tag: differentiation


title: Sample 156

description: Glioblastoma, IDH wildtype


title: P24

description:
P24
processed data file.xlsx

tag: location

tag: t

tag: n


title: WT-input

data_processing:
Trimming and quality control were performed on raw fastq files using Trimmomatic (v0.36) and FastQC (v0.11.4).
The input reads were aligned to the genome using Bowtie (v2.4.5). Samples were normalized based on Drosophila spike-ins.
Peak detection was performed using MACS (v2.2.7.1) with the following options: broad=N, model=Y, paired=Y, qvalue=0.05.
Assembly: GRCh38
Supplementary files format and content: Peak files generated by MACS2 as .xls files


title: P28

description:
P28
processed data file.xlsx

tag: tissue

tag: m

tag: predictive score


title: Sample 140

description: Glioblastoma, IDH wildtype


title: WT-2-36me2

tag: genotype


title: Endoderm Ngn3Cre 21ss b2 096, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_096

tag: strain

tag: time


title: P22

description:
P22
processed data file.xlsx

value: sigmoid colon

tag: risk


title: Sample 134

description: Glioblastoma, IDH wildtype


title: WT-2-27ac

tag: cell line

tag: cell type

tag: chip antibody


title: WT-2-27me3


title: Endoderm Ngn3Cre 21ss b2 097, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_097

value: Ngn3-Cre; Ai6


title: Sample 126

description: Glioblastoma, IDH wildtype


title: P23

description:
P23
processed data file.xlsx

tag: msi status

tag: age


title: P21

description:
P21
processed data file.xlsx

tag: Sex

value: male

tag: bmi


title: Endoderm Ngn3Cre 21ss b2 095, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_095


title: Endoderm Ngn3Cre 21ss b2 101, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_101


title: Endoderm Ngn3Cre 21ss b2 094, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_094


title: D1240A-H3K27me3-Rep1

tag: biological replicates


title: Endoderm Ngn3Cre 21ss b2 100, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_100


title: P20

description:
P20
processed data file.xlsx

tag: differentiation

value: low

tag: location

tag: t


title: WT-1-36me2


title: Sample 121

description: Glioblastoma, IDH wildtype

tag: tissue


title: P19

description:
P19
processed data file.xlsx

value: medium

tag: n

tag: m

tag: predictive score

value: Low


title: Endoderm Ngn3Cre 21ss b2 098, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_098

tag: strain

tag: genotype

tag: time


title: Sample 109

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: P18

description:
P18
processed data file.xlsx

value: colorectal cancer (CRC) specimen

tag: risk


title: Sample 106

description: Glioblastoma, IDH wildtype


title: WT-1-27ac

tag: cell line

tag: cell type

tag: chip antibody


title: Endoderm Ngn3Cre 21ss b2 091, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_091


title: Endoderm Ngn3Cre 21ss b2 092, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_092


title: P17

description:
P17
processed data file.xlsx

tag: msi status

value: MSI

tag: age

tag: Sex

value: rectum


title: Endoderm Ngn3Cre 21ss b2 093, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_093


title: TKO-input


title: Endoderm Ngn3Cre 21ss b2 090, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_090


title: TKO-2-27me3


title: P15

description:
P15
processed data file.xlsx

tag: bmi

tag: differentiation

value: high

value: High


title: Sample 89

description: Glioblastoma, IDH wildtype


title: Sample 100

description: Glioblastoma, IDH wildtype


title: Endoderm Ngn3Cre 21ss b2 089, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_089


title: P16

description:
P16
processed data file.xlsx

value: MSS

tag: location

tag: t


title: Sample 122

description: Glioblastoma, IDH wildtype

tag: tissue


title: TKO-2-27ac


title: Endoderm Ngn3Cre 21ss b2 088, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_088

