title: CEMBA181210_5C_3_CEMBA181210_5C_4_B2_ad002


title: CEMBA181210_5C_3_CEMBA181210_5C_4_B12_ad012

status: Public on Sep 25 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSs

tag: Sex

value: male

tag: age

tag: strain


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title: CEMBA181210_5C_1_CEMBA181210_5C_2_D11_ad007


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D10_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D12_ad004


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D11_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D11_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D12_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D10_ad004


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D11_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D10_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D10_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D11_ad004


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D11_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad007


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad004


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D1_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D2_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad007


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C8_ad004


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C9_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C8_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C8_ad008


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C7_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C8_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C7_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C8_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C8_ad002


title: 1ct_day7_control

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

description: Single-cell RNAseq data

library_source: transcriptomic

data_processing:
The Cell Ranger 3.0.2 Single-Cell Software Suite (10x Genomics) was implemented to process the raw sequencing data from the Illumina HiSeq X run.
This pipeline performed de-multiplexing, alignment (GRCh38/STAR), and barcode processing to generate gene-cell matrices used for downstream analysis.
Genome_build: GRCh38
26 bp Read1 (10x cell barcode and UMI), 8 bp i7 Index (sample index), and 98 bp Read2 (insert)
Supplementary_files_format_and_content: cell ranger count matrix for single cells in each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Colonic Epithelial Cells cultured transfected with shRNA specific for a scrambled control after 7 days

growth_protocol: shAPC and shScramble cells stably expressed in HCEC 1CT were routinely cultured in HCEC culture media (DMEM:M199=4:1) supplemented with EGF (20 ng/mL), hydrocortisone (1ug/mL), insulin (10 ug/mL), Sodium selenite (5nM), transferrin (2 ug/mL), and 2% FBS at 37°C in 5% CO2.

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument  Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' ver 2 Reagent Kit User Guide Rev A
RNA libraries were prepared for sequencing using Single Cell 3' Reagent Kit v2 (10x genomics).

treatment_protocol: For retrovirus transduction, we cultured HCEC 1CT cells in above condition with 1 μg/ml of puromycin after transduction. shAPC and shScrambled cells were harvested at 3-and 7-days after transduction, and stored on ice in PBS before the single cell library preparation.

tag: cell line

value: HCEC

tag: cell type

value: Human colonic epithelial progenitor cells

tag: time point

tag: shRNA

value: shScramble


title: 1ct_day7_shAPC

description: Single-cell RNAseq data

source_name: Colonic Epithelial Cells cultured transfected with shRNA specific for APC after 7 days

value: shAPC


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C7_ad001


title: 1ct_day3_shAPC

description: Single-cell RNAseq data

source_name: Colonic Epithelial Cells cultured transfected with shRNA specific for APC after 3 days


title: K562-FAN-2

city: Xi’an

first: yanmin

last: zhang

state: Shaanxi

address: No. 76, Yanta Weststreet, #54

country: China

institute: School of Medicine, Xi’an Jiaotong University, Xi’an, Shaanxi Province

description:
difference_mRNA_K562_vandetanib_vs_control.xls
lncRNA_difference_K562_vandetanib_vs_control.xlsx

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2).
The clean reads were mapped to the hg19 genome using HISAT2 (v2.0.4).
Then expression level of gene was calculated by STRING TIE (v1.2.3). 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: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include normal count values for each Sample.
Supplementary_files_format_and_content: difference_mRNA_K562_vandetanib_vs_control.xls
Supplementary_files_format_and_content: lncRNA_difference_K562_vandetanib_vs_control.xlsx

molecule: total RNA

source_name: K562 cells, vandetanib

growth_protocol: K562 cells were cultured in IMDM containing 10% fetal bovine serum, 100 U/mL penicillin, and 100 U/mL streptomycin.

extract_protocol:
Total RNA was extracted using the RNAfast200 kit according to the manufacturer’s protocol.
The strand-specific RNA-seq libraries were prepared using a NEBNext® Ultra™ I RNA Library Prep Kit for Illumina (NEB, MA, USA) following the manufacturer’s instructions.

treatment_protocol: Treat with vandetanib (1.56 μM) and control (DMSO) for 48 h.

tag: genotype

value: wild type

tag: treatment

value: vandetanib (1.56 uM)


title: K562-Y-2

source_name: K562 cells, control

value: control (DMSO)


title: K562-FAN-1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad012


title: K562-Y-3


title: 1ct_day3_control

description: Single-cell RNAseq data

source_name: Colonic Epithelial Cells cultured transfected with shRNA specific for a scrambled control after 3 days


title: K562-FAN-3


title: K562-Y-1


title: T2

city: Gent

first: Siebe

last: Loontiens

address: Corneel Heymanslaan 10

department: Center for Medical Genetics

country: Belgium

institute: Ghent University

description:
RNA isolated from T-ALL cells collected from full blown leukemic  hTLX1  zebrafish
rawCountMatrix_SLT.txt.gz
sample_24

data_processing:
First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide
Counts to GRCz10.91.gtf were generated on the fly by STAR
Genome_build: GRCz10
Supplementary_files_format_and_content: txt file with raw counts

organism: Danio rerio

source_name: T-ALL colleted when 90% of zebrafish was taken over by GFP + T-ALL cells.

extract_protocol: Truseq stranded mRNA library prep (illumina, #20020594)

value: T-ALL

value: Tg(rag2:hTLX1; rag2:GFP)

tag: tumor stage

value: Primary T-ALL

tag: lab of sample collection and sequencing

value: Speleman lab


title: T2-2

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from  hTLX1 primary T-ALL 2
rawCountMatrix_SLT.txt.gz
sample_23

value: Transplant T-ALL


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad001


title: T2-2-1

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from  hTLX1 transplant T-ALL 2.2
rawCountMatrix_SLT.txt.gz
sample_21


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad007


title: T2-1

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from  hTLX1 primary T-ALL 2
rawCountMatrix_SLT.txt.gz
sample_20


title: Sadie-D

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (1x50bp, single read)

