title: LUT111PS

description:
Library name: LUT111PS
LUT111PS


title: 19-3_NCI-H128_Day7_DMSO_0

status: Public on Jan 20 2026

type: SRA

city: chiba

first: YINGBO

last: GONG

department: Medicine

country: Japan

institute: CHIBA University

library_source: transcriptomic

data_processing:
Deep sequencing was performed on an Illumina NovaSeq 6000 (paired-end reads) according to the manufacturer’s protocols. Sequenced reads from the RNA-seq experiments were aligned using the Bowtie 2 and TopHat (version 1.3.2), and Cufflinks (version 2.0.2) was used for transcriptome assembly. Gene expression levels were expressed as fragments per kilobase of exons per million mapped sequence reads. DEGs were identified using the R software package (version 4.2.0). Heatmaps and dendrograms were generated using R, GraphPad Prism 9.0, or https://www.chiplot.online/. DEG-related and terms of the KEGG were analyzed by gene set enrichment analysis software (GSEA, version 4.2.3).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: NCI-1417 [H1417] (Cat. No. CRL-5869), NCI-H209 [H209] (HTB-172), SHP-77 (Cat. No. CRL-2195), NCI-H211 (Cat. No. CRL-5824), NCI-H196 (Cat. No. CRL-5823), NCI-H146 (Cat. No. HTB-173), NCI-H187 (Cat. No. CRL-5804), NCI-H69 (Cat. No. HTB-119), NCI-H446 [H446] (Cat. No. HTB-171), DMS 79 (Cat. No. CRL-2049), NCI-H510A [H510A, NCI-H510] (Cat. No. HTB-184), DMS 114 (Cat. No. CRL-2066), DMS 53 (Cat. No. CRL-2062), NCI-H2081 (Cat. No. CRL-5920), NCI-H524 [H524] (Cat. No. CRL-5831), NCI-H128 (Cat. No. HTB-120), NCI-H526 (Cat. No. CRL-5811), and NCI-H1694 (Cat. No. CRL-5888) cell lines were purchased from the American Type Culture Collection. Lu-135 (Cat. No. JCRB0170), COR-L51 (Cat. No. 92031916), CPC-N (Cat. No. ACC 306), and SBC-5 (Cat. No. JCRB0819) cell lines were obtained from the Japanese Collection of Research Bioresources, European Collection of Authenticated Cell Cultures, German Collection of Microorganisms and Cell Cultures GmbH, and Health Science Research Resources Bank, respectively. All of these are small-cell lung cancer cell lines and were cultured in RPMI1640 medium (Cat#: 189-02025, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% FBS (Cat#: 10270106, GIBCO Thermo Fisher Scientific, San Jose, CA) (NCI-1417, NCI-H209, SHP-77, NCI-H211, NCI-H196, Lu-135, and COR-L51), in conditioned, high-glucose RPMI1640 (Wako, Cat#: 187-02705) with 10% FBS (NCI-H146, NCI-H187, NCI-H69, NCI-H446, NCI-H526, NCI-H524, and DMS 79), in McCoy’s 5A (GIBCO, Cat#: 16600-082) with 10% FBS (CPC-N), in minimum essential medium (Cat#: 21442-25, Nacalai Tesque, Kyoto, Japan) with 10% FBS (SBC-5), in F-12K medium (GIBCO, Cat#: 11765-054) with 10% FBS (NCI-H510A), in Waymouth’s medium (GIBCO, Cat#: 11220-035) with 10% FBS (DMS 114 and DMS 53), in IMDM medium (GIBCO, Cat#: 12440-053) with 20% FBS (NCI-H128), or in HITES medium (GIBCO, 11330-032) with 10% FBS, Insulin (FUJIFILM, Cat#: 093-06351), Transferrin (Cat#: 10652202001, Roche Diagnostics, Rotkreuz, Switzerland), Hydrocortisone (Cat#: H6909-10ML, SIGMA-Aldrich, St. Louis, MO, USA), GlutaMAX (GIBCO, Cat#: 35050-061), Sodium Selenite (FUJIFILM, Cat#: 190-10844), and -Estradiol (SIGMA-Aldrich, Cat#: E2758-250MG) (NCI-H2081 and NCI-H1694). INSM1 knockout NCI-H1417 and NCI-H146 cells were generated using CRISPR‒Cas9 genome editing as previously described (Ochiiwa et al., 2021).

extract_protocol:
SCLC cell lines were treated, for the indicated durations, with different LSD1 inhibitors. Total cellular RNA was extracted using a modified chloroform/phenol procedure (TRIzol™, Invitrogen Thermo Fisher Scientific). RNA integrity and concentration were measured using a 4200 TapeStation system for high-throughput automated electrophoresis (Agilent, Santa Clara, CA, USA)
RNA-Seq libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) following the manufacturers’ protocols.

treatment_protocol: The SCLC cell lines were seeded in plates. The following day, LSD1 inhibitors were serially diluted with DMSO and mixed with the culture medium. The mixtures were then added to each well on the plates. The final concentration of DMSO was set at 0.075 %. Cells were maintained with the inhibitors without any medium change.

tag: cell line

tag: cell type

value: small-cell lung cancer

tag: genotype

value: WT

tag: treatment

value: DMSO


title: UTL-011PS

city: Birmingham

first: Zhangli

last: Su

state: Alabama

address: 720 20th Street South

department: Department of Genetics

country: USA

institute: University of Alabama

description:
Library name: UTL-011PS
UTL-011PS

data_processing:
Raw small RNA sequencing reads were trimmed to remove adapter sequences using Cutadapt (v5.1). Adapter-trimmed reads were then mapped and annotated using Unitas (v1.7.3), a specialized tool for comprehensive small RNA annotation. For liver biopsy samples, read count matrices generated by Unitas were imported into DESeq2 (v1.44.0) in R for normalization and differential expression analysis. Prior to analysis, RNAs with zero counts in more than 80% of samples were excluded to reduce low-abundance noise. Data visualization was performed in R using ggplot2 (v3.5.1) and ggpubr (v0.6.0). For perfusate samples, read count matrices generated by Unitas were imported into R and normalized to reads per million (RPM). Given the lower complexity of perfusate libraries relative to biopsy samples, differential expression analysis was performed using Student’s t-tests on RPM values. Data visualization was carried out in R with ggplot2 (v3.5.1) and ggpubr (v0.6.0), and receiver operating characteristic (ROC) curves were generated using the ROCR package (v1.0-11).
Assembly: hg38
Supplementary files format and content: count table including microRNA and tRNA fragments

source_name: liver

extract_protocol:
Total RNA was extracted from needle biopsies using the Direct-zol RNA MicroPrep Kit (Zymo Research, Cat. #R2062) according to the manufacturer’s instructions, including on-column DNase I treatment to remove genomic DNA contamination. For DOPS samples, RNA was isolated from 500 μl of solution using the same kit, following the manufacturer’s protocol for liquid samples, and eluted in 15 μl of RNase-free water. Purified RNA was stored at –80 °C, and repeated freeze–thaw cycles were avoided to minimize RNA degradation.
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Cat. #E7330) following the manufacturer’s instructions. For each sample, 100 ng of tissue RNA or 5 μl of DOPS RNA was used as input. Indexing was performed using the NEBNext Multiplex Oligos for Illumina, with PCR amplification carried out for 15 cycles for tissue RNA libraries and 18 cycles for perfusate RNA libraries. Amplified products were resolved on an 8% polyacrylamide gel (Thermo Fisher Scientific, Cat. #EC6215BOX), and target bands were excised and purified. Equal amounts of libraries were pooled and sequenced on an Illumina NextSeq 500 platform, generating approximately 10 million 75 bp single-end reads per sample.

tag: tissue

value: liver

tag: transplant outcome

value: NF


title: 19-1_NCI-H128_Day7_DMSO_0


title: 19-4_NCI-H128_Day7_TAS1440_300nM


title: mpk_KO_cpd_5

city: Baltimore

first: Mackenzie

last: Kui

state: Maryland

address: 725 N Wolfe Street

department: Physiology

institute: Johns Hopkins

description:
Library name: 23_KOcpd2h
KO_cpd_5

data_processing:
Pooled libraries were sequenced on an Illumina® NovaSeqX Plus instrument using standard protocols for paired end sequencing. 24 samples were multiplexed for an estimated 89 million unique mapped reads per sample. Demultiplexed FASTQ files were generated using bcl-convert v3.7.5.
Transcriptomic data collected by RNA sequencing (RNA-seq) was analyzed to determine the genes that are present in each sample and condition, their expression levels, and the differences between expression levels among experiment conditions, as follows. Sequencing reads were mapped to the mouse genome version GRCm39 with the alignment tool STAR v.2.7.8a (ref-star), which allows for large ‘gaps’ in the alignment, representing introns.
Assembly: The aligned reads were assembled with PsiCLASS v.1.0.2 (ref-psiclass) to create gene and transcript models. Unlike traditional transcript assemblers that process each sample separately, PsiCLASS simultaneously analyzes all samples in the experiment to produce a unified set of transcript annotations to use in the subsequent differential analyses. Transcripts were then assigned to known genes from the GENCODE v.M28 reference gene set. Lastly, DESeq2 (ref-deseq) was used to quantify the expression levels and determine differentially expressed genes. P values were corrected for FDR.
Supplementary files format and content: csv files contain raw counts normalized by gene length

organism: Mus musculus

source_name: kidney cortical collecting duct

growth_protocol: Without transformation (WT) and Gpr39 knockout (KO) mpkCCD cells were seeded onto 12-well transwell inserts and cultured in complete media without dDAVP for 9 days to allow for full polarization. Cells were then switched to simple media for 24 hours prior to treatment.

extract_protocol:
Following treatment, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat# 74104) according to the manufacturer’s instructions. Samples were checked for quality/quantity on Fragment Analyzer and Qubit prior to library preparation.
NEBNext Poly(A) Magnetic Isolation Module (NEB #E7490) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Cat# E7775) were used to generate libraries. Specifically, Poly A RNAs were isolated from total RNAs and fragmented for cDNA synthesis. End repair was performed, and DNA fragments were ligated to sequencing adapters. Ligated fragments were subsequently size selected through purification using Sample Purification Beads PCR amplification was used to prepare the libraries. The Fragment Analyzer was used for quality control of the libraries to ensure adequate concentration and appropriate fragment size. The resulting library insert size was 200bp-500bp with a median size around 300bp. Libraries were barcoded using unique dual indexing (E6440S) and pooled for sequencing.

