title: IUGR Lamb 4

city: Tucson

first: Sean

middle: W

last: Limesand

state: AZ

address: 4101 N Campbell Ave

department: Animal & Comparative Biomedical Sciences

institute: University of Ariziona

description:
ILA_4
14-010

data_processing:
Trimmomatic to remove reads less than 65 bases
Tophat (v2.0.1)  -a 20 -m 1 -I 50000 -g 9 -N 3 -rgl 1 --red 4 -rred 0  fr-unstranded
cufflinks (v2.1.1) -G -b oar3174.fa -u -N -F 0.05  Annotation- Ensembl Ovis_aries.Oar_v3.1.74.gtf
cuffmerge -G oar3174.gtf -s oar3174.fa
cuffquant -u library-type fr-unstranded -b oar3174.fa -max-bundle-frags 10000000 merged.gtf
cuffdiff -N -u -c 12 -FDR 0.05 --library-type fr-unstranded -b oar3174.fa --max-bundle-frags 10000000 -compatible-hits-norm merged.gtf
Genome_build: Ensemble release 74 Ovis_aries.Oar_v3.1.dna_sm.toplevel.fa.gz
Supplementary_files_format_and_content: gene_exp.diff.gz - cuffdiff gene level statistics
Supplementary_files_format_and_content: genes.fpkm.tsv.gz - table of tracking_id, gene ID, locus and FPKM values  from cuffdiff genes.FPKM_tracking

organism: Ovis aries

source_name: Isolated Semitendinosus Muscle

growth_protocol: Columbia-Rambouillet crossbred ewes carrying singleton pregnancies. During pregnancy ewes were fed alfalfa pellets and had ad lib access to water and salt. After birth lambs were removed from the ewes, given colostrum, and reared on lamb milk replacer (ad lib, Milk Specialties Co.).

extract_protocol:
Semitendinosus was dissected from the hindlimb and a mid muscle biopsy was snap frozen in liquid nitrogen and stored at -80C for RNA extraction with Qiagen Microprep RNAeasy
mRNA was selected and double-stranded cDNA libraries with ligated sequencing adapters was constructed with the Illumina TruSeq RNA Sample Prep Kit. Cluster generation was conducted with Illumina TruSeq 100bp PE (paired end) cluster kit

treatment_protocol: IUGR fetuses were generated by exposing pregnant ewes to elevated ambient temperatures (40°C for 12h; 35°C for 12h, dew point 22°C) from 40 ± 2 days gestation age (dGA) until 89 ± 4 dGA (lambs) or 94 ± 5 dGA (fetuses). Control fetuses were from ewes that were pair fed to the average intake of the heat stressed ewes.

tag: stress

value: IUGR

value: postnatal day 28

value: Female

tag: birthweight (kg)

tag: weight at necropsy (kg)

value: isolated semitendinosus muscle


title: IUGR Lamb 5

status: Public on Aug 17 2023

type: SRA

country: USA

description:
ILA_5
15-011

library_source: transcriptomic

molecule: total RNA

tag: age

value: postnatal day 35

tag: Sex

tag: tissue


title: IUGR Lamb 2

description:
ILA_2
13-009

value: postnatal day 33

value: Male


title: Control Lamb 5

description:
CLA_5
15-009

value: Control

value: postnatal day 39


title: Control Lamb 4

description:
CLA_4
15-008

value: postnatal day 29


title: Control 1 - Day 5, rep3

city: Hong Kong

first: Yin Yu

last: Lam

address: 102 Pokfulam Road

department: Department of Paediatrics and Adolescent Medicine

country: China

institute: The University of Hong Kong

description:
hiPSC1_Day5_Rep3
Poly-A mRNA-seq

data_processing:
Raw sequencing reads were filtered, aligned against GRCh38 genome with count matrix generated with Rsubread.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count_Matrix.csv: Comma-separated count matrix.

organism: Homo sapiens

source_name: Human induced pluripotent stem cell-derived cardiomyocytes

extract_protocol:
Total RNA was isolated with TRIzol LS Reagent according to manufacturer's protocol.
Constructed with Illumina Stranded mRNA Prep according to manufacturer's protocol.

tag: cell type

value: Induced pluripotent stem cell-derived APLNR+ in vitro SHF progenitors

tag: disease state

value: Normal

tag: time point

value: 0h post-isolation


title: IUGR Lamb 0

description:
ILA_0
13-005


title: Control 1 - Day 5, rep2

description:
hiPSC1_Day5_Rep2
Poly-A mRNA-seq


title: Control Lamb 3

description:
CLA_3
15-007

value: postnatal day 26


title: IUGR Lamb 1

description:
ILA_1
13-007


title: B01

city: La Jolla

first: Stephanie

last: Cherqui

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
RNA-Seq data were processed using Kallisto (version 0.45.0), Mus musculus genome GRCm38 Ensembl version 94 annotation (Mus_musculus GRCm38.94 chr_patch_hapl_scaff.gtf)
Gene-level TPM values and gene annotations were computed using tximport and the biomaRt R package.
A custom python script was used to organize the data and log reduced using log2(TPM+1).
Assembly: Mus musculus genome GRCm38 Ensembl version 94 annotation (Mus_musculus GRCm38.94 chr_patch_hapl_scaff.gtf)
Supplementary files format and content: tab-separated values files include estimated counts (est_counts) and TPM.

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Hippocampus and cortex were dissected from brains and total RNA was isolated using Rneasy Tissue kit (Qiagen). RNA was assessed for quality using an Agilent Tapestatio 4200, and 50ng of RNA with an RNA Integrity Number greater than 8.0 were used to generate libraries.
RNA sequencing libraries using the Illumina® Stranded mRNA Prep (Illumina) following manufacturer’s instructions.

value: Hippocampus

tag: genotype

tag: treatment

value: Transplanted with GFP+ WT HSPCs


title: Control Lamb 2

description:
CLA_2
14-011

value: postnatal day 27


title: Control Lamb 1

description:
CLA_1
13-016

value: postnatal day 37


title: A01


title: Control Lamb 0

description:
CLA_0
13-008

value: postnatal day 28


title: Control 1 - Day 5, rep1

description:
hiPSC1_Day5_Rep1
Poly-A mRNA-seq


title: IUGR Lamb 3

description:
ILA_3
13-010

value: IUGR

value: Female


title: SF-MSCs, sham, biol rep 3

city: Bunkyo-ku

first: Kentaro

last: Endo

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

data_processing:
SOAPnuke v1.5.2
Remove the reads containing the adaptor, the reads whose N content is greater than 5%, and low-quality reads using SOAPnuke (parameter: -l 15 -q 0.2 -n 0.05).
Trimmed sequence reads were mapped to Rnor_6.0 using HISAT2 v2.0.4 (parameter: --sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF).
Read count extraction and normalization were performed using HISAT2.
Assembly: GCF_000001895.5_Rnor_6.0
Supplementary files format and content: Tab-delimited text files include TPM values for each sample

organism: Rattus norvegicus

source_name: Synovial fluid

growth_protocol: Rat SF-MSCs were cultured in growth medium consisting of α-modified essential medium (α-MEM), 10% fetal bovine serum (FBS), and 1% antibiotic-antimycotic in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, Hilden, German).
Total RNA was used for the construction of sequencing libraries.
mRNA was isolated using oligo dT beads and fragmented.
Single-strand cDNA was generated using random N6-primed reverse transcription, followed by a secondstrand cDNA with dUTP.
After PCR amplification and DNA nanoball synthesis, the products were sequenced by BGISEQ-500.

value: Synovial fluid

tag: group

value: sham

value: mesenchymal stem cells

value: WT


title: liver cells, SMSrKO8

city: Brooklyn

first: Mulin

last: He

state: New York

address: 310 Clarkson Avenue, Apt.615

institute: SUNY Downstate Health Sciences Univ

data_processing:
For liver samples from wild-type (WT) and Smsr-KO mice, the raw data of sequence reads were trimmed using Trimmomatic (v.0.36).
For isolated primary hepatocytes from WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice, the raw sequencing reads were trimmed using SOAPnuke (v.1.5.2).
The trimmed reads were further mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner (v.2.5.2b) and Bowtie2 (v.2.2.5) respectively.
Then, the extracted gene hit counts were used for differential expression analysis using DESeq2 (v.1.30.1).
Assembly: mm10
Supplementary files format and content: raw counts, TPM values, or FPKM values for each sample

source_name: liver

extract_protocol:
For SMSrKO mice, total RNA was extracted from sWAT using an RNeasy Plus Micro Kit (Qiagen). RNA samples were quantified using a Qubit 4 fluorometer (Thermo Fisher Scientific), and RNA integrity was determined using a 4200 TapeStation System (Agilent Technologies).
For SMSrKO mice, the RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit s (NEB) and sequenced on an Illumina HiSeq.
For WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice, hepatocyte samples were isolated from two months old WT, Sms1/Sms2-dKO, and Sms1/Sms2/Smsr-tKO mice (n=3 per group) using a two-step collagenase method.
RNA was extracted from primary hepatocytes with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA integrity was checked using 2200 TapeStation system (Agilent Technologies).

value: liver

value: liver cells

value: SMSrKO


title: Control 2 - Day 9

description: scRNA-seq

data_processing:
Raw sequencing reads filtered and aligned against GRCh38 genome with Cell Ranger 3.0.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (RNA expression levels).
Supplementary_files_format_and_content: barcodes.tsv (Cell identification code).
Supplementary_files_format_and_content: features.tsv (List of genes).

