title: Endothelial cells, chronic pancreatitis tissue_3

city: Tokyo

first: Nobuyoshi

last: Hiraoka

address: 5-1-1 Tsukiji, Chuo-ku

department: Pathology Division

country: Japan

institute: National Cancer Center Research Institute

description: Gene expression

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: The slide was scanned with an Agilent Technologies Scanner G2505C.

data_processing: Agilent Feature Extraction Software (v10.7.3.1) was used for background subtraction.

source_name: Endothelial cells, isolated from chronic pancreatitis tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from the RNA using the Low Input Quick Amp LabellingKit One colour (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer's instructions. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from TECs using an RNeasy-Mini kit (QIAGEN, Valencia, CA) and quantified using a NanoDrop 8000 instrument (Thermo Fisher Scientific, Waltham, MA). The RNA integrity number (RIN) was evaluated by a 2100 Bioanalyzer (Agilent, Santa Clara, CA).

value: chronic pancreatitis tissue

value: Endothelial cells

tag: gender

value: male

tag: age


title: M1_TCR_day10_LCMV_armstrong

status: Public on Nov 10 2020

type: SRA

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

description: Day 10 LCMV armstrong

library_source: transcriptomic

data_processing:
Reads were aligned to mouse reference genome mm10
Single cell TCR data were filtered to select the best TCR alpha and beta chain at the clonal level, based on full length, productive CDR3 regions and expression level
Genome_build: mm10
Supplementary_files_format_and_content: Matrix files were generated using Cell Ranger (10x Genomics).

molecule: total RNA

organism: Mus musculus

extract_protocol:
Chromium single cell 5' kit V2 from 10x genomics
Chromium single cell 5' kit V2 from 10x genomics for single cell gene expression (GEX) and single cell TCR library

treatment_protocol: Activated antigen specific CD4 T cells (CD4+CD44+GP66+) were sorted from five C57BL/6J mice at day 10 post acute LCMV armstrong infection and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 and v3 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the NextSeq 500/550 High Output Kit v2 (150 cycles)

tag: strain

value: C57BL/6 mice

tag: infection

value: LCMV armstrong

tag: tissue

value: spleen


title: Endothelial cells, chronic pancreatitis tissue_2

type: RNA

description: Gene expression

organism: Homo sapiens

tag: cell type

value: female


title: Endothelial cells, chronic pancreatitis tissue_1

description: Gene expression


title: DI1

city: Bodø

first: Jorge

last: Fernandes

address: Universitetsalleen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
Raw data was demultiplexed with bcl2fastq (v2.20.0.422)
Raw fastq files were trimmed adapters using cutadapt (v1.12) and filtered low-quality reads using FASTX-Toolkit (0.0.14); Quality control of raw and clean reads were performed using FastQC (v0.11.5).
Clean reads were mapped to Atlantic salmon genome assembly ICSASG_v2 (GCF_000233375.1) using STAR with version 020201
Read counts were extracted from alignment file "ReadsPerGene.out.tab", and all samples were merged into one matrix
Differential gene expression analysis was performed using DESeq2 (v1.20.0), and plot visualization was achieved using R packages ggplot2 (v3.2.1) and pheatmap (v1.0.12).
Genome_build: ICSASG_v2
Supplementary_files_format_and_content: Tab-delimited matrix containing read counts of each individual samples

organism: Salmo salar

source_name: distal intestine

growth_protocol: Atlantic salmon post smolts of about 70 g were purchased from a commercial producer (Sundsfjord Smolt, Nygårdsjøen, Norway) and maintained at the Research Station of Nord University, Bodø, Norway. Fish were fed a commercial feed (Ewos Micro, Ewos AS, Bergen, Norway) to satiation, and reared in a flow-through sea water system (temperature: 7-8°C, dissolved oxygen saturation: 87-92 %, 24-h light cycle). The fish (average 550g) were starved for 24 h and were killed with an overdose of MS-222. Head kidney (HK) and distal intestine (DI) samples were then collected. Immune cells from head kidney and distal intestine were isolated and grown at 12°C in Leibovitz’s L-15 Medium. The osmolality of cell culture media was adjusted to 380 mOsm by adding a solution consisting of 5% (v/v) 0.41 M NaCl, 0.33 M NaHCO3 and 0.66 (w/v) D-glucose.

extract_protocol:
Total RNA was extracted from adherent cells from HK or DI (< 500,000 cells) using the PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The quality and quantity of total RNA were assessed using Agilent RNA high sensitivity screen tape kits and Bioanalyzer 2200 TapeStation system (Agilent Technologies, Santa Clara, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA library preparation kit with poly (A) mRNA magnetic isolation module (NEB #E7490; New England BioLabs®, Herts, UK), according to the manufacturer’s protocol. For the first and second strand cDNA synthesis, 50 ng of total RNA having high RNA integrity number (RIN > 8) was enriched with Oligo(dT)-conjugated magnetic beads and fragmented to ~200 nt. Thereafter, the resulting cDNA were end-repaired for adaptor ligation. The ligated cDNAs were amplified on a thermal cycler for 14 cycles. The PCR products were purified using AMPure XP beads (Beckman Coulter Inc., Brea, CA, United States) to avoid contamination from residual adapter dimers and unwanted (smaller) fragments. After library preparation, the quality and quantity of individual libraries were assessed using Agilent DNA high sensitivity screen tape kits and Bioanalyzer 2200 TapeStation system.

treatment_protocol: The fish were starved for 24 h and were sacrificed with an overdose of MS-222 (80 mg/L). Head kidney and distal intestine samples were then collected. Immune cells from DI and HK were extracted and grown at 12°C in Leibovitz’s L-15 Medium (L-15). The isolated DI or HK leukocytes were allowed to adhere on a petri dish with 2 mL L-15+ for 2 days at 12°C. After removing the supernatant containing non-adherent cells, the cells adherent on petri dish were detached by washing three times with 1.5 mL ice-cold PBS supplemented with 5 mM EDTA. The cells were centrifuged (500 × g, 5 min, 4°C) and re-suspended with 2 mL L-15+.

value: adherent cells from distal intestine


title: Endothelial cells, pancreatic cancer tissue_3

description: Gene expression

source_name: Endothelial cells, isolated from pancreatic cancer tissue

value: pancreatic cancer tissue


title: Endothelial cells, pancreatic cancer tissue_2

description: Gene expression


title: Offspring from UCP1-KO dam (11)

status: Public on Nov 09 2020

city: Lübeck

first: Rebecca

last: Oelkrug

address: Ratzeburger Allee 160

country: Germany

institute: University of Lübeck

description: Liver gene expression data of offspring from WT and UCP1-KO dams.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Clariom S Mouse Array was used and CEL data was imported into Transcriptome Analysis Console (TAC) 4.0 (Thermo Fisher, Germany) and pre-processed for further analysis in R. Array data was normalized by Robust Multi-chip Analysis (RMA) algorithm with signal space transformation (SST) as indicated by the manufacturer, which contains background adjustment and reduction, quantile normalization and therefore an increase of fold change

label: Biotin

source_name: Liver samples of adult male offspring from UCP1-KO dams.

label_protocol: Affymetrix standard protocol

growth_protocol: Breeding strategy: UCP1-KO and WT female dams were mated with heterozygous (HET) sires at an ambient temperature of 23°C (± 1°C), to obtain heterozygous (HET) offspring from both groups.

extract_protocol: RNA isolation was performed following the manufacturer’s instructions using RNeasy Mini Kit (QIAGEN, Germany).

treatment_protocol: Offspring were kept at 23°C and had free access to a standard chow diet (Altromin, breeding diet, 1314, Germany) and water.

value: 4-5 months

value: liver

tag: genotype offspring

value: HET

tag: genotype dam


title: Offspring from UCP1-KO dam (09)


title: Offspring from UCP1-KO dam (10)


title: Endothelial cells, pancreatic cancer tissue_1

description: Gene expression


title: Offspring from WT dam  (06)

source_name: Liver samples of adult male offspring from WT dams.

value: WT


title: Offspring from UCP1-KO dam (12)


title: Offspring from WT dam (05)


title: Offspring from UCP1-KO dam (08)


title: Offspring from WT dam (03)


title: Offspring 23°C dam (23_15)

description: Liver gene expression data of offspring from dams that were kept at different ambient temperatures only during pregnancy.

source_name: Liver samples of adult male offspring from dams kept at 23°C during pregnancy.

growth_protocol: Breeding strategy: WT dams (C57BL/6NCr)  were acclimated to different ambient temperatures (30°C for 3 weeks, 18°C and 10°C for 2 weeks) prior to the onset of breeding, while sires were exposed to the corresponding ambient temperature only for 3 days. Offspring from breeding pairs kept at 23°C (standard animal house temperature) served as control group.  Importantly, at the day of delivery all dams and their offspring were transferred to 23°C to constrain the influence of ambient temperature to the period of pregnancy. Liver samples obtained from adult male offspring were used for microarray analysis.

tag: gestational temperature

value: 23 degree C


title: Offspring 23°C dam (23_1)


title: Offspring 23°C dam (23_23)


title: Offspring from UCP1-KO dam (07)


title: Offspring 30°C dam (30_7)

source_name: Liver samples of adult male offspring from dams kept at 30°C during pregnancy.

value: 30 degree C


title: Offspring from WT dam (02)


title: Offspring 30°C dam (30_8)


title: Offspring 30°C dam (30_4)


title: Offspring from WT dam (04)


title: Offspring 18°C dam (18_7)

source_name: Liver samples of adult male offspring from dams kept at 18°C during pregnancy.

value: 18 degree C


title: Offspring 23°C dam (23_2)


title: Offspring 30°C dam (30_5)


title: Offspring 18°C dam (18_1)


title: Offspring from WT dam (01)


title: Offspring 23°C dam (23_17)


title: Offspring 30°C dam (30_6)


title: Offspring 18°C dam (18_5)


title: Offspring 10°C dam (10_8)

source_name: Liver samples of adult male offspring from dams kept at 10°C during pregnancy.

value: 10 degree C


title: Offspring 18°C dam (18_3)


title: Offspring 18°C dam (18_4)


title: Offspring 10°C dam (10_6)


title: WT_d14_CD45-CD31+_IL35_ rep3

city: Philadelphia

first: Xiaofeng

last: Yang

state: PA

address: 3500 North Broad Street

department: Cardiovascular Research Center

institute: Temple University

data_processing:
Sequence reads were aligned to mouse mm10 genome using Tophat2, then Cufflinks algorithm was implemented to assemble transcripts and estimate their abundance. Cuffdiff was implemented to statistically assess expression changes in quantified genes in different conditions.
Genome_build: UCSC mm10

source_name: CD45-CD31+ cells from hindlimb muscle

extract_protocol:
Hindlimb skeletal muscle was dissociated into single-cell suspension, then cells were stained with surface antibody anti-CD45 (BioLegend, #103116) and anti-CD31 (BioLegend, #102427) for 30 minutes at room temperature. All cell-sorting experiments were performed using an Aria Cell Sorter (BD Biosciences). The CD45-CD31+ cells were sorted directly into TRIzol, and RNA was extracted using miRNeasy Mini kit (Qiagen).
Total RNA libraries were prepared by using Pico Input SMARTer Stranded Total RNA-Seq Kit (Takara). In short, 250 pg-10 ng total RNA from each sample was reverse-transcribed via random priming and reverse transcriptase. Full-length cDNA was obtained with SMART (Switching Mechanism At 5' end of RNA Template) technology. The template-switching reaction keeps the strand orientation of the RNA. The ribosomal cDNA is hybridized to mammalian-specific R-Probes and then cleaved by ZapR. Libraries containing Illumina adapter with TruSeq HT indexes were subsequently pooled and loaded to the HiSeq 2500.

