title: EC2 TM

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: mRNA

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38).
Reads were aligned to mouse reference genome mm10 by STAR aligner (version 2.6.1a).
Gene counts were quantified by htseq-count (version 0.11.2).
Variations were called based on the aligned file by BCFtools mpileup function (version 1.9-40).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Gene counts by htseq-count with txt format.
Supplementary_files_format_and_content: Site_Pool.csv: Comma-separated values

source_name: mouse endothelial cells

extract_protocol:
Two inducible ADAR1 knockout mice from two independent litters were used for EC isolation. RNA samples were isolated from TM treated and nontreated control cells.
RNA libraries were prepared from 100ng RNA using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems) according to manufacturer’s protocol and were sequenced using NovaSeq6000 platform (Illumina).

tag: model

value: Inducible EC-specific ADAR1 knockout

value: TM

value: Endothelial cells

tag: age

value: Male


title: EC2 CON

status: Public on Dec 27 2021

type: SRA

country: USA

description: mRNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment

value: CON

tag: cell type

tag: strain

tag: Sex


title: Clostridioides difficile 630∆erm∆gdpP_rep1

city: Gif-sur-Yvette

first: Johann

last: Peltier

address: 1, avenue de la terasse

country: France

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2
HtSeqCount was used for counting genes with default parameters
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied with the  630∆erm∆gdpP as a reference for reporting the expression data of 630∆erm∆gdpP∆busR.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Raw Counts and Normalized Counts

organism: Clostridioides difficile 630

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols; Truseq stranded RNA seq kit

tag: strain/genotype

value: vegetative cells


title: Clostridioides difficile 630∆erm∆gdpP_rep2


title: D3-IS-mice1-left kidney tissue

city: Guangzhou

first: Xu-Tao

last: Chen

state: Guangdong

address: 58# Zhongshan Road 2

country: China

institute: The First Affiliated Hospital of Sun Yat-sen University

source_name: kidney tissue

growth_protocol: All mice were individually housed in a biosafety level 2 room until Week 9.

extract_protocol:
Total RNAs were extracted from samples using the RNeasyMini Kit (Qiagen, Hilden, Germany). RNA quality was assessed by using NanoDrop (Thermo Fisher Scientific, Waltham, MA) and Qubit Fluorometer (Invitrogen).
High-quality RNA samples (28 S/18 S = 2.0−2.2, RIN > 9.0) were used to construct sequencing libraries following a standardized procedure on the Illumina HiSeq 2000 Sequencing System.

treatment_protocol: In IRI group, IRI was established by clamping the left renal pedicle for 30 minutes. In IS group, tacrolimus (2.5 mg/kg) and mycophenolic acid (50 mg/kg) were administered by gastric gavage once daily.

value: male

value: All renal cells

value: immunosuppressants

tag: infection

value: mouse polyomavirus (MPyV)

tag: time

value: 3 days

tag: tissue

value: left kidney


title: Oleic Acid Growth - Rep2

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

data_processing:
RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine.
SOAP (v2.21, -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).The rest reads with adaptor， or with unknown bases more than 5%  ,or with more than 20% low-quality bases were cleared by a software developed by BGI group. After, clear reads were mapped to reference genome (Salmonella enterica subsp. enterica serovar Typhimurium SL1344 (https://www.ncbi.nlm.nih.gov/nuccore/NC_016810.1?report=fasta)(https://www.ncbi.nlm.nih.gov/nuccore/NC_016810.1?report=genbank) with Bowtie2： v2.2.5 -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --), and expression value was caculated with RSEM (http://deweylab.biostat.wisc.edu/RSEM）
Genome_build: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, complete genome(https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2) and plasmid (https://www.ncbi.nlm.nih.gov/nuccore/NC_003277.2)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Oleic Acid Growth

growth_protocol: Overnight cultures were grown from a single colony, diluted 1:100 in fresh M9CA minimal medium supplemented with 0.4% Brij-58 and 0.1 % glucose (Group GLU) or 0.1 % oleic acid (Group OAG) , and grown to the OD600 ~ 1.0 at 37°C  with shaking at 220 rpm

extract_protocol:
Bacterial cultures were mixed with 0.2 (v/v) of stop solution (95% ethanol and 5% phenol) and immediately frozen within liquid nitrogen. Total RNA was isolated using the hot phenol method. Briefly, 2.0 OD600 cell pellet was resuspended with 300 μL lysozyme (#L3790, Sigma-Aldrich) at 0.5 mg/mL, 30 μL 10% SDS and 33 μL 3M sodium acetate (pH5.2). Cleared lysate was mixed with 375 μL saturated phenol (pH4.5) and incubated at 64°C for 6 min with shaking. The aqueous phase was collected after centrifuge and mixed with 375 μL chloroform in Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech). RNA was precipitated at -80 °C overnight by mixing the aqueous phase (~350 μL) with 700 μL 30:1 ethanol: sodium acetate (pH 6.5) mix. RNA pellets were washed with 80% ethanol and dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and was quantified using NanoDrop 2000.
Ribosomal RNAs was removed by Biotin-labeled rRNA probe. RNA was fragmented with BGI fragmentation buffer and was reverse transcribed with random hexamer. Double chain cDNA was then blunted and phosphorylated for the 5’ end, and overhang A base in the 3’ end and ligated with T-overhang adapter. After PCR application, samples were sequenced in BGISeq-500 platform

treatment_protocol: Cells from GLU groups were washed twice with PBS at room temperature and resuspend in M9CA minimal medium supplemented with 0.4% Brij-58 and 0.1 % oleic acid and cultivated for 10 min (OAS).

tag: genotype

value: wild-type

value: Oleic Acid Growth (OAG)

value: Bacterial cells


title: EC1 CON

description: mRNA


title: Control group 1

status: Public on Dec 26 2021

type: RNA

city: Beijing

first: Wei

last: Han

address: Dongdansantiao 5

institute: CAMS&PUMC

description: Gene expression after control treatment in U87MG

hyb_protocol: Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent technologies, Santa Clara, CA, US).

organism: Homo sapiens

source_name: U87MG glioma cell, Control group

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: Total RNA containing was extracted from U87MG, T98G and A172 cells by using the Trizol reagent (Invitrogen)  according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: we packaged the recombinant lentivirus vectors expressing shRNAs targeting two variants of HOTAIRM1 simultaneously in stably transduced U87MG, T98G and A172 glioma cell lines. Total RNA was extracted for microarray analysis.

tag: cell line

value: glioma cell


title: Control group 3

description: Gene expression after control treatment in A172

source_name: A172 glioma cell, Control group


title: Control group 2

description: Gene expression after control treatment in T98G

source_name: T98G glioma cell, Control group


title: RE-5299-input

city: Rochester

first: Aditya

last: Bhagwate

state: MN

address: 200 1st Street SW

institute: Mayo Clinic

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10) and sicer
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage siganl

molecule: genomic DNA

source_name: Buffy coat

extract_protocol:
Lysates were clarified from Mnase/sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to ThruPLEX® DNA-seq Kit V2 (Rubicon Genomics, Ann Arbor, MI) according to the manufacturer’s instructions. . Briefly,In the first step, the DNA is repaired and yields molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5’ ends are ligated with high efficiency to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The adaptors cannot ligate to each other and do not have single-strand tails, both of which contribute to non-specific background found with many other NGS preparations. In the final step, the 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes are added through a high-fidelity amplification. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were purified by AMpure reagents. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

value: Buffy coat

tag: histone mark antibody

value: Input sample

tag: ge group

value: Input

tag: disease state

value: Diabetes Mellitus


title: RE-4150-input


title: HOTAIRM1 knockdown 1

description: Gene expression after HOTAIRM1 knockdown in U87MG

source_name: U87MG glioma cell, HOTAIRM1 knockdown


title: RE-6135-k27Ac-29

value: anti-H3K27Ac (CST, Cat. 8173, Lot 1)

value: Normal


title: HOTAIRM1 knockdown 3

description: Gene expression after HOTAIRM1 knockdown in A172

source_name: A172 glioma cell, HOTAIRM1 knockdown


title: HOTAIRM1 knockdown 2

description: Gene expression after HOTAIRM1 knockdown in T98G

source_name: T98G glioma cell, HOTAIRM1 knockdown


title: RE-3589-input


title: RE-6135-input


title: RE-5299-K9Ac-18

value: anti-H3K9Ac (in house EDL, Lot1)

value: Delayed


title: RE-3223-K9Ac-16


title: RE-3589-k27Ac-31

value: Rapid


title: RE-3223-input


title: RE-4150-k27Ac-30


title: RE-2896-K9Ac-13


title: R6369-k27Ac-5


title: RE-2896-input


title: R2260-k27Ac-8


title: R2260-input


title: R6369-K4me3-4

value: anti-H3K4me3 (in house EDL, Lot1)


title: EC1 TM

description: mRNA

value: Inducible EC-specific ADAR1 knockout

value: TM

value: Endothelial cells

value: Male


title: 85-K9Ac-9


title: R6369-input


title: R2260-K4me3-7


title: 85-K4me3-7


title: 85-input


title: 85-K27Ac-8


title: 84-K9Ac-24


title: R6369-K9Ac-6


title: Glucose Growth - Rep1

source_name: Glucose Growth

value: wild-type

value: Glucose Growth (GLU)


title: R2260-K9Ac-9


title: 84-input


title: 5299-K27Ac-38


title: 84-K4me3-23


title: 42-K27Ac-22


title: 84-K27Ac-25


title: 5299-input


title: 5299-k4me3-28


title: 6348-H3K27ac-26


title: 4150-input


title: 42-K9Ac-21


title: 42-K4me3-20


title: 42-input


title: 3715-input


title: 4150-K9Ac-29


title: 35-K9Ac-18


title: 35-K4me3-17


title: 6348-k4me3-25


title: 35-K27Ac-19


title: 6348-H3K9ac-27


title: 3223-k4me3-23


title: 37510-K4me3-13


title: 3223-input


title: 2896-k27Ac-36


title: 2896-k4me3-26


title: 3426-k4me3-22


title: 3426-K27Ac-32


title: 3223-k27Ac-33


title: 2818-K4me3-10


title: 2896-input


title: 6348-input


title: 2818-input


title: 2818-k27Ac-11


title: 17-K9Ac-14


title: 17-K4me3-13


title: 17-K27Ac-15


title: 17-input


title: 105-K9Ac-3


title: 105-K4me3-1


title: 104-K9Ac-27


title: 3426-input


title: 105-input


title: 35-input


title: 105-K27Ac-2


title: 104-K4me3-26


title: 104-K27Ac-28


title: 104-input


title: 103-input


title: 103-K9Ac-6


title: RE-9733_Input

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with default parameters
Peak calling was performed using MASC2 (v2.0.10) and sicer
Genome_build: hg19
Supplementary_files_format_and_content: Peak files from MACS2, and BAM files


