title: MIN6 cell CPA1 Ribo-seq rep3

first: Chien-Wen

last: Chen

address: 2109 Adelbert Road

department: Genetics and Genome Sciences

data_processing:
library strategy: Ribo-seq
The data processing was done in Galaxy platform (usegalaxy.org). 1.) Size selection was done by Clip function; fragments length between 20 to 40 bases with a Linker-A sequence in the 3' end were collected.
2.) QC was done by Filter by quality function; Quality cut-off value was 20, fragments with 95 percent of bases higher than cut-off value were collected.
3.) FASTQ was converted to FASTA by FASTQ to FASTA function.
4.) Alignment was done by Bowtie2 function with the default setting. Output as BAM files.
5.) Gene counts were done by BAM-to-SAM, Cut and Group functions; in brief, each transcribe assigned by Bowtie2 in SAM file was collected. The total number of a transcribe was served as the Gene count of the transcribe.
6.) Reads per Kilobase per Million reads (RPKM) was done by Microsoft Excel. In brief, the Gene count was divied by the RNA length in kilobase according to the reference, GRCm38.P6_rna
Genome_build: GRCm38.P6_rna
Supplementary_files_format_and_content: Gene count, RPM, RPKM

source_name: MIN6 cell CPA1 Ribo-seq

growth_protocol: MIN6 cells were cultured in DMEM containing 4.5g/L glucose, 10% heat-inactivated FBS, 1mM sodium pyruvate, 0.1% β-mercaptoethanol, 2mM L-glutamine and 100U/mL of Penicillin and Streptomycin.

extract_protocol:
For mRNA-seq, poly(A) RNA was enriched from total RNA, then randon digested by alkaline buffer. For Ribo-seq, 50U/ug Rnase If was treated, then monosome was enriched before RNA extraction. RNA fragments length between 15 to 50 bases were recycled for library generation.
Ribo-seq and mRNA-seq libraries were generated by a published in-house protocol (Chen and Tanaka, Cell reports 2018).

treatment_protocol: 200uM CPA was treated directly into culture media for 1 or 18 hours before harvest.

tag: cell line/type

value: Insulinoma MIN6 cell

value: CPA 1 hour

tag: molecule subtype

value: Ribosome footprinting


title: MIN6 cell CPA18 mRNA-seq rep3

status: Public on May 20 2021

type: SRA

city: Cleveland

state: OH

country: USA

institute: Case Western Reserve University

library_source: transcriptomic

data_processing:
The data processing was done in Galaxy platform (usegalaxy.org). 1.) Size selection was done by Clip function; fragments length between 20 to 40 bases with a Linker-A sequence in the 3' end were collected.
2.) QC was done by Filter by quality function; Quality cut-off value was 20, fragments with 95 percent of bases higher than cut-off value were collected.
3.) FASTQ was converted to FASTA by FASTQ to FASTA function.
4.) Alignment was done by Bowtie2 function with the default setting. Output as BAM files.
5.) Gene counts were done by BAM-to-SAM, Cut and Group functions; in brief, each transcribe assigned by Bowtie2 in SAM file was collected. The total number of a transcribe was served as the Gene count of the transcribe.
6.) Reads per Kilobase per Million reads (RPKM) was done by Microsoft Excel. In brief, the Gene count was divied by the RNA length in kilobase according to the reference, GRCm38.P6_rna
Genome_build: GRCm38.P6_rna
Supplementary_files_format_and_content: Gene count, RPM, RPKM

molecule: polyA RNA

organism: Mus musculus

source_name: MIN6 cell CPA18 mRNA-seq

tag: treatment

value: CPA 18 hours


title: MIN6 cell CPA18 Ribo-seq rep3

molecule: total RNA

source_name: MIN6 cell CPA18 Ribo-seq


title: Sample134 [Rectal biopsy]

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Using FastQC, the single end 150 bp reads were trimmed and adapters were removed.
Reads were mapped to human genome hg19 using hisat2.
The aligned reads were converted into read counts per gene with SAMtools and HTSeq in the default union mode.
The raw read counts were normalized via trimmed mean of M-values normalization with the edgeR R package.
Further adjustment and removal of batch effects was performed with SVA and (SNM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for each sample.
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene expression for each sample.

organism: Homo sapiens

source_name: Rectal biopsy

extract_protocol:
Rectal biopsy specimens were obtained during diagnostic colonoscopy. RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced on the Illumina NextSeq as single-end 150-bp reads.

tag: individual

tag: gender

value: F

tag: age at diagnosis

tag: time of sampling

value: Baseline

tag: initial treatment

value: CS-IV

tag: colectomy

tag: disease

value: pediatric ulcerative colitis


title: MIN6 cell CPA1 mRNA-seq rep3

source_name: MIN6 cell CPA1 mRNA-seq


title: MIN6 cell control Ribo-seq rep3

source_name: MIN6 cell control Ribo-seq

value: DMSO 18 hours


title: MIN6 cell control mRNA-seq rep3

source_name: MIN6 cell control mRNA-seq


title: Sample133 [Rectal biopsy]


title: Sample154 [Rectal biopsy]

value: 52wk FU

value: CS-Oral


title: MIN6 cell CPA18 Ribo-seq rep2


title: Sample132 [Rectal biopsy]

value: M


title: 2D_replated_Epicardium-quantseq [Ant_replated-80957.4-quantseq]

city: Vienna

first: Pablo

last: Hofbauer

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

description:
Ant_replated-80957.4-quantseq
mRNA

data_processing:
Trimming was performed for Smart-Seq2 experiments using trim-galore v0.5.0 and for QuantSeq 3' mRNA-Seq experiments using BBDuk v38.06 (ref=polyA.fa.gz,truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10  minlength=20).
Reads mapping to abundant sequences included in the iGenomes UCSC hg38 reference (human rDNA, human mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and UCSC gene annotation provided in the iGenomes UCSC hg38 bundle (https://support.illumina.com/sequencing/sequencing_software/igenome.html). Reads were aligned to the hg38 genome using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting for QuantSeq experiments (-s 1).
Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_counts.tsv: Tab-delimited text files with per gene read counts.

source_name: 2D replated epicardial cells (H9)

growth_protocol: ~70% confluent hPSCs were seeded at 55,000 cells/24 well plate in E8 + ROCKi (Y-27632, Tocris) 24h prior differentiation. Cells were induced with CDM medium (Mendjan et al. 2014) containing FGF2 (30 ng/ml, Cambridge University), LY294002 (7.5 µM, Tocris), BMP4 (10 ng/ml, R&D Systems) and CHIR99021 (1.5 µM, Tocris) (similar to Iyer et al., 2016.). Following 36h-40h, differentiation medium was exchanged to CDM medium containing BMP4 (10ng/ml), FGF2 (8 ng/ml), Insulin (10 µg/ml), IWR-1 (1µM, Tocris) and Retinoic Acid (1 µM, Sigma Aldrich) for 2 days with medium change every day. Subsequently, the medium was changed to CDM medium containing BMP4 (10 ng/ml), Insulin (10 µg/ml) and Retinoic Acid (1 µM) for 5 days with one medium change in-between (similar to Guadix et al., 2017). For maintenance of the obtained epicardium, cells were seeded at the end of differentiation onto Bovine Fibronectin (2 µg/ml, Sigma) coated plates in CDM medium containing Insulin (10 µg/ml) and SB431542 (10 µM, Tocris) supplemented with ROCKi for the first day of seeding. This medium was termed CDM-SBI. The replated epicardium was routinely passaged at 80-90% confluency every 3-5 days at 1:3 ratio;

extract_protocol: RNA was isolated with the RNeasy Mini Kit (Qiagen, #74104). Generation of the RNA-seq libraries was performed according to manufacturer’s instructions with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, #015). After the preparation of the libraries, samples were checked for an adequate size distribution with a fragment analyzer (Advanced Analytical Technologies, Inc) and were submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing. For Smart-Seq2 analysis, 400 cells were sorted into lysis buffer and stored at -80C until further processing. Samples were QC’d/libraries prepared and sequenced by the VBCF NGS facility using a home-made Smart-Seq2 kit.

tag: genotype

value: Wild-type

tag: cell type

value: 2D replated epicardial cells (H9)

tag: sequencing type

value: quant-seq


title: 2D_replated_Epicardium-quantseq [Ant_replated-88627.5-quantseq]

description:
Ant_replated-88627.5-quantseq
mRNA


title: MIN6 cell CPA1 mRNA-seq rep2


title: MIN6 cell CPA1 Ribo-seq rep2


title: Sample131 [Rectal biopsy]


title: Las1L siRNA #1

type: RNA

city: Houston

first: Han

last: Liao

address: 6431 Fannin St.

institute: The University of Texas Health Science Center at Houston

description: Replicate #1

hyb_protocol: Standard hybridization protocol for illumina microarray

scan_protocol: Standard scanning protocol for illumina microarray

data_processing: All analyses were performed using GenomeStudio software (Illumina, Inc.)

label: Biotin

source_name: Las1L siRNA

label_protocol: Standard cRNA biotin labeling protocol for illumina microarray

growth_protocol: Cells were cultured at 37° C with 5% CO2 in Dulbecco's modified Eagle's medium (DMEM) high glucose (Hyclone) supplemented with 5% fetal bovine serum (FBS, Hyclone) and penicillin-streptomycin.

extract_protocol: Total RNA was extracted with Trizol reagent

treatment_protocol: Synthetic short interfering RNA (siRNA) oligonucleotides (Sigma) were delivered into cells with Lipofectamine RNAi Max (Invitrogen). 40 nM of siRNA oligonucleotides were transfected using the reverse transfection protocol according to the manufacturer’s instructions.

tag: cell line

value: Colorectal carcinoma

tag: sirna sequence

value: CUGAUACGCUGUAAGCUCUdTdT

tag: duration


title: Control siRNA Rep1

description: Replicate #1

source_name: Control siRNA

value: GAUCAUACGUGCGAUCAGAdTdT


title: Control siRNA Rep2

description: Replicate #2


title: Sample135 [Rectal biopsy]


title: MIN6 cell CPA18 mRNA-seq rep2

value: Insulinoma MIN6 cell


title: Las1L siRNA #2

description: Replicate #1

value: CAUUUAUACCCAGAGUGGAdTdT


title: MIN6 cell control Ribo-seq rep2

value: Ribosome footprinting


title: MIN6 cell control mRNA-seq rep2


title: Sample130 [Rectal biopsy]

value: F


title: MIN6 cell CPA18 Ribo-seq rep1

value: CPA 18 hours


title: 2D_replated_Epicardium-quantseq [Ant_replated-80956.3-quantseq]

description:
Ant_replated-80956.3-quantseq
mRNA


title: MIN6 cell CPA1 Ribo-seq rep1

value: CPA 1 hour


title: Sample129 [Rectal biopsy]

value: Baseline

value: pediatric ulcerative colitis


title: MIN6 cell control Ribo-seq rep1

value: DMSO 18 hours


title: MIN6 cell CPA1 mRNA-seq rep1


title: 2D_replated_Epicardium-quantseq [Ant_replated-88624.2-quantseq]

description:
Ant_replated-88624.2-quantseq
mRNA


title: 2D_replated_Epicardium-quantseq [Ant_replated-88628.6-quantseq]

description:
Ant_replated-88628.6-quantseq
mRNA


title: Sample127 [Rectal biopsy]


title: Sample128 [Rectal biopsy]


title: Ovary α-FOXL2 ChIP-seq (Ad)