treatment_protocol: Recombinant mouse IL-35 was administered intramuscularly (i.m.) (0.3 µg/gastrocnemius (GC) muscle in 20 µl PBS) at the time of HLI procedure, and three times a week afterwards until the end of observation. The non-surgery limb and PBS control group limb were injected with 20 µl PBS as the internal and experimental control, respectively.

value: Hindlimb skeletal muscle

tag: treatment

value: i.m. injection of IL35

tag: age + days after ischemia

value: 10-12 weeks + 14 days

tag: Sex

value: Male


title: Offspring 10°C dam (10_5)

value: male


title: WT_d14_CD45-CD31+_PBS_ rep3

value: i.m. injection of PBS


title: WT_d14_CD45-CD31+_PBS_ rep2


title: WT_d14_CD45-CD31+_IL35_ rep2


title: WT_d14_CD45-CD31+_PBS_ rep1


title: Offspring 10°C dam (10_4)


title: Offspring 10°C dam (10_2)


title: WT_d0_CD45-CD31+_rep1

value: 10-12 weeks + 0 days


title: WT_d0_CD45-CD31+_rep2


title: NH568

city: Paris

first: Audrey

last: Desgrange

address: 24 boulevard du Montparnasse

country: France

institute: Imagine - Institut Pasteur

data_processing:
Base Calling: Illumina base calling software
Alignement: Hisat2
Abundance mesurement: FeatureCount (R Subread package)
Normalisations / statistical analysis: Deseq2, edgeR, Limma (R packages).
Genome_build: Mouse GRCm38
Supplementary_files_format_and_content: normalised abundance measurements

source_name: microdissected cardiac region

extract_protocol:
RNA was extracted in TRIzol-Chloroform and purified using the RNeasy micro kit. RNA quality and quantity were assessed using RNA Screen Tape 6000 Pico LabChips with the Tape Station (Agilent Technologies). All RINs were higher than 9.0
The library was established using the Nugen Universal Plus mRNA-Seq kit, using 20 ng of total RNAs as recommended by the manufacturer. The oriented cDNAs produced from the poly-A+ fraction were PCR amplified (15-18 cycles). An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina HiSeq2500, with paired-end reads of 130 bases and a mean sequencing depth of 58 millions per sample

treatment_protocol: Embryos were microdissected and the tissue was flash frozen in liquid nitrogen

value: microdissected cardiac region

tag: developmental stage

value: E8.5 embryo

value: mixed genetic background

tag: genotype

value: Hoxb1 Cre/+ ; Nodal flox/nul

value: female


title: NH603


title: NH564


title: WT mouse 3

city: MADRID

first: JUAN

last: DE LA PARRA

address: AV. COMPLUTENSE

country: Spain

institute: COMPLUTENSE UNIVERSITY

description: Gene expression in hippocampus

hyb_protocol: RNA was hybridized to GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions (Affymetrix, Santa Clara, CA) in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Genechip Expression Console Software

label: biotin

source_name: WT mouse 3

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit (Affymetrix, High Wycombe, UK).

extract_protocol: Hippocampi were dissected from hemibrains. Total RNA was extracted using Trizol® reagent (Invitrogen, USA)

value: hippocampus

value: wildtype


title: NH597

value: Hoxb1 +/+ ; Nodal flox/+


title: KO mouse 3

description: Gene expression in hippocampus

source_name: KO mouse 3

value: Ahr-KO


title: NH599


title: WT mouse 1

description: Gene expression in hippocampus

source_name: WT mouse 1


title: WT mouse 2

description: Gene expression in hippocampus

source_name: WT mouse 2


title: NH561


title: NH555


title: KO mouse 2

description: Gene expression in hippocampus

source_name: KO mouse 2


title: WT_d14_CD45-CD31+_IL35_ rep1


title: RNA-seq circulating activated memory B cells DSA+ ABMR+ #2

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCh38 89 version of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools 1.9
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCh38 89 version as GTF file and using unstranded strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 3.5.1 including CPM values for each sample
Genome_build: HISAT2 GRCh38 DNA primary assembly fasta version 89
Supplementary_files_format_and_content: Raw Counts text files in tab-delimited format of each sample combining R1 and R2 generated by Htseq, each file containing a matrix count of all samples of specific cell type

source_name: Activated memory B cells

extract_protocol:
Total RNA was extracted from cTFH and ABCs were FACS-sorted directly into lysis buffer (Trizol). RNA was isolated using miRNeasy Mini Kit (Qiagen).
cDNA synthesis and amplification were performed with a SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara). Libraries were sequenced on an Illumina NextSeq 500 using 75-bp paired-end reads.

value: Activated memory B cells

tag: patients

value: adult kidney transplant recipients


title: RNA-seq circulating activated memory B cells DSA+ ABMR+ #1


title: RNA-seq circulating activated memory B cells DSA+ ABMR- #3


title: dH1f_sgAF10_Rep1

city: Istanbul

first: Kenan

last: Sevinç

address: Rumelifeneri Yolu, Sariyer

department: School of Medicine

country: Turkey

institute: Koç University

data_processing:
Quality check of reads for all samples was carried out using FastQC version 0.11.5.
Reads were mapped to hg19 using HISAT2 version 2.1.0.
Raw read counts were generated using feautureCounts version 1.6.0.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimeted text files with raw counts for all samples.

source_name: Fibroblast cells

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.
RNA libraries were prepared for sequencing using standard NEB protocols.

tag: transduced with

value: OSKM

tag: donor


title: dH1f_sgControl_Rep3


title: dH1f_sgControl_Rep2


title: dH1f_sgControl_Rep1


title: dH1f_sgAF10_Rep2


title: dH1f_sgAF10_Rep3


title: RNA-seq circulating activated memory B cells DSA+ ABMR- #2


title: RNA-seq circulating T follicular helper cells DSA+ ABMR+ #2

source_name: circulating T follicular helper cells

value: circulating T follicular helper cells


title: RNA-seq circulating activated memory B cells DSA- #1


title: RNA-seq circulating T follicular helper cells DSA- #2


title: RNA-seq circulating T follicular helper cells DSA- #1


title: RNA-seq circulating activated memory B cells DSA+ ABMR- #1


title: RNA-seq circulating T follicular helper cells DSA- #3


title: RNA-seq circulating activated memory B cells DSA- #3


title: RNA-seq circulating T follicular helper cells DSA+ ABMR+ #1


title: RNA-seq circulating T follicular helper cells DSA+ ABMR- #1


title: RNA-seq circulating activated memory B cells DSA- #2


title: RNA-seq circulating T follicular helper cells DSA+ ABMR- #3


title: RNA-seq circulating T follicular helper cells DSA+ ABMR- #2


title: Mammary epithelial cell, L72_H12

city: San Antonio

first: Meena

last: Kusi

state: TX

address: 7703 Floyd Curl Dr

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

library_source: genomic

data_processing:
scATAC-seq libraries were sequenced on a NextSeq 500 platform with High Output reagents (Illumina) using paired-end 75-bp reads. Adapter and primer sequences were trimmed and initial quality control checks were performed using FastQC tools. Sequencing reads were aligned to the GRCh37/hg19 assembly of the human genome using Bowtie2 with the parameter ‘-X2000’ to ensure paired reads were within 2 kb of one another. PCR duplicates were eliminated using Picard tools and alignments with mapping quality less than 30 were subsequently removed by samtools. Reads mapped to the mitochondria and unmapped contigs were filtered out and excluded from further analysis.
Peak calling was performed using MACS2 with the following settings: --nomodel --nolambda --keep-dup all --call-summits. Artifact signals were excluded using ENCODE blacklist.
Genome_build: hg19
Bed files represent MACS2 peaks as described above.

molecule: genomic DNA

source_name: Human mammary epithelial cells (HMECs)

extract_protocol:
Single-cell ATAC-seq libraries were prepared on a Fluidigm C1 instrument using ‘ATAC Seq- Cell Load and Stain Rev C’ script. Cells were passed through a 20 μm cell strainer (CellTrics, Sysmex Partac) to remove debris and cell aggregates, and mixed at a ratio of 7:3 with C1 suspension reagent. The resulting single-cell suspension was loaded on C1 Single-Cell Open App IFC chip (1862x, 10-17 μm, Fluidigm) at a concentration of 350 cells/μL. Captured cells were stained with 2 μM green-fluorescent calcein-AM and 4 μM red-fluorescent ethidium homodimer-1 (Molecular Probes) and visualized under an EVOS FL cell imaging station (Life Technologies) to ensure successful capture and to determine cell viability. After cell lysis and Tn5 transposition, 8 cycles of pre-amplification were run on IFC chip.
Pre-amplified PCR products were transferred to 96-well plates and further amplified for an additional 13 cycles using custom Nextera dual-index primers and NEBNext High-Fidelity 2X PCR master mix (New England Biolabs). Individually barcoded libraries were pooled and purified on a single MinElute column (Qiagen). The quality and size distribution of pooled libraries were evaluated on an Agilent 2100 Bioanalyzer using High Sensitivity DNA reagents (Agilent).
Single-cell assay for transposase accessible chromatin followed by sequencing (scATAC-seq)