title: 2818-K9Ac-9


title: RE-8546_Input


title: RE-8546-K9Ac-14_Normal


title: RE-4958_Input


title: RE-4851-K9Ac-17_Delayed


title: RE-49583-k27Ac-28_Delayed


title: RE-4851_Input


title: RE-3885_Input


title: RE-3885-K9Ac-10_Normal


title: RE-4592-k27Ac-32_Normal


title: RE-5921-k27Ac-34_Normal


title: RE-3051_Input


title: RE-3051-K9Ac-15_Delayed


title: RE-4592_Input


title: RE-5921_Input


title: RE-1045_Input


title: RE-1045-K9Ac-12_Normal


title: RE-2931-k27Ac-33_Normal


title: RE-2931_Input


title: RE-0775_Input


title: R6542-K9Ac-18_Normal


title: R6542-K27Ac-17_Normal


title: R5642_Input


title: R6433-K9Ac-15_Delayed


title: R6433-K4me3-13_Delayed


title: R6433_Input


title: R6542-K4me3-16_Normal


title: R6433-K27Ac-14_Delayed


title: RE-0775-K9Ac-11_Delayed


title: R3445-K9Ac-21_Delayed


title: R3445-K27Ac-20_Delayed


title: R3445-K4me3-19_Delayed


title: R3445_Input


title: R1791-K9Ac-9_Rapid


title: R1791_Input


title: R1791-K27Ac-8_Rapid


title: R0412-K9Ac-6_Rapid


title: R0412_Input


title: R0296_K9Ac-3_Normal


title: R0412-K4me3-4_Rapid


title: R0296_Input


title: R0296-k27Ac-2_Normal


title: 8546_Input


title: 8546-k27Ac-31_Normal


title: 9733-k4me3-38_Normal


title: R0296-K4me3-1_Normal


title: 7275_Input


title: 9733_Input


title: 8546-k4me3-21_Normal


title: 7275-H3K4me3-1_Rapid


title: 7275-H3K9Ac-3_Rapid


title: 6149_Input


title: 6149-H3K4me3-21_Rapid


title: 7275-H3K27ac-2_Rapid


title: 6149-H3K9Ac-23_Rapid


title: elegans-him17, rep1

city: Cambridge

first: Francesco Nicola

last: Carelli

address: Henry Wellcome Building of Cancer and Developmental Biology,  Tennis Court Road

country: United Kingdom

institute: University of Cambridge

data_processing:
C. elegans RNA-seq reads were aligned to the WS275 C. elegans genome assembly using STAR (2.7.5a) with the TwoPass mode. Strand-specific wiggle output was converted to BigWig.
Genome_build: WS275
Supplementary_files_format_and_content: Forward and reverse-strand genome-wide read coverage in RPM (reads per million of mapped reads)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: For each of two replicates, approximately 100 wild-type and him-17(me24) (m+z-) young adults grown on agar plates at 20ºC from the starved L1 stage were hand-picked.  him-17(me24) were derived from him-17(me24)/tmC12 [tmIs1194] mothers.

extract_protocol:
Total RNA was extracted using TriPure (Roche) and further purified using an RNeasy column (Qiagen).
poly A was isolated using the NEBNext Poly(A) mRNA Isolation kit and libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (E7760S).

value: Whole worm

value: him-17 mutant

tag: developmental stage

value: young adult

tag: growth condition


title: R1791-K4me3-7_Rapid


title: elegans-wt, rep2

value: N2 (Bristol)

value: wt


title: 6149-H3K27ac-22_Rapid

value: anti-H3K27Ac (CST, Cat. 8173, Lot 1)


title: 5921-K9Ac-17_Normal

value: Normal


title: 5921_Input

value: Input sample

value: Input


title: R0412-K27Ac-5_Rapid

value: Rapid


title: 4958-k9Ac-33_Delayed

value: anti-H3K9Ac (in house EDL, Lot1)

value: Delayed


title: elegans-him17, rep2


title: 4958_Input


title: 4851-k4me3-30_Delayed

value: anti-H3K4me3 (in house EDL, Lot1)


title: elegans-HIM17-rep2

data_processing:
ChIP-seq reads were preprocessed with trim-galore (default settings) and then aligned to the WS275 C. elegans genome assembly using BWA v. 0.7.17 with the BWA-MEM algorithm (Li and Durbin, 2010).
The SAMtools v. 0.1.19 ‘view’ utility (Li et al., 2009) was used to convert the alignments to BAM format and extract mapq10 reads. Coverage normlised bedgraph tracks were generated using MACS2 (2.1.2) and converted to BigWig format.
Genome_build: WS275
Supplementary_files_format_and_content: sequencing depth-normalized genome-wide linear read coverage (from reads with MAPQ value >= 10)

growth_protocol: Wild-type young adults (YA) were prepared by growing synchronized L1s in liquid culture using standard S-basal medium with HB101 E. coli for 60 hr at 20˚C. Adults were sucrose floated, washed in PBS, and flash frozen in liquid nitrogen.

extract_protocol:
Frozen YA worms were ground to a powder, which was incubated in 1.5 mM EGS (Pierce 21565) in PBS for 8 minutes, followed by the addition of formaldehyde to a final concentration of 1%, and incubated for a further 8 minutes. The fixation was quenched for 5 minutes by the addition of 0.125 M glycine. Fixed tissue was washed 2X with PBS with protease inhibitors (Roche EDTA-free protease inhibitor cocktail tablets 05056489001) and once in FA buffer (50 mM Hepes pH7.5, 1 mM EDTA, 1% TritonX-100, 0.1% sodium deoxycholate, and 150 mM NaCl) with protease inhibitors (FA+), then resuspended in 1 ml FA+ buffer per 1 ml of ground worm powder. The extract was sonicated to an average size of ~250 base pairs using a Bioruptor Pico (Diagenode), and 20 ug of DNA was used per ChIP reaction.
ChIP DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads. Illumina TruSeq adaptors and barcodes were used.

tag: growth temperature

tag: chip antibody


title: elegans-wt, rep1


title: 4851-k27Ac-40_Delayed


title: elegans-HIM17-rep1


title: 4592-K9Ac-41_Normal


title: 4851_Input


title: 4495-H3K9Ac-7_Rapid


title: 4495-H3K27ac-6_Rapid


title: 4495-H3K4me3-5_Rapid


title: 4419-H3K4me3-17_Rapid


title: 4419_Input


title: briggsae-lcap-glp1-ya-rep1

data_processing:
Reads were trimmed to 20bp with trim-galore, then mapped on the WS275 C. briggsae genome assemly using the bwa-backtrack algorithm in single-end mode. Reads of low quality (MAPQ < 10) and mapping on any unassembled contig were discarded. bedgraph linear coverage tracks were then generated from this reads filling in the sequences between the first and second read in a pair, then converted to bigWig.
Genome_build: WS275
Supplementary_files_format_and_content: Forward and reverse-strand genome-wide absolute read coverage

organism: Caenorhabditis briggsae

growth_protocol: Wild-type AH16 C. briggsae or glp-1(we58) mutants were grown in liquid culture from the starved L1 to the young adult stage using standard S-basal medium with HB101 bacteria (wt at 20C, glp-1 at 27C), washed in M9, floated on sucrose, washed again in M9, then frozen into "popcorn" by dripping embryo or worm slurry into liquid nitrogen. Popcorn were stored at -80°C until use.

extract_protocol:
RNA was extracted from one million pelleted nuclei by adding 500ul Trizol and 100 µl of Chloroform and shaking samples vigorously for 15 s. Samples were then spun at 12,000 g for 15 min at 4 C and the aqueous phase was transferred into one volume of ice-cold Isopropanol. 0.5 µl of GlycoBlue (AM9515) was added and RNA was left to precipitate overnight at -20 C. Once precipitated, RNA was pelleted (12,000 g for 30 min at 4 C), washed in 1 ml of ice-cold 80% Ethanol and resuspended in 12 µl of RNAse-free water. Concentration was estimated using Qubit. A minimum of 20 ng of total nuclear RNA was used to make long nuclear RNA-seq libraries.
Long nuclear RNA (>200 nt) was isolated using Zymo Clean and Concentrate columns (#R1013) and stranded libraries were prepared using the NEB Next Ultra Directional RNA Library Prep Kit (#E7420S) after removing rRNA using the Ribo-Zero rRNA removal kit (MRZH11124). Long nuclear RNA-seq libraries were made from two biological replicates for each tissue.

value: glp-1 mutant

tag: fraction

value: chromatin-associated long RNA


title: briggsae-lcap-glp1-ya-rep2


title: MCF10A-M2 cells transfected with siOVOL1 (Replicate #2)

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=no”.
The gene annotation used for quantification was Ensembl version 104.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count in TSV format

source_name: pre-malignant human breast cell line

growth_protocol: MCF10A-M2 cells were maintained in DMEM/F12 (GlutaMAX™ Supplement; Thermo Fisher Scientific; Cat. Nr.: 31331028) containing 5% horse serum (Thermo Fisher Scientific; Cat. Nr.: 26050088), 0.1 μg/ml Cholera toxin (Sigma-Aldrich; Cat. Nr.: C8052), 0.02 μg/ml Epidermal Growth Factor (EGF; Sigma-Aldrich; Cat. Nr.: 01-107), 0.5 μg/ml Hydrocortisone (Sigma-Aldrich; Cat. Nr.: H0135), 10 μg/ml Insulin (Sigma-Aldrich; Cat. Nr.: I6634) and 100 U/ml Penicillin/Streptomycin. The cells were mentioned were maintained in a 5% CO2, 37 °C, humidified incubator and tested negative for mycoplasma routinely. The cell line was checked for authenticity by short tandem repeats (STR) profiling.

extract_protocol:
RNA was extracted by a NucleoSpin RNA kit (Macherey Nagel; Cat. Nr.: 740955) according to the manufacturer's instructions.
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI) in China using the DNBSEQ platform.

treatment_protocol: Cells were seeded at 80% confluence and incubated with complex formed by DharmaFECT transfection reagents and siRNAs (10 nM at final concentration). Medium was changed at 24 h post-transfection. RNA samples were collected at 2 days after transfection.