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS v3.3.41/RTA 2.5.2) and bcl2fastq Conversion Software (Illumina; San Diego, CA)
FASTQ-formatted sequence data was analyzed using a standard HISAT (hierarchical indexing for spliced alignment of transcripts)-Cufflinks workflow. RNA-Seq sequence reads (FASTQ format) were aligned to the reference cat genome assembly (Nov. 2014, ICGSC Felis Catus 8.0) using HISAT software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values (Cuffnorm output) were utilized for downstream analysis steps.
Processed data are Cufflinks-Cuffnorm output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: Nov. 2014, ICGSC Felis Catus 8.0
Supplementary_files_format_and_content: Tab-delimited text files include Ensembl ID, FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

organism: Felis catus

source_name: feline chronic gingivostomatitis (FCGS) tissue

extract_protocol:
Total RNA was isolated from matched pairs of chronic gingivostomatitis (FCGS; diseased) and adjacent healthy tissues using the RNeasy Mini Kit (Qiagen, Inc.). RNA quantity and quality were assessed on a NanoDrop spectrophotometer (Thermo Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), respectively.
Transcriptome profiling was performed using a directional, strand-specific mRNA-Seq approach. Briefly, indexed RNA-Seq libraries were prepared from 200 ng total RNA using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Inc.) according to the manufacturer’s standard protocol. Poly-adenylated mRNA was purified from total RNA and ribosomal RNA removed by binding to oligo(dT) beads, which was followed by RNA fragmentation by incubation at 94ºC in the presence of magnesium. Double-stranded cDNA was then generated by random-primed first-strand synthesis and subsequent second strand synthesis in the presence of dUTP for strand marking. The double-stranded cDNA was then 3’-A tailed and indexed, Illumina-compatible adapters were ligated. The libraries were then enriched by high-fidelity PCR amplification (15 cycles) with KAPA HiFi HotStart DNA Polymerase and adapter-specific primers.

tag: subject id

value: Sadie

tag: tissue

value: gingival tissue-diseased

value: diseased

value: inflammatory


title: Jerome-H

source_name: feline healthy gingival tissue

value: Jerome

value: gingival tissue-healthy

value: healthy

value: normal


title: T1

description:
RNA isolated from T-ALL cells collected from full blown leukemic  hTLX1  zebrafish
rawCountMatrix_SLT.txt.gz
sample_19


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C7_ad008

value: SSs

value: male


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad010


title: T1-2

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from  hTLX1 primary T-ALL 1
rawCountMatrix_SLT.txt.gz
sample_18


title: T1-1

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from  hTLX1 primary T-ALL 1
rawCountMatrix_SLT.txt.gz
sample_17


title: PT3

description:
RNA isolated from T-ALL cells collected from full blown leukemic phf6+/-, hTLX1  zebrafish
rawCountMatrix_SLT.txt.gz
sample_15

value: Tg(rag2:hTLX1; rag2:GFP);phf6+/-


title: Bart-H

value: Bart


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad004


title: Jerome-D


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad006


title: PT4

description:
RNA isolated from T-ALL cells collected from full blown leukemic phf6+/-, hTLX1  zebrafish
rawCountMatrix_SLT.txt.gz
sample_16

value: T-ALL


title: PT2-1

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from phf6+/-, hTLX1 primary T-ALL 2
rawCountMatrix_SLT.txt.gz
sample_11


title: PT2-3

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from phf6+/-, hTLX1 primary T-ALL 2
rawCountMatrix_SLT.txt.gz
sample_13


title: Bart-D


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad002


title: PT1

description:
RNA isolated from T-ALL cells collected from full blown leukemic phf6+/-, hTLX1  zebrafish
rawCountMatrix_SLT.txt.gz
sample_10


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C6_ad008


title: PT2-2

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from phf6+/-, hTLX1 primary T-ALL 2
rawCountMatrix_SLT.txt.gz
sample_12


title: Glyc_spo rep 2

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

data_processing:
Base-calling with bcl2fastq2-2.15
alignment done with bowtie version 0.12.7
filter and manipulation with samtools 1.3
Frecuency count htseq-count version 0.6.0.
last filter bedtools v2.25.0
Genome_build: E. coli K-12 MG1655  and S. pombe 972 h-
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest

organism: Schizosaccharomyces pombe

source_name: cells

growth_protocol: liquid culture were incubated to mid exponential growth

extract_protocol:
Cells were collected in log phase and RNA later added and harvested to 5000g for 5 min. Pellet were frozen on -80°C. RNA was harvested using Trizol reagent and precipitated with isopropyl alcohol, samples were treated with DNAses an concentrate with RNA cleaner kit. RRNA were removed with Ribominus bacteria /yeast kit and  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: YE medium was used changed carbon source in each treatment : glucose 2% and  Glycerol : sodium acetate (10 :1) 2%(w/v)

tag: carbon source

value: Glycerol :sodium acetate (10 :1) 2%(w/v)

value: mid exponential growth culture


title: PT2

description:
RNA isolated from T-ALL cells collected from full blown leukemic phf6+/-, hTLX1  zebrafish
rawCountMatrix_SLT.txt.gz
sample_14

value: Primary T-ALL

value: Speleman lab


title: Sadie-H

value: Sadie


title: PT1-3

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from phf6+/-, hTLX1 primary T-ALL 1
rawCountMatrix_SLT.txt.gz
sample_9

value: Transplant T-ALL


title: PT1-2

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from phf6+/-, hTLX1 primary T-ALL 1
rawCountMatrix_SLT.txt.gz
sample_8


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C5_ad012


title: PT1-1

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from phf6+/-, hTLX1 primary T-ALL 1
rawCountMatrix_SLT.txt.gz
sample_7


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C5_ad001


title: Gluc_spo rep 3

value: Glucose 2%  (w/V)


title: AB-thymus-9

description:
RNA of dissected thymi of tg(rag2-GFP) zebrafish
rawCountMatrix_SLT.txt.gz
sample_6

source_name: Healthy dissected  thymus

value: thymocytes


title: Glyc_spo rep 1


title: AB-thymus-7

description:
RNA of dissected thymi of tg(rag2-GFP) zebrafish
rawCountMatrix_SLT.txt.gz
sample_4


title: Glyc_spo rep 3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C5_ad006


title: Gluc_spo rep 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C5_ad008


title: AB-thymus-11

description:
RNA of dissected thymi of tg(rag2-GFP) zebrafish
rawCountMatrix_SLT.txt.gz
sample_2


title: Gluc_spo rep 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_D6_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C5_ad002


