title: RNA-Seq Sample1, Colon, WT, Control

description:
raw_read_count_matrix.txt
s1

data_processing:
Adapter sequences and poor quality bases were trimmed with cutadapt
Data were aligned to joint mm10 and hIL26-BAC reference genome using STAR aligner
Read counts per gene were summarised using featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts per gene, tab delimited

source_name: Colon

growth_protocol: WT (C57BL/6 B6) or TG (C57BL/6 with human IL26 BAC transgene) littermate mice were housed in pathogen-free conditions with regularized day-night cycles and ad-libitum access to sterile food and water

extract_protocol:
Mice were sacrificed at the timepoints specified above, followed by dissection of their colons, tissue homogenized using 1.4mm ceramic beads, and RNA extraction performed using Qiagen MiniPrep RNA isolation kits
Libraries were enriched for mRNA followed by directional strand tagging using the directions for NEBNext Ultra Directional RNA Library Prep Kit for Illumina (#7420). Briefly, mRNA enrichment was followed by fragmentation, generating 250-350 bp fragment sizes, followed by cDNA generation. Following size-based fragment purification, NEB Next Adaptor for Illumina was ligated to the cDNA fragments, purified, followed by PCR to amplify the library, which was then sequenced on a Novaseq 6000 S4 platform

treatment_protocol: Male and Female mice were assessed for development of spontaneous colitis (20-24 weeks) or after exposure for 6 days to 2.5% (w/v) DSS at 10-14 weeks of age.

value: Colon

value: WT

tag: treatment

value: Control


title: Oocyte_1 [CLEVER-seq]

status: Public on Aug 02 2020

type: SRA

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

library_source: genomic

data_processing:
Library strategy: CLEVER-seq
Illumina CASAVA version 1.8 were used to the basecalling.
We used Trim Galore (v0.3.3) to remove adaptors and low quality bases.
Next, reads passed quality control were mapped to human reference genome (version: hg19) using Bismark (v0.13.0). After alignment, PCR duplicates were removed with the command ‘samtools rmdup’ (v0.1.18).
Genome_build: hg19
Supplementary_files_format_and_content: The processed bed files include chromosome, start position, end position, reference genotype, regular CpG ("0") or 5fCpG ("1"), strand.

molecule: genomic DNA

organism: Homo sapiens

source_name: Oocyte

extract_protocol:
The CLEVER-seq experiment was carried out according to the previous study with slight modification. The single cells of human early embryo were transferred into lysis buffer (20 mM Tris, 2 mM EDTA, 20 mM KCl, and 0.3% TritonX-100, 1 mg/ml QIAGEN protease) by mouth pipette. After centrifugation (1 min at 7,000 r.p.m., 4°C), the sample was incubated at 50°C for 3 hr to release the genomic DNA followed by 70°C for 30 min to inactive the protease. Then trace mount of spike-in oligo DNA contain 5fC modification was added into sample. In order to label the 5fC, 150 mM malononitrile (J&K) was used. Mineral oil (15 μl) was add onto the surface of the sample to prevent evaporation. The sample was incubated at 37°C for 20 hr with constant shaking at 850 r.p.m. in the Thermomixer (Eppendorf). Then the single cell genome was amplified by MALBAC (Yikon Genomics) according to the user guide.
The genomic DNA was fragment into ~300 by by covaris S2. The library construction was performed using KAPA Hyper Prep Kit (Kapa Biosystems). The libraries were sequenced on Illumina Hiseq 4000 platform in pair-end 150 bp model (Novogene).

tag: developmental stage

value: MII oocyte


title: LizardD_B12

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 for mouse, and for Pogona vitticeps pvi1.1 from http://georges.biomatix.org/genomics-uc, For annotation a synthetic chromosom. composed of al of Pogona vitticepsl transcript models extracted from  “Pogona_vitticeps.male.cds"  from http://georges.biomatix.org/genomics-uc, extended with 200bp to the 5’ end separated by 20 bp spacers.
Supplementary_files_format_and_content: Tab-delimited file of UMI counts

molecule: polyA RNA

organism: Pogona vitticeps

source_name: brain

extract_protocol:
Fresh frozen and O.C.T (Tissue-Tek) embedded brains were sectioned and 14 μm thick sections collected on agarose membranes. A metal frame was then placed on the slide and used to make a well, filled with O.C.T and quickly frozen on dry ice. The glass slide was removed and
replaced with a second metal frame and the created well was filled with O.C.T and frozen.  In order to mount the sample at a predefined angle we first use a scalpel to remove the sample from the metal frames and then angled using a custom made positioning device. After mounting in the correct angle, he sample was repositioned on the cryostat and 70 μm strips were sliced, collected with a forceps and transferred in a 96-wells plate kept inside the cryostat. The angle of the cryostat sample holder was not changed between samples

tag: slice id (cutting angle and slice index)


title: RNA-Seq Sample21, Colon, TG, DSS

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
raw_read_count_matrix.txt
s21

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: TG

value: DSS


title: ATAC ctrl_14d rep3

city: Pasadena

first: Theodora

last: Koromila

state: CA

address: 1200 E Califonia Blvd

country: USA

institute: California Institute of Technology

data_processing:
ATAC-seq data, the raw 151bp paired-end fastq data were trimmed to before aligned to drosophila dm6 reference genome assembly using Bowtie2 aligner. Aligned bam files were subject to further sorting and duplicate removal using samtools before downstream analysis.
RNA-seq data, the raw 151bp paired-end fastq data were trimmed before aligned to drosophila dm6 reference genome/gene annotation using TOPHAT2. Aligned bam files were subject to gene quantification and differential analysis using cufflinks and cuffdiff pipelines.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig for ATACseq, gene statistics table for RNAseq

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Individual embryos were collected on agar plates from females of the following genotypes: wild-type/control (i.e y w females crossed to sh_opa males), mutant (i.e.MTD-Gal4 x sh_opa), or ectopically-expressing opa (i.e. MTD-Gal4 x UAS-opa). Nuclear morphology was observed under a compount microscope at 20x magnification.Single sh_opa and control embryos were assayed at nc14D (nc14+45’), whereas UAS-opa and control embryos were assayed at nc14B (nc14+20’).  Temperatures for sample collection were maintained at 26C to minimize variation in cell cycle timing. Under these conditions, cell cycle times were indistinguishable. Cell cycles were timed from the onset of anaphase of the previous cell cycle. Each embryo was hand-selected and hand-dechorionated for the analysis.
Fragmentation and amplification of ATAC-seq libraries were performed essentially as described previously (Buenrostro et al., 2015). RNA-seq libraries were constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770) following the manufacturer’s instructions.
Prepared libraries were subject to paired-end sequencing using an Illumina NovaSeq.

value: embryos

tag: age at harvest

value: wt


title: ATAC shOpa_14d rep1

value: Opa shRNAi


title: Sperm_9 [CLEVER-seq]

source_name: Sperm

value: Mature sperm


title: Sperm_10 [CLEVER-seq]


title: LizardD_B11


title: ATAC ctrl_14d rep2


title: Oocyte_5 [CLEVER-seq]


title: Sperm_8 [CLEVER-seq]


title: LizardD_B10


title: RNA-Seq Sample20, Colon, TG, DSS

description:
raw_read_count_matrix.txt
s20


title: Sperm_7 [CLEVER-seq]


title: LizardD_B09


title: RNA-Seq Sample13, Colon, TG, Control

description:
raw_read_count_matrix.txt
s13


title: Sperm_6 [CLEVER-seq]


title: LizardD_B08


title: PHD2/3_KO_03 (PX8830_CAGATC_L001)

city: Houston

first: Xinchun

last: Pi

state: Texas

address: One Baylor Plaza

department: Medicine

institute: Baylor College of Medicine

data_processing:
Data was mapped to the mouse geneome using TopHat2 and the UCSC mm10 mouse genome as reference.
Gene expression was quantified using Cufflinks 2 and the Genecode reference.
Differential gene expression was determined using parametric t-test
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited file contains the FPKM for the Samples after quantile normalization.

source_name: heart tissue

extract_protocol:
A RNeasy Miniprep Kit  (Qiagen) was used to isolate the RNA following the manufacturer's guidelines.
Illumina TruSeq kit was used in library preparation following the manufacturer's guidelines

tag: strain

value: PHD2/3 endothelial knockout

value: heart

tag: age


title: Sperm_5 [CLEVER-seq]


title: RNA-Seq Sample19, Colon, TG, DSS

description:
raw_read_count_matrix.txt
s19


title: PHD2/3_KO_02 (PX8828_GCCAAT_L001)


title: ATAC shOpa_14d rep2


title: LizardD_B07


title: Sperm_4 [CLEVER-seq]


title: PHD2/3_KO_04 (PX8906_ACTTGA_L001)


title: RNA-Seq Sample14, Colon, TG, Control

description:
raw_read_count_matrix.txt
s14


title: LizardD_B06


title: Sperm_2 [CLEVER-seq]


title: RNA-Seq Sample10, Colon, WT, DSS

description:
raw_read_count_matrix.txt
s10


title: Wildtype_04 (PX8826_TGACCA_L001)

value: Wild type


title: RNA-Seq Sample6, Colon, WT, DSS

description:
raw_read_count_matrix.txt
s6


title: Wildtype_03 (PX8825_TTAGGC_L001)


title: LizardD_B05


title: RNA-Seq Sample7, Colon, WT, DSS

description:
raw_read_count_matrix.txt
s7


title: ATAC ctrl_14d rep1


title: PHD2/3_KO_01 (PX8827_ACAGTG_L001)


title: Sperm_3 [CLEVER-seq]


title: LizardD_B04


title: Sperm_1 [CLEVER-seq]


title: RNA-Seq Sample22, Colon, TG, DSS

description:
raw_read_count_matrix.txt
s22


title: LizardD_B03


title: ATAC Zld mut rep2

description:
atac_zld_all.bw
zld_mut2

data_processing:
For both ChIP-seq and ATAC-seq data, the raw fastq data of 50-bp single-end sequencing reads were trimmed using Trimmomatic-0.38 tool to remove Illumina adapter sequence before aligned to drosophila dm6 reference genome assembly using Bowtie2 aligner. Aligned bam files were subject to further sorting and duplicate removal using samtools. Reads mapped to chr2L,chr2R,chr3L, chr3R, chr4, chrX were kept for downstream analysis. Bioligical replicate bam files were merged before generating signal trace files using using bamCoverage function of deepTools, with RPKM method for normalization and 10bp as genomic bin size.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig

source_name: ATAC

extract_protocol:
Embryos produced from either wild-type (D. melanogaster.ZH-86Fb) or mutant sh opa and sh zld were collected on yeasted apple juice agar plates. Individual embryos were selected from plates , and nuclear morphology was observed under a compount microscope at 20x magnification. Temperatures for sample collection were maintained between 22°C and 24°C to minimize variation in cell cycle timing. Under these conditions, cell cycle times were indistinguishable. Cell cycles were timed from the onset of anaphase of the previous cell cycle. The staging of samples at 3-min intervals relies on the synchrony of nuclear divisions  in the early Drosophila embryos. Each embryo was hand-selected and hand-dechorionated for the analysis.
For ChIP-seq, anti-Opa antibodies were raised in two rabbits (E990 and E991) against a truncated recombinant protein spanning from amino acids 125-507 of Opa.
Fragmentation and amplification of ATAC-seq libraries were performed essentially as described previously (Buenrostro et al., 2015).
Prepared libraries were subject to single-end sequencing using an Illumina HiSeq2500.