treatment_protocol: Cells were treated with either 1 µM cpd1324 + 10 µM ZnCl₂ or vehicle control (0.1% DMSO + 10 µM ZnCl₂) for 2 hours in the basolerateral compartment

value: kidney cortical collecting duct

value: mpkCCD

value: epithelial

value: KO

value: 1 µM cpd1324 + 10 µM ZnCl₂

tag: time

value: 2 hours


title: mpk_KO_cpd_4

description:
Library name: 22_KOcpd2h
KO_cpd_4


title: LUT105PS

description:
Library name: LUT105PS
LUT105PS


title: mpk_KO_cpd_3

description:
Library name: 21_KOcpd2h
KO_cpd_3


title: 18-6_CPC-N_Day7_TAS1440_300nM

source_name: CPC-N

value: CPC-N


title: LUT103PS

description:
Library name: LUT103PS
LUT103PS

value: EAD


title: 18-4_CPC-N_Day7_TAS1440_300nM


title: LUT092PS

description:
Library name: LUT092PS
LUT092PS


title: LUT093PS

description:
Library name: LUT093PS
LUT093PS


title: mpk_KO_cpd_1

description:
Library name: 19_KOcpd2h
KO_cpd_1


title: LUT108PS

description:
Library name: LUT108PS
LUT108PS


title: 18-3_CPC-N_Day7_DMSO_0


title: mpk_WT_cpd_6

description:
Library name: 18_WTcpd2h
WT_cpd_6


title: LUT089PS

description:
Library name: LUT089PS
LUT089PS


title: LUT091PS

description:
Library name: LUT091PS
LUT091PS


title: 18-2_CPC-N_Day7_DMSO_0


title: 18-5_CPC-N_Day7_TAS1440_300nM


title: mpk_WT_cpd_4

description:
Library name: 16_WTcpd2h
WT_cpd_4


title: LUT088PS

description:
Library name: LUT088PS
LUT088PS


title: LUT098PS

description:
Library name: LUT098PS
LUT098PS


title: LUT087PS

description:
Library name: LUT087PS
LUT087PS


title: mpk_WT_cpd_5

description:
Library name: 17_WTcpd2h
WT_cpd_5


title: mpk_KO_cpd_2

description:
Library name: 20_KOcpd2h
KO_cpd_2


title: LUT096PS

description:
Library name: LUT096PS
LUT096PS


title: mpk_WT_cpd_2

description:
Library name: 14_WTcpd2h
WT_cpd_2


title: LUT084PS

description:
Library name: LUT084PS
LUT084PS


title: mpk_WT_cpd_3

description:
Library name: 15_WTcpd2h
WT_cpd_3


title: mpk_WT_cpd_1

description:
Library name: 13_WTcpd2h
WT_cpd_1


title: LUT085PS

description:
Library name: LUT085PS
LUT085PS


title: 18-1_CPC-N_Day7_DMSO_0


title: LUT099PS

description:
Library name: LUT099PS
LUT099PS


title: 17-4_NCI-H1694_Day7_TAS1440_300nM


title: 17-5_NCI-H1694_Day7_TAS1440_300nM


title: mpk_KO_veh_6

description:
Library name: 12_KOVeh
KO_veh_6

value: 0.1% DMSO + 10 µM ZnCl₂


title: 17-3_NCI-H1694_Day7_DMSO_0


title: LUT083PS

description:
Library name: LUT083PS
LUT083PS


title: LUT077PS

description:
Library name: LUT077PS
LUT077PS


title: LUT062PS

description:
Library name: LUT062PS
LUT062PS


title: LUT073PS

description:
Library name: LUT073PS
LUT073PS


title: LUT066PS

description:
Library name: LUT066PS
LUT066PS


title: 16-6_NCI-H2081_Day7_TAS1440_300nM


title: LUT068PS

description:
Library name: LUT068PS
LUT068PS


title: LUT060PS

description:
Library name: LUT060PS
LUT060PS


title: LUT070PS

description:
Library name: LUT070PS
LUT070PS


title: 17-6_NCI-H1694_Day7_TAS1440_300nM


title: LUT059PS

description:
Library name: LUT059PS
LUT059PS


title: mpk_KO_veh_4

description:
Library name: 10_KOVeh
KO_veh_4


title: LUT074PS

description:
Library name: LUT074PS
LUT074PS


title: LUT057PS

description:
Library name: LUT057PS
LUT057PS


title: LUT086PS

description:
Library name: LUT086PS
LUT086PS


title: 16-4_NCI-H2081_Day7_TAS1440_300nM


title: mpk_KO_veh_5

description:
Library name: 11_KOVeh
KO_veh_5


title: mpk_KO_veh_3

description:
Library name: 9_KOVeh
KO_veh_3


title: 17-1_NCI-H1694_Day7_DMSO_0


title: LUT056PS

description:
Library name: LUT056PS
LUT056PS


title: LUT061PS

description:
Library name: LUT061PS
LUT061PS


title: LUT072PS

description:
Library name: LUT072PS
LUT072PS


title: LUT055PS

description:
Library name: LUT055PS
LUT055PS


title: mpk_WT_veh_6

description:
Library name: 6_WTVeh
WT_veh_6


title: LUT065PS

description:
Library name: LUT065PS
LUT065PS


title: mpk_KO_veh_2

description:
Library name: 8_KOVeh
KO_veh_2


title: mpk_WT_veh_5

description:
Library name: 5_WTVeh
WT_veh_5


title: LUT052PS

description:
Library name: LUT052PS
LUT052PS


title: 17-2_NCI-H1694_Day7_DMSO_0


title: mpk_KO_veh_1

description:
Library name: 7_KOVeh
KO_veh_1


title: 16-5_NCI-H2081_Day7_TAS1440_300nM


title: LUT049PS

description:
Library name: LUT049PS
LUT049PS


title: 16-3_NCI-H2081_Day7_DMSO_0


title: LUT051PS

description:
Library name: LUT051PS
LUT051PS


title: LUT046PS

description:
Library name: LUT046PS
LUT046PS


title: mpk_WT_veh_4

description:
Library name: 4_WTVeh
WT_veh_4


title: 16-2_NCI-H2081_Day7_DMSO_0


title: LUT047PS

description:
Library name: LUT047PS
LUT047PS


title: LUT048PS

description:
Library name: LUT048PS
LUT048PS


title: mpk_WT_veh_3

description:
Library name: 3_WTVeh
WT_veh_3


title: LUT045PS

description:
Library name: LUT045PS
LUT045PS


title: 16-1_NCI-H2081_Day7_DMSO_0


title: mpk_WT_veh_2

description:
Library name: 2_WTVeh
WT_veh_2


title: LUT044PS

description:
Library name: LUT044PS
LUT044PS


title: LUT042PS

description:
Library name: LUT042PS
LUT042PS


title: 15-6_COR-L51_Day7_TAS1440_300nM


title: LUT040PS

description:
Library name: LUT040PS
LUT040PS


title: Multiplexed sublibrary 3

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 240 Pasteur Drive

department: Orthopaedic Surgery

institute: Stanford University

description:
Library name: Sublibrary B3
Parse Biosciences scRNA library

library_source: transcriptomic single cell

data_processing:
Sequencing files were processed using the Parse Biosciences Pipeline (v1.1,1), debarcoded and aligned to the mouse GRCm39 (mm39) genome to obtain count matrices.
Assembly: mm39
Supplementary files format and content: CSV files containing cell metadata, annotation data matrices in .h5ad format, digital gene expression matrices in .mtx format and CSV of gene IDs/names
Supplementary files format and content: Sample loading table as .xlsm file used for de-barcoding files using Parse pipeline
Supplementary files format and content: .txt file with groups and mouse sample_ids from sample loading table

source_name: Hindlimb knee joint

growth_protocol: Young (3 mo.) and aged male (24-28 mo.) C57BL/6J mice were obtained from Jackson Laboratory and the US National Institute on Aging (NIA) aged colony, respectively.

extract_protocol:
Mouse hind limbs were briefly cleaned to remove skin and muscle surrounding the joint. Knee joints  were then  harvested by trimming approximately 1mm of tissue from the ends of both long bones and enzymatically digested with pronase followed by liberase enzymes (Cat# 5401127001)  at 37ºC for 1 hr and 6 hrs, respectively, as previously described. Single-cell suspensions were immediately fixed using the Evercode Cell Fixation v1 kit (Parse Biosciences, Seattle) according to manufacturer’s instructions. Fixed samples were stored at -80°C until processing.
Library preparation was performed using the Evercode WT Mega v1 kit (Parse Biosciences, Seattle) following manufacturer’s instructions. Sequences from all samples were barcoded and combined into one sublibrary which was sequenced.

treatment_protocol: Aged and young mice were treated for 1 month once a day by intraperitoneal injection with 5mg/kg of SW033291 (SW) (ApexBio cat # A8709) or vehicle. Vehicle and SW were prepared in 10% ethanol, 5% Cremophor EL (Sigma-Aldrich cat # C5135), 85% D5W (Dextrose 5% Water) as previously reported

value: Hindlimb knee joint

tag: strain

tag: developmental stage

value: 3 or 24-28 months old

value: Vehicle or SW (PGDH inhibition)


title: LUT038PS

description:
Library name: LUT038PS
LUT038PS


title: LUT039PS

description:
Library name: LUT039PS
LUT039PS


title: 15-4_COR-L51_Day7_TAS1440_300nM

value: small-cell lung cancer


title: 15-2_COR-L51_Day7_DMSO_0

value: WT


title: 15-5_COR-L51_Day7_TAS1440_300nM


title: LUT015PS

description:
Library name: LUT015PS
LUT015PS


title: LUT031PS

description:
Library name: LUT031PS
LUT031PS


title: 15-3_COR-L51_Day7_DMSO_0

value: DMSO


title: mpk_WT_veh_1

description:
Library name: 1_WTVeh
WT_veh_1


title: CD11b+, IKK2 LoF, Sham 3

city: Ulm

first: Bernd

last: Baumann

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house (Novogene) perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. Hisat was selected as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene, FPKM of each gene was then calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FKPM for each sample

source_name: brain cortex

extract_protocol:
RNA was harvested using RNA-Solv® Reagent kit (omega BIO-TEK)
RNA sequencing and data processing were conducted by Novogene (London, UK). In summary, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After the fragmentation step, random hexamer primers were used for first-strand cDNA synthesis, which was followed by the second-strand cDNA synthesis using dUTP for the directional library. The library was afterward checked by Qubit and real-time PCR for quantification, for size distribution detection, a bioanalyzer was used. Index-coded samples were clustered according to the manufacturer’s instructions. After cluster generation, the library preparations were subsequently sequenced on an Illumina platform.

treatment_protocol: Young adult mice were either subjected to closed head injury (CHI) or sham-operated by surgical incision and sacrificed three days post injury. ACSA-2+ and CD11b+ cells were purified using the MACS Miltenyi system.