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
processed data file:
Supplementary_Table_2.xlsx

library_source: genomic

data_processing:
For each of the experiments, reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). STAR (v2.7.2a), BWA mem (v0.7.12) and HiC-Pro (v2.11.4) were used to map transcriptomic (RNA-seq), genomic (ChIP-seq, ATAC-seq) and 3D (Hi-C) trimmed reads to the GRCm38 (mm10) genome respectively
The GENCODE M23 gene annotation set was used to estimate strand-specific gene expression data in the RNA-seq data with the Bioconductor package RSubread (v1.28.1) and to assign the locations of nearby genes in the ATAC-seq datasets. For ChIP-seq and ATAC-seq experiments, duplicated reads were removed with Picard MarkDuplicates (v2.17.10) and low quality reads (MAPQ < 55) or reads that mapped to the mitochondrial genome were removed with SAMtools (v1.0).
MACS2 (v2.1.1.20160309) was used to call peaks in the ChIP-seq and ATAC-seq datasets using the parameters ‘-call-summits -m 2 20’ and ‘--nomodel –broad’ respectively
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tables of expression values and fold changes in gene expression, bigWig Coverage files and called peaks.

molecule: genomic DNA

source_name: Ovary

extract_protocol: Cells were fixed with 1% methanol-free formaldehyde in PBS (Thermo scientific #28906) for five minutes at RT with rotation.  Fixation was stopped by addition of glycine to 0.125M and rotation at RT for 10 min.  After pelleting, cells were washed in PBS and stored at -80o C until use.  Sertoli cell ChIP was performed with about 2.5 million cells and granulosa cell ChIP with about 1 million cells.  Nuclei were prepared from the fixed cells and chromatin was sheared to an average size of 300-400 bp in a Covaris S220 according to the manufacturer’s recommendations.  After shearing, the lysate was diluted 1:3 with complete DOC RIPA (37) and the sample was centrifuged at 21,000g for ten minutes at 4o C to pellet any insoluble material.  The supernatant was transferred to a fresh siliconized tube and the ChIP was initiated with the addition of ~1 ug of the relevant antibody and rotated at 4o C overnight.  Samples were then spun at 21,000g for 10 min. to pellet insoluble material and supernatant was mixed with 20 ul Protein A Dynabeads (Invitrogen, 10002D) previously blocked with BSA and yeast tRNA to inhibit non-specific binding.  After incubation at 4o C for 60 min. with rotation to allow association of protein A with the antibody, beads were applied to a magnet and washed sequentially as described previously (37).  After elution and cross link reversal, sequencing libraries were prepared using the Hyper Prep Kit (KAPA Biosystems, KK8502). Whole gonad ChIP-seq was performed essentially the same as for primary cells ChIP-seq except gonads from 2-3 animals were pooled and fixed in 1% paraformaldehyde (Electron Microscopy Sciences #15710) for 10 min. (ESR2 and FOXL2) or fixed in 2 mM disuccinimidyl glutarate (DSG, ThermoFisher Scientific #20593) at RT for 45 min. followed by 1% paraformaldehyde fixation at RT for 15 minutes (SOX9).  After quenching the fix with 0.125M glycine, chromatin was sheared to an average size of 300-500 bp using a tip sonicator.

tag: genoype

value: wild type

tag: strain background

value: Mixed 129Sv and C57Bl/6J

tag: tamoxifen time point

tag: antibody

value: AVIVA ARP39574

tag: age

value: Adult


title: MIN6 cell CPA18 mRNA-seq rep1

tag: cell line/type

tag: treatment


title: Ovary α-ESR2 ChIP-seq (Ad)

value: AVIVA ARP37039


title: Epicardium_cardiac_mesoderm-quantseq [Ant_meso-115473.5-quantseq]

description:
Ant_meso-115473.5-quantseq
mRNA

source_name: Epicardium cardiac mesoderm (H9)

value: Epicardium cardiac mesoderm (H9)

value: quant-seq


title: Epicardium_cardiac_mesoderm-quantseq [Ant_meso-80945.4-quantseq]

description:
Ant_meso-80945.4-quantseq
mRNA

value: Wild-type


title: Epicardium_cardiac_mesoderm-quantseq [Ant_meso-80944.3-quantseq]

description:
Ant_meso-80944.3-quantseq
mRNA


title: MV90_D30_Ctrl_5

city: Leipzig

first: Jana

last: Schor

state: Saxony

address: Permoserstr. 15

department: Molecular Systems Biology

country: Germany

institute: Helmholtz Centre for Environmental Research

data_processing:
For demultiplexing we used bcl2fastq (release 2.20), which is provided by Illumina.  Sequencing adapters were trimmed using the cutadapt (release 1.5) software, and subsequent quality control was performed using the fastqc program (release 0.11.2) and the fastx-toolkit (release 0.013). Reads were aligned to the human genome (UCSC Human Dec. 2013 GRCh38/hg38 Assembly) using the hisat2 mapping tool (release 2.1.0) and subsequently sorted by name and genomic location using samtools (release 1.1).
New transcripts were generated with the stringtie tool (release 1.3.3, reference annotation: Gencode v26), and sample wise assemblies were merged applying stringtie-merge. Subsequently, the new transcripts were annotated with respect to their relative genomic position to known genes using cuffcompare (2.2.1). Transcripts that entirely fall within a reference intron, are intergenic, and those that overlap an exon of a known gene on the opposite strand were kept. The number of reads that overlap either a new transcript or a known gene from the reference annotation were counted using the htseq-count program (0.6.1).
Genome_build: UCSC Mouse Dec. 2011 GRCm38/mm10 Assembly
Supplementary_files_format_and_content: Tab-delimited text files include count values for each Sample.

growth_protocol: Retina organoids were differentiated (for protocol see: Völkner et al, Stem Cell Reports, 2016) frompluripotent mESC (E14Tg2a, wildtype)

extract_protocol:
Samples were taken at Day 20 (Ctrl only), 22, 25 and 30 of differentiation. At each timepoint per experimental condition 6 individual organoids were sampled. Organoids were lysed in 100µl TRIzol by mortar-pestle homogenization, RNA was isolated using miRNeasy Kit (Qiagen) and Maxtract High Density tubes (Qiagen), residual DNA was removed using Ambion TURBO DNA-free Kit (Thermo Fisher) and RNA cleaned up by ethanol-precipitation.
The RNA integrity for each sample was controlled with the RNA 6000 Nano Assay and the Agilent 2100 Bioanalyzer (Agilent Technologies). 100ng total RNA was used for rRNA depletion. Ribosomal RNAs were removed from total RNA. A strand-specific library using the Ribo-Zero Gold H/M/R Magnetic Kit (Illumina, San Diego, CA, USA). A strand-specific library was prepared using the ScripSeqv2 Kit (Illumina), was checked by Agilent 2100 Bioanalyzer system with a High Sensitivity DNA Kit (Agilent). Library concentration was determined by Qubit 2.0 instrument using the Quant-iT dsDNA High Sensitivity kit (Thermo Fisher Scientific).  size selected in a range of 200-600 bp using preparative agarose gel in combination with MinElute Gel Extraction Kit (Qiagen).

treatment_protocol: Only solvent water has been added during time

tag: tissue

value: retina

value: Development day 30

value: Control


title: Sample125 [Rectal biopsy]

tag: individual

tag: gender

value: M

tag: age at diagnosis

tag: time of sampling

tag: initial treatment

value: CS-IV


title: Sample126 [Rectal biopsy]

tag: colectomy

tag: disease


title: Epicardium_cardiac_mesoderm-quantseq [Ant_meso-88610.2-quantseq]

description:
Ant_meso-88610.2-quantseq
mRNA

tag: genotype

tag: cell type

tag: sequencing type


title: MV90_D30_Ctrl_3


title: Sample123 [Rectal biopsy]

value: CS-Oral


title: 2D_replated_Epicardium-quantseq [Ant_replated-88623.1-quantseq]

description:
Ant_replated-88623.1-quantseq
mRNA

value: 2D replated epicardial cells (H9)


title: MV90_D30_Ctrl_4


title: MV90_D30_Ctrl_6


title: Epicardium_cardiac_mesoderm-quantseq [Ant_meso-88609.1-quantseq]

description:
Ant_meso-88609.1-quantseq
mRNA


title: MV90_D30_Ctrl_2


title: MV90_D25_Ctrl_6

value: Development day 25


title: MIN6 cell control mRNA-seq rep1

value: Insulinoma MIN6 cell

value: DMSO 18 hours


title: Sample122 [Rectal biopsy]

value: Baseline

value: pediatric ulcerative colitis


title: MV90_D25_Ctrl_4


title: Epicardium_mesoderm_induction-quantseq [Ant_ind-115472.6-quantseq]

description:
Ant_ind-115472.6-quantseq
mRNA

source_name: Epicardium mesoderm induction (H9)

value: Epicardium mesoderm induction (H9)


title: Epicardium_mesoderm_induction-quantseq [Ant_ind-115471.5-quantseq]

description:
Ant_ind-115471.5-quantseq
mRNA


title: Sample121 [Rectal biopsy]

value: F


title: MV90_D25_Ctrl_3


title: RNAi-MTA_Input_Rep3

city: Beijing

first: Leilei

last: Zhou

state: Beijing

address: No. 20 Nanxincun, Xiangshan, Haidian District

department: Institute of botany

country: China

institute: Chinese Academy of Sciences

data_processing:
For data analysis, the quality of raw sequencing reads was initially assessed by FastQC tool (version 0.11.7; http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adaptors and low-quality bases with a score < 20 were trimmed using Cutadapt (version 1.16), and then short reads with a length < 18 nucleotides or reads containing ambiguous nucleotides were filtered out by Trimmomatic (version 0.30).
The remaining reads were aligned to the strawberry reference genome v2.0.a1 (ftp://ftp.bioinfo.wsu.edu/species/Fragaria_vesca/Fvesca-genome.v2.0.a1) by Burrows Wheeler Aligner (BWA; version 0.30). Mapping quality (MAPQ) of all aligned reads was concurrently evaluated, and only uniquely mapped reads with a MAPQ ≥ 13 were retained for subsequent analysis.
The identification of m6A peaks was carried out by MACS software (version 2.0.10), using the corresponding input as a control. High-confidence peaks were obtained by a stringent cutoff threshold for MACS-assigned false discovery rate (FDR) < 0.05.
PeakAnalyzer (version 2.0) was applied to annotate the identified peaks to the strawberry genome annotation file (ftp.bioinfo.wsu.edu/species/Fragaria_vesca/Fvesca-genome.v2.0.a2/genes/).
Genome_build: Fvesca-genome v2.0.a1
Supplementary_files_format_and_content: bigWig files

organism: Fragaria x ananassa

source_name: Total RNA from the RNAi-MTA fruit

growth_protocol: Grown in a standard greenhouse.

extract_protocol:
Total RNA was extracted with the plant RNA extraction kit (Magen, R4165-02) from the MTA RNAi strawberry fruits and the controls, respectively. mRNA was isolated from the total RNA and then fragmented, followed by immunoprecipitation with specific anti-m6A antibody (Synaptic Systems, 202003).
For library construction, 50 ng of immunoprecipitated mRNAs or pre-immunoprecipitated mRNAs (input control) were used for library construction with NEBNext ultra RNA library prepare kit for Illumina (NEB, E7530). High-throughput sequencing was performed on the Illumina HiSeq X sequencer with a paired-end read length of 150 bp according to the standard protocols.