value: Primary mammary epithelial cells

tag: passages


title: RNA-seq circulating T follicular helper cells DSA+ ABMR+ #3


title: Mammary epithelial cell, L72_H11


title: Mammary epithelial cell, L72_H10


title: Mammary epithelial cell, L72_H08


title: Mammary epithelial cell, L72_H09


title: RNA-seq circulating activated memory B cells DSA+ ABMR+ #3


title: Mammary epithelial cell, L72_H07


title: Mammary epithelial cell, L72_H06


title: Mammary epithelial cell, L72_H02


title: Mammary epithelial cell, L72_H03


title: Mammary epithelial cell, L72_H05


title: Mammary epithelial cell, L72_H04


title: Mammary epithelial cell, L72_H01


title: Mammary epithelial cell, L72_G10


title: Mammary epithelial cell, L72_G06


title: Mammary epithelial cell, L72_G05


title: Mammary epithelial cell, L72_G03


title: Mammary epithelial cell, L72_G07


title: Mammary epithelial cell, L72_G04


title: Mammary epithelial cell, L72_G08


title: Mammary epithelial cell, L72_F10


title: Mammary epithelial cell, L72_F11


title: Mammary epithelial cell, L72_G01


title: Mammary epithelial cell, L72_G02


title: Mammary epithelial cell, L72_F07


title: Mammary epithelial cell, L72_F09


title: Mammary epithelial cell, L72_G09


title: Mammary epithelial cell, L72_F08


title: Mammary epithelial cell, L72_G12


title: Mammary epithelial cell, L72_G11


title: Mammary epithelial cell, L72_F04


title: Mammary epithelial cell, L72_F05


title: Mammary epithelial cell, L72_F03


title: Mammary epithelial cell, L72_F06


title: Mammary epithelial cell, L72_F02


title: Mammary epithelial cell, L72_F01


title: Mammary epithelial cell, L72_E11


title: Mammary epithelial cell, L72_E08


title: Mammary epithelial cell, L72_E12


title: Mammary epithelial cell, L72_F12


title: Mammary epithelial cell, L72_E05


title: Mammary epithelial cell, L72_E06


title: Mammary epithelial cell, L72_E04


title: Mammary epithelial cell, L72_D11


title: Mammary epithelial cell, L72_E03


title: Mammary epithelial cell, L72_E01


title: Mammary epithelial cell, L72_D12


title: Mammary epithelial cell, L72_E02


title: Mammary epithelial cell, L72_D09


title: Mammary epithelial cell, L72_D03


title: KO mouse 1

description: Gene expression in hippocampus

source_name: KO mouse 1


title: Mammary epithelial cell, L72_E10


title: Mammary epithelial cell, L72_D05


title: Mammary epithelial cell, L72_D04


title: Mammary epithelial cell, L72_D01


title: Mammary epithelial cell, L72_D07


title: Mammary epithelial cell, L72_D06


title: Mammary epithelial cell, L72_C09


title: Mammary epithelial cell, L72_C11


title: Mammary epithelial cell, L72_C12


title: Mammary epithelial cell, L72_C06


title: Mammary epithelial cell, L72_E09


title: Mammary epithelial cell, L72_C08


title: Mammary epithelial cell, L72_E07


title: Mammary epithelial cell, L72_D02


title: Mammary epithelial cell, L72_C05


title: Mammary epithelial cell, L72_C07


title: Mammary epithelial cell, L72_C10


title: Mammary epithelial cell, L72_D10


title: Mammary epithelial cell, L72_D08


title: Mammary epithelial cell, L72_C03


title: Mammary epithelial cell, L72_C04


title: Mammary epithelial cell, L72_C02


title: Mammary epithelial cell, L72_B10


title: Mammary epithelial cell, L72_C01


title: Mammary epithelial cell, L72_B11


title: Mammary epithelial cell, L72_B12


title: Mammary epithelial cell, L72_B08


title: Mammary epithelial cell, L72_B09


title: Mammary epithelial cell, L72_B07


title: Mammary epithelial cell, L72_A12


title: Mammary epithelial cell, L72_B06


title: Mammary epithelial cell, L72_B01


title: Mammary epithelial cell, L72_B05


title: Mammary epithelial cell, L72_A11


title: Mammary epithelial cell, L72_B02


title: Mammary epithelial cell, L72_B03


title: Mammary epithelial cell, L72_A10


title: Mammary epithelial cell, L72_A05


title: Mammary epithelial cell, L72_A08


title: Mammary epithelial cell, L72_A04


title: Mammary epithelial cell, L72_A09


title: Mammary epithelial cell, L72_A06


title: Mammary epithelial cell, L72_A03


title: Mammary epithelial cell, L72_A07


title: Mammary epithelial cell, L72_A02


title: Mammary epithelial cell, D72_H11


title: Mammary epithelial cell, D72_H10


title: Mammary epithelial cell, D72_H08


title: Mammary epithelial cell, D72_H09


title: Mammary epithelial cell, D72_H12


title: Mammary epithelial cell, L72_B04


title: Mammary epithelial cell, D72_H03


title: Mammary epithelial cell, D72_H05


title: Mammary epithelial cell, D72_H06


title: Mammary epithelial cell, D72_H02


title: Mammary epithelial cell, D72_H01


title: Mammary epithelial cell, D72_H04


title: Mammary epithelial cell, D72_G11


title: Mammary epithelial cell, D72_G12


title: Mammary epithelial cell, D72_G10


title: Mammary epithelial cell, D72_G06


title: Mammary epithelial cell, L72_A01


title: Mammary epithelial cell, D72_G08


title: Mammary epithelial cell, D72_G07


title: Mammary epithelial cell, D72_G05


title: Mammary epithelial cell, D72_G09


title: Mammary epithelial cell, D72_F12


title: Mammary epithelial cell, D72_G04


title: Mammary epithelial cell, D72_F10


title: Mammary epithelial cell, D72_F11


title: Mammary epithelial cell, D72_G02


title: Mammary epithelial cell, D72_G03


title: Mammary epithelial cell, D72_H07


title: Mammary epithelial cell, D72_G01


title: Mammary epithelial cell, D72_F04


title: Mammary epithelial cell, D72_F03


title: Mammary epithelial cell, D72_F07


title: Mammary epithelial cell, D72_F06


title: Mammary epithelial cell, D72_F08


title: Mammary epithelial cell, D72_E12


title: Mammary epithelial cell, D72_E11


title: Mammary epithelial cell, D72_F02


title: Mammary epithelial cell, D72_E10


title: Mammary epithelial cell, D72_F01


title: Mammary epithelial cell, D72_E09


title: Mammary epithelial cell, D72_E07


title: Mammary epithelial cell, D72_F09


title: Mammary epithelial cell, D72_E08


title: Mammary epithelial cell, D72_E01


title: Mammary epithelial cell, D72_E02


title: Mammary epithelial cell, D72_E05


title: Mammary epithelial cell, D72_E04


title: Mammary epithelial cell, D72_D12


title: Mammary epithelial cell, D72_D11


title: Mammary epithelial cell, D72_D08


title: Mammary epithelial cell, D72_D10


title: Mammary epithelial cell, D72_F05


title: Mammary epithelial cell, D72_D07


title: Mammary epithelial cell, D72_D03


title: Mammary epithelial cell, D72_D02


title: Mammary epithelial cell, D72_D01


title: Mammary epithelial cell, D72_D06


title: Mammary epithelial cell, D72_D05


title: Mammary epithelial cell, D72_C11


title: Mammary epithelial cell, D72_D04


title: Mammary epithelial cell, D72_C08


title: Mammary epithelial cell, D72_C10


title: Mammary epithelial cell, D72_C09


title: Mammary epithelial cell, D72_E06


title: Mammary epithelial cell, D72_C07


title: Mammary epithelial cell, D72_E03


title: Mammary epithelial cell, D72_C05


title: Mammary epithelial cell, D72_C06


title: Mammary epithelial cell, D72_B11


title: Mammary epithelial cell, D72_C03


title: Mammary epithelial cell, D72_B12


title: Mammary epithelial cell, D72_C02


title: Mammary epithelial cell, D72_C01


title: Mammary epithelial cell, D72_D09


title: Mammary epithelial cell, D72_B09


title: Mammary epithelial cell, D72_B10


title: Mammary epithelial cell, D72_B08


title: Mammary epithelial cell, D72_C12


title: Mammary epithelial cell, D72_B07


title: Mammary epithelial cell, D72_B06


title: Mammary epithelial cell, D72_B05


title: Mammary epithelial cell, D72_B03


title: Mammary epithelial cell, D72_B04


title: Mammary epithelial cell, D72_B02


title: Mammary epithelial cell, D72_B01


title: Mammary epithelial cell, D72_A10


title: Mammary epithelial cell, D72_A09


title: Mammary epithelial cell, D72_A11


title: Mammary epithelial cell, D72_A07


title: Mammary epithelial cell, D72_A08


title: Mammary epithelial cell, D72_C04


title: Mammary epithelial cell, D72_A03


title: Mammary epithelial cell, D72_A04


title: Mammary epithelial cell, D72_A05


title: Mammary epithelial cell, D72_A02


title: Mammary epithelial cell, U72_H12

value: Untreated


title: Mammary epithelial cell, U72_H11


title: Mammary epithelial cell, U72_H08


title: Mammary epithelial cell, U72_H10


title: Mammary epithelial cell, U72_H06


title: Mammary epithelial cell, U72_H09


title: Mammary epithelial cell, U72_H03


title: Mammary epithelial cell, U72_H07


title: Mammary epithelial cell, U72_H02


title: Mammary epithelial cell, U72_H05


title: Mammary epithelial cell, U72_H01


title: Mammary epithelial cell, U72_G12


title: Mammary epithelial cell, D72_A12


title: Mammary epithelial cell, U72_H04


title: Mammary epithelial cell, D72_A06


title: Mammary epithelial cell, U72_G09


title: Mammary epithelial cell, U72_G11


title: Mammary epithelial cell, U72_G10


title: Mammary epithelial cell, U72_G05


title: Mammary epithelial cell, U72_G03


title: Mammary epithelial cell, U72_G07


title: Mammary epithelial cell, U72_G06


title: Mammary epithelial cell, U72_G01


title: Mammary epithelial cell, D72_A01


title: Mammary epithelial cell, U72_G02


title: Mammary epithelial cell, U72_F12


title: Mammary epithelial cell, U72_F11


title: Mammary epithelial cell, U72_F10


title: Mammary epithelial cell, U72_F09


title: Mammary epithelial cell, U72_F08


title: Mammary epithelial cell, U72_F07


title: Mammary epithelial cell, U72_F05


title: Mammary epithelial cell, U72_F06


title: Mammary epithelial cell, U72_F04


title: Mammary epithelial cell, U72_F03


title: Mammary epithelial cell, U72_F02


title: Mammary epithelial cell, U72_E12


title: Mammary epithelial cell, U72_F01


title: Mammary epithelial cell, U72_E11


title: Mammary epithelial cell, U72_G08


title: Mammary epithelial cell, U72_E08


title: Mammary epithelial cell, U72_E09


title: Mammary epithelial cell, U72_G04


title: Mammary epithelial cell, U72_E10


title: Mammary epithelial cell, U72_E05


title: Mammary epithelial cell, U72_E04


title: Mammary epithelial cell, U72_E07


title: Mammary epithelial cell, U72_E06


title: Mammary epithelial cell, U72_E01


title: Mammary epithelial cell, U72_D12


title: Mammary epithelial cell, U72_E03


title: Mammary epithelial cell, U72_D11


title: Mammary epithelial cell, U72_D10


title: Mammary epithelial cell, U72_D09


title: Mammary epithelial cell, U72_D08


title: Mammary epithelial cell, U72_D07


title: Mammary epithelial cell, U72_D05


title: Mammary epithelial cell, U72_D04


title: Mammary epithelial cell, U72_D02


title: Mammary epithelial cell, U72_D01


title: Mammary epithelial cell, U72_C11


title: Mammary epithelial cell, U72_C12


title: Mammary epithelial cell, U72_E02


title: Mammary epithelial cell, U72_C07


title: Mammary epithelial cell, U72_C06


title: Mammary epithelial cell, U72_C09


title: Mammary epithelial cell, U72_C03


title: Mammary epithelial cell, U72_C04


title: Mammary epithelial cell, U72_C02


title: Mammary epithelial cell, U72_D06


title: Mammary epithelial cell, U72_B11


title: Mammary epithelial cell, U72_B09


title: Mammary epithelial cell, U72_C01


title: Mammary epithelial cell, U72_B10


title: Mammary epithelial cell, U72_B06


title: Mammary epithelial cell, U72_B07


title: Mammary epithelial cell, U72_D03


title: Mammary epithelial cell, U72_B03


title: Mammary epithelial cell, U72_B04


title: Mammary epithelial cell, U72_B05


title: Mammary epithelial cell, U72_B02


title: Mammary epithelial cell, U72_B08


title: Mammary epithelial cell, U72_C08


title: Mammary epithelial cell, U72_B12


title: Mammary epithelial cell, U72_B01


title: Mammary epithelial cell, U72_A12


title: Mammary epithelial cell, U72_C05


title: Mammary epithelial cell, U72_A11


title: Mammary epithelial cell, U72_A08


title: Mammary epithelial cell, U72_A09


title: Mammary epithelial cell, U72_A07


title: Mammary epithelial cell, U72_A06


title: Mammary epithelial cell, U72_A03


title: Mammary epithelial cell, U72_A04


title: Mammary epithelial cell, U72_A01


title: Mammary epithelial cell, U72_A02


title: Mammary epithelial cell, U72_A05


title: Mammary epithelial cell, U72_C10


title: PBS4-2_Riboseq

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

description: Ribosome profiling

data_processing:
Library strategy: Ribo-Seq
RNA-seq and ribosome profiling libraries were analyzed in parallel. Reads were aligned to the mm10 genome using HISAT2 Version 2.1.0. Data was then analyzed by RiboTaper Version 1.3.1a, which confirmed periodicity of ribo-seq data. The RiboTaper script was run using default parameters: 8 cores, read lengths 28, 29, and 30 nucleotides, and an offset value of 12 nucleotides. Htseq Version 0.9.1 was used with default parameters to generate raw counts files from bam files for both RNA-seq and Ribo-seq. Counts were filtered to remove mitochondrial and ribosomal RNAs and differential gene expression analysis was performed using DeSEQ2. For ribosome profiling reads, ribosomal RNA was filtered using Bowtie2, followed by alignment of the non-ribosomal reads to the mm10 genome using HISAT2 Version 2.1.0. Differentially translated ORFs were identified using DeSEQ2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.htseq.txt: Tab-delimited text files include counts.