value: brain cortex

value: GFAP IKK2 Loss-of-function

value: Sham

value: Day 3


title: Multiplexed sublibrary 1

description:
Library name: Sublibrary A4
Parse Biosciences scRNA library


title: LUT004PS

description:
Library name: LUT004PS
LUT004PS

value: liver

value: NF


title: 14-5_Lu-135_Day7_TAS1440_300nM


title: 14-4_Lu-135_Day7_TAS1440_300nM


title: LUT024PS

description:
Library name: LUT024PS
LUT024PS


title: LUT023PS

description:
Library name: LUT023PS
LUT023PS


title: CD11b+, IKK2 LoF, Sham 4


title: LUT132_L2_EAD

description: Library name: LUT132L2

tag: needle biopsy specimen


title: 14-6_Lu-135_Day7_TAS1440_300nM


title: 15-1_COR-L51_Day7_DMSO_0


title: LUT014PS

description:
Library name: LUT014PS
LUT014PS


title: LUT037PS

description:
Library name: LUT037PS
LUT037PS


title: LUT010PS

description:
Library name: LUT010PS
LUT010PS


title: LUT007PS

description:
Library name: LUT007PS
LUT007PS


title: Multiplexed sublibrary 2

description:
Library name: Sublibrary B1
Parse Biosciences scRNA library


title: CD11b+, IKK2 LoF, Sham 2


title: LUT132_L1_EAD

description: Library name: LUT132L1


title: LUT005PS

description:
Library name: LUT005PS
LUT005PS


title: CD11b+, IKK2 LoF, Sham 1


title: LUT130_L2_NF

description: Library name: LUT130L2


title: LUT118_L1_EAD

description: Library name: LUT118L1


title: CD11b+, IKK2 LoF, TBI +3d 2

value: CHI/TBI


title: LUT117_L2_NF

description: Library name: LUT117L2


title: LUT111_L2_NF

description: Library name: LUT111L2


title: 14-2_Lu-135_Day7_DMSO_0


title: LUT110_L1_NF

description: Library name: LUT110L1


title: LUT127_L2_EAD

description: Library name: LUT127L2


title: CD11b+, IKK2 LoF, TBI +3d 4


title: LUT118_L2_EAD

description: Library name: LUT118L2


title: 13-4_NCI-H510A_Day7_TAS1440_300nM


title: LUT127_L1_EAD

description: Library name: LUT127L1


title: LUT106_L2_EAD

description: Library name: LUT106L2


title: CD11b+, IKK2 LoF, TBI +3d 3


title: CD11b+, IKK2 GoF, Sham 3

value: GFAP IKK2 Gain-of-function


title: 14-1_Lu-135_Day7_DMSO_0


title: 13-6_NCI-H510A_Day7_TAS1440_300nM


title: 14-3_Lu-135_Day7_DMSO_0


title: LUT105_L2_NF

description: Library name: LUT105L2


title: LUT130_L1_NF

description: Library name: LUT130L1


title: LUT110_L2_NF

description: Library name: LUT110L2


title: LUT104_L2_EAD

description: Library name: LUT104L2


title: LUT111_L1_NF

description: Library name: LUT111L1


title: 13-5_NCI-H510A_Day7_TAS1440_300nM


title: CD11b+, IKK2 GoF, Sham 5


title: CD11b+, IKK2 GoF, Sham 4


title: LUT104_L1_EAD

description: Library name: LUT104L1


title: CD11b+, IKK2 GoF, Sham 1


title: 13-3_NCI-H510A_Day7_DMSO_0


title: LUT102_L2_EAD

description: Library name: LUT102L2


title: CD11b+, IKK2 GoF, TBI +3d 5


title: LUT102_L1_EAD

description: Library name: LUT102L1


title: 12-6_SBC-5_Day7_TAS1440_300nM


title: CD11b+, IKK2 LoF, TBI +3d 1


title: LUT106_L1_EAD

description: Library name: LUT106L1


title: LUT117_L1_NF

description: Library name: LUT117L1


title: LUT100_L1_EAD

description: Library name: LUT100L1


title: LUT101_L1_NF

description: Library name: LUT101L1


title: LUT100_L2_EAD

description: Library name: LUT100L2


title: 12-3_SBC-5_Day7_DMSO_0


title: CD11b+, IKK2 GoF, TBI +3d 4


title: CD11b+, IKK2 GoF, Sham 2


title: LUT105_L1_NF

description: Library name: LUT105L1


title: 13-1_NCI-H510A_Day7_DMSO_0


title: 12-1_SBC-5_Day7_DMSO_0


title: LUT099_L2_EAD

description: Library name: LUT099L2


title: 12-5_SBC-5_Day7_TAS1440_300nM


title: CD11b+, IKK2 GoF, TBI +3d 3


title: LUT099_L1_EAD

description: Library name: LUT099L1


title: 11-6_DMS114_Day7_TAS1440_300nM


title: LUT101_L2_NF

description: Library name: LUT101L2


title: LUT088_L1_EAD

description: Library name: LUT088L1


title: CD11b+, IKK2 GoF, TBI +3d 2


title: 11-5_DMS114_Day7_TAS1440_300nM


title: CD11b+, Control, Sham 1

value: Control


title: 12-2_SBC-5_Day7_DMSO_0


title: LUT098_L1_EAD

description: Library name: LUT098L1

value: EAD


title: 12-4_SBC-5_Day7_TAS1440_300nM


title: Infant Blood_Control_11

city: Aurora

first: JAMES

middle: R

last: BARDILL

state: CO

department: Surgery

institute: UNIVERSITY OF COLORADO-ANSCHUTZ MED

description:
Library name: Sample 64
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_11

data_processing:
The ACGT101-miR program removed adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA), and repeats.
Unique sequences (18–26 nucleotides) were mapped to species-specific precursors in miRBase 22.0 by BLAST search to identify known and novel 3p- and 5p-derived miRNAs. Sequences mapping to mature miRNAs in hairpin arms were identified as known miRNAs, while those mapping to the opposite arm of known precursors were novel candidates. Remaining sequences were mapped to other selected species’ precursors in miRBase 22.0 and further BLASTed against the Homo sapiens genome to determine their genomic locations.
Assembly: hg38
Supplementary files format and content: Raw Counts Text Files

source_name: Serum

growth_protocol: Third-trimester maternal blood, amniotic fluid, cord blood, and infant blood were collected from CDH-complicated pregnancies. Amniotic fluid and cord blood were collected at the time of delivery. Cord blood collected was a mixture of both venous and arterial blood.

extract_protocol:
Total miRNA was purified using the Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA, USA) per the manufacturer's protocol. miRNA concentrations were measured using the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Quality control analysis and quantification were performed using Agilent Technologies 2100 Bioanalyzer (Agilent, CA, USA), and RNA integrity number >7.0 confirmed sample integrity.
Sequencing was performed by LC Sciences (Houston, Texas, USA). We used 1 µg of total RNA to prepare small RNA libraries with TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Single-end 50bp sequencing was conducted on an Illumina Hiseq 2500 system.

treatment_protocol: Infant blood was collected within the first 24 hours of life. Control samples of cord blood, amniotic fluid, and infant blood were obtained from similar gestational-aged healthy pregnancies after informed consent at the University of Colorado Hospital. Third-trimester maternal serum (n=10, GA 28–40 weeks) was obtained from Lee BioSolutions (Maryland Heights, MO) and served as healthy control samples

value: Serum


title: CD11b+, Control, TBI +3d 3


title: LUT089_L2_NF

description: Library name: LUT089L2


title: CD11b+, Control, Sham 2


title: LUT084_L2_NF

description: Library name: LUT084L2


title: 11-2_DMS114_Day7_DMSO_0


title: CD11b+, Control, TBI +3d 2


title: Infant Blood_Control_10

description:
Library name: Sample 63
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_10


title: LUT087_L2_NF

description: Library name: LUT087L2


title: LUT088_L2_EAD

description: Library name: LUT088L2


title: CD11b+, IKK2 GoF, TBI +3d 1


title: LUT087_L1_NF

description: Library name: LUT087L1


title: CD11b+, Control, TBI +3d 4


title: LUT085_L2_EAD

description: Library name: LUT085L2


title: LUT083_L2_NF

description: Library name: LUT083L2


title: ACSA-2+, IKK2 LoF, Sham 4

value: ACSA-2+ astrocyte


title: LUT098_L2_EAD

description: Library name: LUT098L2


title: Infant Blood_Control_08

description:
Library name: Sample 61
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_08


title: 11-4_DMS114_Day7_TAS1440_300nM


title: LUT085_L1_EAD

description: Library name: LUT085L1


title: Infant Blood_Control_07

description:
Library name: Sample 60
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_07


title: 11-3_DMS114_Day7_DMSO_0


title: 10-5_DMS53_Day7_TAS1440_300nM


title: LUT077_L2_NF

description: Library name: LUT077L2


title: ACSA-2+, IKK2 LoF, Sham 2


title: LUT077_L1_NF

description: Library name: LUT077L1


title: 13-2_NCI-H510A_Day7_DMSO_0


title: 11-1_DMS114_Day7_DMSO_0


title: LUT083_L1_NF

description: Library name: LUT083L1


title: Infant Blood_Control_04

description:
Library name: Sample 57
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_04


title: ACSA-2+, IKK2 LoF, Sham 3


title: LUT073_L1_NF

description: Library name: LUT073L1


title: LUT084_L1_NF

description: Library name: LUT084L1


title: ACSA-2+, IKK2 LoF, TBI +3d 3


title: CD11b+, Control, TBI +3d 1


title: 10-6_DMS53_Day7_TAS1440_300nM


title: 10-2_DMS53_Day7_DMSO_0


title: Infant Blood_Control_06

description:
Library name: Sample 59
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_06


title: Infant Blood_Control_09

description:
Library name: Sample 62
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_09


title: 10-4_DMS53_Day7_TAS1440_300nM


title: LUT073_L2_NF

description: Library name: LUT073L2


title: ACSA-2+, IKK2 LoF, TBI +3d 2


title: Infant Blood_Control_05

description:
Library name: Sample 58
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_05


title: ACSA-2+, IKK2 LoF, TBI +3d 1


title: Infant Blood_Control_01

description:
Library name: Sample 55
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_01


title: ACSA-2+, IKK2 LoF, Sham 1


title: LUT072_L2_NF

description: Library name: LUT072L2


title: Infant Blood_Control_02

description:
Library name: Sample 56
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_Control_02


title: 10-1_DMS53_Day7_DMSO_0


title: LUT072_L1_NF

description: Library name: LUT072L1


title: ACSA-2+, IKK2 LoF, TBI +3d 4


title: LUT089_L1_NF

description: Library name: LUT089L1


title: 9-6_NCI-H69_Day7_TAS1440_300nM


title: 10-3_DMS53_Day7_DMSO_0


title: Cord Blood_CDH_21

description:
Library name: Sample 54
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_21

value: CDH


title: Cord Blood_CDH_19

description:
Library name: Sample 53
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_19


title: 9-5_NCI-H69_Day7_TAS1440_300nM


title: LUT071_L2_EAD

description: Library name: LUT071L2


title: LUT071_L1_EAD

description: Library name: LUT071L1


title: 9-3_NCI-H69_Day7_DMSO_0


title: ACSA-2+, IKK2 GoF, Sham 3


title: 9-4_NCI-H69_Day7_TAS1440_300nM


title: 9-2_NCI-H69_Day7_DMSO_0


title: ACSA-2+, IKK2 GoF, Sham 4


title: LUT070_L2_NF

description: Library name: LUT070L2


title: ACSA-2+, IKK2 GoF, Sham 2


title: ACSA-2+, IKK2 GoF, Sham 5


title: Cord Blood_CDH_14

description:
Library name: Sample 52
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_14


title: ACSA-2+, IKK2 GoF, Sham 1


title: LUT068_L1_NF

description: Library name: LUT068L1


title: 9-1_NCI-H69_Day7_DMSO_0


title: LUT068_L2_NF

description: Library name: LUT068L2


title: Cord Blood_CDH_12

description:
Library name: Sample 50
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_12


title: 8-5_NCI-H526_Day7_TAS1440_300nM


title: 8-6_NCI-H526_Day7_TAS1440_300nM


title: Cord Blood_CDH_13

description:
Library name: Sample 51
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_13


title: LUT070_L1_NF

description: Library name: LUT070L1


title: LUT065_L2_NF

description: Library name: LUT065L2


title: Cord Blood_CDH_09

description:
Library name: Sample 49
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_09


title: ACSA-2+, IKK2 GoF, TBI +3d 4


title: Cord Blood_CDH_07

description:
Library name: Sample 47
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_07


title: ACSA-2+, IKK2 GoF, TBI +3d 5


title: 8-4_NCI-H526_Day7_TAS1440_300nM


title: ACSA-2+, IKK2 GoF, TBI +3d 3


title: LUT065_L1_NF

description: Library name: LUT065L1


title: Cord Blood_CDH_08

description:
Library name: Sample 48
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_08


title: LUT061_L2_NF

description: Library name: LUT061L2


title: Cord Blood_CDH_04

description:
Library name: Sample 46
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_CDH_04


title: 8-3_NCI-H526_Day7_DMSO_0


title: LUT061_L1_NF

description: Library name: LUT061L1


title: LUT057_L2_NF

description: Library name: LUT057L2


title: Cord Blood_Control_11

description:
Library name: Sample 45
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_11


title: ACSA-2+, IKK2 GoF, TBI +3d 2


title: 8-2_NCI-H526_Day7_DMSO_0


title: 8-1_NCI-H526_Day7_DMSO_0


title: Cord Blood_Control_09

description:
Library name: Sample 43
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_09


title: Cord Blood_Control_08

description:
Library name: Sample 42
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_08


title: Cord Blood_Control_10

description:
Library name: Sample 44
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_10


title: ACSA-2+, IKK2 GoF, TBI +3d 1


title: ACSA-2+, Control, Sham 5


title: 7-4_NCI-H524_Day7_TAS1440_300nM


title: 7-6_NCI-H524_Day7_TAS1440_300nM


title: Cord Blood_Control_07

description:
Library name: Sample 41
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_07


title: ACSA-2+, Control, Sham 4


title: LUT053_L2_NF

description: Library name: LUT053L2


title: ACSA-2+, Control, Sham 2


title: Cord Blood_Control_06

description:
Library name: Sample 40
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_06


title: 7-5_NCI-H524_Day7_TAS1440_300nM


title: 7-3_NCI-H524_Day7_DMSO_0


title: LUT052_L2_NF

description: Library name: LUT052L2


title: ACSA-2+, Control, Sham 1


title: LUT053_L1_NF

description: Library name: LUT053L1


title: LUT052_L1_NF

description: Library name: LUT052L1


title: 7-2_NCI-H524_Day7_DMSO_0


title: Cord Blood_Control_04

description:
Library name: Sample 39
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_04