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad007


title: AB-thymus-2-3-5-6

description:
RNA of dissected thymi of tg(rag2-GFP) zebrafish
rawCountMatrix_SLT.txt.gz
sample_3


title: AB-thymus-10

description:
RNA of dissected thymi of tg(rag2-GFP) zebrafish
rawCountMatrix_SLT.txt.gz
sample_1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad006


title: T2-2-3

description:
RNA isolated from T-ALL cells collected from Rag2-/- zebrafish upon transplantation of 5 milion of T-ALL cells originating from  hTLX1 transplant T-ALL 2.2
rawCountMatrix_SLT.txt.gz
sample_22

value: Tg(rag2:hTLX1; rag2:GFP)


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad004


title: 30IEC_CL_2

city: San Francisco

first: Kevin

last: Man

address: 555 Mission Bay Boulevard South

department: Physiology

institute: University of California, San Francisco

data_processing:
Quality of raw sequencing data was assessed using FastQC, and bases with a per base sequencing quality of less than 28 were trimmed with Trimmomatic (parameters: LEADING:15 TRAILING:15 MINLEN:35)
Trimmed reads were pseudoaligned to mouse transcriptome (mm10, Genome Reference Consortium Mouse Build 38) using Kallisto with 100 bootstraps
Differential gene expression was defined as a fold change of ≥1.5, with a false discovery rate of q-value <0.05, and was performed using Sleuth in gene-level mode with likelihood-ratio test as the method for statistical testing
Genome_build: mm10, Genome Reference Consortium Mouse Build 38
Supplementary_files_format_and_content: RawCount_Matrix.txt

extract_protocol:
Epithelial cells were isolated from large intestines after flushing with ice-cold sterile PBS. The entire length of the colon was opened longitudinally and washed with Ca2+/Mg2+-free HBSS supplemented with 2% bovine serum albumin and 10 mM HEPES. The colon was then cut into small pieces (5-10 mm) and immersed in 20 ml of Ca2+/Mg2+-free HBSS with 2% fetal calf serum, 1 mM EDTA, 10 mM HEPES, and 1 mM dithiothreitol, and incubated at 37°C at 200 rpm for 20 minutes and the process was repeated twice. The three fractions of epithelial cells were pooled, passed through a 100 μM mesh nylon filter, and centrifuged at 1,000 g for 5 minutes at 4°C. Lymphocytes and other CD45+ cells were removed from the epithelial cell fraction by overlaying onto a 40-90% Percoll gradient followed by centrifugation at 2,200 rpm for 20 minutes. The remaining epithelial cells were collected and washed with ice-cold HBSS and centrifuged for 1,000 g for 5 minutes at 4°C. The final pellet was then collected as colonocytes, and purity was assessed by flow cytometry using anti-CD45, anti-EpCAM, and anti-cytokeratin-18 antibodies.
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library prep kit following standard Illumina protocols
The pooled libraries were sequenced on NextSeq 500 Illumina sequencer using NextSeq 500/550 High Output Kit v2.5 (75 cycles) (Illumina #20024906) in a single read mode.

treatment_protocol: Mice were pre-treated with beta-3 adrenergic receptor agonist CL 316,243 1mg/kg for two weeks or vehicle prior to oral administration of 4% dextran-sodium sulfate in drinking water.

value: Large intestine epithelial cells

tag: days dss treatment

tag: agonist treatment


title: 30IEC_D0_4

value: vehicle


title: 30IEC_CL_4


title: 30IEC_D3_4


title: 30IEC_CL_D3_3


title: 30IEC_CL_1


title: 30IEC_CL_3


title: 30IEC_CL_D3_2


title: 30IEC_CL_D3_1


title: 30IEC_D0_2


title: 30IEC_D3_1


title: 30IEC_D3_3


title: 30IEC_D3_2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad010

tag: brain region


title: 30IEC_CL_D3_4


title: 30IEC_D0_3


title: M8: tMCAO-R12h-3

type: RNA

city: Nanjing

first: Fangfang

last: Wu

state: Jiangsu

address: Dingjia Qiao 87#

department: Department of Pharmacology

institute: Southeast University

description: T, Mice subjected to transient MCAO were sacrificed at 12 hours of reperfusion after 1 hour occlusion of middle cerebral artery.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: ipsilateral cortex, tMCAO, 12h

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Adult male C57BL/6J mice weighing 21.4~22.1 g were maintained on a 12 h light/dark cycle at 25 °C and provided with free access to commercial rodent chow and tap water before the experiments.

extract_protocol: Total RNA was extracted from the ipsilateral cortex of each mouse using TRIzol reagent (Invitrogen Life Technologies, Carlsbad, USA) according to the manufacturer’s protocol. The RNA quantity and quality were measured by NanoDrop ND-1000 (NanoDrop products, Wilmington, DE, USA). The RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: The MCAO method was described previously, a silicone-rubber-coated 6-0 filament (DOCCOL Co, Redlands, CA) was inserted into the ECA and advanced over 9-11 mm to the carotid bifurcation along the internal carotid artery and to the origin of the middle cerebral artery (MCA). After 1 h occlusion, the filament was removed to restore blood flow of the MCA territory. Sham-operated mice received the same surgery except for the insertion of the filament. Mice subjected to transient MCAO were sacrificed at 12 h of reperfusion.

tag: Sex

value: adult

value: ipsilateral cortex


title: M5: sham-1

description: C, Sham-operated mice served as control. Sham-operated mice received the same surgery except for the insertion of the filament.

