title: HCT116_pladiB_chase_4SU_Seq_rep1

data_processing:
Reads were mapped against the human genome (GRCh38) and rRNA sequences using ContextMap 2.7.9 with BWA as internal alignment program.
Read counts per gene (from Ensembl version 100) were calculated using the featureCounts program from the subread package (v1.4.6-p3).
Genome_build: GRCh38
Supplementary_files_format_and_content: gene read counts

source_name: Human colorectal HCT116 cells in culture

extract_protocol:
Cells were lysed in 3 ml of TriReagent for 5 min at room temperature and then stored at -80°C until further use. Thawed samples were mixed with 1 ml of chloroform, centrifuged 12000g/4°C/20 min and aqueous phase was transferred into new tubes followed by addition of 1.5 ml of precipitation buffer (1.2 M NaCl, 0.8 M sodium citrate) and 1.5 ml of isopropanol. After 10 min at room temparature samples were centrifuged 12000g/4°C/20 min, pellet was washed with 1 ml of 75% EtOH, centrifuged 13000g/4°C/10 min and diluted in 100 ul of RNase-free water. After 10 min at 65°C the samples were immediately cooled on ice and stored at -80°C. Biotinylation was performed similar to (Radle et al., 2013) and (Duffy and Simon, 2016). Reaction consisted of 100 µg of RNA, 0.01 mg/ml MTSEA Biotin-XX (Biotium, 90066), 20 % DMF, 10 mM Tris, pH=7.4, 1 mM EDTA. Samples were incubated at room temparature for 30 min in dark and RNA was extracted twice by chloroform extraction in Phase Lock Gel Heavy tubes (Quantabio, 71386). RNA was precipitated for 10 min at room temparature using 1/10th volume of 5 M NaCl and 1 volume of isopropanol, and centrifuged 20000g/4°C/20 min. RNA was diluted in 80 ul of RNase-free water, heated 65°C/10 min, immediately cooled on ice and 5 ul of wash buffer (100 mM Tris, pH=7.4, 10 mM EDTA, 1 M NaCl, 0.1 % Tween-20) was added. Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65001, 50 ul/sample) were washed twice in 500 ul of RNase-free water, twice with 500 ul of wash buffer and blocked in 440 ul of wash buffer containing 40 ng/ml GlycoBlue (Ambion, AM9516) for 1 h at room temperature in dark. Beads were washed twice with 500 ul of wash buffer, split into new tubes and biotinylated RNA was added. Samples were incubated for 15 min at room temperature in dark, washed 4x with 0.9 ml of wash buffer and eluted for 15 min at room temperature with 100 ul of elution buffer (100 mM Tris, pH=7.4, 1 mM EDTA, 100 mM NaCl, 0.01 % Tween 20). Elution was repeated once and eluates were pooled. Eluate was cleaned using RNeasy MinElute Kit (Qiagen, 74204) with final elution into 25 ul of RNase-free water. Samples (550 ng of RNA) were treated with DNase I (Sigma, AMPD1) according to manufacturer’s protocol. KAPA Pure Beads (Roche, 07983271001, 2.2x sample volume) were used for cleanup, incubated for 15 min at room temperature and washed 2x in 80% ethanol. Samples were eluted into 15 ul of RNase-free water.
Libraries were prepared using 450 ng of RNA and Lexogen SiRV – Set 3 spike-ins (180 pg). Ribosomal RNA depletion was done using RiboCop rRNA Depletion Kit version 1.3 (Lexogen, 037.24) following manufacturer’s instructions. In final step, RNA was eluted into 6.5 ul of RNase-free water and 5 ul of this eluate was used for library preparation. Library was prepared following instructions in NEB Next UltraII Directional RNA Library Kit for Illumina using KAPA Pure Beads.

treatment_protocol: HCT116 cells plated at 50-60% confluency onto 150-cm2 dishes were treated with 186 nM pladi B for 45 min, 50 nM OTS964 for 15 min or DMSO for 15 min in 10 ml of DMEM at 37°C. Five ml of medium was removed and saved. 4SU was added to final concentration of 500 nM and cells were incubated for another 15 min at 37°C. For pulse experiment medium was discarded and cells were lysed. For chase experiment cells were washed once in PBS, saved medium was returned into dishes and cells were incubated for another 2 h at 37°C and then lysed.

tag: treatment before labelling

value: pladiB 186 nM

tag: timepoint before labelling

value: 45 min

tag: labelling

tag: timepoint of labelling

value: 15 min

tag: treatment after labelling

tag: timepoint after labelling


title: db21-aqr-ots964-rep1

status: Public on Jul 09 2022

type: SRA

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

library_source: transcriptomic

data_processing:
library strategy: iCLIP
iCLIP sequencing reads were processed on the iMaps server using the iCount software (https://github.com/tomazc/iCount).
Experimental barcodes were removed and sequencing reads aligned with STAR (Dobin et al., 2013) to hg38 human reference genome (build GRCh38 primary assembly GENCODE version 27), allowing two mismatches and ten secondary alignments.
Unique Molecular Identifiers (UMIs), were used to distinguish and remove PCR duplicates. To determine protein-RNA contact sites, the uniquely mapped sequencing read preceding nucleotide was assigned as the crosslink site event.
Summary of cDNA counts within genes and genic regions was generated with iCount summary function after normalising the counts by the length of corresponding regions.
Significant contact sites were identified as iCLIP peaks, using the iCount peak function, based on false discovery rate (FDR) < 0.05 comparing specific sites within a window of three nucleotides with randomised data (100 permutations) and within co-transcribed regions (https://github.com/tomazc/iCount/blob/master/iCount/analysis/peaks.py).
The significant crosslink signal was normalised by sequencing deep and million of tags (CPM). Combined genome-wide BigWig coverage tracks of U2AF65, SF3B1 and AQR iCLIP were generated using deepTools (Ramirez et al., 2014) normalised by sequencing deep and million of tags (CPM) and binned per nucleotide.
Genome_build: GRCh38 GENCODE version 27 annotation
Supplementary_files_format_and_content: Individual cross-link bed files, individual cross-link peaks bedgraphs,  grouped cross-link bed files  and CPM normalised bigwigs

molecule: total RNA

organism: Homo sapiens

growth_protocol: Human colorectal HCT116 cell line was maintained in DMEM/high glucose media supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2.

extract_protocol:
Described in detail in library construction protocol
iCLIP was performed as previously described (Huppertz et al., 2014) with only minor modifications described below. Each cell pellet (originally from one 150 cm2 plate) was lysed in 1 ml of lysis buffer and the lysate was homogenized by passing three-times through an insulin syringe. Lysate was treated with 4 U/ml Turbo DNase (Thermo Fisher, AM2238), 12 U/ml RNase I (Thermo Fisher, AM2295) shaking at 1100 rpm and 37°C for 3 min. Clarified extracts (21000g for 30 min) were incubated for 2 h with appropriate antibody pre-bound to 50 µl of protein G Dynabeads. After series of stringent washes, adenylated L3 RNA adapter was ligated to the 3’end of crosslinked RNAs. Proteins and crosslinked RNAs were resolved by SDS-PAGE (NuPAGE 4-12% Bis-Tris Protein Gel, Thermo Fisher Scientific, NP0322) and transferred to nitrocellulose membrane. The region of the membrane containing the radioactively labeled crosslinked protein–RNA complexes was excised, RNA was isolated and reverse transcribed to cDNA. cDNA was fractionated using urea denaturing gel electrophoresis and three fractions running between 70-85 nt (L-low), 85-120 nt (M-medium) and 120-200 nt (H-high) were isolated. Each fraction was independently circularized by single-stranded DNA ligase, annealed to an oligonucleotide complementary to the restriction site and cut between the two adapter regions by BamHI. After final PCR amplification using P3 and P5 Solexa primers all three fractions were pooled together in ratio 1:5:5 (L:M:H). Multiplexed libraries were sequenced as 50bp single-end reads on Illumina sequencer (EMBL, Heidelberg).