title: ACSA-2+, Control, Sham 3


title: LUT057_L1_NF

description: Library name: LUT057L1


title: ACSA-2+, Control, TBI +3d 3


title: LUT051_L2_NF

description: Library name: LUT051L2


title: 7-1_NCI-H524_Day7_DMSO_0


title: Cord Blood_Control_01

description:
Library name: Sample 37
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_01


title: LUT051_L1_NF

description: Library name: LUT051L1


title: Cord Blood_Control_03

description:
Library name: Sample 38
column name in Table8.5_CDH_CBvsCTL_CB.txt:  Cord Blood_Control_03


title: 6-6_NCI-H446_Day7_TAS1440_300nM


title: 6-3_NCI-H446_Day7_DMSO_0


title: 6-4_NCI-H446_Day7_TAS1440_300nM


title: Amniotic Fluid_CDH_21

description:
Library name: Sample 36
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_21

source_name: Amniotic Fluid

value: Amniotic Fluid


title: Amniotic Fluid_CDH_14

description:
Library name: Sample 34
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_14


title: Amniotic Fluid_CDH_13

description:
Library name: Sample 33
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_13


title: LUT045_L2_NF

description: Library name: LUT045L2


title: LUT046_L2_NF

description: Library name: LUT046L2


title: ACSA-2+, Control, TBI +3d 1


title: 6-2_NCI-H446_Day7_DMSO_0

value: small-cell lung cancer


title: LUT048_L2_NF

description: Library name: LUT048L2


title: Amniotic Fluid_CDH_12

description:
Library name: Sample 32
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_12


title: Amniotic Fluid_CDH_19

description:
Library name: Sample 35
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_19


title: ACSA-2+, Control, TBI +3d 2


title: T3

city: Xi'an

first: Yulong

last: Chen

state: Shaanxi

address: No 1. Xinwang Road

country: China

institute: Xi'an Medical University

description:
Library name: Sample 6
Column name in raw_counts.txt: T3

data_processing:
RNA sequencing was performed on a BGISEQ-2000RS platform
The raw data obtained from sequencing was filtered using SOAPNuke (version 2.2.1)
HISAT2 software (v 2.2.1) was used to align clean reads to Ensembl mouse genomes
The expression level of genes was calculated by RSEM (v 1.3.1)
read counts were input into DEseq2 (v 1.40.2) to calculate differential gene expression and the statistical significance.
Assembly: GRCm38
Supplementary files format and content: tab-delimitd text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Total RNAs were isolated using an RNA 6000 Nano Kit (5067-1511, Agilent, CA, USA).
RNA library was prepared using the MGIEasy RNA Library Prep Kit (#1000006384, MGI Tech Co., Ltd, Shenzhen, China)

treatment_protocol: feeding high cholesterol diet for 12 weeks

value: Liver

value: YAPHep KOapoE-/-

value: High cholesterol diet


title: Amniotic Fluid_CDH_09

description:
Library name: Sample 30
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_09


title: C3

description:
Library name: Sample 3
Column name in raw_counts.txt: C3

value: YAPflox/floxapoE-/-mice


title: 5-6_NCI-H211_Day7_TAS1440_300nM

value: WT


title: 5-5_NCI-H211_Day7_TAS1440_300nM


title: ACSA-2+, Control, TBI +3d 4

value: brain cortex

value: Day 3


title: T1

description:
Library name: Sample 4
Column name in raw_counts.txt: T1

value: YAPHep koapoE-/-


title: 6-1_NCI-H446_Day7_DMSO_0

value: DMSO


title: 6-5_NCI-H446_Day7_TAS1440_300nM


title: C2

description:
Library name: Sample 2
Column name in raw_counts.txt: C2


title: Amniotic Fluid_CDH_10

description:
Library name: Sample 31
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_10


title: T2

description:
Library name: Sample 5
Column name in raw_counts.txt: T2


title: LUT045_L1_NF

description: Library name: LUT045L1

value: liver

value: NF


title: LUT048_L1_NF

description: Library name: LUT048L1


title: LUT046_L1_NF

description: Library name: LUT046L1


title: C1

description:
Library name: Sample 1
Column name in raw_counts.txt: C1


title: LUT044_L2_EAD

description: Library name: LUT044L2

value: EAD


title: LUT044_L1_EAD

description: Library name: LUT044L1


title: Amniotic Fluid_CDH_08

description:
Library name: Sample 29
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_08


title: 5-4_NCI-H211_Day7_TAS1440_300nM


title: 13-3B5 rep4

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description: Library name: 13-3B5_rep4

data_processing:
Reads were trimmed and quality filtered by TrimGalore (v.0.6.6, Cutadapt v.2.10), using default parameters
Consequently, reads were mapped to the Genome Reference Consortium Mouse Build 38, using STAR Aligner (v.2.7.6a)
A gene expression counts table was generated with HTSeq (v.0.12.4)
Data were normalized for sequencing depth with the median of ratios method and consequently analyzed for differential expression in the DESeq2 R package (v.1.32.0)
Assembly: GRCm38
Supplementary files format and content: .csv file with raw counts

growth_protocol: C2C12 myoblasts were maintained in DMEM Glutamax with 10% FBS and 1% pen/strep. For diferentiation into myotubes, myoblasts were grown until 90-95% confluency and switched to DMEM glutamax with 2% adult horse serum and 1% pen/strep for 5 days.

extract_protocol:
RNA was harvested using the miRNAeasy Mini Kit (Qiagen). >0.9 ug of total RNA was used for the construction of the sequencing libraries
Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero kit according to manufacturers instructions.  30 million reads were sequenced with the NovaSeq 6000 PE 150 system

treatment_protocol: C2C12 myotubes were treated for 16 hours with the following conditions: 7.7 nM b12 hIgG4 (negative control antibody); 7.7 nM 13-3B5 hIgG4 (activating MuSK antibody); 0.1 nM neural agrin + 7.7 nM b12 hIgG4 (natural activator + negative control antibody); 0.1 nM neural agrin + 7.7 nM 13-3B5xb12 (natural activator + monovalent inhibiting MuSK antibody); 0.1 nM neural agrin + 7.7 nM 11-3F6xb12 (natural activator + monovalent inhibiting MuSK antibody).

value: myotube cells


title: Agrin b12 rep4

description: Library name: Agrin_b12_rep4

value: 0.1 nM neural agrin + 7.7 nM b12 hIgG4


title: LUT038_L1_NF

description: Library name: LUT038L1


title: Amniotic Fluid_CDH_04

description:
Library name: Sample 27
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_04

value: CDH


title: Agrin 13-3B5xb12 rep4

description: Library name: Agrin_13-3B5xb12_rep4

value: 0.1 nM neural agrin + 7.7 nM 13-3B5xb12


title: LUT039_L2_EAD

description: Library name: LUT039L2


title: 5-3_NCI-H211_Day7_DMSO_0

value: small-cell lung cancer


title: Amniotic Fluid_CDH_07

description:
Library name: Sample 28
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_CDH_07

value: Amniotic Fluid


title: 5-2_NCI-H211_Day7_DMSO_0


title: Amniotic Fluid_Control_11

description:
Library name: Sample 26
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_11

value: Control


title: Agrin 11-3F6xb12 rep4

description: Library name: Agrin_11-3F6xb12_rep4

value: 0.1 nM neural agrin + 7.7 nM 11-3F6xb12


title: LUT038_L2_NF

description: Library name: LUT038L2


title: LUT039_L1_EAD

description: Library name: LUT039L1


title: 5-1_NCI-H211_Day7_DMSO_0


title: 4-4_NCI-H196_Day7_TAS1440_300nM


title: Amniotic Fluid_Control_08

description:
Library name: Sample 23
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_08


title: b12 rep4

description: Library name: b12_rep4

value: 7.7 nM b12 hIgG4


title: Agrin 11-3F6xb12 rep3

description: Library name: Agrin_11-3F6xb12_rep3


title: Amniotic Fluid_Control_10

description:
Library name: Sample 25
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_10


title: 4-5_NCI-H196_Day7_TAS1440_300nM

value: WT


title: Agrin 13-3B5xb12 rep3

description: Library name: Agrin_13-3B5xb12_rep3


title: LUT024_L2_EAD

description: Library name: LUT024L2


title: 4-6_NCI-H196_Day7_TAS1440_300nM


title: LUT024_L1_EAD

description: Library name: LUT024L1


title: Amniotic Fluid_Control_09

description:
Library name: Sample 24
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_09


title: Amniotic Fluid_Control_07

description:
Library name: Sample 22
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_07


title: LUT023_L2_EAD

description: Library name: LUT023L2


title: Agrin b12 rep3

description: Library name: Agrin_b12_rep3


title: 4-3_NCI-H196_Day7_DMSO_0


title: Amniotic Fluid_Control_06

description:
Library name: Sample 21
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_06


title: 13-3B5 rep3

description: Library name: 13-3B5_rep3


title: LUT023_L1_EAD

description: Library name: LUT023L1


title: 4-2_NCI-H196_Day7_DMSO_0


title: 4-1_NCI-H196_Day7_DMSO_0


title: Amniotic Fluid_Control_05

description:
Library name: Sample 20
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_05


title: Amniotic Fluid_Control_03

description:
Library name: Sample 19
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_03


title: 3-5_NCI-H187_Day7_TAS1440_300nM


title: Maternal Serum 3rd Trimester_CDH_19

description:
Library name: Sample 17
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_19

value: Serum


title: Agrin 13-3B5xb12 rep2

description: Library name: Agrin_13-3B5xb12_rep2


title: b12 rep3

description: Library name: b12_rep3


title: Amniotic Fluid_Control_01

description:
Library name: Sample 18
column name in Table8.3_CDH_AFvsCTL_AF.txt:  Amniotic Fluid_Control_01


title: 3-4_NCI-H187_Day7_TAS1440_300nM


title: LUT015_L2_NF

description: Library name: LUT015L2


title: Agrin 11-3F6xb12 rep2

description: Library name: Agrin_11-3F6xb12_rep2


title: Agrin b12 rep2

description: Library name: Agrin_b12_rep2


title: 13-3B5 rep2

description: Library name: 13-3B5_rep2


title: b12 rep2

description: Library name: b12_rep2


title: Agrin 11-3F6xb12 rep1

description: Library name: Agrin_11-3F6xb12_rep1


title: 3-1_NCI-H187_Day7_DMSO_0


title: 3-2_NCI-H187_Day7_DMSO_0


title: LUT014_L1_NF

description: Library name: LUT014L1


title: Maternal Serum 3rd Trimester_CDH_13

description:
Library name: Sample 15
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_13


title: Maternal Serum 3rd Trimester_CDH_12

description:
Library name: Sample 14
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_12


title: 3-3_NCI-H187_Day7_DMSO_0


title: LUT010_L2_NF

description: Library name: LUT010L2


title: LUT015_L1_NF

description: Library name: LUT015L1


title: Maternal Serum 3rd Trimester_CDH_10

description:
Library name: Sample 13
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_10


title: LUT010_L1_NF

description: Library name: LUT010L1


title: LUT017_L1_NF

description: Library name: LUT017L1


title: LUT017_L2_NF

description: Library name: LUT017L2


title: 2-6_SHP-77_Day7_TAS1440_300nM


title: 3-6_NCI-H187_Day7_TAS1440_300nM


title: Maternal Serum 3rd Trimester_CDH_09

description:
Library name: Sample 12
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_09


title: Maternal Serum 3rd Trimester_CDH_14

description:
Library name: Sample 16
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_14


title: 2-5_SHP-77_Day7_TAS1440_300nM


title: LUT014_L2_NF

description: Library name: LUT014L2


title: Agrin b12 rep1

description: Library name: Agrin_b12_rep1


title: Agrin 13-3B5xb12 rep1

description: Library name: Agrin_13-3B5xb12_rep1


title: LUT007_L1_EAD

description: Library name: LUT007L1


title: 2-4_SHP-77_Day7_TAS1440_300nM


title: 2-3_SHP-77_Day7_DMSO_0


title: b12 rep1

description: Library name: b12_rep1


title: LUT005_L2_EAD

description: Library name: LUT005L2


title: 2-2_SHP-77_Day7_DMSO_0


title: Maternal Serum 3rd Trimester_Control_10

description:
Library name: Sample 10
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_10


title: LUT007_L2_EAD

description: Library name: LUT007L2


title: 2-1_SHP-77_Day7_DMSO_0


title: 1-6_DMS79_Day7_TAS1440_300nM


title: Maternal Serum 3rd Trimester_Control_09

description:
Library name: Sample 9
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_09


title: Fucoidan_PBMC_biol_rep2

city: Guangzhou

first: Linpeng

last: Li

state: Guangdong

address: Tianhe District

institute: Jinan University

description:
Library name: Sample_7
Column name in gene_count.txt: Fucoidan_2

data_processing:
Raw reads were demultiplexed and adapter sequences were removed using Cutadapt (v4.0)
Clean reads were aligned to the mouse reference genome using HISAT2 (v2.2.1).
followed by quality trimming of low-quality bases (Phred score < 20 at the 3′ end) using Trimmomatic (v0.39)
Clean reads were aligned to the mouse reference genome (GRCm39/mm39) using HISAT2 (v2.2.1)
Assembly: GRCm39 (mm39)
Supplementary files format and content: Excel file containing gene-level raw read counts for all PBMC RNA-seq samples.