molecule: polyA RNA

source_name: Human induced pluripotent stem cell derived cardiomyocytes

extract_protocol:
Embryoid bodies were dissociated with 1X TrypLE at 37oC for 15 minutes. Dissociated cells were resuspended in RPMI/B27 for cell encapsulation.
Constructed with Chromium Single Cell 3' Reagent Kit v3.1 according to manufacturer's protocol.

value: Normal

value: Day 9 of in vitro cardiac differentiation


title: Control 2 - Day 5

description: scRNA-seq

value: Human induced pluripotent stem cell derived cardiomyocytes

value: Day 5 of in vitro cardiac differentiation


title: SF-MSCs, sham, biol rep 2


title: liver cells, SMSrKO7


title: SF-MSCs, sham, biol rep 1


title: Control 2 - Day 4

description: scRNA-seq

value: Day 4 of in vitro cardiac differentiation


title: liver cells, SMSrKO6


title: SF-MSCs, pMx, biol rep 2

value: pMx


title: IUGR Fetus 0

description:
IFE_0
11-056

value: gestational day 133

value: Not Applicable

value: isolated semitendinosus muscle


title: SF-MSCs, pMx, biol rep 3


title: Control Fetus 3

description:
CFE_3
11-058

value: Control

value: Female


title: liver cells, WT4


title: Control Fetus 2

description:
CFE_2
11-057

value: gestational day 135

value: Male


title: Control 1 - Day 5

description: scRNA-seq


title: liver cells, SMSrKO5


title: SF-MSCs, pMx, biol rep 1

value: Synovial fluid

value: mesenchymal stem cells

value: WT


title: liver cells, WT3

value: liver

value: liver cells


title: Control Fetus 1

description:
CFE_1
11-040

value: gestational day 132


title: IUGR Fetus 3

description:
IFE_3
12-026

value: IUGR

value: gestational day 134


title: SF-MSCs, intact, biol rep 3

value: intact


title: liver cells, WT2


title: Control 1 - Day 4

description: scRNA-seq

value: Human induced pluripotent stem cell derived cardiomyocytes

value: Normal

value: Day 4 of in vitro cardiac differentiation


title: IUGR Fetus 2

description:
IFE_2
12-014

value: gestational day 133

value: Not Applicable

value: isolated semitendinosus muscle


title: Control Fetus 0

description:
CFE_0
11-038

value: Control


title: SF-MSCs, intact, biol rep 1


title: liver cells, WT1


title: SF-MSCs, intact, biol rep 2


title: Control 1 - Day 2

description: scRNA-seq

value: Day 2 of in vitro cardiac differentiation


title: IUGR Fetus 1

description:
IFE_1
12-013

value: gestational day 135

value: Male


title: Control 2 - Day 2

description: scRNA-seq


title: Control 1 - Day 9

description: scRNA-seq

value: Day 9 of in vitro cardiac differentiation


title: WT3

status: Public on Aug 16 2023

city: London

first: Tobias

last: Warnecke

address: Du Cane Road

country: United Kingdom

institute: Imperial College

data_processing:
Untrimmed reads were mapped using Bowtie2 for A. aeolicus (single end reads) and using BWA for B. bacteriovorus (paired-end). Read counts of all genes were estimated using the python package HTSeq
Assembly: B.bacteriovorus : GCA_000196175.1; A.aeolicus : GCF_000008625.1
Supplementary files format and content: Aquifex-aeolicus_readcounts; Readcounts and gene Length
Supplementary files format and content: HIID13_WT_Count_and_RPKM: Read counts and gene length

organism: Bdellovibrio bacteriovorus

source_name: strain HID13

growth_protocol: RNA extraction from B. bacteriovorus HID13, cells were diluted in 10 mL of fresh YP medium at an OD of 0.1 and grown until reaching a density of 0.6 (20 hours at 30°C with shaking). For each replicate, 2 mL of culture were spun at maximum speed, snap frozen and kept at -80°C until RNA extraction. ; Aquifex aeolicus pellets were purchased from the Archaeenzentrum Regensburg, Germany

extract_protocol:
RNEasy kit (Qiagen), including DNase I treatment. RNA quality was assessed using an Agilent 2100 Bioanalyser.
For the B. bacteriovorus samples (all RIN scores > 9.5), ribosomal RNA was depleted using the NEBNext®rRNA Depletion Kit (Bacteria), and NGS libraries made using the NEBNext® Ultra™ II Directional RNALibrary Prep Kit for Illumina® according to manufacturer’s instructions. Paired-end 55bp reads were generated on a NextSeq 2000 with dual 8bp indexing. For the A. aeolicus samples (all RIN scores > 5), rRNA was depleted using Illumina Ribozero Kit (Bacteria), and NGS libraries made using the TruSeq Stranded Total RNA LT Kit according to manufacturer’s instructions. Single End 50bp reads were generated on a MiSeq with single 6bp indexing.

value: strain HID13

tag: cell line

value: No treatment


title: WT1


title: WT2


title: DAP-seq, Halo-ZmAuxIAA8,rep2

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

description: Magne HaloTag Beads, Promega (G7281)

library_source: genomic

data_processing:
RNA-sequencing data of 150 bp paired-end raw reads were trimmed and quality filtered by trim_galore, and mapped to maize transcriptome (NCBI B73-REFERENCE NAM-5.0) using Salmon (v1.10.2) software.
Differentially expressed genes (DEGs) were called using R package of DESeq2 with s-value threshold of 0.005.
DAP-seq data of ZmAux/IAA8 were preprocessed similarly to the above RNA-seq reads, and aligned to maize genome using Bowtie2 (v2.5.1) software
BigWig files were generated using bamCoverage (v3.5.1) with normalization of sequencing depth to 10 millions.
Assembly: NCBI B73-REFERENCE NAM-5.0
Supplementary files format and content: text, gene expression values determined by Salmon.
Supplementary files format and content: BigWig, genomic track of DAP-seq read density.
Library strategy: DAP-seq

molecule: genomic DNA

organism: Zea mays

source_name: leaf tissues at three-leaf stage

extract_protocol:
Total RNA from the maize leaf samples was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, United States). Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The Halo-ZmCCT or Halo-ZmAux/IAA8 fusion protein was expressed using the TNT SP6 Coupled Wheat Germ Extract System (Promega, USA) and then purified with Magne HaloTag Beads (Promega, USA). Genomic DNA (gDNA, 5 μg in 130 μL TE buffer) was fragmented to an average of 200 bp using a Covaris M220 (Woburn, USA) according to the manufacturer’s recommended settings. The fragmented gDNA was then purified using MICH DNA Clean Beads (Bluescape, China) at a DNA to beads ratio of 0.7-1.1. The beads were incubated with the gDNA for 5 min at room temperature and placed on a magnet (Bluescape, China) to immobilize the beads. The supernatant was then removed. The beads were washed twice with 200 μL of 80% ethanol and allowed to dry. Once dry, they were resuspended in 22 μL resuspension buffer, incubated at room temperature for 5 min, and placed on the magnet. The DNA-containing supernatant was then transferred to a new tube.
Briefly, mRNA was purified by using poly-T oligo-attached magnetic beads. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
DAP-seq libraries were constructed using the MICH TLX DNA-seq Kit (Bluescape, China) according to the manufacturer’s instructions. After the beads with bound proteins were incubated with DNA fragments at room temperature for 1 h, they were washed three times with wash buffer to remove unbound DNA fragments. The HaloTag beads were resuspended in 30-μl elution buffer and then heated at 98 °C for 10 min to denature the protein and release the bound DNA fragment into the solution.

value: leaf tissues at three-leaf stage

value: primary tissue of leaf

value: WT ZmCCT

value: normal


title: DAP-seq, Halo-ZmAuxIAA8,rep1

description: Magne HaloTag Beads, Promega (G7281)


title: Input of DAP-seq, Halo-ZmAuxIAA8

description: Magne HaloTag Beads, Promega (G7281)


title: TEinsertion,drought,RNA,rep1

data_processing:
RNA-sequencing data of 150 bp paired-end raw reads were trimmed and quality filtered by trim_galore, and mapped to maize transcriptome (NCBI B73-REFERENCE NAM-5.0) using Salmon (v1.10.2) software.
Differentially expressed genes (DEGs) were called using R package of DESeq2 with s-value threshold of 0.005.
DAP-seq data of ZmAux/IAA8 were preprocessed similarly to the above RNA-seq reads, and aligned to maize genome using Bowtie2 (v2.5.1) software
BigWig files were generated using bamCoverage (v3.5.1) with normalization of sequencing depth to 10 millions.
Assembly: NCBI B73-REFERENCE NAM-5.0
Supplementary files format and content: text, gene expression values determined by Salmon.
Supplementary files format and content: BigWig, genomic track of DAP-seq read density.

value: TE insertion in the promoter of ZmCCT

value: drought


title: TEinsertion,drought,RNA,rep2


title: deltaTE,drought,RNA,rep3


title: deltaTE,drought,RNA,rep2


title: deltaTE,drought,RNA,rep1


title: WSB007

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: Microglia were sorted from Live viable dye negative, CD45 positive, CD11b positive isolated from brain single cells suspension

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: brain microglia

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Cells were sort-purified using specificed markers from brain of 5XFAD and 5XFAD B2m KO mice