tag: cultivar

value: Benihoppe

value: Fruits with the removal of attached achenes

tag: developmental stage

value: large green (LG)

tag: genotype/variation

value: RNAi-MTA


title: RNAi-MTA_Input_Rep2

tag: antibody


title: MV90_D25_Ctrl_2

value: retina

tag: age


title: Epicardium_mesoderm_induction-quantseq [Ant_ind-80940.3-quantseq]

description:
Ant_ind-80940.3-quantseq
mRNA

value: Wild-type

value: quant-seq


title: RNAi-MTA_Input_Rep1


title: Sample124 [Rectal biopsy]

value: M

value: CS-IV


title: MV90_D30_Ctrl_1

value: Development day 30

value: Control


title: Sample119 [Rectal biopsy]


title: RNAi-MTA_IP_Rep3

value: anti-m6A antibody


title: Sample117 [Rectal biopsy]

value: CS-Oral


title: 3D_aggregated_epicardium-quantseq [ANT_3D-115498.8-quantseq]

description:
ANT_3D-115498.8-quantseq
mRNA

source_name: 3D aggregated epicardial cells (H9)

growth_protocol: For the generation of aggregated epicardium used in the engulfment assay, day 8.5 epicardial cells were dissociated using TrypLE Express Enzyme (Gibco) and re-seeded as aggregates in AggreWell400 plates (Stem Cell Technologies) at 1000 cells/well in CDM-SBI and 5% FBS (PAA). After 2 days, on average 8-12 formed aggregates/well were transferred to ultra-low cluster 96-well plates (Corning) containing CDM-SbI, put on a shaker at 58 rpm, 37C and 5% CO2, and cultured for 1 week with medium refreshed every second day.

value: 3D aggregated epicardial cells (H9)


title: MV90_D22_Ctrl_6

value: Development day 22


title: Epicardium_mesoderm_induction-quantseq [Ant_ind-88603.1-quantseq]

description:
Ant_ind-88603.1-quantseq
mRNA

value: Epicardium mesoderm induction (H9)


title: MV90_D25_Ctrl_1

value: Development day 25


title: Sample118 [Rectal biopsy]

value: Baseline

value: pediatric ulcerative colitis


title: RNAi-MTA_IP_Rep2

value: Benihoppe

value: Fruits with the removal of attached achenes

value: large green (LG)


title: Sample116 [Rectal biopsy]

value: F


title: MV90_D25_Ctrl_5

value: retina


title: MV90_D22_Ctrl_4


title: 3D_aggregated_epicardium-quantseq [ANT_3D-115497.7-quantseq]

description:
ANT_3D-115497.7-quantseq
mRNA

value: quant-seq


title: Sample115 [Rectal biopsy]

value: CS-IV


title: MV90_D22_Ctrl_3


title: Control_Input_Rep3

source_name: Total RNA from the control fruit


title: RNAi-MTA_IP_Rep1

value: RNAi-MTA


title: Epicardium_mesoderm_induction-quantseq [Ant_ind-80941.4-quantseq]

description:
Ant_ind-80941.4-quantseq
mRNA

value: Wild-type


title: 3D_aggregated_epicardium-quantseq [ANT_3D-115496.6-quantseq]

description:
ANT_3D-115496.6-quantseq
mRNA


title: Sample114 [Rectal biopsy]

value: M


title: Sample120 [Rectal biopsy]

value: CS-Oral


title: MV90_D22_Ctrl_2

value: Control


title: Control_Input_Rep2


title: Sample113 [Rectal biopsy]


title: 3D_aggregated_epicardium-quantseq [ANT_3D-115495.5-quantseq]

description:
ANT_3D-115495.5-quantseq
mRNA

value: 3D aggregated epicardial cells (H9)


title: Control_Input_Rep1


title: 3D_aggregated_epicardium-quantseq [ANT_3D-88636.4-quantseq]

description:
ANT_3D-88636.4-quantseq
mRNA


title: MV90_D22_Ctrl_5

value: Development day 22


title: MV90_D22_Ctrl_1


title: Epicardium_mesoderm_induction-quantseq [Ant_ind-88604.2-quantseq]

description:
Ant_ind-88604.2-quantseq
mRNA

value: Epicardium mesoderm induction (H9)


title: MV90_D20_6

value: Development day 20


title: Control_IP_Rep3

value: anti-m6A antibody


title: 3D_aggregated_epicardium-quantseq [ANT_3D-88635.3-quantseq]

description:
ANT_3D-88635.3-quantseq
mRNA


title: Control_IP_Rep2

value: Benihoppe


title: MV90_D20_4


title: Control_IP_Rep1

value: Fruits with the removal of attached achenes


title: MV90_D20_5


title: 3D_aggregated_epicardium-quantseq [ANT_3D-88632.2-quantseq]

description:
ANT_3D-88632.2-quantseq
mRNA


title: MV90_D20_3


title: 3D_aggregated_epicardium-quantseq [ANT_3D-88631.1-quantseq]

description:
ANT_3D-88631.1-quantseq
mRNA


title: MV90_D20_2


title: induced_Pluripotent Stem Cells_WTC-smartseq [Pluri_WTC-103366.1-smartseq]

description:
Pluri_WTC-103366.1-smartseq
mRNA

source_name: induced pluripotent stem cells (WTC)

growth_protocol: Human pluripotent stem cell lines (H9, WiCell; WT and modified WTC, Allen Institute for Cell Science) were cultured in a modified in-house medium based on the E8 culture system (Thomson 2008). The original E8 recipe was supplemented with 0.5% BSA (Europa Biosciences) and in-house produced FGF2. Cells were grown on either Corning or Eppendorf tissue culture-treated plates coated with Vitronectin (Stem Cell Technologies) and passaged using either TrypLE Express Enzyme (Gibco) or PBS-EDTA every 3-4 days.

value: induced pluripotent stem cells (WTC)


title: induced_Pluripotent Stem Cells_WTC-smartseq [Pluri_WTC-103367.3-smartseq]

description:
Pluri_WTC-103367.3-smartseq
mRNA


title: Sample109 [Rectal biopsy]

value: F

value: Baseline

value: pediatric ulcerative colitis


title: Sample107 [Rectal biopsy]


title: Sample106 [Rectal biopsy]


title: MV90_D20_1

value: retina


title: induced_Pluripotent Stem Cells_WTC-smartseq [Pluri_WTC-103365.2-smartseq]

description:
Pluri_WTC-103365.2-smartseq
mRNA


title: Sample105 [Rectal biopsy]


title: Sample111 [Rectal biopsy]


title: 3D GFP-/Tomato- cells from CMEC organoid-smartseq [Neither_WTC-103370.3-smartseq]

description:
Neither_WTC-103370.3-smartseq
mRNA

source_name: Non-Cardiomyocyte/Non-Endothelial population from cardiac organoids containing cardiomyocytes and endothelial cells (WTC)

growth_protocol: Pluripotency maintenance medium was refreshed 6h prior to seeding cells. Then, 2500-3000 hPSC were seeded into ultra-low cluster 96-well plates (Corning) in FLyAB(Ins) medium with CHIR99021 (5-6 µM for WTC, 1.5 µM for H9) and ROCKi (5 µM) for 36h-40h. Next, medium was exchanged to BFIIWPRa with the addition of VEGF-A (200 ng/ml, Peprotech) for 4 days with medium exchanged every day. Subsequently, medium was exchanged to BFI + VEGF-A (100 ng/ml) for 2 days with a medium change after 1 day. For maintenance, CDM medium with 100 ng/ml of VEGF-A was used and exchanged every second day. For Smart-Seq2 analysis, Day 7.5 organoids containing cardiomyocytes and endothelial cells were dissociated using the StemDiff cardiomyocyte dissociation kit (Stem Cell Technologies, Catalog #05010) and GFP+ CMs and Tomato+ ECs as well as GFP-/Tomato- cells were FACS-sorted into lysis buffer.


title: bre1-3

first: Huan

last: Wang

address: NO.1 Beichen West Road

institute: institute of microbiology

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 (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Verticillium dahliae VdLs.17 (assembly ASM15067v2)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Verticillium dahliae

source_name: conidia

extract_protocol:
Fungal sample were collected from 5 days cultures grown on liquid Czapek-Dox medium. Total RNA was extracted using fungal RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain


title: Sample112 [Rectal biopsy]

value: CS-IV


title: Sample104 [Rectal biopsy]


title: Dux KO #2 mESC doxorubicin, 2

city: Salt Lake City

first: Edward

middle: John

last: Grow

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

institute: University of Utah

data_processing:
Bbduk adapter Trimming
Tophat2 (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant)
and counts for each transcript were generated using “Get datasets”
Differential expression analysis was performed using DESEq2.
Genome_build: mm10
Supplementary_files_format_and_content: 20190106-fpkm-matrix-RNAseq-with-DEseq-results-v12 (FPKM and statistical analysis), 20190102-count-file-mESC-C4dox-vsDUXKOdox-v10 (raw counts used for DESeq2)

source_name: E14 mouse embryonic stem cells

growth_protocol: Mycoplasma-free E14 mESCs were cultured on gelatin in 2i+LIF medium containing Gibco KO-DMEM with nonessential amino acids, 2-mercaptoethanol, and dipeptide glutamine, and were supplemented with 15% ES-grade FBS, leukemia inhibitory factor (LIF) (Thermo Fisher), 1 mM PD0325901 (Sigma-Aldrich), and 3 mM CHIR99021 (Sigma-Aldrich). Stable cell lines were selected using puromycin (Thermo Fisher Scientific A11138-03) at 0.5-1 ug/mL, Geneticin (Life Technologies 10131-035) at 100-200ug/mL, or Blasticidin (Fisher Scientific B12150-0.1) at 1.5-3ug/mL.

extract_protocol:
Trizol
libraries generated according to manufacturer instructions: poly-A selected RNA using NEB-next kit (New England Biolabs e7500s).

treatment_protocol: mESC were treated with 1uM doxorubicin for 6 hours and then media was replaced with non-drug containing media. Control cells were treated with DMSO vehicle control for 6 hours and then media was replaced.

value: Dux KO

value: mESC

tag: agent

value: doxorubicin


title: Sample110 [Rectal biopsy]

source_name: Rectal biopsy

tag: individual

value: M


title: Dux KO #1 mESC doxorubicin, 1


title: bre1-2


title: Sample103 [Rectal biopsy]

tag: gender


title: 3D GFP-/Tomato- cells from CMEC organoid-smartseq [Neither_WTC-103362.2-smartseq]

description:
Neither_WTC-103362.2-smartseq
mRNA

value: Non-Cardiomyocyte/Non-Endothelial population from cardiac organoids containing cardiomyocytes and endothelial cells (WTC)


title: 3D GFP-/Tomato- cells from CMEC organoid-smartseq [Neither_WTC-103359.1-smartseq]

description:
Neither_WTC-103359.1-smartseq
mRNA


title: bre1-1


title: Sample102 [Rectal biopsy]

tag: age at diagnosis

value: CS-Oral


title: Control 1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: 4hr CHX treatment

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Agilent Arabidopsis thaliana Gene Expression Microarray 8x60K (AMADID No: 37661) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX : 75th percentile shift method.

organism: Arabidopsis thaliana

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: 9-day-old seedlings grown on MS media.

extract_protocol: RNA was prepared using the Spectrum Plant Total RNA Kit following the manufacturer's recommendations.

treatment_protocol: 4hr of CHX or CHX + DEX treatment in liquid 1/2MS media under continuous agitation.