source_name: ipsilateral cortex, sham, 12h

value: male

tag: age


title: M7: sham-3

source_name: ipsilateral cortex, sham,12h

tag: strain


title: M4: tMCAO-R12h-2


title: M6: sham-2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad008

value: SSs


title: M2: tMCAO-R12h-1


title: 30IEC_D0_1


title: 22IEC_D3_4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C4_ad002


title: 22IEC_D3_2


title: 22IEC_D3_3


title: 22IEC_D0_4


title: 22IEC_D0_3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad007


title: 22IEC_D0_1


title: repeat 2 -WT mouse fed normal chow diet (NC) for 4 weeks

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC. Reaper version 15-065 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides.
Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.5.2b with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.1. Only genes with a minimum fold change of +- 1.5 (log2 +-0.59), a maximum Benjamini-Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
The Ensemble annotation was enriched with UniProt data (release 24.03.2017) based on Ensembl gene identifiers.
Genome_build: mm10
Supplementary_files_format_and_content: library-size normalized counts

source_name: white adipocyte

extract_protocol:
Total RNA was isolated using the RNeasy lipid tissue Mini Kit (Qiagen, Valencia, CA, USA), and DNA was removed using the QIAGEN RNase-Free DNaseSet following the manufacturer’s instructions.
20ng of total RNA was used as starting material for ribosomal depletion with RiboGone-Mammalian (Clontech) followed by library preparation using SMARTer Stranded Total RNA Sample Prep Kit (Clontech).

tag: genotype/variation

value: WT

tag: diet

value: normal


title: repeat 2 -Ad-Yap/Taz-KO mouse (KO) mouse fed normal chow diet (NC) for 4 weeks

value: Ad-Yap/Taz-KO


title: repeat 1 -WT mouse fed normal chow diet (NC) for 4 weeks


title: 22IEC_D0_2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad010


title: repeat 2 -WT mouse fed HFD for 4 weeks

value: HFD


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad006


title: Adult bone marrow monocytes 2

first: Daniel

last: Bunis

state: California

address: 35 Medical Center Way, Regeneration Medicine Building 903B

hyb_protocol: Cy3-coupled aRNA was fragmented and hybridized overnight to a SurePrint G3 Human GE v2 8x60K microarray, which was washed and scanned per the manufacturer’s instructions (Agilent Technologies)

scan_protocol: Per manufacturer’s instructions

data_processing:
Data were processed with Agilent Feature Extraction Software (v10.7.3.1)
Probes with at least 70% missing data were filtered, then any other missing data was imputed. Data were then quantile normalized using the normalizeBetweenArrays function of the Limma package (Ritchie et al., 2015), followed by filtering of probes without expression above a 2^7 background for every replicate in at least one sample group, followed by median scaling per gene.
The normalized and filtered data sets are available on the series record. Background subtracted signal (gProcessedSignal column of raw files) are included in the sample data table.

source_name: bone marrow

label_protocol: Total RNA extract was subjected to two rounds of linear amplification and Cy3 labelling using the Aminoallyl MessageAmp II aRNA Amplification kit (Invitrogen).

extract_protocol: Fetal UCB was collected from the umbilical cord after sterile preparation with antiseptic swabs. mLN tissue were mechanically compressed in media and filtered to form a single-cell suspension. Samples were ficolled to obtain the mononuclear cell layer, then viably cryopreserved. Naïve CD4 T cells were FACSorted (CD3+CD4+CD25-CD45RA+CD27+) and re-sorted to a purity of greater than 99%. RNA was isolated using the RNAqueous-Micro kit (Life Technologies).

value: bone marrow

tag: cell type

value: monocytes

tag: developmental stage

tag: sample type

value: control

tag: sample linkage


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: Adult bone marrow monocytes 3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad002


title: Fetal bone marrow monocytes 4

value: fetal


title: repeat 2 -Ad-Yap/Taz-KO mouse (KO) fed HFD for 4 weeks


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad004


title: repeat 1 -Ad-Yap/Taz-KO mouse (KO) mouse fed normal chow diet (NC) for 4 weeks


title: Adult bone marrow monocytes 1


title: 22IEC_D3_1


title: Adult bone marrow monocytes 4


title: repeat 1 -Ad-Yap/Taz-KO mouse (KO) fed HFD for 4 weeks


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C3_ad008


title: Fetal bone marrow monocytes 3


title: Fetal bone marrow monocytes 1


title: Tumor-182

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labeled RNA samples were hybridized to the LNA-enhanced miRCURY™ microarray version 11.0 (Exiqon, Denmark), which contained capture probes targeting all human miRNAs registered in   miRBASE version 13.0 at the Sanger Institute at the time of the analysis. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: After hybridization, washing and drying, the microarray slides were scanned in an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the resulting images were quantified by ImaGene v.8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10)3 and normalized using the global LOWESS (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: Adrenocortical carcinoma biopsy

label_protocol: 450 ng total RNA from sample and a common reference pool was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: RNA was extracted from 50-100 mg of tumor using the Qiagen miRNeasy Kit.

tag: condition

value: Adrenocortical carcinoma

source_name: Common reference pool

value: common reference


title: Adult peripheral blood monocytes 5

source_name: peripheral blood

value: peripheral blood

value: experimental


title: Fetal bone marrow monocytes 2


title: Tumor-163


title: repeat 1 -WT mouse fed HFD for 4 weeks


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad001


title: Tumor-146


title: Tumor-173


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad007


title: Tumor-137


title: Tumor-131


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad012


title: Adult peripheral blood monocytes 2


title: Adult peripheral blood monocytes 4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad006


title: Tumor-113


title: Tumor-108


title: Tumor-149


title: Tumor-130


title: Tumor-141


title: Adult peripheral blood monocytes 1


title: Tumor-135


title: Tumor-129


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C12_ad004


title: Tumor-127


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad008


title: Tumor-118


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C2_ad004


title: Tumor-114


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C12_ad012


title: Tumor-136


title: Normal-NB 400

source_name: Normal adrenal biopsy

value: Normal adrenal


title: Tumor-106


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C12_ad008


title: Fetal peripheral blood monocytes 5

source_name: umbilical cord blood

value: umbilical cord blood


title: Fetal peripheral blood monocytes 3


title: Adult peripheral blood monocytes 3

value: adult


title: Fetal peripheral blood monocytes 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C12_ad010

value: male


title: Normal-NB 40A


title: Tumor-122


title: Normal-NB 299


title: Fetal mesenchymal lymph node naïve CD4 T cells 4

source_name: mesenchymal lymph node

value: mesenchymal lymph node

value: CD4 T cells


title: Normal-NB 6


title: Fetal peripheral blood monocytes 4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C12_ad007