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain


title: WSB008


title: WSB005


title: TEinsertion,normal,RNA,rep3


title: TEinsertion,normal,RNA,rep2


title: TEinsertion,normal,RNA,rep1


title: WSB003


title: WSB004


title: deltaTE,normal,RNA,rep2


title: deltaTE,normal,RNA,rep1


title: deltaTE,normal,RNA,rep3


title: HeLa shTra2b 2nd

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

description: expressed_gene_FPKM.txt; expressed_gene_reads.txt

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then, adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (version 0.0.13). The short reads less than 16nt were also dropped. The clean reads were then aligned to the GRch38 genome by TopHat2, allowing 4 mismatches. Uniquely mapped reads were used for gene read number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) .
The R Bioconductor packages edgeR and DESeq were utilized to screen out the DEGs. A false discovery rate <0.05 and fold change > 2 or < 0.5 were set as the cut-off criteria for identifying DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline, as described previously. In brief, ABLas detection of 10 types of ASEs was based on the splice junction reads, including exon skipping (ES), alternative 5' splice site (A5SS), alternative 3'splice site (A3SS), intron retention (IR), mutually exclusive exons (MXEs), mutually exclusive 5'UTRs (5pMXEs), mutually exclusive 3'UTRs (3pMXEs), cassette exon, A3SS&ES, and A5SS&ES.
To assess RBP-regulated ASE, Student’s t-test was used to evaluate the significance of the ratio alteration of ASEs. Those events that were significant at the P value cut-off corresponding to a false discovery rate cut-off of 5% were considered RBP-regulated ASEs.
To sort out functional categories of DEGs, gene ontology (GO) terms and KEGG pathways were identified using the KOBAS 2.0 server. The hypergeometric test and Benjamin-Hochberg FDR controlling procedure were used to define the enrichment of each term.
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: ovarian cells

growth_protocol: HeLa, HO8910 and A2780 cells were seeded in 24-well culture plates. When the cells reached 70% confluence, the cells were transfected with the vector using Lipofectamine 2000 according to the manufacturer's protocol. The cells were then incubated at 37℃ for 48 h, and viable cells were harvested and washed twice with phosphate-buffered saline (PBS). Viable cells were double-stained with fluorescein isothiocyanate (FITC)-conjugated Annexin V and 7-amino actinomycin D (7-AAD; Biotech Co., Ltd., Suzhou, Jiangsu, China). The percentage of cell apoptosis was defined as the sum of the right lower and upper quadrants. The induction of apoptosis was detected using the Annexin V/PI Apoptosis Detection Kit (Nan Jing Key Gen Biotech Co, Jiangsu, China) according to the manufacturer's instructions. Briefly, the cells were cultured at a density of 1.0×105 cells/mL, treated with TRA2B-shRNA/TRA2B-siRNA and cultured for 12 h at 37℃ with 5 % CO2. All samples were analyzed using a FACSort Flow Cytometer (Becton Dickinson, USA).

extract_protocol:
The HeLa cells were ground into fine powder before RNA extraction. Total RNA was extracted with TRIzol (Ambion, Shanghai, China). The RNA was further purified with two phenol-chloroform treatments, then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were re-determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, Hercules, California, USA). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of the total RNA was used for RNA-seq library preparation using the VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme, Nanjing, Jiangsu, China). Polyadenylated mRNAs were purified and fragmented, then converted into double strand cDNA. After end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200–500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified, and stored at -80℃before sequencing.

treatment_protocol: To explore whether TRA2B could influence the invasive ability of ovarian cancer cells using the mothod of Transwell assay. The upper chamber was covered by100μl Matrigel (1mg/ml)(BD, USA). After Matrigel dried into gel, 200 μl cell suspension was added into transwell upper chamber and cultured for 24 hours at 37℃. Then, cells on the upper chamber were removed and cells from the lower surface were fixed with 7% ice ethanol, stained with 0.5% crystal violet for 30 mins. The cells were counted by ImagePro Plus.

value: HeLa

tag: transfection


title: WSB006


title: WSB001


title: HeLa shTra2b 1st


title: HeLa shCtrl 2nd

value: shCtrl


title: TEinsertion,drought,RNA,rep3


title: HeLa shCtrl 1st


title: aco-mutant-BA

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

library_source: transcriptomic single cell

data_processing:
The scRNA-Seq FASTQ files (10x Genomics 3' version 3) were aligned to the Zebrafish Ensembl version 91 reference genome (GRCz11) and transcriptome, using Cell Ranger version 3.1.0. Cell Ranger filtered feature sparse matrix counts files from all samples (HDF5 format) were supplied to AltAnalyze141 version 2.1.4 for unsupervised analysis using the EnsMart 91 zebrafish database and ICGS2 algorithm with default parameters. Cell-type predictions were initially obtained from ICGS2 based on marker enrichment and then further refined based on manual curation with literature-associated markers. The obtained ICGS2 clusters were filtered to include muscle, endothelial and epithelial clusters for downstream UMAP visualization.
Assembly: GRCz11
Supplementary files format and content: HDF5 filtered sparse matrix

organism: Danio rerio

source_name: bulbus arteriosus

growth_protocol: Single cell preparations were prepared similar to previously published protocols designed to dissociate rigid elastic tissue with minor variations. The SV and BA were dissected from using fine forceps and pooled in a Tyrode’s solution (pH 7.4) following washing in 1X PBS.

extract_protocol:
The pooled tissue was washed 3 times in Tyrode’s before the addition of Liberase IV (0.29U/ml, Roche, 05401020001), Elastase (1.0 U/ml, Sigma, E7885), and Pronase E (0.92 U/ml, Sigma, P5147). Dissociation of the tissues was facilitated via incubation at 37°C and gentle trituration with pipettes of descending tip diameter (first 2.0 mm followed by 0.8 mm. Can also use filtered P1000 and P20 tips, respectively). The dissociation reaction was halted by transferring the cells to a modified Kraft-Brühe solution (pH 6.9) and the cells were spun down to a pellet before being resuspended in a final 1% BSA solution in 1X PBS.
Single cells were submitted to the CCHMC Gene Expression Core using the 10x 3' version 3.1 Chromium platform.
Paired-end sequencing using an Illumina NovaSeq 6000 SP Flow Cell was performed

value: bulbus arteriosus nr2f1a mutant


title: aco-mutant-SV

source_name: sinus venosus

value: sinus venosus nr2f1a mutant


title: SV-WT

value: sinus venosus WT


title: DMSO_3

city: Boston

first: Kiran

last: Kurmi

state: MA

address: Department of Cell Biology, Harvard Medical School, LHRRB, Room 314, 240 Longwood Avenue

department: Cell Biology

institute: Harvard Medical School

data_processing:
For read counts, the RNA-seq analysis pipeline was performed with the bcbio-nextgen framework (https://doi.org/10.5281/zenodo.3564938) using default parameters for bulk RNA-seq analysis with the Mus musculus genome reference GRCm38 Ensembl version 99.  Reads were aligned with star and salmon, kallisto was used to quantify expression counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: CD4+ T cells

growth_protocol: Naive CD4+ T cells were activated for six hours with 2 mg/mL anti-CD3/anti-CD28 mAbs in RPMI-1640 supplemented with 10% heat-inactivated FBS, 10 mM HEPES, 0.05 mM 2-mercaptoethanol, and 1% penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using RNeasy Micro Kit (Qiagen, cat. #74004) according to the manufacturer’s instructions and protocols. RNA was eluted in RNase-free water, and sample concentrations and RNA quality were determined by NanoDrop and Bioanalyzer (Agilent), respectively. All samples scored RIN values of >9.0.
RNA-seq library preparation was performed with the High Throughput TruSeq Stranded mRNA Library Prep kit (Illumina), following the manufacturer’s instructions. Each sample input of 500 ng RNA was used with 10 μl of 1:1,000 diluted ERCC Spike-In Mix 1 (Ambion). Libraries were amplified for eleven cycles during the final amplification step and quantified using the Qubit dsDNA HS assay (Thermo Fisher Scientific). Library size and quality were spot-checked for a subset of samples using Bioanalyzer (Agilent). Libraries were pooled at equimolar concentrations, and then the pool was quantitated using the KAPA library quantification kit (Kapa Biosystems).

treatment_protocol: DMSO, 2 nM pyrvinium pamoate (Sigma #P0027), or 25 nM rotenone (Tocris #3616) was treated for 1 hr prior to sample collection.

tag: strain background

value: female

value: WT

value: CD4+ T cells


title: PP_2


title: PP_3


title: PP_1


title: Rotenone_2


title: Rotenone_3


title: DMSO_2


title: N1IC model, replicate 1, scRNAseq

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: Microwell-based scRNA-seq, 8-base index read, 26-base read 1, 58-base read 2

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were then aligned to GRCm38 (GENCODE v.M10) with sequence of Cre recombinase using STAR v.2.5.0 with parameters "-- sjdbOverhang 57 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
Genome build:  GRCm38 (mm10) with sequence of Cre recombinase
supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

source_name: Brain tumor tissue resection

growth_protocol: Mice were bred in house and housed under standard conditions. Correct expression of transgenes was confirmed by genotyping from genomic DNA.

extract_protocol:
Mouse brain tumor resections were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) according to the manufacturer’s instructions.
mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.

treatment_protocol: Mice were sacrificed for collecting brain tumor tissues when when endstage criteria were met. Freshly resected tumor tissues were kept in ice-cold PBS for transportation prior to dissociation.

