title: DataTOgi_ELOFKOrep1_16h_SSPE_TagDir

description:
genomic DNA (ChIP)
genome used for mapping:
Hg19

value: 16 hours

value: RNAPII-S2 clone 3E10 (Millipore)


title: E17_FJW161014001_E05

status: Public on Apr 20 2021

type: SRA

city: Chuo-ku, Kobe

first: Hironobu

last: Fujiwara

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (v1.0) for NextSeq.
fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-L 42 -l 36 -k 4.0 -q 30' for HiSeq 1500, '-L 50 -l 36 -k 4.0 -q 30' for HiSeq 2500 and '-L 75 -l 36 -k 4.0 -q 30' for NextSeq. The reads were mapped to the mouse genome (mm10) using HISAT2 (version 2.0.4) with the parameters '-p 4 --end-to-end'. Transcript levels were quantified as Transcripts Per Kilobase Million (TPM) with Sailfish (version 0.10.0) using GENCODE vM14 annotation file.
outside of the mean minus three standard deviations of the number of mapped reads to a sailfish index (Sailfish) or the number of assigned reads to gene regions (featureCounts, function of Subread version 1.5.0); over 10% reads assigning to mitochondrial RNA (featureCounts); abnormal gene body coverage of sequencing reads by human curation (RseQC, version 2.6.4).
for count table, after convert Ensemble transcript_id to Gene_id, each isoform expression were summarized on gene level.
Genome_build: mm10
Supplementary_files_format_and_content: txt

molecule: total RNA

organism: Mus musculus

source_name: E17.0_whisker follicles cells

extract_protocol:
Single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa).
RamDA-seq sequencing libraries were prepared by using the advanced method of RamDA-seq (refer to the Methods section in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs" DOI: https://doi.org/10.1038/s41467-018-02866-0).

tag: Stage

tag: cell type

value: whisker follicles cells

tag: data quality

value: ok


title: E17_FJW161014001_E06


title: E17_FJW161014001_F04


title: DataTOgi_ELOFKOrep2_8h_SSPE_TagDir

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

library_source: genomic

data_processing:
ChIP-seq, BrU-seq and ATAC-seq data analyses: For RNAPII-Ser2 ChIP-seq, low-quality sequence reads and adapters were filtered out by Trimmomatic (v3.36) (A. M. Bolger et al, 2014). The trimmed reads were aligned to the human reference genome (GRC h37/hg19) with the Burrows-Wheeler Aligner (BWA-v0.7.12-r1039) (H. Li et al, 2013). Biobambam2 (v2.0.72) (G. Tischler et al, 2014) was used to remove duplicate reads from the aligned reads. Sequence reads were locally realigned and base-quality scores were recalibrated with the IndelRealigner and BaseRecalibrator programs in Genome Analysis Toolkit (GATK-v3.5) (McKenna et al, 2010).
For pan-RNAPII ChIP-seq, BrU-seq and ATAC-seq, reads were aligned to the Human Genome 38 (Hg38) using bwa-mem tools (BWA (Version 0.7.16a) or STAR (Version 2.5.3a)) (H. Li et al, 2013; Dobin et al, 2013). Only high-quality reads (> q30) were included in the analyses and duplicates were removed using Samtools (Version 1.6) with fixmate -m and markdup -r settings (Table S7). Bam files were converted into stranded TagDirectories and UCSC genome tracks using HOMER tools (Version 4.8.2) (S. Heinz et al, 2010). A list of 49,948 genes was obtained from the UCSC genome database (https://genome.ucsc.edu/cgi-bin/hgTables) selecting the knownCanonical table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes should be non-overlapping with at least 2 kb between genes. Subsequent selection of sets of genes is described per analysis.
For ChIP-seq, binding profiles within selected areas of individual genes (e.g. around TSS or TTS), were defined using the AnnotatePeaks.pl tool of HOMER using the default normalization to 10mln reads. Metagene profiles were defined using the makeMetaGeneProfile.pl tool of HOMER, using default settings. Read densities in input samples were subtracted from individual ChIP-seq datasets to background-correct our data in which negative values were converted to 0, to prevent the use of impossible negative read densities in further calculations. Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 3.5.3) (R. Core Team, R, 2019). ChIP-seq binding and metagene profiles were averaged per set of genes and profiles were normalized to area under the curve to allow proper comparison of the profiles without effects of overall differences in read density.
ATAC-seq and BrU-seq heatmaps were generated as described for ChIP-seq analyses, except for the input subtraction and removal of negative values. BrU-seq aggregated profiles, were defined using the AnnotatePeaks.pl tool or makeMetaGeneProfile.pl tool of HOMER using the default normalization to 10mln reads, as for ChIP-sequencing. Genes were selected on size and strongest binding of RNAPII at the TSS in undamaged condition, as for ChIP-sequencing. Averaged binding profiles were subsequently normalized to nascent transcript levels, as quantified by 5-EU labelling, relative to the control in their specific cell type. For example, WT cells 3 h after UV irradiation showed 35% RNA relative to WT control cells, so we multiplied the expression of the bins by 0.35.  RNA-seq analyses: Obtained sequencing reads were cleaned by 5'-end quality trimming and Illumina-adapter clipping by Trimmomatic (A. M. Bolger et al, 2014). Pre-alignment quality control of the cleaned sequencing reads was done with FastQC. The alignment to reference genome hg19 of trimmed sequencing reads was done with Hisat2, guided by gene annotation in the refGene UCSC table (D. Kim et al, 2015). The generated SAM files were converted to the binary counterpart BAM, followed by BAM sorting and indexing with SAMtools (H. Li et al, 2009).  Counting reads to the UCSC's genomic features hg19 was performed by Subread/featureCounts (Y. Liao et al, 2014). Differential expression analysis was carried out, using edgeR (M. D. Robinson et al, 2010). Only genes indicating at least 2 counts per million in at least 20% of samples were included in the analysis. Data were normalized for sample specific effects by the trimmed mean of M-values. This was followed by estimating the dispersion and determining the differentially expressed genes using the general linear model (GLM). FDR-adjusted p-values < 0.05 were considered significant.
Genome_build: hg19 or hg38 as indicated per sample
Supplementary_files_format_and_content: excel tables providing stranded metagene profiles for the top 3000 genes for each individual sample, and the BrU-seq counts versus distance from the TSS for genes of 25-50Kb, 50-100Kb and >100Kb

molecule: genomic DNA

organism: Homo sapiens

source_name: RPE1-iCas9 ELOF1-KO

growth_protocol: DMEM GlutaMAX +10% Fetal Calf Serum + antibiotics

extract_protocol:
ATAC-seq: For each experimental condition 50.000 cells were harvested and washed with cold PBS containing protease inhibitors (Roche). The cells were resuspended in 50  l Transposase mixture, containing 1x Tagment DNA buffer Illumina Kit, #20034197), 0.5  l Tagment DNA enzyme (Illumina Kit, #20034197) and 0,2  g/ l Digitonin (Promega, #G9441), and incubated at 37  C for 30 min. Fragmented DNA was purified using a Qiagen MinElute kit (#28204).  BrU-seq: For BrU(DRB)-seq, cells were pre-treated with 100  M DRB for 1-3hrs (as indicated per sample) after which cells were washed with PBS and immdeidately, or 30 min later, incubated with 2 mM bromouridine (Bru) at 37 C for 15 or 30 min. For regular BrU-seq, cells were either mock-treated or irradiated with UV-C light (9 J/m2). Cells were then incubated in conditioned media for different periods of time before being incubated with 2 mM bromouridine (Bru) at 37 C for a 30 min. The cells were then lysed in TRIzol reagent (Invitrogen) and Bru-containing RNA isolated as previously described (Andrade-Lima et al., 2015). ChIP-seq: Cells were mock treated or UV-irradiated with 9 J/m2 and incubated in conditioned media for different periods of time (1, 4, 8, 16 h). Cells were crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed with PBS and crosslinked with 1% PFA for 20 min at room temperature. Fixation was stopped by adding 1.25 M Glycin in PBS to a final concentration of 0.1 M for 3 minutes at room temperature. Cells were washed with cold PBS and lysed and collected in a buffer containing 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6). Chromatin was pelleted in 5 min at 400 g and incubated in a buffer containing 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) for 10 minutes at 4 C. Chromatin was again pelleted for 5 min at 400 g and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6)) to a final concentration of 15x106 cells/ml. Chromatin was sonicated to approximately 1 nucleosome using a Bioruptor waterbath sonicator (Diagenode). Chromatin of ~5x106 cells was incubated with 3  g antibody (Antibodies are listed in Table S3) overnight at 4 C, followed by a 1.5 h protein-chromatin pull-down with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D and 10003D). ChIP samples were washed extensively, followed by decrosslinking for 4 h at 65 C in the presence of proteinase K. DNA was purified using a Qiagen MinElute kit.  RNA-seq: Cells were UV-irradiated (254 nm, 9 J/m2) or mock-treated and harvested 24 h later. Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's protocol. Up to 5   106 cells per sample were lysed in RLT buffer. For quantification purposes, 24 ng of the eight ArrayControl(tm) RNA Spikes (Thermo Fisher Scientific) were added to each sample (3 ng/spike).
ATAC-seq: Libraries were prepared by PCR using NEBNext High-Fidelity 2x PCR Master Mix (New England Labs, #M0541) and Nextera XT index Kit v2 (Illumina). Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. BrU-seq: cDNA libraries were made from the Bru-labeled RNA using the Illumina TruSeq library kit and paired-end 151 bp sequenced using the Illumina NovaSeq platform at the University of Michigan Advanced Genomics Core. Indicated is whether single-end or paired-end sequencing data was used for downstream analyses ChIP-seq: For RNAPII-Ser2 ChIP-seq sample libraries were prepared from 1 ng ChIPed DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) and index primer sets (NEB, E7335S). Strand-biased library amplification was performed using high-fidelity KAPA HiFi Enzyme (Roche, KK2102). The prepared libraries were sequenced on an Illumina HiSeq 2500 system (Illumina), resulting in 150 bp paired-end reads. For the remaining ChIP-seq samples, libraries were prepared using kapa hyper prep kit (Roche) and A-T mediated ligation of full Y-shaped IDT adapters. Samples were sequenced on an Illumina HiSeq X system (Macrogen), resulting in 150 bp paired-end reads. RNA-seq: Samples were purified using the KAPA mRNA Hyperprep kit (Roche) and prepared for sequencing using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's instructions, and sequenced in a single lane on an Illumina HiSeq4000.

treatment_protocol: DNA damage was induced by irradiating cells with varying doses of UV-C as indicated per sample; samples were assayed at different time-periods after UV treatment as indicated per sample.