source_name: Fetal cortex

extract_protocol:
We employed a modified version of the ribosome profiling protocol described by McGlincy et al. Flash-frozen embryonic brain tissue was thawed in 400 ml lysis buffer (150 mM NaCl, 20 mM Tris, pH 7.4, 5mM MgCl2, 1mM DTT, 100 mg/ml cyclohexamide, 1% v/v Triton X-100, and 25 U/ml Turbo DNase I (ThermoFisher Scientific)). Tissue was pipetted ten times in lysis buffer and incubated for 10 minutes on ice. Tissue was then triturated ten times through a 26-gauge needle. Lysate were clarified by centrifugation for 10 min at 20000 × g at 4°C and supernatant was recovered.
Total RNA purified using the Direct-zol RNA MiniPrep kit (Zymo) with DNaseI treatment. RNA-seq libraries were prepared from 10 ng total RNA using the SMARTer® Stranded Total RNA-Seq Kit v2 (Takara) and sequenced on a Next-seq 500 using paired-end 2 x 37nt sequencing runs. For ribosome profiling, 1.5ml RNase I (10U/ml, ThermoFisher Scientific) was add to lysate containing 30 mg RNA and incubated for 45 minutes at room temperature with gentle agitation. 10 µl SUPERaseIn RNase inhibitor (20U/ml, ThermoFisher Scientific) was added after 45 minutes and samples transferred to ice to stop nuclease digestion. Lysate was transferred to a polycarbonate ultracentrifuge tube and underlayed with 0.9 ml sucrose cushion (1 M sucrose, 20 U/ml SUPERaseIn in Polysome buffer, 150 mM NaCl, 20 mM Tris, pH 7.4, 5mM MgCl2, 1mM DTT, 100 mg/ml cycohexamide). Ribosome-protected RNAs were pelleted by centrifugation at 52,000 rpm, 4°C for 2 h. Supernatant was removed, and pellet resuspended in 300 µl TRIzol reagent. RNA fragments were purified using a Direct-zol RNA MiniPrep kit (Zymo Research) and eluted in 100 µl RNase-free water. RNA was precipitated with one volume of isopropanol, 30 µg GlycoBlue, and 100 mM NaOAc pH 5.5 (300 µl total volume), and chilled at −20°C for at least 2 hours, or overnight. RNA was pelleted by centrifugation for 30 min at 20000 × g, 4°C, supernatant was removed, and pellets were air-dried for 10 min. Purified RNA was resuspended in 5 µl 10 mM Tris pH 8, and RNA 17-34 nucleotides was size selected using a 15% TBE-Urea gel (Life Technologies). RNA was extracted from gel sections in 400 ul RNA extraction buffer (300 mM NaOAc, pH 5.5, 1mM EDTA, 0.25% v/v SDS), then precipitated with 30 µg GlycoBlue and one volume of isopropanol. Precipitations were left at −20°C overnight. Size-selected RNA was resuspended in 4 µl 10 mM Tris pH 8 and transferred to a clean non-stick RNase-free microfuge tube. Size-selected RNA was dephosphorylated with T4 PNK (NEB) at 37°C for 1 hour. The reaction was brought up to 50 µl with nuclease-free water and purified using 1.8 volumes of Agencourt RNAClean XP beads (Beckman Coulter) and 5.4 volumes of isopropanol. Beads were captured on a magnetic rack and washed twice with 85% EtOH. Beads were air-dried and resuspended in 7 µl nuclease-free water. Supernatant containing purified RNA was removed from beads and quantified by Qubit RNA assay (ThermoFisher Scientific). Sequencing libraries prepared using the SMARTer® smRNA-Seq Kit for Illumina® (Takara). Libraries were sequenced on a Novaseq 6000 using single-end 1 x 50 nt sequencing runs.

tag: strain/background

value: Embryonic day 18

value: PBS

value: Fetal cortex

value: missing


title: Mammary epithelial cell, U72_A10


title: PBS1_Riboseq

description: Ribosome profiling


title: PBS1-2_Riboseq

description: Ribosome profiling


title: MIA8_Riboseq

description: Ribosome profiling

value: Maternal immune activation (MIA)


title: MIA6_Riboseq

description: Ribosome profiling


title: Rspo1_Axin2pos_rep1

city: Cardiff

first: Eider

last: Valle-Encinas

state: Cardiff

address: Sir Martin Evans Building, Museum Avenue

department: Biosciences

country: United Kingdom

institute: Cardiff University

data_processing:
Sequences were trimmed with Trimmomatic 0.35 and assessed for quality using FastQC 0.11.2 (bolger et al., 2014).
On average, 99% of the total reads were mapped to the mouse GRCm38 reference genome using STAR 2.5.1b. and counts were assigned to transcripts using featureCounts with the GRCm38.84 Ensembl gene build GTF (Dobin et al., 2012) (Liao et al., 2014).
Counts per million (CPM) and fragments per kilobase per million (FPKM) were calculated for each gene using Deseq2 packages.  Both the reference genome and GTF were downloaded from the Ensembl FTP site (Data Hub, Cardiff University, Cardiff, CF14 4AXN).
Genes with <0.5 average FPKM in all biological groups were considered as not expressed and discarded from the analysis.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text files include ensembl Gene ID and Gene names anotations and their assigned raw counts and FPKM values for each Sample
Supplementary_files_format_and_content: csv files include Deseq2 differential expression analysis of pairwise comparisions

source_name: differentiated bile duct organoids

growth_protocol: Organoids were originated and expanded following Huch et al (2013) indications

extract_protocol:
Organoids were collected, incubated for 7min at 37°C with TriplE and dissociated into single cells and re-suspended in AdDMEM/F12 containing 2 mM EDTA for sorting. Cells were sorted into 0.5 ml of expansion media or 0.5 ml of Trizol. Total RNA was isolated following Trizol Reagent (Life Technologies) RNA extraction method coupled with RNaesy MinElute columns (Qiagen).
Single-end 75bp sequencing was performed with 100ng of total RNA input determined by a Hi-sensitivity Qubic kit on a NextSeq-500 sequencer where equi-molar libraries were pooled in the Genomic Hub of Cardiff University (Cardiff University, CF103AX, UK).

treatment_protocol: Organoids were expanded for 2 to 4 days and differentiated following Huch et al (2013) protocol for 11 days. During the last 24h of culture, differentiation media was supplemented with 3 uM dexamethasone, 500 nM 4-OHT (Sigma) with or without 100ng/ml Rspo1 (Prepotech) when indicated.

value: differentiated bile duct organoids

tag: strain

value: mixed genetic background

value: Male

value: Axin2CreERT2+/-; R26-LSL-tdTom+/-

tag: organoid passage

tag: tdtom expression

value: tdTom positive


title: PBS6_Riboseq

description: Ribosome profiling

tag: tissue


title: PBS4_Riboseq

description: Ribosome profiling


title: PBS7_Riboseq

description: Ribosome profiling


title: Untreated_Axin2neg_rep3

value: Control

value: tdTom negative


title: Rspo1_Axin2neg_rep3


title: Rspo1_Axin2neg_rep2


title: Rspo1_Axin2neg_rep1


title: Untreated_Axin2neg_rep2


title: Untreated_Axin2neg_rep1


title: MIA2_Riboseq

description: Ribosome profiling


title: MIA1_Riboseq

description: Ribosome profiling


title: PBS7_RNAseq

data_processing:
RNA-seq and ribosome profiling libraries were analyzed in parallel. Reads were aligned to the mm10 genome using HISAT2 Version 2.1.0. Data was then analyzed by RiboTaper Version 1.3.1a, which confirmed periodicity of ribo-seq data. The RiboTaper script was run using default parameters: 8 cores, read lengths 28, 29, and 30 nucleotides, and an offset value of 12 nucleotides. Htseq Version 0.9.1 was used with default parameters to generate raw counts files from bam files for both RNA-seq and Ribo-seq. Counts were filtered to remove mitochondrial and ribosomal RNAs and differential gene expression analysis was performed using DeSEQ2. For ribosome profiling reads, ribosomal RNA was filtered using Bowtie2, followed by alignment of the non-ribosomal reads to the mm10 genome using HISAT2 Version 2.1.0. Differentially translated ORFs were identified using DeSEQ2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.htseq.txt: Tab-delimited text files include counts.


title: PBS4_RNAseq


title: PBS6_RNAseq


title: PBS1-2_RNAseq


title: PBS3_RNAseq


title: PBS3_Riboseq

description: Ribosome profiling


title: Rspo1_Axin2pos_rep2


title: Rspo1_Axin2pos_rep3


title: PBS1_RNAseq


title: MIA3_Riboseq

description: Ribosome profiling


title: MIA6_RNAseq


title: MIA8_RNAseq


title: MIA3_RNAseq


title: PBS4-2_RNAseq


title: MIA4_RNAseq


title: KC+UNC_ATAC

first: Keisuke

last: Tateishi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, The University of Tokyo

data_processing:
Sequence reads were trimmed and aligned to the mouse genome (mm10) using BWA.
PCR duplicates were removed using Picard’s Mark Duplicates.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated  by normalizing to RPKM and smoothed by 150bp sliding windows with 20bp bin size using bamCoverage.

source_name: Pancreas organoids

growth_protocol: Organoids were cultured in vitro as previously described. The culture medium was based on AdDMEM/F12 (Invitrogen) supplemented with B27 (Invitrogen), 1.25 μM N-acetylcysteine (Wako), 50 ng/mL EGF (Wako), 100 ng/mL Fgf10 (Wako), 10% Wnt3a-conditioned medium, 10% RSPO1-conditioned medium, 10 nM gastrin (Sigma-Aldrich), and 10 mM nicotinamide (Sigma-Aldrich). Additionally, for 4 days after seeding, the cells were supplemented with 100 ng/mL Noggin (PeproTech). Cells were coated with Matrigel (BD Bioscience).

extract_protocol:
Harvested organoids were gently digested into single cell suspension using TrypLE and DNaseI, and 50,000 cells were used for ATAC-seq.
Library preparation was performed as previously described (2013 Buenrostro). Breifly, cells were washed lysed using lysis buffer followed by transposase reaction with Tagment DNA TDE1 Enzyme and Buffer Small Kit (Illumina). Transposed DNA was purified using MinElute PCR Purification kit (Qiagen) and amplified using NEBNext High-Fidelity 2X PCR Master Mix(NEB)  followed by size selection with AMPure Beads (Beckman Coulter).Libraries were sequenced using NextSeq500 (Illumina)with paired-end 50bp+25bp reads.