value: late nc14


title: LizardD_B02


title: Wildtype_01 (PX8823_ATCACG_L001)


title: ATAC Zld mut rep1

description:
atac_zld_all.bw
zld_mut1


title: RNA-Seq Sample3, Colon, WT, Control

description:
raw_read_count_matrix.txt
s3


title: RNA-Seq Sample12, Colon, TG, Control

description:
raw_read_count_matrix.txt
s12


title: LizardD_B01


title: RNA-Seq Sample2, Colon, WT, Control

description:
raw_read_count_matrix.txt
s2


title: ATAC Opa mut rep2

description:
atac_opa_all.bw
opa_mut2


title: LizardD_A11


title: LizardD_A12


title: ATAC Opa mut rep1

description:
atac_opa_all.bw
opa_mut1


title: ATAC ctrl rep2

description:
atac_ctrl_all.bw
ctrl2


title: RNA-Seq Sample11, Colon, TG, Control

description:
raw_read_count_matrix.txt
s11


title: ATAC ctrl rep1

description:
atac_ctrl_all.bw
ctrl1


title: LizardD_A09


title: LizardD_A08


title: WT_input

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
RNA:Clean Reads mapped to reference  genome using Hisat2 v2.0.4
RNA:count counting
ChIP: Clean Reads mapped to reference  genome using bowtie2
ChIP: peaks were called using macs2
Genome_build: GRCm38
Supplementary_files_format_and_content: RNA:TXT file contain counts for each sample
Supplementary_files_format_and_content: ChIP:bed files were generated using macs2

source_name: KPC1199 cells infected with lentivirus expressing sgLacZ as WT

growth_protocol: KPC1199 cells were cultured in DMEM containing 10% FBS and 1% penicillin/streptomycin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Chromatin was prepared from isolated acinar cells or cell lines using standard protocol of ChIP Kit (Active Motif). In brief, cells were fixed by 1% formaldehyde for 10 min and terminated by glycine for 5 min (final concentration = 0.125 M). After 2 times washing by pre-cooling PBS (protease inhibitor containing), cells were scraped and resuspended in SDS-lysis buffer respectively (50 mM Tris-HCl Ph 7.5, 10 mM EDTA, 1% SDS and protease inhibitor), and sonicated to shear crosslinked DNA to about 200-bp. Fifty micrograms of fragmented chromatin was incubated overnight with 2.5 μl of anti-H3K36me3 antibody (Abcam, ab9050) and normal IgG (used as negative control). Complexes were isolated using pre-cleaned protein G agarose (1 hour at 4 ℃). Immunoprecipitated DNA was prepared as a standard illumine library according to Illumina's instructions.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: KPC1199 cells were infected with lentivirus expressing both Cas9 enzyme and sgRNA against LacZ and Setd2, respectively. Monoclonal cells were selected with 2μg/ml puromycin treatment for 2 weeks.

tag: genotype/variation

tag: cell line

tag: antibody

value: IgG


title: ChIP wce late rep2

description:
ChIP_Opa_late.bw
wce_late_2

value: 4h embryo collection (mid nc14 to gastrulation)

tag: chip antibody


title: WT_IP

value: infected with lentivirus expressing sgLacZ

value: anti-H3K36me3 antibody (Abcam, ab9050)


title: KO_input

source_name: Setd2 knockout KPC1199 cells using CRISPR/Cas9, as KO

value: Setd2 knockout using CRISPR/Cas9


title: Wildtype_02 (PX8824_CGATGT_L001)


title: ChIP wce late rep1

description:
ChIP_Opa_late.bw
wce_late_1


title: mice 9,3-3 (mRNA)

type: RNA

first: Zhenlin

last: Huang

state: Shanghai

address: 1200 Cailun Road, Zhangjiang High Tech Park

department: Institute of Chinese Materia Medica

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 9 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: 330mg/kg MCT group

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology). Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: Mice were supplied with standard laboratory diet and water ad libitum at a temperature 22±1 °C with a 12 h light–dark cycle (6:00–18:00) and 65±5% humidity. All mice were received humane care in compliance with the institutional animal care guidelines approved by the Experimental Animal Ethical Committee, Shanghai University of Traditional Chinese Medicine.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Twenty-four C57BL/6 male mice were randomly divided into 3 groups: (1) vehicle control (n=8), (2) 270 mg/kg MCT (n=8), (3) 330 mg/kg MCT (n=8). Mice were fasted for 12 h before orally given with different doses of MCT (270, 330mg/kg, intragastric administration), but allowed water ad libitum. Mice were allowed food and water ad libitum after MCT administration. Animals were sacrificed 48 h after MCT administration, and blood and livers were collected.

tag: Sex

value: male

value: 6 weeks

value: liver

tag: agent

value: Monocrotaline

tag: dose


title: LizardD_A07


title: ChIP Opa late rep2

description:
ChIP_Opa_late.bw
opa_late_2

value: In-house anti-Opa antibody


title: mice 8,3-2 (mRNA)

institute: Shanghai University of Traditional Chinese Medicine


title: RNA-Seq Sample4, Colon, WT, Control

description:
raw_read_count_matrix.txt
s4

value: Colon

value: WT

value: Control


title: WT-2

description:
all.counts.txt
WT_2


title: LizardD_A06


title: ChIP Opa late rep1

description:
ChIP_Opa_late.bw
opa_late_1

value: wt


title: WT-1

description:
all.counts.txt
WT_1


title: LizardD_A10


title: LizardD_A05


title: LizardD_A04


title: KO_IP


title: ChIP wce early rep2

description:
ChIP_Opa_early.bw
wce_early_2

value: 3h embryo collection  (nc13 to mid nc14)


title: KO2-2

description:
all.counts.txt
KO2_2


title: ChIP wce early rep1

description:
ChIP_Opa_early.bw
wce_early_1


title: KO2-1

description:
all.counts.txt
KO2_1


title: ChIP Opa early rep2

description:
ChIP_Opa_early.bw
opa_early_2


title: mice 4,2-1 (mRNA)

source_name: 270mg/kg MCT group


title: LizardD_A03


title: mice 6,2-3 (mRNA)


title: mice 7,3-1 (mRNA)


title: mice 3,1-3 (mRNA)

source_name: control group

value: saline

value: control


title: mice 5,2-2 (mRNA)


title: mice 2,1-2 (mRNA)


title: mice 1,1-1 (mRNA)


title: LizardD_A02


title: KO1-2

description:
all.counts.txt
KO1_2


title: LizardD_A01


title: ChIP Opa early rep1

description:
ChIP_Opa_early.bw
opa_early_1


title: KO1-1

description:
all.counts.txt
KO1_1


title: Tx_Ribavirin_2

city: Ciudad de México

first: Alfredo

last: Hidalgo-Miranda

state: CDMX

address: Periferico Sur #4809

department: Cancer Genomic

country: Mexico

institute: INMEGEN

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, USA).

data_processing: Array signal intensities were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

label: biotin

label_protocol: SensationPlus™ FFPE Amplification and WT Labeling Kit were used to generate the biotinylated cRNA starting from 100ng of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

growth_protocol: The cutaneous T-cell lymphoma was grown in RPMI +10% fetal bovine serum prior to treatment with Ribavirin.

extract_protocol: Trizol method was used to extract the total RNA.

treatment_protocol: Hut78 cell line was treated with 50 μM of Ribavirin for 120 h. As control (C), cells without treatment were used.

tag: cell type

value: Cutaneous T-cell lymphocyte

value: Ribavirin


title: dfr-14_BRGC-4

status: Public on Aug 01 2020

first: Bo

middle: G

last: Lindberg

address: Svante Arrhenius väg 20 C

department: MBW

institute: Stockholm University

data_processing:
fastq files were aligned to Ensembl release 95 of Drosophila melanogaster reference genome BDGP6 using STAR after being trimmed with TrimGalore
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Transcripts with average counts below 1 in at least one group were filtered out using the keep function in the edgeR package in R
Expression data was normalized using the calcNormFactors function in the edgeR package in R
Common dispersion and tagwise dispersions were estimate in one run using the estimateDisp function in edgeR
Differentially expressed genes (5% false discovery rate) in BRGC and body were identified by separate analyses using Exact test in edgeR.
Genome_build: Ensembl release 95 of Drosophila melanogaster reference genome BDGP6
Supplementary_files_format_and_content: Excel file includes normalized gene counts and counts adjusted to zero baseline for each sample, exact test and annotation

source_name: Brain-ring gland complex

growth_protocol: Larvae were reared at 25 degrees C at 60 % rel. Humidity

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using a HiSeq2500 (Illumina TruSeq Stranded mRNA) with Poly-A selection

tag: background strain

value: untreated


title: dfr-14_body-4

source_name: Rest of body

value: wild-type

tag: treatment


title: dfr-14_BRGC-2


title: dfr-14_BRGC-1


title: dfr-14_body-2


title: control_BRGC-4


title: dfr-14_body-3


title: control_BRGC-2


title: control_body-4


title: control_BRGC-1


title: Control_2

source_name: Control


title: control_BRGC-3


title: control_body-1


title: control_body-3


title: Tx_Ribavirin_1


title: dfr-14_BRGC-3


title: dfr-14_body-1


title: control_body-2


title: Control_1


title: SM_Dropseq

city: Davis

first: Celina

middle: E

last: Juliano

state: California

address: 149 Briggs Hall

department: MCB

institute: University of California Davis

description:
HMT-3522/MEF 1:1 mix for species mixing experiment
SM_UMIcounts.txt

data_processing:
Data was processed using Drop-seq tools v1.01, according to Drop-seq protocol v3.1 (http://www.dropseq.org/). Read 2 was aligned with Bowtie2 v 2.2.6 to Ensembl GRCh38 using release 92 gene models. Each aligned read was tagged with its mate-pair UMI and cell barcode (which comprise Read 1). Each aligned exonic read was tagged with a gene name. Cell barcodes were corrected for synthesis errors. A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. The first inflection point was estimated on a cumulative sum plot of the digital expression matrix to determine the number of cells in the sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file of UMI counts

organism:
Homo sapiens
Mus musculus

source_name: Human Caucasian breast epithelial/Mouse embryonic fibroblasts

growth_protocol: HMT-3522 cell lines were maintained in DMEM/ F12 (Gibco) supplemented with prolactin, insulin, sodium selenite, hydrocortisone, β-estrogen, transferrin.

extract_protocol:
Cells were encapsulated using a standard Drop-seq apparatus. Lysis occurred in droplets in Drop-seq lysis buffer (www.drop-seq.org)
Libraries were prepared according to Drop-seq Protocol v3.1 (12/28/2015), with 12–15 cycles of PCR amplification and 100 STAMPs per PCR reaction.

treatment_protocol: Prior to Drop-seq cells were dissociated with 0.25% trypsin/ EDTA and rinsed into phosphate buffered saline. Cells were washed and resuspended in PBS + 0.05% BSA.


title: nasopharyngeal carcinoma, specimen T2-3

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description: Gene expression of nasopharyngeal carcinoma, specimen T2-3

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: nasopharyngeal carcinoma, specimen

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

value: nasopharyngeal carcinoma

tag: gender

value: female


title: nasopharyngeal carcinoma, specimen T4-2

description: Gene expression of nasopharyngeal carcinoma, specimen T4-2


title: nasopharyngeal carcinoma, specimen T2-2

description: Gene expression of nasopharyngeal carcinoma, specimen T2-2

value: male


title: nasopharyngeal carcinoma, specimen T4-1

description: Gene expression of nasopharyngeal carcinoma, specimen T4-1


title: PB_preDC, WTCHG_324058_712507

city: Newcastle upon Tyne

first: Anastasia

last: Resteu

address: M3.127, 3rd Floor Leech Building, Framlington Place

institute: Newcastle University

data_processing:
Trimmed with Trimmomatic v 0.36
Aligned reads with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 60bp were dropped
Counts were obtained with HTSEQ v 0.6.1
Further processing was performed in R 3.3.3. The cells were filtered based on precentage of ERCC counts (<25%), mitochondrial percentage (<30%), total features (>3000 and <5000), total counts (>25000)
Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files with HTSEQ counts
Supplementary_files_format_and_content: PB_preDC_flow_channel_values.csv: Channel values produced when sorting the individual cells for scRNA-Seq.