tag: cell line

tag: genotype

tag: uv-c dose

tag: time after uv-c

value: 8 hours

tag: chip-antibody


title: DataTOgi_ELOFKOrep2_16h_SSPE_TagDir


title: E17_FJW161014001_E04


title: E17_FJW161014001_E02


title: E17_FJW161014001_E11


title: E17_FJW161014001_E03


title: DataTOgi_ELOFKOrep2_1h_SSPE_TagDir

value: 1 hour


title: E17_FJW161014001_D10


title: DataTOgi_ELOFKOrep1_4h_SSPE_TagDir

value: 4 hours


title: DataTOgi_ELOFKOrep1_1h_SSPE_TagDir


title: E17_FJW161014001_D12


title: DataTOgi_ELOFKOrep2_4h_SSPE_TagDir


title: DataTOgi_ELOFKOrep2_mock_SSPE_TagDir

value: mock

value: not applicable


title: DataTOgi_ELOFKOrep1_mock_SSPE_TagDir


title: E17_FJW161014001_E01


title: DataTOgi_CSBKOrep1_16h_SSPE_TagDir

source_name: RPE1-iCas9 CSB-KO

value: CSB-KO


title: E17_FJW161014001_E09


title: E17_FJW161014001_D09


title: E17_FJW161014001_D08


title: DataTOgi_ELOFKOrep1_8h_SSPE_TagDir


title: E17_FJW161014001_D07


title: DataTOgi_CSBKOrep2_8h_SSPE_TagDir


title: E17_FJW161014001_D06


title: E17_FJW161014001_D05


title: DataTOgi_CSBKOrep1_8h_SSPE_TagDir


title: E17_FJW161014001_D03


title: E17_FJW161014001_D11

value: low


title: E17_FJW161014001_D04


title: DataTOgi_CSBKOrep1_4h_SSPE_TagDir


title: DataTOgi_CSBKOrep2_4h_SSPE_TagDir


title: DataTOgi_CSBKOrep2_1h_SSPE_TagDir


title: DataTOgi_CSBKOrep2_16h_SSPE_TagDir


title: DataTOgi_CSBKOrep2_mock_SSPE_TagDir


title: DataTOgi_CSBKOrep1_1h_SSPE_TagDir


title: E17_FJW161014001_C12


title: DataTOgi_CSBKOrep1_mock_SSPE_TagDir


title: E17_FJW161014001_C11


title: E17_FJW161014001_D01


title: E17_FJW161014001_C10


title: E17_FJW161014001_C09


title: E17_FJW161014001_D02


title: DataTOgi_WTrep1_16h_SSPE_TagDir

source_name: RPE1-iCas9 WT

value: WT


title: E17_FJW161014001_C08


title: DataTOgi_WTrep1_8h_SSPE_TagDir


title: DataTOgi_WTrep2_8h_SSPE_TagDir


title: DataTOgi_WTrep2_4h_SSPE_TagDir


title: DataTOgi_WTrep1_4h_SSPE_TagDir


title: E17_FJW161014001_C06


title: E17_FJW161014001_C07


title: DataTOgi_WTrep2_1h_SSPE_TagDir


title: E17_FJW161014001_C03


title: E17_FJW161014001_C04


title: E17_FJW161014001_C05


title: DataTOgi_WTrep2_mock_SSPE_TagDir


title: DataTOgi_WTrep1_mock_SSPE_TagDir


title: E17_FJW161014001_C01


title: E17_FJW161014001_C02


title: DataTOgi_WTrep1_1h_SSPE_TagDir


title: DataTOgi_WTrep2_16h_SSPE_TagDir


title: E17_FJW161014001_B12


title: E17_FJW161014001_B11


title: ProliHH_P5_3D_Hep_1_32

city: Beijing

first: Cheng-ran

last: Xu

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

department: School of Basic Medical Sciences

country: China

institute: Peking University

data_processing:
Sequencing reads were aligned to the Homo sapiens reference genome (hg38) with TopHat (v2.1.0).
HTSeq (v0.6.0) was used to quantify the reads that mapped to each gene.
Gene expression levels were evaluated as transcripts per million (TPM).
Genome_build: hg38
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

source_name: Liver

growth_protocol: Human endoderm stem cells were generated from hPSCs and maintained in serum-free conditions as described previously (Cheng et al., 2012). For the hepatocyte differentiation, the EnSCs were dissociated into a single-cell suspension with 0.25% trypsin-EDTA, and then the cells were suspended in a 500 mL spinner flask at a density of 1×106 cells per milliliter in 300 mL hepatic specification medium, mixed with Matrigel at the final concentration of 4%, that contained ascorbic acid (Wako), MTG (Sigma), bFGF (10 ng/ml), TGF-α (20 ng/ml), EGF (10 ng/ml), VEGF (10 ng/ml), BMP4 (50 ng/ml), HGF (25 ng/ml), dexamethasone (Dex) (40 ng/ml, Sigma), and 1% DMSO (Sigma) (from day 0 to day 6, Stage I). From day 6 to day 12 (Stage II), the medium was replaced with hepatoblast formation medium containing ascorbic acid, MTG, bFGF (10 ng/ml), HGF (25 ng/ml), EGF (20 ng/ml), VEGF (10 ng/ml), oncostatin M (OSM) (20 ng/ml), Dex (40 ng/ml), 1% DMSO, Compound E (0.1 μM, Millipore), A83-01 (0.5 μM, Selleck), and Vitamin K1 (6 g/ml, Sangon). Then, the medium was changed to maturation medium, which contained ascorbic acid, MTG, HGF (25 ng/ml), OSM (20 ng/ml, PeproTech), Dex (40 ng/ml), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and erlotinib HCl (EGFi) (2 μM, Stemgent) (from day 12 to day 24, Stage 3H). The above differentiation medium was SFD-based (Cheng et al., 2012). From day 24, the hepatic spheres were cultured in hepatocyte culture medium (HCM, Lonza) that consisted of ascorbic acid, MTG, 8 bromo-cAMP (1 mM, Biolog), Compound E (0.1 μM), A83-01 (0.5 μM), Vitamin K1 (6 g/ml), and EGFi (2 μM) (from day 24 to day 30, Stage 4H). The medium was changed every 2 days. The cells were maintained in a 5% CO2, 5% O2, 90% N2 environment (from day 0 to day 18), and then in a 5% CO2/ambient air environment (from day 18 to day 30). The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise. For the cholangiocyte differentiation, the hepatoblasts were generated from EnSCs using the method as aforementioned. After hepatoblast formation, the hepatic spheres were cultured in SFD-based cholangiocyte specification medium containing ascorbic acid, MTG, FGF10 (50 ng/ml), Activin A (50 ng/ml), and retinoic acid (3 μM, Sigma) (from day 12 to day 15, Stage 3C). Then, the medium was changed to maturation medium, which contained HGF (25 ng/ml), EGF (50 ng/ml), TGF-β (5 ng/ml, PeproTech), Dex (40 ng/ml), and TPPB (0.5 μM, Calbiochem) (from day 16 to day 21, Stage 4C). The basic medium used for this final stage was biliary differentiation medium (BDM) (Sampaziotis et al., 2015). The cells were cultured in a 5% CO2, 5% O2, 90% N2 environment. The hepatic spheres were stirred at the optimal speed of 60 rpm. All cytokines were human and purchased from R&D Systems, unless stated otherwise.

extract_protocol:
Single-cell RNA-seq was performed according to the Smart-seq2 protocol as reported previously (Picelli et al., 2014). After the cells were digested into a single-cell suspension, each single-cell sample was manually selected under a microscope with a mouth pipette and transferred into lysis buffer containing 1.9 µl of 0.2% Triton X-100 (Sigma), 1 µl of 10 µM oligo (dT) primer, 1 µl of 10 mM dNTP mix (New England Biolabs), 0.1 µl of 40 U/µl RNase inhibitor (New England Biolabs) and 0.05 µl of ERCC spike-in RNA (a dilution of 1:300,000, Life Technologies). After single-cell lysis, the sample was mixed with 0.29 µl H2O, 2 µl of 5× Superscript II first-strand buffer, 2 µl of 5 M Betaine (Sigma), 0.5 µl of 100 mM DTT, 0.06 µl of 1 M MgCl2, 0.1 µl of 100 µM TSO primer, 0.25 µl of 40 U/µl RNase inhibitor and 0.5 µl of 200 U/µl SuperScript II reverse transcriptase (Invitrogen). After reverse transcription was performed, 2.25 µl H2O, 12.5 µl KAPA HiFi HotStart ReadyMix (KAPA Biosystems) and 0.25 µl of 10 µM IS PCR primer were added to the sample. Then, PCR preamplification was conducted for 18 cycles. Next, cDNA samples were purified with VAHTS DNA Clean Beads XP beads (Vazyme).
Purified cDNA (2 ng) was prepared for library construction using a TruePrep DNA Library Prep Kit (Vazyme) with a 0.4× standard reaction system, and PCR amplification was conducted for 8 cycles. Finally, the library was purified and size-selected, and fragments with a peak size of ~350 bp were analyzed with an Advanced Analytical Fragment Analyzer.

value: Hepatocyte derived from ProliHH P5 (Passage 2) through 3D maturation; ProliHH P5 were generated from human primary hepatocytes and passaged to P5


title: E17_FJW161014001_B10


title: ProliHH_P5_3D_Hep_1_28


title: ProliHH_P5_3D_Hep_1_29


title: ProliHH_P5_3D_Hep_1_30


title: E17_FJW161014001_B07


title: ProliHH_P5_3D_Hep_1_25


title: ProliHH_P5_3D_Hep_1_26


title: E17_FJW161014001_B06


title: ProliHH_P5_3D_Hep_1_24


title: E17_FJW161014001_B05


title: E17_FJW161014001_B04


title: E17_FJW161014001_B09


title: ProliHH_P5_3D_Hep_1_23


title: E17_FJW161014001_B03


title: E17_FJW161014001_B08


title: E17_FJW161014001_B01


title: E17_FJW161014001_A11


title: E17_FJW161014001_A10


title: ProliHH_P5_3D_Hep_1_19


title: ProliHH_P5_3D_Hep_1_21


title: ProliHH_P5_3D_Hep_1_20


title: E17_FJW161014001_A09


title: ProliHH_P5_3D_Hep_1_17


title: ProliHH_P5_3D_Hep_1_27


title: E17_FJW161014001_A08


title: ProliHH_P5_3D_Hep_1_18


title: ProliHH_P5_3D_Hep_1_16


title: E17_FJW161014001_A07


title: ProliHH_P5_3D_Hep_1_14


title: ProliHH_P5_3D_Hep_1_15


title: E17_FJW161014001_A06


title: ProliHH_P5_3D_Hep_1_13


title: E17_FJW161014001_A03


title: E17_FJW161014001_A04


title: ProliHH_P5_3D_Hep_1_12


title: ProliHH_P5_3D_Hep_1_22


title: E17_FJW161014001_A02


title: ProliHH_P5_3D_Hep_1_10


title: E17_FJW161014001_A01


title: E17_FJW161014001_B02


title: E15_FJW161014003_H11

source_name: E15.0_whisker follicles cells


title: ProliHH_P5_3D_Hep_1_08


title: ProliHH_P5_3D_Hep_1_07


title: E15_FJW161014003_H10


title: E15_FJW161014003_H09


title: ProliHH_P5_3D_Hep_1_06


title: ProliHH_P5_3D_Hep_1_05


title: ProliHH_P5_3D_Hep_1_03


title: E17_FJW161014001_A05


title: E15_FJW161014003_H08


title: E15_FJW161014003_H07


title: E15_FJW161014003_H06


title: E15_FJW161014003_H04


title: ProliHH_P5_3D_Hep_1_04


title: E15_FJW161014003_H05


title: ProliHH_P5_3D_Hep_1_31


title: ProliHH_P5_3D_Hep_1_11


title: ProliHH_P5_3D_Hep_1_09


title: ProliHH_P2_3D_Hep_1_20

value: Hepatocyte derived from ProliHH P2 (Passage 2) through 3D maturation; ProliHH P2 were generated from human primary hepatocytes and passaged to P2