tag: tissue

value: Seedlings

value: 9 days old

tag: treatment

value: Cycloheximide


title: Dux KO #1 mESC control, 1

value: control


title: Dux KO #2 mESC control, 2


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88969.8-smartseq]

description:
HCMEC-88969.8-smartseq
mRNA

growth_protocol: Human cardiac microvascular endothelial cells (HCMEC) were obtained from PromoCell (PC-C-12285 HCMEC-c) and cultured according to manufacturer’s instruction using Endothelial Cell Growth Medium MV (PromoCell, PC-C-22020). For Smart-Seq2 analysis, HCMEC were dissociated with TrypLE Express Enzyme (Gibco) and FACS-sorted into lysis buffer.

value: Wild-type


title: Control 2

description: 4hr CHX treatment


title: Treated 1

description: 4hr CHX + DEX treatment

value: Cycloheximide + Dexamethasone


title: Sample101 [Rectal biopsy]

value: F

tag: time of sampling

tag: initial treatment

tag: colectomy


title: V592-3

tag: genotype

value: wild type


title: V592-2


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88968.7-smartseq]

description:
HCMEC-88968.7-smartseq
mRNA

tag: cell type

tag: sequencing type


title: p53 KO #1 mESC doxorubicin, 1

value: p53 KO


title: Sample100 [Rectal biopsy]

value: Baseline

tag: disease

value: pediatric ulcerative colitis


title: V592-1


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88967.6-smartseq]

description:
HCMEC-88967.6-smartseq
mRNA


title: Treated 2

description: 4hr CHX + DEX treatment


title: Sample099 [Rectal biopsy]


title: p53 KO #2 mESC control, 2


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88965.4-smartseq]

description:
HCMEC-88965.4-smartseq
mRNA


title: p53 KO #1 mESC control, 1


title: A10KO_14

city: Nanjing

first: Zichun

last: Hua

address: Xianlin Road 163# Nanjing University Xianlin Campus

department: School of Life Science

institute: Nanjing University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Melanoma

extract_protocol:
Total RNAs from WT and ANXA10 KO B16F10 cells were extracted using a Trizol reagent kit (Invitrogen, USA), followed by DNase I (TaKaRaBio, Japan) treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88966.5-smartseq]

description:
HCMEC-88966.5-smartseq
mRNA


title: A10KO_13


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88964.3-smartseq]

description:
HCMEC-88964.3-smartseq
mRNA


title: WT mESC doxorubicin, 2

value: WT


title: WT_3


title: WT mESC control, 2

value: mESC


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88962.1-smartseq]

description:
HCMEC-88962.1-smartseq
mRNA


title: A10KO_1


title: p53 KO #2 mESC doxorubicin, 2

value: doxorubicin


title: WT mESC doxorubicin, 1


title: Sample097 [Rectal biopsy]

value: M


title: WT mESC control, 1


title: 2D Human cardiac microvascular endothelial cells (HCMEC)-smartseq [HCMEC-88963.2-smartseq]

description:
HCMEC-88963.2-smartseq
mRNA


title: Sample093 [Rectal biopsy]

value: CS-IV


title: Sample095 [Rectal biopsy]


title: Sample096 [Rectal biopsy]


title: Sample094 [Rectal biopsy]


title: WT_2


title: 3D Tomato+ Endothelial cells from CMEC organoid-smartseq [EC_WTC_Tomato-103364.4-smartseq]

description:
EC_WTC_Tomato-103364.4-smartseq
mRNA

source_name: Endothelial cells from cardiac organoids containing cardiomyocytes and endothelial cells (WTC)


title: 3D Tomato+ Endothelial cells from CMEC organoid-smartseq [EC_WTC_Tomato-103369.3-smartseq]

description:
EC_WTC_Tomato-103369.3-smartseq
mRNA

value: Endothelial cells from cardiac organoids containing cardiomyocytes and endothelial cells (WTC)


title: 3D Tomato+ Endothelial cells from CMEC organoid-smartseq [EC_WTC_Tomato-103361.2-smartseq]

description:
EC_WTC_Tomato-103361.2-smartseq
mRNA


title: WT_1


title: E18.5_female_genitalia_1

city: Research Triangle Park

first: Ciro

middle: Maurizio

last: Amato

state: NC

address: 111 Tw Alexander Dr

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

description: cell disassociation protocol: Cell were disassociated with a 1.2 U/mL Dispase II, 1mgl/mL Collangenase IV, and 5U/mL DNAaseI cocktail.

data_processing:
Sequences were aligned with CellRanger
Data were filtered, clustered, visualized, and analyzed with Seurat V4.0
Data were analyzed with Seurat for male, female, and male+female (combined)
To analyze stage-dependent changes in gene expression, data was extracted from Seurat and processed with base R.
Genome_build: mm10
Supplementary_files_format_and_content: barcode, feature, and matrix files exported from CellRanger
Supplementary_files_format_and_content: sheet of assigned clusters for each step of analysis

source_name: external genitalia

extract_protocol: 10x Genomics

value: external genitalia

tag: genetic background

value: Sf1cre; Rosa-tdTomato; Runx1-eGFP


title: E18.5_female_genitalia_2


title: Sample091 [Rectal biopsy]


title: dQ_snf5_Stv_pH5_4

city: New York

first: Gregory

last: Brittingham

state: NY

address: 435 East 30th street

department: Cell Biology

institute: NYU Institute for Systems Genetics

description: RNA minus rRNA

data_processing:
Illumina software used for basecalling by the NYU GTC core
Sequenced reads were aligned to the sacCer2 genome using standard kallisto methods
Downstream visualization and analysis was done using R (3.2.2). Differential gene expression analysis, heat maps and volcano plots were created using DESeq2using a generalized linear negative binomial model on raw counts where a wald test was used to determine differentially expressed genes and Euclidean distance to calculate clustering for heat maps. For the purpose of this submission, the median of ratios was used to create normalized read counts.
Genome_build: SacCer2
Supplementary_files_format_and_content: Counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene for each sample (standard DESeq2 protocol). I would use abundance.tsv data calculated in kallisto then create a deseq2 object using the run_metadata.txt file to analyze.

organism: Saccharomyces cerevisiae

growth_protocol: Most experiments, unless indicated, were performed in synthetic complete media (13.4 g/L yeast nitrogen base and ammonium sulfate; 2 g/L amino acid mix and 2% glucose). Carbon starvation media was synthetic complete without dextrose and supplemented with sorbitol, a non-fermentable carbon source to avoid osmotic shock during glucose-starvation (6.7 g/L YNB + ammonium sulfate; 2g/L Amino acid mix and 100 mM Sorbitol). pH was adjusted using 5 M NaOH.

extract_protocol:
Total RNA was extracted from WT, ΔQ-snf5 and HtoA-snf5 strains during exponentially growth (+Glu) and after 4 hours of glucose starvation using a Roche Hi-Pure RNA extraction kit. Next, Poly-A selection was performed using Dynabeads and libraries were performed following manufactures indications.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Glucose starvation: Cultures were incubated in a rotating incubator at 30ΟC and grown overnight (14-16 h) to an OD between 0.2 and 0.3. Note: it is extremely important to prevent culture OD from exceeding 0.3 – and results are different if cells are allowed to saturate and then diluted back. Thus, it is imperative to obtain log phase cultures directly to obtain reproducible results. 3 milliliters of OD 0.2-0.3 culture were centrifuged at 6000 RPM for 3 minutes, re-suspended in SC Sorbitol at different pHs and washed 2 times. Finally, cells were re-suspended in 3 milliliters of SC Sorbitol. For flow cytometry, aliquots of 200 uL were taken for each time point in 96 well plates. During the course of time lapse experiments, culture aliquots were set aside at 4ΟC. LSR II – HTS were used for all measurements. 10,000 cells were measured for each time point.

value: dQ

value: Stv


title: HtoA_snf5_Stv_pH5_4

description: RNA minus rRNA

value: HtoA


title: Sample089 [Rectal biopsy]


title: 3D Tomato+ Endothelial cells from CMEC organoid-smartseq [EC_WTC_Tomato-103358.1-smartseq]

description:
EC_WTC_Tomato-103358.1-smartseq
mRNA


title: E18.5_male_genitalia_2


title: HtoA_snf5_Dex_4

description: RNA minus rRNA

value: Dex


title: E18.5_male_genitalia_1


title: Sample090 [Rectal biopsy]

value: CS-Oral


title: WT_Stv_pH7_4

description: RNA minus rRNA


title: WT_Stv_pH5_4

description: RNA minus rRNA


title: dQ_snf5_Dex_4

description: RNA minus rRNA


title: E16.5_female_genitalia_1


title: 3D GFP+ Cardiomyocytes from CMEC organoid-smartseq [CM_WTC_GFP-103360.2-smartseq]

description:
CM_WTC_GFP-103360.2-smartseq
mRNA

source_name: Cardiomyocytes from cardiac organoids containing cardiomyocytes and endothelial cells (WTC)


title: WT_Dex_4

description: RNA minus rRNA


title: E16.5_male_genitalia_2


title: 3D GFP+ Cardiomyocytes from CMEC organoid-smartseq [CM_WTC_GFP-103368.3-smartseq]

description:
CM_WTC_GFP-103368.3-smartseq
mRNA

value: Cardiomyocytes from cardiac organoids containing cardiomyocytes and endothelial cells (WTC)


title: E16.5_female_genitalia_2


title: 3D GFP+ Cardiomyocytes from CMEC organoid-smartseq [CM_WTC_GFP-103363.4-smartseq]

description:
CM_WTC_GFP-103363.4-smartseq
mRNA


title: Sample088 [Rectal biopsy]

value: F


title: Sample087 [Rectal biopsy]

value: Baseline


title: Sample092 [Rectal biopsy]

value: pediatric ulcerative colitis


title: E16.5_male_genitalia_1


title: 3D GFP+ Cardiomyocytes from CMEC organoid-smartseq [CM_WTC_GFP-103357.1-smartseq]

description:
CM_WTC_GFP-103357.1-smartseq
mRNA


title: Sample086 [Rectal biopsy]


title: HtoA_snf5_Stv_pH5_3

description: RNA minus rRNA


title: Sample084 [Rectal biopsy]


title: E14.5_female_genitalia_2


title: Sample083 [Rectal biopsy]


title: E14.5_female_genitalia_1


title: WT_Stv_pH7_2

description: RNA minus rRNA

value: WT


title: Sample085 [Rectal biopsy]


title: 2D_Anterior endothelial cells-smartseq [2D_ANT-88949.3-smartseq]

description:
2D_ANT-88949.3-smartseq
mRNA

source_name: Anterior endothelial cells differentiated from pluripotent stem cells (H9)

growth_protocol: Pluripotent stem cells were seeded at 100,000 cells/24well coated with vitronectin (Stemcell Technologies, #7180) in E8 medium supplemented with 10 µM ROCK-inhibitor (R&D/Tocris, #1254). On the following day, cells were induced with FLyABCH(Ins), 1- 3 µM CHIR99021 (R&D/Tocris, #RD-4423/10), and incubated for 36 – 40 hours. For the following two days, medium was exchanged to BFIIWPRa. Subsequently, differentiation medium comprised CDM with 200 ng/ml VEGF (Peprotech, #AF-100-20) and 2 µM Forskolin (Sigma-Aldrich, #F3917) for 2 days followed by one day of culture in CDM + 100 ng/ml VEGF. ECs were maintained in CDM supplemented with 100 ng/ml VEGF.