value: SSs


title: Tumor-196


title: Fetal peripheral blood monocytes 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C11_ad012


title: Fetal mesenchymal lymph node naïve CD4 T cells 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C12_ad001


title: AB-thymus-8

description:
RNA of dissected thymi of tg(rag2-GFP) zebrafish
rawCountMatrix_SLT.txt.gz
sample_5

value: thymocytes

tag: genotype

tag: tumor stage

value: healthy

tag: lab of sample collection and sequencing

value: Speleman lab


title: Fetal mesenchymal lymph node naïve CD4 T cells 3

tag: tissue


title: Tumor-192a


title: Tumor-184a


title: Tumor-194a


title: Fetal mesenchymal lymph node naïve CD4 T cells 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C11_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C11_ad010


title: Normal-NB 5


title: Tumor-180b


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C11_ad002


title: Tumor-171


title: Tumor-175


title: Tumor-165


title: Tumor-169b


title: Tumor-179a


title: Tumor-160


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C11_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C10_ad010


title: Tumor-153a


title: MDCKII AVL9-KD4 2D-D4 RNA-seq

city: ATHENS

first: Shaying

last: Zhao

state: GA

address: B304B Life Sciences, 120 Green Street

institute: University of Georgia

data_processing:
Read pairs were aligned to the dog reference genome canFam3 with HISAT v2.1.0.
Cufflinks v2.2.1 was used to quantify gene expression in FPKM, guided by canine gene annotation CanFam3.1.84 downloaded from UCSC genome browser
Genome_build: canFam3
Supplementary_files_format_and_content: Tab-delimited files with expression values in FPKM for each sample

organism: Canis lupus familiaris

source_name: MDCKII cells

growth_protocol: MDCKII cells were maintained in Eagle’s minimal essential medium with 5% fetal bovine serum, 10 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin; For 3D cultures, cells were grown on top of matrigel. For 2D cultures, cells were seeded on transwell inserts grown until over-confluence. The cells for seeding were regarded as day0 samples.

extract_protocol:
Cysts grown for 24h, 3, 5, 8, 14 days, cells for seeding (day 0) and over-confluent cells were collected and RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen)
RNA-seq libraries were constructed using KAPA Stranded mRNA-Seq Kit

tag: cell line

value: MDCKII

tag: culturing time

value: day 4


title: Tumor-151a


title: MDCKII AVL9-KD1 2D-D4 RNA-seq


title: MDCKII DENND5A-KD2 2D-D7 RNA-seq

value: day 7


title: Adult peripheral blood naïve CD4 T cells 4


title: Adult peripheral blood naïve CD4 T cells 2


title: Adult peripheral blood naïve CD4 T cells 5


title: Fetal peripheral blood naïve CD4 T cells 5

value: fetal


title: Adult peripheral blood naïve CD4 T cells 3


title: MDCKII DENND5A-KD2 2D-D4 RNA-seq


title: Adult peripheral blood naïve CD4 T cells 1


title: Fetal peripheral blood naïve CD4 T cells 4


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C10_ad004

tag: brain region


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C10_ad002

tag: Sex


title: MDCKII DENND5A-KD1 2D-D4 RNA-seq


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad012

tag: age


title: MDCKII AVL9-KD4 D0 RNA-seq

value: day 0


title: MDCKII DENND5A-KD2 D0 RNA-seq


title: Normal-NB 3

value: common reference


title: KO-3

city: shanghai

first: min

last: liu

address: huashan road

institute: shanghaijiaotong university

data_processing:
Illumina sequencing with paired-ends 2x150 as the sequencing mode
The clean reads were mapped to the mouse genome (assembly GRCm38) using the HISAT2 software
Gene expression levels were estimated using FPKM (fragments per kilobase of exon per million fragments mapped) by StringTie
To annotate genes with gene ontology (GO) terms, ClusterProfiler (R package) was used
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file including RPKM values for each Sample

source_name: Intestinal epithelial cells

extract_protocol:
IECs were isolated from Setd2f/f and Setd2Vil-KO mice treated for 4 d with DSS by EDTA-based isolation. Each sample contained 3 independent repeated animals
NEB Next Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) was used for the construction of sequencing libraries.

tag: strain

value: Two-month-old


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C10_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad007


title: KO-2


title: KO-1


title: MDCKII AVL9-KD1 D0 RNA-seq


title: Fetal peripheral blood naïve CD4 T cells 2

value: experimental


title: MDCKII 2D-D11-3 RNA-seq

value: wildtype

value: day 11


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad010

value: male


title: Tumor-121

value: Adrenocortical carcinoma


title: MDCKII DENND5A-KD1 D0 RNA-seq


title: MDCKII 2D-D11-2 RNA-seq


title: MDCKII DENND5A-KD1 2D-D7 RNA-seq


title: WT-3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad006


title: MDCKII 2D-D11-1 RNA-seq


title: MDCKII 2D-D4-3 RNA-seq


title: Fetal peripheral blood naïve CD4 T cells 3

value: umbilical cord blood

value: CD4 T cells


title: Fetal peripheral blood naïve CD4 T cells 1


title: WT-2


title: MDCKII 2D-D4-2 RNA-seq


title: WT-1


title: MDCKII 3D-D8-2 RNA-seq

value: day 8


title: MDCKII 3D-D5-2 RNA-seq

value: day 5


title: INPUT-KO

data_processing:
Illumina NextSeq 500 used for sequencing
The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 (v2.2.6) software
Peak detection was performed using the MACS (v2.1.1)  peak finding algorithm with 0.01 set as the p-value cutoff.
Annotation of peak sites to gene features was performed using the ChIPseeker R package.
Genome_build: mm10
Supplementary_files_format_and_content: This table is a file obtained by annotating the peak with the ChIPseeker package in the original file KO_peaks.narrowPeak.chr.xlsx after MACS2 search.

extract_protocol:
Intestinal epithelial cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti- H3K36me3 antibodies.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NextSeq 500 with single-end 1x75 as the sequencing mode.