title: ProliHH_P5_3D_Hep_1_01


title: ProliHH_P2_3D_Hep_1_22


title: E15_FJW161014003_H03


title: ProliHH_P5_3D_Hep_1_02


title: E15_FJW161014003_H02


title: E15_FJW161014003_H01


title: E15_FJW161014003_G12


title: ProliHH_P2_3D_Hep_1_18


title: ProliHH_P2_3D_Hep_1_21


title: E15_FJW161014003_G11


title: ProliHH_P2_3D_Hep_1_17


title: ProliHH_P2_3D_Hep_1_16


title: E15_FJW161014003_G10


title: E15_FJW161014003_G09


title: E15_FJW161014003_G08


title: ProliHH_P2_3D_Hep_1_15


title: E15_FJW161014003_G07


title: E15_FJW161014003_G05


title: E15_FJW161014003_G06


title: ProliHH_P2_3D_Hep_1_13


title: E15_FJW161014003_G03


title: E15_FJW161014003_G04


title: ProliHH_P2_3D_Hep_1_12


title: ProliHH_P2_3D_Hep_1_19


title: E15_FJW161014003_G01


title: E15_FJW161014003_F12


title: ProliHH_P2_3D_Hep_1_08


title: ProliHH_P2_3D_Hep_1_11


title: ProliHH_P2_3D_Hep_1_10


title: E15_FJW161014003_G02


title: ProliHH_P2_3D_Hep_1_09


title: E15_FJW161014003_F10


title: ProliHH_P2_3D_Hep_1_07


title: E15_FJW161014003_F09


title: ProliHH_P2_3D_Hep_1_06


title: ProliHH_P2_3D_Hep_1_04


title: ProliHH_P2_3D_Hep_1_05


title: ProliHH_P2_3D_Hep_1_03


title: ProliHH_P2_3D_Hep_1_14


title: E15_FJW161014003_F08


title: E15_FJW161014003_F07


title: ProliHH_P2_3D_Hep_1_02


title: ProliHH_P2_3D_Hep_1_01


title: E15_FJW161014003_F06


title: PHH_5C_1_94

value: 5C-condition cultured human primary hepatocyte


title: E15_FJW161014003_F11


title: PHH_5C_1_95


title: E15_FJW161014003_F04


title: E15_FJW161014003_F03


title: E15_FJW161014003_F02


title: PHH_5C_1_93


title: PHH_5C_1_92


title: E15_FJW161014003_E12


title: PHH_5C_1_91


title: PHH_5C_1_90


title: E15_FJW161014003_E10


title: PHH_5C_1_88


title: E15_FJW161014003_F01


title: PHH_5C_1_89


title: E15_FJW161014003_E11


title: PHH_5C_1_87


title: E15_FJW161014003_F05


title: E15_FJW161014003_E09


title: PHH_5C_1_85


title: PHH_5C_1_86


title: E15_FJW161014003_E08


title: E15_FJW161014003_E07


title: E15_FJW161014003_E06


title: E15_FJW161014003_E05


title: PHH_5C_1_84


title: PHH_5C_1_96


title: PHH_5C_1_82


title: E15_FJW161014003_E04


title: E15_FJW161014003_E03


title: PHH_5C_1_83


title: E15_FJW161014003_E02


title: PHH_5C_1_80


title: PHH_5C_1_81


title: E15_FJW161014003_D12


title: E15_FJW161014003_E01


title: PHH_5C_1_79


title: PHH_5C_1_78


title: E15_FJW161014003_D10


title: PHH_5C_1_75


title: PHH_5C_1_76


title: PHH_5C_1_74


title: E15_FJW161014003_D06


title: E15_FJW161014003_D05


title: E15_FJW161014003_D07


title: E15_FJW161014003_D03


title: PHH_5C_1_72


title: PHH_5C_1_73


title: E15_FJW161014003_D04


title: E15_FJW161014003_D02


title: PHH_5C_1_70


title: PHH_5C_1_71


title: PHH_5C_1_77


title: E15_FJW161014003_D11


title: PHH_5C_1_68


title: E15_FJW161014003_C11


title: PHH_5C_1_67


title: E15_FJW161014003_C10


title: PHH_5C_1_66


title: PHH_5C_1_65


title: E15_FJW161014003_C09


title: PHH_5C_1_69


title: PHH_5C_1_64


title: E15_FJW161014003_D01


title: PHH_5C_1_63


title: E15_FJW161014003_C08


title: E15_FJW161014003_C06


title: E15_FJW161014003_C07


title: E15_FJW161014003_D08


title: E15_FJW161014003_C12


title: E15_FJW161014003_C05


title: PHH_5C_1_61


title: PHH_5C_1_60


title: PHH_5C_1_59


title: E15_FJW161014003_C03


title: PHH_5C_1_55


title: PHH_5C_1_58


title: E15_FJW161014003_B12


title: E15_FJW161014003_C01


title: E15_FJW161014003_B11


title: E15_FJW161014003_C04


title: E15_FJW161014003_B09


title: PHH_5C_1_53


title: PHH_5C_1_52


title: E15_FJW161014003_B08


title: E15_FJW161014003_B07


title: PHH_5C_1_50


title: E15_FJW161014003_B10


title: PHH_5C_1_62


title: PHH_5C_1_51


title: E15_FJW161014003_B06


title: PHH_5C_1_49


title: E15_FJW161014003_B05


title: PHH_5C_1_48


title: E15_FJW161014003_B04


title: PHH_5C_1_57


title: E15_FJW161014003_B03


title: E15_FJW161014003_C02


title: PHH_5C_1_46


title: E15_FJW161014003_B01


title: PHH_5C_1_56


title: E15_FJW161014003_B02


title: PHH_5C_1_47


title: E15_FJW161014003_A10


title: PHH_5C_1_42


title: PHH_5C_1_43


title: PHH_5C_1_54


title: E15_FJW161014003_A09


title: E15_FJW161014003_A11


title: PHH_5C_1_44


title: PHH_5C_1_45


title: E15_FJW161014003_A06


title: PHH_5C_1_39


title: PHH_5C_1_41


title: E15_FJW161014003_A07


title: PHH_5C_1_40


title: PHH_5C_1_38


title: E15_FJW161014003_A05


title: PHH_5C_1_37


title: E15_FJW161014003_A03


title: PHH_5C_1_36


title: E15_FJW161014003_A02


title: E15_FJW161014003_A01


title: PHH_5C_1_34


title: E15_FJW161014002_H10


title: E15_FJW161014002_H12


title: PHH_5C_1_33


title: E15_FJW161014002_H08


title: PHH_5C_1_31


title: PHH_5C_1_32


title: E15_FJW161014002_H07


title: PHH_5C_1_30


title: E15_FJW161014002_H06


title: PHH_5C_1_29


title: E15_FJW161014002_H04


title: PHH_5C_1_28


title: E15_FJW161014002_H03


title: PHH_5C_1_27


title: E15_FJW161014002_H05


title: PHH_5C_1_26


title: E15_FJW161014002_G11


title: E15_FJW161014002_H01


title: PHH_5C_1_22


title: PHH_5C_1_23


title: PHH_5C_1_24


title: PHH_5C_1_35


title: E15_FJW161014002_G10


title: E15_FJW161014002_G12


title: PHH_5C_1_21


title: E15_FJW161014002_H09


title: E15_FJW161014002_G09


title: PHH_5C_1_20


title: E15_FJW161014002_G07


title: PHH_5C_1_19


title: E15_FJW161014002_G02


title: PHH_5C_1_17


title: PHH_5C_1_18


title: E15_FJW161014002_H02


title: PHH_5C_1_16


title: PHH_5C_1_25


title: PHH_5C_1_14


title: E15_FJW161014002_F11


title: PHH_5C_1_15


title: PHH_5C_1_13


title: PHH_5C_1_12


title: E15_FJW161014002_F10


title: E15_FJW161014002_F09


title: PHH_5C_1_10


title: PHH_5C_1_09


title: PHH_5C_1_08


title: E15_FJW161014002_F08


title: E15_FJW161014002_F06


title: E15_FJW161014002_F07


title: E15_FJW161014002_G08


title: E15_FJW161014002_F05


title: PHH_5C_1_06


title: E15_FJW161014002_F03


title: E15_FJW161014002_G04


title: E15_FJW161014002_G01


title: E15_FJW161014002_F04


title: PHH_5C_1_07


title: E15_FJW161014002_F01


title: PHH_5C_1_04


title: E15_FJW161014002_E11


title: E15_FJW161014002_F12


title: E15_FJW161014002_E10


title: PHH_5C_1_02


title: PHH_5C_1_03


title: PHH_5C_1_11


title: E15_FJW161014002_E09


title: PHH_5C_1_01


title: Immature_Hepatocyte_1_31

source_name: EnSC

value: EnSC-derived immature hepatocyte


title: Immature_Hepatocyte_1_30


title: E15_FJW161014002_E08


title: Immature_Hepatocyte_1_29


title: E15_FJW161014002_E06


title: Immature_Hepatocyte_1_28


title: E15_FJW161014002_E05


title: E15_FJW161014002_E03


title: E15_FJW161014002_E02


title: PHH_5C_1_05


title: Immature_Hepatocyte_1_26


title: Immature_Hepatocyte_1_27


title: Immature_Hepatocyte_1_24


title: Immature_Hepatocyte_1_25


title: E15_FJW161014002_D11


title: E15_FJW161014002_E04


title: Immature_Hepatocyte_1_22


title: Immature_Hepatocyte_1_23


title: Immature_Hepatocyte_1_21


title: E15_FJW161014002_D12


title: E15_FJW161014002_E01


title: E15_FJW161014002_D08


title: E15_FJW161014002_D09


title: E15_FJW161014002_E07


title: E15_FJW161014002_D10


title: Immature_Hepatocyte_1_19


title: E15_FJW161014002_D06


title: Immature_Hepatocyte_1_20


title: E15_FJW161014002_D07


title: E15_FJW161014002_D05


title: Immature_Hepatocyte_1_17


title: Immature_Hepatocyte_1_18


title: E15_FJW161014002_D04


title: E15_FJW161014002_D03


title: E15_FJW161014002_D01


title: E15_FJW161014002_D02


title: E15_FJW161014002_C11


title: Immature_Hepatocyte_1_13


title: Immature_Hepatocyte_1_16


title: Immature_Hepatocyte_1_14


title: Immature_Hepatocyte_1_12


title: Immature_Hepatocyte_1_15


title: Immature_Hepatocyte_1_11


title: E15_FJW161014002_C10


title: Immature_Hepatocyte_1_10


title: E15_FJW161014002_C09


title: E15_FJW161014002_C07


title: E15_FJW161014002_C08


title: E15_FJW161014002_C04


title: E15_FJW161014002_C05


title: Immature_Hepatocyte_1_09


title: E15_FJW161014002_C06


title: Immature_Hepatocyte_1_08


title: Immature_Hepatocyte_1_07


title: Immature_Hepatocyte_1_03


title: Immature_Hepatocyte_1_06


title: E15_FJW161014002_C03


title: E15_FJW161014002_C02


title: Immature_Hepatocyte_1_01


title: Immature_Hepatocyte_1_02


title: E15_FJW161014002_C12


title: E15_FJW161014002_B12


title: ESC_Derived_HLC_1_140

source_name: ESC

value: Human embryonic stem cell-derived hepatocyte-like cell


title: ESC_Derived_HLC_1_139


title: E15_FJW161014002_B11


title: E15_FJW161014002_B09


title: ESC_Derived_HLC_1_138


title: E15_FJW161014002_B10


title: Immature_Hepatocyte_1_05


title: ESC_Derived_HLC_1_136


title: E15_FJW161014002_B08


title: ESC_Derived_HLC_1_135


title: ESC_Derived_HLC_1_137


title: E15_FJW161014002_B04


title: ESC_Derived_HLC_1_134


title: E15_FJW161014002_B05


title: ESC_Derived_HLC_1_132


title: E15_FJW161014002_B03


title: E15_FJW161014002_C01


title: ESC_Derived_HLC_1_129


title: ESC_Derived_HLC_1_130


title: E15_FJW161014002_B02


title: E15_FJW161014002_B01


title: ESC_Derived_HLC_1_131


title: E15_FJW161014002_A10


title: E15_FJW161014002_A09


title: ESC_Derived_HLC_1_128


title: E15_FJW161014002_A08


title: Immature_Hepatocyte_1_04


title: E15_FJW161014002_A06


title: E15_FJW161014002_A07


title: E15_FJW161014002_B07


title: ESC_Derived_HLC_1_127


title: ESC_Derived_HLC_1_124


title: ESC_Derived_HLC_1_126


title: E15_FJW161014002_A05


title: ESC_Derived_HLC_1_123


title: E15_FJW161014002_A04


title: E15_FJW161014002_A03


title: E15_FJW161014002_A11


title: E15_FJW161014002_A02


title: E15_FJW161014002_A01


title: ESC_Derived_HLC_1_125


title: ESC_Derived_HLC_1_117


title: ESC_Derived_HLC_1_116


title: ESC_Derived_HLC_1_121


title: ESC_Derived_HLC_1_118


title: ESC_Derived_HLC_1_122


title: ESC_Derived_HLC_1_119


title: ESC_Derived_HLC_1_120


title: ESC_Derived_HLC_1_113


title: ESC_Derived_HLC_1_115


title: ESC_Derived_HLC_1_114


title: Mouse_SmartSeq2_GhrlCFP_P0_2

data_processing:
We aligned sequenced reads to the mouse reference genome (mm10) with TopHat (v2.1.0) using the parameters ‘‘-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq’’.
We quantified the reads assigned to each gene using HTSeq (v0.6.0) with parameters ‘‘-f bam -r pos -s no -a 30’’.
The read count was normalized to transcripts per million (TPM). To avoid transcriptomic perturbations due to individual highly expressed genes, we excluded genes that comprised greater than 10% of transcripts in at least 10 single-cell samples (Ins1, Ins2, Gcg, Sst, Ghrl, Ppy, Iapp, Pyy, Yam1) during the total transcript count calculation.
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample
Supplementary_files_format_and_content: values tab-delimited text files include UMI and TP0.1M values for each sample

molecule: polyA RNA

source_name: Pancreas

extract_protocol:
The Smart-seq2 procedure was the same as previously described (Yu et al., 2019, The EMBO Journal), which follows the Smart-seq2 method (Picelli et al., 2014, Nature Protocols).
The mRNA was reverse transcribed into cDNA for library construction using a TruePrep DNA Library Prep Kit (Vazyme, TD502).