value: Brain tumor tissue resection

value: M

tag: tumor stage

value: end-stage

tag: background mice


title: N1IC model, replicate 2, scRNAseq


title: liver-HFD-AN1284 5mg treated, rep3

city: Jerusalem

first: Rinat

last: Abramovitch

address: Hadassah Ein Kerem

department: Institute for Gene Therapy

country: Israel

institute: Hadassah Medical Organization

data_processing:
Quality and adapter trimming with cutadapt, v1.18, using parameters -q 28,28 -O 1 --match-read-wildcards -m 15.
Filtering low quality reads with fastq_quality_filter (FASTX package, v0.0.14), using parameters -q 20 -p 90.
Alignment with TopHat, v2.1.1, using parameters -G genes.gtf (from Ensembl release 95) -N 6 --read-gap-length 5 --read-edit-dist 11 --segment-length 20 --read-realign-edit-dist 3 --no-coverage-search --library-type fr-firststrand.
Counts per gene with htseq-count, v0.6.0, using parameters -s 'reverse' and genes from Ensembl release 95. Final raw counts were the sum of counts in each individual sequencing run.
Genes with less than 10 reads were discarded prior to normalization with DESeq2, v1.22.1. Differential expression (with DESeq2) was done with default parameters except setting independentFiltering=F. A combined single factor was used to test pairwise comparisons between specific combinations of diet and dose, while a two factors design (Diet and Dose) was used for global comparisons between levels of each factor (e.g. HFD vs. ND).
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2_final.xlsx, an Excel file with a header row, followed by data rows for each gene. Columns A-L have general details; M-AE have the raw counts (for each sample); AF-AX the normalized counts; AY is the mean expression in the system; AZ-BE are the results of comparing HFD to ND; BF-BK are for dose 1mg vs. Saline; BL-BQ for dose 5mg vs. Saline; BR-BW for 5mg vs. 1mg; BX-CC for HFD vs. ND, given saline; CD-CI for HFD vs. ND, given 1mg; CJ-CO for HFD vs. ND, given 5mg; CP-CU for 1mg vs. Saline, under ND; CV-DA for 5mg vs. Saline, under ND; DB-DG for 5mg vs. 1mg, under ND; DH-DM for 1mg vs. Saline, under HFD; DN-DS for 5mg vs. Saline, under HFD; DT-DY for 5mg vs. 1mg, under HFD; DZ-EL have either "yes" or "no" indicating for each of the comparisons if the gene was included in the list of significant genes for that comparison.

source_name: liver-HFD-AN1284 5mg treated

growth_protocol: Male C57BL/6JOlaHsd mice aged four weeks were used for NASH experiments. The normal diet (ND) consisted of Teklad 2918SC radiated pellets (ENVIGO) that contained 13.9% kcal from fat, 62.9% from carbohydrates and 23.1% from protein. The high fat diet (HFD50; Envigo-Teklad TD.150235) contained 50.5% kcal from fat, 38% from carbohydrates and 11.5% from protein. To this diet was added sucrose (20%), fructose (10%), cholesterol (1.25%), reduced choline (900 mg/kg), a high content of trans-fat (12% of fatty acids) and saturated fat (50% of fatty acids). Prior to commencement of the experiments all animals were fed ad libitum with a ND. The 2 diets were given for four months.

extract_protocol:
Total liver RNA was extracted from snap-frozen liver tissues (4-5 mice per group) using the miRNeasy Micro Kit (Qiagen, Hilden, Germany)
Libraries were constructed with the KAPA Stranded RNA-Seq Kit, after poly-A selection, with Illumina'a TruSeq adapters. Samples were pooled and sequenced in two runs of the NextSeq machine.

treatment_protocol: Under ketamine /xylazine anesthesia the mice were implanted with the micro-osmotic pumps containing saline or AN1284 at a dose of 1 or 5 mg/kg/day,  that was given for a further eight weeks.

value: liver

tag: nutrition

value: high fat diet 4 month

value: mouse model of NASH

value: AN1284 5mg in mini-pump


title: p53 model, replicate 1, scRNAseq


title: p53 model, replicate 2, scRNAseq


title: liver-HFD-AN1284 5mg treated, rep2


title: BA-WT

value: bulbus arteriosus WT


title: liver-HFD-AN1284 1mg treated, rep1

source_name: liver-HFD-AN1284 1mg treated

value: AN1284 1mg in mini-pump


title: liver-HFD-saline treated, rep3

source_name: liver-HFD-saline treated

value: saline in mini-pump


title: liver-HFD-AN1284 1mg treated, rep3


title: liver-HFD-AN1284 1mg treated, rep4


title: liver-HFD-AN1284 1mg treated, rep2


title: Rotenone_1


title: liver-ND-AN1284 1mg treated, rep2

source_name: liver-ND-AN1284 1mg treated

value: Normal diet

value: control


title: liver-HFD-saline treated, rep1


title: liver-ND-AN1284 1mg treated, rep3


title: liver-ND-AN1284 5mg treated, rep3

source_name: liver-ND-AN1284 5mg treated


title: liver-ND-AN1284 5mg treated, rep1


title: liver-ND-AN1284 5mg treated, rep2


title: liver-ND-AN1284 1mg treated, rep1


title: DMSO_1


title: liver-ND-saline treated, rep3

source_name: liver-ND-saline treated


title: liver-ND-saline treated, rep2


title: liver-HFD-AN1284 5mg treated, rep1


title: liver-HFD-saline treated, rep2


title: Exp0_F3058C56_Plate1_K1A3_N715_S506, Child

city: Sydney

first: Fabio

last: Luciani

state: NSW

address: Kensington Campus

country: Australia

institute: UNSW Sydney

description:
ELT5411_A92
genes.fpkm_table
genes.attr_table
samples.table

data_processing:
VDJPuzzle was run to extract TCR and quantify gene expression (FPKM)
Assembly: hg38
Supplementary files format and content: Matrix of FPKM values per sample, per gene
Supplementary files format and content: List of gene names in matrix
Supplementary files format and content: List of sample names in matrix

source_name: PBMCs

extract_protocol:
Single influenza A2/M158-specific CD8+ T cells were sorted using flow cytometry, with RNA isolation and sequencing library construction performed according to the Smart-seq2 protocol.
Single cell RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMCs

value: Bulk C1R

value: Bulk C1R cell line

tag: epitope

value: Child

tag: phenotype


title: Exp0_F3058C56_Plate1_K1B3_N715_S507, Child

description:
ELT5411_A93
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

tag: age

value: Tcm


title: Exp0_F3058C56_Plate1_K1B4_N701_S515, Child

description:
ELT5411_A97
genes.fpkm_table
genes.attr_table
samples.table

tag: tissue


title: Exp0_F3058C56_Plate1_K1A4_N701_S513, Child

description:
ELT5411_A96
genes.fpkm_table
genes.attr_table
samples.table

tag: cell type


title: Exp0_F3058C56_Plate1_K1D3_N715_S508, Child

description:
ELT5411_A94
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1H2_N715_S505, Child

description:
ELT5411_A91
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1F2_N715_S502, Child

description:
ELT5411_A89
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1B2_N714_S507, Child

description:
ELT5411_A85
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1D2_N714_S510, Child

description:
ELT5411_A87
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1E2_N714_S511, Child

description:
ELT5411_A88
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: Exp0_F3058C56_Plate1_K1G2_N715_S503, Child

description:
ELT5411_A90
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C4_N701_S516, Child

description:
ELT5411_A98
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1D1_N712_S511, Child

description:
ELT5411_A80
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1D4_N701_S517, Child

description:
ELT5411_A99
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H10_N712_S507, Newborn

description:
ELT5411_A77
genes.fpkm_table
genes.attr_table
samples.table

value: Newborn

value: Tnaive


title: Exp0_F3058C56_Plate1_K1E1_N714_S502, Child

description:
ELT5411_A81
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1G1_N714_S505, Child

description:
ELT5411_A83
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1B1_N712_S508, Child

description:
ELT5411_A78
genes.fpkm_table
genes.attr_table
samples.table

value: Tscm


title: Exp0_CB149_Plate1_C1G10_N712_S506, Newborn

description:
ELT5411_A76
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C1_N712_S510, Child

description:
ELT5411_A79
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E10_N712_S503, Newborn

description:
ELT5411_A74
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1F1_N714_S503, Child

description:
ELT5411_A82
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1H3_N715_S511, Child

description:
ELT5411_A95
genes.fpkm_table
genes.attr_table
samples.table


title: liver-ND-saline treated, rep1

value: liver

tag: disease state


title: Exp0_CB149_Plate1_C1C10_N711_S511, Newborn

description:
ELT5411_A72
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F10_N712_S505, Newborn

description:
ELT5411_A75
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1H1_N714_S506, Child

description:
ELT5411_A84
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B10_N711_S510, Newborn

description:
ELT5411_A71
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F9_N711_S505, Newborn

description:
ELT5411_A67
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E9_N711_S503, Newborn

description:
ELT5411_A66
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C2_N714_S508, Child

description:
ELT5411_A86
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1G9_N711_S506, Newborn

description:
ELT5411_A68
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D9_N711_S502, Newborn

description:
ELT5411_A65
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H9_N711_S507, Newborn

description:
ELT5411_A69
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A10_N711_S508, Newborn

description:
ELT5411_A70
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1C9_N710_S511, Newborn

description:
ELT5411_A64
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1G8_N710_S506, Newborn

description:
ELT5411_A60
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F8_N710_S505, Newborn

description:
ELT5411_A59
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H7_N707_S507, Newborn

description:
ELT5411_A53
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A8_N707_S508, Newborn

description:
ELT5411_A54
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells


title: Exp0_CB149_Plate1_C1G7_N707_S506, Newborn

description:
ELT5411_A52
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D8_N710_S502, Newborn

description:
ELT5411_A57
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B8_N707_S510, Newborn

description:
ELT5411_A55
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D10_N712_S502, Newborn

description:
ELT5411_A73
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1C8_N707_S511, Newborn

description:
ELT5411_A56
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F7_N707_S505, Newborn