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. The Pladienolide B inhibitor was purchased from Cayman Chemical (#16538) and diluted in DMSO. HCT116 cells were plated onto 150 cm2 plates to reach 75 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO), 50 nM OTS964, 186nM Pladienolide B for 1 h. The cells were than crosslinked by UV-C (254 nm, 200 mJ/cm2).

tag: cell line background

tag: treatment

tag: group


title: HCT116_pladiB_chase_4SU_Seq_rep2

tag: cell type

value: HCT116 (wild type)


title: db21-u2af65-plad-rep2

value: PLAD


title: db21-u2af65-dmso-rep2

value: DMSO


title: db21-aqr-dmso-rep1


title: db21-aqr-dmso-rep2


title: db21-u2af65-ots964-rep2


title: HCT116_pladiB_pulse_4SU_Seq_rep1


title: db21-u2af65-ots964-rep1


title: HCT116_OTS964_chase_4SU_Seq_rep2

value: OTS964 50nM


title: HCT116_OTS964_pulse_4SU_Seq_rep2


title: db21-u2af65-dmso-rep1


title: HCT116_OTS964_chase_4SU_Seq_rep1


title: db21-u2af65-plad-rep1


title: HCT116_DMSO_chase_4SU_Seq_rep2

value: DMSO (solvent)


title: HCT116_OTS964_pulse_4SU_Seq_rep1


title: HCT116_DMSO_RNAPII_ChIP_seq_rep2

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38) using BWA.
Sequence reads with an alignment score <20 reads were discarded.
Resulting bam files were converted into bedgraph format using the genomecov command of bedtools.
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

source_name: HCT116 cells in culture, 4h after treatment

extract_protocol:
Protein G Dynabeads (Thermo Fisher Scientific, 10009D) were pre-blocked with BSA for 4 h, washed 3 times with RIPA buffer (50 mM Tris-Cl, pH 8, 150 mM NaCl, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1x protease inhibitors, Sigma, P8340), followed by the incubation with specific antibody for 4 h at 4°C. Cells were crosslinked with 1% formaldehyde for 10 min, reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed twice with ice-cold PBS, scraped, and pelleted. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20 x 7s (amp 0.85) using 5/64 probe (QSonica Q55A). Clarified extracts (13,000g for 10 min) were precleared with protein G Dynabeads rotating for 2-4 h at 4°C and then incubated overnight with antibody pre-bound to protein G Dynabeads. For each ChIP-seq experiment we performed 2 technical replicates and pooled them together.
ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2, NEB E7335S, E7500S).

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. HCT116 cells were plated onto 150 cm2 plates to reach 75 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO) or 30 nM OTS964 for 4 h.

tag: time point

tag: chip antibody

value: Rpb1 NTD (D8L4Y) Rabbit mA (Cell Signaling, #14958)


title: HCT116_DMSO_P-Ser5_ChIP_seq_rep2

value: RNA pol II CTD phospho Ser5 antibody (Active Motif #61085)


title: HCT116_pladiB_pulse_4SU_Seq_rep2


title: HCT116_DMSO_pulse_4SU_Seq_rep2


title: db21-sf3b1-plad-rep1


title: HCT116_DMSO_chase_4SU_Seq_rep1


title: db21-sf3b1-ots964-rep2


title: HCT116_DMSO_pulse_4SU_Seq_rep1


title: HCT116_DMSO_RNA_seq_rep2

molecule: nuclear RNA

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, pelleted at 500g for 3 min and treated for 5 min with 500 µl of cytoplasmic lysis buffer (10 mM Tris-Cl, pH=8, 0.32 M sucrose, 3 mM CaCl2, 2 mM MgCl2, 0.1 mM EDTA, 0.5 % TritonX-100, supplemented with 40 U/ml RNase inhibitor). Cytoplasmic RNA present in the supernatant was removed by centrifugation (500g for 3 min). Nuclear RNA was isolated from the remaining nuclear pellet using Tri-Reagent (Sigma, 93289).
For each sample, 600 ng of DNase treated RNA (Sigma, AMPD1) was used for rRNA depletion using RiboCop rRNA Depletion Kit (Lexogen, #144). Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760) according to the manufacturer protocol.

treatment_protocol: The OTS964 inhibitor was purchased from MedChem Express (HY-12467) and diluted in DMSO. HCT116 cells were plated onto 10 cm2 plates to reach 50 % confluency at the day of teatment. Next day cells were treated with solvent (DMSO) or 30 nM OTS964 for 4 h.


title: HCT116_DMSO_RNA_seq_rep1


title: DC no_migration 3 [Sample_N3]

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

country: USA

institute: M. D. Anderson Cancer Center

data_processing:
Sequence reads were trimmed for adaptor sequence (using cutadapt) low-quality sequences removed (using fastp)
Trimmed sequence reads were mapped to hg38 transcriptome using salmon v0.14.1
Raw counts and normalized TPM generated by salmon for each sample were combined into processed gene expression tables
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM and raw count values for each Sample

source_name: blood

extract_protocol:
cDNA was synthesized and amplified using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA), following the manufacturer’s instructions
RNA-seq libraries were generated from cDNA using the Illumina Nextera XT DNA Sample Preparation Kit. cDNA library quality was assessed using an Agilent 2100 Bioanalyzer

tag: tissue

value: blood

tag: cell line

value: dendritic cells

value: mature dendritic cells

tag: genotype

value: wild type

value: CCL19 gradient


title: DC migrate_out 2 [Sample_P2]


title: DC migrate_out 1 [Sample_P1]


title: DC no_migration 1 [Sample_N1]


title: DC no_migration 2 [Sample_N2]


title: DC migrate_out 3 [Sample_P3]


title: Epididyaml primary adipocytes - old Crtc2 AKO_rep2

city: Seoul

first: Seung-Hoi

last: Koo

address: 145 Anam-Ro, Seongbuk-Gu

department: Life Sciences

country: South Korea

institute: Korea University

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the NCBI. And then, transcript assembly of known transcripts was processed by StringTie v1.3.4d.
Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample.
Assembly: mm10

organism: Mus musculus

source_name: Epididyaml primary adipocytes

extract_protocol:
Total RNA concentration was calculated by Quant-IT RiboGreen(Invitrogen, #R11490). To assess the integrity of the total RNA, samples are run on the TapeStation RNA screentape(Agilent). Only high-quality RNA preparations, with RIN greater than 7.0, were used for RNA library construction.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq mRNA Sample Prep kit (Illumina, Inc., San Diego, CA, USA). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T oligo‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature.
The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase(Invitrogen) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the indexing adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using the TapeStation D1000 ScreenTape  (Agilent Technologies, Waldbronn, Germany). Indexed libraries were then sequenced using the HiSeq4000 platform (Illumina,San Diego, USA) by the Macrogen Incorporated.