tag: tissue

value: Pancreas

tag: cell source

tag: developmental time point


title: Mouse_SmartSeq2_GhrlCre_E17.5_1

value: Ghrl-Cre;Rosa-RFP+


title: Mouse_SmartSeq2_GcgPos_GhrlPos_E15.5_2


title: Mouse_SmartSeq2_GhrlCFP_P0_1


title: Mouse_SmartSeq2_GcgPos_GhrlPos_E15.5_1


title: Mouse_SmartSeq2_GhrlCFP_P3_1


title: Mouse_SmartSeq2_GhrlCFP_E18.5_2


title: Mouse_SmartSeq2_GhrlCFP_P3_2


title: Mouse_SmartSeq2_GhrlCFP_E18.5_1


title: Mouse_SmartSeq2_GhrlCFP_E17.5_2


title: ESC_Derived_HLC_1_111


title: ESC_Derived_HLC_1_107


title: ESC_Derived_HLC_1_110


title: Mouse_SmartSeq2_Ngn3High_GhrlPos_E14.5_1


title: ESC_Derived_HLC_1_108


title: ESC_Derived_HLC_1_112


title: ESC_Derived_HLC_1_109


title: Mouse_SmartSeq2_GhrlCFP_E16.5_1


title: Mouse_SmartSeq2_GhrlCFP_E15.5_2


title: Mouse_SmartSeq2_GhrlCFP_E17.5_1


title: Mouse_SmartSeq2_GhrlCFP_E16.5_3


title: Mouse_SmartSeq2_GhrlCFP_E16.5_2


title: Mouse_SmartSeq2_GhrlCFP_E15.5_1


title: ESC_Derived_HLC_1_102


title: ESC_Derived_HLC_1_103


title: Mouse_SmartSeq2_GhrlCFP_E14.5_1


title: Mouse_SmartSeq2_PpymNeptune_P3_2


title: ESC_Derived_HLC_1_105


title: Mouse_SmartSeq2_GhrlCFP_E13.5_1


title: Mouse_SmartSeq2_PpymNeptune_P3_1


title: ESC_Derived_HLC_1_106


title: ESC_Derived_HLC_1_104


title: ESC_Derived_HLC_1_099


title: ESC_Derived_HLC_1_100


title: ESC_Derived_HLC_1_101


title: Mouse_SmartSeq2_GhrlCFP_E14.5_2


title: ESC_Derived_HLC_1_097


title: ESC_Derived_HLC_1_098


title: ESC_Derived_HLC_1_096


title: Mouse_SmartSeq2_PpymNeptune_P0_2


title: Mouse_SmartSeq2_PpymNeptune_P0_1


title: RNA sequencing Chicken3-skeletal-muscle biological replicate 3

city: Chengdu

first: jin

last: long

address: Hui ming

institute: Sichuan Agricultural University

description:
Chicken3-skeletal-muscle
chicken_exp.txt

data_processing:
Gene-level expression was estimated as transcripts per million (TPM) using the high-speed transcript quantification tool Kallisto (version 0.43.0).
Genome_build: Felis_catus_6.2, Gallus_gallus-5.0, CanFam3.1, Cavpor3.0, Mmul_8.0.1, GRCm38.p5, OryCun2.0, Rnor_6.0, Oar_v3.1
Supplementary_files_format_and_content: genes expression level (TPM) text file

organism: Gallus gallus

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
We used an rRNA depletion protocol (Ribo-Zero kit, Epicentre) coupled with the Illumina TruSeq stranded RNA-Seq library protocol to construct the RNA-Seq libraries. All libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit (Invitrogen) and sequenced on HiSeq X Ten (Illumina) platform to produce average ~ 49 million 150-bp paired-end raw reads and ~ 48 million high-quality reads for each library.

tag: breed

value: Tibetan chicken

value: skeletal muscle

tag: age

value: Adult

tag: Sex

value: female


title: RNA sequencing Chicken3-Spleen biological replicate 3

description:
Chicken3-Spleen
chicken_exp.txt

source_name: Spleen

value: Spleen


title: RNA sequencing Chicken3-Liver biological replicate 3

description:
Chicken3-Liver
chicken_exp.txt

value: Liver


title: RNA sequencing Chicken3-Lung biological replicate 3

description:
Chicken3-Lung
chicken_exp.txt

source_name: Lung

value: Lung


title: ESC_Derived_HLC_1_095


title: RNA sequencing Chicken3-Kidney biological replicate 3

description:
Chicken3-Kidney
chicken_exp.txt

source_name: Kidney

value: Kidney


title: Mouse_SmartSeq2_PpymNeptune_E18.5_2


title: RNA sequencing Chicken3-Heart biological replicate 3

description:
Chicken3-Heart
chicken_exp.txt

source_name: Heart

value: Heart


title: ESC_Derived_HLC_1_094


title: Mouse_SmartSeq2_PpymNeptune_E18.5_1


title: ESC_Derived_HLC_1_093


title: RNA sequencing Chicken2-Spleen biological replicate 2

description:
Chicken2-Spleen
chicken_exp.txt


title: RNA sequencing Chicken2-Lung biological replicate 2

description:
Chicken2-Lung
chicken_exp.txt


title: Mouse_SmartSeq2_PpymNeptune_E17.5_1


title: RNA sequencing Chicken2-Liver biological replicate 2

description:
Chicken2-Liver
chicken_exp.txt


title: RNA sequencing Chicken2-skeletal-muscle biological replicate 2

description:
Chicken2-skeletal-muscle
chicken_exp.txt


title: ESC_Derived_HLC_1_092


title: ESC_Derived_HLC_1_090


title: RNA sequencing Chicken2-Adipose biological replicate 2

description:
Chicken2-Adipose
chicken_exp.txt

source_name: Adipose

value: Adipose


title: RNA sequencing Chicken1-Spleen biological replicate 1

description:
Chicken1-Spleen
chicken_exp.txt


title: ESC_Derived_HLC_1_091


title: ESC_Derived_HLC_1_089


title: Mouse_SmartSeq2_PpymNeptune_E16.5_3


title: Mouse_SmartSeq2_PpymNeptune_E16.5_2


title: RNA sequencing Chicken1-Liver biological replicate 1

description:
Chicken1-Liver
chicken_exp.txt


title: RNA sequencing Chicken1-Lung biological replicate 1

description:
Chicken1-Lung
chicken_exp.txt


title: RNA sequencing Chicken1-Kidney biological replicate 1

description:
Chicken1-Kidney
chicken_exp.txt


title: ESC_Derived_HLC_1_088


title: ESC_Derived_HLC_1_087


title: Mouse_SmartSeq2_PpymNeptune_E16.5_1


title: Mouse_SmartSeq2_SstBFP_P3_3


title: RNA sequencing Chicken1-Heart biological replicate 1

description:
Chicken1-Heart
chicken_exp.txt


title: RNA sequencing Chicken3-Adipose biological replicate 3

description:
Chicken3-Adipose
chicken_exp.txt


title: Mouse_SmartSeq2_PpymNeptune_E17.5_2


title: ESC_Derived_HLC_1_086


title: RNA sequencing Chicken2-Heart biological replicate 2

description:
Chicken2-Heart
chicken_exp.txt


title: RNA sequencing Chicken1-Adipose biological replicate 1

description:
Chicken1-Adipose
chicken_exp.txt


title: Mouse_SmartSeq2_SstBFP_P3_2


title: RNA sequencing Chicken2-Kidney biological replicate 2

description:
Chicken2-Kidney
chicken_exp.txt


title: Mouse_SmartSeq2_SstBFP_P3_1


title: ESC_Derived_HLC_1_085


title: cor_sal_1w_424

city: Copenhagen

first: Gitte

middle: Moos

last: Knudsen

address: 9 Blegdamsvej

department: Neurobiology Research Unit

country: Denmark

institute: Copenhagen University Hospital, Rigshospitalet

data_processing:
fastp v0.20.0 was used to trim adapters etc from the raw 150bp PE reads (default settings except: –detect_adapter_for_pe –correction –trim_poly_x –cut_tail –trim_front1 12 –trim_front2 12 –trim_tail1 1 –trim_tail2 1).
Trimmed reads were mapped to the susScr11 genome assembly using STAR (v2.6c) in two-pass mode allowing for overlapping read mates and guided by an ENSEMBL (UCSC, Feb.10 2019) gene annotation (settings: –sjdbOverhang 100 –twopassMode Basic –outSAMtype BAM SortedByCoordinate –outSAMattributes All –outSAMunmapped Within –outFilterMismatchNoverLmax 0.1 –outFilterMatchNmin 25 –outFilterMismatchNmax 10 –peOverlapNbasesMin 20).
Mapped reads were assigned to ENSEMBL (UCSC, Feb.10 2019) genes with featureCounts (v1.5.1, settings: –primary -p -B -O –fraction -s 0 -J) generating the raw count table.
note: pigs were split evenly in two batches (’2xx’ and ’4xx’).
note: pig ’257’ (=animal ID) 1 day saline is excluded, as the raw fastq file was corrupted and the original file could not be recovered from sequencing facility.
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Prefrontal cortex tissue

growth_protocol: 20kg pigs, standard housing condition, weight-adjusted food twice daily, free access to water

extract_protocol:
Whole brain extracted immediately after euthanasia and snap frozen in powdered dry-ice
NEBNext Ultra 2 RNA with poly-A selection

treatment_protocol: One iv injection of saline or 0.08mg/kg psilocybin while awake and freely roaming. Euthanasia by iv pentobarbital overdose