title: INPUT-WT


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad008

value: SSs


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B9_ad001


title: MDCKII 3D-D3-2 RNA-seq

value: MDCKII

value: day 3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad002


title: MDCKII 3D24h-3 RNA-seq

value: 24 hour


title: MDCKII 3D24h-2 RNA-seq


title: MDCKII D0-3 RNA-seq


title: H3K36me3-KO


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B9_ad007


title: MDCKII 3D-D5-3 RNA-seq


title: H3K36me3-WT


title: MDCKII D0-4 RNA-seq


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B9_ad010


title: MDCKII D0-2 RNA-seq


title: day0_2 ATAC-seq

data_processing:
Sequencing reads were mapped to the Canfam3 genome using BWA v0.7.10.
Mitochondrial reads were removed.
ATAC-seq peaks were identified using MACS v2.1.1 (FDR 0.05).
Genome_build: canFam3
Supplementary_files_format_and_content: Bigwig files for each sample

growth_protocol: MDCKII cells were maintained in Eagle’s minimal essential medium with 5% fetal bovine serum, 10 mM HEPES, 2 mM glutamine, 100 U/ml penicillin, 100 mg/ml streptomycin; For 3D cultures, cells were grown on top of matrigel for 19 days. For 2D cultures, cells were seeded on transwell inserts grown until over-confluence (day4). The cells for seeding were regarded as day0 samples.

extract_protocol:
Day 0 and 2D cells were collected using cell scraper, and 3D cysts were isolated from m3atrigel with cell recovery solution (Corning). After washing with cold PBS, the cells were dissociated in lysis buffer (1% NP40, 10mM Tris pH7.5, 10mM NaCl, 3mM MgCl2, 1mM EDTA) using syringe. The samples were filtered with miracloth. Crude nuclei were sorted by flow cytometer (Beckman Coulter MoFlo XDP) with DAPI. The nuclei were pelleted and resuspended in the transposase reaction mix (25 μl 2xTagmentation buffer, 2.5 μL transposase and 22.5 μL nuclease-free water), and incubated at 37°C for 30 min.
Immediately following transposition, transposed DNA was purified with Qiagen minElute Reaction Cleanup Kit, and amplified using Phusion DNA polymerase (NEB) for 10-13 cycles.

value: day 1


title: day0_1 ATAC-seq

value: day 0


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B9_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_C1_ad004


title: 2D_1 ATAC-seq

value: day 4


title: 2D_2 ATAC-seq


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B9_ad008


title: 3D_2 ATAC-seq

value: day 20


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad012


title: 3D_1 ATAC-seq

value: day 19


title: ABI8plus

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

data_processing:
FastQC
Tophat2
Cufflinks
Supplementary_files_format_and_content: FPKM

organism: Brachypodium distachyon

source_name: ABI plus

extract_protocol:
RNA extraction using Sigma Spectrum Plant total RNA kit; library prep with Illumina TruSeq kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MTL-OX

tag: treatment

value: MeJA


title: ABI7plus


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad001

value: male


title: day0_3 ATAC-seq

value: day 2


title: ABI6minus

source_name: ABI minus

value: mock


title: ABI5minus


title: WT4plus

source_name: WT plus

value: WT


title: WT3plus


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad007


title: WT2minus

source_name: WT minus


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad010


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad004


title: WT1minus


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad002


title: depol 2 hours 4 [k2h4.small.rna]

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

data_processing:
Ribo-Seq:
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2.
Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, sequencing adapters were trimmed, low quality 3 prime nucleotides (Phred33 < 28) were removed and single 5 prime nucleotides were trimmed.
Reads were aligned to abundant short non-coding RNAs (rRNA, snRNA, snoRNA, miRNA) using 'Bowtie2' version 2.2.6. Unaligned reads were retained for further analysis.
Reads were mapped to the hg38 reference genome using 'Tophat2' version 2.1.1, and reads aligning to features were counted with 'HTSeq' version 0.7.2.
Counts were normalized using EdgeR version 3.8
mRNA-Seq:
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2.
Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, low quality 3 prime nucleotides (Phred33 < 28) were removed.
Reads were mapped to the hg38 reference genome using 'Tophat2' version 2.1.1, and reads aligning to features were counted with 'HTSeq' version 0.7.2.
Counts were normalized using EdgeR version 3.8
Small RNA-Seq:
Bcl files were demultiplexed and converted to fastq format using 'Bcl2fastq' version 2.2.
Lane data for each sample were merged.
Using 'Cutadapt' version 1.14, sequencing adapters were trimmed and low quality 3 prime nucleotides (Phred33 < 28) were removed.
For identification of tRNA-derived small RNA fragments, reads were aligned and counted against a reference file containing mature and precursor sequences obtained from gtRNAdb using 'tDR Mapper'.
For identification of microRNA, reads were mapped to the hg38 reference genome using 'Bowtie2' version 2.2.6 and reads aligning to mature microRNA (miRBase gtf file) were counted with 'HTSeq' version 0.7.2.
Counts were normalized using EdgeR version 3.8
Genome_build: hg38
Supplementary_files_format_and_content: cpm.mrna.r.0h.2h.txt: tab delimited text file containing mRNA-Seq gene-level counts per million
Supplementary_files_format_and_content: cpm.ribo.r.0h.2h.txt: tab delimited text file containing Ribo-Seq gene-level counts per million
Supplementary_files_format_and_content: cpm.mirna.r.0h.2h.txt: tab delimited text file containing microRNA counts per million
Supplementary_files_format_and_content: cpm.trna.r.0h.2h.txt: tab delimited text file containing tRNA-derived small RNA counts per million

source_name: depol 2 hours 4

growth_protocol: SH-SY5Y cultures were neuronally differentiated using all-trans retinoic acid (ATRA; Sigma-Aldrich) (Encinas et al. 2000). One day prior to differentiation (day -1), cells were seeded at a density of 25,000 cells/cm2 in complete culture medium. The next day (day 0), standard culture medium was replaced with ATRA-supplemented medium (10µM final) and cells were wrapped in foil to protect from light exposure. ATRA-medium was subsequently replaced on days 2, 4 and 6, after which the methods were continued as described on day 7.