value: Endoderm


title: WT-1-27me3

value: TKO


title: P14

description:
P14
processed data file.xlsx

value: female

tag: n

tag: m


title: Sample 79

description: Pilocytic astrocytoma


title: TKO-1-36me2

value: plasma cell


title: P13

description:
P13
processed data file.xlsx

value: ascending colon

tag: predictive score


title: Sample 77

description: Glioblastoma, IDH wildtype


title: TKO-1-27me3

tag: genotype


title: P12

description:
P12
processed data file.xlsx


title: Endoderm Ngn3Cre 21ss b2 086, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_086

tag: strain

value: Ngn3-Cre; Ai6

tag: time


title: TKO-1-27ac

tag: cell line


title: Sample 76

description: Glioblastoma, IDH wildtype


title: TKO-2-36me2

tag: cell type


title: P11

description:
P11
processed data file.xlsx

value: sigmoid colon

tag: risk


title: Sample 68

description: Ganglioglioma


title: Sample 90

description: Glioblastoma, IDH wildtype


title: Sample 54

description: Oligodendroglioma, IDH-mutant  and  1p/19q-codeleted, grade 2


title: Endoderm Ngn3Cre 21ss b2 084, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_084


title: F1295A-2-36me2

tag: chip antibody


title: Sample 35

description: Glioblastoma, IDH wildtype


title: P9

description:
P9
processed data file.xlsx

tag: msi status

tag: age

value: male


title: P10

description:
P10
processed data file.xlsx

tag: Sex

tag: bmi

value: medium


title: Endoderm Ngn3Cre 21ss b2 087, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_087


title: P8

description:
P8
processed data file.xlsx

tag: differentiation

tag: location

value: Low


title: Endoderm Ngn3Cre 21ss b2 083, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_083

tag: tissue


title: F1295A-2-27me3


title: F1295A-input


title: Endoderm Ngn3Cre 21ss b2 082, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_082


title: Sample 8

description: Glioblastoma, IDH wildtype

value: Brain tumor


title: Endoderm Ngn3Cre 21ss b2 081, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_081


title: F1295A-1-36me2


title: P6

description:
P6
processed data file.xlsx

value: colorectal cancer (CRC) specimen

tag: t

tag: n


title: Sample 2

description: Glioblastoma, IDH wildtype


title: P7

description:
P7
processed data file.xlsx

tag: m

tag: predictive score


title: F1295A-2-27ac

tag: genotype


title: Endoderm Ngn3Cre 21ss b2 080, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_080

tag: strain

tag: time


title: P5

description:
P5
processed data file.xlsx


title: Endoderm Ngn3Cre 21ss b2 085, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_085


title: F1295A-1-27me3

tag: cell line

tag: cell type


title: Endoderm Ngn3Cre 21ss b2 079, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_079


title: F1295A-1-27ac

tag: chip antibody


title: P4

description:
P4
processed data file.xlsx

tag: msi status

tag: risk


title: Sample 460


title: Sample 458

description: Glioblastoma, IDH wildtype


title: Sample 24

description: Glioblastoma, IDH wildtype


title: D1240A-input


title: P3

description:
P3
processed data file.xlsx

tag: age

tag: Sex

value: descending colon


title: D1240A-2-36me2


title: Sample 440


title: Sample 439

description: Glioblastoma, IDH wildtype


title: P2

description:
P2
processed data file.xlsx

tag: bmi

tag: differentiation

value: rectum


title: D1240A-2-27me3


title: Sample 438

description: Glioblastoma, IDH wildtype

tag: tissue


title: P1

description:
P1
processed data file.xlsx

value: high

tag: location

tag: t


title: Endoderm Ngn3Cre 21ss b2 075, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_075


title: Endoderm Ngn3Cre 21ss b2 076, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_076