value: Prefrontal cortex

tag: treatment

value: saline

tag: time following treatment

value: 1 week

tag: batch


title: cor_sal_1w_254


title: RNA sequencing Chicken1-skeletal-muscle biological replicate 1

description:
Chicken1-skeletal-muscle
chicken_exp.txt


title: ESC_Derived_HLC_1_084


title: cor_sal_1w_426


title: cor_sal_1w_252


title: Mouse_SmartSeq2_SstBFP_P0_1


title: ESC_Derived_HLC_1_083


title: cor_sal_1w_245


title: cor_sal_1d_420

value: 1 day


title: cor_sal_1d_416


title: Mouse_SmartSeq2_SstBFP_E17.5_3


title: cor_sal_1d_418


title: Mouse_SmartSeq2_SstBFP_E17.5_2


title: cor_sal_1d_260


title: ESC_Derived_HLC_1_081

value: Human embryonic stem cell-derived hepatocyte-like cell


title: cor_sal_1d_256


title: cor_sal_1w_428


title: cor_psi_1w_427

value: psilocybin


title: cor_psi_1w_425


title: Mouse_SmartSeq2_SstBFP_E16.5_4

value: Pancreas


title: ESC_Derived_HLC_1_080


title: ESC_Derived_HLC_1_079


title: cor_psi_1w_253


title: cor_psi_1w_423


title: Mouse_SmartSeq2_SstBFP_E16.5_2


title: cor_psi_1w_251


title: cor_psi_1w_246


title: Mouse_SmartSeq2_SstBFP_P0_2


title: cor_psi_1d_419


title: ESC_Derived_HLC_1_133


title: cor_psi_1d_415


title: cor_psi_1d_417


title: ESC_Derived_HLC_1_076


title: Mouse_SmartSeq2_SstBFP_E16.5_1


title: cor_psi_1d_258


title: cor_psi_1d_259


title: Mouse_SmartSeq2_SstBFP_E15.5_4


title: Mouse_SmartSeq2_SstBFP_E17.5_1


title: RNA sequencing gpig-Spleen biological replicate 1

description:
gpig-Spleen
gpig_exp.txt

organism: Cavia porcellus

value: Guinea pig


title: Mouse_SmartSeq2_SstBFP_E15.5_3


title: cor_psi_1d_255


title: ESC_Derived_HLC_1_075


title: RNA sequencing gpig-Skeletal-muscle biological replicate 1

description:
gpig-Skeletal-muscle
gpig_exp.txt

source_name: Skeletal muscle

value: Skeletal muscle


title: RNA sequencing gpig-Liver biological replicate 1

description:
gpig-Liver
gpig_exp.txt

value: Adult


title: Mouse_SmartSeq2_SstBFP_E15.5_2


title: ESC_Derived_HLC_1_078


title: Mouse_SmartSeq2_SstBFP_E16.5_3


title: ESC_Derived_HLC_1_077


title: RNA sequencing gpig-Lung biological replicate 1

description:
gpig-Lung
gpig_exp.txt

value: female


title: ESC_Derived_HLC_1_074


title: ESC_Derived_HLC_1_073


title: RNA sequencing gpig-Kidney biological replicate 1

description:
gpig-Kidney
gpig_exp.txt


title: Mouse_SmartSeq2_SstBFP_E15.5_1


title: RNA sequencing gpig-Heart biological replicate 1

description:
gpig-Heart
gpig_exp.txt


title: RNA sequencing gpig-Adipose biological replicate 1

description:
gpig-Adipose
gpig_exp.txt


title: Mouse_SmartSeq2_SstBFP_E14.5_2


title: ESC_Derived_HLC_1_071


title: ESC_Derived_HLC_1_072


title: RNA sequencing Cat3-Lung biological replicate 3

description:
Cat3-Lung
cat_exp.txt

organism: Felis catus

value: A native breed of cat from Chengdu  city


title: RNA sequencing Cat3-Skeletal-muscle biological replicate 3

description:
Cat3-Skeletal-muscle
cat_exp.txt


title: RNA sequencing Cat3-Liver biological replicate 3

description:
Cat3-Liver
cat_exp.txt

value: Liver


title: ESC_Derived_HLC_1_069


title: RNA sequencing Cat3-Kidney biological replicate 3

description:
Cat3-Kidney
cat_exp.txt


title: ESC_Derived_HLC_1_068


title: Mouse_SmartSeq2_GcgGFP_P3_2


title: RNA sequencing Cat3-Heart biological replicate 3

description:
Cat3-Heart
cat_exp.txt


title: Mouse_SmartSeq2_GcgGFP_P3_1


title: ESC_Derived_HLC_1_067


title: Mouse_SmartSeq2_GcgGFP_E17.5_1


title: RNA sequencing Cat2-Spleen biological replicate 2

description:
Cat2-Spleen
cat_exp.txt

value: Spleen


title: RNA sequencing Cat2-Skeletal-muscle biological replicate 2

description:
Cat2-Skeletal-muscle
cat_exp.txt


title: ESC_Derived_HLC_1_066


title: RNA sequencing Cat2-Lung biological replicate 2

description:
Cat2-Lung
cat_exp.txt

value: Lung


title: RNA sequencing Cat3-Spleen biological replicate 3

description:
Cat3-Spleen
cat_exp.txt


title: ESC_Derived_HLC_1_070


title: Mouse_SmartSeq2_Ngn3CreER2D_E17.5_1

value: Ngn3-CreER;Rosa-RFP+ (TM 2D)


title: ESC_Derived_HLC_1_065


title: RNA sequencing Cat2-Kidney biological replicate 2

description:
Cat2-Kidney
cat_exp.txt

value: Kidney


title: Mouse_SmartSeq2_Ngn3CreER2D_E15.5_2


title: RNA sequencing Cat2-Liver biological replicate 2

description:
Cat2-Liver
cat_exp.txt


title: ESC_Derived_HLC_1_064


title: Mouse_SmartSeq2_SstBFP_E14.5_1


title: RNA sequencing Cat1-Spleen biological replicate 1

description:
Cat1-Spleen
cat_exp.txt


title: RNA sequencing Cat2-Adipose biological replicate 2

description:
Cat2-Adipose
cat_exp.txt

value: Adipose


title: Mouse_SmartSeq2_Ngn3CreER2D_E15.5_1


title: RNA sequencing Cat1-Skeletal-muscle biological replicate 1

description:
Cat1-Skeletal-muscle
cat_exp.txt


title: RNA sequencing Cat1-Lung biological replicate 1

description:
Cat1-Lung
cat_exp.txt


title: RNA sequencing Cat3-Adipose biological replicate 3

description:
Cat3-Adipose
cat_exp.txt


title: RNA sequencing Cat1-Kidney biological replicate 1

description:
Cat1-Kidney
cat_exp.txt


title: Mouse_SmartSeq2_Ngn3CreER2D_E14.5_5


title: Mouse_SmartSeq2_Ngn3CreER2D_E14.5_6


title: ESC_Derived_HLC_1_062


title: RNA sequencing Cat1-Heart biological replicate 1

description:
Cat1-Heart
cat_exp.txt

value: Heart


title: ESC_Derived_HLC_1_061


title: Mouse_SmartSeq2_Ngn3CreER2D_E14.5_4


title: Mouse_SmartSeq2_Ngn3CreER2D_E14.5_3


title: RNA sequencing Cat2-Heart biological replicate 2

description:
Cat2-Heart
cat_exp.txt


title: ESC_Derived_HLC_1_060


title: WT_SFZ

city: Tokyo

first: Yuji

last: Maenohara

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

department: Orthopaedic department

institute: University of Tokyo

data_processing:
Reads were mapped to the mm10 using HISAT2
Clean reads were mapped to reference using Bowtie2 and gene expression level was caliclated with RSEM
Gene expression level is represented as FPKM (fragments per kilobase of exon per million fragments mapped) value.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

extract_protocol:
SFZ cells were isolated as described previously.Briefly, both ends of the femur and proximal end of the tibia were dissected from 5-day-old mice, and ligaments, tendons, and synovium were excised. Cartilage tissues were incubated with 0.25% trypsin for 1 hour, followed by 1.5 hours of digestion with 173 U/mL type I collagenase. Dissociated cells were seeded on fibronectin-coated culture dishes. Total RNA was purified using an RNeasy Mini Kit
RNA libraries were prepared By BGI

tag: strain

value: Superficial zone cells of cartilage

value: post natal day 5

value: wild type


title: Mouse_SmartSeq2_Ngn3CreER2D_E14.5_2


title: Prg4KO_SFZ

tag: cell type


title: Mouse_SmartSeq2_Ngn3CreER2D_E14.5_1


title: ESC_Derived_HLC_1_059

value: Human embryonic stem cell-derived hepatocyte-like cell


title: ESC_Derived_HLC_1_057


title: ESC_Derived_HLC_1_058


title: Mouse_SmartSeq2_Ngn3CreER1D_E18.5_2

value: Pancreas

value: Ngn3-CreER;Rosa-RFP+ (TM 1D)


title: ESC_Derived_HLC_1_063


title: RNA sequencing Cat1-Liver biological replicate 1

description:
Cat1-Liver
cat_exp.txt


title: ESC_Derived_HLC_1_056


title: Mouse_SmartSeq2_Ngn3CreER1D_E18.5_1


title: Mouse_SmartSeq2_Ngn3CreER1D_E17.5_3


title: ESC_Derived_HLC_1_054


title: Mouse_SmartSeq2_Ngn3CreER1D_E17.5_2


title: ESC_Derived_HLC_1_053


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47284]

type: RNA

city: Beerse

first: Marianne

last: Tuefferd

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica

description: PBMC patient 2_24Weeks

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).

scan_protocol: Images were analyzed using the GeneChip® Command Console Software (AGCC) (Affymetrix).

data_processing: All microarray data were processed using the statistical computing program R (R version 3.2.2) as well as Bioconductor tools. The gene expression values were normalized using RMA. Grouping of the individual probes into gene-specific probe sets was performed based on Entrez Gene using the metadata package hgu219hsentrezg (version 20.0.0).

label: Biotin

source_name: PBMCs

label_protocol: All microarray-related steps for target preparation, including the amplification of total RNA and labeling, were carried out as described in the GeneChip®3’ IVT Express Kit User Manual (Affymetrix 2004). Biotin-labeled target samples were hybridized to the GeneChip® HG-U219 containing probes for 18492 genes.

extract_protocol: Trizol (Invitrogen)

tag: patient

tag: time


title: Mouse_SmartSeq2_Ngn3CreER1D_E17.5_1


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47289]

description: PBMC patient 8_24Weeks


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47290]

description: PBMC patient 9_24Weeks


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47286]

description: PBMC patient 4_24Weeks


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47287]

description: PBMC patient 6_24Weeks


title: ESC_Derived_HLC_1_052


title: Mouse_SmartSeq2_Ngn3CreER1D_E16.5_4


title: ESC_Derived_HLC_1_051


title: ESC_Derived_HLC_1_055


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47270]

description: PBMC patient 6_ EOT

value: EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47274]

description: PBMC patient 7_ EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47278]

description: PBMC patient 8_ EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47283]

description: PBMC patient 1_24Weeks


title: ESC_Derived_HLC_1_050


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47288]

description: PBMC patient 7_24Weeks


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47262]

description: PBMC patient 4_ EOT


title: Mouse_SmartSeq2_Ngn3CreER1D_E16.5_3


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47258]

description: PBMC patient 3_ EOT


title: Mouse_SmartSeq2_Ngn3CreER1D_E16.5_2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47250]

description: PBMC patient 1_ EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47254]

description: PBMC patient 2_ EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47266]

description: PBMC patient 5_ EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47282]

description: PBMC patient 9_ EOT


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47277]

description: PBMC patient 8_ 1 week


title: ESC_Derived_HLC_1_049


title: Mouse_SmartSeq2_Ngn3CreER1D_E16.5_1


title: Mouse_SmartSeq2_Ngn3CreER1D_E15.5_3


title: ESC_Derived_HLC_1_048


title: ESC_Derived_HLC_1_047


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47281]

description: PBMC patient 9_ 1 week


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47285]

description: PBMC patient 3_24Weeks


title: Mouse_SmartSeq2_Ngn3CreER1D_E15.5_1


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47269]

description: PBMC patient 6_ 1 week


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47265]

description: PBMC patient 5_ 1 week


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47261]

description: PBMC patient 4_ 1 week


title: ESC_Derived_HLC_1_045


title: Mouse_SmartSeq2_Ngn3CreER1D_E14.5_2


title: ESC_Derived_HLC_1_043


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47257]

description: PBMC patient 3_ 1 week


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47273]

description: PBMC patient 7_ 1 week


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47249]

description: PBMC patient 1_ 1 week


title: Mouse_SmartSeq2_Ngn3CreER1D_E14.5_1


title: ESC_Derived_HLC_1_046


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47253]

description: PBMC patient 2_ 1 week


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47276]

description: PBMC patient 8_Day2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47280]

description: PBMC patient 9_Day2


title: Mouse_SmartSeq2_Ngn3CreER1D_E13.5_2


title: ESC_Derived_HLC_1_044


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47272]

description: PBMC patient 7_Day2


title: ESC_Derived_HLC_1_042


title: ESC_Derived_HLC_1_082


title: Mouse_SmartSeq2_Ngn3CreER1D_E15.5_2


title: Mouse_SmartSeq2_Ngn3CreER1D_E13.5_1


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47260]

description: PBMC patient 4_Day2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47252]

description: PBMC patient 2_Day2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47256]

description: PBMC patient 3_Day2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47264]

description: PBMC patient 5_Day2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47248]

description: PBMC patient 1_Day2


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47279]

description: PBMC patient 9_BL

value: Baseline


title: ESC_Derived_HLC_1_041


title: HNF6 ChIP Input Foxa1L/L;2L/L   2

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

country: USA

institute: University of Pennsylvania

description: processed data file: WT_5412_peaks.txt

data_processing:
DNA methylation data was analyzed by using 100 bp single-end sequencing reads that were trimmed and quality filtered by trim galore software (v.0.3.3) using the following command:
trim_galore sample_R1.fastq.gz
Read alignment (genome build mm9) and extraction of single-base resolution methylation levels were carried out by BSMAP v.2.74  using the following commands:
bsmap -a sample_R1_val_1.fq.gz  -d mm9_AllGenome.fa -o bam_file -R -p12
python methratio.py -i “no-action” -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file
DNA methylation scores were calculated on FoxA2 binding sites obtained by ChIP-exo-seq  at different distances from FoxA2 peak center. Methylation score in each window is the average methylation levels of CpGs located in the window per sample. Then, average of two biological samples was calculated.
Genome_build: mm9

source_name: Liver, Foxa1L/L;2L/L

growth_protocol: All procedures involving mice were conducted under a protocol approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Pennsylvania. 8 weeks-old mice Foxa1L/L;Foxa2L/L with or without Cre Alfp were used for dissecting the role of Foxa1/2 in liver development. In the case of FoxA1/2 ablation in adulthood, a total of 1 × 1011genome copies of AAV8 carrying the gene for Cre under the hepatocyte-specific Tbg promoter (Penn vector) were injected into the superficial temporal vein of Foxa1L/L;Foxa2L/L 8-weeks-old mice for 1 month.