description:
ELT5411_A51
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E7_N707_S503, Newborn

description:
ELT5411_A50
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A7_N706_S510, Newborn

description:
ELT5411_A47
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D7_N707_S502, Newborn

description:
ELT5411_A49
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B7_N706_S511, Newborn

description:
ELT5411_A48
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H6_N706_S508, Newborn

description:
ELT5411_A46
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F6_N706_S506, Newborn

description:
ELT5411_A44
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1G6_N706_S507, Newborn

description:
ELT5411_A45
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B9_N710_S510, Newborn

description:
ELT5411_A63
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A9_N710_S508, Newborn

description:
ELT5411_A62
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E6_N706_S505, Newborn

description:
ELT5411_A43
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1C6_N706_S502, Newborn

description:
ELT5411_A41
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H8_N710_S507, Newborn

description:
ELT5411_A61
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2F10_N729_S510, Older adult

description:
ELT5411_A379
genes.fpkm_table
genes.attr_table
samples.table

value: Older adult


title: Exp0_CB149_Plate1_C1D6_N706_S503, Newborn

description:
ELT5411_A42
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E10_N729_S508, Older adult

description:
ELT5411_A378
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2G10_N729_S511, Older adult

description:
ELT5411_A380
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E8_N710_S503, Newborn

description:
ELT5411_A58
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B6_N705_S511, Newborn

description:
ELT5411_A40
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H5_N705_S508, Newborn

description:
ELT5411_A38
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D10_N729_S507, Older adult

description:
ELT5411_A377
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D9_N728_S510, Older adult

description:
ELT5411_A371
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E9_N728_S511, Older adult

description:
ELT5411_A372
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B10_N729_S505, Older adult

description:
ELT5411_A375
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C9_N728_S508, Older adult

description:
ELT5411_A370
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1G5_N705_S507, Newborn

description:
ELT5411_A37
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A10_N729_S503, Older adult

description:
ELT5411_A374
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A8_N728_S506, Older adult

description:
ELT5411_A368
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2G6_N728_S503, Older adult

description:
ELT5411_A366
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2F6_N728_S502, Older adult

description:
ELT5411_A365
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B9_N728_S507, Older adult

description:
ELT5411_A369
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E6_N727_S511, Older adult

description:
ELT5411_A364
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C6_N727_S508, Older adult

description:
ELT5411_A362
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B6_N727_S507, Older adult

description:
ELT5411_A361
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A6_N727_S506, Older adult

description:
ELT5411_A360
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2G5_N727_S505, Older adult

description:
ELT5411_A359
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2F5_N727_S503, Older adult

description:
ELT5411_A358
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D6_N727_S510, Older adult

description:
ELT5411_A363
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D5_N726_S511, Older adult

description:
ELT5411_A356
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F5_N705_S506, Newborn

description:
ELT5411_A36
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2G4_N726_S506, Older adult

description:
ELT5411_A352
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E5_N727_S502, Older adult

description:
ELT5411_A357
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A5_N726_S507, Older adult

description:
ELT5411_A353
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C10_N729_S506, Older adult

description:
ELT5411_A376
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C5_N726_S510, Older adult

description:
ELT5411_A355
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E4_N726_S503, Older adult

description:
ELT5411_A350
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2F4_N726_S505, Older adult

description:
ELT5411_A351
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A7_N728_S505, Older adult

description:
ELT5411_A367
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A6_N705_S510, Newborn

description:
ELT5411_A39
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C4_N724_S511, Older adult

description:
ELT5411_A348
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A4_N724_S508, Older adult

description:
ELT5411_A346
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2G3_N724_S507, Older adult

description:
ELT5411_A345
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B4_N724_S510, Older adult

description:
ELT5411_A347
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E5_N705_S505, Newborn

description:
ELT5411_A35
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D4_N726_S502, Older adult

description:
ELT5411_A349
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E3_N724_S505, Older adult

description:
ELT5411_A343
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2F3_N724_S506, Older adult

description:
ELT5411_A344
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D3_N724_S503, Older adult

description:
ELT5411_A342
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C3_N724_S502, Older adult

description:
ELT5411_A341
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D5_N705_S503, Newborn

description:
ELT5411_A34
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B5_N726_S508, Older adult

description:
ELT5411_A354
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2A3_N723_S510, Older adult

description:
ELT5411_A339
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B3_N723_S511, Older adult

description:
ELT5411_A340
genes.fpkm_table
genes.attr_table
samples.table

value: Tem


title: Exp0_DMC018_Plate2_E2F2_N723_S507, Older adult

description:
ELT5411_A337
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2E2_N723_S506, Older adult

description:
ELT5411_A336
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2D2_N723_S505, Older adult

description:
ELT5411_A335
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2G2_N723_S508, Older adult

description:
ELT5411_A338
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1C5_N705_S502, Newborn

description:
ELT5411_A33
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2B2_N723_S502, Older adult

description:
ELT5411_A333
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G10_N722_S510, Older adult

description:
ELT5411_A331
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1H10_N722_S511, Older adult

description:
ELT5411_A332
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2C2_N723_S503, Older adult

description:
ELT5411_A334
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E10_N722_S507, Older adult

description:
ELT5411_A329
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F10_N722_S508, Older adult

description:
ELT5411_A330
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C10_N722_S505, Older adult

description:
ELT5411_A327
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B10_N722_S503, Older adult

description:
ELT5411_A326
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1H9_N721_S511, Older adult

description:
ELT5411_A324
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E9_N721_S507, Older adult

description:
ELT5411_A321
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D9_N721_S506, Older adult

description:
ELT5411_A320
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F9_N721_S508, Older adult

description:
ELT5411_A322
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G9_N721_S510, Older adult

description:
ELT5411_A323
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A10_N722_S502, Older adult

description:
ELT5411_A325
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B5_N704_S511, Newborn

description:
ELT5411_A32
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate2_E2F9_N729_S502, Older adult

description:
ELT5411_A373
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B9_N721_S503, Older adult

description:
ELT5411_A318
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C9_N721_S505, Older adult

description:
ELT5411_A319
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A9_N721_S502, Older adult

description:
ELT5411_A317
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1H8_N720_S511, Older adult

description:
ELT5411_A316
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D10_N722_S506, Older adult

description:
ELT5411_A328
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D8_N720_S506, Older adult

description:
ELT5411_A312
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B8_N720_S503, Older adult

description:
ELT5411_A310
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G8_N720_S510, Older adult

description:
ELT5411_A315
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E8_N720_S507, Older adult

description:
ELT5411_A313
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A5_N704_S510, Newborn

description:
ELT5411_A31
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A8_N720_S502, Older adult

description:
ELT5411_A309
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F8_N720_S508, Older adult

description:
ELT5411_A314
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1H7_N719_S511, Older adult

description:
ELT5411_A308
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B7_N719_S505, Older adult

description:
ELT5411_A303
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C7_N719_S506, Older adult

description:
ELT5411_A304
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A7_N719_S503, Older adult

description:
ELT5411_A302
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D7_N719_S507, Older adult

description:
ELT5411_A305
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1H6_N719_S502, Older adult

description:
ELT5411_A301
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G7_N719_S510, Older adult

description:
ELT5411_A307
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G6_N718_S511, Older adult

description:
ELT5411_A300
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H4_N704_S508, Newborn

description:
ELT5411_A30
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C6_N718_S507, Older adult

description:
ELT5411_A297
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D6_N718_S508, Older adult

description:
ELT5411_A298
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F5_N718_S502, Older adult

description:
ELT5411_A293
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F6_N718_S510, Older adult

description:
ELT5411_A299
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B6_N718_S506, Older adult

description:
ELT5411_A296
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D5_N716_S510, Older adult

description:
ELT5411_A291
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G5_N718_S503, Older adult

description:
ELT5411_A294
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C5_N716_S508, Older adult

description:
ELT5411_A290
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C8_N720_S505, Older adult

description:
ELT5411_A311
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1G4_N704_S507, Newborn

description:
ELT5411_A29
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A6_N718_S505, Older adult

description:
ELT5411_A295
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E5_N716_S511, Older adult

description:
ELT5411_A292
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B5_N716_S507, Older adult

description:
ELT5411_A289
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F7_N719_S508, Older adult

description:
ELT5411_A306
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C4_N729_S521, Older adult

description:
ELT5411_A284
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F4_N716_S503, Older adult

description:
ELT5411_A286
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G3_N729_S517, Older adult

description:
ELT5411_A281
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G4_N716_S505, Older adult

description:
ELT5411_A287
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A5_N716_S506, Older adult

description:
ELT5411_A288
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B4_N729_S520, Older adult

description:
ELT5411_A283
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A4_N729_S518, Older adult

description:
ELT5411_A282
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E4_N716_S502, Older adult

description:
ELT5411_A285
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E3_N729_S515, Older adult

description:
ELT5411_A279
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F3_N729_S516, Older adult

description:
ELT5411_A280
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C3_N728_S522, Older adult

description:
ELT5411_A278
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B3_N728_S521, Older adult

description:
ELT5411_A277
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G2_N728_S518, Older adult

description:
ELT5411_A275
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1A3_N728_S520, Older adult

description:
ELT5411_A276
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F2_N728_S517, Older adult

description:
ELT5411_A274
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E2_N728_S516, Older adult

description:
ELT5411_A273
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C2_N728_S513, Older adult

description:
ELT5411_A271
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B2_N727_S522, Older adult

description:
ELT5411_A270
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1G1_N727_S521, Older adult

description:
ELT5411_A269
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1E1_N727_S518, Older adult

description:
ELT5411_A267
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1F1_N727_S520, Older adult