title: Sample 363

description: Astrocytoma, IDH-mutant, grade 3


title: D1240A-1-36me2


title: D1240A-2-27ac


title: 22Rv1- Scramble_2

city: OMAHA

first: Jyoti

middle: Bala

last: Kaushal

state: NE

address: 42nd and Emile

institute: UNMC

data_processing:
Raw sequences were processed for quality control using both FastQC and MultiQC
Alignment was done usingHISAT2
Expression quantification was done in R using "featureCounts"
Differential expression analysis was run in R using the DESeq2
Assembly: GRCh38 release 84 version of H. sapiens (human) from Ensembl
Supplementary files format and content: tab-delimited text file includes raw counts (counts_data_22RV1.csv)

source_name: Prostate Cancer

growth_protocol: Human prostate cancer cell line 22Rv1 supplemented with 5% fetal bovine serum (FBS; R&D Systems Cat#S11550H) and 1% penicillin-streptomycin (Invitrogen Cat#15140-122). Cells were incubated in a humidified incubator at 37 °C and supplied with 5% CO2. Cells were subcultured by trypsin-EDTA treatment.

extract_protocol:
22Rv1-Gsk3β shRNA4 or 22Rv1-scramble cells were lysed using RNA lysis buffer provided with the mirVana RNA isolation kit (Cat#AM1561, Thermo Fischer Scientific; n=3). Total RNA was isolated by following the manufacturer’s protocol.
Library preparation was achieved using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s protocol

treatment_protocol: The 22Rv1 cells with stable Gsk3β knockdown and scramble control were generated using a human shRNA (Gsk3β shRNA) lentiviral particle system from ORIGENE. The lentiviral and polybrene mixture were used in each well for transduction. 72 hrs after transfection, GFP+-transfected 22Rv1 cells were sorted using FACS Aria II (BD Biosciences). Sorted GFP-positive cells were subsequently selected for puromycin-containing media.

value: Prostate Cancer

value: Epithelial cells

value: Gsk3beta-wild type

tag: treatment

value: Scramble-lentiviral transduction


title: 22Rv1- Scramble_3


title: Endoderm Ngn3Cre 21ss b2 073, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_073

value: Endoderm


title: 22Rv1- Scramble_1


title: D1240A-1-27me3

value: TKO

value: plasma cell


title: Sample 255

description: Astrocytoma, IDH-mutant, grade 3


title: D1240A-1-27ac


title: Endoderm Ngn3Cre 21ss b2 072, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_072

value: Ngn3-Cre; Ai6


title: Endoderm Ngn3Cre 21ss b2 078, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_078


title: Endoderm Ngn3Cre 21ss b2 071, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_071


title: 22Rv1- Gsk3β shRNA4_3

value: Gsk3β-shRNA lentiviral transduction


title: Endoderm Ngn3Cre 21ss b2 074, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_074


title: Sample 254

description: Supratentorial ependymoma, NOS


title: Endoderm Ngn3Cre 21ss b2 077, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_077


title: 22Rv1- Gsk3β shRNA4_2


title: Endoderm Ngn3Cre 21ss b2 070, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_070


title: Sample 102

description: Supratentorial ependymoma, NOS


title: 22Rv1- Gsk3β shRNA4_1


title: Endoderm Ngn3Cre 21ss b2 069, scRNA-seq

description:
Smart-seq3xpress
Ngn3Cre_21ss_b2_069


title: Sample 92

description: Glioblastoma, IDH wildtype


title: TKO-WT-1

data_processing:
Trimming and quality control were performed on raw fastq files using Trimmomatic (v0.36) and FastQC (v0.11.4).
The reads were aligned to the transcriptome using STAR (v2.7.9a) and quantified using RSEM (v1.3.1)
Differential expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: RSEM raw gene counts in .csv file

extract_protocol:
Total RNA was extracted with the Direct-zol RNA MiniPrep Plus Kit
Poly(A) RNA sequencing were performed by the University of Florida Interdisciplinary Center for Biotechnology Research core

tag: biological replicate

tag: vector

value: NSD2 expression vector


title: TKO-F1295A-3

tag: genotype

value: NSD2 p.F1295A expression vector