extract_protocol:
Mice were anesthetized, sacrificed, and subjected to liver perfusion. Whole liver was then digested by collagenase (Roche) and hepatocytes removed and isolated by means of a percoll gradient (18). This yielded a population of relatively pure (>95%) hepatocytes. DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH 8), 2 mM ethylenediaminetetraacetic acid, 0.2% sodium dodecyl sulfate, 200 mM NaCl) supplemented with 300 μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
For ChIP analysis, chromatin was fixed and sheared with the M220 Focused-ultrasonicator™ (Covaris®) using the microTube snap-cap. Ten micrograms of chromatin was then immunoprecipitated with 2 μg of or HNF6 (Santa Cruz, sc-13050) antibodies. Libraries were generated using the NEBNext Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs).

tag: genotype/variation


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47268]

description: PBMC patient 6_Day2


title: ESC_Derived_HLC_1_040


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47275]

description: PBMC patient 8_BL


title: ESC_Derived_HLC_1_039


title: ESC_Derived_HLC_1_037


title: HNF6 ChIP Input Foxa1L/L;2L/L   1

description: processed data file: WT_5406_peaks.txt


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47267]

description: PBMC patient 6_BL


title: HNF6 ChIP Bound Foxa1L/L;2L/L   2

description: processed data file: WT_5412_peaks.txt


title: HNF6 ChIP Bound Foxa1L/L;2L/L   1

description: processed data file: WT_5406_peaks.txt


title: ESC_Derived_HLC_1_036


title: HNF6 ChIP Input Foxa1L/L;2L/L   3

description: processed data file: WT_5868_peaks.txt


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47334]

description: FNAB patient9_24weeks

source_name: FNABs

label_protocol: All microarray-related steps for target preparation, including the amplification of total RNA and labeling, were carried out as described in the GeneChip®3’ IVT Pico Kit User Manual (12 PCR cycles, Affymetrix). Biotin-labeled target samples were hybridized to the GeneChip® HG-U219 containing probes for 18492 genes.

tag: time point


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47251]

description: PBMC patient 2_BL


title: HNF6 ChIP Input Foxa1L/L;2L/L Alfp Cre 2

description: processed data file: DKO_5227_peaks.txt

source_name: Liver, Foxa1L/L;2L/L Alfp Cre

value: Foxa1L/L;2L/L Alfp Cre


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47247]

description: PBMC patient 1_BL


title: HNF6 ChIP Bound Foxa1L/L;2L/L   3

description: processed data file: WT_5868_peaks.txt


title: ESC_Derived_HLC_1_034


title: ESC_Derived_HLC_1_038


title: ESC_Derived_HLC_1_035


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47259]

description: PBMC patient 4_BL


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47271]

description: PBMC patient 7_BL


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47255]

description: PBMC patient 3_BL


title: PBMCs, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47263]

description: PBMC patient 5_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47328]

description: FNAB patient2_24weeks


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47332]

description: FNAB patient7_24weeks


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47333]

description: FNAB patient8_24weeks


title: ESC_Derived_HLC_1_033


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47329]

description: FNAB patient3_24weeks


title: HNF6 ChIP Bound Foxa1L/L;2L/L Alfp Cre 2

description: processed data file: DKO_5227_peaks.txt


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47331]

description: FNAB patient6_24weeks


title: HNF6 ChIP Input Foxa1L/L;2L/L Alfp Cre 1

description: processed data file: DKO_5222_peaks.txt


title: ESC_Derived_HLC_1_032


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47318]

description: FNAB patient7_EOT


title: HNF6 ChIP Input Foxa1L/L;2L/L AAV Cre 2

description: processed data file: 5005_2_peaks.txt

source_name: Liver, Foxa1L/L;2L/L AAV Cre

value: Foxa1L/L;2L/L AAV Cre


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47327]

description: FNAB patient1_24weeks


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47322]

description: FNAB patient8_EOT


title: HNF6 ChIP Bound Foxa1L/L;2L/L AAV Cre 2

description: processed data file: 5005_2_peaks.txt

value: Liver


title: HNF6 ChIP Bound Foxa1L/L;2L/L AAV Cre 1

description: processed data file: 5007_1_peaks.txt


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47306]

description: FNAB patient4_EOT


title: ESC_Derived_HLC_1_028


title: ESC_Derived_HLC_1_029


title: ESC_Derived_HLC_1_030


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47326]

description: FNAB patient9_EOT


title: WGBS Foxa1L/L;2L/L AAV Cre 2

description: processed data file: Methylation_scores_at_FoxA_sites_AAV_Cre.txt

source_name: Hepatocytes, Foxa1L/L;2L/L AAV Cre

extract_protocol:
Mice were anesthetized, sacrificed, and subjected to liver perfusion. Whole liver was then digested by collagenase (Roche) and hepatocytes removed and isolated by means of a percoll gradient (18). This yielded a population of relatively pure (>95%) hepatocytes. DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH 8), 2 mM ethylenediaminetetraacetic acid, 0.2% sodium dodecyl sulfate, 200 mM NaCl) supplemented with 300 μg/mL proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
WGBS libraries were prepared using the Ovation® Ultralow Methyl-Seq Library System (NuGEN Technologies Inc.) as per the manufacturer’s instructions. One hundred and fifty nanograms of genomic DNA was sheared with the M220 Focused-ultrasonicator™(Covaris®) using the 200 bp snap-cap protocol and subsequently purified with AMPure XP beads. After end repair, adaptor ligation, and final repair, DNA was bisulfite converted with the EpiTect Fast DNA Bisulfite Kit (Qiagen GmbH) following the cycling conditions specified in the Ovation® Ultralow Methyl-Seq Library System protocol. Libraries were then amplified, purified, pooled, and sequenced on the Illumina HiSeq with 100 bp single-end sequencing. Sequencing was conducted by the University of Pennsylvania Next-Generation Sequencing Core (Philadelphia, PA, USA) at a depth that exceeds the 20-fold commonly achieved in WGBS databases.

value: Hepatocytes


title: HNF6 ChIP Bound Foxa1L/L;2L/L Alfp Cre 1

description: processed data file: DKO_5222_peaks.txt


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47302]

description: FNAB patient3_EOT


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47310]

description: FNAB patient5_EOT


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47298]

description: FNAB patient2_EOT


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47321]

description: FNAB patient8_1week


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47313]

description: FNAB patient6_1week


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47309]

description: FNAB patient5_1week


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47330]

description: FNAB patient4_24weeks


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47314]

description: FNAB patient6_EOT


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47317]

description: FNAB patient7_1week


title: ESC_Derived_HLC_1_026


title: WGBS Foxa1L/L;2L/L AAV Cre 1


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47305]

description: FNAB patient4_1week


title: ESC_Derived_HLC_1_025


title: HNF6 ChIP Input Foxa1L/L;2L/L AAV Cre 1

description: processed data file: 5007_1_peaks.txt


title: ESC_Derived_HLC_1_031


title: ESC_Derived_HLC_1_027


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47301]

description: FNAB patient3_1week


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47294]

description: FNAB patient1_EOT


title: WGBS Foxa1L/L;2L/L Alfp Cre 1

description: processed data file: Methylation_scores_FoxA_Alfp.txt

source_name: Hepatocytes, Foxa1L/L;2L/L Alfp Cre


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47297]

description: FNAB patient2_1week


title: ESC_Derived_HLC_1_024

source_name: ESC


title: ESC_Derived_HLC_1_023


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47325]

description: FNAB patient9_1week


title: WGBS Foxa1L/L;2L/L  2

source_name: Hepatocytes, Foxa1L/L;2L/L


title: ESC_Derived_HLC_1_022


title: WGBS Foxa1L/L;2L/L  1


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47316]

description: FNAB patient7_Day2


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47308]

description: FNAB patient5_Day2


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47312]

description: FNAB patient6_Day2


title: WGBS Foxa1L/L;2L/L Alfp Cre 2


title: ESC_Derived_HLC_1_021


title: ESC_Derived_HLC_1_020


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47320]

description: FNAB patient8_Day2


title: UCBPP-PA14_Pep1018_1

city: Burnaby

first: Amy

middle: H.

last: Lee

state: BC

address: 8888 University Drive

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

description: bacterial cells from the edge of swarming colony treated with peptide1018

data_processing:
FastQC v0.11.5 and MulitQC v0.8.dev were used to obtain the quality score for FASTQ files
STAR aligner was used to align reads to the UCBPP-PA14 genome (GCF_000014625.1)
Read count tables were then generated with HTseq-count v0.6.1p1
DESeq2 was used to estimate the fold-change in gene expression between untreated edge and centre cells, and peptide-treated cells under swarming conditions
with thresholds of adjusted p-value ≤ 0.05 and absolute fold change ≥ 1.5
Genome_build: P. aeruginosa UBCPP-PA14 (GCF_000014625.1)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

organism: Pseudomonas aeruginosa UCBPP-PA14

growth_protocol: The standard swarming assay for P. aeruginosa involved inoculating 1 μl of mid-log phase sub-culture into the centre of a polystyrene plate containing BM2 swarming agar. PAO1 swarming assays were conducted on BM2 swarming agar with 0.5% CAA instead of 0.1% CAA, which was used for PA14.

extract_protocol:
Bacterial cells were collected and mixed 1:2 volume-wise with RNA protect Bacteria Reagent (QIAGEN). RNA was extracted using RNeasy mini kit (QIAGEN).
RNA was quantified using a Nanodrop-1000 (ThermoFisher). RNA quality and quantity were assessed on an Agilent Bioanalyzer. rRNA was depleted (Ribo-Zero depletion kit, Illumina), and cDNA libraries were prepared using the KAPA RNA HyperPrep Kit (KAPA Biosystems) and sequenced through the University of British Columbia Sequencing Consortium (Illumina HiSeq-2500)

treatment_protocol: Peptide 1018 was incorporated directly into the agar when necessary. Swarming plates were incubated for 20 h prior to RNA extraction.

value: Swarming edge with peptide

tag: media

value: BM2 swarming agar and 0.75 ug/ml peptide 1018

tag: replicate


title: ESC_Derived_HLC_1_019


title: UCBPP-PA14_Swarm_E3

description: bacterial cells from the edge of swarming colony

value: Swarming edge

value: BM2 swarming agar


title: UCBPP-PA14_Swarm_E1

source_name: bacterial cells from the edge of swarming colony


title: ESC_Derived_HLC_1_018


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47304]

description: FNAB patient4_Day2


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47300]

description: FNAB patient3_Day2


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47293]

description: FNAB patient1_1week


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47324]

description: FNAB patient9_Day2


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47292]

description: FNAB patient1_Day2


title: UCBPP-PA14_Swarm_C3

description: bacterial cells from the center of swarming colony

value: Swarming centre


title: ESC_Derived_HLC_1_017


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47315]

description: FNAB patient7_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47319]

description: FNAB patient8_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47323]

description: FNAB patient9_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47311]

description: FNAB patient6_BL


title: ESC_Derived_HLC_1_016


title: UCBPP-PA14_Swarm_C1

source_name: bacterial cells from the center of swarming colony


title: ESC_Derived_HLC_1_015


title: ESC_Derived_HLC_1_014


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47299]

description: FNAB patient3_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47307]

description: FNAB patient5_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47296]

description: FNAB patient2_Day2


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47295]

description: FNAB patient2_BL


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47303]

description: FNAB patient4_BL


title: EE9_t4_rep3

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

data_processing:
standard illumina base-calling and demultiplexing
bowtie2 v2.4.2 mapping on WCFS1 genome (accession numbers NC_006375.1, NC_006376.1, NC_006377.1, and NC_004567.2)
Supplementary_files_format_and_content: The textfile contain the raw counts of reads mapped to the WCFS1 genome, the fastq files contain the raw data as produced by the Illumina Novaseq 6000 machine

organism: Lactiplantibacillus plantarum

source_name: L. plantarum culture

growth_protocol: growt in in MRS at 37 C until late exponential phase

extract_protocol:
RNA sequencing was performed on the wild type strain L. plantarum NZ3400, the auto-aggregating strains IA01t0 and PA4_02 and the non-aggregating IA01t4. Pre-cultures were performed in MRS broth at 30°C overnight. Experiments were performed in triplicates for NZ3400, IA01t0 and IA01t4 and in duplicate for and PA4_02. Cultures were inoculated from an overnight pre-culture and grown until OD600nm=2.6-2.7. The growth phase was validated via pH measurements and HPLC analysis of glucose and lactate concentrations. Total RNA was extracted based on a chloroform/phenol extraction followed by purification using the High Pure RNA isolation kit (Roche Diagnostics, Rotkreuz, Switzerland) as described previously (58). RNA quantity, purity and integrity were verified using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Samples with an RNA integrity number (RIN) > 9 and a 16S/23S-rRNA ratio > 1.5 were selected for rRNA depletion. Thereafter, EDTA was added to 1 mM and depletion was performed using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Life Technologies Europe BV, Zug, Switzerland) following the manufacturer’s instructions. Concentrations of depleted samples were determined in a TapeStation and normalized to 100 ng/ml using in Tris-HCl (10 mM, pH=8.5).
Sequencing of 100 bp single reads was done on Illumina Novaseq 6000 (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). The library was prepared according to the Illumina Truseq Total RNA protocol.