description:
ELT5411_A268
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D1_N727_S517, Older adult

description:
ELT5411_A266
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E4_N704_S505, Newborn

description:
ELT5411_A27
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1C1_N727_S516, Older adult

description:
ELT5411_A265
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H10_N727_S513, Adult

description:
ELT5411_A263
genes.fpkm_table
genes.attr_table
samples.table

value: Adult


title: Exp0_CB149_Plate1_C1F4_N704_S506, Newborn

description:
ELT5411_A28
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1B1_N727_S515, Older adult

description:
ELT5411_A264
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C10_N726_S517, Adult

description:
ELT5411_A258
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F10_N726_S521, Adult

description:
ELT5411_A261
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G10_N726_S522, Adult

description:
ELT5411_A262
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F9_N724_S521, Adult

description:
ELT5411_A253
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B10_N726_S516, Adult

description:
ELT5411_A257
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E10_N726_S520, Adult

description:
ELT5411_A260
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D4_N704_S503, Newborn

description:
ELT5411_A26
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G9_N724_S522, Adult

description:
ELT5411_A254
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D10_N726_S518, Adult

description:
ELT5411_A259
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A10_N726_S515, Adult

description:
ELT5411_A256
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C9_N724_S517, Adult

description:
ELT5411_A250
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_DMC018_Plate1_E1D2_N728_S515, Older adult

description:
ELT5411_A272
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D9_N724_S518, Adult

description:
ELT5411_A251
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E9_N724_S520, Adult

description:
ELT5411_A252
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H8_N724_S513, Adult

description:
ELT5411_A247
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H9_N726_S513, Adult

description:
ELT5411_A255
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G8_N723_S522, Adult

description:
ELT5411_A246
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B9_N724_S516, Adult

description:
ELT5411_A249
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A9_N724_S515, Adult

description:
ELT5411_A248
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1C4_N704_S502, Newborn

description:
ELT5411_A25
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E8_N723_S520, Adult

description:
ELT5411_A244
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B4_N703_S511, Newborn

description:
ELT5411_A24
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A8_N723_S515, Adult

description:
ELT5411_A240
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F8_N723_S521, Adult

description:
ELT5411_A245
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D8_N723_S518, Adult

description:
ELT5411_A243
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B8_N723_S516, Adult

description:
ELT5411_A241
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C8_N723_S517, Adult

description:
ELT5411_A242
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G7_N722_S522, Adult

description:
ELT5411_A238
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E7_N722_S520, Adult

description:
ELT5411_A236
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B7_N722_S516, Adult

description:
ELT5411_A233
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G6_N721_S522, Adult

description:
ELT5411_A230
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C7_N722_S517, Adult

description:
ELT5411_A234
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A4_N703_S510, Newborn

description:
ELT5411_A23
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D7_N722_S518, Adult

description:
ELT5411_A235
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F6_N721_S521, Adult

description:
ELT5411_A229
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B6_N721_S516, Adult

description:
ELT5411_A225
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C6_N721_S517, Adult

description:
ELT5411_A226
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G5_N720_S522, Adult

description:
ELT5411_A222
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E6_N721_S520, Adult

description:
ELT5411_A228
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H5_N721_S513, Adult

description:
ELT5411_A223
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D5_N720_S520, Adult

description:
ELT5411_A220
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E5_N720_S521, Adult

description:
ELT5411_A221
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A6_N721_S515, Adult

description:
ELT5411_A224
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A7_N722_S515, Adult

description:
ELT5411_A232
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H7_N723_S513, Adult

description:
ELT5411_A239
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H4_N720_S515, Adult

description:
ELT5411_A216
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C5_N720_S518, Adult

description:
ELT5411_A219
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F7_N722_S521, Adult

description:
ELT5411_A237
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G4_N720_S513, Adult

description:
ELT5411_A215
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F4_N719_S522, Adult

description:
ELT5411_A214
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E4_N719_S521, Adult

description:
ELT5411_A213
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D4_N719_S520, Adult

description:
ELT5411_A212
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H6_N722_S513, Adult

description:
ELT5411_A231
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B4_N719_S517, Adult

description:
ELT5411_A210
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1G3_N703_S507, Newborn

description:
ELT5411_A21
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D6_N721_S518, Adult

description:
ELT5411_A227
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C4_N719_S518, Adult

description:
ELT5411_A211
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1H3_N703_S508, Newborn

description:
ELT5411_A22
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A4_N719_S516, Adult

description:
ELT5411_A209
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F3_N718_S522, Adult

description:
ELT5411_A206
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H3_N719_S515, Adult

description:
ELT5411_A208
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D3_N718_S520, Adult

description:
ELT5411_A204
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C3_N718_S518, Adult

description:
ELT5411_A203
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B5_N720_S517, Adult

description:
ELT5411_A218
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A3_N718_S516, Adult

description:
ELT5411_A201
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G3_N719_S513, Adult

description:
ELT5411_A207
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E3_N718_S521, Adult

description:
ELT5411_A205
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H2_N718_S515, Adult

description:
ELT5411_A200
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2A5_N720_S516, Adult

description:
ELT5411_A217
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B3_N718_S517, Adult

description:
ELT5411_A202
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E2_N716_S521, Adult

description:
ELT5411_A197
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2F2_N716_S522, Adult

description:
ELT5411_A198
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G2_N718_S513, Adult

description:
ELT5411_A199
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D2_N716_S520, Adult

description:
ELT5411_A196
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1F3_N703_S506, Newborn

description:
ELT5411_A20
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B2_N716_S517, Adult

description:
ELT5411_A194
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2H1_N716_S516, Adult

description:
ELT5411_A193
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2G1_N716_S515, Adult

description:
ELT5411_A192
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2D1_N715_S522, Adult

description:
ELT5411_A190
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2E1_N716_S513, Adult

description:
ELT5411_A191
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C1_N715_S521, Adult

description:
ELT5411_A189
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2B1_N715_S520, Adult

description:
ELT5411_A188
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E3_N703_S505, Newborn

description:
ELT5411_A19
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A10_N715_S515, Child

description:
ELT5411_A185
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D10_N715_S518, Child

description:
ELT5411_A187
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D9_N715_S513, Child

description:
ELT5411_A184
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B10_N715_S516, Child

description:
ELT5411_A186
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2C9_N714_S522, Child

description:
ELT5411_A183
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A9_N714_S520, Child

description:
ELT5411_A181
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D8_N714_S518, Child

description:
ELT5411_A180
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B9_N714_S521, Child

description:
ELT5411_A182
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B8_N714_S516, Child

description:
ELT5411_A178
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2C8_N714_S517, Child

description:
ELT5411_A179
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A8_N714_S515, Child

description:
ELT5411_A177
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1D3_N703_S503, Newborn

description:
ELT5411_A18
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A7_N712_S520, Child

description:
ELT5411_A173
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B7_N712_S521, Child

description:
ELT5411_A174
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D7_N714_S513, Child

description:
ELT5411_A176
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_KK2_Plate2_A2C2_N716_S518, Adult

description:
ELT5411_A195
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D6_N712_S518, Child

description:
ELT5411_A172
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B6_N712_S516, Child

description:
ELT5411_A170
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1C3_N703_S502, Newborn

description:
ELT5411_A17
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A6_N712_S515, Child

description:
ELT5411_A169
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B5_N711_S521, Child

description:
ELT5411_A166
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2C5_N711_S522, Child

description:
ELT5411_A167
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D5_N712_S513, Child

description:
ELT5411_A168
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D4_N711_S518, Child

description:
ELT5411_A164
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A5_N711_S520, Child

description:
ELT5411_A165
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2C4_N711_S517, Child

description:
ELT5411_A163
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2B4_N711_S516, Child

description:
ELT5411_A162
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2E3_N711_S513, Child

description:
ELT5411_A160
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1B3_N702_S511, Newborn

description:
ELT5411_A16
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2D3_N710_S522, Child

description:
ELT5411_A159
genes.fpkm_table
genes.attr_table
samples.table


title: DKO_DOX_rep3

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DOX knockout vs 3 DMSO control samples (DOX knockout vs DMSO control with 3 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes
Supplementary files format and content: count

growth_protocol: RPMI-8402 cells stably expressing Cas9  were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the qiazol and miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of paired-end, 100-bp-long reads by the DNBSEQ platform were performed at the BGI Genomics.