source_name: Peripheral blood mononuclear cells

growth_protocol: Male C57BL/6J mice were housed at 25°C under a 12 h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Peripheral blood mononuclear cells were isolated by density-gradient centrifugation. Total RNA was extracted from mouse PBMCs using the Illumina TruSeq RNA Sample Prep V2 Kit (#RS-122-2001).
Library preparation and RNA sequencing were conducted by Beijing Novogene Corporation. Messenger RNA underwent poly(A) selection from ~1 μg total RNA via oligo(dT)-coupled magnetic beads, followed by fragmentation and first-strand cDNA synthesis. Double-stranded cDNA was generated, ligated with barcoded adapters using the VAHTS Universal V6 RNA-seq Library Prep Kit (#NR604-02, Vazyme), and quantified via Qubit 2.0 Fluorometer (Thermo Fisher). Library fragment size distribution was assessed using an Agilent 2100 Bioanalyzer. Paired-end sequencing (2 × 150 bp) was performed on the Illumina NovaSeq 6000 platform, yielding 40–50 million reads per library.

treatment_protocol: Mice received daily oral gavage of saline for 1 month.

value: Peripheral blood mononuclear cells

value: wt

tag: Sex

value: male

value: Daily oral gavage with fucoidan (200 mg/kg)

value: 1 month

tag: batch


title: Fucoidan_PBMC_biol_rep1

description:
Library name: Sample_6
Column name in gene_count.txt: Fucoidan_1


title: LUT005_L1_EAD

description: Library name: LUT005L1

value: liver

value: EAD


title: Maternal Serum 3rd Trimester_Control_06

description:
Library name: Sample 6
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_06


title: Maternal Serum 3rd Trimester_CDH_08

description:
Library name: Sample 11
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_CDH_08


title: Maternal Serum 3rd Trimester_Control_07

description:
Library name: Sample 7
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_07


title: LUT004_L2_NF

description: Library name: LUT004L2

value: NF


title: Saline_PBMC_biol_rep5

description:
Library name: Sample_5
Column name in gene_count.txt: Saline_5

value: Oral gavage with saline


title: LUT004_L1_NF

description: Library name: LUT004L1


title: 1-5_DMS79_Day7_TAS1440_300nM


title: shREN_DOX_D7_R3

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: Library name: shREN_DOX_D7_R3

data_processing:
Reads in fastq files were filtered (for quality (phred score > 20) and length (>20 bases)) and trimmed (Illumina adapters) using TrimGalore (v0.6.6) in single-end mode with the following flags (--phred33 --fastqc --quality 20 --length 20).
Filtered and trimmed reads were then aligned to the human genome (GRCh38.p13) using the STAR aligner (v2.7.5b) with the following flags (--outSAMattributes Standard --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within). A STAR index was generated prior to alignment using gencode v36 gene annotations (--runMode genomeGenerate).
Coordinate sorted binary alignment files (BAM) were indexed and mapping statistics were generated using samtools (v1.9) (index/flagstat).
Read counts in indexed BAM files were then quantified at the gene level using the featureCounts utility from subread (v2.0.6) with default flags using gencode v36 gene annotations.
Raw counts were normalised by total library size and gene length (Transcripts Per Million) using R (v4.0.2).
Assembly: GRCh38 (GRCh38.p13)
Supplementary files format and content: A tab-delimited text file that includes raw gene count values for each sample.
Supplementary files format and content: A tab-delimited text file that includes TPM normalised gene count values for each sample.

molecule: polyA RNA

source_name: lung cancer

growth_protocol: Non-small cell lung cancer cell lines NCI-H661 and NCI-H1299 were cultured in RPMI-1640 (Gibco), A427 and HuTu80 with EMEM (Gibco), DMS114 with Waymouth (Gibco) and Cov318 with DMEM (Gibco) growth medium, all supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1x penicillin/streptomycin at 37℃, 5% CO2. Cells were routinely passaged to maintain exponential growth, using Trypsin-Low EDTA (LE) Express (Gibco) to detach cells each time. Cells were regularly tested for mycoplasma contamination using the Mycoplasma PCR Detection Kit (abcam, #ab289834). NSCLC cell lines were also STR profiled to ensure authenticity. NCI-H661, NCI-H1299, A427, HuTu80, DMS114 and Cov318 were purchased from ATCC.

extract_protocol:
RNA extraction was performed on cell pellets collected from each cell line, using the Monarch Total RNA miniprep kit (NEB #T2010S) with DNAse I treatment according to the manufacturers instructions. RNA was quantified using the Qubit™ RNA High Sensitivity (HS) Assay Kit (Invitrogen) on a Qubit 3.0 flourometer.
Following RNA quantitation, 1 microgram of RNA was used as input for PolyA+ directional RNA-seq library preparation using the NEBNext Ultra II Directional RNA-seq Kit (#E7765, NEB) with the PolyA mRNA magnetic isolation module (#E7490, NEB) according to the manufacturers instructions. Following adaptor ligation, the final PCR used to incorportate multiplexing oligos for Illumina libraries using the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1-4) was ran for a total of 8 cycles. Individual and pooled libraries were quantified and quality controlled using the dsDNA high sensitivity (HS) Qubit assay (Invitrogen) on the Qubit 3.0 fluorometer (Invitrogen) and D1000 High Sensitivity DNA kit (Agilent) on the TapeStation 2200 (Agilent).The pooled library was sequenced on an Illumina NextSeq 500 or NextSeq 2000 either as single-end 75bp or 100bp configurations respectively.

treatment_protocol: For NCI-H661 CRISPR knockouts, cells were electroporated using Neon™ Transfection System (ThermoFisher) with Cas9 RNP (loaded with a single guide RNA targeted to DPPA2 or DPPA4. Post electroporation, cells were seeded at low density (1 cell/well in a 384-well plate) to isolate monoclonal populations. After 3 weeks in single-cell dilution, populations were screened by PCR and edits identified by Sanger sequencing. Based on sequencing data, clones were selected for further genotype evaluation.Clones with an indel knockout on all alleles were expanded, cryopreserved, and tested for mycoplasma. For NCI-H661 inducible shRNA knockdowns miR30 based shRNAs were expressed using a tetracycline-inducible PiggyBac transposon system (pCLIIPi-iRFP-shRNA-pGK-mVenus), as previously described (Eckersley-Maslin et al. 2020). Established shRNA sequences against either; Renilla luciferase (non-targeting control) (#713), human DPPA2 (#760) or DPPA4 (#1993) were cloned by first annealing complementary oligo’s and ligating them into a digested pMSCV-miR30 backbone3 , followed by PCR, digestion and ligation into the pCLIIPi backbone. Stable cell lines were generated by transfecting NCI-H661 cells with the shRNA vectors along with PiggyBac transposase (pRM1024), waiting for 2 weeks, then sorting mVenus positive cells twice with expansion in between, collecting the top 50% of mVenus positive cells each time as a bulk population for further experiments. The mVenus DPPA4 shRNA construct underwent additional cloning to replace mVenus with tagBFP to allow for selection of cells containing both DPPA2 and DPPA4 inducible shRNA. To generate the double inducible knockdown line, stable shDPPA2 (mVenus+) cells were transfected with the shDPPA4 (tagBFP) vector and selected as above for both mVenus+/tagBFP+ cells. To induce shRNA expression, cells were treated with 2μg/ml doxycycline (Dox) for 7 days. For NCI-H661, A427, HuTu80, DMS114 and Cov318 siRNA knockdowns, 10uL Lipofectamine 2000 (ThermoFisher, #11668027) and 200pmol of non-targeted and DPPA2/4 targeted siRNA twice over 96 hours (first dose at day 0, second dose at day 2, collection on day 4) using SMARTpool siRNA (containing 4 siRNAs per pool) (Horizon/Dharmacon, Non-targeting; #D-001810-10-05, DPPA2; #L-018977-01-0005, DPPA4; #L-020766-01-0005). Lipofectamine 2000 and siRNA complexes were first formed with reduced-serum OptiMEM medium (Gibco) for 20 mins at room temperature, prior to addition to cells grown in complete medium. For the drug treatment experiment, NCI-H661 cells were treated with either a vehicle control (DMSO) or the p300/CBP inhibitor A-485 (10uM) for 24 hours.

value: lung cancer

value: lung large cell carcinoma

value: shREN stable

value: Doxycyline 2ug/mL 7 days


title: Maternal Serum 3rd Trimester_Control_08

description:
Library name: Sample 8
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_08

value: Control


title: Maternal Serum 3rd Trimester_Control_05

description:
Library name: Sample 5
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_05


title: shREN_DOX_D7_R2

description: Library name: shREN_DOX_D7_R2


title: Maternal Serum 3rd Trimester_Control_04

description:
Library name: Sample 4
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_04


title: 1-1_DMS79_Day7_DMSO_0

value: small-cell lung cancer

value: DMSO


title: 1-4_DMS79_Day7_TAS1440_300nM

value: WT


title: Fucoidan_PBMC_biol_rep3

description:
Library name: Sample_8
Column name in gene_count.txt: Fucoidan_3

value: Peripheral blood mononuclear cells


title: Saline_PBMC_biol_rep4

description:
Library name: Sample_4
Column name in gene_count.txt: Saline_4

value: wt


title: 1-3_DMS79_Day7_DMSO_0


title: shREN_CTRL_D7_R3

description: Library name: shREN_CTRL_D7_R3

value: H20 7 days


title: 13-3B5 rep1

description: Library name: 13-3B5_rep1

value: myotube cells


title: Day7-3_H1417_Day7_TAS1440_300nM_rep3


title: Saline_PBMC_biol_rep2

description:
Library name: Sample_2
Column name in gene_count.txt: Saline_2

value: male

value: 1 month


title: Maternal Serum 3rd Trimester_Control_03

description:
Library name: Sample 3
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_03

value: Serum


title: Saline_PBMC_biol_rep1

description:
Library name: Sample_1
Column name in gene_count.txt: Saline_1


title: Saline_PBMC_biol_rep3

description:
Library name: Sample_3
Column name in gene_count.txt: Saline_3


title: Maternal Serum 3rd Trimester_Control_02

description:
Library name: Sample 2
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_02


title: shREN_CTRL_D7_R2

description: Library name: shREN_CTRL_D7_R2


title: shREN_CTRL_D7_R1

description: Library name: shREN_CTRL_D7_R1


title: HCT116-CSE-3

city: Chongqing

first: Shasha

last: Wu

address: No.1 Youyi Road, Yuzhong District

department: Gastroenterology

institute: The First Affiliated Hospital of Chongqing Medical University

description: Library name: Sample 6

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Assembly: GRCh38
Supplementary files format and content: xls files include TPM values for each sample