tag: aggregation

value: no


title: WT_rep3

value: WT


title: EE9_t4_rep2


title: EE9_t4_rep1


title: WT_rep2


title: EE9_t0_rep4

value: yes


title: EE9_t0_rep3


title: ESC_Derived_HLC_1_011

value: Human embryonic stem cell-derived hepatocyte-like cell


title: WT_rep4


title: ESC_Derived_HLC_1_010


title: 6_B6_rep2


title: UCBPP-PA14_Pep1018_3

source_name: bacterial cells from the edge of swarming colony treated with peptide1018

value: BM2 swarming agar and 0.75 ug/ml peptide 1019


title: ESC_Derived_HLC_1_013


title: Fine Needle Aspirate, IFN-free DAA therapy in HCV treatment-naïve patients, (5 longitudinal samples/patient) [47291]

description: FNAB patient1_BL


title: ESC_Derived_HLC_1_012


title: cell line CLBL, control, replicate 3

city: Columbus

first: Ayse

middle: Selen

last: Yilmaz

state: OH

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU

description: 0C CLBL1

hyb_protocol: Then 5.2 μg of fragmented and labeled ss-cDNA were hybridized to Affymetrix GeneChip CanGene 1.0 ST array for 16 hours at 45°C rotating at 60 rpm.

scan_protocol: Arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing:
Microarray data was analyzed using the robust multiarray averaging (RMA) method in the R statistical programming environment version 3.1.2.   Differential expression analysis was performed with the R ‘limma’ package and graphically visualization of heat maps was performed with the R basic plots and ‘pheatmap
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = CanGene-1_0-st
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

organism: Canis lupus familiaris

source_name: cell line CLBL, control

label_protocol: A 100 ng aliquot of total RNA was linearly amplified and labeled using the Affymetrix WT Plus Reagent Kit (Thermo Fisher Scientific, Waltham, MA).

growth_protocol: Cell lines were cultured in complete RPMI 1640 medium supplemented with 10% heat inactivated fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine (Invitrogen, Carlsbad, CA), 100 units/ml of penicillin and streptomycin (Gibco), and cultured at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted using the Total RNA Purification Kit (Norgen) and QIAshredder Columns (Qiagen). RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Cell lines CLBL-1 and 17-71 were treated with 100 nM of PR220, a selective protein arginine methyltransferase (PRMT5) inhibitor. Cell line CLBL-1 was collected at day 2 and cell line 17-71 was collected at day 4, according to cell line sensitivity and biomarker analysis of global protein symmetric di-methylation and H4R3me2s.

tag: cell line

tag: tissue source

value: lymph node

value: canine B-cell lymphoma cell line

tag: condition

value: Control


title: cell line CLBL, control, replicate 1

description: 0A CLBL1


title: EE9_t0_rep2


title: cell line CLBL, control, replicate 2

description: 0B CLBL1


title: 6_B6_rep3


title: 1000 ppm PB for 7 days, biological rep5

city: Osaka

first: Ayako

last: Ohara

address: 1-98, Kasugade-naka 3-chome, Konohana-ku

institute: Sumitomo Chemical Co., Ltd.

description: gene expression data from humanized liver of chimeric mouse fed diets containing 1000 ppm PB for 7 days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, mixtures were hybridized to SurePrint G3 Rat Gene Expression 8x60K Microarrays, SurePrint G3 Mouse GE 8x60K Microarrays or SurePrint G3 Human GE v2 8x60K Microarrays for 17 hours at 65°C in a rotating 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 (Agilent) using one color scan setting for 8x60K array slides. The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: The processed signal intensities were log2-transformed and normalized to the 75th percentile using GeneSpring software (version 14.9.1) (Agilent).

source_name: liver of chimeric mouse with human hepatocytes fed diets containing 1000 ppm PB for 7 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop 2000/2000c Spectrophotometer.

growth_protocol: The animals were housed in a barrier maintained animal room. The environmental conditions in the animal room were set to maintain a temperature range of 22 - 26°C and a relative humidity range of 40 - 70%, and a 12 hour light (8:00 - 20:00)/ 12 hour dark (20:00 - 8:00) illumination cycle. A commercially available pulverized diet and filtered tap water were provided ad libitum.

extract_protocol: The livers were stored in RNAlater RNA Stabilization Reagent (Life Technologies Corporation, Carlsbad, CA) at -20°C. Total RNA was prepared using Isogen solution (Nippon Gene) and RNeasy Mini Kits (Qiagen) following the manufacturer's instructions. Total RNA was quantified using a NanoDrop 2000/2000c Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Male chimeric mice with human hepatocytes (4-5 animals/dose) were fed diets containing 0 (control), 500 or 1000 ppm PB for 7 days.

tag: gender

value: male

tag: tissue

value: liver


title: ESC_Derived_HLC_1_006


title: ESC_Derived_HLC_1_007


title: ESC_Derived_HLC_1_005


title: ESC_Derived_HLC_1_009


title: cell line 17-71, treated 100, replicate 3

description: 17-71 100.C

source_name: cell line 17-71, 100 nM of PR220

value: 100 nM of PR220


title: HeLa cells, siTRMT2A rep_3

city: Aveiro

first: Ana

last: Soares

address: Campus de Santiago

country: Portugal

institute: University of Aveiro

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality was examined by FastQC and trimmed reads (pass Illumina quality  filter, trimmed 5’,3’-adaptor bases by cutadapt) were aligned allowing for 1 mismatch only to the  mature tRNA sequences, then reads that did not map were aligned allowing for 1 mismatch only to precursor  tRNA sequences with bowtie software.
The abundance of tRF & tiRNA was evaluated using their sequencing counts and was normalized as counts per million of total aligned reads  (CPM). The tRFs & tiRNAs differentially expressed were screened based on the count value  with R package edgeR.
Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn  plots, Hierarchical clustering, Scatter plots and Volcano plots were performed in R or perl environment for  statistical computing and graphics of the expressed tRF & tiRNA.
Genome_build: GtRNAdb
Supplementary_files_format_and_content: Excel files containing tRF and tiRNA ID, sequence, type, length of sequence, alignment information, read count and CPM, the counts of per million mapped reads:
[Expression]  contains all the expressed tRFs and tiRNAs sequenced in all samples
[Up_siTRMT2A vs siCtrl]  contains tRFs and tiRNAs upregulated in the siTRMT2A condition
[Down_siTRMT2A vs siCtrl]  contains tRFs and tiRNAs downregulated in the siTRMT2A condition

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, Cat.11965084), supplemented with 10% of Fetal Bovine Serum (FBS) (Sigma, Cat.F1051) and 1% of Pen-Strep-Glut (Gibco, Cat.15070063). Cells were maintained in culture in an incubator at 37°C with 5% of CO2 and 95% of humidity.

extract_protocol:
The total RNA was extracted using the mirVanaTM miRNA Isolation kit (Ambion) or TRIsure™ (Bioline) according to manufacturer´s instructions. The integrity and quantity of each RNA sample were assessed using a Bioanalyzer.
Total RNA samples were first pretreated as following to remove some  RNA modifications that interfere with small RNA-seq library construction: 3’-aminoacyl (charged)  deacylation to 3’-OH for 3’-adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’  -adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’-adaptor ligation, m1A and  m3C demethylation for efficient reverse transcription. Then pretreated total RNA was used to prepare  the sequencing library in the following steps: 1) 3’-adapter ligation; 2) 5’-adapter ligation; 3) cDNA  synthesis; 4) PCR amplification; 5) size selection of 134_x0018_160bp PCR amplified fragments (corresponding  to 14_x0018_40nt small RNA size range). The libraries were denatured as single-stranded DNA molecules,  captured on Illumina flow cells, amplified in situ as sequencing clusters and sequenced for 50 cycles on  Illumina NextSeq 500 system per the manufacturer’s instructions.
Small-RNA Seq

treatment_protocol: A siGenome SMARTpool human siRNA targeting the tRNA-modifying enzyme TRMT2A (siTRMT2A) and a negative control siGenome SMARTpoll human siRNA (siCtrl) were obtained from Dharmacon (ThermoScientific) and reversely transfected into HeLa cells in 24 well plates. SMARTpools are a mixture of 4 siRNAs against the gene of interest provided as a single reagent, increasing potency and specificity. Briefly, 12 µL of 500 nM siRNA duplex in 88 µL of Opti-MEM (Alfagene, Cat.31985062) was added to each well, followed by the addition of 1 µL/well of lipofectamine RNAimax (Invitrogen, Cat.13778075) mix. After an incubation for 30 minutes, 4x10e4 cells/mL were added to each well in complete growth medium without antibiotics. Finally, cells were incubated for 72 hours at 37°C in a CO2 incubator.

value: HeLa

value: cervical cancer cell

tag: treatment

value: Cells transfected with a siTRMT2A


title: 1000 ppm PB for 7 days, biological rep4


title: ESC_Derived_HLC_1_008


title: ESC_Derived_HLC_1_004


title: cell line CLBL, treated 100, replicate 1

description: 100A CLBL1

source_name: cell line CLBL, 100 nM of PR220


title: cell line CLBL, treated 100, replicate 2

description: 100B CLBL1


title: 1000 ppm PB for 7 days, biological rep3


title: 1000 ppm PB for 7 days, biological rep1


title: 500 ppm PB for 7 days, biological rep3

description: gene expression data from humanized liver of chimeric mouse fed diets containing 500 ppm PB for 7 days

source_name: liver of chimeric mouse with human hepatocytes fed diets containing 500 ppm PB for 7 days


title: cell line 17-71, treated 100, replicate 1

description: 17-71 100.A


title: cell line 17-71, control, replicate 1

description: 17-71 0.A

source_name: cell line 17-71, control


title: 500 ppm PB for 7 days, biological rep4


title: 500 ppm PB for 7 days, biological rep5


title: HeLa cells, siTRMT2A rep_2


title: ESC_Derived_HLC_1_003


title: E15_FJW161014001_H12

description: EWF-E15_FJW161014001_H12_TCGACGT-TCTCTCC_L006

source_name: E15.0_whisker follicles cells

tag: Stage

value: whisker follicles cells

tag: data quality

value: ok


title: E15_FJW161014001_H11

description: EWF-E15_FJW161014001_H11_TGCAGCT-TCTCTCC_L006


title: cell line 17-71, treated 100, replicate 2

description: 17-71 100.B


title: E15_FJW161014001_H10

description: EWF-E15_FJW161014001_H10_CGATCAG-TCTCTCC_L006


title: HeLa cells, siCtrl rep_3

value: Cells transfected with a siCtrl


title: HeLa cells, siTRMT2A rep_1


title: 1000 ppm PB for 7 days, biological rep2


title: 0 ppm (control) for 7 days, biological rep4

description: gene expression data from humanized liver of chimeric mouse fed diets containing 0 ppm (control) for 7 days