source_name: peripheral blood

growth_protocol: primary cells

extract_protocol:
none
Smart-seq2 and Nextera XT

tag: passed cell qc

value: YES


title: nasopharyngeal carcinoma, specimen T2-1

description: Gene expression of nasopharyngeal carcinoma, specimen T2-1

tag: tissue


title: nasopharyngeal carcinoma, specimen T3-2

description: Gene expression of nasopharyngeal carcinoma, specimen T3-2


title: PB_preDC, WTCHG_324058_712508

value: early pre-DC2


title: PB_preDC, WTCHG_324058_712517


title: amphotericin B treated cultures, reference strain

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

description: transcriptome of 16.5 h cultures treated with 2 mM AmB at 16h; total RNA from three biological replicates were pooled

hyb_protocol: Fragmented cRNA samples (1650 ng; specific activity >20.0 pmol Cy3/mg cRNA) were applied to the individual arrays. Slides were hybridized at 65°C and 10 rpm for 17 h in an Agilent hybridization oven.

scan_protocol: After washing (with GE Wash Buffer 1 at room temperature and GE Wash buffer 2 at 37°C) slides were dried by brief centrifugation and were scanned immediately on the Agilent DNA Microarray Scanner (FE SW 11.1) using one color scan setting for 1x44k array slides (Extended Dynamic Range, Scan Area 61x21.6 mm, Scan resolution 5 m, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: Prenormalised microarray data were obtained with Agilent's Feature Extraction software (version 12.0.3.1) using default one-color high density protocol. Prenormalised data were background corrected using the normexp+offset method  followed by quantile normalization between arrays.

organism: Aspergillus nidulans

source_name: mycelia, amB treated cultures

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol. Dye incorporation and cRNA yield were checked with NanoDrop.

growth_protocol: A. nidulans strains were grown in submerged cultures. All submerged cultivations were carried out in 500 ml flasks containing 100 ml Barratt’s minimal broth at 37 °C and at 3.7 Hz shaking frequency. Cultures were inoculated with 100 × 106 freshly harvested conidia.

extract_protocol: Total RNA was isolated from lyophilized mycelia according to Chomczynski (Emri et al. Methods Mol Biol. 2017;1542:345-365. doi: 10.1007/978-1-4939-6707-0_23).

treatment_protocol: 16 h cultures were treated with 2 mM AmB, 0.2 mM CdCl2 as well as 10 mM CR or were kept untreated for 0.5 h.

tag: sample type

value: reference strain

tag: genotype

value: pyrG89, AfupyrG+; pyroA+; veA+


description: Gene expression of normal nasopharyngeal tissue, specimen N-5

source_name: normal nasopharyngeal tissue, specimen

value: normal nasopharyngeal tissue


title: PB_preDC, WTCHG_324058_712506


title: CdCl2 treated cultures, delta-atfA mutant

description: transcriptome of 16.5 h cultures treated with 0.2 mM CdCl2 at 16h; total RNA from three biological replicates were pooled

source_name: mycelia, CdCl2 treated cultures

value: delta-atfA mutant

value: (pyrG89, AfupyrG+; pyroA4; DatfA::pyroA; veA+


title: PB_preDC, WTCHG_324058_712504


title: nasopharyngeal carcinoma, specimen T3-5

description: Gene expression of nasopharyngeal carcinoma, specimen T3-5


description: Gene expression of normal nasopharyngeal tissue, specimen N-4


title: nasopharyngeal carcinoma, specimen T3-3

description: Gene expression of nasopharyngeal carcinoma, specimen T3-3


title: amphotericin B treated cultures, delta-atfA mutant


description: Gene expression of normal nasopharyngeal tissue, specimen N-2


description: Gene expression of normal nasopharyngeal tissue, specimen N-3


title: untreated cultures, delta-atfA mutant

description: transcriptome of 16.5 h cultures; total RNA from three biological replicates were pooled

source_name: mycelia, untreated cultures


title: PB_preDC, WTCHG_324058_712505

value: pre-pDC

value: NO


title: CdCl2 treated cultures, reference strain


title: nasopharyngeal carcinoma, specimen T3-4

description: Gene expression of nasopharyngeal carcinoma, specimen T3-4


title: nasopharyngeal carcinoma, specimen T3-1

description: Gene expression of nasopharyngeal carcinoma, specimen T3-1


description: Gene expression of normal nasopharyngeal tissue, specimen N-6


title: Congo Red treated cultures, reference strain

description: transcriptome of 16.5 h cultures treated with 10 mM CR at 16h; total RNA from three biological replicates were pooled

source_name: mycelia, CR treated cultures


title: PB_preDC, WTCHG_324058_712503


title: Congo Red treated cultures, delta-atfA mutant


title: PB_preDC, WTCHG_324058_712502


title: untreated cultures, reference strain


title: PB_preDC, WTCHG_324058_711502


title: PB_preDC, WTCHG_324058_711505


title: PB_preDC, WTCHG_324058_710508


title: PB_preDC, WTCHG_324058_711507


title: PB_preDC, WTCHG_324058_711506


title: PB_preDC, WTCHG_324058_711504


title: PB_preDC, WTCHG_324058_711517


title: PB_preDC, WTCHG_324058_710517


title: PB_preDC, WTCHG_324058_710504


title: PB_preDC, WTCHG_324058_711503


title: PB_preDC, WTCHG_324058_710505


title: PB_preDC, WTCHG_324058_710502


title: PB_preDC, WTCHG_324058_710506


description: Gene expression of normal nasopharyngeal tissue, specimen N-1


title: PB_preDC, WTCHG_324058_709507


title: PB_preDC, WTCHG_324058_710503


title: PB_preDC, WTCHG_324058_709505


title: PB_preDC, WTCHG_324058_711508


title: PB_preDC, WTCHG_324058_708508


title: PB_preDC, WTCHG_324058_708507


title: PB_preDC, WTCHG_324058_708505


title: PB_preDC, WTCHG_324058_708504


title: PB_preDC, WTCHG_324058_710507


title: PB_preDC, WTCHG_324058_708502


title: PB_preDC, WTCHG_324058_707508


title: PB_preDC, WTCHG_324058_707505


title: PB_preDC, WTCHG_324058_707504


title: PB_preDC, WTCHG_324058_707517


title: PB_preDC, WTCHG_324058_707506


title: PB_preDC, WTCHG_324058_709508


title: PB_preDC, WTCHG_324058_706507


title: PB_preDC, WTCHG_324058_706505


title: PB_preDC, WTCHG_324058_706504


title: PB_preDC, WTCHG_324058_709506


title: PB_preDC, WTCHG_324058_707503


title: PB_preDC, WTCHG_324058_707502


title: PB_preDC, WTCHG_324058_706508


title: PB_preDC, WTCHG_324058_706506


title: PB_preDC, WTCHG_324058_709504


title: PB_preDC, WTCHG_324058_708517


title: PB_preDC, WTCHG_324058_706502


title: PB_preDC, WTCHG_324058_709502


title: PB_preDC, WTCHG_324058_708506


title: PB_preDC, WTCHG_324058_705517


title: PB_preDC, WTCHG_324058_705508


title: PB_preDC, WTCHG_324058_705507


title: PB_preDC, WTCHG_324058_705505


title: PB_preDC, WTCHG_324058_708503


title: PB_preDC, WTCHG_324058_705503


title: PB_preDC, WTCHG_324058_704517


title: PB_preDC, WTCHG_324058_704505


title: PB_preDC, WTCHG_324058_704506


title: PB_preDC, WTCHG_324058_704504


title: PB_preDC, WTCHG_324058_704507


title: PB_preDC, WTCHG_324058_704503


title: PB_preDC, WTCHG_324058_706503


title: PB_preDC, WTCHG_324058_703517


title: PB_preDC, WTCHG_324058_707507


title: PB_preDC, WTCHG_324058_703508


title: PB_preDC, WTCHG_324058_702517


title: PB_preDC, WTCHG_324058_703502


title: PB_preDC, WTCHG_324058_703505


title: PB_preDC, WTCHG_324058_702506


title: PB_preDC, WTCHG_324058_703507


title: PB_preDC, WTCHG_324058_703506


title: PB_preDC, WTCHG_324058_705506


title: PB_preDC, WTCHG_324058_702508


title: PB_preDC, WTCHG_324058_702504


title: PB_preDC, WTCHG_324058_702507


title: PB_preDC, WTCHG_324058_703503


title: PB_preDC, WTCHG_324058_702503


title: PB_preDC, WTCHG_324058_702505


title: PB_preDC, WTCHG_324058_702502


title: PB_preDC, WTCHG_324058_701508


title: PB_preDC, WTCHG_324058_701507


title: PB_preDC, WTCHG_324058_701506


title: PB_preDC, WTCHG_324058_704502


title: PB_preDC, WTCHG_324058_701505


title: PB_preDC, WTCHG_324058_701504


title: PB_preDC, WTCHG_324058_701502


title: PB_preDC, WTCHG_282156_712506


title: PB_preDC, WTCHG_324058_703504


title: PB_preDC, WTCHG_282156_712508


title: PB_preDC, WTCHG_282156_712507


title: PB_preDC, WTCHG_282156_712503


title: PB_preDC, WTCHG_282156_712505


title: PB_preDC, WTCHG_282156_712504


title: PB_preDC, WTCHG_282156_711504


title: PB_preDC, WTCHG_282156_711506


title: PB_preDC, WTCHG_282156_711517


title: PB_preDC, WTCHG_282156_711507


title: PB_preDC, WTCHG_282156_710517


title: PB_preDC, WTCHG_282156_711508


title: PB_preDC, WTCHG_282156_712502


title: PB_preDC, WTCHG_282156_711505


title: PB_preDC, WTCHG_282156_710506


title: PB_preDC, WTCHG_282156_711503


title: PB_preDC, WTCHG_282156_710508


title: PB_preDC, WTCHG_282156_710505


title: PB_preDC, WTCHG_282156_710507


title: PB_preDC, WTCHG_282156_710504


title: PB_preDC, WTCHG_282156_710503


title: PB_preDC, WTCHG_282156_710502


title: PB_preDC, WTCHG_282156_709506


title: PB_preDC, WTCHG_282156_709505


title: PB_preDC, WTCHG_282156_709507


title: PB_preDC, WTCHG_282156_709502


title: PB_preDC, WTCHG_282156_709508


title: PB_preDC, WTCHG_282156_708507


title: PB_preDC, WTCHG_282156_708508


title: PB_preDC, WTCHG_282156_708517


title: PB_preDC, WTCHG_282156_708506


title: PB_preDC, WTCHG_282156_708504


title: PB_preDC, WTCHG_282156_708503


title: PB_preDC, WTCHG_282156_707506


title: PB_preDC, WTCHG_282156_707517


title: PB_preDC, WTCHG_324058_706517


title: PB_preDC, WTCHG_282156_707507


title: PB_preDC, WTCHG_282156_707505


title: PB_preDC, WTCHG_282156_706508


title: PB_preDC, WTCHG_282156_707508


title: PB_preDC, WTCHG_282156_706507


title: PB_preDC, WTCHG_282156_707504


title: PB_preDC, WTCHG_282156_707503


title: PB_preDC, WTCHG_282156_709504


title: PB_preDC, WTCHG_282156_706504


title: PB_preDC, WTCHG_282156_706505


title: PB_preDC, WTCHG_282156_706517


title: PB_preDC, WTCHG_282156_706502


title: PB_preDC, WTCHG_282156_706503


title: PB_preDC, WTCHG_282156_706506


title: PB_preDC, WTCHG_282156_708505


title: PB_preDC, WTCHG_282156_705506


title: PB_preDC, WTCHG_282156_705507


title: PB_preDC, WTCHG_282156_705505


title: PB_preDC, WTCHG_282156_705508


title: PB_preDC, WTCHG_282156_704508


title: PB_preDC, WTCHG_282156_704517


title: PB_preDC, WTCHG_282156_705503


title: PB_preDC, WTCHG_282156_707502


title: PB_preDC, WTCHG_282156_704502


title: PB_preDC, WTCHG_282156_704503


title: PB_preDC, WTCHG_282156_704505


title: PB_preDC, WTCHG_282156_704507


title: PB_preDC, WTCHG_282156_704504


title: PB_preDC, WTCHG_282156_703507


title: PB_preDC, WTCHG_282156_703517


title: PB_preDC, WTCHG_282156_704506


title: PB_preDC, WTCHG_282156_703504


title: PB_preDC, WTCHG_282156_703508


title: PB_preDC, WTCHG_282156_703506


title: PB_preDC, WTCHG_282156_703505


title: PB_preDC, WTCHG_282156_702517


title: PB_preDC, WTCHG_282156_703503


title: PB_preDC, WTCHG_282156_702506


title: PB_preDC, WTCHG_282156_702507


title: PB_preDC, WTCHG_282156_703502


title: PB_preDC, WTCHG_282156_702508


title: PB_preDC, WTCHG_282156_705517


title: PB_preDC, WTCHG_282156_702505


title: PB_preDC, WTCHG_282156_702504


title: PB_preDC, WTCHG_282156_702502


title: PB_preDC, WTCHG_282156_701507


title: PB_preDC, WTCHG_282156_701508


title: PB_preDC, WTCHG_282156_701505


title: PB_preDC, WTCHG_282156_701504


title: WTCHG_603210_294166

data_processing:
Trimmed with Trimmomatic v 0.36
Aligned reads with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 60bp were dropped
Counts were obtained with HTSEQ v 0.6.1
Further processing was performed in R 3.3.3. The cells were filtered based on precentage of ERCC counts (<70%), mitochondrial percentage (<15%), total features (>1700), total counts (>50000)
Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files with HTSEQ counts
Supplementary_files_format_and_content: BM_preDC_flow_channel_values.csv: Channel values produced when sorting the individual cells for scRNA-Seq.