title: dQ_snf5_Stv_pH5_3

description: RNA minus rRNA


title: E14.5_male_genitalia_2


title: 2D_Anterior endothelial cells-smartseq [2D_ANT-88948.3-smartseq]

description:
2D_ANT-88948.3-smartseq
mRNA

value: Anterior endothelial cells differentiated from pluripotent stem cells (H9)


title: 2D_Anterior endothelial cells-smartseq [2D_ANT-88947.2-smartseq]

description:
2D_ANT-88947.2-smartseq
mRNA


title: HtoA_snf5_Stv_pH5_2

description: RNA minus rRNA


title: E14.5_male_genitalia_1


title: Sample081 [Rectal biopsy]


title: 2D_Anterior endothelial cells-smartseq [2D_ANT-88946.1-smartseq]

description:
2D_ANT-88946.1-smartseq
mRNA


title: Sample082 [Rectal biopsy]


title: K12

city: Milwaukee

first: Meetha

last: Medhora

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Radiation oncology

institute: Medical College of Wisconsin

data_processing:
Data QC and trim with trim_galore version 0.2.5
read alignment with bowtie version 1.1.1
microRNA identification with miRanalyzer version 0.3
Genome_build: rn4
Supplementary_files_format_and_content: microRNA read counts

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Kidneys were removed and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012,RS-200-0024,RS-200-0036) was used with 1 ug of total RNA for the construction of sequencing libraries.
MicroRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Un-anesthetized 11- to 12-week-old female WAG/RijCmcr rats weighing approximately 155 g were immobilized in a plastic jig and irradiated with 320-kVp orthovoltage system X-rays, with a half-value layer (HVL) of 1.4 mm Cu with a dose-rate of 1.75 Gy per min for total dose of 13 Gy to the whole body, except for one hind limb that was carefully externalized and shielded from the chamber (leg-out PBI). Rats were randomized into 3 groups (1) nonirradiated controls (0 Gy). (2) Irradiation only group (13 Gy). (3) Irradiation + lisinopril group (13 Gy + lisinopril). Lisinopril were added to the drinking water at a dose of ~24 mg m-2 day-1, which is comparable to that approved for clinical use, starting from day 7 after radiation and continued till the termination. Rats were also given daily subcutaneous injection of saline (40 ml kg-1 day-1) from days 3-7 and enrofloxacin (10 mg kg-1 day-1) up to 14 days after irradiation as supportive care.

value: Wistar - WAG/RijCmcr

value: Kidney

tag: time point

value: 35 days after irradiation

tag: radiation

value: 13 Gy leg-out PBI

tag: medication

value: Lisinopril

tag: group name

value: 13 Gy leg-out PBI + Lisinopril

value: female


title: Sample080 [Rectal biopsy]

tag: individual

tag: gender

value: M


title: K11

tag: strain

tag: tissue


title: dQ_snf5_Stv_pH5_2

description: RNA minus rRNA

value: dQ

tag: treatment

value: Stv


title: ATAC_Sperm_Sevo_7d_F2_rep1

first: Hsiao-Lin

middle: V.

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format.
Paired reads were aligned to mouse reference genome mm10 using Bowtie2, using default parameters except -X 2000 -m 1. Duplicates were removed using Picard Tools.
To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS) and mono-nucleosome (Nucleosome) fragments, we chose reads 1-115 bp 180-247 bp in length, respectively.
MACS was used for peak calling with nucleosome-free reads (Liu 2014).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage (--binSize 1 -- normalizeUsing RPGC)

source_name: Sperm

extract_protocol:
OmniATAC-seq protocol was used and Tn5 tagmented genomic DNA was extracted with phenol chloroform extraction. Per experiment, 100,000 sperm were used.
OmniATAC-seq libraries were prepared for sequencing using standard protocol.

value: Sperm

tag: condition

tag: replicate


title: Sample079 [Rectal biopsy]

tag: age at diagnosis

tag: time of sampling

value: 52wk FU

tag: initial treatment

value: CS-Oral

tag: colectomy


title: K13


title: HtoA_snf5_Dex_2

description: RNA minus rRNA

tag: genotype

value: HtoA

value: Dex


title: WT_Stv_pH5_2

description: RNA minus rRNA

value: WT


title: ATAC_Sperm_Sevo_7d_F1_rep2

tag: cell type


title: K10

tag: time point


title: K9

tag: radiation


title: WT_Dex_2

description: RNA minus rRNA


title: Sample078 [Rectal biopsy]

value: F

value: Baseline

tag: disease

value: pediatric ulcerative colitis


title: Sample077 [Rectal biopsy]


title: ATAC_Sperm_Sevo_7d_F1_rep1


title: WT_Stv_pH7_1

description: RNA minus rRNA


title: Sample076 [Rectal biopsy]


title: K8

value: Wistar - WAG/RijCmcr

value: Kidney

value: 35 days after irradiation

tag: medication

tag: group name


title: WT_Stv_pH5_1

description: RNA minus rRNA


title: ATAC_Sperm_Sevo_1d_F1_rep2


title: HtoA_snf5_Dex_1

description: RNA minus rRNA


title: K7

value: 13 Gy leg-out PBI

tag: gender


title: ATAC_Sperm_Sevo_1d_F1_rep1

tag: strain


title: ATAC_Sperm_Sevo_7d_F2_rep2


title: K6

tag: tissue

value: female


title: dQ_snf5_Dex_2

description: RNA minus rRNA

tag: treatment


title: ATAC_Sperm_control_rep2

tag: condition

value: control


title: dQ_snf5_Dex_1

description: RNA minus rRNA

value: dQ


title: ATAC_Sperm_control_rep1

tag: replicate


title: K5


title: Sample073 [Rectal biopsy]

tag: individual

tag: age at diagnosis


title: YAP+R34P-Tumor [YR3447]

city: pittsburgh

last: Prochownik

state: PA

address: 4401 Penn Avenue

department: Section of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh

description:
YR3447
YAP+R34P

data_processing:
CLC Genomics Workbench v12.0
Genome_build: Reference sequence = Mus_musculus_ensembl_v80_Sequence Gene track = mus_musculus_refseq_GRCm38.p6_Genes  mRNA track = mus_musculus_refseq_GRCm38.p6_mRNA
Supplementary_files_format_and_content: Expression Browser.xlsx

source_name: Tumor

extract_protocol:
RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic organisms or eukaryotic organisms' long-non-coding libraries, rRNA is removed using the Ribo-Zero kit that leaves the mRNA. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: FVB

tag: hdtvi plasmids


title: Sample098 [Rectal biopsy]

value: M

tag: time of sampling

tag: initial treatment

tag: colectomy


title: Sample072 [Rectal biopsy]

value: CS-IV


title: Sample071 [Rectal biopsy]


title: YAP+R34P-Tumor [YR3445]

description:
YR3445
YAP+R34P


title: K2

tag: time point

value: age matched non-radiation control

value: 0 Gy


title: Gluta neurons 4C-seq

city: München

first: Daniel

last: Lam

address: Ismaninger Straße 22

institute: Technical University Munich

data_processing:
Library strategy: 4C-seq
ATAC-seq: Reads were trimmed and aligned with bowtie2 (Langmead and Salzberg 2012), with standard parameters and a maximum fragment length of 2,000. Duplicate reads were removed with Picard.
ATAC-seq: De-duplicated reads were filtered for high quality (samtools (Li et al. 2009), MAPQ ≥ 30), nonmitochondrial chromosome, non-Y chromosome, and proper pairing (samtools flag 0 × 2).
ATAC-seq: Peaks were called with macs2 (Zhang et al. 2008, 2), and filtered out with IDR threshold of 0.1 (Li et al. 2011) and blacklist of artifactual regions in hg19.
ATAC-seq: Libraries were quality controlled by downsampling to 5 million reads and evaluating transcription start site enrichment (RefSeq) and fraction of reads in peaks.
4C-seq: Reads were trimmed with Trimmomatic v0.36 (Bolger et al. 2014), aligned with bowtie2 (Langmead and Salzberg 2012) and subsequently processed, filtered, analyzed and visualized according to Basic4Cseq (Walter et al. 2014) in R v 4.0.2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig, bedGraph

source_name: Glutamatergic neurons

growth_protocol: iPSC were maintained in mTeSR culture media (STEMCELL Technologies) on cell culture dishes coated with Matrigel (Corning) or Geltrex (Thermo Fisher). NSC cultured in complete StemPro NSC SFM (Thermo Fisher) consisting of KnockOut D-MEM/F-12 with StemPro Neural Supplement, EGF, bFGF, and GlutaMAX on Geltrex-coated cell culture dishes.

extract_protocol:
ATAC-seq: Adherent cells were dissociated with TrypLE Select Enzyme and centrifuged at 500 g for 5 min at 4°C. The cell pellet was resuspended in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged for 20 min at 500 g at 4°C. 4C-seq: Cells were dissociated to single cells with TrypLE Express and fixed in 2% formaldehyde in DPBS (Thermo Fisher) for 10 min. Glycine was added to a final concentration of 222 mM to quench the cross-linking reaction. Cells were centrifuged for 10 minutes at 400g at 4°C, the supernatant discarded, and the cell pellet resuspended in cold lysis buffer (50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, cOmplete protease inhibitor cocktail, Roche) and incubated on ice for 30 minutes. To ensure complete lysis, cells were stained with methyl green pyronin (Dianova). In the case of efficient lysis, nuclei are stained blue and cytoplasm pink. Next, lysed cells were centrifuged and the pellet was washed with DPBS and resuspended in water. NEBuffer and SDS (0.3% final concentration) were added and the samples were incubated at 37°C for 1 hr while shaking at 900 rpm with occasional pipetting to break cell aggregates. Triton X-100 (Biomol) was added to a concentration of 2.5% and samples were again incubated at 37°C for 1 hr while shaking. The first round of digestion was done with DpnII (New England Biolabs) at 37°C overnight. Digest efficiency was checked on an agarose gel. DpnII was inactivated by incubating for 20 min at 65°C. Ligation was performed with T4 ligase (Thermo Fisher) overnight at 16°C and checked on an agarose gel. Samples were then decrosslinked with Proteinase K at 65°C overnight. After DNA purification with phenol-chloroform, the second round of digestion was performed with Csp6I (Thermo Fisher). Digestion was followed by overnight ligation with T4 ligase at 16°C. Samples were purified using Amicon Ultra-15 columns (Millipore) and DNA quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher).
ATAC-seq: Purified samples were then amplified by PCR (maximum 12 cycles) using barcoded primers from the Nextera Index Kit (Illumina). To determine the optimal number of cycles for each sample, samples were first amplified for 5 cycles (5 min at 72°C, 30 sec at 98°C, and 5 cycles of 10 sec at 98°C, 30 sec at 63°C, and 1 min at 72°C). Samples amplified for 5 cycles were then subjected to qPCR (SYBR Green, Thermo Fisher). The additional number of cycles required was the number of cycles required to reach one quarter of the maximal fluorescence intensity in the first 5 cycles. The remainder of each sample was subsequently amplified for an additional 5-7 cycles. Amplified samples were purified with SPRI beads (Beckman Coulter) at a ratio 1:1.8 sample:beads, and fragment size was checked using the High Sensitivity DNA kit (Agilent). Libraries were sequenced on a HiSeq 4000 (Illumina), two samples per lane, 100 bp paired end reads. 4C-seq: To generate 4C libraries, we used 3.2 µg of DNA for PCR amplification divided into 16 PCR reactions, using Expand Long Template PCR System (Sigma Aldrich). PCR primers were designed using the MEIS1 promoter as a viewpoint and included TruSeq adapters. Primer genomic targets are shown in Fig. S3 and sequences in Table S1. PCR conditions were 2 min at 94°C, 30 cycles of 15 sec at 94°C, 1 min at 55°C, and 3 min at 68°C followed by 5 min at 68°C. Pooled libraries were purified using SPRI beads (Beckman Coulter) at a ratio of 1:1.8 sample:beads, and fragment size was checked using the High Sensitivity DNA kit (Agilent). The libraries were sequenced on an Illumina MiSeq.