tag: cell type

value: MCF10A cells (normal human breast epithelial cell line) transformed with HA-Ras

tag: treatment

value: transfected with siRNA tagrgeting OVOL1 (siOVOL1)

value: OVOL1 depletion


title: MCF10A-M2 cells transfected with siOVOL1 (Replicate #1)


title: briggsae-lcap-wt-ya-rep2

value: Whole worm

tag: strain


title: MCF10A-M2 cells transfected with siOVOL2 (Replicate #2)

value: transfected with siRNA tagrgeting OVOL2 (siOVOL2)

value: OVOL2 depletion


title: MCF10A-M2 cells transfected with siNT (Replicate #3)

value: transfected with non-targeting siRNA (siNT)

value: control


title: MCF10A-M2 cells transfected with siOVOL1 (Replicate #3)


title: MCF10A-M2 cells transfected with siNT (Replicate #2)


title: 4419-H3K27ac-18_Rapid

value: anti-H3K27Ac (CST, Cat. 8173, Lot 1)


title: briggsae-glp1-rep2

data_processing:
Reads were trimmed using trim_galore, and aligned using bwa in single-end mode.
Low-quality (q<10) reads and reads mapping to non-assembled contigs mtDNA were discarded.
Normalised coverage was calculated using MACS2: --format BAM --bdg --SPMR --gsize ce --nolambda --nomodel --extsize 150 --shift -75 --keep-dup all
Genome_build: WS275
Supplementary_files_format_and_content: Coverage depth-normalized genome-wide accessibility profiles.

growth_protocol: Wild-type AF16 C. briggsae or glp-1(we58) mutants were grown in liquid culture from the starved L1 to the young adult stage using standard S-basal medium with HB101 bacteria (wt at 20C, glp-1 at 27C), washed in M9, floated on sucrose, washed again in M9, then frozen into "popcorn" by dripping embryo or worm slurry into liquid nitrogen. Popcorn were stored at -80°C until use.

extract_protocol:
Frozen worms were broken by grinding in a mortar and pestle or smashing using a Biopulverizer, then the frozen powder was thawed in 10 ml Egg buffer (25 mM HEPES pH 7.3, 118 mM NaCl, 48 mM KCl, 2 mM CaCl2, 2 mM MgCl2). Ground worms were pelleted by spinning at 1500 g for 2 minutes, then resuspended in 10ml working Buffer A (0.3M sucrose, 10 mM Tris pH 7.5, 10 mM MgCl2, 1mM DTT, 0.5 mM spermidine 0.15 mM spermine, protease inhibitors (Roche complete, EDTA free) containing 0.025% IGEPAL CA-630. The sample was dounced 10X in a 14ml stainless steel tissue grinder (VWR), then the sample spun 100g for 6 min to pellet large fragments. The supernatant was kept and the pellet resuspended in a further 10 ml Buffer A, then dounced for 25 strokes. This was spun 100g for 6 min to pellet debris and the supernatants, which contain the nuclei, were pooled, spun again at 100g for 6 min to pellet debris, and transferred to a new tube. Nuclei were counted using a hemocytometer. One million nuclei were transferred to a 1.5 ml tube and spun 2000g for 10min to pellet.
ATAC-seq was performed essentially as in (Buenrostro et al. 2013). The one million nuclei were resuspended in 47.5 ul of tagmentation buffer, incubated for 30 minutes at 37°C with 2.5 ul Tn5 enzyme (Illumina Nextera kit), and then tagmented DNA purified using a MinElute column (Qiagen) and converted into a library using the Nextera kit protocol. Typically, libraries were amplified using 12–16 PCR cycles.

value: young adult


title: 3885-k4me3-25_Normal

value: Normal


title: briggsae-lcap-wt-ya-rep1

value: wt


title: 3885-k27Ac-35_Normal


title: MCF10A-M2 cells transfected with siNT (Replicate #1)


title: MCF10A-M2 cells transfected with siOVOL2 (Replicate #1)


title: 3885_Input

value: Input sample

value: Input


title: MCF10A-M2 cells transfected with siOVOL2 (Replicate #3)


title: 4592_Input


title: 4495_Input


title: briggsae-glp1-rep1


title: 3536_Input


title: briggsae-wt-rep2


title: 3536-H3K9Ac-11_Rapid

value: anti-H3K9Ac (in house EDL, Lot1)

value: Rapid


title: 4419-H3K9Ac-19_Rapid


title: briggsae-wt-rep1


title: 3536-H3K4me3-9_Rapid

value: anti-H3K4me3 (in house EDL, Lot1)


title: 3536-H3K27ac-10_Rapid


title: 3051-k4me3-29_Delayed

value: Delayed


title: 3051-k27Ac-39_Delayed


title: 2931-K9Ac-49_Normal


title: 2931_Input


title: 3051_Input


title: 2028_Input


title: 2447-K9Ac-1_Rapid


title: Viral_rep2

city: Nangjing

first: Jing

last: Wu

address: Medical School, Nanjing University, 22# Hankou Road, Nanjing, Jiangsu Province

institute: Nanjing University

description: HeLa cells were pre-exposed to DMSO for 48 h and then infected with VSV (MOI=1) for 24 h

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: HeLa cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HeLa cells

tag: treatment 1

value: DMSO treatment for 3 days

tag: treatment 2

value: VSV (MOI=1) infected for 24 hours


title: Viral_rep1


title: Mock_rep3

description: HeLa cells were pre-exposed to DMSO for 72 h


title: Mock_rep1


title: Mock_rep2


title: 2447_Input


title: Viral_rep3


title: Bap_Viral_rep1

description: HeLa cells were pre-exposed to Bap at 10 μM for 48 h and then infected with VSV (MOI=1) for 24 h

value: Bap (10uM) exposure for 3 days


title: Bap_Viral_rep3


title: BaP_rep3

description: HeLa cells were pre-exposed to Bap at 10 μM for 72 h


title: BaP_rep2


title: 2028-H3K4me3-13_Rapid


title: 2028-H3K9Ac-15_Rapid


title: Sample7

city: Sydney

first: Ji

last: Tu

email: ji.tu@unsw.edu.au, ji.tu@outlook.com

state: NSW

address: High St, Kensington

country: Australia

institute: University of New South Wales

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each cell

source_name: nucleus pulposus

extract_protocol:
The nucleus pulposus tissues were surgically removed from patients and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 500 U/mL collagenase I (SangonBiotech) , 150 U/mL collagenase II (SangonBiotech) , 50U/mL collagenase IV (SangonBiotech) ,0.1mg/ml hyaluronidase (SangonBiotech),30U/mL DNaseI (SangonBiotech) and 5% Fetal Bovine Serum Oringin South America(Yeasen) for 95 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences). The single-cell suspension was further enriched with a MACS dead cell removal kit (Miltenyi Biotec).
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.
scRNA-seq

value: nucleus pulposus

tag: degeneration grades

value: Grade IV


title: Sample8

tag: tissue


title: BaP_rep1


title: Sample6

value: Grade III


title: 1045-k4me3-24_Normal


title: 1045-k27Ac-34_Normal

value: anti-H3K27Ac (CST, Cat. 8173, Lot 1)


title: 2028-H3K27ac-14_Rapid


title: 1045_Input


title: Sample5


title: 2447-K4me3-2_Rapid


title: Bap_Viral_rep2


title: Sample4

value: Grade II


title: 0775-k27Ac-37_Delayed


title: 0775-k4me3-27_Delayed


title: Sample3


title: Sample2

value: Grade I


title: Sample1


title: 0775_Input


title: Naive2

status: Public on Dec 25 2021

city: Glasgow

first: Miguel

last: Pineda

address: 120 university avenue

institute: University of Glasgow

data_processing:
FastQC was used for initial quality control checks on raw sequence data coming from high throughput sequencing pipelines.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCM38 mouse reference using Hisat2 v2.1.0.
Featurecounts version 1.4.6 was used to quantify reads counts.
Genome_build: GRCM38
Supplementary_files_format_and_content: tab-delimited text files include read counts values for each sample generated with feature counts.

source_name: mouse synovium

extract_protocol:
Mouse SFs were expanded and grown ex vivo were. Cells were seeded in culture plates, RNA was extracted after treatment.
library preparation was done using polyA selection (TruSeq stranded mRNA kit)

value: synovium

tag: condition

value: Naive health (control)


title: IL-1β 1

value: IL-1Beta treated (experimental)


title: Naive1


title: IL-1β 2


title: siRNA IL-1β 1

value: IL-1Beta treated ARNO knock down (experimental)


title: Naive3


title: IL-1β 3


title: siRNA IL-1β 3


title: run3_210602_G1_CreTomFl_Tuft_D1_3

city: Boston

first: Adam

last: Haber

state: Massachusetts

address: 665 Huntington Ave, HSPH Building 1, Room 305

institute: Harvard T. H. Chan School of Public Health

description: Run3 210602 G1 CreTomFl Tuft D1 3

data_processing:
Full-length RNAseq (SMART-Seq2)
Tophat
Bowtie
RSEM
PCA (prcomp in R)
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million (TPM) expression values (derived from RSEM  for each gene (rows) in each sample (columns)

source_name: Nasal tuft cells

extract_protocol: Full length RNAseq (SMART-Seq2)