treatment_protocol: UNC0638 was purchased from Selleck (Houston USA).Organoids were cultured either with fresh media or with 5µM UNC0638 for 24hours prior to experiments.

value: Pancreas

tag: cell type

value: Pancreas ductal cell

value: Ptf1aCre/; KrasG12D

value: 5µM UNC0638 for 24hours


title: MIA2_RNAseq


title: KC_ATAC


title: Skin_cDNA

city: Guangzhou

first: Jin-Xin

last: Bei

state: Guangdong

address: 651 Dongfeng Road East, Yuexiu District, Guanzhou, P.R. China

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina-implemented software bcl2fastq (version v2.19.0.316) was used for basecalling.
cDNA sequencing reads were aligned to the human reference genome (hg38) and digital gene expression matrix was built using STAR algorithm in CellRanger (“count” option; version 3.0.1; 10x Genomics).
Genome_build: hg38
Supplementary_files_format_and_content: Each sample was represented by tab-delimited text files including raw counts of each gene for each cell.

molecule: polyA RNA

source_name: An adult male donor who died of a traumatic brain injury

extract_protocol:
Viable single cells were prepared from the tissue samples of 15 different organs of a research-consented adult donor.
The concentration of single cell suspension was determined using a Cellometer Auto 2000 instrument (Cellometer) and adjusted to 1,000 cells/μl. Approximately 14,000 cells were loaded into a CHROMIUM instrument (10x Genomics, CA, USA) according to the standard protocol of the Chromium single cell V(D)J kit (v1) in order to capture 5,000 ~ 10,000 cells per channel. In brief, mRNA transcripts from each sample were ligated with barcoded indexes at 5'-end and reverse transcribed into cDNA, using GemCode technology (10x Genomics, USA). cDNA libraries including the enriched fragments spanning the full-length V(D)J segments of T cell receptors (TCR) or B cell receptor (BCR), and 5'-end fragments for gene expression were separately constructed, which were subsequently subjected for high-throughput sequencing.

value: Skin

value: male

tag: age

value: 31 years


title: MIA7_Riboseq

description: Ribosome profiling

value: Embryonic day 18

value: Fetal cortex


title: Trachea_cDNA

value: Trachea


title: K_ATAC


title: Spleen_cDNA

value: Spleen


title: Stomach_cDNA

value: Stomach


title: Rectum_cDNA

value: Rectum


title: BK_MIAPBS_E14E18

description: single cell isolation by Indrops

data_processing:
Transcripts were processed according to the pipeline in Macosko et al. (2015). Briefly, this pipeline was used to build a custom transcriptome from Ensembl GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1, after filtering the annoatation gtf file (gencode.v17.annotation.gtf filtered for feature_type=îgeneî, gene_type="protein_coding" and gene_status="KNOWN"). Read quality control and mapping against this transcriptome was performed. Unique molecular identifiers (UMIs) were used to link sequence reads back to individual captured molecules. All steps of the pipeline were run using default parameters unless explicitly stated.
Genome_build: mm10
Supplementary_files_format_and_content: transcript counts

extract_protocol:
Embryonic cortices at E14 and E18 were transferred to dissociation media: HBSS (Life Technologies), 10 mM Hepes (Sigma), 172 mg/L kynurenic acid (Sigma), 0.86 g/L MgCl2·6H2O (Sigma), and 6.3 g/L D-glucose (Sigma). This solution was saturated with 95% oxygen and 5% CO2 and was pH-adjusted to 7.35 before use. Papain (20 U/mL; Worthington), Pronase from Streptomyces griseus (1 mg/mL; Sigma), proteinase XXIII from Aspergillus melleus (3 mg/mL; Sigma), and DNase (2 mg/mL; Worthington) were added to the dissociation media. Dissociation was carried out at 37 °C for 1 h. The samples were then triturated, filtered, and spun at 300 × g for 5 min. The pellet was resuspended in trypsin inhibitor solution (dissociation media with 1% BSA and 1% ovomucoid). Following gradient centrifugation (70 × g for 10 min), the cells were washed in dissociation media containing 0.04% BSA and resuspended in dissociation media containing 0.04% BSA and 15% OptiPrep (Sigma). Individual cells were captured and barcoded using the inDrops platform as previously described.30 Briefly, single-cell suspensions were fed into a microfluidic device that packaged the cells with barcoded hydrogel microspheres and reverse transcriptase/lysis reagents. After cell encapsulation, primers were photo-released by UV exposure. Indexed libraries were pooled and sequenced on a NextSeq 500 (Illumina).
Individual cells were captured and barcoded using the inDrops platform as previously described. Briefly, single-cell suspensions were fed into a microfluidic device that packaged the cells with barcoded hydrogel microspheres and reverse transcriptase/lysis reagents. After cell encapsulation, primers were photo-released by UV exposure. Two libraries of approximately 5000 cells each were collected for each sample. Indexed libraries were pooled and sequenced on a Nextseq 500 (Illumina).

value: mixed sample (non-demultiplexed)

value: Embryonic days 14 and 18


title: Marrow_cDNA

value: Marrow


title: Muscle_cDNA

value: Muscle


title: Lymph.node_cDNA

value: Lymph node


title: Esophagus_cDNA

value: Esophagus


title: Heart_cDNA

value: Heart


title: Liver_cDNA

value: Liver


title: Common.bile.duct_cDNA

value: Common bile duct


title: Bladder_cDNA

value: Bladder

value: male


title: Blood_cDNA

value: Blood

value: 31 years


title: MIA7_RNAseq

value: Embryonic day 18

value: Maternal immune activation (MIA)

value: Fetal cortex

value: missing


title: N92

city: Beijing

first: Chen

last: Wu

address: 17 Panjiayuan Nanli, Chaoyang District

institute: Cancer Hospital, Chinese Academy of Medical Sciences

description:
S246
ACGEJ123pairs_gene_expression_hg19.txt

data_processing:
We used HISAT2 (v2.1.0) to align RNA sequence reads to the UCSC hg19 human genome and then used StringTie (v1.3.3b) to re-assemble transcriptome and quantify the expression level of each gene in each sample. The assembly process was guided by the reference annotations from GENCODE (v19). Gene expression levels were quantified by Transcript per Million (TPM).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ACGEJ123pairs_gene_expression_hg19.txt: Tab-delimited text file containing the expression abundance (TPM) of each gene in each sample.

source_name: Adjacent normal tissue sample

extract_protocol:
Total RNA were extracted from tissue samples using the AllPrep DNA/RNA Kit (Qiagen).
RNA degradation and contamination were monitored on 1% agarose gels. RNA concentration was measured by Qubit® RNA Assay Kit in Qubit® 2.0. RNA library preparation used NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina and 3 nanograms RNA per sample as the initial materials. Ribosomal RNA was removed using Epicentre Ribo-ZeroTM Gold Kits. Library fragments were purified using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China).

value: Adjacent normal tissue

tag: patient

tag: population

value: Chinese


title: MIA1_RNAseq

tag: treatment


title: N88

description:
S245
ACGEJ123pairs_gene_expression_hg19.txt


title: Small.intestine_cDNA

value: Small intestine

tag: Sex


title: N84

description:
S244
ACGEJ123pairs_gene_expression_hg19.txt


title: N80

description:
S241
ACGEJ123pairs_gene_expression_hg19.txt


title: N81

description:
S242
ACGEJ123pairs_gene_expression_hg19.txt


title: N75

description:
S239
ACGEJ123pairs_gene_expression_hg19.txt


title: N65

description:
S233
ACGEJ123pairs_gene_expression_hg19.txt


title: N72

description:
S238
ACGEJ123pairs_gene_expression_hg19.txt


title: N7

description:
S236
ACGEJ123pairs_gene_expression_hg19.txt


title: N67

description:
S234
ACGEJ123pairs_gene_expression_hg19.txt


title: N70

description:
S237
ACGEJ123pairs_gene_expression_hg19.txt


title: N68

description:
S235
ACGEJ123pairs_gene_expression_hg19.txt


title: N63

description:
S232
ACGEJ123pairs_gene_expression_hg19.txt


title: N82

description:
S243
ACGEJ123pairs_gene_expression_hg19.txt


title: N79

description:
S240
ACGEJ123pairs_gene_expression_hg19.txt


title: N58

description:
S230
ACGEJ123pairs_gene_expression_hg19.txt


title: N57

description:
S229
ACGEJ123pairs_gene_expression_hg19.txt


title: N52

description:
S227
ACGEJ123pairs_gene_expression_hg19.txt


title: N40

description:
S222
ACGEJ123pairs_gene_expression_hg19.txt


title: N55

description:
S228
ACGEJ123pairs_gene_expression_hg19.txt


title: N41

description:
S223
ACGEJ123pairs_gene_expression_hg19.txt


title: N51

description:
S226
ACGEJ123pairs_gene_expression_hg19.txt


title: N49

description:
S225
ACGEJ123pairs_gene_expression_hg19.txt


title: N43

description:
S224
ACGEJ123pairs_gene_expression_hg19.txt


title: N59

description:
S231
ACGEJ123pairs_gene_expression_hg19.txt


title: N35

description:
S220
ACGEJ123pairs_gene_expression_hg19.txt


title: N346

description:
S219
ACGEJ123pairs_gene_expression_hg19.txt


title: N39

description:
S221
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title: N306

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title: N313

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title: N308

description:
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title: N310

description:
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title: N321

description:
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title: N312

description:
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title: N301

description:
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title: N300

description:
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title: N297

description:
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title: N295

description:
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title: N292

description:
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title: N29

description:
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title: N294

description:
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title: N287

description:
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title: N285

description:
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title: N284

description:
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title: N280

description:
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title: N291

description:
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title: N281

description:
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title: N282

description:
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title: N288

description:
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title: N275

description:
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title: ecw_yiepko_w_3hp_2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

data_processing:
Sequencing: Illumina platform
Mapping: Sequence reads generated from RNA-seq were mapped onto the reference genome (NC_017635.1) using bowtie with the maximum insert size of 1000 bp, and 2 maximum mismatches after trimming 3 bp at 3’ ends
SAM: SAM files generated from bowtie.
Cufflinks: run Cufflinks (http://cufflinks.cbcb.umd.edu/) to calculate fragments per kilobase of exon per million fragments (FPKM) with default options with the library type of dUTP RNA-seq and the default normalization method (classic-fpkm)
Genome_build: Genome build: reference genome(NC_017635.1)
Supplementary_files_format_and_content: tab-seperated text files include various values for each sample(The column name is shown on the first line)

organism: Escherichia coli W

source_name: bacteria

extract_protocol:
Total RNA from culture cells was extracted by RNA isolation Protocol (NucleoSpin RNA XS from Macherey-Nagel Corporations.)
The sequencing library is prepared by random fragmentation of DNA or cDNA sample, follewed by 5' and 3' adapter ligation (TruSeq stranded mRNA kits, Microbe )

value: deletion yiep

tag: growth condition

value: with 3HP


title: ecw_yiepko_wo_3hp_2

tag: genotype

value: without 3HP


title: N279

description:
S177
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title: N274

description:
S175
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title: ecw_wt_w_3hp_2