treatment_protocol: RPMI-8402 cells stably expressing Cas9 were treated with either DMSO (Control) or Doxycline to induce expression of sgRNAs against MYC for 72 hours.   Cells were then harvested and total RNA were extracted for library preparation and RNA-Seq analysis

value: T-ALL

value: Doxycycline


title: Exp0_F3058C56_Plate2_K2C7_N712_S522, Child

description:
ELT5411_A175
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: Exp0_F3058C56_Plate2_K2C3_N710_S521, Child

description:
ELT5411_A158
genes.fpkm_table
genes.attr_table
samples.table


title: DKO_DOX_rep1


title: Exp0_F3058C56_Plate2_K2C6_N712_S517, Child

description:
ELT5411_A171
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate2_K2A4_N711_S515, Child

description:
ELT5411_A161
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk C1R


title: Exp0_F3058C56_Plate2_K2E2_N710_S517, Child

description:
ELT5411_A155
genes.fpkm_table
genes.attr_table
samples.table


title: DKO_DMSO_rep2

value: DMSO

value: control


title: Exp0_F3058C56_Plate2_K2B3_N710_S520, Child

description:
ELT5411_A157
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Child


title: DKO_DMSO_rep3


title: Exp0_F3058C56_Plate2_K2D2_N710_S516, Child

description:
ELT5411_A154
genes.fpkm_table
genes.attr_table
samples.table

value: Temra


title: RPMI_MYC_KO_DOX_rep3

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DOX knockout vs 3 DMSO control samples ( DOX knockout vs  DMSO control with 3 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes
Supplementary files format and content: count


title: RPMI_MYC_KO_DMSO_rep2


title: Exp0_F3058C56_Plate2_K2E1_N710_S513, Child

description:
ELT5411_A152
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: RPMI_MYC_KO_DMSO_rep3


title: DKO_DMSO_rep1


title: Exp0_F3058C56_Plate2_K2C2_N710_S515, Child

description:
ELT5411_A153
genes.fpkm_table
genes.attr_table
samples.table


title: RPMI_MYC_KO_DMSO_rep1


title: Exp0_F3058C56_Plate2_K2A3_N710_S518, Child

description:
ELT5411_A156
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk C1R cell line


title: Exp0_F3058C56_Plate2_K2C1_N707_S521, Child

description:
ELT5411_A150
genes.fpkm_table
genes.attr_table
samples.table


title: RPMI_MYC_KO_DOX_rep1


title: Exp0_F3058C56_Plate2_K2B1_N707_S520, Child

description:
ELT5411_A149
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1H10_N707_S518, Child

description:
ELT5411_A148
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1F10_N707_S517, Child

description:
ELT5411_A147
genes.fpkm_table
genes.attr_table
samples.table


title: DKO_DOX_rep2


title: RPMI_MYCN_KO_DMSO_rep3

data_processing:
RNA-seq datasets were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DOX overexpression vs 3 DMSO control samples (DOX overexpression vs DMSO control with 3 replicates).
Assembly: hg19
Supplementary files format and content: txt file for differentially expressed genes
Supplementary files format and content: count

treatment_protocol: RPMI-8402 cells stably expressing Cas9 were treated with either DMSO (Control) or Doxycline to induce expression of sgRNAs against MYCN for 72 hours.   Cells were then harvested and total RNA were extracted for library preparation and RNA-Seq analysis


title: Exp0_F3058C56_Plate1_K1E10_N707_S516, Child

description:
ELT5411_A146
genes.fpkm_table
genes.attr_table
samples.table


title: RPMI_MYCN_KO_DOX_rep3


title: RPMI_MYCN_KO_DMSO_rep2


title: RPMI_MYCN_KO_DOX_rep2


title: Exp0_F3058C56_Plate1_K1H9_N706_S520, Child

description:
ELT5411_A141
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1A3_N702_S510, Newborn

description:
ELT5411_A15
genes.fpkm_table
genes.attr_table
samples.table

value: Newborn


title: RPMI_MYC_KO_DOX_rep2


title: Exp0_F3058C56_Plate2_K2D1_N707_S522, Child

description:
ELT5411_A151
genes.fpkm_table
genes.attr_table
samples.table


title: RPMI_MYCN_KO_DOX_rep1


title: RPMI_MYCN_KO_DMSO_rep1


title: Exp0_CB149_Plate1_C1H2_N702_S508, Newborn

description:
ELT5411_A14
genes.fpkm_table
genes.attr_table
samples.table

value: Tnaive


title: Exp0_F3058C56_Plate1_K1A10_N706_S521, Child

description:
ELT5411_A142
genes.fpkm_table
genes.attr_table
samples.table


title: RPMI_DOX_Neg_HiChIP

data_processing:
Hi-ChIP data were aligned and processed using HiC-Pro pipeline version 2.11.1, and the reads in the fastq files were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 version 2.4.1.
The restriction sites ^GATC and G^ANTC across the human genome were cut and utilized by HiC-Pro using the HiC-Pro Utilities Python script “digest genome”.
HiC-Pro configuration on ligation site were set to be ^GATC and G^ANTC optimize for ARIMA kit data. The aligned data were further processed using hichipper to call interactions.
Hichipper version 2.7.9 was used to extract the valid interactions from the HiC-Pro data and generate the bedpe interaction file by utilizing anchors from peaks called by MACS2 broadPeak using the dangling-end and self-cycle Hi-ChIP read pairs with the following parameters: --keep-dup all -p 1e-9 --extsize 147 --nomodel -f bed.
Hichipper used to process interactions using the following parameters: -l 50 -mi 5000 -ma 2000000.
Assembly: hg19
Supplementary files format and content: *_allValidPairs txt file output from HiC-Pro
Supplementary files format and content: *.intra.loop_counts.bedpe bedpe file output from hichipper
Supplementary files format and content: *.anchors.bed anchor used by hichipper
Library strategy: Hi-ChIP

growth_protocol: Jurkat and RPMI-8402  cells stably expressing dCAS9-KRAB  were cultured in RPMI-1640 medium supplemented with 10% tetracycline-free FBS and Pen/Strep.

extract_protocol:
Library construction from the H3K27ac Hi-ChIP-seq samples and sequencing of paired-end 100-bp-long reads by the DNBSEQ platform were performed at BGI Genomics.
Paired-end Hi-ChIP

treatment_protocol: The cells were cross-linked with formaldehyde, lysed with Hi-C buffer, and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis.

tag: chip antibody

value: H3K27ac Antibody (Abcam; ab4729)


title: Exp0_F3058C56_Plate1_K1E9_N706_S516, Child

description:
ELT5411_A138
genes.fpkm_table
genes.attr_table
samples.table


title: Jurkat_DOX_Pos_HiChIP

source_name: Jurkat

value: Jurkat


title: RPMI_DOX_Pos_HiChIP


title: Exp0_F3058C56_Plate1_K1B10_N706_S522, Child

description:
ELT5411_A143
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1D9_N706_S515, Child

description:
ELT5411_A137
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C9_N706_S513, Child

description:
ELT5411_A136
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1D10_N707_S515, Child

description:
ELT5411_A145
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1G9_N706_S518, Child

description:
ELT5411_A140
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1F9_N706_S517, Child

description:
ELT5411_A139
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1H8_N705_S520, Child

description:
ELT5411_A133
genes.fpkm_table
genes.attr_table
samples.table


title: LAM MVPC Majka_43_03_2016

city: Denver

first: Susan

middle: M

last: Majka

email: majkas@njhealth.org, susanmajka@mac.com

state: co

address: 1400 Jackson St, Goodman Bldg K810a

department: Medicine

institute: NJH

hyb_protocol: Complimentary DNA generated from amplified RNA was hybridized to duplicate Affymetrix Human gene 1.0 st chips (Santa Clara, CA).

scan_protocol: Affymetrix protocol

data_processing: Differential expression analysis was carried out using Bioconductor (v3.2, R 3.2.2). Raw probe level data were read in, using packages oligo and pd.hugene.1.0.st.v1.  After normalization with RMA, moderated t-test implemented in limma package was employed for differential expression testing. A minimal fold change of 1.7X, up or down and p<0.05 were employed as criteria for defining differentially expressed genes. Expression values for these genes are represented in a heatmap; generated using the pheatmap function in R.

source_name: VU LAM 01

label_protocol: Affymetrix protocol

growth_protocol: MVPC isolation and culture protocol published by Majka lab; Adult samples from VUMC and fetal from Dr. Gomperts; Human lung plastic adherent cells were isolated from ex-plant lung tissue post autopsy or transplant by collagenase digest (Vanderbilt IRB Protocol 9401) to form a suspen-sion. The cells were stained with antibodies to sort CD45neg ABCG2pos cells (lung mesenchymal progenitors) using a BD FACSAria III (BD Biosciences, San Jose, California). Techniques were previously described and ABCG2 was validated as a cell surface marker for both murine eGFP labeled and human MVPC.Antibodies for flow  cytometry were purchased form eBiosciences, (San Diego, CA) or Thermo Fisher (Waltham, MA). Human MVPC were isolated from explanted lung tissue via ABCG2 enrichment and characterized as previously described, expressing mesen-chymal cell surface determinants, lacking hematopoietic, and endothelial determinants as well as forming colonies (CFU-F) . Global gene expression profiling with hi-erarchical clustering and GO analysis was performed.

extract_protocol: total RNA was prepared with Qiagen RNA Isolation Kit reagents (Qiagen, Valencia, CA) for total RNA isolation and analysis of gene expression.

treatment_protocol: Microarray analysis of primary human lung MVPC was performed in triplicate or with an n of three or greater independent patient samples.