treatment_protocol: For differentiation, iPSCs were grown to 90% confluence and then dissociated with TrypLE Select Enzyme for 5 minutes at 37°C. 500,000 iPS cells were plated per well of a 24 well plate in mTeSR supplemented with RevitaCell (Thermo Fisher). The next day (day 1), the medium was replaced with neural induction medium (NIM) consisting of DMEM/F12, N-2, B-27, and GlutaMAX supplements, MEM Non-Essential Amino Acids, 0.11 mM 2-mercaptoethanol, 0.05% (v/v) Bovine Serum Albumin Fraction V Solution, Penicillin-Streptomycin (all Thermo Fisher), 100 nM LDN193189 and 10 μM SB431542 (Cayman Chemical), and 2 μM XAV939 (R & D Systems). NIM was changed daily until day 5, when it was replaced with 75% NIM/25% N2 medium (DMEM/F12, N-2 supplement, 0.15% (w/v) dextrose, 55 μM 2-mercaptoethanol, Penicillin-Streptomycin). On day 7, cells were fed with 50% NIM/50% N2, and on day 9 with 25% NIM/75% N2. On day 10, cells were dissociated into a single cell suspension with TrypLE Express Enzyme and plated onto Matrigel-coated 24-well plates in 25% NIM/75% N2 supplemented with RevitaCell at 2 million cells per well. At this stage some material was harvested for (NPC stage, day 10). On day 11 the medium was replaced with N2/B27 medium (N2 medium with B-27 supplement) containing 0.65 µM purmorphamine (Cayman Chemical). On day 19-23, cells were fed daily with N2/B27 medium without purmorphamine. On day 24, cells were harvested (GE, day 24).

tag: cell type

value: iCell GlutaNeurons (Cellular Dynamics)


title: Sample070 [Rectal biopsy]

tag: disease


title: K1

tag: radiation

tag: medication


title: Sample075 [Rectal biopsy]

tag: gender


title: GABA neurons 4C-seq

source_name: GABA neurons

value: iCell GABANeurons (Cellular Dynamics)


title: YAP+L30P-Tumor [YL3450]

description:
YL3450
YAP+L30P

value: F

tag: strain


title: GE 4C-seq rep2

source_name: Ganglionic eminence cells

value: iPSC-derived GE (d24)


title: Sample069 [Rectal biopsy]

value: Baseline

value: pediatric ulcerative colitis


title: Sample074 [Rectal biopsy]


title: Δ(90)+YAP+NFE2L2_WT-Tumor [W3522]

description:
W3522
Δ(90)+YAP+NFE2L2_WT


title: Sample068 [Rectal biopsy]


title: WT_Dex_1

description: RNA minus rRNA

tag: genotype

value: wild type

value: Dex


title: Sample067 [Rectal biopsy]


title: M46018_3

first: Hongjian

address: No.1 Wenyuan Road, Xianlin University Town, Nanjing

institute: Nanjing Normal University

data_processing:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA).
PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
Genome_build: dm6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: M. luteus infected CR46018-overexpressing

extract_protocol:
RNA integrity was assessed with the RNA nano 6000 assay kit for the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Briefly, mRNA was purified from total RNA with poly T oligo-attached magnetic beads. Fragmentation was conducted at high temperature with divalent cations in 5× first-strand synthesis reaction buffer. To select cDNA fragments 370–420 bp long, library fragments were purified in an AMPure XP system (Beckman Coulter, Beverly, MA, USA). PCR was performed with Phusion high-fidelity DNA polymerase, universal PCR primers, and index (X) primer. The PCR products were purified in the AMPure XP system (Beckman Coulter, Beverly, MA, USA) and library quality was assessed in the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA). Index-coded samples were clustered on a cBot cluster generation system using a TruSeq PE cluster kit v3-cBot-HS (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The reference genome index was built and paired-end clean reads were aligned to the reference genome with Hisat2 v2.0.5. FeatureCounts v. 1.5.0-p3 enumerated the reads mapped to each gene. Differential expression analysis was performed in the DESeq2 package of R v. 1.20.0 (R Core Team, Vienna, Austria).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gal80ts; Tub> CR46018

tag: treatment

value: 12 hours after injection of M. luteus

tag: developmental stage

value: adult

tag: Sex

value: male


title: Δ(90)+YAP+NFE2L2_WT-Tumor [W3464]

description:
W3464
Δ(90)+YAP+NFE2L2_WT

value: FVB


title: K4

value: Wistar - WAG/RijCmcr

tag: tissue

value: Kidney

value: 35 days after irradiation

tag: group name

value: female


title: Δ(90)+YAP+NFE2L2_WT-Tumor [W3460]

description:
W3460
Δ(90)+YAP+NFE2L2_WT

value: M

tag: hdtvi plasmids


title: M46018_1


title: NPC 4C-seq rep1

source_name: Neural progenitor cells

value: iPSC-derived NPC (d10)


title: K3

value: age matched non-radiation control

value: 0 Gy


title: YAP+R34P-Tumor [YR3443]

description:
YR3443
YAP+R34P


title: M25C_3

source_name: M. luteus infected control flies

value: Gal80ts; Tub-Gal4/P{CaryP}attP40


title: iPSC 4C-seq rep2

source_name: Induced pluripotent stem cells

value: Induced pluripotent stem cells


title: Δ(90)+YAP+NFE2L2_WT-Tumor [W3425]

description:
W3425
Δ(90)+YAP+NFE2L2_WT


title: Sample064 [Rectal biopsy]

address: 950 Atlantic Drive

institute: Georgia Institute of Technology

data_processing:
Using FastQC, the single end 150 bp reads were trimmed and adapters were removed.
Reads were mapped to human genome hg19 using hisat2.
The aligned reads were converted into read counts per gene with SAMtools and HTSeq in the default union mode.
The raw read counts were normalized via trimmed mean of M-values normalization with the edgeR R package.
Further adjustment and removal of batch effects was performed with SVA and (SNM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for each sample.
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene expression for each sample.

extract_protocol:
Rectal biopsy specimens were obtained during diagnostic colonoscopy. RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced on the Illumina NextSeq as single-end 150-bp reads.

tag: individual

tag: age at diagnosis

tag: time of sampling

value: Baseline

value: CS-IV

value: pediatric ulcerative colitis


title: Sample065 [Rectal biopsy]

tag: initial treatment

value: CS-Oral

tag: colectomy


title: Δ(90)+YAP+NFE2L2_WT-Tumor [W3423]

description:
W3423
Δ(90)+YAP+NFE2L2_WT


title: iPSC 4C-seq rep1

tag: cell type


title: Gluta neurons ATAC-seq rep2

data_processing:
ATAC-seq: Reads were trimmed and aligned with bowtie2 (Langmead and Salzberg 2012), with standard parameters and a maximum fragment length of 2,000. Duplicate reads were removed with Picard.
ATAC-seq: De-duplicated reads were filtered for high quality (samtools (Li et al. 2009), MAPQ ≥ 30), nonmitochondrial chromosome, non-Y chromosome, and proper pairing (samtools flag 0 × 2).
ATAC-seq: Peaks were called with macs2 (Zhang et al. 2008, 2), and filtered out with IDR threshold of 0.1 (Li et al. 2011) and blacklist of artifactual regions in hg19.
ATAC-seq: Libraries were quality controlled by downsampling to 5 million reads and evaluating transcription start site enrichment (RefSeq) and fraction of reads in peaks.
4C-seq: Reads were trimmed with Trimmomatic v0.36 (Bolger et al. 2014), aligned with bowtie2 (Langmead and Salzberg 2012) and subsequently processed, filtered, analyzed and visualized according to Basic4Cseq (Walter et al. 2014) in R v 4.0.2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig, bedGraph

value: iCell GlutaNeurons (Cellular Dynamics)


title: M25C_1

value: 12 hours after injection of M. luteus

value: adult

value: male


title: GE 4C-seq rep1

value: iPSC-derived GE (d24)


title: NPC 4C-seq rep2


title: Sample063 [Rectal biopsy]

tag: disease


title: M46018_2

value: Gal80ts; Tub> CR46018


title: Sample062 [Rectal biopsy]

value: F


title: M25C_2


title: Sample061 [Rectal biopsy]

value: M


title: GABA neurons ATAC-seq rep2

value: iCell GABANeurons (Cellular Dynamics)


title: Δ(90)+YAP-Tumor [s2139]

description:
s2139
Δ(90)+YAP

value: FVB


title: Δ(90)+YAP-Tumor [s1800]

description:
s1800
Δ(90)+YAP


title: Δ(90)+YAP-Tumor [s2138]

description:
s2138
Δ(90)+YAP


title: GABA neurons ATAC-seq rep1


title: Sample066 [Rectal biopsy]


title: Δ(90)+YAP-Tumor [s1799]

description:
s1799
Δ(90)+YAP


title: Sample060 [Rectal biopsy]


title: Δ(90)+YAP-Tumor [s1758]

description:
s1758
Δ(90)+YAP


title: NSC ATAC-seq rep2

source_name: Neural stem cells

value: Human neural stem cells derived from H9 (WA09) human embryonic stem cells (ThermoFisher)


title: Sample058 [Rectal biopsy]

source_name: Rectal biopsy


title: Gluta neurons ATAC-seq rep1


title: Sample059 [Rectal biopsy]


title: Δ(90)+YAP+R34P-Tumor [R3496]

description:
R3496
Δ(90)+YAP+R34P


title: NSC ATAC-seq rep1


title: Δ(90)+YAP+R34P-Tumor [R3494]

description:
R3494
Δ(90)+YAP+R34P


title: GE ATAC-seq rep2


title: Sample057 [Rectal biopsy]


title: Mixture of blood samples from three dairy cows with 7 dpi

city: Yinchuan

first: Xing-Ping

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

description:
Cow_08-I
Peripheral blood from the cow at 7 day of post infected with S. aureus

data_processing:
Illumina HiSeq2500 used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. And reads were trimmed and cleaned by removing the sequences smaller than 18 nt or longer than 30 nt. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and new miRNA predicted by comparing with known miRNAs from miRBase. Randfold tools soft was used for new miRNA secondary structure prediction.
Prior to differential gene expression analysis, for each sequenced library, differential expression analysis of two samples was performed using the IDEG6. Pvalue was adjusted using q value (Storey et al, 2003). qvalue<0.005 & |log2 （foldchange） |≥1 was set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of the differentially expressed genes (DEGs) was implemented by the GOseq R packages based Wallenius non-central hyper-geometric distribution.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Matrix table with information of miRNA and expression level (TPM) of miRNA for every sample.

organism: Bos taurus

source_name: blood

growth_protocol: On the day 0, 1, 3, 5, and 7 after S. aureus infection, peripheral blood was collected from the jugular vein.