value: Nasal tuft cells

value: Inhaled Alternaria Alternata extracts

tag: time point

value: 24 hr

tag: genotype

value: ChAT-CRE TdTomato LTC4 Synthase flox/flox


title: run3_210602_D1_CreTomFl_Tuft_D3_1

description: Run3 210602 D1 CreTomFl Tuft D3 1

value: 72 hr


title: run3_210602_F1_CreTomFl_Tuft_D0_3

description: Run3 210602 F1 CreTomFl Tuft D0 3


title: run3_210602_C5_CreTomFl_Tuft_D1_2

description: Run3 210602 C5 CreTomFl Tuft D1 2


title: run3_210602_H9_CreTomFl_Tuft_D3_3

description: Run3 210602 H9 CreTomFl Tuft D3 3


title: run3_210602_A9_CreTomFl_Tuft_D0_1

description: Run3 210602 A9 CreTomFl Tuft D0 1


title: run3_210602_C1_CreTomFl_Tuft_D1_1

description: Run3 210602 C1 CreTomFl Tuft D1 1


title: run3_210602_H7_CreTomFl_EpcamHi_D3_2

description: Run3 210602 H7 CreTomFl EpcamHi D3 2

source_name: EpCAM-high nasal epithelial cells

value: EpCAM-high nasal epithelial cells


title: run3_210602_G3_CreTomFl_EpcamHi_D1_3

description: Run3 210602 G3 CreTomFl EpcamHi D1 3


title: run3_210602_A11_CreTomFl_EpcamHi_D0_1

description: Run3 210602 A11 CreTomFl EpcamHi D0 1


title: run3_210602_D3_CreTomFl_EpcamHi_D3_1

description: Run3 210602 D3 CreTomFl EpcamHi D3 1


title: siRNA IL-1β 2


title: run3_210602_B3_CreTomFl_EpcamHi_D0_2

description: Run3 210602 B3 CreTomFl EpcamHi D0 2


title: run3_210602_C3_CreTomFl_EpcamHi_D1_1

description: Run3 210602 C3 CreTomFl EpcamHi D1 1


title: run3_210602_B1_CreTomFl_Tuft_D0_2

description: Run3 210602 B1 CreTomFl Tuft D0 2


title: run3_210602_H11_CreTomFl_EpcamHi_D3_3

description: Run3 210602 H11 CreTomFl EpcamHi D3 3


title: run3_210602_C7_CreTomFl_EpcamHi_D1_2

description: Run3 210602 C7 CreTomFl EpcamHi D1 2


title: run3_210602_E9_CreTom_Tuft_D0_4

description: Run3 210602 E9 CreTom Tuft D0 4

value: ChAT-CRE TdTomato


title: run3_210602_C9_CreTom_Tuft_D3_1

description: Run3 210602 C9 CreTom Tuft D3 1


title: run3_210602_F5_NewCreTom_Tuft_D1_3

description: Run3 210602 F5 NewCreTom Tuft D1 3


title: run3_210602_F9_CreTom_Tuft_D1_4

description: Run3 210602 F9 CreTom Tuft D1 4


title: run3_210602_F3_CreTomFl_EpcamHi_D0_3

description: Run3 210602 F3 CreTomFl EpcamHi D0 3


title: run3_210602_B9_CreTom_Tuft_D1_2

description: Run3 210602 B9 CreTom Tuft D1 2


title: run3_210602_H5_CreTomFl_Tuft_D3_2

description: Run3 210602 H5 CreTomFl Tuft D3 2


title: run3_210602_A5_NewCreTom_Tuft_D0_2

description: Run3 210602 A5 NewCreTom Tuft D0 2


title: run3_210602_H3_CreTom_EpcamHi_D3_4

description: Run3 210602 H3 CreTom EpcamHi D3 4


title: run3_210602_G5_NewCreTom_Tuft_D3_2

description: Run3 210602 G5 NewCreTom Tuft D3 2


title: run3_210602_G9_CreTom_Tuft_D3_2

description: Run3 210602 G9 CreTom Tuft D3 2


title: run3_210602_E11_CreTom_EpcamHi_D0_4

description: Run3 210602 E11 CreTom EpcamHi D0 4


title: run3_210602_A7_NewCreTom_EpcamHi_D0_2

description: Run3 210602 A7 NewCreTom EpcamHi D0 2


title: run3_210602_B5_CreTom_Tuft_D1_1

description: Run3 210602 B5 CreTom Tuft D1 1


title: run3_210602_H1_CreTom_Tuft_D3_4

description: Run3 210602 H1 CreTom Tuft D3 4


title: run3_210602_G11_CreTom_EpcamHi_D3_2

description: Run3 210602 G11 CreTom EpcamHi D3 2


title: run3_210602_G7_NewCreTom_EpcamHi_D3_2

description: Run3 210602 G7 NewCreTom EpcamHi D3 2


title: run3_210602_B11_CreTom_EpcamHi_D1_2

description: Run3 210602 B11 CreTom EpcamHi D1 2


title: run3_210602_C11_CreTom_EpcamHi_D3_1

description: Run3 210602 C11 CreTom EpcamHi D3 1


title: run3_210602_A3_CreTom_EpcamHi_D0_1

description: Run3 210602 A3 CreTom EpcamHi D0 1


title: run3_210602_A1_CreTom_Tuft_D0_1

description: Run3 210602 A1 CreTom Tuft D0 1


title: run3_210602_B7_CreTom_EpcamHi_D1_1

description: Run3 210602 B7 CreTom EpcamHi D1 1


title: run2_210423_F1_CreTomFl_Tuft_D0_4

description: Run2 210423 F1 CreTomFl Tuft D0 4


title: run2_210423_E9_CreTomFl_Tuft_D0_3

description: Run2 210423 E9 CreTomFl Tuft D0 3


title: run2_210423_H9_CreTomFl_Tuft_D3_4

description: Run2 210423 H9 CreTomFl Tuft D3 4


title: run2_210423_A9_CreTomFl_Tuft_D0_1

description: Run2 210423 A9 CreTomFl Tuft D0 1


title: run2_210423_B1_CreTomFl_Tuft_D0_2

description: Run2 210423 B1 CreTomFl Tuft D0 2


title: run3_210602_E7_CreTom_EpcamHi_D0_3

description: Run3 210602 E7 CreTom EpcamHi D0 3


title: run2_210423_D5_CreTomFl_Tuft_D3_1

description: Run2 210423 D5 CreTomFl Tuft D3 1


title: run2_210423_G1_CreTomFl_Tuft_D1_3

description: Run2 210423 G1 CreTomFl Tuft D1 3


title: run2_210423_G5_CreTomFl_Tuft_D1_4

description: Run2 210423 G5 CreTomFl Tuft D1 4


title: run2_210423_C5_CreTomFl_Tuft_D1_2

description: Run2 210423 C5 CreTomFl Tuft D1 2


title: run2_210423_C1_CreTomFl_Tuft_D1_1

description: Run2 210423 C1 CreTomFl Tuft D1 1


title: run2_210423_D9_CreTomFl_Tuft_D3_2

description: Run2 210423 D9 CreTomFl Tuft D3 2


title: run2_210423_F3_CreTomFl_EpcamHi_D0_4

description: Run2 210423 F3 CreTomFl EpcamHi D0 4


title: run2_210423_B3_CreTomFl_EpcamHi_D0_2

description: Run2 210423 B3 CreTomFl EpcamHi D0 2


title: run2_210423_E11_CreTomFl_EpcamHi_D0_3

description: Run2 210423 E11 CreTomFl EpcamHi D0 3


title: run2_210423_A11_CreTomFl_EpcamHi_D0_1

description: Run2 210423 A11 CreTomFl EpcamHi D0 1


title: run2_210423_H5_CreTomFl_Tuft_D3_3

description: Run2 210423 H5 CreTomFl Tuft D3 3


title: run3_210602_F11_CreTom_EpcamHi_D1_4

description: Run3 210602 F11 CreTom EpcamHi D1 4


title: run2_210423_E1_CreTom_Tuft_D0_3

description: Run2 210423 E1 CreTom Tuft D0 3


title: run2_210423_H1_CreTom_Tuft_D3_4

description: Run2 210423 H1 CreTom Tuft D3 4


title: run2_210423_D11_CreTomFl_EpcamHi_D3_2

description: Run2 210423 D11 CreTomFl EpcamHi D3 2


title: run2_210423_H7_CreTomFl_EpcamHi_D3_3

description: Run2 210423 H7 CreTomFl EpcamHi D3 3


title: run2_210423_D1_CreTom_Tuft_D3_2

description: Run2 210423 D1 CreTom Tuft D3 2


title: run3_210602_F7_NewCreTom_EpcamHi_D1_3

description: Run3 210602 F7 NewCreTom EpcamHi D1 3


title: run2_210423_H11_CreTomFl_EpcamHi_D3_4

description: Run2 210423 H11 CreTomFl EpcamHi D3 4


title: run2_210423_G3_CreTomFl_EpcamHi_D1_3

description: Run2 210423 G3 CreTomFl EpcamHi D1 3


title: run2_210423_C9_CreTom_Tuft_D3_1

description: Run2 210423 C9 CreTom Tuft D3 1


title: run2_210423_D7_CreTomFl_EpcamHi_D3_1

description: Run2 210423 D7 CreTomFl EpcamHi D3 1


title: run2_210423_F5_CreTom_Tuft_D1_3

description: Run2 210423 F5 CreTom Tuft D1 3


title: run2_210423_B9_CreTom_Tuft_D1_2

description: Run2 210423 B9 CreTom Tuft D1 2


title: run2_210423_A3_CreTom_EpcamHi_D0_1

description: Run2 210423 A3 CreTom EpcamHi D0 1


title: run2_210423_B5_CreTom_Tuft_D1_1

description: Run2 210423 B5 CreTom Tuft D1 1


title: run2_210423_E3_CreTom_EpcamHi_D0_3

description: Run2 210423 E3 CreTom EpcamHi D0 3


title: run2_210423_F9_CreTom_Tuft_D1_4

description: Run2 210423 F9 CreTom Tuft D1 4


title: run2_210423_H3_CreTom_EpcamHi_D3_4

description: Run2 210423 H3 CreTom EpcamHi D3 4


title: run2_210423_A5_CreTom_Tuft_D0_2

description: Run2 210423 A5 CreTom Tuft D0 2


title: run2_210423_G9_CreTom_Tuft_D3_3

description: Run2 210423 G9 CreTom Tuft D3 3


title: run2_210423_A1_CreTom_Tuft_D0_1

description: Run2 210423 A1 CreTom Tuft D0 1


title: run2_210423_C11_CreTom_EpcamHi_D3_1

description: Run2 210423 C11 CreTom EpcamHi D3 1


title: run2_210423_B11_CreTom_EpcamHi_D1_2

description: Run2 210423 B11 CreTom EpcamHi D1 2


title: run1_200128_G5_LTC4Sflfl_DC_4

description: Run1 200128 G5 LTC4Sflfl DC 4

source_name: Nasal dendritic cells

value: Nasal dendritic cells

value: LTC4 Synthase flox/flox


title: run1_200128_F8_LTC4Sflfl_Mf_3

description: Run1 200128 F8 LTC4Sflfl Mf 3

source_name: Nasal macrophages

value: Nasal macrophages


title: run2_210423_D3_CreTom_EpcamHi_D3_2

description: Run2 210423 D3 CreTom EpcamHi D3 2


title: run2_210423_F7_CreTom_EpcamHi_D1_3

description: Run2 210423 F7 CreTom EpcamHi D1 3


title: run1_200128_G2_LTC4Sflfl_DC_1

description: Run1 200128 G2 LTC4Sflfl DC 1


title: run2_210423_E7_CreTom_EpcamHi_D0_4

description: Run2 210423 E7 CreTom EpcamHi D0 4


title: run1_200128_F7_LTC4Sflfl_Mf_2

description: Run1 200128 F7 LTC4Sflfl Mf 2


title: run2_210423_F11_CreTom_EpcamHi_D1_4

description: Run2 210423 F11 CreTom EpcamHi D1 4


title: run1_200128_F9_LTC4Sflfl_Mf_4

description: Run1 200128 F9 LTC4Sflfl Mf 4


title: run2_210423_A7_CreTom_EpcamHi_D0_2

description: Run2 210423 A7 CreTom EpcamHi D0 2


title: run1_200128_G3_LTC4Sflfl_DC_2

description: Run1 200128 G3 LTC4Sflfl DC 2


title: run1_200128_F6_LTC4Sflfl_Mf_1