extract_protocol:
Total RNA was extracted using the Total RNA Extractor（Trizol）kit (B511311, Sangon, China) according to the manufacturer’s protocol, and treated with RNase-free DNase I to remove genomic DNA contamination. RNA integrity was evaluated with a 1.0% agarose gel. Thereafter, the quality and quantity of RNA were assessed using a NanoPhotometer ® spectrophotometer (IMPLEN, CA, USA) and a Qubit® 2.0 Flurometer (Invitrogen). The high quality RNA samples were subsequently submitted to the Sangon Biotech (Shanghai) Co., Ltd. for library preparation and sequencing.
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: Colorectal cancer

value: CSE treated


title: QBM-44

city: Tampa

first: Xiaoxian

last: Liu

state: FL

address: 13131 USF Magnolia Drive

institute: Moffitt Cancer Center

description: Library name: GMB-F44

data_processing:
The Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v7.1.0 software
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: eye

extract_protocol:
Uveal melanomas were harvested from GnaqCA; Bap1CKO; MycCKI mice when ocular enlargement was visibly apparent. Mice were euthanized, and eyes were enucleated using fine scissors and forceps under a dissection microscope. After removal, each eye was placed in ice-cold sterile PBS. Under a stereomicroscope, extraocular tissues (conjunctiva, optic nerve), lens, and vitreous were removed. Tumor tissue arising from the choroid and adjacent structures was dissected out with fine-tipped forceps and immediately transferred into the enzyme solution. Enzymatic dissociation was performed using the Tumor Dissociation Kit (Miltenyi Biotec, RRID:SCR_020285) according to the manufacturer’s instructions. Tissues were incubated at 37°C for 30–45 minutes with intermittent gentle agitation. The resulting cell suspension was washed with PBS containing 2% FBS and centrifuged at 300 x g for 5 minutes. Cells were resuspended in sterile PBS, Cell viability and counts were obtained by AO/PI dual fluorescent staining and visualization on the Nexcelom Cellometer K2 (Nexcelom Bioscience LLC, RRID:SCR_018656). Cell viability >80% was used for inclusion in sequencing.
10x genomics Gel Bead-in-Emulsion (GEM) library construction protocol

value: eye


title: Day7-1_H1417_Day7_TAS1440_300nM_rep1


title: Day7-2_H1417_Day7_TAS1440_300nM_rep2


title: shDPPA4_DOX_D7_R2

description: Library name: shDPPA4_DOX_D7_R2

value: lung cancer

value: lung large cell carcinoma

value: shDPPA4 stable


title: 1-2_DMS79_Day7_DMSO_0


title: shDPPA4_DOX_D7_R3

description: Library name: shDPPA4_DOX_D7_R3

value: Doxycyline 2ug/mL 7 days


title: Maternal Serum 3rd Trimester_Control_01

description:
Library name: Sample 1
column name in Table8.7_CDH_MS3vsCTL_MS3.txt:  Maternal Serum 3rd Trimester_Control_01

value: Control


title: shREN_DOX_D7_R1

description: Library name: shREN_DOX_D7_R1

value: shREN stable


title: HCT116-CSE-2

description: Library name: Sample 5


title: QBM-43

description: Library name: GMB-F43


title: Day5-2_H1417_Day5_TAS1440_300nM_rep2

value: small-cell lung cancer

value: WT


title: shDPPA4_CTRL_D7_R3

description: Library name: shDPPA4_CTRL_D7_R3


title: HCT116-3

description: Library name: Sample 3


title: HCT116-CSE-1

description: Library name: Sample 4


title: QBM-21

description: Library name: GMB-L21


title: QBM-22

description: Library name: GMB-L22


title: QBM-42

description: Library name: GMB-M42


title: Day3-3_H1417_Day3_TAS1440_300nM_rep3


title: RKO-shCKAP2L-3

description: Library name: Sample 12

source_name: RKO

value: RKO


title: Day5-3_H1417_Day5_TAS1440_300nM_rep3


title: shDPPA4_CTRL_D7_R1

description: Library name: shDPPA4_CTRL_D7_R1

value: H20 7 days


title: Day5-1_H1417_Day5_TAS1440_300nM_rep1


title: QBM-23

description: Library name: GMB-L23


title: HCT116-1

description: Library name: Sample 1


title: YAP5SA, Cardiomyocytes, rep 2

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

description: Library name: Y2

data_processing:
Reads were mapped to the mouse genome (mm10, Ensembl GRCm38.94) using STAR. Lowly expressed genes were removed within each condition using median log2-transformed counts per gene per million mapped reads of 1, and a union set of genes was generated from each condition.
Differential expression analysis was performed using edgeR using a general linear model framework with an additional covariate to mitigrate an apparent batch effect.
Assembly: GRCm38.94
Supplementary files format and content: ReadSummary.txt: tab-delimited file containing genes (ensembl ID) and then gene counts from STAR for each of the libraries
Supplementary files format and content: ResultsTable.xlsx: 3-way Comparison = GFP vs. YAP5SA vs. YAP6SA. YAP6SA vs. GFP alone

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Two hearts from each virus were collected at P9 and cardiomyocyte nuclei were enriched using anti-PCM1 pulldown. RNA was extracted using the RNeasy Plus Micro kit following manufacturer specifications.
Library construction was performed by Novogene Inc. Poly-A enriched, non-directional libraries

treatment_protocol: Wildtype ICR mice were subcutaneously injected with 1*10^11 viral genomes of AAV9 virus containing cTnT-GFP, cTnT-YAP5SA, or cTnT-YAP6SA expression constructs at P6.

value: Heart

value: Cardiomyocyte

value: Wildtype


title: HCT116-2

description: Library name: Sample 2


title: shDPPA4_DOX_D7_R1

description: Library name: shDPPA4_DOX_D7_R1


title: Day3-1_H1417_Day3_TAS1440_300nM_rep1


title: shDPPA2_DOX_D7_R2

description: Library name: shDPPA2_DOX_D7_R2

value: shDPPA2 stable


title: Day2-3_H1417_Day2_TAS1440_300nM_rep3


title: RKO-shCKAP2L-1

description: Library name: Sample 10

value: Colorectal cancer


title: YAP5SA, Cardiomyocytes, rep 1

description: Library name: Y1


title: Day3-2_H1417_Day3_TAS1440_300nM_rep2


title: RKO-shCKAP2L-2

description: Library name: Sample 11


title: Day2-2_H1417_Day2_TAS1440_300nM_rep2


title: shDPPA2_DOX_D7_R1

description: Library name: shDPPA2_DOX_D7_R1


title: Day1-3_H1417_Day1_TAS1440_300nM_rep3


title: RKO-NC-3

description: Library name: Sample 9

value: negative control


title: RKO-NC-1

description: Library name: Sample 7


title: shDPPA2_CTRL_D7_R3

description: Library name: shDPPA2_CTRL_D7_R3


title: GFP Cardiomyocytes, rep 2

description: Library name: G2


title: shDPPA4_CTRL_D7_R2

description: Library name: shDPPA4_CTRL_D7_R2


title: HCT116-CKAP2L-2

description: Library name: Sample 5

value: CKAP2L overexpression


title: Day2-1_H1417_Day2_TAS1440_300nM_rep1


title: shDPPA2_CTRL_D7_R1

description: Library name: shDPPA2_CTRL_D7_R1

value: lung cancer


title: YAP6SA, Cardiomyocytes, rep 1

description: Library name: P1


title: shDPPA2_DOX_D7_R3

description: Library name: shDPPA2_DOX_D7_R3

value: lung large cell carcinoma


title: Day1-1_H1417_Day1_TAS1440_300nM_rep1


title: shDPPA2_CTRL_D7_R2

description: Library name: shDPPA2_CTRL_D7_R2


title: YAP6SA, Cardiomyocytes, rep 2

description: Library name: P2


title: HCT116-CKAP2L-3

description: Library name: Sample 6


title: Day1-2_H1417_Day1_TAS1440_300nM_rep2


title: TA, Hypothyroid diet, day 14

city: Los Angeles

first: Paola

last: Aguiari

address: 4650 W Sunset Blvd

institute: Children's Hospital, Los Angeles

description: Library name: HYPO_14

data_processing:
scRNA-seq data were analyzed with Partek™ Flow™ software, v11.0
Sequencing files were aligned to the Mus musculus reference genome mm39 using Cell Ranger - Gene Expression aligner.
Transcript abundance was estimated using the Partek™ Flow™ algorithm based on GENCODE release M30 transcript model with default settings.
To filter out low-quality cells, we applied thresholds based on the total UMI count (<100 or >8,000), detected gene count (<500 or >50,000), and mitochondrial UMI proportion (1-15%).
Read counts per gene in all samples were normalized by log2 counts per million and adding 1 for values of zero.
Assembly: mm39
Supplementary files format and content: tab-limited text files includes normalized counts for each sample

source_name: male Tibialis Anterior Muscle

growth_protocol: Hypothyroidism was induced by feeding 3-5 month-old mice a iodine-deficient diet containing propylthiouracil (PTU; 0.15% w/w) (TD.08259, Envigo Teklad). Control mice received a matched diet (TD.120461, Envigo Teklad).

extract_protocol:
Approximately 5,000 cells were captured on a 10x Chromium device using a 10X V3 Single Cell 3′ Solution kit.
RNA libraries for scRNA sequencing were prepared using Chromium Single Cell 3’ Regent kit V3 Chemistry from 10xGenomics following manufacturer's instructions.

treatment_protocol: Muscle injury was induced through injection of cardiotoxin (CTX, 50 μg/ml) in the right Tibialis Anterior muscle.

value: male Tibialis Anterior Muscle

value: Hypothyroid diet (low iodine + 0.15% PTU)

value: day 14


title: GFP Cardiomyocytes, rep 1

description: Library name: G1


title: TA, Hypothyroid diet, day 5

description: Library name: HYP_05d

value: day 5


title: TA, Control diet, day 14

description: Library name: CTRL_14d

value: Control diet


title: RKO-NC-2

description: Library name: Sample 8


title: HCT116-Vector-3

description: Library name: Sample 3

value: control


title: shDKD_CTRL_D7_R3

description: Library name: shDKD_CTRL_D7_R3

value: shDKD stable


title: QBM-41

description: Library name: GMB-M41

value: eye


title: Day0-2_H1417_Day0_rep2

value: small-cell lung cancer

value: WT


title: shDKD_DOX_D7_R2

description: Library name: shDKD_DOX_D7_R2

value: Doxycyline 2ug/mL 7 days


title: shDKD_DOX_D7_R3

description: Library name: shDKD_DOX_D7_R3


title: Day0-3_H1417_Day0_rep3


title: HCT116-CKAP2L-1

description: Library name: Sample 4


title: shDKD_CTRL_D7_R1

description: Library name: shDKD_CTRL_D7_R1

value: H20 7 days


title: TA, Hypothyroid diet, day 0

description: Library name: HYPO_NI

value: day 0


title: shDKD_DOX_D7_R1

description: Library name: shDKD_DOX_D7_R1


title: HCT116-Vector-1

description: Library name: Sample 1

value: Colorectal cancer


title: RNA-Seq of Homo sapiens: NHDF, 0.251 μM retinoic acid,rep3

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

description:
Library name: AA3
processed data in column D, the ID name is AA3

data_processing:
Assess raw reads using FastQC
Gene and transcript expression read counts were calculated using featureCounts and StringTie. Subsequently, FPKM values for genes and transcripts were computed. During this process, we applied basic filtering criteria:Genes or transcripts with a length shorter than 100 bp were removed;Genes or transcripts with an FPKM value less than 0.0001 were considered as not expressed (FPKM = 0).Genes that were not expressed (FPKM = 0) in all samples were excluded from further analysis.
Assembly: GRCh38
Supplementary files format and content: rawcount file contains raw read counts of gene expression for each sample
Supplementary files format and content: fpkm file provides normalized gene expression values using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method

source_name: skin

growth_protocol: Normal human dermal fibroblasts (NHDF; BioCell Biotechnology, CHN) and the human embryonic kidney cell line (HEK293T; Center for Type Culture Collection, SCSP-502, CHN) were cultured in Dulbecco’s Modified Eagle’s Medium with high glucose (DMEM/High Glucose; CGM101.05, Cellmax, CHN), supplemented with 10% fetal bovine serum (FBS; 04-001-1ACS, BI, IL) and 100 U/mL penicillin with 100 μg/mL streptomycin (P1400, Solarbio, CHN).