tag: strain

value: Epididyaml primary adipocytes

value: Crtc2 adipocyte-specific KO


title: Epididyaml primary adipocytes - old Crtc2 f/f_rep1

value: WT


title: Epididyaml primary adipocytes - old Crtc2 f/f_rep2


title: gWAT_+CACS_rep9

city: New York

first: Charles

last: Murphy

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

description:
Goncalves-MG-7833_2019_10_25_HTSeq.gene.counts.csv
Goncalves-MG-7833_2019_10_25_genes-fpkm.csv

data_processing:
Raw sequenced reads were aligned to the mouse reference GRCm38 using STAR (v2.4.1d, 2-pass mode) aligner and Raw counts were obtained using HTSeq (v0.6.1) (Engström et al., 2013; Teng et al., 2016). The principal component analysis (PCA) was performed using R Studio Version 3.6.3 and DEBrowser shinny application (Kucukural et al., 2019). Genes with <10 CPM were filtered out and batch effect correction was achieved using the Combat method (Johnson et al., 2007). The differentially expressed genes (DEG) were obtained using DESeq2 and were considered statistically significant when FDR < 0.05 and Log2(FC) > 1.5. The list of DEG was then used for KEGG pathway enrichment analysis using the R package clusterProfiler (Yu et al., 2012). The probability of browning in the WAT was assessed using the online webtool BATLAS (Perdikari et al., 2018).
Genome_build: GRCm38
Supplementary_files_format_and_content: Files ending in "genes-fpkm.csv" are comma-delimited file containing FPKM values for each sample. Files ending in "HTSeq.gene.counts.csv" are comma-delimited file containing per-gene counts for each sample.

source_name: Gonadal white adipose tissue

extract_protocol:
Total RNA was extracted from gastrocnemius (whole muscle) and WAT (whole depot) using TRIzol (Thermo Fisher), followed up by a clean-up step using RNeasy kit (Qiagen).
One microgram of total RNA of each sample was submitted to the WCM Genomics Resources Core Facility.

tag: Sex

value: M

tag: cacs status

value: Positive

tag: weight loss

tag: sequencing batch


title: Epididyaml primary adipocytes - young Crtc2 AKO_rep2


title: Epididyaml primary adipocytes - young Crtc2 AKO_rep1


title: Epididyaml primary adipocytes - old Crtc2 AKO_rep1


title: Epididyaml primary adipocytes - old Crtc2 f/f_rep3


title: gWAT_+CACS_rep7


title: gWAT_+CACS_rep8


title: Epididyaml primary adipocytes - young Crtc2 f/f_rep2


title: Epididyaml primary adipocytes - young Crtc2 AKO_rep3


title: gWAT_+CACS_rep5


title: Epididyaml primary adipocytes - young Crtc2 f/f_rep1


title: gWAT_+CACS_rep6


title: Epididyaml primary adipocytes - young Crtc2 f/f_rep3


title: gWAT_-CACS_rep10

value: Negative


title: HCT116_OTS964_RNA_seq_rep2

value: HCT116 (wild type)

value: OTS964 30nM


title: 7_E8_VASA_dP_MEG3_DMR

city: Rehovot

first: Yonatan

last: Stelzer

address: Herzl 234

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: PBAT DNA sequencing of bisulfite converted DNA

data_processing:
1. Sequences were demultiplexerd using bcl2fastq/2.15.0.4
2. Bismark was used for conversion of mm10 genome
3. Sequences were mapped to the genome using bowtie2
4. Methylation percentages were extracted with bismark_methylation_extractor
Assembly: mm10
Supplementary files format and content: Tab-separated text file for each sample, containing a row per genomic CpG with the following columns: 'chrs', 'start','end', # coordinates of profiled C, 'methylation_percentage'  - # percentage of methylated C in CpG context
Library strategy: PBAT

source_name: tail

extract_protocol:
DNA was isolated by lysing cells in lysis buffer (0.1M Tris buffer, 0.2M NaCl, 0.005M EDTA, 0.2% SDS) with 10mg/ml Proteinease K at 55°C, precipitated with Iso-Propanol, washed with 70% Ethanol and resuspended in TE buffer. Bisulfite conversion of DNA was established using the EZ DNA Methylation-Lightning Kit (Zymo Research cat#D5031).
Converted DNA samples were subjected to an End repair reaction containing End repair mix and buffer (NEB cat#E6050) and 0.2-150ng DNA. DNA was purified using 2.5X SPRI Agencourt AMPure XP beads (Beckman Coulter cat#A63881). The eluted product was next subjected to an A-tail reaction including 10mM dATPs and Klenow Fragment 3´5´ exo- (NEB cat#M0212). DNA was purified with 2.5X SPRI beads. The clean DNA was tagged with an index oligo adapter in a ligation reaction using the Quick ligase Kit (NEB cat#M2200). Tagged products were then cleaned using 1.3X SPRI beads, and amplified for library preparation with 14 PCR cycles using the KAPA HiFi HotStart Ready Mix kit (Kapa Biosystems cat#KK2601), following the manufacturer’s protocol. The reaction mix was then cleaned with 0.7X beads. Final libraries were pooled and sequenced on an Illumina NextSeq system using the 150-bp high-output sequencing kit.

value: tail

value: IG-CGI paternal deletion

tag: developmental stage


title: 8_E7_VASA_dP_MEG3_DMR


title: HCT116_OTS964_RNA_seq_rep1


title: Epididyaml primary adipocytes - old Crtc2 AKO_rep3


title: gWAT_-CACS_rep9


title: 7_E7_VASA_dP_MEG3_DMR


title: VASA_Pupclone50_dP_live_MEG3_DMR


title: VASA_Pupclone51_WT_MEG3_DMR


title: VASA_clone74_E9_dBi_MEG3_DMR

value: IG-CGI biallelic deletion


title: gastro_+CACS_rep2

source_name: Gastrocnemius


title: gastro_+CACS_rep4


title: gastro_+CACS_rep3


title: gastro_+CACS_rep1


title: VASA_clone74_E8_dP_MEG3_DMR


title: gastro_-CACS_rep5


title: VASA_clone74_E6_WT_MEG3_DMR


title: VASA_clone74_E5_dM_MEG3_DMR

value: IG-CGI maternal deletion


title: VASA_clone74_E7_dP_MEG3_DMR


title: C57BL/6J mice, Brown adipose tissue,control [ND3]

city: Hangzhou

first: Fei

last: Yang

address: 866 Yu-hang-tang Road

country: China

institute: Zhejiang University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads  containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base  quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored  in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2  (v2.0.4) .
After that, Ericscript (v0.5.5)   and rMATS (V3.2.5) were used to detect  fusion genes and differential splicing genes (DSGs), respectively.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text file including expression quantities for each sample

source_name: Brown adipose tissue

extract_protocol:
Total RNA was extracted from the BAT using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) , and was used for the construction of sequencing libraries.
Bowtie2 (v2.2.5)   was applied to align the clean reads to the gene set, a database built by BGI (Beijing  Genomic Institute in ShenZhen), in which known and novel, coding and noncoding  transcripts were included, then expression level of gene was calculated by RSEM  (v1.2.12) .