source_name: bone marrow

extract_protocol: Smart-seq2 and Nextera XT


title: WTCHG_603210_293155


title: WTCHG_603210_295179


title: WTCHG_603210_296107


title: WTCHG_603210_294167


title: WTCHG_603210_296191

value: Mono


title: WTCHG_603210_294131


title: WTCHG_603210_295119


title: WTCHG_603210_293143


title: WTCHG_603210_293154


title: WTCHG_603210_292143


title: WTCHG_603210_291130


title: WTCHG_603210_291131

value: pDC


title: WTCHG_603210_290179


title: WTCHG_603210_290118


title: WTCHG_603210_291167


title: WTCHG_603210_292142


title: WTCHG_603210_290119


title: PB_preDC, WTCHG_282156_702503


title: PB_preDC, WTCHG_282156_701506


title: WTCHG_603210_288190


title: WTCHG_603210_288189


title: WTCHG_603210_289106


title: WTCHG_603210_289107


title: WTCHG_603210_287178


title: WTCHG_603210_295178


title: WTCHG_603210_288108


title: WTCHG_603210_292155


title: WTCHG_603210_287177


title: WTCHG_603210_285144


title: WTCHG_603210_286166


title: WTCHG_603210_285153


title: WTCHG_603210_286165


title: WTCHG_603210_285154


title: WTCHG_603210_287120


title: WTCHG_603210_286132


title: WTCHG_603210_284156


title: WTCHG_603210_284142


title: WTCHG_603210_289191


title: WTCHG_603210_282180


title: WTCHG_603210_281192


title: WTCHG_603210_282118


title: WTCHG_603210_284141


title: WTCHG_603210_283130


title: WTCHG_603210_280188


title: WTCHG_603210_280109


title: WTCHG_603210_281105


title: WTCHG_603210_280189


title: WTCHG_603210_279176


title: WTCHG_603210_279177


title: WTCHG_603210_279121


title: WTCHG_603210_278165


title: WTCHG_603210_278164


title: WTCHG_603210_278133


title: WTCHG_603210_277153


title: WTCHG_603210_277152


title: WTCHG_603210_276157


title: WTCHG_603210_277145


title: WTCHG_603210_275129


title: WTCHG_603210_274116


title: WTCHG_603210_274181


title: WTCHG_603210_275128


title: WTCHG_603210_273105


title: WTCHG_603210_276141


title: WTCHG_603210_272188


title: WTCHG_603210_283168


title: WTCHG_603210_271175


title: WTCHG_603210_271122


title: WTCHG_603210_272187


title: WTCHG_603210_272110


title: WTCHG_603210_269151


title: WTCHG_603210_270163


title: WTCHG_603210_274117


title: WTCHG_603210_269146


title: WTCHG_603210_270164


title: WTCHG_603210_267127


title: WTCHG_603210_273193


title: WTCHG_603210_268139


title: WTCHG_603210_268158


title: WTCHG_603210_266182


title: WTCHG_603210_268140


title: PB_preDC, WTCHG_324058_704508


title: WTCHG_603210_266116


title: WTCHG_603210_276140


title: WTCHG_603210_265103


title: WTCHG_603210_265104


title: WTCHG_603210_265194


title: WTCHG_603210_264187


title: WTCHG_603210_264111


title: WTCHG_603210_269152


title: WTCHG_603210_263174


title: WTCHG_603210_263123


title: WTCHG_603210_263175


title: WTCHG_603210_261151


title: WTCHG_603210_261150


title: WTCHG_603210_261147


title: WTCHG_603210_267128


title: WTCHG_603210_260159


title: WTCHG_603210_262135


title: WTCHG_603210_262162


title: WTCHG_603210_260138


title: WTCHG_603210_259126


title: WTCHG_603210_258183


title: WTCHG_603210_259127


title: WTCHG_603210_259171


title: WTCHG_603210_258115


title: WTCHG_603210_258114


title: WTCHG_603210_257195


title: WTCHG_603210_257103


title: WTCHG_603210_264186


title: WTCHG_603210_262163


title: WTCHG_603210_257102


title: WTCHG_603210_256186


title: WTCHG_603210_256112


title: WTCHG_603210_256185


title: WTCHG_603210_255173


title: WTCHG_603210_255124


title: WTCHG_603210_254162


title: WTCHG_603210_254136


title: WTCHG_603210_253150


title: WTCHG_603210_254161


title: WTCHG_603210_253148


title: WTCHG_603210_252137


title: WTCHG_603210_252160


title: WTCHG_603210_251126


title: WTCHG_603210_251125


title: WTCHG_603210_248196


title: WTCHG_603210_249196


title: WTCHG_603210_250184


title: WTCHG_603210_250114


title: WTCHG_603210_249102


title: WTCHG_603210_249101


title: WTCHG_603210_248185


title: WTCHG_603210_248101


title: WTCHG_603210_247173


title: WTCHG_603210_247184


title: WTCHG_603210_255174


title: WTCHG_603210_247113


title: WTCHG_603210_246172


title: WTCHG_603210_246161


title: WTCHG_603210_246125


title: WTCHG_603210_245149


title: WTCHG_603210_245160


title: WTCHG_603210_245137


title: WTCHG_603210_244149


title: WTCHG_603210_252138


title: WTCHG_603210_244137


title: WTCHG_603210_243161


title: WTCHG_603210_243136


title: WTCHG_603210_243125


title: WTCHG_603210_250113


title: WTCHG_603210_242173


title: WTCHG_603210_242124


title: WTCHG_603210_241112


title: WTCHG_603210_239183


title: WTCHG_603210_241101


title: WTCHG_603210_238172


title: WTCHG_603210_240195


title: WTCHG_603210_239184


title: WTCHG_603210_240102


title: WTCHG_603210_241185


title: WTCHG_603210_239114


title: WTCHG_603210_238171


title: WTCHG_603210_238126


title: WTCHG_603210_237159


title: WTCHG_603210_237160


title: WTCHG_603210_235162


title: WTCHG_603210_244148


title: WTCHG_603210_235136


title: WTCHG_603210_242113


title: WTCHG_603210_234123


title: WTCHG_603210_233186


title: WTCHG_603210_240196


title: WTCHG_603210_231183


title: WTCHG_603210_232194


title: WTCHG_603210_232195


title: urine_ultracentrifugation_5

city: Nijmegen

first: Ilse

last: Rood

address: PO Box 9101

country: Netherlands

institute: Radboudumc

description: MiRNA profiling in microvesicles isolated with ultracentrifugation

hyb_protocol: Hi-RPM buffer and hybridization time with 20 hours at 55°C with 20 rpm

scan_protocol: Using miRBase v20 custom Agilent SurePring G3 human miRNA (8x60K) microarrays

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent)

label: Cyanine 3-Cytidine biphosphate

label_protocol: Cyanine 3-Cytidine biphosphate (pCp) for labeling using 100 ng total RNA or equivalent input per array

extract_protocol: Microvesicles were isolated with different protocols: ExoRNeasy (according to the manufacturer's recommendation), modified ExoRNeasy (Alvarez et al. Kidney Int 2012;82:1024-32) and ultracentrifugation (UC; Rood et al Kidney Int 2010;78:810-816). Total miRNA was extracted from raw urine and microvesicles obtained by UC using the miRNeasy Serum/Plasma Kit (Qiagen GmbH, Hilden, Germany); the exoRNeasy Serum/Plasma Kit was used for extraction of miRNA from microvesicles obtained by (modified) ExoRNeasy (according to the manufacturer's recommendation).

value: urine


title: urine_Ultracentrifugation_10


title: urine_Ultracentrifugation_9


title: urine_ultracentrifugation_7


title: WTCHG_603210_233112


title: urine_Ultracentrifugation_8


title: urine_modified ExoRNeasy_7

description: MiRNA profiling in microvesicles isolated with modified protocol of ExoRNeasy

source_name: urine_modified ExoRNeasy_7


title: WTCHG_603210_231182


title: WTCHG_603210_232103


title: WTCHG_603210_236147


title: WTCHG_603210_236148


title: urine_modified ExoRNeasy_10

source_name: urine_modified ExoRNeasy_10


title: WTCHG_603210_236150


title: urine_Modified ExoRNeasy_8

source_name: urine_Modified ExoRNeasy_8


title: WTCHG_603210_235135


title: WTCHG_603210_231115


title: urine_modified ExoRNeasy_6

source_name: urine_modified ExoRNeasy_6


title: WTCHG_603210_230171


title: urine_Modified ExoRNeasy_9

source_name: urine_Modified ExoRNeasy_9


title: WTCHG_603210_230170


title: WTCHG_603210_233111


title: urine_ExoRNeasy_8

description: MiRNA profiling in microvesicles isolated with ExoRNeasy


title: urine_ExoRNeasy_10


title: urine_Ultracentrifugation_6


title: WTCHG_603210_230127


title: urine_ExoRNeasy_7


title: WTCHG_603210_229158


title: WTCHG_603210_229159


title: WTCHG_603210_228147


title: WTCHG_603210_228146


title: WTCHG_603210_227135


title: urine_ExoRNeasy_5


title: WTCHG_603210_226175


title: WTCHG_603210_227134


title: WTCHG_603210_229139


title: WTCHG_603210_228151


title: urine_raw_8

description: MiRNA profiling using raw urine


title: WTCHG_603210_226123


title: urine_ExoRNeasy_9


title: urine_ExoRNeasy_6


title: urine_raw_9

description: MiRNA profiling using raw urine


title: urine_raw_5

description: MiRNA profiling using raw urine


title: urine_ultracentrifugation_1


title: urine_raw_6

description: MiRNA profiling using raw urine


title: WTCHG_603210_225187


title: urine_Ultracentrifugation_2


title: WTCHG_603210_227163


title: WTCHG_603210_225110


title: urine_raw_10

description: MiRNA profiling using raw urine


title: urine_Ultracentrifugation_4


title: WTCHG_603210_224194


title: urine_raw_7

description: MiRNA profiling using raw urine


title: WTCHG_603210_224193


title: urine_modified ExoRNeasy_1

source_name: urine_modified ExoRNeasy_1


title: WTCHG_603210_224104


title: WTCHG_603210_223182


title: urine_Modified ExoRNeasy_3

source_name: urine_Modified ExoRNeasy_3


title: WTCHG_603210_223116


title: WTCHG_603210_223181


title: WTCHG_603210_222170


title: urine_modified ExoRNeasy_2

source_name: urine_modified ExoRNeasy_2


title: WTCHG_603210_222128


title: urine_Modified ExoRNeasy_4

source_name: urine_Modified ExoRNeasy_4


title: WTCHG_603210_221157


title: WTCHG_603210_222169


title: urine_ExoRNeasy_2


title: urine_ExoRNeasy_1


title: urine_ExoRNeasy_3


title: urine_ExoRNeasy_4


title: WTCHG_603210_221140


title: urine_raw_3

description: MiRNA profiling using raw urine


title: urine_raw_4

description: MiRNA profiling using raw urine


title: urine_raw_1

description: MiRNA profiling using raw urine


title: WTCHG_603210_220152


title: NEC_Id

city: Uppsala

first: Miyuki

last: Nakamura

address: Ulls Grand1

institute: Swedish University of Agricultural Sciences

data_processing:
Library strategy: CUT&RUN
After removing low quality reads by fastq_quality_filter (-q 20 -p 80 -Q 33), reads were mapped by bwa mem -P (bwa-0.7.17). The paired-end reads mapped on the different contigs were discarded. Then, merged paired-end fragments shorter than 701 bp were selected. The reads were processed by bedtools and bedGraphToBigWig.
Genome_build: Pabies1.0-genome.fa (ftp://plantgenie.org/Data/ConGenIE/Picea_abies/v1.0/FASTA/GenomeAssemblies/)
Supplementary_files_format_and_content: Bigwig