extract_protocol:
Cells were exposed to cycloheximide (0.1mg/mL) prior to detergent lysis and scraping as per the Illumina TruSeq Ribo Profile kit manual.
Production of ribosome protected mRNA fragments (RPFs) and library preparation were then performed using the Illumina TruSeq Ribo Profile kit (H/M/R), with minor amendments to the manufacturer’s protocol. Briefly, 300µL clarified lysate was treated with 9µL RNase I (45 min) to digest unprotected RNAs, after which reactions were stopped with 15µL SUPERase inhibitor (Invitrogen). Small RNA fragments were then enriched using MicroSpin S-400 columns (GE Life Sciences), prior to ribosomal RNA depletion, RPF size selection, end repair, adapter ligation, reverse transcription and PAGE purification, conducted according to the manufacturer’s instructions. RPF cDNA amplicons were subsequently produced with 12x PCR cycles, adapter dimers were removed via 8% native polyacrylamide gel and samples were quantified via Agilent high sensitivity DNA chip. For sequencing, samples were pooled in equal volumes and concentrations, denatured with NaOH (0.2mM) and diluted to a final concentration of 1.8pM in Tris-HCl (200mM, pH 7) and HT1 buffer. RPF libraries were then subjected to 76 single-end sequencing cycles using the Illumina NextSeq 500 benchtop sequencer.

treatment_protocol: Depolarised cells were incubated in Hank's Balanced Salt Solution (35mM NaCl, 0.6mM MgSO4.7H2O, 2.5 mM CaCl2.2H2O, 10mM HEPES, 6mM Glucose) supplemented with stimulating concentrations of KCl (100mM). Cells were incubated for 3 min at room temp, then rested at standard culturing conditions for 10 min. A total of 4 consecutive stimulus-rest cycles were conducted, after which cells were harvested either immediately or 2 hours after the final stimulus-rest cycle.

value: Neuronally differentiated SH-SY5Y

tag: passages

tag: depolarised

value: Yes

tag: molecule subtype

value: small RNA


title: depol 2 hours 4 [k2h4.ribo]

tag: cell type

value: ribosome-protected mRNA


title: Control-2

city: Hong Kong

first: Honglin

last: Chen

address: Rm 5-19, 5/F, Lab block, 21 Sassoon Road, Pokfulam

department: Department of Microbiology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples with each sample having an average throughput of 87.7Gb and a total throughput of 11.7Gb. In terms of sequence quality, an average of 94% of the bases achieved a quality score of Q30 where Q30 denotes the accuracy of a base call to be 99.9%.
Fastq reads were subsequently aligned to the Golden Hamster and SARS-CoV-2 genome (NCBI Reference Sequence: NC_045512.2 ) with STAR (V2.7.2a) and counts were generated through its in-built htseq-count algorithm. (STAR parameters used: --readFilesCommand gunzip -c --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts).
Genes with a total read count below 10 were excluded from downstream analysis.
Differential Expression Analysis utilised DESeq2 which also was used to normalised expression values.
All analysis was performed through the R environment.
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Raw counts and normalized expression tables are in comma-separated (.csv) format with genes distributed as rows and samples as columns.

organism: Mesocricetus auratus

source_name: Hamster Lung Tissue

growth_protocol: Viruses were isolated from 5 confirmed COVID-19 patients for this study.  For animal challenge, viral stocks were prepared after two serial passages in Vero E6 cells (ATCC; CRL-15786) in Dulbecco’s Modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 5% Fetal Bovine Serum (Thermo Fisher Scientific), and 100 IU penicillin G/ml and 100 ml streptomycin sulfate/ml, (Thermo Fisher Scientific).

extract_protocol:
Lung left inferior lobe from hamsters were cut into pieces and lysed with RA1 lysis buffer provided with the NucleoSpin® RNA Plus kit (Macherey-nagel), RNA extraction was performed according the manufacture’s instruction, including an on-column genomic DNA digestion step.
1 µg of high-quality total RNA (RIN>8) was used as starting material for cDNA library preparation with KAPAmRNA HyperPrep Kit. In brief, Poly-A containing mRNA was collected by using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented to 200 – 300 bp by incubating at 94oC for 6 min in the presence of magnesium ions. The fragmented mRNA was then applied as template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds cDNA underwent, 3’ adenylation and indexed adaptor ligation. The adaptor-ligated libraries were enriched by 10 cycles of polymerase chain reaction (PCR). The libraries were denatured and diluted to optimal concentration.

treatment_protocol: Virus stock was diluted with Phosphoate-buffered saline (PBS) to 2 x 104 PFU/ml.  Hamsters with anesthetized and then intranasally inoculation with 50 ul of diluted viruses containing 103 PFU of viruses.  Nasal washes were collected from hamster at 3 dpi and 5 dpi.

value: Lung

tag: gender

value: Female

value: 8-9 weeks

tag: viral titre


title: depol 2 hours 4 [k2h4.mrna]

value: Poly(A) mRNA


title: IL-7Rα high reversed 2

city: Seoul

first: Hang-Rae

last: Kim

address: 103 Daehak-ro, Jongno-gu

department: Anatomy and Cell Biology

institute: Seoul National University College of Medicine

description: healthy individual 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalized with robust spline normalization (rsn) method in R

label: biotin

source_name: IL-2 reversed IL-7Rα high

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

value: effector memory (EM) CD8+ T cells

value: peripheral blood

tag: sample type

value: IL-2 reversed IL-7Rα high


title: Control-1


title: IL-7Rα low reversed 1

description: healthy individual 1

source_name: IL-2 reversed IL-7Rα low

value: IL-2 reversed IL-7Rα low


title: IL-7Rα low fresh 2

description: healthy individual 2

source_name: fresh IL-7Rα low

value: fresh IL-7Rα low


title: IL-7Rα low reversed 2

description: healthy individual 2

value: male


title: IL-7Rα high fresh 2

description: healthy individual 2

source_name: fresh IL-7Rα high

value: fresh IL-7Rα high


title: depol 2 hours 3 [k2h3.ribo]

source_name: depol 2 hours 3


title: depol 2 hours 3 [k2h3.small.rna]


title: HK-95-1

value: 2 x 10 4 PFU/ml.


title: IL-7Rα high fresh 1

description: healthy individual 1


title: HK-95-2


title: IL-7Rα high reversed 1

description: healthy individual 1


title: IL-7Rα low fresh 1

description: healthy individual 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B7_ad008