source_name: liver of chimeric mouse with human hepatocytes fed diets containing 0 ppm (control) for 7 days


title: ESC_Derived_HLC_1_001


title: ESC_Derived_HLC_1_002


title: cell line 17-71, control, replicate 2

description: 17-71 0.B


title: 0 ppm (control) for 7 days, biological rep3


title: 500 ppm PB for 7 days, biological rep2


title: 0 ppm (control) for 7 days, biological rep1


title: 0 ppm (control) for 7 days, biological rep2


title: 500 ppm PB for 7 days, biological rep1


title: E15_FJW161014001_H09

description: EWF-E15_FJW161014001_H09_CCTAAGA-TCTCTCC_L006


title: E15_FJW161014001_H08

description: EWF-E15_FJW161014001_H08_ACTGAGC-TCTCTCC_L006


title: DE_1_15

value: Definitive endoderm


title: E15_FJW161014001_H06

description: EWF-E15_FJW161014001_H06_ATGCGCA-TCTCTCC_L006


title: HeLa cells, siCtrl rep_1


title: E15_FJW161014001_H05

description: EWF-E15_FJW161014001_H05_TACGCTG-TCTCTCC_L006


title: E15_FJW161014001_H02

description: EWF-E15_FJW161014001_H02_GGAGCTA-TCTCTCC_L006


title: E15_FJW161014001_H04

description: EWF-E15_FJW161014001_H04_CGGAGCC-TCTCTCC_L006


title: DE_1_13


title: DE_1_12


title: E15_FJW161014001_H01

description: EWF-E15_FJW161014001_H01_ACTCGCT-TCTCTCC_L006

value: low


title: DE_1_14


title: Day 90 organoids proximal  SARS 4DPI Rep 1

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
Sequencing of pooled libraries were done using NextSeq 500 (Illumina). The quality of the raw data was assessed using FastQC v.0.11.7. Sequence reads were aligned to a combination of the human genome reference (GRCh38) and SARS-CoV-2 sequence, using STAR v.2.6.0c. Counts per gene were summarized using the featureCounts function from the subread package v.1.6.2.
Ensembl v67 gene annotations were used for gene counts, gene counts were obtain using STAR v2.6
Raw gene counts were normalized using limma/voom method
Genome_build: GRCh38 with SARS_CoV2 genome and tdtomato
Supplementary_files_format_and_content: Matrix of counts per million reads per sample

source_name: BU1CG human iPSC

growth_protocol: To derive proximal and colonic intestinal epithelial cells/organoids, PSCs were first dissociated into single cells suspension and 1.8-2X106 cells were plated per well (triplicate wells, n=3) of a 6-well tissue culture plate coated with Matrigel for 24 hours in mTeSR media containing ROCK inhibitor (RI) prior to differentiation into definitive endoderm differentiation using the Definitive Endoderm Kit (Stem Cell Technologies, 05110) for 3 days (day 0-3). To drive further maturation of definitive endoderm, day 3 cells were then passed 1:3-1:6 to a new plate in complete serum free differentiation medium (cSFDM) described in Gouon-Evans et al. (2006) supplemented with 2mM of dorsomorphin (DS, Stemgent, 040024) and 10mM SB431543 (SB, Biotechne, 1614) (together constituting DS/SB media) for 3 days (day 3-6) plus 10mM RI for the first 24 hrs. On day 6, cells were re-fed with cSFDM media supplemented with 3mM CHIR (Biotechne, 4423) 100nM retinoic acid (Sigma-Aldrich, R2625), and 10ng/mL rhBMP4 (BioTechne, 314BP) for specification of intestinal lineages. On day 15, cells were single-cell dissociated by trypsin for fluorescence activated cell sorting a CDX2-eGFP reporter (BU1CG, Mithal et al 2020). Cells were then cultured in three dimensional matrigel droplets, either CK+DCI (colon) or IM+CK (intestinal) to regionally pattern HIOs.

extract_protocol:
Following cell sorting for desired cell population, biological triplicate (n=3) samples of purified RNA was harvested using Qiazol and RNA Sample Preparation Kit v2 (QIAGEN).
Total mRNA was isolated using magnetic beads-based poly(A) selection, fragmented, and randomly fragmented for reverse transcription, followed by synthesis of cDNA fragments. cDNA fragments were then end-paired, and ligated to Illumina Paired-End sequencing adapters. The products were end-paired and PCR-amplified to create the final cDNA library.

treatment_protocol: After maturation of HIOs, HIOs were infected with purified SARS-CoV-2 stock at MOI 0.4. 100 μl inoculum was prepared in CK+DCI or IM+CK media for colonic or proximal HIOs, respectively (or mock-infected with medium-only). To facilitate infection, HIOs were isolated from matrigel.  Briefly, media was removed from wells containing HIOs, 0.5 mL Cell Recovery Solution (Corning) was added to the cells in matrigel, and plates were incubated at 4oC for 30 minutes.  The dissolved matrigel and cells in the Cell Recovery Solution were then transferred to 2 mL Sarstedt tubes .  Cells were pelleted by low speed centrifugation (300xg, 5 minutes).  Supernatant was removed and virus-free or virus-containing media were added to the corresponding tubes.  Cell pellets were mechanically disrupted to facilitate viral access.  HIOs were then incubated for 1 hour at 37oC and 5% CO2.  After the adsorption period, cells were pelleted by low speed centrifugation (300xg, 5 minutes) and the inoculum was removed.  Cells were subsequently re-plated in matrigel droplets with media and incubated at 37oC for the indicated times of infection. After 1 and 4 dpi, cells were lysed in Trizol and removed from the BSL4 lab, where RNA extraction was performed as per manufacterers recommended protocols

tag: developmental stage

value: Day 90 proximal organoid directed differentiation

tag: culture media

value: IM+CK

value: SARS-CoV-2 infected

tag: days post treatment

tag: isolation method

value: whole organoids


title: E15_FJW161014001_G12

description: EWF-E15_FJW161014001_G12_TCGACGT-CGTCTAA_L006

tag: cell type


title: Day 90 organoids proximal  Mock 4DPI Rep 3

value: Mock


title: DE_1_11


title: E15_FJW161014001_G10

description: EWF-E15_FJW161014001_G10_CGATCAG-CGTCTAA_L006


title: E15_FJW161014001_G11

description: EWF-E15_FJW161014001_G11_TGCAGCT-CGTCTAA_L006


title: DE_1_10


title: E15_FJW161014001_G08

description: EWF-E15_FJW161014001_G08_ACTGAGC-CGTCTAA_L006


title: E15_FJW161014001_G07

description: EWF-E15_FJW161014001_G07_TAGCGCT-CGTCTAA_L006


title: Day 90 Organoids proximal  Mock 4DPI Rep 2


title: Day 90 organoids proximal  SARS 4DPI Rep 3


title: E15_FJW161014001_G04

description: EWF-E15_FJW161014001_G04_CGGAGCC-CGTCTAA_L006


title: Day 90 organoids proximal  Mock 4DPI Rep 1


title: E15_FJW161014001_G05

description: EWF-E15_FJW161014001_G05_TACGCTG-CGTCTAA_L006


title: E15_FJW161014001_G06

description: EWF-E15_FJW161014001_G06_ATGCGCA-CGTCTAA_L006


title: DE_1_08


title: Day 90 organoids proximal  SARS 4DPI Rep 2


title: E15_FJW161014001_H03

description: EWF-E15_FJW161014001_H03_GCGTAGT-TCTCTCC_L006


title: E15_FJW161014001_G03

description: EWF-E15_FJW161014001_G03_GCGTAGT-CGTCTAA_L006


title: E15_FJW161014001_G01

description: EWF-E15_FJW161014001_G01_ACTCGCT-CGTCTAA_L006


title: Day 90 organoids proximal  SARS 1DPI Rep 3


title: E15_FJW161014001_F11

description: EWF-E15_FJW161014001_F11_TGCAGCT-CTAAGCC_L006


title: E15_FJW161014001_F12

description: EWF-E15_FJW161014001_F12_TCGACGT-CTAAGCC_L006


title: DE_1_07


title: E15_FJW161014001_F10

description: EWF-E15_FJW161014001_F10_CGATCAG-CTAAGCC_L006


title: DE_1_06


title: Day 90 organoids proximal  SARS 1DPI Rep 2


title: DE_1_09


title: Day 90 organoids proximal  SARS 1DPI Rep 1


title: E15_FJW161014001_F07

description: EWF-E15_FJW161014001_F07_TAGCGCT-CTAAGCC_L006


title: E15_FJW161014001_F05

description: EWF-E15_FJW161014001_F05_TACGCTG-CTAAGCC_L006


title: E15_FJW161014001_F09

description: EWF-E15_FJW161014001_F09_CCTAAGA-CTAAGCC_L006


title: E15_FJW161014001_F06

description: EWF-E15_FJW161014001_F06_ATGCGCA-CTAAGCC_L006


title: Day 90 organoids proximal  Mock 1DPI Rep 3


title: DE_1_05


title: DE_1_04


title: E15_FJW161014001_F04

description: EWF-E15_FJW161014001_F04_CGGAGCC-CTAAGCC_L006


title: DE_1_02


title: E15_FJW161014001_F03

description: EWF-E15_FJW161014001_F03_GCGTAGT-CTAAGCC_L006


title: DE_1_03


title: E15_FJW161014001_F02

description: EWF-E15_FJW161014001_F02_GGAGCTA-CTAAGCC_L006


title: Day 90 organoids proximal  Mock 1DPI Rep 1


title: E15_FJW161014001_F01

description: EWF-E15_FJW161014001_F01_ACTCGCT-CTAAGCC_L006


title: Day 90 organoids Colonic SARS 4DPI Rep 3

value: Day 90 colonic organoid directed differentiation

value: CK+DCI


title: E15_FJW161014001_F08

description: EWF-E15_FJW161014001_F08_ACTGAGC-CTAAGCC_L006


title: E15_FJW161014001_E11

description: EWF-E15_FJW161014001_E11_TGCAGCT-AAGGAGT_L006


title: Day 90 organoids Colonic SARS 4DPI Rep 2


title: DE_1_01


title: E15_FJW161014001_E10

description: EWF-E15_FJW161014001_E10_CGATCAG-AAGGAGT_L006


title: E15_FJW161014001_E09

description: EWF-E15_FJW161014001_E09_CCTAAGA-AAGGAGT_L006


title: Day 90 Organoids proximal  Mock 1DPI Rep 2


title: Day 90 organoids Colonic Mock 4DPI Rep 3


title: E15_FJW161014001_E08

description: EWF-E15_FJW161014001_E08_ACTGAGC-AAGGAGT_L006


title: E15_FJW161014001_E05

description: EWF-E15_FJW161014001_E05_TACGCTG-AAGGAGT_L006


title: E15_FJW161014001_E04

description: EWF-E15_FJW161014001_E04_CGGAGCC-AAGGAGT_L006


title: E15_FJW161014001_E06

description: EWF-E15_FJW161014001_E06_ATGCGCA-AAGGAGT_L006


title: E15_FJW161014001_E07

description: EWF-E15_FJW161014001_E07_TAGCGCT-AAGGAGT_L006


title: E15_FJW161014001_E12

description: EWF-E15_FJW161014001_E12_TCGACGT-AAGGAGT_L006


title: E15_FJW161014001_E03

description: EWF-E15_FJW161014001_E03_GCGTAGT-AAGGAGT_L006


title: E15_FJW161014001_E02

description: EWF-E15_FJW161014001_E02_GGAGCTA-AAGGAGT_L006


title: E15_FJW161014001_D12

description: EWF-E15_FJW161014001_D12_TCGACGT-ACTGCAT_L006


title: Day 90 organoids Colonic SARS 4DPI Rep 1


title: Day 90 organoids Colonic Mock 4DPI Rep 1


title: Day 90 organoids Colonic SARS 1DPI Rep 3


title: E15_FJW161014001_D11

description: EWF-E15_FJW161014001_D11_TGCAGCT-ACTGCAT_L006


title: E15_FJW161014001_D10

description: EWF-E15_FJW161014001_D10_CGATCAG-ACTGCAT_L006


title: E15_FJW161014001_D09

description: EWF-E15_FJW161014001_D09_CCTAAGA-ACTGCAT_L006