organism: Picea abies

source_name: Non-embryonic callus after somatic embryo induction

growth_protocol: Seedlings were germinated and grown in quarter-strength SH medium (von Arnold & Clapham, 2008) for 2 months in dark at 22˚C. Somatic embryonic calli and non-embryonic calli were proliferated in half-strength LP medium (von Arnold & Clapham, 2008) in dark at 22˚C.

extract_protocol:
Digested genomic DNA by pA-MNase were collected by ethanol precipitation. Subsequently, larger fragments were removed from extracted DNA by x 0.6 volume Agencourt AMPure XP and then the remaining DNA was recovered by x 3.0 volume AMpure XP.
Libraries were constructed using MicroPlex Library Preparation Kit v2 following the manufacturer's procedure.

treatment_protocol: For somatic induction treatment, somatic embryonic and non-embryonic calli were incubated in BMI-SI medium for 1 week.

tag: cultivar

value: Svenska Skogsplantor AB

value: Non-embryonic callus

tag: condition

value: After somatic embryo induction


title: SEC_Ni

source_name: Somatic embryonic callus before somatic embryo induction

value: Embryonic callus

value: Before somatic embryo induction


title: WTCHG_603210_219164

value: YES


title: Seedlings

source_name: Seedlings

value: Seedlings


title: NEC_Ni

source_name: Non-embryonic callus before somatic embryo induction


title: WTCHG_603210_260139


title: SEC_Id

source_name: Somatic embryonic callus after somatic embryo induction


title: WTCHG_603210_220146


title: WTCHG_603210_219134


title: WTCHG_603210_218121


title: WTCHG_603210_217110


title: WTCHG_603210_218176


title: WTCHG_603210_216193


title: 5AZA Day 6_1

city: Los Alamos

first: Christina

middle: Rene

last: Steadman

state: NM

address: MS888 PO Box 1663

department: Biosciences

institute: Los Alamos National Laboratory

description: 5-aza-2'deoxycytidine treated sample from Day 6 in culture_replicate 1

data_processing:
Sequencing reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software and then analyzed using bismark bowtie2 for alignment. The --non_directional parameter was applied while running bismark.
Methylation calling was performed using MethylDackel (https://github.com/dpryan79/MethylDackel/) using default settings. Parameters were also used to find sites in a CHG and CHH context.
Index files were constructed by bismark_genome_preparation command using the entire reference genome of P. soloecismus (GenBank PJAJ00000000).

organism: Picochlorum sp. 'soloecismus'

growth_protocol: Picochlorum soloecismus cells were grown in 250 mL shaker flasks, maintained at ambient temperature, under 300 µmolm-2s-1 fluorescent light with a 16h/8h light:dark cycle in modified f/2 media with 8.8 mM sodium nitrate. Cultures were shaken and supplemented with 1% CO2.

extract_protocol:
Sterile sampling was used for obtaining aliquots on a daily basis. A modified, combined protocol was generated from the manufacturer’s instructions using E.Z.N.A. Plant DNA DS Mini Kit (D2411-01; Omega Bio-tek Inc, Norcross, GA) and Quick-DNA Fungal/Bacterial Miniprep kit (D6005; Zymo Research, Irvine, CA).
P. soloecismus samples were processed and analyzed using the Methyl-MaxiSeq library preparation, sequencing, and bioinformatics pipeline from Zymo Research.

treatment_protocol: 5-aza-2’-deoxycytidine (5AZA) was purchased from Sigma (A3656). 5AZA was prepared in 50% DMSO and 50% ice cold MilliQ water in the least possible volume for a final concentrations of 20 µM in 250 ml shaker flasks. Stock solutions of 5AZA were stored at -20ºC. Treatment with 20 µM 5-aza-2'-deoxycytidine occured every day in culture, 4-5 hr into the light cycle prior to DNA replication in P. soloecismus.

value: treated (5-aza-2'-deoxycytidine)

tag: time in culture

value: Day 6

tag: biological replicate


title: 5AZA Day 10_1

description: 5-aza-2'deoxycytidine treated sample from Day 10 in culture_replicate 1

value: Day 10


title: 5AZA Day 5_3

description: 5-aza-2'deoxycytidine treated sample from Day 5 in culture_replicate 3

value: Day 5


title: 5AZA Day 7_2

description: 5-aza-2'deoxycytidine treated sample from Day 7 in culture_replicate 2

value: Day 7


title: 5AZA Day 7_3

description: 5-aza-2'deoxycytidine treated sample from Day 7 in culture_replicate 3


title: 5AZA Day 10_3

description: 5-aza-2'deoxycytidine treated sample from Day 10 in culture_replicate 3


title: 5AZA Day 7_1

description: 5-aza-2'deoxycytidine treated sample from Day 7 in culture_replicate 1


title: WTCHG_603210_216192


title: WTCHG_603210_215181


title: 5AZA Day 10_2

description: 5-aza-2'deoxycytidine treated sample from Day 10 in culture_replicate 2


title: 5AZA Day 5_2

description: 5-aza-2'deoxycytidine treated sample from Day 5 in culture_replicate 2


title: WTCHG_603210_215180


title: 5AZA Day 5_1

description: 5-aza-2'deoxycytidine treated sample from Day 5 in culture_replicate 1


title: WTCHG_603210_215117


title: 5AZA Day 4_3

description: 5-aza-2'deoxycytidine treated sample from Day 4 in culture_replicate 3

value: Day 4


title: WTCHG_603210_214169


title: WTCHG_603210_218122


title: 5AZA Day 4_2

description: 5-aza-2'deoxycytidine treated sample from Day 4 in culture_replicate 2


title: WTCHG_603210_214168


title: 5AZA Day 4_1

description: 5-aza-2'deoxycytidine treated sample from Day 4 in culture_replicate 1


title: WTCHG_603210_214129


title: WTCHG_603210_217109


title: 5AZA Day 6_3

description: 5-aza-2'deoxycytidine treated sample from Day 6 in culture_replicate 3


title: Control Day 10_3

description: control sample from Day 10 in culture_replicate 3

source_name: control sample from Day 10 in culture

value: untreated


title: 5AZA Day 6_2

description: 5-aza-2'deoxycytidine treated sample from Day 6 in culture_replicate 2


title: WTCHG_603210_213157


title: WTCHG_603210_216105


title: WTCHG_603210_212145


title: WTCHG_603210_213141


title: WTCHG_603210_211133


title: Control Day 7_3

description: control sample from Day 7 in culture_replicate 3

source_name: control sample from Day 7 in culture


title: WTCHG_603210_212144

source_name: bone marrow


title: Control Day 10_1

description: control sample from Day 10 in culture_replicate 1


title: WTCHG_603210_213156


title: WTCHG_603210_212153


title: Control Day 7_2

description: control sample from Day 7 in culture_replicate 2


title: Control Day 6_3

description: control sample from Day 6 in culture_replicate 3

source_name: control sample from Day 6 in culture


title: Control Day 10_2

description: control sample from Day 10 in culture_replicate 2


title: Control Day 7_1

description: control sample from Day 7 in culture_replicate 1


title: Control Day 6_2

description: control sample from Day 6 in culture_replicate 2


title: WTCHG_603210_211132


title: WTCHG_603210_210177


title: urine_modified ExoRNeasy_5

description: MiRNA profiling in microvesicles isolated with modified protocol of ExoRNeasy

source_name: urine_modified ExoRNeasy_5


title: WTCHG_603210_210121


title: WTCHG_603210_210120


title: Control Day 5_3

description: control sample from Day 5 in culture_replicate 3

source_name: control sample from Day 5 in culture


title: Control Day 5_2

description: control sample from Day 5 in culture_replicate 2


title: WTCHG_603210_209189


title: WTCHG_603210_209109


title: Control Day 4_3

description: control sample from Day 4 in culture_replicate 3

source_name: control sample from Day 4 in culture


title: Control Day 4_2

description: control sample from Day 4 in culture_replicate 2


title: WTCHG_603210_209108


title: Control Day 4_1

description: control sample from Day 4 in culture_replicate 1


title: WTCHG_603210_208192

value: Mono


title: WTCHG_603210_208191


title: WTCHG_603210_207179


title: Control Day 6_1

description: control sample from Day 6 in culture_replicate 1


title: WTCHG_603210_206130


title: CRL1790_miR890.1_miRNA

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

hyb_protocol: Nanostring miRNA hybridization-ligation protocol

scan_protocol: Nanostring Human miRv3 expression panel

data_processing: Data were normalized with Nanostring nSolver 4.0 global normalization

source_name: in vitro  cell culture, adherent

label_protocol: Nanostring Human miRv3 expression panel

extract_protocol: Qiagen miRNeasy kit

tag: experimental treatment

tag: biological replicate.plate replicate

tag: corresponding gse132501 raw  file

tag: transfection concentration

tag: cell line


title: WTCHG_603210_207118


title: WTCHG_603210_206167


title: WTCHG_603210_207180


title: Control Day 5_1

description: control sample from Day 5 in culture_replicate 1


title: WTCHG_603210_205156


title: CRL1790_miR155.1_miRNA


title: CRL1790_miR18b.4_miRNA

value: miR18b, 100nM


title: CRL1790_Control.5_miRNA

value: Control


title: WTCHG_603210_205142


title: CRL1790_cel67.5_miRNA


title: WTCHG_603210_205155


title: CRL1790_miR890.6_miRNA


title: CRL1790_miR142.2_miRNA


title: CRL1790_cel67.3_miRNA


title: WTCHG_603210_204154


title: WTCHG_603210_204144


title: WTCHG_603210_204143


title: CRL1790_miR155.3_miRNA


title: CRL1790_Control,4_miRNA


title: CRL1790_miR155.2_miRNA


title: WTCHG_603210_208106


title: CRL1790_miR142.3_miRNA


title: WTCHG_603210_203166


title: CRL1790_miR890.5_miRNA


title: WTCHG_603210_203132

value: pDC


title: WTCHG_603210_203131


title: WTCHG_603210_202120


title: WTCHG_603210_202178


title: WTCHG_603210_202119


title: WTCHG_603210_201190


title: EndoC-βH1 cells_rep3

city: Paris

first: Latif

last: Rachdi

address: 123 bvd Port-Royal

country: France

institute: Institut Cochin - Bat. Cassini

description: human beta cell line

data_processing:
STAR alignment with default parameters, on the Ensembl reference GRCh38
STAR --genomeDir /path/to/Index/Genome --sjdbGTFfile /path/to/GTF --runThreadN 14 --readFilesIn /path/to/fq1 /path/to/fq2 --outFileNamePrefix $prefix --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
Counting has been made with featureCount
Normalization and Differential analyses have been processed with the DESeq2 package, standard script and default parameters, with the « contrast » function between our two groups
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Results from DESeq2, tab-delimited file with the Gene Symbol, Description, baseMean, Fold-Change, lfcSE, stat, pvalue, adjusted pvalue, log2FoldChange and GeneID