description: Run1 200128 F6 LTC4Sflfl Mf 1


title: run2_210423_G11_CreTom_EpcamHi_D3_3

description: Run2 210423 G11 CreTom EpcamHi D3 3


title: run1_200128_E12_LTC4Sflfl_EpCAM.int_1

description: Run1 200128 E12 LTC4Sflfl EpCAM.int 1

source_name: EpCAM-intermediate nasal epithelial cells


title: run1_200128_F1_LTC4Sflfl_EpCAM.int_2

description: Run1 200128 F1 LTC4Sflfl EpCAM.int 2

value: EpCAM-intermediate nasal epithelial cells


title: run1_200128_F5_LTC4Sflfl_EpCAM.int_5

description: Run1 200128 F5 LTC4Sflfl EpCAM.int 5


title: run2_210423_B7_CreTom_EpcamHi_D1_1

description: Run2 210423 B7 CreTom EpcamHi D1 1


title: run1_200128_G4_LTC4Sflfl_DC_3

description: Run1 200128 G4 LTC4Sflfl DC 3


title: run1_200128_F2_LTC4Sflfl_EpCAM.int_3

description: Run1 200128 F2 LTC4Sflfl EpCAM.int 3


title: run1_200128_F3_LTC4Sflfl_EpCAM.int_4

description: Run1 200128 F3 LTC4Sflfl EpCAM.int 4


title: run2_210423_G7_CreTomFl_EpcamHi_D1_4

description: Run2 210423 G7 CreTomFl EpcamHi D1 4


title: run1_200128_E8_LTC4Sflfl_EpCAM.high.CD45.low_6

description: Run1 200128 E8 LTC4Sflfl EpCAM.high.CD45.low 6

source_name: EpCAM-high CD45-low nasal tuft cells

value: EpCAM-high CD45-low nasal tuft cells


title: run1_200128_E10_LTC4Sflfl_l_EpCAM.high.CD45.neg_2

description: Run1 200128 E10 LTC4Sflfl l EpCAM.high.CD45.neg 2

source_name: EpCAM-high CD45-negative nasal epithelial cells


title: run1_200128_E11_LTC4Sflfl_l_EpCAM.high.CD45.neg_4

description: Run1 200128 E11 LTC4Sflfl l EpCAM.high.CD45.neg 4

value: EpCAM-high CD45-negative nasal epithelial cells


title: run2_210423_C3_CreTomFl_EpcamHi_D1_1

description: Run2 210423 C3 CreTomFl EpcamHi D1 1


title: run1_200128_E4_LTC4Sflfl_EpCAM.high.CD45.low_2

description: Run1 200128 E4 LTC4Sflfl EpCAM.high.CD45.low 2


title: run1_200128_F4_LTC4Sflfl_EpCAM.int_6

description: Run1 200128 F4 LTC4Sflfl EpCAM.int 6


title: run1_200128_E5_LTC4Sflfl_EpCAM.high.CD45.low_3

description: Run1 200128 E5 LTC4Sflfl EpCAM.high.CD45.low 3


title: run1_200128_E7_LTC4Sflfl_EpCAM.high.CD45.low_5

description: Run1 200128 E7 LTC4Sflfl EpCAM.high.CD45.low 5


title: run1_200128_E6_LTC4Sflfl_EpCAM.high.CD45.low_4

description: Run1 200128 E6 LTC4Sflfl EpCAM.high.CD45.low 4


title: run1_200128_F12_ChATCre_LTC4Sflfl_Mf_3

description: Run1 200128 F12 ChATCre LTC4Sflfl Mf 3

value: ChAT-CRE LTC4 Synthase flox/flox


title: run1_200128_G7_ChATCre_LTC4Sflfl_DC_2

description: Run1 200128 G7 ChATCre LTC4Sflfl DC 2


title: run1_200128_G1_ChATCre_LTC4Sflfl_Mf_4

description: Run1 200128 G1 ChATCre LTC4Sflfl Mf 4


title: run1_200128_E2_ChATCre_LTC4Sflfl_EpCAM.int_6

description: Run1 200128 E2 ChATCre LTC4Sflfl EpCAM.int 6


title: run1_200128_E9_LTC4Sflfl_l_EpCAM.high.CD45.neg_1

description: Run1 200128 E9 LTC4Sflfl l EpCAM.high.CD45.neg 1


title: run1_200128_F10_ChATCre_LTC4Sflfl_Mf_1

description: Run1 200128 F10 ChATCre LTC4Sflfl Mf 1


title: run1_200128_E1_ChATCre_LTC4Sflfl_EpCAM.int_5

description: Run1 200128 E1 ChATCre LTC4Sflfl EpCAM.int 5


title: run1_200128_F11_ChATCre_LTC4Sflfl_Mf_2

description: Run1 200128 F11 ChATCre LTC4Sflfl Mf 2


title: run1_200128_D9_ChATCre_LTC4Sflfl_EpCAM.int_1

description: Run1 200128 D9 ChATCre LTC4Sflfl EpCAM.int 1


title: run1_200128_E3_LTC4Sflfl_EpCAM.high.CD45.low_1

description: Run1 200128 E3 LTC4Sflfl EpCAM.high.CD45.low 1


title: run1_200128_D10_ChATCre_LTC4Sflfl_EpCAM.int_2

description: Run1 200128 D10 ChATCre LTC4Sflfl EpCAM.int 2


title: run1_200128_D8_ChATCre_LTC4Sflfl_EpCAM.high.CD45.neg_4

description: Run1 200128 D8 ChATCre LTC4Sflfl EpCAM.high.CD45.neg 4


title: run1_200128_G8_ChATCre_LTC4Sflfl_DC_3

description: Run1 200128 G8 ChATCre LTC4Sflfl DC 3


title: run1_200128_G9_ChATCre_LTC4Sflfl_DC_4

description: Run1 200128 G9 ChATCre LTC4Sflfl DC 4


title: run1_200128_D6_ChATCre_LTC4Sflfl_EpCAM.high.CD45.neg_1

description: Run1 200128 D6 ChATCre LTC4Sflfl EpCAM.high.CD45.neg 1


title: run1_200128_G6_ChATCre_LTC4Sflfl_DC_1

description: Run1 200128 G6 ChATCre LTC4Sflfl DC 1


title: run1_200128_D12_ChATCre_LTC4Sflfl_EpCAM.int_4

description: Run1 200128 D12 ChATCre LTC4Sflfl EpCAM.int 4


title: run1_200128_D2_ChATCre_LTC4Sflfl_EpCAM.high.CD45.low_3

description: Run1 200128 D2 ChATCre LTC4Sflfl EpCAM.high.CD45.low 3


title: run1_200128_D11_ChATCre_LTC4Sflfl_EpCAM.int_3

description: Run1 200128 D11 ChATCre LTC4Sflfl EpCAM.int 3


title: run1_200128_D7_ChATCre_LTC4Sflfl_EpCAM.high.CD45.neg_2

description: Run1 200128 D7 ChATCre LTC4Sflfl EpCAM.high.CD45.neg 2


title: run1_200128_D3_ChATCre_LTC4Sflfl_EpCAM.high.CD45.low_4

description: Run1 200128 D3 ChATCre LTC4Sflfl EpCAM.high.CD45.low 4


title: run1_200128_D1_ChATCre_LTC4Sflfl_EpCAM.high.CD45.low_2

description: Run1 200128 D1 ChATCre LTC4Sflfl EpCAM.high.CD45.low 2


title: run1_200128_C12_ChATCre_LTC4Sflfl_EpCAM.high.CD45.low_1

description: Run1 200128 C12 ChATCre LTC4Sflfl EpCAM.high.CD45.low 1


title: run1_200128_D4_ChATCre_LTC4Sflfl_EpCAM.high.CD45.low_5

description: Run1 200128 D4 ChATCre LTC4Sflfl EpCAM.high.CD45.low 5


title: DMSO_PolyRNA_rep1

city: Melbourne

first: Lorey

middle: K

last: Smith

state: VIC

address: 4/30 Mater St

institute: Peter MacCallum Cancer Centre

data_processing:
Library strategy: Polysome profiling
Sequencing reads were aligned with Tophat2, and reads counts were obtained with htseq (Anders et al, 2015) with the human genome as reference (human_g1k_v37) using an in-house bioinformatics pipeline, seqliner (http://bioinformatics.petermac.org/seqliner/).
Transcript levels were quantified using the rpkmForGenes script (Ramskold et al. PLoS Comput. Biol 2009) with options -readCount, -fulltranscript and -onlycoding.
Analysis of RNAseq data was performed using anota2seq as described in Oertlin et al., Nucleic Acids Research, 2019. The following modifications were made: Genes with an average read count lower than 30 were removed from the analysis and data was normalized using the TMM-log2 approach and a batch effect (replicate number) was included in the models.
Genome_build: human_g1k_v37
Supplementary_files_format_and_content: Normalized_readcount_matrix.txt: Matrix table with normalized read counts for every gene and every sample.

source_name: A375 melanoma cell line

growth_protocol: A375 melanoma cells were routinely cultured in RPMI with 10% FBS (Life Technologies). Low passage (P8) cells were used for all biological replicates.

extract_protocol:
For polysome profiling, cells were pre-treated with 100µg/mL cycloheximide for 5 mins, washed with ice cold PBS containing 100µg/mL cycloheximide and lysed in a hypotonic lysis buffer (5 mM Tris-HCl (pH 7.5), 2.5mM MgCl2, 1.5 mM KCl, 100 µg/mL cycloheximide, 2mM DTT, 0.5% Triton X-100, and 0.5% sodium deoxycholate). Lysates were pre-cleared by centrifugation to remove nuclei, and the cytoplasm was collected and 20% volume was collected to control for input. The remaining sample volume was loaded onto a 10-40% linear sucrose density gradient (containing 20 mM Tris-HCL (pH 7.6), 100 mM KCl, 5 mM MgCl2) and centrifuged at 36,000 rpm [SW40 Ti rotor (Beckman Coulter, Inc)] for 2.15h at 4°C. Gradients were fractionated and collected (14 fractions per sample), and optical density was continuously recorded at 260nm using an ISCO Tris and UA-6 UV/VIS detector (Teledyne). Input RNA (20% lysate volume) was used to control for total amount of RNA per sample. RNA was isolated from sucrose fractions using phenol-chloroform extraction. For RNAseq, RNA pellets from fractions 9-14 (corresponding to polysome fractions) were pooled and further purified using RNeasy Mini Kits (QIAGEN), according to the manufacturer’s directions for RNA clean up.
RNA quality and quantity were confirmed using Agilent Tapestation (Agilent Technologies), and all samples had an RNA integrity number (RIN) of 8.8 or higher. Approximately 1µg of RNA was used for library preparation using the TruSeq Stranded Total RNA Preparation Kit with Ribo-Zero Gold (Illumina). Briefly, ribosomal RNA (rRNA) was removed using biotinylated, target specific oligos and magnetic beads. The RNA was then fragmented using divalent cations under elevated temperature and reverse transcribed to cDNA with random primers. Indexed adaptors were then ligated and the library was amplified. Samples were then pooled and sequenced on a NextSeq500 (Illumina) high output flow cell to generate approximately 25 million single-end 75bp reads per sample. Library preparation and sequencing procedures were performed by the Molecular Genomics core facility at Peter MacCallum Cancer Centre.