value: Brown adipose tissue

value: A regular chow diet


title: C57BL/6J mice, Brown adipose tissue,control [ND4]


title: gastro_-CACS_rep4


title: C57BL/6J mice, Brown adipose tissue,obesity-prone [HFDhigh2]

value: A high-fat diet


title: C57BL/6J mice, Brown adipose tissue,control  [ND1]


title: gastro_-CACS_rep3


title: C57BL/6J mice, Brown adipose tissue,control [ND2]


title: VASA_clone74_E4_dP_MEG3_DMR


title: gastro_-CACS_rep1


title: C57BL/6J mice, Brown adipose tissue,obesity-prone [HFDhigh3]


title: gastro_+CACS_rep5


title: C57BL/6J mice, Brown adipose tissue,obesity-resistant [HFDlow3]


title: VASA_clone74_E3_dP_MEG3_DMR


title: C57BL/6J mice, Brown adipose tissue,obesity-prone [HFDhigh1]


title: VASA_clone74_E2_dP_MEG3_DMR


title: gWAT_-CACS_rep8

description:
Marcus5878_2018_05_24_17_HTSeq.gene.counts.csv
Marcus5878_2018_05_24_17_genes-fpkm.csv


title: C57BL/6J mice, Brown adipose tissue,obesity-resistant [HFDlow2]


title: C57BL/6J mice, Brown adipose tissue,obesity-resistant [HFDlow1]


title: gWAT_-CACS_rep7


title: VASA_clone115_E8_dP_MEG3_DMR


title: DNK rep3

city: Beijing

first: Jun-jie

last: Hou

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

department: Institute of molecular medicine

institute: Peking University

data_processing:
Illumina Casava2.1.7 software used for basecalling.
Raw reads were pre-processed with TrimGalore(v0.6.0), using default settings. Filtered reads for each library were mapped using HISAT2 (v.2.1.0) against the zebrafish reference genome assembly GRCz11, which was downloaded from Ensembl.
With the matching gene annotation (v.97) from Ensembl, the read counts of each gene were measured by HTSeq (v.0.6.1), using the option ‘–stranded = no’.
Genes were further filtered with at least 10 reads total in all samples using DEseq2(v1.22.2).
Differential analysis was conducted with DEseq2(v1.22.2), and genes with adjusted p value < 0.05 and absolute logFC > 1 were taken as significantly differentially expressed genes in DNF data and CKF data
Genome_build: Danio_rerio.GRCz11.fa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: cardiac endothelial cell

extract_protocol:
~15 adult zebrafish hearts were isolated and washed in cold PBS with 10U/ml heparin (H8060; solarbio). After the atrium and bulbuls were removed, the ventricles were cut gently into small pieces using forceps and collected into 1.5-ml centrifuge tubes containing cold PBS with 5 mM glucose. The sliced tissues were then transferred to a glass tube along with a magnetic stir bar and 1.5-ml digestion buffer in DMEM consisting of collagenase type II (250 U/ml) (17101015; gibco), collagenase type IV (300 U/ml) (17104019; gibco) and DNase I (30 μg/ml) (A3778; AppliChem). The glass tube was then transferred into a 32°C water bath with stirring and incubated for 1 minute. After incubation, the glass tube was removed from the water bath and left at room temperature until the tissue settled on the bottom. The supernatant were discarded to remove blood cells from the samples, followed by washing with cold PBS once. The samples were followed by a series of digestion steps with 1.5-ml digestion buffer. Each digestion step spent for 10 minutes of digestion followed by 3-minute sedimentation. The supernatants were collected in a 15-ml falcon tube containing 2 ml ice-cold FBS kept on ice. The cell suspensions were centrifuged at 300 g for 5 minutes at 4°C, and the cell pellets were gently resuspended in 1-ml PBS kept on ice for FACS. Cardiac endothelial cells were FACS sorted out through the GFP channel and were collected into a collection tube containing 0.5-ml PBS with 10% FBS. The cells were centrifuged at 500 g for 5 minutes at 4°C, and the cell pellets were collected and kept on ice and ready for RNA isolation. The RNA from heart endothelial cells from CtrlF sibling and DNF mutant ventricles at 7 dpa were purified using Magen RNA Nano Kit (R4125; Magen), and RNA was reverse-transcribed to cDNA using MAL-BAC amplification methods described previously (Chapman et al., 2015). 1 ug of cDNA was used for construction of sequencing libraries
1 ug of cDNA was used for next-generation library preparation under manufacture guidelines of NEBNext Ultra DNA Library Prep Kit for Illumina (E7370, NEB).

treatment_protocol: Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:CreER; kdrl:eGFP) (DNK) and Tg(ubi:loxp-DsRed-stop-loxp-DN-xBrg1; kdrl:eGFP) (CtrlK) were treated with 4-HT for 3 days before ventricular resection. The kdrl:eGFP GFP positive endothelial cells sorted by FACS (fluorescence-activated cell sorting) from CKF and DNF hearts at 7 dpa were subjected to RNA-seq analysis.

value: Tu

value: endothelial-overexpression dominant-negative Xenopus Brg1

tag: heart regeneration stage

value: 7 days post heart amputation


title: VASA_clone115_E6_dBi_MEG3_DMR


title: gastro_-CACS_rep2


title: CtrlK rep3

value: untreated


title: CtrlK rep2


title: gWAT_-CACS_rep6


title: gWAT_-CACS_rep5


title: CtrlK rep1


title: Ikkb knockout + I/R d14  replicate 3 (mouse 11+12)

city: Kiel

first: Eileen

last: Dahlke

state: Schleswig-Holstein

address: Otto-Hahn-Platz 8

department: Anatomisches Institut

institute: Christian-Albrechts-Universität Kiel

data_processing:
our in-house RNA-Seq pipeline to map and align the sequenced data (https://github.com/nf-core/rnaseq)
processed the raw data from the sequencer with FastQC v0.11 and Trimgalore v0.4. aligned the reads with STAR v2.5.2b and generated gene counts with featurecounts v1.5.2 and StringTie v1.3.3b
Quality control was assessed throughout with RSeqQC dupRadar, Preseq and MultiQC v1.4
Differentially expressed genes were identified by comparing expression profiles of the different genotypes.
Statistical analysis preformed using R v3.6.3.To identify differentially expressed genes between groups and time points, we used DESeq2 R package v1.26.0. DESeq2 was used for executing pairwise comparisons between genotypes.
Assembly: Genome Reference Consortium Mouse Build 38 and GenBank Assembly ID: GCA_000001635.8
Supplementary files format and content: merged gene counts as tab delimited text file

source_name: kidney

extract_protocol:
RNA was harvested using NucleoSpin(Macherey-Nagel). 0.5 ug of total RNA was used for the construction of sequencing libraries.
TrueSeq stranded mRNA

value: kidney

value: Ikkb knockout

value: I/R d14


title: gWAT_+CACS_rep3

value: M

value: Positive


title: gWAT_+CACS_rep4


title: Ikkb knockout + I/R d14  replicate 2 (mouse 9+10)


title: Ikkb knockout + I/R d14  replicate 1 (mouse 7+8)


title: control + I/R d14  replicate 3 (mouse 5+6)

value: WT


title: VASA_clone115_E3_dM_MEG3_DMR

value: tail


title: gWAT_+CACS_rep2


title: VASA_clone115_E2_dBi_MEG3_DMR


title: VASA_clone74_E1_dbi_MEG3_DMR


title: control + I/R d14  replicate 2 (mouse 3+4)


title: DNK rep2


title: gWAT_+CACS_rep1


title: control + I/R d14 replicate 1 (mouse 1+2)


title: VASA_clone115_E1_dP_MEG3_DMR

value: IG-CGI paternal deletion


title: Ikkb knockout + I/R d2  replicate 3 (mouse 11+12)

value: I/R d2


title: DNK rep1


title: Ikkb knockout + I/R d2  replicate 2 (mouse 9+10)


title: gWAT_-CACS_rep4

value: Negative


title: control + I/R d2  replicate 3 (mouse 5+6)


title: VASA_clone115_E5_dBi_MEG3_DMR

value: IG-CGI biallelic deletion


title: gWAT_-CACS_rep3


title: control + I/R d2 replicate 1 (mouse 1+2)


title: control + I/R d2  replicate 2 (mouse 3+4)


title: Ikkb knockout replicate 3 (mouse 11+12)

value: x


title: Ikkb knockout replicate 2 (mouse 9+10)


title: gWAT_-CACS_rep2


title: 7_E4_VASA_dP_IG_DMR


title: Ikkb knockout replicate 1 (mouse 7+8)


title: gWAT_-CACS_rep1


title: control replicate 3 (mouse 5+6)


title: 8_E5_VASA_dP_IG_DMR


title: Ikkb knockout + I/R d2  replicate 1 (mouse 7+8)