tag: gender

value: F

value: Primary MVPC


title: LAM MVPC Majka_44_03_2016


title: Exp0_F3058C56_Plate1_K1F8_N705_S517, Child

description:
ELT5411_A131
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1E8_N705_S516, Child

description:
ELT5411_A130
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C10_N707_S513, Child

description:
ELT5411_A144
genes.fpkm_table
genes.attr_table
samples.table


title: Jurkat_DOX_Neg_HiChIP

value: T-ALL

tag: treatment


title: fetal MVPC Majka_6_03_2016

value: 17-22 weeks gestation

value: M


title: Exp0_F3058C56_Plate1_K1G8_N705_S518, Child

description:
ELT5411_A132
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: Exp0_F3058C56_Plate1_K1B9_N705_S522, Child

description:
ELT5411_A135
genes.fpkm_table
genes.attr_table
samples.table

value: Tscm


title: LIGHTCART_T48_RNA

first: Jahan

last: Rahman

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

data_processing:
RNA FASTQ reads were processed using Cellranger v7.0.0 count workflow to generate gene expression count matrices. Cite-seq-Count v1.3.4 was used to generate ADT and HTO count matrices.
Resultant sparse count matrices were loaded into R v4.0.0 as Seurat v4.0.6 objects for downstream filtering and analyses.
The RNA data was normalized using SCTransform and integrated across conditions using Seurat. The ADT data was normalized using centered log-ratio transformation across cells. Dimensional reduction, identification of multimodal neighbors, UMAP visualization based on a weighted combination of RNA and ADT data, and graph-based clustering were performed using Seurat’s weighted nearest neighbor workflow. The clusters were annotated based on conserved gene and surface protein markers identified across conditions using the FindConservedMarkers function as well as previously known markers.
Differential gene and surface protein expression analyses between subsets of interest were performed using Seurat’s FindMarkers function which utilizes Wilcoxon rank-sum test.
Gene set enrichment analysis against gene ontology (GO) terms was performed using the fgsea package.
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Raw count matrices:  RNA_counts.csv.gz, ADT_counts.csv.gz
Supplementary files format and content: Cell ID human sample assignments:  cell_sample_assign.csv.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Peripheral blood

extract_protocol:
Cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability. Following QC, the single cell suspension was loaded onto Chromium Next GEM Chip K (10X Genomics PN 1000286) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 10,000 cells proceeded using the Chromium Next GEM Single Cell 5’ Kit v2 (10X Genomics PN 1000263) according to the manufacturer’s protocol. cDNA amplification included 13 cycles and 50 ng of the material was used to prepare sequencing libraries with 14 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S4 Reagent Kit (200 cycles) (Illumina). An average of 22,500 reads was generated per cell.
Amplification products generated using the methods described above included both cDNA and feature barcodes tagged with cell barcodes and unique molecular identifiers. Smaller feature barcode fragments were separated from longer amplified cDNA using a 0.6X cleanup using aMPure XP beads (Beckman Coulter catalog # A63882). Libraries were constructed using the 5’ Feature Barcode Kit (10X Genomics PN 1000256) according to the manufacturer’s protocol with 8 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/88 run using the NovaSeq 6000 S4 Reagent Kit (200 cycles) (Illumina). An average of 82 million paired reads was generated per sample.

value: Peripheral blood

tag: library type

value: mRNA

tag: multiplexed

value: Y

tag: antibodies/tags


title: CART_T48_ADT_HTO

library_source: other

molecule: protein

value: ADT/HTO

value: Total-Seq C ADT Cocktail   and Total-Seq C hashing oligos


title: Exp0_F3058C56_Plate1_K1A8_N704_S521, Child

description:
ELT5411_A126
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells

value: Child


title: LAM MVPC Majka_42_03_2016


title: fetal MVPC Majka_7_03_2016


title: LIGHTCART_T48_ADT_HTO


title: Exp0_F3058C56_Plate1_K1A9_N705_S521, Child

description:
ELT5411_A134
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Tnaive


title: Exp0_F3058C56_Plate1_K1C8_N705_S513, Child

description:
ELT5411_A128
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1B8_N704_S522, Child

description:
ELT5411_A127
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: LIGHTCART_T0_ADT_HTO


title: Exp0_CB149_Plate1_C1G2_N702_S507, Newborn

description:
ELT5411_A13
genes.fpkm_table
genes.attr_table
samples.table

value: Newborn


title: Exp0_F3058C56_Plate1_K1D8_N705_S515, Child

description:
ELT5411_A129
genes.fpkm_table
genes.attr_table
samples.table


title: fetal MVPC Majka_8_03_2016

value: Primary MVPC


title: Control MVPC Majka_49_03_2016

source_name: VU HD07


title: CART_T0_ADT_HTO


title: CART_T48_RNA


title: Control MVPC Majka_50_03_2016


title: CART_T0_RNA


title: Exp0_F3058C56_Plate1_K1E7_N704_S517, Child

description:
ELT5411_A123
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1G7_N704_S520, Child

description:
ELT5411_A125
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1D7_N704_S516, Child

description:
ELT5411_A122
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1F7_N704_S518, Child

description:
ELT5411_A124
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C7_N704_S515, Child

description:
ELT5411_A121
genes.fpkm_table
genes.attr_table
samples.table


title: LIGHTCART_T0_RNA


title: LIS49 hPSCs maintained in primed conditions scATAC-seq

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

institute: Weizmann Institute of Science

library_source: genomic single cell

data_processing:
Sequencing output were demultiplexed using Cell-Ranger-arc V2.0 (10X Genomics) mkfastq command, and counts were estimated with Cell-Ranger count software.
Data were pre-processed and filtered with Seurat 4.0 R package. Cells with very high (>10000) or very low (<1000) number of overlapping peaks were filtered out, as well as cells with high (>3) nucleosome signal score, or low TSS enrichment score (<2).
ATAC data was normalized by term frequency inverse document frequency (TF-IDF) and partial singular value decomposition (SVD) was performed using RunSVD by Signac.
Batch effect correction was performed using RunHarmony by harmony package (https://portals.broadinstitute.org/harmony/index.html), while the cell line type was excluded from the correction and reduction was based on latent semantic indexing (LSI) produce by SVD. UMAP was performed on the harmony corrected 2:50 dimensions.
Construction of the weighted nearest neighbor was perform using FindMultiModalNeighbors by Seurat based on RNA PC1:30 and ATAC harmony 2:50.
Assembly: hg38

growth_protocol: HENSM and Primed scRNA-seq was processed alongside scATAC-seq measured from the same cells (multimodal strategy), in a protocol described below:  LIS49 and WIBR3 hESCs were cultured for 3 passages in HENSM and primed conditions on Matrigel coated plates.

extract_protocol:
Cell nuclei were isolated using the multiomics protocol provided by 10X genomics (cat CG000365), aiming for ~6000 nuclei.
10X Genomic library preparation was performed via the protocol provided by 10X genomics (cat CG000338) and sequenced by 2 units of NovaSeq SP sequencing system (100 cycles).

tag: cell line

value: Human embryonic stem cells

value: Primed (TeSR)


title: Exp0_F3058C56_Plate1_K1B7_N704_S513, Child

description:
ELT5411_A120
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1G6_N703_S521, Child

description:
ELT5411_A118
genes.fpkm_table
genes.attr_table
samples.table


title: WIBR3 hPSCs maintained in primed conditions scATAC-seq


title: Control MVPC Majka_51_03_2016

value: F


title: WIBR3 hPSCs maintained in naïve conditions scATAC-seq

value: Human Enhanced Naïve Stem Cell Medium (HENSM)


title: Exp0_CB149_Plate1_C1F2_N702_S506, Newborn

description:
ELT5411_A12
genes.fpkm_table
genes.attr_table
samples.table

value: PBMCs


title: Exp0_F3058C56_Plate1_K1F6_N703_S520, Child

description:
ELT5411_A117
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1E6_N703_S518, Child

description:
ELT5411_A116
genes.fpkm_table
genes.attr_table
samples.table


title: LIS49 hPSCs maintained in naïve conditions scATAC-seq


title: Patient 2 DAPT Repeat 2

first: Jay

last: Thiagarajah

address: 300 Longwood Avenue, EN620

department: Gastroenterology

institute: Boston Children's Hospital

data_processing:
preprocessed using FASTP
Filtered reads mapped to  GRCh41 genome assembly using HISAT2 (All alignment greater than 90%)
Transcripts were quantified using Salmon
Assembly: GRCh41
Supplementary files format and content: tab-delimited file including TPM values for each sample

source_name: Duodenal

growth_protocol: Cultured as 50 μl domes in 24-well plates with growth factor (Wnt, R-spondin, Noggin) supplemented media

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen).

value: Duodenal

value: Enteroid

tag: genotype

value: Patient with Myo5B mutation

value: MVID

tag: individual

value: Patient 2

value: DAPT


title: Patient 2 DAPT Repeat 3


title: Patient 2 DAPT Repeat 1


title: Patient 1 DAPT Repeat 3

value: Patient 1


title: Patient 2 Untreated Repeat 3

value: Untreated


title: Patient 1 DAPT Repeat 1


title: Exp0_F3058C56_Plate1_K1D6_N703_S517, Child

description:
ELT5411_A115
genes.fpkm_table
genes.attr_table
samples.table

value: CD8+ T cell

value: Child


title: Patient 1 Untreated Repeat 2


title: Patient 1 DAPT Repeat 2


title: Exp0_F3058C56_Plate1_K1H5_N702_S522, Child

description:
ELT5411_A111
genes.fpkm_table
genes.attr_table
samples.table

value: Tcm


title: Patient 1 Untreated Repeat 3


title: Exp0_F3058C56_Plate1_K1G5_N702_S521, Child

description:
ELT5411_A110
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1C6_N703_S516, Child

description:
ELT5411_A114
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1B6_N703_S515, Child

description:
ELT5411_A113
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1A7_N703_S522, Child

description:
ELT5411_A119
genes.fpkm_table
genes.attr_table
samples.table

value: Bulk Naive CD8+ T cells


title: Patient 1 Untreated Repeat 1


title: Patient 2 Untreated Repeat 1


title: Exp0_F3058C56_Plate1_K1A6_N703_S513, Child

description:
ELT5411_A112
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_F3058C56_Plate1_K1F5_N702_S520, Child

description:
ELT5411_A109
genes.fpkm_table
genes.attr_table
samples.table


title: Exp0_CB149_Plate1_C1E2_N702_S505, Newborn

description:
ELT5411_A11
genes.fpkm_table
genes.attr_table
samples.table

value: Newborn

value: Tnaive


title: Exp0_F3058C56_Plate1_K1E5_N702_S518, Child

description:
ELT5411_A108
genes.fpkm_table
genes.attr_table
samples.table