treatment_protocol: For treatment prior to RNA extraction, cells were seeded in 15cm dishes at 5x10^6 cells for DMSO (control) and 1x10^6 for Vem treated dishes. Multiple 15cm dishes per treatment condition were harvested to ensure enough material for sequencing.

tag: cell line

value: DMSO

tag: sample type

value: Polysome-bound RNA


title: 40hVem_TotalRNA_rep4

data_processing:
Sequencing reads were aligned with Tophat2, and reads counts were obtained with htseq (Anders et al, 2015) with the human genome as reference (human_g1k_v37) using an in-house bioinformatics pipeline, seqliner (http://bioinformatics.petermac.org/seqliner/).
Transcript levels were quantified using the rpkmForGenes script (Ramskold et al. PLoS Comput. Biol 2009) with options -readCount, -fulltranscript and -onlycoding.
Analysis of RNAseq data was performed using anota2seq as described in Oertlin et al., Nucleic Acids Research, 2019. The following modifications were made: Genes with an average read count lower than 30 were removed from the analysis and data was normalized using the TMM-log2 approach and a batch effect (replicate number) was included in the models.
Genome_build: human_g1k_v37
Supplementary_files_format_and_content: Normalized_readcount_matrix.txt: Matrix table with normalized read counts for every gene and every sample.

value: 40h Vem

value: Input


title: 24hVem_PolyRNA_rep3

value: 24h Vem


title: DMSO_PolyRNA_rep4


title: 24hVem_PolyRNA_rep2


title: 40hVem_PolyRNA_rep4


title: 24hVem_PolyRNA_rep1


title: Sample146_YFP2-LIB3_Index_N711_S506

city: Charlottesville

first: Alexandre de

middle: Goes

last: Martini

state: VA

address: 409 Lane Road, MR4

department: Pediatrics Nephrology

institute: University of Virginia

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N711_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt

data_processing:
Read quality was assessed for each sample and quality control (QC) report generated by the Java application fastqc/0.11.5
High quality reads were submitted to trimming. Paired-end Nextera adaptors were clipped out by Trimmomatic/0.39 (NexteraPE-PE.fa:2:30:10 Leading:3, Trailing:3, SlidingWindow:4:15, Minlen:36)
Alignment to the reference transcriptome (Ensembl: Mus_musculus.GRCm38.p6.cdna.fa) was performed by Salmon/0.11.2
Tximport R package imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for the downstream analysis
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file includes the matrix table with raw gene counts for every gene and every sample

source_name: KO renin (null) cell

extract_protocol:
Sorted YFP-positive cells were loaded and captured onto the C1 Fluidigm System. Lysis, reverse transcription and PCR were performed according to the SMART-Seq® v4 Ultra® Low Input RNA kit for the Fluidigm® System (Clontech Laboratories, Inc.)
Libraries were prepared using the Nextera XT DNA Library Preparation kit (FC-131-1096) and the Nextera XT Index kit (FC-131-1001)

value: kidney

tag: reporter

value: YFP


title: run1_200128_D5_ChATCre_LTC4Sflfl_EpCAM.high.CD45.low_6

description: Run1 200128 D5 ChATCre LTC4Sflfl EpCAM.high.CD45.low 6


title: Sample147_YFP2-LIB3_Index_N712_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N712_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample145_YFP2-LIB3_Index_N712_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N712_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample144_YFP2-LIB3_Index_N712_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N712_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: 24hVem_TotalRNA_rep2


title: 40hVem_TotalRNA_rep1


title: 24hVem_TotalRNA_rep4


title: 24hVem_TotalRNA_rep3


title: 24hVem_TotalRNA_rep1


title: 40hVem_TotalRNA_rep3


title: DMSO_TotalRNA_rep4


title: 40hVem_PolyRNA_rep2


title: 40hVem_PolyRNA_rep3


title: DMSO_TotalRNA_rep1


title: DMSO_PolyRNA_rep2


title: 40hVem_PolyRNA_rep1


title: 24hVem_PolyRNA_rep4


title: 40hVem_TotalRNA_rep2


title: Sample143_YFP2-LIB3_Index_N711_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N711_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample142_YFP2-LIB3_Index_N710_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N710_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: DMSO_TotalRNA_rep2


title: Sample140_YFP2-LIB3_Index_N711_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N711_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample134_YFP2-LIB3_Index_N709_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N709_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample135_YFP2-LIB3_Index_N711_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N711_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample136_YFP2-LIB3_Index_N710_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N710_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample141_YFP2-LIB3_Index_N712_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N712_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample131_YFP2-LIB3_Index_N709_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N709_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample137_YFP2-LIB3_Index_N710_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N710_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample128_YFP2-LIB3_Index_N708_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N708_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: WT

city: RTP

first: Xiaojiang

last: Xu

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

data_processing:
Raw base call (BCL) files were demultiplexed with bcl2fastq; Cell Ranger (version 3.1) from 10x genomics was used to align reads, generate feature-barcode matrices for WT samples
cellranger mkfastq was used to generate FASTQ files
cellranger count performs alignment, filtering, barcode counting, and UMI counting
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_bc_matrix

source_name: P8 Testis

extract_protocol: scRNA-seq libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics) according to the manufacturer’s instructions at the NIEHS Genomic Core Facility. Briefly, cells obtained from FACS were mixed with a suspension containing barcoded beads and UMI (unique molecular identifier) elements that allow specific tagging of messenger RNA. After partitioning thousands of cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and barcoding, full-length barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Libraries were constructed by fragmentation, end repair, A-tailing, adaptor ligation and index PCR. After ensuring adequate quality of the cDNA libraries, the samples were sequenced at the NIEHS Genomic sequencing Core Facility.

treatment_protocol: WT  mice were treated with tamoxifen (25ug/day) from P1 to P3,  then CD9+ spermatogonia cells were enriched by FACS at P8.

value: Testis

value: CD9+ spermatogonia

value: WT

tag: age

value: postnatal day 8 (P8)


title: Sample139_YFP2-LIB3_Index_N710_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N710_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample138_YFP2-LIB3_Index_N709_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N709_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample_7-HIF2-TAM-K3

city: Houston

first: Yanqing

last: Huang

state: TX

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

description: FSF-KrasG12D/+; Trp53frt/frt; Pdx1-Flp; Hif2fl/fl; αSMACreERT2/+

data_processing:
bcl2fastq to demultiplex and generate fastq files
RSEM package was used to quantitate transcript abundance from RNA-seq fastq files.
RSEM expected counts were imported into DESeq2 and differential expression analysis was performed using DESeq2 package
Genome_build: mm9
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: csv file with normalized gene counts for every gene and every sample

source_name: Pancreatic tumor

extract_protocol:
30mg Pancreatic tumor from KPF-CAF HIF2 WT and KO mice were homogenized and RNA was purified using an RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once weaned, mice were fed with normal chow or tamoxifen chow to generate KPF CAF-HIF WT and KPF CAF-HIF KO mice

value: mixed background

value: Pancreatic tumor

value: FSF-KrasG12D/+; Trp53frt/frt; Pdx1-Flp; Hif2fl/fl; alphaSMACreERT2/+

value: Tamoxifen chow


title: Sample_5-HIF2-TAM-K1


title: Sample129_YFP2-LIB3_Index_N706_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N706_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample124_YFP2-LIB3_Index_N707_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N707_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample133_YFP2-LIB3_Index_N708_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N708_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample_8-HIF2-TAM-K5


title: Sample126_YFP2-LIB3_Index_N708_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N708_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample130_YFP2-LIB3_Index_N709_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N709_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample123_YFP2-LIB3_Index_N706_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N706_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample_6-HIF2-TAM-K2


title: Sample132_YFP2-LIB3_Index_N708_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N708_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: run2_210423_C7_CreTomFl_EpcamHi_D1_2

description: Run2 210423 C7 CreTomFl EpcamHi D1 2

value: EpCAM-high nasal epithelial cells

value: Inhaled Alternaria Alternata extracts

value: 24 hr

value: ChAT-CRE TdTomato LTC4 Synthase flox/flox


title: Sample_3-HIF2-TAM-C3

value: normal chow


title: Sample122_YFP2-LIB3_Index_N707_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N707_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample125_YFP2-LIB3_Index_N706_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N706_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample_4-HIF2-TAM-C5


title: Sample_2-HIF2-TAM-C2


title: Sample121_YFP2-LIB3_Index_N707_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N707_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample127_YFP2-LIB3_Index_N707_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N707_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample_1-HIF2-TAM-C1


title: Sample120_YFP2-LIB3_Index_N706_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N705_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample119_YFP2-LIB3_Index_N705_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N706_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample117_YFP2-LIB3_Index_N704_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N704_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample118_YFP2-LIB3_Index_N705_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N705_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Old MS7080 Parabiosis-3

city: Toon

first: Daisuke

last: Yamashita

address: Shitsukawa

department: Neurosurgery

country: Japan

institute: Ehime University Graduate School of Medicine

description:
QD345-12
processed data file: TMM_normalized_reads_count_per_million.xlsx

data_processing:
Fastqc software was used to check the data quality of original sequencing data. Fastqc report was saved in 01report_of_fastq_data_quality.
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 [1] Langmead B et al., Fast gapped-read alignment with Bowtie 2, Nat Methods 9:357-9 (2012).
The gene expression level was estimated using RSEM v1.2.15.[2] Li B et al., RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics 12:1-16 (2011).
Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed [3] Robinson MD et al, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics 26:139-140 (2010).
Goseq was used to perform the GO enrichment analysis [4] Matthew DY et al., Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biology 11:R14 (2010).
Kobas was used to perform the pathway analysis. [5] Chen X et al., KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases, Nucleic Acids Res 39:316-322 (2011).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TMM_normalized_reads_count_per_million.xlsx: Excel file

source_name: Brain tumor tissue

extract_protocol:
Total RNA was extracted from cells using the TRIzol Plus RNA Purification System (Invitrogen).
RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used. Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumina Inc., San Diego, CA).