title: control replicate 1 (mouse 1+2)


title: control replicate 2 (mouse 3+4)


title: 6_E2_VASA_dP_IG_DMR


title: 8_E1_VASA_dP_IG_DMR


title: RNA-seq, Resis, Vehicle, 3

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

description:
Resis_Vehicle tumor cells were harvested from mice with resistant tumors treated with  vehicle for 2 weeks.
RNAseq5_mouse_Resis_E64_VS_Vehicle_result_all.csv

data_processing:
Sequenced reads were mapped to mm10 or hg19 whole genome using STAR_2.6.0a
Counts were normalized by Transcript per million (TPM)
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: csv files with gene TPM

molecule: polyA RNA

source_name: resistant tumor from recipient mice with vehicle treatment

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicates


title: 6_E1_VASA_dP_IG_DMR


title: VASA_Pupclone51_WT_IG_DMR


title: mouse_Res_Vehicle

description: Vehicle treated chemoresistant bladder tumors were harvested from mice  treated with 8 cycles vehicle

library_source: transcriptomic single cell

data_processing:
ScRNA-seq alignment process was completed by cellranger (version 3.0.0)
Seurat V3 workflow
Assembly: mm10
Supplementary files format and content: txt files with gene counts for scRNA-seq

source_name: chemoresistant tumor from MIBC recipient mice treated with Vehicle

extract_protocol:
Preparation: collect the fresh tumor tissue from vehicle or E64 treated mouse chemo resistant tumors and wash the samples with PBS for 3 times. After the tissue preparation, collagen I (0.5mgml-1) and collagen IV (1mgml-1) was combined to digest the samples with 2 hours in 37℃. The 400g centrifuge was used with 6 minutes. After discarding the supernatant, 10 ml trypsin was used to resuspend with 15 minutes in 37℃. The 10% FBS was added to medium, and filter the mixture through 100μm. Then 400g centrifuge was used. After discarding the supernatant, 4ml 1XACK was used to resuspend the cells on the ice with 3 minutes. And 200 μl 0.04%BSA-PBS was used to resuspend cells. After quantifying the cell number, adjusting the concentration to the 800-1200 cells/μl and ensuring the cell activity > 85%, we used the 10X genomics platform to construct the single cell library of samples.
Follwed by v3 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

tag: library strategy

value: scRNA-seq

tag: agent

value: vehicle


title: mouse_Res_E64

description: E64 treated chemoresistant bladder tumors were harvested from mice treated with 8 cycles E64 (20mg/kg)

source_name: chemoresistant tumor from MIBC recipient mice treated with E64


title: VASA_clone115_E4_WT_MEG3_DMR


title: RNA-seq, Resis, Vehicle, 2

value: resistant tumor from recipient mice with vehicle treatment


title: RNA-seq, Resis, E64, 3

description:
Resis_E64 tumor cells were harvested from mice with resistant tumors treated with E64  for 2 weeks.
RNAseq5_mouse_Resis_E64_VS_Vehicle_result_all.csv

source_name: resistant tumor from recipient mice with E64 treatment


title: zf_library_8h_3

city: Kansas City

first: Hua

last: Li

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Paired end reads were merged with FLASH using default parameters, reads that could not be merged were discarded.
Next, using Cutadapt, the constant regions (5’ = ATGGTGAGCAAGGGCGAGGAGCTGTCCCTCGAG and 3’ = TCTAGATAG) were removed to keep only the library variable region. Reads without these regions were discarded.
Then, reads were separated by length (read length = 297, expected length based on sequence design) and mapped them to the library with salmon to quantify expression at each time point
Mapped reads represent the perfect sequences that we designed. Then, the reads that were not mapped (read length = 297, nucleotide substitutions) were merged with the reads that have a different sequence length (read length < 297 or > 297, insertions and/or deletions). All these reads were called the “imperfect” set. The constant regions that were removed in the first steps of the analysis were added back and therefore every unique read contains a coding sequence which starts in the first ATG (start codon). The codon composition was counted as consecutive triplet until it finds a stop codon. The occurrences of each unique read were counted at every time point to calculate transcript abundance (transcripts per million).
Assembly: reference.fasta
Supplementary files format and content: csv files include TPM values for each sample
Library strategy: Targeted Deep Sequencing

source_name: Zebrafish embryo

extract_protocol:
Injected zebrafish embryos were collected in Buffer RLT (QIAGEN RNeasy kit), followed by vortexing for 1 min and stored at -70°C until extraction. RNA was thawed at 37°C, extracted following the manufacturer’s protocol, and eluted in 50 μL. mRNA was isolated with Dynabeads oligo-(dT) mRNA purification kit following the manufacturer’s protocol. mRNA was eluted in 10 μl of 10 mM Tris-HCl, pH 7.5. 5 μL of purified mRNA were used for cDNA synthesis using the SuperScript IV Reverse Transcriptase kit, utilizing a specific oligo that binds to the 3’ Illumina adapter (GTAGTGACTGGAGTTCAGAC). The cDNA was cleaned with the Qiagen MinElute PCR purification kit and eluted in 20 μL of water.
We tested different PCR cycles to amplify the library using specific oligos that target the surrounding Illumina adapters. We selected 16 cycles for the samples at 2 and 5 hpi, and 18 cycles for 8 hpi. The barcoded libraries were cleaned using AMPure XP beads and resuspended in 20 μL of buffer EB (Qiagen). The libraries were sequenced in an Illumina MiSeq instrument 250bp pair-end with 10% of PhiX as spike-in.

treatment_protocol: 10 pg of library mRNA were injected into 1-cell stage zebrafish embryos in 3 independent replicates. Each replicate utilized an independent needle, injection mix, and breeding. 25 embryos were collected at 2, 5, and 8 hours post-injection

value: Zebrafish embryo

tag: treatment

value: Injected zebrafish embryos


title: zf_library_8h_2


title: zf_library_8h_1


title: zf_library_5h_3


title: RNA-seq, Resis, E64, 2

value: resistant tumor from recipient mice with E64 treatment


title: RNA-seq, Resis, E64, 1


title: zf_library_5h_2


title: VASA_clone74_E8_dP_IG_DMR


title: VASA_Pupclone50_dP_live_IG_DMR


title: zf_library_5h_1


title: RNA-seq, normal, bladder, 2

description:
Normal_bladder organoids were derived from mouse normal bladder
RNAseq1_mouse_Sen_vs_normal_result_all.csv

source_name: organoids of normal mouse bladder

value: organoids of normal mouse bladder


title: VASA_clone74_E7_dP_IG_DMR


title: RNA-seq, normal, bladder, 1


title: zf_library_2h_3


title: RNA-seq, mouse, Sensitive, 3

description:
Sensitive MIBC organoids were harvested from the recipient mice.
RNAseq2_mouse_Resis_vs_Sen_result_all.csv;RNAseq1_mouse_Sen_vs_normal_result_all.csv

source_name: chemosensitive tumor from recipient mice


title: RNA-seq, Resis, Vehicle, 1


title: RNA-seq, mouse, Sensitive, 1

value: chemosensitive tumor from recipient mice


title: RNA-seq, mouse, Sensitive, 2


title: VASA_clone74_E6_WT_IG_DMR


title: VASA_clone74_E5_dM_IG_DMR

value: IG-CGI maternal deletion


title: zf_library_2h_2


title: VASA_clone74_E4_dP_IG_DMR


title: zf_library_2h_1


title: RNA-seq, mouse, Resis, 2

description:
Resistant MIBC organoids were harvested from the recipient mice.
RNAseq2_mouse_Resis_vs_Sen_result_all.csv