extract_protocol:
TRIzoL kit (Invitrogen, Carlsbad, CA, USA) was used to extract total RNA from blood at different induction times (0, 1, 3, 5, and 7 days) according to the manufacturer’s instructions.
A total of 1.5 μg of qualified RNA was taken, and EBNext®Ultra™ sRNA sample pre kit was used to construct the miRNA library according to the product instructions.

treatment_protocol: Blood samples of different individuals with the same induction time were mixed and stored using RNALater™ RNA stabilization reagent for blood (Beyotime Biotechnology, Tianjin, China). The samples were frozen and stored at -80℃ for further analysis.

tag: breed

value: half-sib Chinese Holstein cows

value: S. aureus infection

tag: dpi

value: 7 dpi

value: peripheral blood


title: Δ(90)+YAP+R34P-Tumor [R3490]

description:
R3490
Δ(90)+YAP+R34P

tag: gender

tag: strain


title: Sample056 [Rectal biopsy]

first: Angela

value: Baseline

value: pediatric ulcerative colitis


title: GE ATAC-seq rep1


title: Sample055 [Rectal biopsy]


title: Δ(90)+R34P-Tumor [NR3429]

description:
NR3429
Δ(90)+R34P


title: Δ(90)+YAP+R34P-Tumor [R3488]

description:
R3488
Δ(90)+YAP+R34P


title: Sample054 [Rectal biopsy]

value: CS-IV


title: 22Rv1 cell with KIF15 knockdown

city: Jinan

first: Lin

last: Gao

address: No.44, Wenhua Xi Road

institute: shandong university

description: This sample is of 22Rv1 transfected with siRNA of KIF15.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After being washed in an ozone-free environment, image capture was performed with Ageilent DNA Microarray Scanner and uploaded into Agilent Feature Extraction (v11.0.0.1), and Cy3 label intensities determined.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the Agilent GeneSpring GX software package, version 12.1 .

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and streptomycin. Cell cultures were held in a humid, 37℃ and 5% CO2 cell culture incubator.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: 22Rv1 cells transfected with siRNA are referred as 22Rv1_NC and 22Rv1_siKIF15.

tag: cell line

tag: genotype/variation

value: KIF15 knocked down


title: NPC ATAC-seq rep2

value: iPSC-derived NPC (d10)


title: Mixture of blood samples from three dairy cows with 3 dpi

description:
Cow_06-I
Peripheral blood from the cow at 3 day of post infected with S. aureus

tag: treatment

value: 3 dpi


title: 22Rv1 cell as control

description: This sample is of 22Rv1 transfected with siRNA of negtive control.

value: negative control


title: Δ(90)+R34P-Tumor [NR3427]

description:
NR3427
Δ(90)+R34P


title: iPSC ATAC-seq rep2

value: Induced pluripotent stem cells


title: NPC ATAC-seq rep1


title: H2228 with EML4-ALK siRNA

city: Tianjin

first: Yongwen

last: Li

address: No.154, Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

description: Gene expression data from H2228 cells expressing EML4-ALK siRNAs

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Analysis of the microarray expression data was done using the R/Bioconductor through a graphical user interface, Chipster 3.12.5. Normalization was performed using custom chip description file for hgu133Aplus2. Intensity data were log2-transformed, and quantile normalized using robust multi-array average (RMA).

label: biotin

source_name: lung cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were transfected with EML4-ALK V3 plasimids or EML4-ALK siRNAs or negative controls for 48 hours. Then cells were use for this experiment.

tag: transfection

value: EML4-ALK siRNA


title: H2228 with negative control

description: Gene expression data from H2228 cells expressing negative control


title: HEK293 with EML4-ALK V3 plasimids

description: Gene expression data from HEK293 cells expressing EML4-ALK plasmids

source_name: Human embryonic kidney cells

value: EML4-ALK plasmids


title: HEK293 with negative control

description: Gene expression data from HEK293 cells expressing negative control


title: Sample053 [Rectal biopsy]

city: Atlanta

last: Mo

value: F

value: CS-Oral


title: iPSC ATAC-seq rep1


title: Mixture of blood samples from three dairy cows with 0 dpi

description:
Cow_04-I
Peripheral blood from the cow at 0 day of post infected with S. aureus

value: 0 dpi

tag: tissue


title: Δ(90)+L30P-Tumor [NL3438]

description:
NL3438
Δ(90)+L30P

value: FVB

tag: hdtvi plasmids


title: Sample051 [Rectal biopsy]

tag: individual


title: Input-2

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were cleaned with trim-galore and aligned to the human genome, hg19, using bowtie2. PCR duplicated reads were removed by SAMtools
ChIP-seq peaks were identified by MACS2 with the parameter of narrow peak for H1.4 peaks, and broad peak calling for H3K36 methylations.
Genome_build: hg19

source_name: Astrocyte

growth_protocol: T/C28a2 cell, which was the immortalized human juvenile costal chondrocyte, was cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Cells were crosslinked by 1% formaldehyde for 10 mins, and then quenched in 125 mM glycine for 5mins. After washing with cold TBS twice, cells were incubated in lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) for 10 mins on ice. Nuclei were washed and resuspended in MNase digestion buffer (20 mM Tris-HCl, pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) supplemented with 1,000 units of MNase (NEB) and incubated at 37 °C with continuous mixing for 20 mins. The reaction was stopped by adding of 2XSTOP buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), followed by sonication for 10 mins (30 secs on / 30 secs off). For spike-in ChIP-seq, the MNase digested chromatin from drosophila S2 cells was added to 1% to 5% of total chromatin. The chromatin was incubated with antibodies at 4 °C overnight and then subjected to 30 μl of protein G-magnetic beads for additional 2 hours. The beads were extensively washed and bound DNA was eluted with elution buffer (10 mM Tris-HCl, pH8.0, 10 mM EDTA, 150 mM NaCl, 5 mM DTT, 1% SDS) and reverse-crosslinked at 65 °C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen) after treatment of proteinase K and RNase A.
Sequencing libraries were prepared using TruPrep DNA library prep kit (Vazyme) following the manufacturer’s instructions.
The library was sequenced on an Illumina HiSeq 4000 platform with single-end read of 50bp

value: immortalized juvenile costal chondrocyte cell line T/C 28a2

tag: mutation

value: WT

tag: chip antibody


title: Δ(90)+L30P-Tumor [NL3436]

description:
NL3436
Δ(90)+L30P


title: miRXplore_mDOT-seq 2U_replicate2

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
Reads were filtered by length and presence of the adaptors using cutadapt (-m 10 --discard-untrimmed –max-n 0) and later deduplicated using custom Unix script.
To count the reads corresponding to each miRNA, custom reference libraries were created using an in-house Unix script and miRNAs counted by exact match.
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for all samples.

organism: synthetic construct

extract_protocol: miRXplore Universal Reference (Miltenyi Biotec) RNA was denaturated in the presence of EDTA, modified with azide group and 3' alkyne-adapter/RT primer via the click reaction. The resulting RNA-DNA conjugate was used for RNA library preparation according to the NEXTflex Small RNA-seq Kit v3 (PerkinElmer) starting from Step B with the following modifications: at Step D ¼ dilution of NEXTflex 5' 4N adapter was used, at Step G 18 cycles of PCR were performed and Step H1 was proceeded with Step H2.

tag: source


title: Sample050 [Rectal biopsy]

value: M

tag: age at diagnosis

tag: time of sampling

tag: initial treatment

tag: colectomy


title: miRXplore_mDOT-seq 2U_replicate1

source_name: miRXplore Universal Reference (Miltenyi Biotec)


title: Δ(90)+YAP+L30P-Tumor [L3493]

description:
L3493
Δ(90)+YAP+L30P


title: Input-1


title: miRXplore_mDOT-seq 2C_replicate2

value: miRXplore Universal Reference (Miltenyi Biotec)


title: Mixture of blood samples from three dairy cows with 5 dpi

description:
Cow_07-I
Peripheral blood from the cow at 5 day of post infected with S. aureus

tag: breed

value: half-sib Chinese Holstein cows

value: S. aureus infection

tag: dpi

value: 5 dpi

value: peripheral blood


title: Sample049 [Rectal biopsy]

tag: gender

value: Baseline

tag: disease

value: pediatric ulcerative colitis


title: Mixture of blood samples from three dairy cows with 1 dpi

description:
Cow_05-I
Peripheral blood from the cow at 1 day of post infected with S. aureus

value: 1 dpi


title: Δ(90)+YAP+L30P-Tumor [L3491]

description:
L3491
Δ(90)+YAP+L30P

tag: strain


title: IgG-2

tag: cell line

value: Rabbit IgG


title: IgG-1


title: miRXplore_mDOT-seq 2C_replicate1


title: Sample048 [Rectal biopsy]


title: H1.4-2


title: Δ(90)+YAP+L30P-Tumor [L3487]

description:
L3487
Δ(90)+YAP+L30P


title: Sample052 [Rectal biopsy]


title: H1.4-1


title: miRXplore_mDOT-seq 1U_replicate1


title: Sample047 [Rectal biopsy]


title: miRXplore_mDOT-seq 1C_replicate2


title: Δ(90)+YAP+L30P-Tumor [L3485]

description:
L3485
Δ(90)+YAP+L30P


title: NFD-Liver [c7]

source_name: Liver

value: no injection


title: Sample045 [Rectal biopsy]


title: miRXplore_mDOT-seq 1C_replicate1


title: Sample046 [Rectal biopsy]

value: F

value: CS-IV


title: Sample044 [Rectal biopsy]


title: H3K36me3-2


title: L. casei BL23_mDOT-seq C_replicate 2

description:
BL23 C-2
50-500 nt RNA

data_processing:
Sequenced reads were trimmed for adaptors and low quality bases using cutadapt (v2.9) and deduplicated using BBMAP package (v38.41). UMI extraction was performed with UMI-tools (v1.0.1).
Reads were mapped to L. casei BL23 reference genome using hisat2 (2.2.0, options –no-spliced-alignment -a -I 0 -X 1000).
sRNAs were predicted using R (3.5.1) package APERO (1.0.3) and manually curated.
Raw counts were generated using featureCounts from Rsubread package. CPM’s were generated using edgeR package (R 3.5.1)
Genome_build: NC_010999.1
Supplementary_files_format_and_content: Tab-delimited text files include raw counts of all predicted sRNAs for all samples.

organism: Lacticaseibacillus casei

source_name: cells

growth_protocol: Lactobacillus casei BL23 was grown in 200 ml of BD™ Difco™ Lactobacilli MRS Broth at 37 °C to an OD 600 nm of 0.2, 0.9, 3.1, 6.0, 8.5 and 10.0.

extract_protocol:
Total RNA was extracted from bacteria collected at six growth points with RNAzol RT (RN 190) (Molecular Research Center, Inc.). Traces of DNA were removed with DNase I, RNase free (Thermo Scientific). rRNAs were depleted using the modified RiboMinus Transcriptome Isolation Kit, bacteria (Invitrogen). 50-500 nt RNAs were isolated after polyacrylamide gell electrophoresis and treated with RNA 5´ Pyrophosphohydrolase (RppH) (New England Biolabs).
For mDOT-seq U and C libraries RNA was denaturated in the presence of EDTA, modified with azide group and attached to 3' alkyne-adapter/RT primer via the click reaction. The resulting RNA-DNA conjugate was further processed according to the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer) starting from the Step B with couple modifications listed: at Step D ¼ dilution of NEXTflex 5' 4N adapter was used, at Step E incubation at 42 °C was extended to 60 min, at Step G 15 PCR cycles were performed and Steps F and H1 were carried out as described in alternative protocol for Preparing Libraries without Size Selection. For N libraries, RNA was processed according to the NEXTflex Small RNA-Seq Kit v3 (PerkinElmer) with modifications in Steps E, F and H1 identical to mDOT-seq protocol except for Step G were only 12 PCR cycles were performed.