extract_protocol:
Total RNA was extracted using TRIzol reagent (CW0580S, Cowin, CHN) following the manufacturer’s protocol, and the RNA was subsequently used for Illumina sequencing.
The mRNA sequencing library preparation process is initiated by selecting qualified Total RNA as the starting material. The workflow sequentially includes: mRNA purification and fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair/dA-tailing, adapter ligation, and PCR amplification. The PCR products are then accurately quantified using the Qubit DNA HS Assay Kit.

treatment_protocol: NHDF cells were treated with either DMSO (1% v/v) as the vehicle control or 0.1 μg/mL 9-cis HPR OR 0.251 μM retinoic acid for 24 hours.

value: skin

value: Normal human dermal fibroblasts (NHDF)

value: fibroblast

value: 0.251 μM retinoic acid


title: Day7-3_H146_Day7_TAS1440_300nM_rep3


title: Day7-1_H146_Day7_TAS1440_300nM_rep1


title: eWAT, HFD, CD9 myeloid-knockout, rep 4

city: Philadelphia

first: David

last: Hill

state: PA

address: Abramson Research Building, 1208B, 3615 Civic Center Blvd.

department: Division of Allergy and Immunology

institute: Children's Hospital of Philadelphia

description: Library name: Sample 11

data_processing:
Bulk RNAseq reads were aligned to the GRCmm39/mm10 genome using the nf-core RNAseq pipeline version 3.14.0. In brief, FastQC was used to assess the quality of reads and Trim Galore! was used for adapter and quality trimming. Alignment was performed with STAR version 2.7.10a followed by quantification with RSEM version 1.3.1. Duplicates were removed using Picard MarkDuplicates. Low expression genes were filtered with the R package edgeR, followed by differential expression analysis
Assembly: GRCmm39/mm10 genome
Supplementary files format and content: CSV file containing log normalized counts per million (cpm) for each sample

source_name: whole epididymal adipose tissue

growth_protocol: Experiments were performed using sex and age-matched littermate controls. Mice were provided with ad libitum access to water and diet. Mice were fed a high fat diet containing 60 kcal% fat (Research Diets D12492, New Brunswick, NJ) from 6 to 18 weeks of age.

extract_protocol:
[ex vivo adipose tissue macrophages] For bulk RNA-seq of sort-purified cell populations, RNA was isolated using standard Trizol protocol.  [whole eWAT] Total RNA was isolated from snap-frozen tissue samples. RNA extraction was performed using the Maxwell RSC simply RNA Tissue Kit (Promega, AD1340). Briefly, tissue was homogenized in a Thioglycerol Homogenization Solution using the Maxwell RSC Instrument (Promega).
[ex vivo adipose tissue macrophages] For bulk RNA-seq of sort-purified cell populations, libraries were prepared using the SMARTer Stranded RNA-seq kit (Clontech) and TruSeq RNA library prep kit (Illumina).   [whole eWAT] RNA libraries were prepared using the standard Illumina protocol.

treatment_protocol: [ex vivo adipose tissue macrophages] Epididymal white adipose tissue (eWAT) depots were isolated from mice. Adipose samples were placed in 1 mL of DMEM and individual depots were finely minced under sterile conditions with a razorblade prior to digestion in 5 mL DMEM with 6 mg/1 mL collagenase D (Roche) or 3 mg/1 mL collagenase IV (Gibco) at 37° C in a shaking incubator for 30 min. Cells were pelleted at 700g and adipocyte fraction removed. After resuspension of the stromal fraction in 5mL of MACS buffer (1x PBS, 2% calf serum, 25 mM HEPES, 2 mM EDTA) for cell sorting, cells were purified through a 100 μm filter (Falcon), pelleted at 700g, and re-suspended in 1 mL of RBC lysis buffer (0.15 M NH4Cl, .01 M NaHCO3, 0.0013 M EDTA) for 5 minutes at room temperature. Cells were washed again in MACS buffer prior to staining for sorting.  [whole eWAT] whole eWAT was isolated amd snap-frozen.

value: whole epididymal adipose tissue

value: CD9 fl/fl LysMCre-/+ on a C57BL/6J backgroun

value: High fat diet (12 weeks)


title: TA, Control diet, day 0

description: Library name: CTRL_NI

value: male Tibialis Anterior Muscle

value: Control diet


title: NCIH661_WT_c52_3

description: Library name: NCIH661_WT_c52_3

value: lung cancer

value: lung large cell carcinoma

value: Wild type clone c52


title: shDKD_CTRL_D7_R2

description: Library name: shDKD_CTRL_D7_R2

value: shDKD stable


title: NCIH661_WT_c52_2

description: Library name: NCIH661_WT_c52_2


title: eWAT, HFD, CD9 myeloid-knockout, rep 3

description: Library name: Sample 10


title: RNA-Seq of Homo sapiens: NHDF, 0.1 μg/mL 9-cis HPR,rep3

description:
Library name: B3
processed data in column G, the ID name is B3

value: 0.1 μg/mL 9-cis HPR


title: RNA-Seq of Homo sapiens: NHDF, 0.251 μM retinoic acid,rep2

description:
Library name: AA2
processed data in column C, the ID name is AA2


title: Day5-3_H146_Day5_TAS1440_300nM_rep3

value: small-cell lung cancer

value: WT


title: Day0-1_H1417_Day0_rep1


title: Day5-2_H146_Day5_TAS1440_300nM_rep2


title: eWAT, HFD, CD9 myeloid-knockout, rep 1

description: Library name: Sample 8


title: Day5-1_H146_Day5_TAS1440_300nM_rep1


title: NCIH661_WT_c51_2

description: Library name: NCIH661_WT_c51_2

value: Wild type clone c51


title: RNA-Seq of Homo sapiens: NHDF, 0.251 μM retinoic acid,rep1

description:
Library name: AA1
processed data in column B, the ID name is AA1

value: skin


title: TA, Control diet, day 5

description: Library name: CTRL_05d

value: day 5


title: HCT116-Vector-2

description: Library name: Sample 2

value: Colorectal cancer

value: control


title: Day3-3_H146_Day3_TAS1440_300nM_rep3


title: Day7-2_H146_Day7_TAS1440_300nM_rep2


title: Day3-2_H146_Day3_TAS1440_300nM_rep2


title: NCIH661_WT_c51_1

description: Library name: NCIH661_WT_c51_1


title: RNA-Seq of Homo sapiens: NHDF, Control,rep3

description:
Library name: C3
processed data in column J, the ID name is C3

value: Normal human dermal fibroblasts (NHDF)

value: fibroblast

value: Control


title: eWAT, HFD, Control,rep 2

description: Library name: Sample 5

value: whole epididymal adipose tissue

value: CD9 fl/fl LysMCre-/- on a C57BL/6J backgroun

value: High fat diet (12 weeks)


title: eWAT, HFD, CD9 myeloid-knockout, rep 2

description: Library name: Sample 9

value: CD9 fl/fl LysMCre-/+ on a C57BL/6J backgroun


title: RNA-Seq of Homo sapiens: NHDF, 0.1 μg/mL 9-cis HPR,rep1

description:
Library name: B1
processed data in column E, the ID name is B1


title: RNA-Seq of Homo sapiens: NHDF, Control,rep1

description:
Library name: C1
processed data in column H, the ID name is C1


title: eWAT, HFD, Control,rep 4

description: Library name: Sample 7


title: RNA-Seq of Homo sapiens: NHDF, 0.1 μg/mL 9-cis HPR,rep2

description:
Library name: B2
processed data in column F, the ID name is B2


title: NCIH661_PAR_3

description: Library name: NCIH661_PAR_3

value: lung cancer

value: lung large cell carcinoma

value: Parental


title: NCIH661_WT_c52_1

description: Library name: NCIH661_WT_c52_1

value: Wild type clone c52


title: Infant Blood_CDH_21

description:
Library name: Sample 74
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_21

value: Serum

value: CDH


title: eWAT, HFD, Control,rep 1

description: Library name: Sample 4


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.1% Retinoic acid, rep2

description: Library name: Positive_control_group2_2

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version2.20).
Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger, version 3.1.0) .
Assembly: mm10
Supplementary files format and content: matrix.mtx file, store the gene expression matrix in sparse format, representing counts of UMIs (unique molecular identifiers) for each gene (row) in each cell barcode (column).
Supplementary files format and content: barcodes.tsv file, list of cell barcodes (columns of matrix)
Supplementary files format and content: features.tsv file, feature annotations (rows of matrix: gene ID, name, type).

growth_protocol: Ten to twelve-week-old female SKH-1 mice (2311A01051, Charles River Laboratories, USA), weighing between 22 and 25 g, were bred and housed in a controlled environment at the Experimental Animal Center of Zhejiang University. They were maintained on a 12-hour light-dark cycle, with temperatures ranging from 23°C to 27°C and humidity between 40% and 70%, with free access to food and water.

extract_protocol:
The dorsal skin from a consistent area of the female SKH-1 mice was rapidly removed, placed in a container with cold PBS, and cut into small fragments. These fragments were washed three times before being immersed in a digestive mixture containing collagenase I, collagenase II, and Dispase® (all from Sigma, USA). After digestion, the mixture of liquid and tissue was transferred to a centrifuge tube, rinsed with DMEM, and centrifuged at 4°C at 350 g for 7 minutes. Next, 1-2 mL of trypsin was added, and the mixture was incubated at room temperature for 3-5 minutes before resuspension. After digestion, the cell suspension was strained through a 70 µm sieve (Miltenyi, GER). The resulting filtrate was centrifuged at 350 g for 7 minutes at 4°C, and the supernatant was discarded. The pellet was treated with a lysis reagent, resuspended, and chilled on ice for 2-3 minutes. To halt the lysis, 5 mL of DMEM containing 10% FBS was added, followed by centrifugation at 350 g for 7 minutes at 4°C. The pellet was then washed and resuspended according to its volume. Single cells were isolated using the 10× Genomics Chromium Single Cell 3′ Solution (10× Genomics, USA).
Single-cell suspensions were loaded to 10x Chromium to capture single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by LC-Bio Technology co.ltd., (HangZhou,China) at a minimum depth of 20,000 reads per cell.

value: skin

value: SKH-1 mice

value: UVR and treated with 0.1% Retinoic acid


title: Day2-1_H146_Day2_TAS1440_300nM_rep1

data_processing:
Deep sequencing was performed on an Illumina NovaSeq 6000 (paired-end reads) according to the manufacturer’s protocols. Sequenced reads from the RNA-seq experiments were aligned using the Bowtie 2 and TopHat (version 1.3.2), and Cufflinks (version 2.0.2) was used for transcriptome assembly. Gene expression levels were expressed as fragments per kilobase of exons per million mapped sequence reads. DEGs were identified using the R software package (version 4.2.0). Heatmaps and dendrograms were generated using R, GraphPad Prism 9.0, or https://www.chiplot.online/. DEG-related and terms of the KEGG were analyzed by gene set enrichment analysis software (GSEA, version 4.2.3).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
SCLC cell lines were treated, for the indicated durations, with different LSD1 inhibitors. Total cellular RNA was extracted using a modified chloroform/phenol procedure (TRIzol™, Invitrogen Thermo Fisher Scientific). RNA integrity and concentration were measured using a 4200 TapeStation system for high-throughput automated electrophoresis (Agilent, Santa Clara, CA, USA)
RNA-Seq libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) with the SPRIselect reagent (Cat. No. B23318, Beckman Coulter, Indianapolis, IN, USA) following the manufacturers’ protocols.