value: Wild Type


title: ecw_wt_wo3hp_2


title: N271

description:
S173
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title: ecw_yiepko_w_3hp_1


title: N269

description:
S171
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title: N270

description:
S172
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title: ecw_wt_w_3hp_1


title: ecw_wt_wo3hp_1


title: N267

description:
S170
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title: N265

description:
S169
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title: N264

description:
S168
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title: N258

description:
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title: N26

description:
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title: N260

description:
S165
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title: N261

description:
S166
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title: N252

description:
S161
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title: human_costal_cartilage_h1451

city: St. Louis, MO 63110

first: Farshid

last: Guilak

state: MO

address: Campus Box 8233, Couch Research Bldg, Room 3121

department: Orthopaedic Surgery

institute: Washington University in Saint Louis

data_processing:
Reads were processed using an in-house pipeline and open-source R packages as previously described. Raw reads were first trimmed using Cutadapt to remove low quality bases and reads. After trimming, processed reads were aligned to the human reference genome GRCh38 (version 90) by STAR, and the number of aligned reads to each annotated genes or transcripts (GENCODE v21) was performed using featureCounts from the Subread package (v1.4.6).
After quality control, un-normalized gene counts were read into DESeq2 R package by DESeqDataSetFromMatrix function as instructed by the package tutorial. Genes that were expressed by less than 10 cells were then removed. Next, we used DESeq and results functions which implement Wald test in DESeq2 to determine the differentially expressed genes (DEGs) between two consecutive differentiation stages. In this process, the estimation of size factors (i.e., controlling for differences in the sequencing depth of the samples), the estimation of dispersion values for each gene, and fitting a generalized linear model were performed. The Gene counts were also averaged from three hiPSC lines. Top 20 DEGs between two consecutive stages were selected and visualized using ComplexHeatmap R package. To observe the temporal expression of a given gene for each hiPSC line, the count matrix was regularized-logarithm transformed via rlog function first, and we used plotCounts function in DESeq2 to visualize the expression pattern of the gene. Furthermore, regularized-logarithm transformed counts were also used for principle component analysis (PCA) and PCA plots were visualized by ggplot function in ggplot2 R package.
Genome_build: GRCh38 (version 90)
Supplementary_files_format_and_content: gene counts files (x_gene_counts.txt)

source_name: healthy human costal cartilage

growth_protocol:
hiPSCs were induced into mesodermal differentiation in monolayer at 40% confluency. Each day, cells were rinsed with wash medium consisting of 50% IMDM GlutaMAX (IMDM, Fisher Scientific, #31980097) and 50% Ham’s F12 Nutrient Mix (F12, Fisher Scientific, #31765092) to remove previous medium. hiPSCs were then fed daily to sequentially drive mesodermal differentiation similar to those identified in embryonic development with various sets of growth factors and small molecules supplemented in mesodermal differentiation medium consisting of IMDM and F12 with 1% chemically defined lipid concentrate (Gibco), 1% insulin/human transferrin/selenous acid (ITS+, Corning, #354352), 1% P/S (Thermo Fisher Scientific, #15140-122), and 450 μM 1-thioglycerol (Sigma–Aldrich, #M6145). Cells were induced to the anterior primitive streak with 30 ng ml-1 of Activin A (R&D Systems, #338-AC), 4 µM CHIR99021 (Stemgent, #04-0004), and 20 ng ml-1 human fibroblast growth factor (FGF; R&D Systems, #233-FB-025/CF) for 24 hours. On the second day, cells were driven to paraxial mesoderm with 2 µM SB-505124 (Tocris, #3263), 3 µM CHIR99021, 20 ng ml-1 FGF, and 4 µM dorsomorphin (Stemgent, #04-0024). Then, cells were treated with 2 µM SB5, 4 µM DM, 1 µM Wnt-C59 (C59; Cellagent Technology, #C7641-2s), and 500 nM PD173074 (Tocris, #3044) to become early somite on the third day. For the fourth through sixth days, cells were driven to the sclerotome with daily feedings of 2 µM purmorphamine (Stemgent, #04-0009) and 1 µM C59. Finally, for six days, cells were driven to the chondroprogenitor stage (Cp) with 20 ng ml-1 of human bone morphogenetic protein 4 (BMP4; R&D Systems, #314-BP-010/CF) daily.
At each stage, some cells were dissociated using TrypLE (Gibco, #12604013) at 37ºC for 3 mins followed by adding an equal part of neutralizing medium consisting of DMEM/F-12, GlutaMAXTM (DMEM/F12; Thermo Fisher Scientific, #10565042) with 10% FBS (Atlanta Biologicals) and 1% P/S. The dissociated cells were either used for bulk RNA-seq, scRNA-seq, chondrogenic differentiation, or fluorescence-activated cell sorting (FACS) as appropriate.
Cells dissociated at Cp stage were re-suspended at 5 x 105 cells per mL in chondrogenic medium consisting of DMEM/F-12, 1% FBS, 1% ITS+, 55 µM -mertcaptoethanol, 100 nM dexamethasone (DEX; Sigma-Aldrich, #D4902), 1% NEAA (Gibco, #11140050), 1% P/S, 10 ng ml-1 human transforming growth factor beta 3 (TGF-3; R&D Systems, #243-B3-010), 50 μg ml-1 L-ascorbic acid 2-phosphate (ascorbate; Sigma-Aldrich, #A8960), and 40 μg ml-1 L-Proline (proline; Sigma-Aldrich, #P5607). Cells were then centrifuged for 5 min at 300x g to form a pellet. Chondrogenic pellets were cultured at 37ºC for up to 42 days.

extract_protocol:
To determine transcriptome profiles over the course of differentiation, three unique hiPSCs lines (ATCC, BJFF, and STAN) as biological replicates at various differentiation stages (6 mesodermal and 5 chondrogenic stages per cell line; i.e., total 33 samples) were collected for bulk RNA-seq. Cell samples were thawed on ice, and pellet samples were homogenized with zirconia beads (BioSpec Products, # 11079110zx) and a miniature bead beater. RNA was then isolated from all samples using the Total RNA Purification Kit according to the manufacture’s protocol (Norgen Biotek, #37500). RNA was eluted in 20 µl of diethylpyrocarbonate-treated water. The quality and quantity of RNA from each sample was evaluated by RNA Analysis ScreenTape (Agilent, #5067-5576) on bioanalyzer (Agilent 4200 Tapestation). Only samples with a RIN value larger than 0.8 were submitted to the Genome Technology Access Center (GTAC sequencing core) at Washington University in St. Louis for library preparation and bulk RNA-seq. Libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). Sequencing was performed on a Illumina HiSeq 2500 (1 x 50 bp reads) with a sequencing depth of 30 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
Bulk RNA-seq

value: healthy human costal cartilage

tag: individual

value: male, 75yrs, caucasian

tag: Cause of death

value: COPD


title: human_costal_cartilage_h1452

value: female, 74yrs, caucasian


title: N256

description:
S162
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title: ATCC_d42

source_name: hiPSC-derived chondrogenic pellet_day 42

tag: cell line

value: hiPSC line ATCC


title: BJFF_d28

source_name: hiPSC-derived chondrogenic pellet_day 28

value: hiPSC line BJFF


title: human_costal_cartilage_h1454

value: male, 62yrs, caucasian

value: COPD/Emphysema


title: BJFF_d42

value: hiPSC-derived chondrogenic pellet_day 42


title: ATCC_d28

value: hiPSC-derived chondrogenic pellet_day 28


title: N272

description:
S174
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value: Adjacent normal tissue


title: Stan_d28

value: hiPSC line Stan


title: ecw_yiepko_wo_3hp_1


title: N250

description:
S160
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value: Chinese


title: N249

description:
S159
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title: N247

description:
S158
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title: Stan_d21

source_name: hiPSC-derived chondrogenic pellet_day 21


title: ATCC_d21

value: hiPSC-derived chondrogenic pellet_day 21


title: BJFF_d21


title: Stan_d14

source_name: hiPSC-derived chondrogenic pellet_day 14


title: N263

description:
S167
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title: N244

description:
S156
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title: Stan_d42


title: N24

description:
S155
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title: BJFF_d14

value: hiPSC-derived chondrogenic pellet_day 14


title: N212

description:
S153
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title: ATCC_d14


title: N236

description:
S154
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title: BJFF_d7

source_name: hiPSC-derived chondrogenic pellet_day 7

value: hiPSC-derived chondrogenic pellet_day 7


title: N167

description:
S151
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title: N157

description:
S147
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title: BJFF_cp

source_name: hiPSC-derived chondroprogenitor stage

value: hiPSC-derived chondroprogenitor stage


title: Stan_cp


title: N156

description:
S146
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title: ATCC_cp


title: N166

description:
S150
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title: N245

description:
S157
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title: ATCC_scl

source_name: hiPSC-derived sclerotome stage

value: hiPSC-derived sclerotome stage


title: ATCC_d7


title: N163

description:
S149
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title: BJFF_scl


title: Stan_scl


title: N145

description:
S143
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title: N153

description:
S145
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title: N142

description:
S142
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title: N141

description:
S141
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title: N162

description:
S148
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title: Stan_d7


title: ATCC_es

source_name: hiPSC-derived early somite stage

value: hiPSC-derived early somite stage


title: N140

description:
S140
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title: Stan_par

source_name: hiPSC-derived paraxial mesodermal stage

value: hiPSC-derived paraxial mesodermal stage


title: N18

description:
S152
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title: MIA4_Riboseq

description: Ribosome profiling

tag: developmental stage

value: Embryonic day 18

value: Maternal immune activation (MIA)

value: Fetal cortex

value: missing


title: N138

description:
S139
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title: N133

description:
S138
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title: N131

description:
S137
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title: Stan_ap

source_name: hiPSC-derived anterior primitive streak stage


title: Stan_es


title: BJFF_es

value: hiPSC line BJFF


title: ATCC_par

value: hiPSC line ATCC


title: N13

description:
S135
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title: BJFF_ap

value: hiPSC-derived anterior primitive streak stage


title: N126

description:
S133
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value: Adjacent normal tissue


title: Stan_hiPSC

source_name: human foreskin fibroblasts

value: hiPSC line Stan

value: Undifferentiated stem cell stage


title: BJFF_hiPSC


title: N148

description:
S144
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value: Chinese


title: N115

description:
S131
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title: ATCC_hiPSC


title: N125

description:
S132
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title: N112

description:
S130
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title: BJFF_par


title: N11

description:
S129
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title: C59-D14_scRNA-seq