source_name: EndoC-βH1 cells

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 800 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin

value: Fetus


title: WTCHG_603210_201108


title: ECN90 cells_rep3

description: human beta cell line

value: New Born


title: CRL1790_cel67.2_miRNA


title: CRL1790_Control.6_miRNA


title: ECN90 cells_rep2

description: human beta cell line


title: CRL1790_miR18b.2_miRNA


title: EndoC-βH1 cells_rep1

description: human beta cell line


title: EndoC-βH1 cells_rep2

description: human beta cell line


title: WTCHG_603210_201107


title: ECN90 cells_rep1

description: human beta cell line


title: WTCHG_401612_292231

data_processing:
Trimmed with Trimmomatic v 0.36
Aligned reads with STAR v 2.4.0 - bases with quality scores below Q10 (inferred base cell accuracy below 90%) were trimmed and reads shorter than 60bp were dropped
Counts were obtained with HTSEQ v 0.6.1
Further processing was performed in R 3.3.3. The cells were filtered based on precentage of ERCC counts (<30%), mitochondrial percentage (<25%), total features (>2500), total counts (>50000)
Genome_build: GRCh38.p7 (GENCODE release 25)
Supplementary_files_format_and_content: csv files with HTSEQ counts
Supplementary_files_format_and_content: BM_CD34_flow_channel_values.csv: Channel values produced when sorting the individual cells for scRNA-Seq.

value: LMPP CD117+

value: NO


title: WTCHG_401612_292229

value: YES


title: WTCHG_401612_292228


title: WTCHG_401612_292227


title: WTCHG_401612_292226


title: CRL1790_miR142.6_miRNA


title: WTCHG_401612_292225


title: H9ESC_BA_Day24 [ATAC-seq]

city: Athens

first: Liang

last: Zhang

state: GA

address: 325 Riverbend Road

department: Biochemistry and Molecular Biology, Center for Molecular Medicine

institute: University of Georgia

data_processing:
Constructed libraries were sequenced in illumina NextSeq 500 platform and basecalling was perfomed in Real-Time Analysis (RTA) System V2 (illumina).
FastQC was used to check overall sequence data quality. Fastq files were then mapped to human hg38 genome build in Bowtie2 with parameter “--very-sensitive -p 16 --local -N 1 --phred33”. Duplicate reads were removed using Picard tools and unmapped read and mitochondrial read were filtered out using Samtools and command line. For each sample, peak calling was performed using MACS2 (Zhang et al., 2008) with parameter “-g hs -q 0.01 nomodel --bdg --shift -100 --extsize 200 –nolambda –keep-dup all -f BAM –call-summits”.
The MACS2 output narrowPeak files were then merged in HOMER (Heinz et al., 2010) using ‘mergePeaks’ function to first create a union peakset that covers all peaks in the samples and merged overlapping peaks. Read count of each sample in the union peakset was quantified in HOMER using ‘makeTagDirectory’ and ‘annotatePeak’ function. The count matrix was then imported and processed in R Studio.
Genome_build: hg38
Supplementary_files_format_and_content: bed file format; narrow peak file from MACS2

source_name: Derived from human embryonic stem cells (WA09 WiCell, WAe009-A)

growth_protocol: The human embryonic stem cell (hESCs) WA09 (Sex: female, WiCell, WAe009-A) were cultured at polystyrene culture plates coated with Geltrex LDEV-free hESC qualified reduced growth factor basement membrane.  Media for PSC maintenance, sphere formation, paraxial mesoderm and brown adipocyte differentiations were accomplished using a defined base medium (DM) supplemented with specific factors. DM was composed of DMEM/F-12 w/o glutamine supplemented with 2% Probumin,1x Antibiotic-Antimyotic, 1x MEM non-essential amino acids,1x Trace Elements A,1x Trace Elements B,1x Trace Elements C,50 mg/mL Ascorbic Acid, 10 mg/mL Transferrin, 0.1 mM 2-mercaptoethanol and 1x glutagro. The hPSC complete maintenance medium (CMM) was composed of DM supplemented with 8 ng/mL human basic-FGF 200 ng/mL LONG® R3 human IGF-I,10 ng/mL Activin A and 10 ng/mL human Heregulin-β 1. hESCs and hiPSCs were cultured in CMM with media changes every 24 hrs and passaged at 90% confluency using Accutase.

extract_protocol:
The ATAC-Seq samples were prepared following the Omni-ATAC Seq protocol (Corces et al., 2017). In brief, single cell suspension of PM cells and BA cells were generated using Accumax and collagenase Mix as described in the cell culture and differentiation session of method. 50,000 cells were pelleted at 500 RCF at 4 °C for 5 mins. After removal of supernatant, pellet was resuspended in sterile water-based resuspension buffer containing 10 mM Tris-HCl pH=7.4 (Thermo Fisher, 15567-027), 10 mM NaCl (Thermo Fisher, AM9760G), 3 mM MgCl2 (Thermo Fisher, AM9530G), 0.1% NP-40 (Abcam, ab142247), 0.1% Tween-20 and 0.01% Digitonin (Thermo Fisher, BN2006) and incubated on ice for 3 minutes. Subsequent to incubation, lysis was washed by a water-based washing buffer containing 10 mM Tris-HCl pH=7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20. The lysis was then subject to centrifuge at 500 RCF at 4 °C for 5 mins. After removal of supernatant, pellet was resuspended in 50 μl of transposition mixture consisting of 25 μl 2X TD Buffer (illumina, 15027866), 2.5 μl Tn5 transposase (illumina, 15027865), 16.5 μl PBS, 0.5 μl 1% Digitonin, 0.5 μl 10% Tween-20, 5 μl H2O and incubated at 37 °C for 30 minutes. The reaction mix was later cleaned up using Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4014).
Library was then constructed by PCR amplification as instructed in the Omin-ATAC protocol and purified by Omega Mag-Bind RXNPure plus beads (Omega, M1386-01).
Single-end libraries were construced and then sequenced in NextSeq platform with read length 75 bp. Each sample has more than 30 millions read per end.

treatment_protocol: Paraxial mesoderm (PM) cells were generated in a three-step process using rotational suspension culture. First a single-cell suspension containing one million cells/mL was seeded in 6-well suspension plates at a volume of 5.5 mL in hPSC MM plus 10 mM Y-27632 dihydrochloride. The plate was then placed on an Innova 2000 platform shaker at 97 RPM in a 5% CO2, 37°C incubator for 24 hrs. The following day, medium was replaced with hPSC CMM for an additional 24 hrs and maintained in suspension culture. After 24 hrs in CMM, the medium was exchanged for mesoderm induction medium (MesoIM) and cultured for further 48 hrs with medium changes every day. Mesoderm induction medium was composed of DM supplemented with 10 ng/mL BMP4, 20 ng/mL bFGF, 200 ng/mL LONG® R3 human IGF-I and 250 nM rapamycin. After MIM, cells were washed once with DM and then switched to paraxial mesoderm medium (PM) for an additional 96 hrs in suspension with daily medium changes. PMP was composed of DM supplemented with the following factors: 20 ng/mL bFGF, 200 ng/mL LONG® R3 human IGF-I, 250 nM Rapamycin, 25 ng/mL WNT3a, 50 ng/mL Noggin, 2 mM (2'Z,3'E)-6-Bromoindirubin-3'-oxime (BIO) and 5 mM forskolin. Brown adipocyte (BA) differentiation from a PM precursor was performed in two steps using sequential media formulations designated as brown adipocyte 'priming' medium (BA1) and brown adipocyte 'maturation' medium (BA2). PM spheres were disassociated into single cells suspension using Accumax and seeded on Geltrex coated plate with BA1 medium. BA1 was composed of DM supplemented with the 8 ng/mL bFGF, 100 ng/mL BMP7, 200 ng/mL LONG® R3 human IGF-I, 10 mM Y-27632 dihydrochloride, 2uM Rosiglitazone,1 mM Dexamethasone, 1 nM T3 thyroid hormone, 500 mM IBMX (3-Isobutyl-1-methylxanthine) and 10 mM SB. Cells were cultured in BA1 for 8 days with media changes every 48 hrs. After initial priming stage, medium was switched to BA2. BA2 is formulated the same as BA1 excluding SB 431542 and supplemented with 1:500 Chemically Defined Lipid. Cells are maintained in BA2 with daily medium change for additional 35-40 days.

tag: cell identity

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm at differentiation time point day 24

tag: differentiation method

value: Brown adipocytes differentition using defined differentiation medium as described in the protocol section.

tag: differentiation stage

tag: molecule subtype

value: Tn5-transposases-tagged genomic DNA


title: H9ESC_PM [ATAC-seq]

value: Paraxial mesoderm derived from H9 (WA09) human embryonic stem cells

value: PM differentiation using a 3-step method described in the protocol section.

value: Paraxial Mesoderm


title: H9ESC_BA_Day4 [ATAC-seq]

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm at differentiation time point day 4


title: H9ESC_BA_Day8 [ATAC-seq]

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm at differentiation time point day 8


title: H9ESC_BA_Day15 [ATAC-seq]

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm at differentiation time point day 15


title: WTCHG_603210_220145

tag: passed cell qc


title: WTCHG_401612_291232


title: WTCHG_401612_291230


title: H5N1_PM10_2

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

country: India

institute: IISER Bhopal

data_processing:
FastQC was used to assess the quality of reads.
Trimmomatic was used for filtering and trimming of bad quality reads and sequences.
Kallisto was used to allign reads to human genome (hg38).
Tximport was used to obtain gene level abundance counts.
Limma R package was used for Differential Expression analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files containg tpm values for each gene.

source_name: A549 cell line

growth_protocol: A549 cells were cultured in DMEM media supplemented with 10% FBS in 100 mm cell culture dishes. For PM10 treatment and H5N1 infection, cells were cultures in a 12 well cell culture plate.

extract_protocol:
Total RNA was isolated with the help of Trizol reagent (Invitrogen)
Library was constructed with the help of Illumina TruSeq library preparation kit v2.

treatment_protocol:
Treatment: Cells were mock treated for 24 hours and infected with H5N1 for 36 hours  in group 1 and treated with PM10 for 24 hours  and infected with H5N1 for 36 hours in group 2 respectively
Infection: Cell monolayer were washed with PBS after PM10 and mock treatment then infected with  MOI 2 of H5N1 virus for 1 hour in serum free DMEM. Cells were washed again with PBS and cultured in DMEM supplemented with 1% FBS after infection.