source_name: chemoresistant tumor from recipient mice


title: RNA-seq, mouse, Resis, 3

value: chemoresistant tumor from recipient mice


title: 4007-02

city: leuven

first: Panagiotis

middle: Cristophe

last: Karras

state: belgium

address: Herestraat 49

country: Belgium

institute: VIB Center for Cancer Biology

data_processing:
scRNAseq: CellRanger v.3.1.0
bulk RNAseq: RSEM
Assembly: mm10 for mouse and hg19 for human

organism: Mus

extract_protocol: Libraries for scRNA-seq were created using the 10X Genomics Chromium platform according to the manufacturer’s instructions. Library construction was performed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (n = 16; 10x Genomics, catalog number 1000092) or the Chromium Single Cell A Chip Kit and 5′ Library & Gel Bead Kit (10x Genomics, catalog number 1000014). We opted for high target recovery (median 5000, range 5000-10000), keeping within the range of optimal input concentration per target recovery, as recommended by the manufacturer. In brief, cells were partitioned into gel bead-in-emulsions (GEMs) at limiting dilutions, where lysis and reverse transcription occurred, yielding uniquely barcoded full-length cDNA from polyadenylated mRNA. GEMs were subsequently broken, and the pooled fraction was amplified and subjected to fragmentation, end repair and adaptor ligation of size-selected fractions.For bulk RNAseq about 500 pg of RNA per sample was reverse-transcribed and amplified using a modified SMARTseq2 protocol (Rambow et al. 2018). Prior to generating sequencing libraries using the NexteraXT kit (Illumina, cat. no. FC-131-10), cDNA profiles were monitored using the Bioanalyzer. Sequencing was performed on a Nextseq500 platform (Illumina, SE75bp). Differential analyses between siPRRX1 and siCtrl samples were executed using the DeSeq2 pipeline.

value: skin

tag: tumor

value: melanoma

tag: tumor stage

value: primary tumor

tag: description

value: tdTomato+ fraction from primary tumours2 days (early labelled) post-TAM


title: VASA_clone74_E3_dP_IG_DMR

tag: tissue

value: tail

value: IG-CGI paternal deletion


title: 4007-03

value: lung

value: lung metastasis

value: tdTomato+ fraction from lung metastasis 2 days (early labelled) post-TAM


title: CMA320

value: tdTomato+ fraction from lung metastasis  30-days (late labelled) post-TAM


title: VASA_clone74_E2_dP_IG_DMR


title: RNA-seq, normal, bladder, 3


title: C2-MM047-siPRRX1-2

tag: cell line

value: in vitro


title: RNA-seq, mouse, Resis, 1


title: RNA-seq, mouse, DDP4, 3

description:
mouse_DDP4 tumor cells were harvested from mice with sensitive bladder tumor treated with 4 cycles cisplatin-based chemotherapy
RNAseq3_mouse_DDP_result_all.csv

source_name: mouse chemosensitive tumor with 4 cycles chemotherapy


title: CMA318

value: tdTomato+ fraction from primary tumour  30-days (late labelled) post-TAM


title: B12-MM047-siScr-2


title: CMA332

description: BRAF/Pten

value: tail skin


title: VASA_clone115_E8_dP_IG_DMR

tag: genotype


title: VASA_clone115_E4_WT_IG_DMR

value: WT


title: RNA-seq, human, BC20200617, Tumor

description:
MIBC PDXs were generated from  MIBC patients 0617
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0617) mice of MIBC patient


title: CMA338

source_name: NRASQ61K/°;Ink4a-/- melanoma cells

value: cultured in the presence of Bend3 cells for 48h


title: CMA336


title: VASA_clone115_E3_dM_IG_DMR

value: IG-CGI maternal deletion


title: CMA298

description: BRAF/Pten


title: ATAC-seq, Sen, 3

description: Sensitive MIBC organoids were harvested from the recipient mice.

data_processing:
ATAC-Seq reads were aligned to the mm10 genome assembly using Bowtie2(2.2.1)
HMMRATAC was used to call peaks
Genome_build: mm10
Supplementary_files_format_and_content: gappedPeak files for ATAC-Seq

source_name: chemosensitive tumor from MIBC recipient mice

extract_protocol:
The sensitive and resistant organoids were harvested at 3 days after culture, and were gently digested into single cell suspension using TrypLE. 20,000 cells were used for ATAC-seq.
Library preparation was performed as previously described (2013 Buenrostro). Briefly, cells were washed lysed using lysis buffer followed by transposase reaction  (Novoprotein). Transposed DNA was purified using MinElute PCR Purification kit (Qiagen) and amplified using NEBNext High-Fidelity 2X PCR Master Mix(NEB) followed by purified using MinElute PCR Purification kit (Qiagen).


title: RNA-seq, human, BC20200528, Tumor

description:
MIBC PDXs were generated from  MIBC patients 0528
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0528) mice of MIBC patient


title: RNA-seq, human, BC20200617, DDP3

description:
MIBC PDXs were generated from  MIBC patients 0617, treated with 3 cycles cisplatin-based chemotherapy in mice.
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0617) mice of MIBC patient with 3 cycles chemotherapy


title: ATAC-seq, Sen, 2

value: chemosensitive tumor from MIBC recipient mice


title: 7_E6_VASA_dP_IG_DMR

source_name: tail


title: Kif1b-beta neurite

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Fastq files were extracted using bcl2fastq v2.20.
Gene expression was quantitated using kallisto 0.43.0.
TPM values were loess normalized using the R function "cyclicLoess".
Assembly: mm10 (GRCm38)
Supplementary files format and content: TPM.xlsx contains TPM values for each transcript in each sample.
Supplementary files format and content: LR.xlsx contains localization ratios (log2 neurite/soma) for transcript with at least 5 TPM in all conditions.

growth_protocol: 10% FBS in DMEM.

extract_protocol:
Quick-RNA Microprep Kit (Zymo, R1050).
NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7530L).

treatment_protocol: Transfections of plasmids were performed using TransIT X2 (Mirus, MIR6003).

tag: cell type

value: Neuroblastoma

value: Transfection of Kif1b-beta tail

tag: sample type

value: Neurite


title: Kif1c soma

value: Transfection of Kif1c tail

value: Soma


title: Kif1c neurite


title: VASA_clone115_E1_dP_IG_DMR

value: tail

value: IG-CGI paternal deletion


title: B11-MM047-siScr-1

value: melanoma


title: C1-MM047-siPRRX1-1


title: Kif1b-alpha neurite

value: Transfection of Kif1b-alpha tail


title: RNA-seq, mouse, DDP4, 2

value: mouse chemosensitive tumor with 4 cycles chemotherapy


title: scrCMA085_mm10

source_name: NRASQ61K/°;Ink4a-/- primary lesion

value: skin

value: primary tumor


title: RNA-seq, human, BC20200528, 2, DDP5

description:
MIBC PDXs were generated from  MIBC patients 0528_2, treated with 5 cycles cisplatin-based chemotherapy in mice.
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0528-2) mice of MIBC patient with 5 cycles chemotherapy


title: Kif1b-alpha soma


title: Kif1b-beta soma


title: scrCMA084_mm10


title: RNA-seq, human, BC20200528, DDP6

description:
MIBC PDXs were generated from  MIBC patients 0528, treated with 6 cycles cisplatin-based chemotherapy in mice.
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0528) mice of MIBC patient with 6 cycles chemotherapy


title: RNA-seq, human, BC20200528, 2, Tumor

description:
MIBC PDXs were generated from  MIBC patients 0528_2
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0528-2) mice of MIBC patient


title: scrCMA086_mm10


title: RNA-seq, human, BC20190927, Tumor

description:
MIBC PDXs were generated from  MIBC patients 0927
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0927) mice of MIBC patient


title: RNA-seq, mouse, DDP4, 1


title: ATAC-seq, Sen, 1


title: DT480 neurite

value: Transfection of DT480 plasmid


title: RNA-seq, mouse, DDP2, 3

description:
mouse_DDP2  tumor cells were harvested from mice with sensitive bladder tumor treated with 2 cycles cisplatin-based chemotherapy
RNAseq3_mouse_DDP_result_all.csv

source_name: mouse chemosensitive tumor with 2 cycles chemotherapy


title: scrCMA083_mm10


title: RNA-seq, mouse, DDP2, 2

value: mouse chemosensitive tumor with 2 cycles chemotherapy


title: scrCMA079_mm10


title: scrCMA081_mm10


title: ATAC-seq, resis, 2

description: Resistant MIBC organoids were harvested from the recipient mice.