description: C59 treated_hiPSC-derived chondrogenic pellet_day 14

data_processing:
Paired-end sequencing reads were processed by Cell Ranger (10x Genomics software, version 2.0.0). Reads were aligned to the GRCh38 (version 90) for genome annotation, demultiplexing, barcode filtering, and gene quantification. Cell Ranger also removes any barcode that has less than 10% of the 99th percentile of total unique molecular identifiers (UMI) counts per barcode as these barcodes are considered to be associated with empty droplets. After this quality control, gene barcode matrices for each sample were generated by counting the number of UMIs for a given gene (as row) in individual cell (as column). For each sample, ~2,200-2,500 cells were captured.
To assess the difference in composition of cell populations, we performed global unsupervised clustering analysis scRNA-seq datasets. First, gene barcode matrices were input into Seurat R package (version 2.4). We then removed the low-quality cells with less than 200 or more than 7,000 detected genes, or if their mitochondrial gene content was more than 5%. Note that the cutoff criteria were adjusted in few cases due to the sequencing depth and the variations in mitochondrial gene content from datasets. Genes that were detected in less than 3 cells were filtered out. After filtering out low-quality cells or cell doublets, the gene expression was then natural log transformed and normalized for scaling the sequencing depth to 10,000 molecules per cell. Next, to reduce the variance introduced by unwanted sources, we regressed out variation in gene expression driven by cell cycle stages and mitochondrial gene expression with vars.to.regress argument in function ScaleData in Seurat. We then used FindVariableGenes function in Seurat to identify highly variable genes across cells for downstream analysis. These steps resulted in (1) total 17,334 cells with average 1,972 highly variable genes from stages of hiPSCs and CP, as well as TGF-3-treated pellets (d1, d3, d7, d14, d28, and d42), and (2) total 7,997 cells with average 1,886 highly variable genes from C59-treated pellets (d7, d14, d28, and d42) for downstream analysis. Dimensionality reduction on the data was then performed by computing the significant principal components on highly variable genes. We then performed unsupervised clustering by using FindClusters function in Seurat with the resolution argument set to 0.6 and clusters were then visualized in tSNE plot.
Genome_build: GRCh38 (version 90)
Supplementary_files_format_and_content: gene list (_genes.tsv) and cell barcodes (_barcodes.tsv) as well as gene/barcode matrices (_matrix.mtx) are provided for each time point

growth_protocol: Discarded and deidentified waste tissue from the iliac crests of adult bone marrow transplant donors were collected in accordance with the institutional review board of Washington University in Saint Louis. Human bone marros-derived MSCs (hMSCs) were isolated by their physical adherence to plastic culture vessels. Cells were expanded and maintained in expansion medium consisting of DMEM-low glucose (Thermo Fisher Scientific, #11885092), 1% penicillin/streptomycin (P/S, Thermo Fisher Scientific, #15140-122), 10% lot-selected fetal bovine serum (FBS; Atlanta Biologicals, #S11550), and 1 ng ml-1 basic fibroblast growth factor (R&D Systems, #233-FB). Three individual donors were used as biologic replicates in subsequent experiments.    hiPSCs were induced into mesodermal differentiation in monolayer at 40% confluency. Each day, cells were rinsed with wash medium consisting of 50% IMDM GlutaMAX (IMDM, Fisher Scientific, #31980097) and 50% Ham’s F12 Nutrient Mix (F12, Fisher Scientific, #31765092) to remove previous medium. hiPSCs were then fed daily to sequentially drive mesodermal differentiation similar to those identified in embryonic development with various sets of growth factors and small molecules supplemented in mesodermal differentiation medium consisting of IMDM and F12 with 1% chemically defined lipid concentrate (Gibco), 1% insulin/human transferrin/selenous acid (ITS+, Corning, #354352), 1% P/S (Thermo Fisher Scientific, #15140-122), and 450 μM 1-thioglycerol (Sigma–Aldrich, #M6145). Cells were induced to the anterior primitive streak with 30 ng ml-1 of Activin A (R&D Systems, #338-AC), 4 µM CHIR99021 (Stemgent, #04-0004), and 20 ng ml-1 human fibroblast growth factor (FGF; R&D Systems, #233-FB-025/CF) for 24 hours. On the second day, cells were driven to paraxial mesoderm with 2 µM SB-505124 (Tocris, #3263), 3 µM CHIR99021, 20 ng ml-1 FGF, and 4 µM dorsomorphin (Stemgent, #04-0024). Then, cells were treated with 2 µM SB5, 4 µM DM, 1 µM Wnt-C59 (C59; Cellagent Technology, #C7641-2s), and 500 nM PD173074 (Tocris, #3044) to become early somite on the third day. For the fourth through sixth days, cells were driven to the sclerotome with daily feedings of 2 µM purmorphamine (Stemgent, #04-0009) and 1 µM C59. Finally, for six days, cells were driven to the chondroprogenitor stage (Cp) with 20 ng ml-1 of human bone morphogenetic protein 4 (BMP4; R&D Systems, #314-BP-010/CF) daily.       At each stage, some cells were dissociated using TrypLE (Gibco, #12604013) at 37ºC for 3 mins followed by adding an equal part of neutralizing medium consisting of DMEM/F-12, GlutaMAXTM (DMEM/F12; Thermo Fisher Scientific, #10565042) with 10% FBS (Atlanta Biologicals) and 1% P/S. The dissociated cells were either used for bulk RNA-seq, scRNA-seq, chondrogenic differentiation, or fluorescence-activated cell sorting (FACS) as appropriate.     Cells dissociated at Cp stage were re-suspended at 5 x 105 cells per mL in chondrogenic medium consisting of DMEM/F-12, 1% FBS, 1% ITS+, 55 µM -mertcaptoethanol, 100 nM dexamethasone (DEX; Sigma-Aldrich, #D4902), 1% NEAA (Gibco, #11140050), 1% P/S, 10 ng ml-1 human transforming growth factor beta 3 (TGF-3; R&D Systems, #243-B3-010), 50 μg ml-1 L-ascorbic acid 2-phosphate (ascorbate; Sigma-Aldrich, #A8960), and 40 μg ml-1 L-Proline (proline; Sigma-Aldrich, #P5607). Cells were then centrifuged for 5 min at 300x g to form a pellet. Chondrogenic pellets were cultured at 37ºC for up to 42 days.     For C59 treatment for WNT inhibition during chondrogenesis, pellets were treated with either 10 ng ml-1 TGF-3 (control group) or a combination of 10 ng ml-1 TGF-3 and 1 M C59 in chondrogenic medium from d0 to d42 as appropriate.

extract_protocol:
Cells were thawed at 37ºC and resuspended in PBS + 0.04% BSA at concentration of 2,000 cells per l. Cell suspensions were submitted to the GTAC sequencing core at Washington University in St. Louis for library preparation and sequencing. In brief, 10,000 cells per sample were loaded on a Chromium Controller (10x Genomics) for single capture. Libraries were prepared using Single Cell 3′ Library & Gel Bead Kit v2 (#120237 10x Genomics) following manufacture’s instruction. A single cell emulsion (Gel Bead-In-EMulsions, GEMs) is created by making barcoded cDNA unique to each individual emulsion. Recovery agent was added to break GEM and cDNA was then amplified. A library is produced via end repair, dA-tailing, adaptor ligation, post-ligation cleanup with SPRIselect, and sample index PCR. The quality and concentration of the amplified cDNA was evaluated by Bioanalyzer (Agilent 2100) on a High Sensitivity DNA chip (Agilent, #5065-4401). Only cDNA with average library size 260-620 bp were used for sequencing. Sequencing was performed by Illumina HiSeq2500 with the following read length: 26 bp for Read1, 8 bp for i7 Index, and 98 bp for Read2. We generally acquired ~180 million reads per library (sample).  A species mixing experiment (mouse adipose stem cells and human iPSCs, 1:1 mixture) was also performed prior to running on actual sample to ensure good quality of single cell capture (i.e., cell doublet rate < 5%.).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: C59-D28_scRNA-seq

description: C59 treated_hiPSC-derived chondrogenic pellet_day 28


title: C59-D42_scRNA-seq

description: C59 treated_hiPSC-derived chondrogenic pellet_day 42


title: C59-D7_scRNA-seq

description: C59 treated_hiPSC-derived chondrogenic pellet_day 7


title: N108

description:
S128
ACGEJ123pairs_gene_expression_hg19.txt


title: D42_scRNA-seq

description: hiPSC-derived chondrogenic pellet_day 42


title: N130

description:
S136
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title: ATCC_ap


title: D28_scRNA-seq

description: hiPSC-derived chondrogenic pellet_day 28


title: N107

description:
S127
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title: 3_24: 3-control artery

city: Suita City

first: Mika

last: Kushamae

state: Osaka

address: 6-1 Kishibeshinmachi

department: Department of Molecular Pharmacology

institute: Research Institute, National Cerebral and Cardiovascular Center

data_processing:
Illumina software (CASAVA) used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rn6 whole genome using CLC genomics workbench software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rnor6.0
Supplementary_files_format_and_content: excel file

organism: Rattus norvegicus

source_name: 3-control artery

extract_protocol:
Dissected rupture-prone aneurysms and the remaining circle of Willis from the same animal were grinded and homogenized in liquid nitrogen at the 63rd day after surgical manipulations. The total RNA was isolated from homogenized samples using an RNeasy fibrous tissue mini kit (QIAGEN, Hilden, Germany) with an on-column DNase treatment, according to the manufacturer’s instructions.
mRNA-seq libraries were produced using standard protocol of the Truseq stranded mRNA prep kit.

treatment_protocol: To induce IAs, rats were subjected to a bilateral ovariectomy, a ligation of the left carotid artery, the right external carotid artery, and the right pterygopalatine artery, and systemic hypertension was achieved by the combination of a high salt diet and the ligation of the left renal artery 4 under general anesthesia, which was induced by the combination of an intraperitoneal injection of pentobarbital sodium (50 mg/kg) with inhalation of isoflurane (1.5~2 %). Immediately after surgical manipulations, animals were fed chow containing 8% sodium chloride and 0.12 % 3-aminopropionitrile , an irreversible inhibitor of Lysyl Oxidase catalyzing the cross-linking of collagen and elastin.

value: Sprague Dawley (SD)

value: the remaining circle of Willis


title: N104

description:
S125
ACGEJ123pairs_gene_expression_hg19.txt


title: 3_23: 3-intracranial aneurysm lesion

source_name: 3-intracranial aneurysm lesion

value: unruptured aneurysm


title: 2_19: 2-control artery

source_name: 2-control artery


title: D14_scRNA-seq

description: hiPSC-derived chondrogenic pellet_day 14


title: 1_11: 1-control artery

source_name: 1-control artery


title: D7_scRNA-seq

description: hiPSC-derived chondrogenic pellet_day 7

value: hiPSC-derived chondrogenic pellet_day 7


title: N100

description:
S124
ACGEJ123pairs_gene_expression_hg19.txt

source_name: Adjacent normal tissue sample


title: 2_18: 2-intracranial aneurysm lesion

source_name: 2-intracranial aneurysm lesion


title: 1_10: 1-intracranial aneurysm lesion

source_name: 1-intracranial aneurysm lesion


title: Cp_scRNA-seq

description: hiPSC-derived chondroprogenitor stage

value: hiPSC-derived chondroprogenitor stage


title: D1_scRNA-seq

description: hiPSC-derived chondrogenic pellet_day 1

source_name: hiPSC-derived chondrogenic pellet_day 1

value: hiPSC-derived chondrogenic pellet_day 1


title: T92

description:
S123
ACGEJ123pairs_gene_expression_hg19.txt

source_name: Tumor tissue sample

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue


title: wild-type C57BL6 GMP 1

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

country: Denmark

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

description: Granulocyte-Monocyte Progenitor (GMP)

hyb_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin using the Affymetrix/ThermoFisher Fluidics Station 450, and the arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images

scan_protocol: Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix).

data_processing: For normalization and batch correction of murine microarray data, microarray CEL files of our own sorted inv(16)/KITD816Y AML GMP replicates were normalized together with 21 public available microarray CEL files of normal murine BM populations (GSE15907). Briefly, we applied the Robust Multichip Average (RMA) method for normalization of all microarray CEL files partitioned by origins, and applied the empirical Bayes method ?Combat? in an R package to eliminate potential lab batch effects. Batches were defined as the study number, while the covariate was defined as the type of cell population.