value: small-cell lung cancer

value: WT


title: NCIH661_DPPA4_KO_c79_2

description: Library name: NCIH661_DPPA4_KO_c79_2

value: DPPA4 KO clone c79


title: Spatial Transcriptomics: skin, UVR and treated with 0.1% Retinol (upper), UVR and treated with 0.03% 9-cis HPR (lower)

description: Library name: Administration

data_processing:
Each sequenced spatial transcriptomics library was processed and aligned to  (mm10 mous) reference genome using Space Ranger software  (version 2.0.0) from 10x Genomics, with UMI counts summarized for each spot.
After imported into R, the filtered UMI count matrix was analyzed using the R package Seurat (version 4.1.0).
Assembly: mm 10
Supplementary files format and content: matrix.mtx file, Sparse gene expression matrix (genes × spots)
Supplementary files format and content: barcodes.tsv file, List of spatial barcodes (spots)
Supplementary files format and content: features.tsv file, Gene annotations (ID, symbol, type)
Supplementary files format and content: scalefactors_json.json file, Image-to-coordinate scale metadata
Supplementary files format and content: spatial_tissue_hires_image.png file, High-res histological tissue image
Supplementary files format and content: tissue_positions.csv file, Spatial coordinates and tissue/spot mapping
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh frozen OCT-embedded skin biopsies were cryosectioned and placed onto Visium slides (10× Genomics). The slides were placed in a cassette, and 100 μL of 0.1 N HCl (H1758, Sigma-Aldrich, USA) was added to each well for a 15 minutes incubation at 42℃. Following incubation, the HCl was removed from each well, and decrosslinking buffer was added, followed by an hour incubation at 95℃. The pre-hybridization mix was added to each well and incubated for 15 minutes at room temperature. After incubation, the pre-hybridization mix was removed, and 100 μL of hybridization mix was added. The slide was incubated with the hybridizaion mix at 50℃ overnight.
Library preparation, including probe ligation, probe release and extension, probe elution, and Formalin-Fixed Paraffin-Embedded (FFPE) library construction, followed the “Visium Spatial Gene Expression for FFPE reagent kit” user guide (10× Genomics). Sequencing was performed on a Novaseq6000 (Illumina), with read lengths of 28 base pairs for read 1 and 91 base pairs for read 2.

value: UVR and treated with 0.1% Retinol skin of SKH-1 mice (upper), UVR and treated with 0.03% 9-cis HPR skin of SKH-1 mice (lower)


title: NCIH661_PAR_1

description: Library name: NCIH661_PAR_1


title: NCIH661_WT_c51_3

description: Library name: NCIH661_WT_c51_3

value: Wild type clone c51


title: NCIH661_DPPA4_KO_c79_3

description: Library name: NCIH661_DPPA4_KO_c79_3


title: Infant Blood_CDH_19

description:
Library name: Sample 73
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_19


title: Day2-2_H146_Day2_TAS1440_300nM_rep2


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.1% Retinoic acid, rep1

description: Library name: Positive_control_group2_1


title: Infant Blood_CDH_12

description:
Library name: Sample 70
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_12


title: Day1-2_H146_Day1_TAS1440_300nM_rep2


title: Infant Blood_CDH_14

description:
Library name: Sample 72
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_14


title: Day3-1_H146_Day3_TAS1440_300nM_rep1


title: Day1-3_H146_Day1_TAS1440_300nM_rep3


title: Day2-3_H146_Day2_TAS1440_300nM_rep3


title: RNA-Seq of Homo sapiens: NHDF, Control,rep2

description:
Library name: C2
processed data in column I, the ID name is C2

value: Normal human dermal fibroblasts (NHDF)

value: fibroblast

value: Control


title: Infant Blood_CDH_13

description:
Library name: Sample 71
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_13


title: NCIH661_PAR_2

description: Library name: NCIH661_PAR_2

value: lung cancer


title: NCIH661_DPPA4_KO_c79_1

description: Library name: NCIH661_DPPA4_KO_c79_1

value: lung large cell carcinoma


title: Day0-3_H146_Day0_rep3


title: NCIH661_DPPA4_KO_c78_1

description: Library name: NCIH661_DPPA4_KO_c78_1

value: DPPA4 KO clone c78


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.1% 9-cis HPR, rep2

description: Library name: Middle_dose_2

value: UVR and treated with 0.1% 9-cis HPR


title: NCIH661_DPPA4_KO_c78_3

description: Library name: NCIH661_DPPA4_KO_c78_3


title: Day1-1_H146_Day1_TAS1440_300nM_rep1


title: eWAT, HFD, Control,rep 3

description: Library name: Sample 6

value: whole epididymal adipose tissue

value: CD9 fl/fl LysMCre-/- on a C57BL/6J backgroun

value: High fat diet (12 weeks)


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.1% Retinol, rep2

description: Library name: Positive_control_group1_2

value: skin

value: SKH-1 mice

value: UVR and treated with 0.1% Retinol


title: Day0-1_H146_Day0_rep1

value: small-cell lung cancer

value: WT


title: NCIH661_DPPA2_KO_c42_3

description: Library name: NCIH661_DPPA2_KO_c42_3

value: DPPA2 KO clone c42


title: Infant Blood_CDH_08

description:
Library name: Sample 67
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_08

value: Serum

value: CDH


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.1% Retinol, rep1

description: Library name: Positive_control_group1_1


title: Day0-2_H146_Day0_rep2


title: NCIH661_DPPA2_KO_c42_1

description: Library name: NCIH661_DPPA2_KO_c42_1


title: Infant Blood_CDH_10

description:
Library name: Sample 69
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_10


title: Infant Blood_CDH_04

description:
Library name: Sample 65
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_04


title: H1417_GSK2879552_3000nM_Day7_rep3


title: Infant Blood_CDH_07

description:
Library name: Sample 66
column name in Table8.4_CDH_IBvsCTL_IB.txt:  Infant Blood_CDH_07


title: NCIH661_DPPA4_KO_c78_2

description: Library name: NCIH661_DPPA4_KO_c78_2


title: scRNA-seq of Mus musculus: skin, UVR

description: Library name: model

value: UVR


title: scRNA-seq of Mus musculus: skin, UVR and treated with 0.1% 9-cis HPR, rep1

description: Library name: Middle_dose_1


title: H1417_ORY-1001_100nM_Day7_rep3


title: Spatial Transcriptomics: skin, UVR (upper), Control (lower)

description: Library name: Model-Blank

value: UVR skin of SKH-1 mice (upper), and normal skin of SKH-1 mice (lower)


title: SD6010-4

city: NEW HAVEN

first: Museog

last: Choe

state: CT

address: 10 Amistad Street, Ste 214J

department: Genetics

institute: Yale University

description:
Library name: RNA-seq sample12
truseq stranded mrna library

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in)
Assembly: GRCh38
Supplementary files format and content: For RNA-seq, csv file including TPM. For scRNA-seq, matrix, features and barcode files.

source_name: brain organoid

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 10,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P standard  v3.1 (Next GEM)  protocol (10X Genomics)

value: brain organoid

tag: disease state

value: Angelman syndrome


title: NCIH661_DPPA2_KO_c42_2

description: Library name: NCIH661_DPPA2_KO_c42_2

value: lung cancer

value: lung large cell carcinoma


title: SD6010-3

description:
Library name: RNA-seq sample11
truseq stranded mrna library


title: scRNA-seq of Mus musculus: skin, control

description: Library name: blank

value: normal


title: scRNA-seq of mice pit: POMC-WT

city: Montreal

first: Kevin

last: Sochodolsky

state: QC

address: 110 Av des Pins O

department: Molecular Genetic

country: Canada

institute: Institut de recherche clinique de Montreal

description: Library name: POMC-WT

data_processing:
Reads were aligned on the mm10 mouse reference genome with 10x Genomics Cell Ranger 5.0.1 using the default parameters. Data analyses, filtering, normalization and scaling, dimensionality reduction, standard unsupervised clustering was performed using the Seurat R package v3.1 (32). Low quality cells were excluded using these parameters: 1500 > nFeature counts > 4000; nCount RNA > 10,000; 5 > mitochondrial DNA > 0.5. The samples were then combined using the merge function in Seurat. Transcript counts were normalized for total read depth. Cell clusters were identified by principal component analysis and visualized by uniform manifold approximation and projection (UMAP) embedding and unsupervised graph-based clustering with the Louvain algorithm with a resolution of 0.8. UMAP identified cell clusters were annotated based on differential expression of key pituitary marker genes.
Assembly: mm10
Supplementary files format and content: normalised.merged.rds ; Contains R object of both normalised samples merged with Feature count per barcode with clustering.

source_name: Pituitary

extract_protocol:
Dissociated pituitary cells were processed using Chromium Single Cell 3′ v3 Reagent (10x Genomics, Pleasanton, CA) following the manufacturer’s instructions.
8000 cells from two 380 days old animals of each genotype. Pituitary cells were partitioned into gel beads in emulsion for cell lysis and barcoded with oligo-dT priming and reverse transcribed. cDNA libraries were amplified, fragmented and size selected. Samples were controlled at multiple steps during the procedure by running on BioAnalyzer. Resulting libraries were sequenced on Illumina HiSeq 4000 S1 PE28x91 generating ≈3x10^6 reads/sample.

value: Pituitary


title: SingleCell Vista KO gene expression

city: Cleveland

first: Lily

last: Wang

address: 9500 Euclid Ave

institute: Cleveland Clinic

description:
Library name: KO_gex
5' mRNA library read 1 contains cell barcode and UMI; read 2 contains transcript
poly A RNA

data_processing:
Processed files are direct outputs of alignment via uase of CellRanger software.
Seurat object is downstream processed using Seurat V4 includiing those cells used in the study.
Assembly: mouse_mm10-2020-A, vdj_GRCm38_alts_ensembl-5.0.0
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: VDJ (TCR seq)

source_name: tumor tissue

extract_protocol:
B16 melanoma tumors were pooled and digested to obtain single cell suspensions. Tumor infiltrating CD8  and CD4 T cells were stained with anti-CD8 antibody and purified by FACS sorting. 10e4 sorted viable T cells  were loaded into a Chromium Controller (10X Genomics).
Viable sorted T cells were washed three times before being processed using 10X genomics Feature barcoding protocol and workflow with v3.1 3’ technology. The single-cell RNAseq libraries are prepared by the Genomics Core facility at Lerner Research Institute. The single-cell RNAseq libraries are prepared according to the manufacturer’s Chromium Single Cell 3ʹ v3.1 with Feature Barcode technology for Cell Surface Protein (CSP) protocol. Briefly, cDNA for the 3’ gene expression library was initially synthesized from poly-adenylated mRNA, and DNA for the CSP library was synthesized from the cell surface protein feature Barcode. A minimum of 1 nanogram of cDNA was used to begin fragmentation, followed by end-repair, adapter ligation, and sample indexing. Each sequencing library including the CSP library was tagged with a dual index (10-nucleotide long each) sample barcode that identifies from which sample a sequence was derived. In addition, a 12-base unique molecular indexes (UMIs) were introduced to reduce duplicate reads. Constructed libraries are pooled and quantified using a Quantabio Q cycler. NovaSeq 6000 RapidRun flow cells are used to sequence a minimum of 20,000 read pairs per cell for the Gene expression library and a minimum of 5,000 read pairs per cell for the Cell surface protein library using specifications recommended by the manufacturer (10X Genomics, document # CG000317).
Separate feature barcoding libraries sequenced targeting 5,000 reads per cell at 10,000 cells per sample and were mapped to cells using cellranger software. Antibody counts were compiled with gene expression data in Seurat V4.0 software and normalized via CLR normalization methods for plotting.

value: tumor tissue

value: tumor infiltrating T cells

tag: library type

value: RNA


title: NCIH661_DPPA2_KO_c40_2

description: Library name: NCIH661_DPPA2_KO_c40_2

value: DPPA2 KO clone c40


title: H1417_GSK2879552_3000nM_Day7_rep2

city: chiba

first: YINGBO

last: GONG

institute: CHIBA University

value: small-cell lung cancer