source_name: chemoresistant tumor from MIBC recipient mice


title: RNA-seq, human, BC20190927, DDP12

description:
MIBC PDXs were generated from  MIBC patients 0927, treated with 12 cycles cisplatin-based chemotherapy in mice.
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0927) mice of MIBC patient with 12 cycles chemotherapy


title: ATAC-seq, resis, 3

value: chemoresistant tumor from MIBC recipient mice


title: scRNA-seq, human, resistant

description: human resistant tumor was derived from MIBC patients received 4 cycles GP treatment and tumor evaluation was PD

data_processing:
ScRNA-seq alignment process was completed by cellranger (version 3.0.0)
Seurat V3 workflow
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: txt files with gene counts for scRNA-seq

source_name: chemoresistant tumor from MIBC patient

extract_protocol:
Preparation: collect the fresh tumor tissue from MIBC patients and wash the samples with PBS for 3 times. After the tissue preparation, collagen I (0.5mgml-1) and collagen IV (1mgml-1) was combined to digest the samples with 2 hours in 37℃. The 400g centrifuge was used with 6 minutes. After discarding the supernatant, 10 ml trypsin was used to resuspend with 15 minutes in 37℃. The 10% FBS was added to medium, and filter the mixture through 100μm. Then 400g centrifuge was used. After discarding the supernatant, 4ml 1XACK was used to resuspend the cells on the ice with 3 minutes. And 200 μl 0.04%BSA-PBS was used to resuspend cells. After quantifying the cell number, adjusting the concentration to the 800-1200 cells/μl and ensuring the cell activity > 85%.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

value: chemoresistant tumor from MIBC patient


title: ATAC-seq, resis, 1


title: scRNA-seq, human, sensitive

description: human primaty tumor was derived from MIBC patients without any treatment

source_name: chemosensitive tumor from MIBC patient

value: chemosensitive tumor from MIBC patient


title: scrCMA080_mm10


title: scRNA-seq, mouse, sensitive

description: chemosensitive bladder tumors were generated from normal organoids with Trp53,Pten knockout and c-Myc

extract_protocol:
Preparation: collect the fresh tumor tissue from mouse MIBC and wash the samples with PBS for 3 times. After the tissue preparation, collagen I (0.5mgml-1) and collagen IV (1mgml-1) was combined to digest the samples with 2 hours in 37℃. The 400g centrifuge was used with 6 minutes. After discarding the supernatant, 10 ml trypsin was used to resuspend with 15 minutes in 37℃. The 10% FBS was added to medium, and filter the mixture through 100μm. Then 400g centrifuge was used. After discarding the supernatant, 4ml 1XACK was used to resuspend the cells on the ice with 3 minutes. And 200 μl 0.04%BSA-PBS was used to resuspend cells. After quantifying the cell number, adjusting the concentration to the 800-1200 cells/μl and ensuring the cell activity > 85%.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

value: chemosensitive tumor from MIBC recipient mice


title: 234

status: Public on Jul 08 2022

city: Auburn

first: Marie

middle: E

last: Strader

state: AL

address: 101 Rouse Life Sciences, Biological Sciences Department

department: Biological Sciences

institute: Auburn University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Acropora millepora genome (v2.01) using bowtie2(v.2.2.9) --local --no-hd --no-sq --no-unal -k 5
gene counts were compiled using a custom perl script enabling samcounts. Script found at https://github.com/z0on/tag-based_RNAseq
Genome_build: Acropora millepora genome (v2.01)
Supplementary_files_format_and_content: txt files including gene counts values for each sample
Supplementary_files_format_and_content: VCF files for SNP calls

organism: Acropora tenuis

source_name: juvenile tissue

extract_protocol:
RNAqueous kit (Ambion)
tag-seq: https://github.com/z0on/tag-based_RNAseq

tag: cross

value: CUxSB

tag: temperature treatment

value: Ambient

tag: life-stage

value: juvenile

tag: symbiont

value: SED


title: RNA-seq, human, BC20190927, DDP19

description:
MIBC PDXs were generated from  MIBC patients 0927, treated with 19 cycles cisplatin-based chemotherapy in mice.
RNAseq4_human_DDP_result_all.csv

source_name: tumor from PDX(0927) mice of MIBC patient with 19 cycles chemotherapy


title: 233


title: 232

value: SS


title: DMPKS soma

value: Neuroblastoma

value: Transfection of DMPKS plasmid

value: Soma


title: scRNA-seq, mouse, resistant

description: chemoresistant bladder tumors were harvested from mice with chemosensitive tumors treated with 8 cycles cisplatin-based chemotherapy


title: PanB_KO2

city: Nanjing

first: Yuchao

last: Jing

state: Jiangsu

address: 101 Longmian Ave Jiangning District

department: Immunology

institute: Nanjing Medical University

data_processing:
Raw fastq data is trimmed by trimmomatic and get Clean fastq data
Clean fastq data is mapped by Star and get Bam data
Bam data is counted by Htseqcount and get count file
Differential expression calculate use DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: counts file of each sample

source_name: PanB

extract_protocol:
Germinal center B cells were filtered using FACS.Activated B cells were get first enriched B cells from spleen using PanB biotin and SA beads, then activated B cells . RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

tag: strain

value: Jmjd1c B KO

value: spleen with in vitro stimulation

value: Activated B cells


title: PanB_KO1


title: PanB_WT2

value: WT


title: scrCMA082_mm10

value: skin

value: melanoma

value: primary tumor


title: 227


title: 235


title: 228


title: RNA-seq, mouse, DDP2, 1

value: mouse chemosensitive tumor with 2 cycles chemotherapy

tag: replicates


title: 157

value: DRxSB

value: Hot


title: CMA001


title: DT480 soma

value: Transfection of DT480 plasmid


title: DMPKS neurite

value: Neurite


title: 94

value: SBxSB

value: juvenile


title: 220

value: CUxSB

value: Ambient


title: PanB_WT1


title: vitamin D treated colon_rep 6

city: Piscataway

first: Michael

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
27_D_Colon_Rep5

data_processing:
Alignment: RNA-seq: Kallisto v0.45.0.
RNA-seq Transcript Import: tximport 1.16.1
DESeq 1.28.1
Genome_build: RefSeq mm9
Supplementary_files_format_and_content: RNA-Seq: results table for reporting mean of normalized counts for all samples and through comparison of the treated condition vs untreated condition, log2 fold change, standard error, Wald statistic, Wald test p-value, and Benjamini-Hochberg adjusted p-value
Supplementary_files_format_and_content: RNA-Seq: fpkm table outputted by DESeq2 for fragment counts normalized per kilobase of feature length per million mapped fragments