source_name: Bone marrow

label_protocol: Purified RNA was analyzed on expression arrays. RNA was processed using Mouse Gene 1.0 ST Reagent Kit. RNA was reverse transcribed and used for cRNA synthesis, labelling and hybridization with Mouse Gene 1.0 ST Array (ThermoFisher) according to the manufacturer’s protocol.

growth_protocol: Untreated fresh BM of sorted GMPs

extract_protocol: RNA was extracted from 200000 sorted GMPs using miRNeasy KIT (Qiagen) according to the manufacturer's instructions

value: WT C57BL6

value: granulocyte macrophage progenitor (GMP) cells

tag: cell markers

value: Lin- IL7R- Sca1- ckit+ FcgRhiCD34+


title: wild-type C57BL6 GMP 3

description: Granulocyte-Monocyte Progenitor (GMP)


title: Scl_scRNA-seq

description: hiPSC-derived sclerotomal stage

source_name: hiPSC-derived scletorome

value: hiPSC-derived sclerotomal stage


title: IMX2109 replicate 2

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

data_processing:
RNA-seq reads were aligned to IMF17 reference using STAR version 2.5.4a
resulted sequence alignment map file (SAM) converted in sorted BAM file with samtools
The sorted BAM file was processed with featureCounts for quantification
raw counts normalized with RPKM from edgeR and low expressed genes were filtered out (mean_IMF17 OR > 10 mean_IMX2109 > 10 are kept)
For differential analysis the raw counts (from the kept genes) were processed with DESeq2
Genome_build: IMF17 Nanopore assembled genome (PRJNA596648; CP063255)
Supplementary_files_format_and_content: Comma delimited file, normalized transcript counts

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cell culture

growth_protocol: Strains IMF17 and IMX2109 were inoculated from a freezer stock in 100 mL selective minimal glucose medium in a 500 mL shake flask (aerobic). The strains were transferred in biological triplicate to fresh medium and grown until mid-exponential phase at an OD660 of 8.

extract_protocol:
RNA was extracted with hot-phenol method as described by Schmitt et al. (1990)
cDNA libraries were prepared using the TruSeq stranded mRNA kit (illumina) and sequenced on HISeq 2500 (illumina) at Macrogen

treatment_protocol: Cultures were sampled into liquid nitrogen and processed as described by Piper et al. (2002)

tag: strain

tag: replicate

value: Replicate 2


title: inv(16):KitD816Y L-GMP 3

description: Granulocyte-Monocyte Progenitor (GMP)

value: Lin- Sca1- ckit+ CD41- FcgR+ CD150-


title: T88

description:
S122
ACGEJ123pairs_gene_expression_hg19.txt


title: N106

description:
S126
ACGEJ123pairs_gene_expression_hg19.txt

value: Adjacent normal tissue


title: IMF17 replicate 3

value: Replicate 3


title: hiPSC_scRNA-seq

description: Undifferentiated stem cell stage

source_name: human forskin fibroblasts

value: Undifferentiated stem cell stage


title: IMX2109 replicate 1

value: Replicate 1


title: N128

description:
S134
ACGEJ123pairs_gene_expression_hg19.txt

value: Chinese


title: wild-type C57BL6 GMP 2

description: Granulocyte-Monocyte Progenitor (GMP)


title: T84

description:
S121
ACGEJ123pairs_gene_expression_hg19.txt


title: T82

description:
S120
ACGEJ123pairs_gene_expression_hg19.txt


title: IMF17 replicate 1


title: Dif_NSCs__Qk_KO.rep2

city: Higashi-Osaka

first: Kei

last: IIDA

address: Kowakae 3-4-1

institute: Kindai University

data_processing:
Basecalls performed using Torrent Suite version 5.0.4
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d
Genome_build: mm10
Supplementary_files_format_and_content: Expression values for refseq gene models (GRCm38.p4) were calcurated with RSEM (ver. 1.3.0).

source_name: glial progenitors day1

extract_protocol:
Total RNA from cerebral cortical regions of brains or neuronal stem cells were extracted using Rneasy Plus Midi kit (Qiagen) according to the manufacturer’s instructions.
Libraries were prepared according to Life Techonology's instructions accompanying the Ion AB Library Builder™ System and Library Builder. Briefly, total RNA was treated with Dynabeads® mRNA DIRECT™ Microkit to prepare PolyA-selected messenger RNA. RNA libraries were then prepared using the Life Techonology Ion Total RNA-Seq Kit for the AB Library Builder™ System and Library Builder. High-throughput sequencing was performed using the Ion Proton System. Sfpq mRNA level was down-regulated less than 10% in Neuro-2a treated with Sfpq-siRNA comparing those of Luc-siRNA.

value: Neural stem cells

tag: time

value: 24 hr after induced glial differentiation

value: cerebral cortex of embyonic brains


title: inv(16):KitD816Y L-GMP 2

description: Granulocyte-Monocyte Progenitor (GMP)


title: input_minus

city: Wuhan

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

data_processing:
The transcriptome sequencing project was completed on Illumina sequencing platform, Illumina PE library (~300bp) was constructed for sequencing, quality control was carried out on the obtained sequencing data, and then the transcriptome data was analyzed by means of bioinformatics
ChIP-seq reads were aligned to the hg18/Ch37 genome
The original image data sequenced by Illumina Hiseq was transformed into sequence data via Base Calling, namely in FASTQ format, to obtain the most original sequencing data file. FASTQ format file can record the base and its mass fraction of read. FASTQ format is stored as a unit of sequencing read segments, with each read segment accounting for 4 lines. The first and third lines are composed of sequence identifiers and read segment names (the first line begins with "@" and the third line begins with "+"). In the third line, ID can be omitted, but "+" cannot be omitted), the second behavior base sequence, and the fourth behavior the sequencing quality fraction of the corresponding position base.
Genome_build: human Ch37
Supplementary_files_format_and_content: After the sequencing data is taken off the machine, the original sequencing sequence of each sample, which we call raw data or raw reads, is stored in FASTQ (fq for short) file format. Raw data is evaluated for quality (software: FastQC). FastQC is a data quality visualization software that aims to provide an easy way to evaluate data quality to guide downstream analysis on whether or how to proceed.

source_name: human breast cancer cell

growth_protocol: Cells were cucltured into DMEM medium with 10% FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-BAP18.
The steps of DNA library construction are as follows:1.Fix the ends of the DNA from the IP with base A,and repair to add A DNA add sequencing joint processing;2.Magnetic beads were used to recover the target size fragment and PCR amplification was performed to obtain the library to be sequenced;3.The libraries were examined by agarose electrophoresis;4.Qubit 2.0 was used to quantify the library to determine whether the library concentration was suitable for computer;5.After the libraries passed the quality inspection, different libraries were sequenced on Illumina sequencer according to the requirements of effective concentration and target data volume.

treatment_protocol: MCF7 cells were treated with or without 10nM estrodiol in culture medium for 48 hours

tag: antibody

value: without estrogen


title: Dif_NSCs__Cont.rep2

tag: cell type

value: wild type

tag: tissue


title: input_plus

value: with estrogen


title: T81

description:
S119
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: patient


title: IMX2109 replicate 3


title: IP_plus


title: T80

description:
S118
ACGEJ123pairs_gene_expression_hg19.txt

tag: population


title: Dif_NSCs__Cont.rep1


title: P7_Ctx__Qk_KO.rep1

data_processing:
Basecalls performed using Torrent Suite version 4.0.2
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d
Genome_build: mm10
Supplementary_files_format_and_content: Expression values for refseq gene models (GRCm38.p4) were calcurated with RSEM (ver. 1.3.0).

source_name: P7 mouse cerebral cortex

value: cerebral cortex of brain

tag: age

value: postnatal day 7


title: T79

description:
S117
ACGEJ123pairs_gene_expression_hg19.txt


title: IMF17 replicate 2


title: P7_Ctx__Cont.rep1


title: IP_minus

tag: treatment


title: P7_Ctx__Cont.rep3


title: P7_Ctx__Cont.rep2


title: P7_Ctx__Qk_KO.rep2


title: Dif_NSCs__Qk_KO.rep1


title: T75

description:
S116
ACGEJ123pairs_gene_expression_hg19.txt


title: Mouse Islet 16 [exon-level]

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

hyb_protocol: Sample set 01 hybridized to Mouse Exon 1.0 ST arrays at 45°C for 16 hrs O/N following all procedures outlined in the GeneChip WT Terminal Labeling and Hybridization User Manual ( P/N 702808 Rev.6)  for Mouse Exon 1.0 ST Arrays

scan_protocol: GeneChips post processed on the AFX Fluidics 450 Station according to all AFX protocols  and procedures defined for the Mouse Exon 1.0 ST Array (FS450 _0001) as outlined  GeneChip Expression Wash,Stain and Scan user Manual (P/N 702731 rev.3)  GC scanned on the GC3000 G7 Scanner (S/N 50205130).

data_processing:
Raw probe cell intesity data was analyzed at both the gene- and exon-level using the Robust Multichip Analysis (RMA) algorithm within the Affymetrix Expression Console 1.3 software package. Data extracted and processed using Affymetrix Command Console version 3.2.4.1515W.
affymetrix-algorithm-name = rma-exon-full : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20

source_name: WT High Fat Diet

label_protocol: Ambion GeneChip WT Expression kit ( Lot#4440536) used for labeling. Targeted 200ng RNA in-put for each sample. All protocols and procedures followed as outlined in the Ambion WT Expression Kit manual (Manual P/N 4425209 Rev. D ). All samples carried through to 16 hour IVT O/N reaction. Upon completion of IVT reactions, samples cleaned up according to the protocol and procedures outlined in the Ambion WT Expression manual and quantified on the NanoDrop  Ten ug cRNA used for template input for round 2 of ss cDNA synthesis  Round two ss cDNA samples purified according to the protocol and procedures outlined in the Ambion WT manual and quantified on the NanoDrop. Samples set up for fragmentation with a 5.5ug template in-put.  Samples fragmented with a 5.5ug template in-put, upon completion of fragmentation 45ul transferred to new 0.2ml tube for end-terminus labeling, the remaining vol. to be used for Agilent  Fragmented cDNA samples stored at -20°C  1ul used for analysis on the Agilent RNA Nano chip – tested samples look similar and within the recommended nt range  All samples end-terminus labeled.

growth_protocol: Pancreatic islets were isolated from 37-40-week-old experimental mice (WT or GazKO; control-or HFD-fed;  N=5 per  group)  using  a  collagenase  digestion  procedure  previously  described4.  A  stereomicroscope was  used  to  hand-pick  islets  from  contaminating  acinar  tissue  into  a  microfuge  tubecontaining  1  ml phosphate-buffered saline (PBS) and washed one additional time in PBS, with pulse centrifugation used to pellet the islets.

extract_protocol: The PBS was aspirated, and 200 μl RLT buffer (Qiagen) added. Islets were lysed using a plastic micropestle homogenizer and RNA purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions. RNA quality was assessed by electrophoresis using a Eukaryote Total RNA Pico cartridge and Bioanalyzer 2100 instrument (Agilent). The minimum RNA Integrity Score (RIN) of samples subject to microarray analysis was 7.40, with most samples having RIN scores of 8.0 or above.

value: 6 months

tag: Sex

value: male

value: WT

tag: diet

value: High Fat

value: Pancreatic islets


title: Mouse Islet 17 [exon-level]

source_name: KO High Fat Diet

tag: genotype

value: Gaz KO