title: NFD-Liver [c12]


title: Δ(90)+YAP+L30P-Tumor [L3489]

description:
L3489
Δ(90)+YAP+L30P

source_name: Tumor


title: H3K36me3-1


title: miRXplore_mDOT-seq 1U_replicate2


title: NFD-Liver [c4]


title: NFD-Liver [c17]


title: L. casei BL23_mDOT-seq C_replicate 3

description:
BL23 C-3
50-500 nt RNA


title: OPCs-ZJU-37-rep1

first: Jingwei

last: Zhao

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in house perlscripts. In this step, clean data (clean reads) were obtained
Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5 .
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference based approach.
FeatureCounts v 1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Rattus_norvegicus_Ensemble_96
Supplementary_files_format_and_content: all_compare.txt (counts, fkpms)

source_name: oligodendrocyte precursor cells (OPCs)

growth_protocol: 2 P0 SD rat cerebral cortices were dissected out and digested in 0.25% trypsin, after 7 days culture in DMEM/F12 containing 10% FBS, OPCs were purified by shaking on a shaker at 250 rpm for 16-18 hours. Then the OPCs were replaced on 6 cm dishes and cultured in Neurobasal containing B27 and N2.

extract_protocol:
Total RNA was extracted from OPCs using TRIzolTM Reagent (#15596026, InvitrogenTM). Then mRNA was purified form total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illlumina® (#E7770, NEB) and index codes were added to attribute sequences to each sample. The index-coded samples clustering was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructios.

treatment_protocol: OPCs were treated with 5 μM ZJU-37 or equal volume of DMSO for 36 hours.

value: Sprague Dawley

tag: cell type

value: primary cultured OPCs

tag: treatment


title: Sample041 [Rectal biopsy]


title: OPCs-ZJU-37-rep2


title: Sample042 [Rectal biopsy]


title: OPCs-ZJU-37-rep3


title: L. casei BL23_mDOT-seq C_replicate 1

description:
BL23 C-1
50-500 nt RNA


title: NFD-Liver [c1]

value: FVB

tag: hdtvi plasmids


title: L. casei BL23_conventional RNA-seq_replicate 2

description:
BL23 N-2
50-500 nt RNA


title: Sample040 [Rectal biopsy]

tag: individual


title: Control_rep2

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Cultured ESC organoid

extract_protocol:
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via an Illumina NovaSeq instrument.
10X Genomics single cell RNA sequencing

value: Cultured ESC organoid

tag: agent

value: control


title: L. casei BL23_conventional RNA-seq_replicate 1

description:
BL23 N-1
50-500 nt RNA


title: DUX_rep2

value: DUX-pulsed


title: OPCs-DMSO-rep1

value: DMSO


title: OPCs-DMSO-rep2


title: Sample039 [Rectal biopsy]


title: Sample043 [Rectal biopsy]


title: Sample038 [Rectal biopsy]

value: M


title: Sample037 [Rectal biopsy]

value: CS-Oral


title: Control_rep1


title: L. casei BL23_mDOT-seq U_replicate 3

description:
BL23 U-3
50-500 nt RNA


title: DUX_rep1


title: WT late 2-cell rep #6

data_processing:
Bbduk adapter Trimming
Tophat2 (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant)
and counts for each transcript were generated using “Get datasets”
Differential expression analysis was performed using DESEq2.
Genome_build: mm10
Supplementary_files_format_and_content: 20200423-SMRT-seq-DESEq-FPKM-table.txt

source_name: mouse embryo

growth_protocol: Animal experiments performed at the University of Utah were first approved by IACUC and Institutional approval, the protocol # is 18-07014. The Trp53 KO allele has already been described and was obtained as Trp53 flox allele flanking exons 2-10 and maintained on a mixed Bl6/C57 background. Trp53 flox/flox mice were mated to Ddx4::Cre driver to remove the flox cassette leaving the floxed allele. Male Trp53 KO mice were mated to female +/floxed Trp53 mice to generate Trp53 KO females. To generate Trp53 MZ-KO embryos, Trp53 KO females were mated to Trp53 KO males (which were previously confirmed to be fertile). The Trp53 WT control embryos were Trp53 flox/flox animals. Trp53 floxed KO alelles were detected using PCR before weaning of animals and confirmed after sacrifice of animals (see Supplementary Table X for genotyping primer sequences). For Trp53 MZ-KO embryos vs controls stained with DUX antibodies, females were injected with 5U of PSMG followed by 5U of hCG 48 hours later. Zygotes were harvested at 24 hours post hCG injection, washed in M2 media to remove cumulus cells, and then cultured in pre-equilibrated KSOM media under mineral oil. Early 2-cell stage embryos were harvested 2-3 hours after cytokinesis, typically 28-32 hours post hCG injection. Late 2-cell stage embryos were cultured cultured in KSOM after zygote harvest, confirmation of cytokinesis by 32 hours post hCG injection through visual inspection and collected for SMRT-seq libraries 48 hours post hCG

extract_protocol:
individual embryos or eggs were lysed in 5uL of lysis buffer (SMRT-seq v4)
SMRT-seq v4 library using 15 cycles of LD, followed by Nexterna DNA library prep tagmentation into ds-cDNA and PCR
RNAseq via Tn5 tagmentation of cDNA

treatment_protocol: embryos were cultured in KSOM prior to harvest

tag: genotype

value: WT

tag: tissue

value: embryo

tag: tag

value: late 2-cell


title: L. casei BL23_mDOT-seq U_replicate 2

description:
BL23 U-2
50-500 nt RNA


title: Sample036 [Rectal biopsy]

tag: age at diagnosis

tag: time of sampling

value: Baseline

value: pediatric ulcerative colitis


title: L. casei BL23_mDOT-seq U_replicate 1

description:
BL23 U-1
50-500 nt RNA


title: L. casei BL23_conventional RNA-seq_replicate 3

description:
BL23 N-3
50-500 nt RNA


title: OPCs-DMSO-rep3


title: WT late 2-cell rep #4


title: P8 lumbar motor neuros rep3

first: Catarina

last: Catela

state: Illinois

address: Abbott Hall 402,

department: Neurobiology

institute: University of Chicago

data_processing:
Reads were analyzed for quality control
Reads were align to the mouse genome using HISAT program
Reads were counted using FeatureCounts algorythm
Differential expression data generated with DESeq2 program
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with differential expression generated by DESeq2

source_name: Motor neurons

extract_protocol:
Spinal cords were isolated and dissociated with papain. Motor neurons were sorted by FACS (GFP and TdTomato). Motor neuron RNA was extracted using the Arcturus Picopure Extraction Buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: Wildtype

tag: spinal cord region

value: Lumbar


title: Sample035 [Rectal biopsy]

tag: initial treatment

tag: colectomy


title: E12.5 Hoxc8 MNΔ rep3

value: Hoxc8 MN[delta]

value: Brachial


title: E12.5 Hoxc8 MNΔ rep1


title: P8 lumbar motor neuros rep2


title: day9.Il17dko4

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

description: microbial DNA

data_processing:
Library strategy: 16S
Raw reads were filtered to remove adaptors and low-quality and ambiguous bases, and then paired-end reads were added to tags by the Fast Length Adjustment of Short reads program (FLASH, v1.2.11) to get the tags.
The tags were clustered into OTUs with a cutoff value of 97% using UPARSE software (v7 .0.1090) and chimera sequences were compared with the Gold database using UCHIME (v4.2.40) to detect.
OTU representative sequences were taxonomically classified using Ribosomal Database Project (RDP) Classifier v.2.2 with a minimum confidence threshold of 0.6, and trained on the Greengenes database v201305 by QIIME v1.8.0
The USEARCH_global was used to compare all Tags back to OTU to get the OTU abundance statistics table of each sample.
Alpha and beta diversity were estimated by MOTHUR (v1.31.2) and QIIME (v1.8.0) at the OTU level, respectively. Sample cluster was conducted by QIIME (v1.8.0) based on UPGMA.
Genome_build: Greengenes

organism: Microbiota

source_name: microbiota

extract_protocol: microbial DNA was isolated from stools of indicated mice by using QiAamp DNA Stool Mini Kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: WT and Il17d-deficient mice treated with or without colitis

tag: state

value: colitis

tag: mouse genotype

value: Il17d KO

tag: source

value: mouse feces


title: Sample034 [Rectal biopsy]

tag: gender

value: F

tag: disease


title: P8 lumbar motor neuros rep1


title: WT late 2-cell rep #2

first: Edward

address: 2000 Circle of Hope Dr

institute: University of Utah


title: day9.Il17dko1

description: microbial DNA


title: day9.Il17dko3

description: microbial DNA


title: Sample032 [Rectal biopsy]


title: day9.Il17dko2

description: microbial DNA


title: E12.5 Hoxc8 MNΔ rep2


title: WT late 2-cell rep #1


title: WT early 2-cell rep #8

value: early 2-cell


title: day9.WT3

description: microbial DNA

value: Wild type


title: Sample031 [Rectal biopsy]

value: M


title: P8 thoracic motor neuros rep3

value: Thoracic


title: Sample030 [Rectal biopsy]

value: CS-Oral


title: P8 thoracic motor neuros rep2


title: WT late 2-cell rep #5

value: WT

value: embryo


title: day9.WT2

description: microbial DNA


title: WT early 2-cell rep #7


title: P8 brachial motor neuros rep3


title: Sample029 [Rectal biopsy]

value: Baseline


title: WT late 2-cell rep #3

value: late 2-cell


title: Sample033 [Rectal biopsy]

value: CS-IV

value: pediatric ulcerative colitis


title: Sample028 [Rectal biopsy]


title: WT early 2-cell rep #6


title: day9.WT1

description: microbial DNA


title: P8 brachial motor neuros rep2

value: Wildtype


title: Sample027 [Rectal biopsy]


title: WT early 2-cell rep #5


title: day0.Il17dko4

description: microbial DNA

value: steady state


title: P8 brachial motor neuros rep1

value: Brachial


title: WT early 2-cell rep #3


title: WT early 2-cell rep #4


title: day0.Il17dko3

description: microbial DNA

value: Il17d KO


title: E12.5 motor neurons rep6


title: day9.WT4

description: microbial DNA

value: colitis

value: mouse feces


title: Sample025 [Rectal biopsy]


title: E12.5 motor neurons rep4


title: WT early 2-cell rep #2

value: early 2-cell


title: day0.Il17dko2

description: microbial DNA


title: E12.5 motor neurons rep3


title: E12.5 motor neurons rep5


title: Sample024 [Rectal biopsy]

value: F


title: day0.WT2

description: microbial DNA

value: Wild type


title: Sample021 [Rectal biopsy]

value: M


title: day0.Il17dko1

description: microbial DNA


title: WT early 2-cell rep #1


title: day0.WT1

description: microbial DNA


title: day0.WT4

description: microbial DNA


title: Sample020 [Rectal biopsy]

value: CS-Oral


title: Sample023 [Rectal biopsy]


title: Trp53 MZ-KO late 2-cell rep #3

value: Trp53 MZ-KO


title: Trp53 MZ-KO late 2-cell rep #6

value: embryo


title: Sample026 [Rectal biopsy]

value: Baseline


title: Sample018 [Rectal biopsy]