source_name: vitamin D treated colon

extract_protocol:
Intestinal tissues were harvested from mice. About 10-15 cm of the proximal half of small intestine were used for the duodenum crypts and villi samples, and the entire colon tissues from the terminal cecum to rectum were used for colon samples. After flushing with cold PBS, the intestines were cut opened longitudinally, cut into 1 cm pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. The solution was discarded and the tissues were incubated with fresh 3mM EDTA/PBS in rotator for 10 min at 4 0C. After shaking the tubes gently for 10 times, the intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS, rotated for 30 min at 4 0C, then were shaken 30 times. The supernatant containing the whole epithelium tissues (crypts and villi) were collected and spun down at 200 rcf for 3 min at 4 0C. Resuspended the pellet with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes at 200 rcf for 3 mins at 4 0C and at 300 rcf for 30 seconds at 40C in order to remove any residual PBS. Proceeded to RNA extraction. For the colon samples, on an ice-cold plate, the colon was cut from the terminal end of the cecum to the rectum.   An 18-gauge needle attached to a 30 ml syringe was used to flush the feces out of the colon. The colon was cut open longitudinally and rinsed with cold PBS. Afterwards, the colon was scraped with a glass slide and a glass cover slip. The colon was scraped until the tissue turned transparent and only the muscle tissue was left. The scraped epithelial cell pellet was then collected in a 1.5 ml Eppendorf tube coated with 0.5% BSA and filled with 1ml of cold PBS. After pelleting the colon intestinal cell pellet in cold PBS at 300 rcf for 3 minutes in 4C twice, the supernatant was removed. Trizol was quickly added to the pellet by pipetting up and down until the pellet dissolved in the Trizol.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions. All nucleic acid extracts were gDNA Eliminator Solution for 15 s at 37 °C, in order to remove contaminating chromosomal DNA. Resulting RNA was analyzed for quantity and quality with a NanoDrop spectrophotometer ND-1000 (Isogen Life Science, Utrecht, The Netherlands).
RNA quality was examined via Agilent 2100, mRNA was enriched and reverse transcribed, and DNA nanoball synthesis was conducted by BGI. Sequencing was performed on BGISEQ-500 with paired-end, 100bp reads.

treatment_protocol: 12 – 14 week old vitamin D deficient mice were randomly separated and injected with either 0.1 ml vehicle (9:1 mix of propylene glycol and ethanol) or 1,25(OH)2D3 (from Cayman Chemical Company Ann Arbor, MI)  (ip 10ng/g body weight) and killed 4h after the injection

value: wild type

tag: background strain

value: Intestinal Epithelium

tag: Sex

value: pooled male and female

tag: age


title: 219


title: vitamin D treated colon_rep 4

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
D_Colon_Rep4


title: vitamin D treated colon_rep 3

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
D_Colon_Rep3


title: vitamin D treated colon_rep 2

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
D_Colon_Rep2


title: vehicle-treated colon_rep 6

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
6_Veh_Colon_Rep1

source_name: vehicle-treated colon


title: 212

value: LSxCU

value: SED


title: 218


title: vitamin D treated colon_rep 1

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
D_Colon_Rep1


title: vitamin D treated colon_rep 7

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
3_D_Colon_Rep1


title: vehicle-treated colon_rep 5

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
30_Veh_Colon_Rep5


title: 209

value: DRxCU


title: 226

value: SS


title: vehicle-treated colon_rep 3

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
Veh_Colon_Rep3


title: 217


title: 211


title: vehicle-treated colon_rep 1

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
Veh_Colon_Rep1


title: vehicle-treated colon_rep 2

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
Veh_Colon_Rep2


title: 208

value: CUxDR


title: 210


title: vitamin D treated crypts_rep 6

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
D-Crypts-Rep6

source_name: vitamin D treated crypts


title: vehicle-treated colon_rep 4

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
Veh_Colon_Rep4


title: vitamin D treated crypts_rep 5

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
D-Crypts-Rep5


title: 206


title: vitamin D treated colon_rep 5

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Colon.txt, Results_VDR_VitDvsNoVitD_Colon.txt
sample name in processed data file:
D-Colon-Rep5


title: 207


title: 203


title: vitamin D treated crypts_rep 4

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
D_Crypts_Rep4


title: vitamin D treated crypts_rep 3

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
D_Crypts_Rep3


title: vitamin D treated crypts_rep 1

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
D_Crypts_Rep1


title: 202


title: vehicle-treated crypts_rep 5

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
Veh-Crypts-Rep5

source_name: vehicle-treated crypts


title: 205


title: vehicle-treated crypts_rep 4

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
Veh_Crypts_Rep4


title: 198


title: vehicle-treated crypts_rep 6

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
Veh-Crypts-Rep6


title: vitamin D treated crypts_rep 2

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
D_Crypts_Rep2


title: 196


title: 200


title: 57

value: BKxBK


title: vehicle-treated crypts_rep 1

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
Veh_Crypts_Rep1


title: 93


title: vitamin D treated villi_rep 6

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
D-Villi-Rep6

source_name: vitamin D treated villi


title: 194


title: vehicle-treated crypts_rep 3

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
Veh_Crypts_Rep3


title: 201


title: 193


title: 199

value: DRxSB


title: 179


title: 197


title: vitamin D treated villi_rep 5

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
26_D_Villi_Rep5


title: 178


title: vitamin D treated villi_rep 1

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
D_Villi_Rep1


title: 195


title: vitamin D treated villi_rep 3

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
D_Villi_Rep3


title: vitamin D treated villi_rep 2

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
D_Villi_Rep2


title: vehicle-treated villi_rep 5

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
29_Veh_Villi_Rep5

source_name: vehicle-treated villi


title: 176


title: vehicle-treated villi_rep 6

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
5_Veh_Villi_Rep1


title: 175


title: vehicle-treated crypts_rep 2

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Crypts.txt, Results_VDR_VitDvsNoVitD_Crypts.txt
sample name in processed data file:
Veh_Crypts_Rep2


title: 174


title: 171


title: vitamin D treated villi_rep 4

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
D_Villi_Rep4


title: 172


title: vehicle-treated villi_rep 2

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
Veh_Villi_Rep2


title: vehicle-treated villi_rep 1

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
Veh_Villi_Rep1


title: 169


title: 170


title: 30

value: Hot


title: 225


title: 168


title: 224


title: 166


title: 204


title: 177


title: 180


title: 149


title: 164


title: 146


title: 147


title: 143


title: vehicle-treated villi_rep 4

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
Veh_Villi_Rep4


title: 173


title: 144


title: 142


title: 145


title: vehicle-treated villi_rep 3

description:
Intestinal tissues were harvested from mice. After flushing with cold PBS, the intestines were opened and cut into pieces in cold PBS for washing, and then incubated with 3mM EDTA/PBS in rotator for 5 min at 4 0C. Discarded the solution and incubated with 3mM EDTA/PBS in rotator for 10 min at 4 0C. Intestinal pieces were transferred to new tube prepared with cold 3mM EDTA/PBS and rotated for 30 min at 4 0C and then were shaken 15 times. Collected the supernatant and spin down at 170 rcf for 3 min at 4 0C. Resuspended with cold PBS and separated villi from crypts with 70 µm filter. Collected both villi and crypts in different Eppendorf tubes. Centrifuged tubes twice at 200 rcf in 4 0C and removed the supernatant. Proceeded to RNA extraction.RNeasy Plus Universal Kit was used for villi and crypts with RiboZol RNA extraction reagent (Amresco, Solon, Ohio), according to manufacturer’s instructions.
FPKM_VDR_VitDvsNoVitD_Villi.txt, Results_VDR_VitDvsNoVitD_Villi.txt
sample name in processed data file:
Veh_Villi_Rep3


title: 140


title: 139


title: 138


title: 141


title: 135


title: 136


title: 131


title: 148


title: 130


title: 137