treatment_protocol: All animal experiments were performed at the UAB under an Institutional Animal Care and Use Committee (IACUC)-approved protocol according to NIH guidelines (#20295). Young (2 months) C57BL/6 mice were purchased from Charles River and Jackson Laboratory. Old (16 months) C57BL/6 mice were supported by NIA (Myriam Gorospe). Mice were housed 3 per cage with food and water on a 12:12 light:dark cycle. For intracranial injection, mice were anesthetized with ketamine/xylazine and fixed in place and dissociated BC cells were stereotactically injected into the striatum of mice. Mice were placed on a stage warmed at 37°C until they were fully awake. For parabiosis, female mice were placed in a cage for two weeks to assure peaceful cohabitation. Two animals were anesthetized using 1-5 to 2% isoflurane, shaved at approximately 1 cm above the elbow to 1 cm below the knee, prepared by thoroughly wiping (3x) with Betadine soaked wipes followed by alcohol wipes, and placed on a heated pad covered by a sterile pad. For analgesia, Carprofen and Buprenorphine were administered subcutaneously at a dose of 10 mg/kg and 0.1 mg/kg respectively. Longitudinal skin incisions were performed to the shaved sides of each animal starting at 0.5 cm above the elbow all the way to 0.5 cm below the knee joint. Following the incision, the skin was gently detached from the subcutaneous fascia by holding it up with a pair of curved forceps. The fascia was then separated with a second pair to create 0.5 cm of free skin. The left olecranon of one animal will be joined to the right olecranon of the other. Both olecranons and knee joints were clearly distinguishable following the skin incision. To facilitate the joining, the elbow of the first mouse was bent and a needle of the non- absorbable 3-0 suture will be passed under the olecranon. Following the attachment of the joints, the skin of the two animals was joined with continuous absorbable 5-0 Vicryl suture starting ventrally from the elbow towards the knee. To prevent skin rupture and separation tight suture closure of the skin in the area around the elbows and knees was performed. To prevent dehydration, 0.5 ml of 0.9% NaCl was administered subcutaneously to each mouse, and animals were kept on a heated pad until recovery. Following recovery, analgesics carprofen and buprenorphine were given by subcutaneous injection every 12 hr for 48 hr at the same doses described above. Animals were monitored for signs of pain and given Sulfamethoxazole/Trimethoprim in drinking water (2 mg sulfa/ml +0.4 mg trim/ml) for 10 days. For NMN administration, water consumption was measured prior to the start of NMN administration. NMN was administered in drinking water at 300 mg/kg/day, based on the previously measured water consumption. The NMN solution was prepared twice weekly by dissolving NMN into autoclaved water at the respective doses and sterilized by filtering. Water bottles and cages were changed twice weekly.

tag: Sex

value: Female

tag: group

value: Old-parabiosis rejuvenation

value: Brain tumor

value: Parabiosis


title: Old MS7080 Parabiosis-2

description:
QD345-11
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Sample116_YFP2-LIB3_Index_N705_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N705_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt

value: kidney

value: YFP


title: Sample115_YFP2-LIB3_Index_N704_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N704_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample111_YFP2-LIB3_Index_N704_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N704_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Old MS7080 NMN-1

description:
QD345-07
processed data file: TMM_normalized_reads_count_per_million.xlsx

value: Old-NMN rejuvenation

value: NMN


title: Old MS7080 NMN-2

description:
QD345-08
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Old MS7080 NMN-3

description:
QD345-09
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Sample113_YFP2-LIB3_Index_N704_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N704_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample114_YFP2-LIB3_Index_N703_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N703_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample110_YFP2-LIB3_Index_N703_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N703_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Old MS7080 CTR-2

description:
QD345-05
processed data file: TMM_normalized_reads_count_per_million.xlsx

value: Old


title: Old MS7080 CTR-3

description:
QD345-06
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Old MS7080 Parabiosis-1

description:
QD345-10
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Old MS7080 CTR-1

description:
QD345-04
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Sample108_YFP2-LIB3_Index_N702_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N702_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Young MS7080 CTR-1

description:
QD345-01
processed data file: TMM_normalized_reads_count_per_million.xlsx

value: Young


title: Young MS7080 CTR-2

description:
QD345-02
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Young MS7080 CTR-3

description:
QD345-03
processed data file: TMM_normalized_reads_count_per_million.xlsx


title: Sample109_YFP2-LIB3_Index_N702_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N702_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample107_YFP2-LIB3_Index_N702_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N702_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample106_YFP2-LIB3_Index_N703_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N703_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample105_YFP2-LIB3_Index_N703_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N703_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample104_YFP2-LIB3_Index_N701_S506

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N701_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample102_YFP2-LIB3_Index_N702_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N702_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample101_YFP2-LIB3_Index_N701_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N701_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample103_YFP2-LIB3_Index_N701_S504

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N701_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample100_YFP1-LIB_1_Index_N711_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N711_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample99_YFP2-LIB3_Index_N701_S503

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N701_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample98_YFP1-LIB_1_Index_N712_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N712_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample112_YFP2-LIB3_Index_N705_S505

description:
FCH7W2YBBXX_L6_YFP2-LIB3_Index_N705_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample95_YFP1-LIB_1_Index_N710_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N710_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample96_YFP1-LIB_1_Index_N711_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N711_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample97_YFP1-LIB_1_Index_N712_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N712_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample93_YFP1-LIB_1_Index_N711_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N711_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample92_YFP1-LIB_1_Index_N711_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N711_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample86_YFP1-LIB_1_Index_N709_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N709_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample88_YFP1-LIB_1_Index_N709_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N709_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample87_YFP1-LIB_1_Index_N709_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N709_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample91_YFP1-LIB_1_Index_N712_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N712_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample84_YFP1-LIB_1_Index_N708_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N708_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample83_YFP1-LIB_1_Index_N709_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N709_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample78_YFP1-LIB_1_Index_N706_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N706_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample79_YFP1-LIB_1_Index_N707_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N707_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample89_YFP1-LIB_1_Index_N710_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N710_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample90_YFP1-LIB_1_Index_N710_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N710_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample77_YFP1-LIB_1_Index_N708_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N708_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample80_YFP1-LIB_1_Index_N708_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N708_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample82_YFP1-LIB_1_Index_N707_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N707_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample76_YFP1-LIB_1_Index_N707_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N707_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample94_YFP1-LIB_1_Index_N712_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N712_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample71_YFP1-LIB_1_Index_N706_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N706_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample74_YFP1-LIB_1_Index_N706_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N706_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample73_YFP1-LIB_1_Index_N706_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N706_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample72_YFP1-LIB_1_Index_N705_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N705_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample70_YFP1-LIB_1_Index_N704_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N704_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample69_YFP1-LIB_1_Index_N705_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N705_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample85_YFP1-LIB_1_Index_N710_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N710_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample68_YFP1-LIB_1_Index_N704_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N704_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample67_YFP1-LIB_1_Index_N705_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N705_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample65_YFP1-LIB_1_Index_N704_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N704_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample81_YFP1-LIB_1_Index_N708_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N708_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample63_YFP1-LIB_1_Index_N703_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N703_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample64_YFP1-LIB_1_Index_N703_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N703_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample61_YFP1-LIB_1_Index_N704_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N704_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample56_YFP1-LIB_1_Index_N701_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N701_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample60_YFP1-LIB_1_Index_N703_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N703_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample62_YFP1-LIB_1_Index_N702_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N702_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample59_YFP1-LIB_1_Index_N703_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N703_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample57_YFP1-LIB_1_Index_N701_S506

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N701_S506
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample58_YFP1-LIB_1_Index_N702_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N702_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample75_YFP1-LIB_1_Index_N707_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N707_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample55_YFP1-LIB_1_Index_N702_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N702_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: 101027 edge2 [edge2]

description:
processed data file:
Clone raw counts.xlsx
edge2_USR17009709L_HCCVFDMXX

data_processing:
bcl2fastq version 1.8.4 software from Illumina to create the Fastq files
Raw FASTQ files were trimmed with TrimGalore! version 0.6.2 with parameters --paired --trim1
Trimmed FASTQ files were aligned with STAR version 2.5.4b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated with Cufflinks version 2.2.1 with parameters --library-type fr-firststrand -G -L
Differential expression was calculated with Cuffdiff using default parameters
Genome_build: Gencode GRCh38 p7 Release25
Supplementary_files_format_and_content: tab delimited Excel files containing raw count values for each sample and Ensembl gene identifier

source_name: Edge clone

extract_protocol:
Total RNA was extracted from cells using the TRIzol Plus RNA Purification System (Invitrogen).
RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).  RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).  RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).  RNA integrity was checked by Agilent Bioanalyzer 2100, only samples with clean rRNA peaks were used.  Libraries for RNA-seq were prepared according to KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system. Final library quality and quantity were analyzed by Agilent Bioanalyzer 2100 and Life Technologies Qubit3.0 Fluorometer, respectively. 150 bp Paired-end sequencing was performed on Illumina HiSeq 4000 (Illumnia Inc., San Diego, CA).

tag: tisue/cell type

value: Edge clone


title: 101027 edge3 [edge3]

description:
processed data file:
Clone raw counts.xlsx
edge3_USR17009710L_HCCTGDMXX


title: 101027 edge6 [edge6]

description:
processed data file:
Clone raw counts.xlsx
edge6_USR17009711L_HCCTGDMXX


title: Sample54_YFP1-LIB_1_Index_N702_S504

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N702_S504
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample53_YFP1-LIB_1_Index_N701_S505