tag: treatment

tag: agent

value: Influenza (H5N1)


title: H5N1_2

value: Mock


title: WTCHG_401612_291226


title: H5N1_1


title: WTCHG_401612_291225


title: H5N1_PM10_1


title: WTCHG_401612_290232


title: WTCHG_401612_291228


title: WTCHG_401612_290231


title: HCT116_CHX+

city: Cambridge

first: Tamara

last: Ouspenskaia

state: Massachusetts

address: 415 Main St

institute: Broad Institute

description: ribosome-protected mRNA fragments

data_processing:
Library strategy: Ribo-seq
Illumina adapters were removed using fastx_clipper from the FASTX-Toolkit.
Ribosomal RNA and tRNA were removed using Bowtie version 1.0.0
Remaining reads were aligned to the genome (hg19 / GRCh37) and transcriptome using STAR version 2.5.3a (--alignIntronMin 20 --alignIntronMax 100000 --outFilterMismatchNmax 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic). For the transcriptome annotation, a combination of GENCODE v26lift37 transcriptome annotation was combined with transcripts annotated as tstatus “unannotated” from MiTranscriptome annotation.
RibORF offsetCorrect script was used to correct the RPF offsets for each read length, generating an output BAM file with a single nucleotide for each read located at the offset-corrected position.
Translated nuORFs were discovered using RibORF and PRICE.
ORF translation was quantified using an improved translation quantification method based on Ribo-seq reads, which incorporates multi-mapping information and translated frame information.
Genome_build: hg19
Supplementary_files_format_and_content: RibORF offsetCorrect script was used to correct the RPF offsets for each read length, generating an output BAM file with a single nucleotide for each read located at the offset-corrected position. These offset corrected BAM files were used for ORF discovery using RibORF. The offset corrected BAM files were combined for B721.221 cells across HLA alleles, for HCT116 cells across conditions, and for HMel replicates and converted in BigWig files using bamCoverage (--binSize 1, --filterRNAstrand forward or --filterRNAstrand reverse). The BigWig files are useful for visualizing translated ORFs in genome browser, where each peak represents the number of Ribo-seq reads supporting each codon. The offset corrected BAM files were also used to calculate the translation levels in TPM using a novel method that takes into account the frame and accounts for multimapping reads. .tpm files are tab-separated files containing translation levels (TPM) for all B721.221 samples combined, or for each HMel sequencing run.

extract_protocol:
Culture media was removed, cells were washed with ice-cold PBS containing cycloheximide (0.1mg/ml) and lysed in Lysis Buffer according to the Illumina protocol (RPHMR12126).
Ribosomes containing ribosome-protected mRNA fragments (RPFs) were enriched using MicroSpin S-400 columns (GE Healthcare, catalog # 27-5140-01). Ribo-zero rRNA Removal Kit (Illumina, MRZH11124, discontinued) was used to deplete rRNA from RPFs. The entire RPF sample was loaded on a 15% urea-polyacrylamide gel. Gel fragments in 28-32 nucleotide range were cut from the gel. Samples were eluted from the gel overnight at 4°C. Subsequently, end repair, adapter ligation and reverse transcription were carried out according to the manufacturer’s protocol. For the cDNA gel purification, the reverse transcription reaction was loaded on a 10% urea-polyacrylamide gel. The samples were eluted from the gel overnight at room temperature. Subsequently, RPFs were circularized and 5 μl of circDNA was used for library amplification. The number of amplification cycles was determined based on the observed sample quality and expected yield, but usually ranged between 8 and 10 cycles. Following amplification, the library was gel-purified using 4% E-Gel EX Agarose Gel (ThermoFisher G401004) and Zymoclean Gel DNA Recovery Kit (Zymo Research D4007), with 4 volumes of ADB buffer to accommodate 4% agarose gel. The resulting libraries were analyzed for quality using Agilent Bioanalyzer 2100 and sequenced for 51 cycles on the Illumina NextSeq platform, using NextSeq 500 high output kit, V2, 75 cycles.

tag: cell type

value: colorectal carcinoma cell line

value: cycloheximide 10 minutes, 0.1mg/ml


title: Hmel_rep1

description: ribosome-protected mRNA fragments

source_name: Hmel

value: Hmel

value: Epidermal Melanocytes, neonatal

value: cycloheximide 5 minutes, 0.1mg/ml


title: HCT116_CHX-

description: ribosome-protected mRNA fragments


title: Hmel_rep2

description: ribosome-protected mRNA fragments


title: WTCHG_401612_290230

value: LMPP CD117+

value: YES


title: A375

description: ribosome-protected mRNA fragments

value: malignant melanoma cell line


title: WTCHG_401612_290229


title: B721.221_B4402

description: ribosome-protected mRNA fragments

value: B-lymphoblastoid cell line

tag: hla allele


title: WTCHG_401612_291231


title: B721.221_B1501

description: ribosome-protected mRNA fragments


title: WTCHG_401612_291227


title: Hmel_rep3

description: ribosome-protected mRNA fragments


title: WTCHG_401612_290228


title: WTCHG_401612_289228


title: WTCHG_401612_290225


title: WTCHG_401612_289230


title: WTCHG_401612_289226


title: WTCHG_401612_290226


title: B721.221_A0101

description: ribosome-protected mRNA fragments


title: B721.221_A3303

description: ribosome-protected mRNA fragments


title: K3iPSC_BA_Day50FSK_Rep1

data_processing:
Constructed libraries were sequenced in illumina NextSeq 500 platform and basecalling was perfomed in Real-Time Analysis (RTA) System V2 (illumina).
Sequence data (fastq) were mapped to hg19 using STAR (V2.6.1.C) on default setting with "-quantMode GeneCounts" to obtain read count of each sample.
Raw readcount of each samples were collected and analyzed in R Studio (Version 1.0.143) with RNA-Seq analysis package "limma_3.32.10 ","edgeR_3.18.1" and "DESeq2_1.16.1" following published analytic pipelines (Law, Charity W et al. 2016; Love, Michael et al. 2014) .
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include raw read counts of each sample.

source_name: Derived from human induced pluripotent stem cells (K3, Si-Yayeb et al., 2010)

growth_protocol: The human embryonic stem cell (hESCs) WA09 (Sex: female, WiCell, WAe009-A) and induced pluripotent stem cell (hiPSCs) line K3 (Sex: male, Si-Tayeb et al., 2010) were cultured at polystyrene culture plates coated with Geltrex LDEV-free hESC qualified reduced growth factor basement membrane.  Media for PSC maintenance, sphere formation, paraxial mesoderm and brown adipocyte differentiations were accomplished using a defined base medium (DM) supplemented with specific factors. DM was composed of DMEM/F-12 w/o glutamine supplemented with 2% Probumin,1x Antibiotic-Antimyotic, 1x MEM non-essential amino acids,1x Trace Elements A,1x Trace Elements B,1x Trace Elements C,50 mg/mL Ascorbic Acid, 10 mg/mL Transferrin, 0.1 mM 2-mercaptoethanol and 1x glutagro. The hPSC complete maintenance medium (CMM) was composed of DM supplemented with 8 ng/mL human basic-FGF 200 ng/mL LONG® R3 human IGF-I,10 ng/mL Activin A and 10 ng/mL human Heregulin-β 1. hESCs and hiPSCs were cultured in CMM with media changes every 24 hrs and passaged at 90% confluency using Accutase.

extract_protocol:
Total RNA were extracted using E.Z.N.A. Total RNA kit I (Omega, R6834), according to manufacture's protocol.
RNA samples with RNA Integrity number above 8.0 were seleced for library preparation in Geogia Genomic and Bioinformatic Core (https://dna.uga.edu/). KAPA Stranded mRNA-Seq Kit  for Illumina® Platforms (KR0960-v5.17) were used for library constructions of all RNA-Seq samples included in this study.
Pair-end stranded libraries were construced and then sequenced in NextSeq platform with read length 75 bp. Each sample has more than 30 millions read per end.

value: Brown adipocytes differentiated from K3iPSC derived paraxial mesoderm

tag: time

value: differentiation time point day 50

value: Brown adipocytes differentition using defined differentiation medium as described in the protocols section.

tag: forskolin treatment

value: Yes


title: WTCHG_401612_289225


title: WTCHG_401612_289227


title: K3iPSC_BA_Day50CTR_Rep1

value: NO


title: H9ESC_BA_Day50FSK Rep2

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm


title: H9ESC_BA_Day50FSK_Rep1


title: WTCHG_401612_280232


title: WTCHG_401612_280231


title: H9ESC_BA_Day44

value: differentiation time point day 44


title: WTCHG_401612_280230


title: WTCHG_401612_280229


title: WTCHG_401612_280228


title: H9ESC_BA_Day38

value: differentiation time point day 38


title: H9ESC_BA_Day32

value: differentiation time point day 32


title: H9ESC_BA_Day24

value: differentiation time point day 24


title: WTCHG_401612_280227


title: H9ESC_BA_Day20 [ATAC-seq]

value: Brown adipocytes differentiated from H9ESC derived paraxial mesoderm at differentiation time point day 20

value: Brown adipocytes differentition using defined differentiation medium as described in the protocol section.

value: Tn5-transposases-tagged genomic DNA


title: H9ESC_BA_Day20

value: differentiation time point day 20


title: WTCHG_401612_280226

value: LMPP CD117+

value: YES


title: WTCHG_401612_280225


title: H9ESC_BA_Day15

value: differentiation time point day 15


title: WTCHG_401612_279232


title: H9ESC_BA_Day8

value: differentiation time point day 8


title: H9ESC_BA_Day4

value: differentiation time point day 4


title: WTCHG_401612_279231


title: K3iPSC_PM_Rep1

value: Paraxial mesoderm derived from K3 induced human pluripotent stem cells

value: PM differentiation using a 3-step method described in the protocols section.


title: K3iPSC_PM_Rep2

value: NO


title: H9ESC_PM

value: Paraxial mesoderm derived from H9 (WA09) human embryonic stem cells


title: WTCHG_401612_279229


title: WTCHG_401612_279228


title: WTCHG_401612_279227


title: T4S1_Dropseq

description:
HMT-3522-T4-2/HMT-3522-S1 co-culture, mixed at 70:30 ratio
UMIcounts.txt

source_name: Human Caucasian breast epithelial

tag: tissue

value: Human Caucasian breast epithelial

tag: strain


title: WTCHG_401612_279226


title: T4_Dropseq

description: UMIcounts.txt


title: S1a_Dropseq

description: UMIcounts.txt


title: WTCHG_401612_278230


title: WTCHG_401612_278232


title: WTCHG_401612_279225


title: WTCHG_401612_278229


title: WTCHG_401612_278227


title: WTCHG_401612_278228


title: WTCHG_401612_278225


title: WTCHG_401612_277229


title: WTCHG_401612_277228


title: S1_Dropseq

description: UMIcounts.txt


title: WTCHG_401612_277227


title: WTCHG_401612_276232


title: WTCHG_401612_277226


title: WTCHG_401612_276231


title: WTCHG_401612_276229


title: WTCHG_401612_276230


title: WTCHG_401612_276227


title: WTCHG_401612_278226


title: WTCHG_401612_277225


title: WTCHG_401612_276226


title: [gene] PBMC-control diagnosis-UC subject-447 biological rep-29

city: Indianapolis

first: Boyd

last: Steere

state: IN

address: Lilly Corporate Center

department: Immunology

institute: Lilly

description:
subject-ID_447
@52084400980523112917428617726999

hyb_protocol: 5 μg of biotin-labeled cDNA per HTA2 platform standard procedure

scan_protocol: Scanning performed with Affymetrix GeneChip station under default settings followed by CEL file derivation from Affymetrix GeneChip Command Console (AGCC)

data_processing:
Background correction and quantile normalization of the gene expression data obtained from the Affymetrix Human Transcriptome Array 2.0 (HTA2) platform were performed by the RMA method while controlling for batch.  Summarization was performed with RLM.  Annotations were defined by the Affymetrix NetAffx(TM) NA35 release, which is based on the GRCh37 human reference genome. Differential expression at the gene-level was performed using the empirical Bayes method implemented in LIMMA{Ritchie:ef}controlling for donor in the model.
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

source_name: PBMC-control

label_protocol: Minimum RNA input was 100ng with a concentration range of 10 ng/μl to 50 ng ng/μl.  Label molecule was biotin.  Amplification performed using standard protocol from Affymetrix WT Express Kit.

growth_protocol: Whole blood was collected into EDTA-containing tubes. PBMC were purified using Ficoll-Paque density gradient purification. The absolute number of cells was determined using a haemocytometer (Marienfeld).

extract_protocol: Total RNA was extracted from cultured cells, using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s protocol. The RNA yield was determined by quantifying the samples on an Agilent Bioanalyzer.  Only samples with a 28S/18S ratio of 0.8 to 3.0 and a RIN Score of >= 6.0 passed QC metrics and were accepted for analysis.