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N701_S505
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: 101027 core5 [core5]

description:
processed data file:
Clone raw counts.xlsx
core5_USR17009713L_HCCVFDMXX

source_name: Core clone

value: Core clone


title: 101027 core6 [core6]

description:
processed data file:
Clone raw counts.xlsx
core6_USR17009714L_HCCTGDMXX


title: Sample 51_N712_N506_CELL51

description:
Index_N712_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt

source_name: WT renin cell


title: 101027 core4 [core4]

description:
processed data file:
Clone raw counts.xlsx
core4_USR17009712L_HCCTGDMXX


title: 1051 edge11 [OtC1042]

description:
processed data file:
Clone raw counts.xlsx
OtC1042_GGCTAC_L001-L002


title: 1051 edge9 [OtC1095]

description:
processed data file:
Clone raw counts.xlsx
OtC1095_ACAGTG_L001-L002


title: Sample 49_N712_N504_CELL49

description:
Index_N712_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample66_YFP1-LIB_1_Index_N705_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N705_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample52_YFP1-LIB_1_Index_N701_S503

description:
FCH7W7CBBXX_L1_YFP1-LIB_1_Index_N701_S503
processed data file: Counts_Ren1c_YFP_KO_salmon_01292021.txt


title: Sample 50_N712_N505_CELL50

description:
Index_N712_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 48_N712_N503_CELL48

description:
Index_N712_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 edge1 [OtB0400]

description:
processed data file:
Clone raw counts.xlsx
OtC0400_ATCACG_L001-L002


title: 1051 edge13 [OtB8866]

description:
processed data file:
Clone raw counts.xlsx
OtB8866_ATGTCA_L002


title: 1051 edge12 [OtB8865]

description:
processed data file:
Clone raw counts.xlsx
OtB8865_AGTTCC_L002


title: Sample 46_N711_N505_CELL46

description:
Index_N711_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 45_N711_N504_CELL45

description:
Index_N711_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 44_N711_N503_CELL44

description:
Index_N711_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 edge7 [OtB8863]

description:
processed data file:
Clone raw counts.xlsx
OtB8863_CTTGTA_L002


title: 1051 edge8 [OtB8864]

description:
processed data file:
Clone raw counts.xlsx
OtB8864_AGTCAA_L001-L002


title: Sample 41_N710_N504_CELL41

description:
Index_N710_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 42_N710_N505_CELL42

description:
Index_N710_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 edge2 [OtB0401]

description:
processed data file:
Clone raw counts.xlsx
OtC0401_CGATGT_L001-L002


title: 1051 core11 [OtB8861]

description:
processed data file:
Clone raw counts.xlsx
OtB8861_TAGCTT_L002


title: 1051 core9 [OtB8860]

description:
processed data file:
Clone raw counts.xlsx
OtB8860_GATCAG_L002


title: 1051 core8 [OtB8859]

description:
processed data file:
Clone raw counts.xlsx
OtB8859_ACTTGA_L002


title: Sample 39_N709_N506_CELL39

description:
Index_N709_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 43_N710_N506_CELL43

description:
Index_N710_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 edge5 [OtB8862]

description:
processed data file:
Clone raw counts.xlsx
OtB8862_R1_combined


title: Sample 38_N709_N505_CELL38

description:
Index_N709_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 47_N711_N506_CELL47

description:
Index_N711_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 core4 [OtB8857]

description:
processed data file:
Clone raw counts.xlsx
OtB8857_GCCAAT_L002


title: Sample 40_N710_N503_CELL40

description:
Index_N710_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 core2 [OtB8856]

description:
processed data file:
Clone raw counts.xlsx
OtB8856_ACAGTG_L002


title: Liver_tumor_patient 28

city: Tuebingen

first: Srinivas

middle: Reddy

last: Pallerla

state: Baden-Württemberg

address: Wilhelmstraße 27

department: Institute for Tropical Medicine

country: Germany

institute: Universitätsklinikum Tübingen

data_processing:
The normalization using three house keeping genes and fold chage gene expression between the tumor (T) and adjacent nontumor (NT) pair was determined using the relative quantification 2^-ΔΔCt method
For the normalization it uses the average of three housekeeping genes (HKG): GAPDH, ACTB, and TBP
Target gene signals normalized to housekeeping genes; deltaCt, where deltaCt = (Ct_tumor or nontumor − Ct_HKG)
Delta delta Ct (ΔΔCt)= delta Ct[tumor] - delta Ct[nontumor]

label: SYBR Green

source_name: hepatocellular carcinoma

label_protocol: For cDNA synthesis, one microgram of total RNA from each sample was reverse transcribed in 20 µL reaction using the RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. The cDNA was diluted to 1:10 with nuclease-free water and subjected to quantitative real-time PCR. The quantitative real-time PCR was performed with the LightCycler 480 Instrument II (Roche, Basel, Switzerland) in 96 well plates using a 10 µL final volume containing 0.3 µmol/L of forward and reverse primers, 2 µL of diluted cDNA and 1X SensiFAST™ SYBR® No-ROX Kit (Bioline, Memphis, TN, USA). PCR cycle parameters were initial denaturation at 94 °C for 2 min, 40 cycles at 95 °C for 10 s, and 60°C for 25 s, with the fluorescence signal acquired at the end of each cycle. A melting curve analysis was performed at the end of the amplification. All 23 genes (20 genes under investigation plus 3 housekeeping genes) were quantified in duplicates in 96 well plates having a couple of non-template reactions with ACTB primers. The primer sequences used are given in the supplementary table.

extract_protocol: Total RNA was extracted from approximately 5 mm3 of HCC tumor or adjacent normal liver tissue using 1 mL TRIzol™ reagent (Thermo Fisher Scientific, Waltham, MA, USA). Next, the tissues were homogenized with a Dounce homogenizer, and RNA was isolated according to the manufacturer’s instructions.

value: Tumor

tag: gender

value: Male

tag: aspartate aminotransferase (sgot)

tag: alanine aminotransferase (sgpt)

tag: bilirubintp

tag: bilirubintt

tag: protein

tag: albumin

tag: alpha-fetoprotein  (ng/ml)

tag: carcino embryonic antigen (ng/ml)

tag: carbohydrate antigen 19-9  (u/ml)


title: Liver_nontumor_patient 29

tag: tissue

value: Non-tumor


title: Liver_tumor_patient 30


title: Liver_tumor_patient 29


title: Liver_nontumor_patient 28


title: Sample 37_N709_N504_CELL37

description:
Index_N709_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt

tag: strain


title: Liver_tumor_patient 27


title: Liver_nontumor_patient 30


title: Sample 36_N709_N503_CELL36

description:
Index_N709_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt

tag: reporter


title: Liver_nontumor_patient 27

tag: age


title: Liver_tumor_patient 26


title: 1085 Normal [OtB8894]

description:
processed data file:
Tissue raw counts.xlsx
OtB8894_ATGTCA_L001-L002

source_name: Non-neoplastic cortical tissue

value: Non-neoplastic cortical tissue


title: 1032 Normal [OtB8893]

description:
processed data file:
Tissue raw counts.xlsx
OtB8893_AGTTCC_L001-L002


title: Liver_tumor_patien t25


title: 1210 Normal [OtB8892]

description:
processed data file:
Tissue raw counts.xlsx
OtB8892_OtB8892_AGTCAA_L002


title: 1051 core6 [OtB8858]

description:
processed data file:
Clone raw counts.xlsx
OtB8858_CAGATC_L002


title: Sample 34_N708_N505_CELL34

description:
Index_N708_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 24


title: Liver_nontumor_patient 25


title: Sample 35_N708_N506_CELL35

description:
Index_N708_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 23


title: 1078 Normal [OtB8891]

description:
processed data file:
Tissue raw counts.xlsx
OtB8891_CTTGTA_L001-L002


title: Sample 32_N708_N503_CELL32

description:
Index_N708_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 24


title: Sample 33_N708_N504_CELL33

description:
Index_N708_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 0573 Edge [OtB6798]

description:
processed data file:
Tissue raw counts.xlsx
OtB6798_ATTCCT_L001-L002

source_name: GBM edge tissue

value: GBM edge tissue


title: 1053 Edge [OtB6446]

description:
processed data file:
Tissue raw counts.xlsx
OtB6446_AGTTCC_L001-L002


title: 0573 Core [OtB6447]

description:
processed data file:
Tissue raw counts.xlsx
OtB6447_ATGTCA_L001-L002

source_name: GBM core tissue

value: GBM core tissue


title: Liver_tumor_patient 21


title: Liver_tumor_patient 22


title: Liver_nontumor_patient 22


title: Sample 31_N707_N506_CELL31

description:
Index_N707_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 23


title: Liver_nontumor_patient 26


title: 1053 Core [OtB6445]

description:
processed data file:
Tissue raw counts.xlsx
OtB6445_AGTCAA_L001-L002


title: Liver_nontumor_patient 21


title: Sample 29_N707_N504_CELL29

description:
Index_N707_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: 1051 Core [OtB6444]

description:
processed data file:
Tissue raw counts.xlsx
OtB6444_R1_combined


title: Liver_tumor_patient 20

value: Female


title: Sample 28_N707_N503_CELL28

description:
Index_N707_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 19


title: Liver_nontumor_patient 20


title: Liver_tumor_patient 19


title: Liver_tumor_patient 18


title: Liver_nontumor_patient 18


title: 1051 Edge [OtB6443]

description:
processed data file:
Tissue raw counts.xlsx
OtB6443_GGCTAC_L001-L002


title: Liver_tumor_patient 17


title: Sample 27_N706_N506_CELL27

description:
Index_N706_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 25_N706_N504_CELL25

description:
Index_N706_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 30_N707_N505_CELL30

description:
Index_N707_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 17


title: Liver_nontumor_patient 15


title: Liver_tumor_patient 16


title: Liver_tumor_patient 15


title: Liver_nontumor_patient 16


title: Liver_tumor_patient 14


title: Liver_tumor_patient 13


title: Liver_tumor_patient 12


title: Sample 22_N705_N505_CELL22

description:
Index_N705_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 12


title: Liver_nontumor_patient 13


title: Sample 21_N705_N504_CELL21

description:
Index_N705_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 11


title: Liver_tumor_patient 11


title: Sample 19_N704_N506_CELL19

description:
Index_N704_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 10


title: Liver_nontumor_patient 10


title: Sample 18_N704_N505_CELL18

description:
Index_N704_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 9


title: Sample 26_N706_N505_CELL26

description:
Index_N706_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 8


title: Liver_nontumor_patient 9


title: Sample 17_N704_N504_CELL17

description:
Index_N704_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 24_N706_N503_CELL24

description:
Index_N706_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 7


title: Sample 23_N705_N506_CELL23

description:
Index_N705_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 7


title: Liver_nontumor_patient 14


title: Sample 15_N703_N507_CELL15

description:
Index_N703_N507
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 5


title: Liver_tumor_patient 5


title: Sample 20_N705_N503_CELL20

description:
Index_N705_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 4


title: Sample 14_N703_N506_CELL14

description:
Index_N703_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 13_N703_N505_CELL13

description:
Index_N703_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_tumor_patient 6


title: Liver_tumor_patient 3


title: Liver_nontumor_patient 4


title: Liver_nontumor_patient 8


title: Sample 12_N703_N504_CELL12

description:
Index_N703_N504
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 11_N703_N503_CELL11

description:
Index_N703_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 10_N702_N507_CELL10

description:
Index_N702_N507
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 2


title: Liver_tumor_patient 2


title: Liver_nontumor_patient 1


title: Liver_tumor_patient 1


title: Sample 9_N702_N506_CELL9

description:
Index_N702_N506
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 16_N704_N503_CELL16

description:
Index_N704_N503
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Sample 8_N702_N505_CELL8

description:
Index_N702_N505
processed data file: Counts_Ren1c_YFP_WT_salmon_01292021.txt


title: Liver_nontumor_patient 6


title: Liver_nontumor_patient 3