treatment_protocol: For stimulation assays, 0.5×10^6 to 1×10^6 PBMC were cultured in 200 μl medium in duplicates in round bottom 96-well plates and exposed to ultrapure 200 ng/ml LPS (Enzo Life Sciences; Cat.# ALX-581-008), 200 ng/ml L18MDP (Invivogen) 10 μg/ml anti-IL-10R (Biolegend; clone: 3F9), and/or anti-CD3/anti-CD28 beads (Invitrogen) for 16 hours in complete RPMI with L-glutamine (Sigma) supplemented with 10 % human serum (Sigma; Cat.# H4522), non-essential amino acids (Gibco); 1 mM Sodium-Pyruvate (Gibco) and 100 U/ml penicillin and 10 μg/ml streptomycin (Sigma).

tag: stimulation

value: PBMC-control

tag: diagnosis

value: UC

tag: Sex

value: M

tag: batch

value: peripheral PBMC


title: [gene] PBMC-control diagnosis-UC subject-429 biological rep-28

description:
subject-ID_429
@52084400978709110317428272788114


title: [gene] PBMC-control diagnosis-UC subject-2031 biological rep-34

description:
subject-ID_2031
@52084400980524112917428617727087


title: [gene] PBMC-control diagnosis-UC subject-531 biological rep-30

description:
subject-ID_531
@52084400978710110317428272788155


title: WTCHG_401612_276225


title: [gene] PBMC-control diagnosis-UC subject-369 biological rep-27

description:
subject-ID_369
@52084400978328102417428100272938

value: F


title: [gene] PBMC-control diagnosis-UC subject-2001 biological rep-33

description:
subject-ID_2001
@52084400978711110317428272788256


title: [gene] PBMC-control diagnosis-UC subject-1628 biological rep-32

description:
subject-ID_1628
@52084400980525112917428617727159


title: WTCHG_401612_276228


title: WTCHG_401612_275231


title: [gene] PBMC-control diagnosis-UC subject-113 biological rep-26

description:
subject-ID_113
@52084400973514011718428996209060


title: [gene] PBMC-control diagnosis-CD subject-1018 biological rep-18

description:
subject-ID_1018
@52084400978711110317428272788236

value: CD


title: [gene] PBMC-control diagnosis-CD subject-1600 biological rep-21

description:
subject-ID_1600
@52084400978326102417428100272827


title: [gene] PBMC-control diagnosis-CD subject-1180 biological rep-19

description:
subject-ID_1180
@52084400978328102417428100272955


title: [gene] PBMC-control diagnosis-IBDu subject-104 biological rep-23

description:
subject-ID_104
@52084400978711110317428272788221

value: IBDu


title: [gene] PBMC-control diagnosis-Other subject-464 biological rep-25

description:
subject-ID_464
@52084400978710110317428272788149

value: Other


title: WTCHG_401612_275229

value: LMPP CD117+

value: YES


title: [gene] PBMC-control diagnosis-CD subject-1253 biological rep-20

description:
subject-ID_1253
@52084400980525112917428617727163


title: [gene] PBMC-control diagnosis-IBDu subject-293 biological rep-24

description:
subject-ID_293
@52084400980522112917428617726988


title: [gene] PBMC-control diagnosis-UC subject-1014 biological rep-31

description:
subject-ID_1014
@52084400980522112917428617726962


title: [gene] PBMC-control diagnosis-CD subject-1864 biological rep-22

description:
subject-ID_1864
@52084400978709110317428272788111


title: [gene] PBMC-control diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400978709110317428272788075


title: WTCHG_401612_275228


title: [gene] PBMC-control diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
@52084400978328102417428100272960


title: WTCHG_401612_275232


title: [gene] PBMC-control diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
@52084400980525112917428617727131


title: WTCHG_401612_275227


title: WTCHG_401612_275226


title: WTCHG_401612_275230


title: WTCHG_401612_274231


title: WTCHG_401612_274227


title: WTCHG_401612_274229


title: WTCHG_401612_274228


title: WTCHG_401612_274226


title: [gene] PBMC-control diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400978328102417428100272949


title: WTCHG_401612_274225


title: WTCHG_401612_275225


title: WTCHG_401612_273230


title: WTCHG_401612_273229


title: WTCHG_401612_273227


title: WTCHG_401612_274230


title: WTCHG_401612_273228


title: [gene] PBMC-control diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
@52084400978708110317428272788057


title: WTCHG_401612_273226


title: [gene] PBMC-control diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
@52084400980522112917428617726939


title: [gene] PBMC-control diagnosis-CD subject-280 biological rep-6

description:
subject-ID_280
@52084400978709110317428272788079


title: [gene] PBMC-control diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400980523112917428617727012


title: [gene] PBMC-control diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400980525112917428617727130


title: [gene] PBMC-control diagnosis-CD subject-243 biological rep-5

description:
subject-ID_243
@52084400978327102417428100272906


title: [gene] PBMC-control diagnosis-CD subject-528 biological rep-10

description:
subject-ID_528
@52084400978710110317428272788169


title: [gene] LPS aIL10R diagnosis-UC subject-2031 biological rep-38

description:
subject-ID_2031
@52084400980522112917428617726974


title: [gene] PBMC-control diagnosis-CD subject-423 biological rep-8

description:
subject-ID_423
@52084400978709110317428272788100


title: WTCHG_401612_273225


title: [gene] PBMC-control diagnosis-CD subject-232 biological rep-4

description:
subject-ID_232
@52084400978709110317428272788085


title: WTCHG_388581_256280


title: WTCHG_388581_256279


title: [gene] PBMC-control diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400978326102417428100272828


title: [gene] PBMC-control diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978328102417428100272941


title: WTCHG_388581_256277


title: WTCHG_388581_256276


title: WTCHG_388581_256278

value: CMP 33-


title: WTCHG_388581_256275


title: [gene] PBMC-control diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978708110317428272788058


title: WTCHG_388581_256274


title: [gene] LPS aIL10R diagnosis-UC subject-2001 biological rep-37

description:
subject-ID_2001
@52084400978708110317428272788014


title: WTCHG_388581_256208

value: HSC/MPP CD90-


title: WTCHG_388581_256273


title: WTCHG_388581_256207

value: HSC/MPP CD90+


title: WTCHG_388581_256206


title: [gene] LPS aIL10R diagnosis-UC subject-1338 biological rep-35

description:
subject-ID_1338
@52084400978711110317428272788255


title: WTCHG_388581_256205


title: WTCHG_388581_256204


title: [gene] LPS aIL10R diagnosis-UC subject-1014 biological rep-34

description:
subject-ID_1014
@52084400978711110317428272788220


title: [gene] LPS aIL10R diagnosis-UC subject-1628 biological rep-36

description:
subject-ID_1628
@52084400978711110317428272788223


title: WTCHG_388581_256203


title: [gene] LPS aIL10R diagnosis-Other subject-464 biological rep-27

description:
subject-ID_464
@52084400978328102417428100272954


title: [gene] LPS aIL10R diagnosis-CD subject-1600 biological rep-23

description:
subject-ID_1600
@52084400978326102417428100272857


title: [gene] LPS aIL10R diagnosis-IBDu subject-293 biological rep-26

description:
subject-ID_293
@52084400978708110317428272788015


title: [gene] LPS aIL10R diagnosis-CD subject-1864 biological rep-24

description:
subject-ID_1864
@52084400978326102417428100272820


title: WTCHG_388581_256202


title: [gene] LPS aIL10R diagnosis-UC subject-369 biological rep-29

description:
subject-ID_369
@52084400978329102417428100273014


title: [gene] LPS aIL10R diagnosis-UC subject-554 biological rep-33

description:
subject-ID_554
@52084400978326102417428100272847


title: [gene] LPS aIL10R diagnosis-UC subject-531 biological rep-32

description:
subject-ID_531
@52084400978709110317428272788102


title: [gene] LPS aIL10R diagnosis-UC subject-447 biological rep-31

description:
subject-ID_447
@52084400978710110317428272788173


title: [gene] LPS aIL10R diagnosis-UC subject-113 biological rep-28

description:
subject-ID_113
@52084400978710110317428272788185


title: [gene] LPS aIL10R diagnosis-CD subject-1180 biological rep-21

description:
subject-ID_1180
@52084400978710110317428272788177


title: WTCHG_388581_255279


title: WTCHG_388581_255278


title: WTCHG_388581_255280


title: [gene] LPS aIL10R diagnosis-CD subject-1018 biological rep-19

description:
subject-ID_1018
@52084400980524112917428617727066


title: WTCHG_388581_255276


title: WTCHG_388581_255275


title: [gene] LPS aIL10R diagnosis-IBDu subject-104 biological rep-25

description:
subject-ID_104
@52084400978708110317428272788028


title: WTCHG_388581_255277


title: [gene] LPS aIL10R diagnosis-CD subject-1045 biological rep-20

description:
subject-ID_1045
@52084400978711110317428272788212


title: WTCHG_388581_255274


title: WTCHG_388581_255208


title: WTCHG_388581_255273


title: [gene] LPS aIL10R diagnosis-CD subject-1253 biological rep-22

description:
subject-ID_1253
@52084400980523112917428617727023


title: WTCHG_388581_255207


title: [gene] LPS aIL10R diagnosis-CD subject-670 biological rep-14

description:
subject-ID_670
@52084400978708110317428272788047


title: [gene] LPS aIL10R diagnosis-CD subject-843 biological rep-17

description:
subject-ID_843
@52084400978328102417428100272953


title: [gene] LPS aIL10R diagnosis-CD subject-891 biological rep-18

description:
subject-ID_891
@52084400978329102417428100273003


title: [gene] LPS aIL10R diagnosis-CD subject-701 biological rep-15

description:
subject-ID_701
@52084400978328102417428100272980


title: WTCHG_388581_255206


title: [gene] LPS aIL10R diagnosis-CD subject-792 biological rep-16

description:
subject-ID_792
@52084400980524112917428617727101


title: WTCHG_388581_255205


title: [gene] LPS aIL10R diagnosis-CD subject-558 biological rep-11

description:
subject-ID_558
@52084400980524112917428617727110


title: [gene] LPS aIL10R diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
@52084400980524112917428617727096


title: [gene] LPS aIL10R diagnosis-CD subject-649 biological rep-13

description:
subject-ID_649
@52084400978326102417428100272818


title: [gene] PBMC-control diagnosis-CD subject-508 biological rep-9

description:
subject-ID_508
@52084400980523112917428617727029


title: WTCHG_388581_255204


title: [gene] LPS aIL10R diagnosis-CD subject-643 biological rep-12

description:
subject-ID_643
@52084400978709110317428272788112


title: WTCHG_388581_255201


title: WTCHG_388581_255203


title: WTCHG_388581_255202


title: WTCHG_388581_254280


title: WTCHG_388581_254279


title: WTCHG_388581_254277


title: WTCHG_388581_254276


title: [gene] LPS aIL10R diagnosis-CD subject-423 biological rep-8

description:
subject-ID_423
@52084400978711110317428272788261


title: [gene] LPS aIL10R diagnosis-UC subject-429 biological rep-30

description:
subject-ID_429
@52084400980525112917428617727162


title: WTCHG_388581_254274


title: [gene] LPS aIL10R diagnosis-CD subject-372 biological rep-7

description:
subject-ID_372
@52084400978710110317428272788134


title: [gene] LPS aIL10R diagnosis-CD subject-138 biological rep-2

description:
subject-ID_138
@52084400978327102417428100272879


title: [gene] LPS aIL10R diagnosis-CD subject-186 biological rep-3

description:
subject-ID_186
@52084400978709110317428272788115


title: [gene] LPS aIL10R diagnosis-CD subject-129 biological rep-1

description:
subject-ID_129
@52084400978709110317428272788098


title: [gene] LPS aCD3-aCD28 aIL10R diagnosis-UC subject-2001 biological rep-37

description:
subject-ID_2001
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