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

value: SSs


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad012


title: depol 2 hours 3 [k2h3.mrna]

value: Neuronally differentiated SH-SY5Y


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad001


title: depol 2 hours 2 [k2h2.small.rna]

source_name: depol 2 hours 2

value: Yes


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad007


title: depol 2 hours 1 [k2h1.small.rna]

source_name: depol 2 hours 1

value: small RNA


title: depol 2 hours 2 [k2h2.mrna]


title: HK-92-3


title: depol 2 hours 2 [k2h2.ribo]

value: ribosome-protected mRNA


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad010


title: HK-92-2

value: Lung


title: depol 2 hours 1 [k2h1.ribo]


title: depol 0 hours 4 [k0h4.ribo]

source_name: depol 0 hours 4


title: depol 0 hours 4 [k0h4.small.rna]


title: depol 2 hours 1 [k2h1.mrna]


title: depol 0 hours 4 [k0h4.mrna]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad006


title: HK-92-1

value: Female


title: depol 0 hours 3 [k0h3.small.rna]

source_name: depol 0 hours 3


title: depol 0 hours 3 [k0h3.ribo]


title: HK-15-3

value: 8-9 weeks


title: depol 0 hours 3 [k0h3.mrna]

value: Poly(A) mRNA


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad004


title: HK-15-2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad002


title: depol 0 hours 2 [k0h2.ribo]

source_name: depol 0 hours 2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B6_ad008


title: depol 0 hours 2 [k0h2.small.rna]


title: depol 0 hours 1 [k0h1.small.rna]

source_name: depol 0 hours 1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B5_ad012


title: depol 0 hours 1 [k0h1.ribo]


title: depol 0 hours 1 [k0h1.mrna]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B5_ad001


title: HK-13-2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B5_ad010


title: HK-13-1


title: HK-13-3


title: resting 4 [r4.small.rna]

source_name: resting

value: No


title: resting 4 [r4.ribo]


title: resting 4 [r4.mrna]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B5_ad007


title: HK-8-3


title: resting 3 [r3.ribo]


title: resting 3 [r3.small.rna]


title: resting 3 [r3.mrna]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B5_ad006


title: depol 0 hours 2 [k0h2.mrna]


title: HK-15-1


title: resting 2 [r2.ribo]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B5_ad008


title: resting 2 [r2.small.rna]


title: HK-8-2


title: resting 2 [r2.mrna]


title: resting 1 [r1.small.rna]


title: resting 1 [r1.ribo]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad012


title: resting 1 [r1.mrna]


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad001


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad007


title: stage4 rep7

city: Cambridge

first: Ya

last: Min

state: Massachusetts

address: 16 Divinity Ave.

institute: Harvard University

description: apex of floral bud consumed by developing carpel primordia

data_processing:
Sequencing was conducted at Novogene (Beijing, China) using the 150 bp paired-end Illumina HiSeq4000 sequencing platform.
The raw sequencing reads were filtered by removing adapters and low-quality reads using Trim Galored v0.6.5 17 (quality Phred score cutoff = 20) and mapped to the Aquilegia coerulea ‘Goldsmith’ v3.1 reference transcriptome (https://phytozome.jgi.doe.gov/) using Kallisto v0.46.118.
Supplementary_files_format_and_content: Tab Separated Value files including estimated counts and tpm for each sample.

organism: Aquilegia coerulea

source_name: floral meristems

growth_protocol: Seeds of Aquilegia coerulea ‘Kiragami’ were purchased from Swallowtail Garden Seeds (Santa Rosa, CA, USA). Seeds were germinated in wet soil and seedlings were grown under conditions of 16h daylight at 18˚C and 8 h dark at 13˚C.

extract_protocol:
Once the plants developed approx. six true leaves, they were transferred into vernalization conditions (16h daylight at 6˚C and 8h dark at 6˚C) for three to four weeks, and subsequently moved back to the regular growth condition. Once the inflorescences started to develop, axillary FMs were quickly dissected on ice using surgical needles and flash frozen in liquid nitrogen. Three sepals were removed from every floral bud collected. The total RNA of all samples was extracted using the RNeasy Micro Kit (Qiagen, Netherlands).
Sequencing libraries were prepared by the Bauer Core facility of Harvard University using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA, Inc., CA, USA) for cDNA synthesis and Illumina Nextera XT (Illumina) for library preparation. Libraries were fragmented to an average size of 350 bp.

treatment_protocol: all wild-type

tag: cultivar

value: Kiragami

value: floral meristems

tag: developmental stage

value: developmental stage4

tag: genotype

value: wild-type


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad006

city: La Jolla

value: male


title: stage4 rep4

tag: tissue


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad010


title: stage4 rep6


title: HCEC 1CT_APC KD-1

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

address: 291, Daehak-ro

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Colonic Epithelial Cells

growth_protocol: HCEC 1CT_WT and APC KD cells were routinely cultured in HCEC culture media (DMEM:M199=4:1) supplemented with EGF (20 ng/mL), hydrocortisone (1ug/mL), insulin (10 ug/mL), Sodium selenite (5nM), transferrin (2 ug/mL), and 2% FBS at 37°C in 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: No Treatment

tag: cell line

value: HCEC

value: Human colonic epithelial progenitor cells

value: APC KD


title: HCEC 1CT_APC KD-3


title: HCEC 1CT_WT-3

value: WT


title: HCEC 1CT_WT-1


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad002

tag: brain region

value: SSs


title: stage4 rep3


title: HK-8-1

value: 2 x 10 4 PFU/ml.


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B3_ad012

tag: Sex


title: stage4 rep1


title: stage4 rep2


title: HCEC 1CT_APC KD-2


title: stage4 rep8


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B3_ad001

tag: age


title: siCM1_sample1

city: Taipei

first: Yi-Shuian

last: Huang

state: Nangang

address: 128 Academia Road, Section 2

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

hyb_protocol: Cy3-label cRNA was fragmented to ~50-100 nt, which were used for hybridization to Agilent SurePrint Microarray (whole rat genome 4x44K microarray) at 65°C for 17 h.

scan_protocol: After washing, the microarrays were dried by nitrogen air and canned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: The scanned images were analyzed by Feature extraction 10.7.3.1 software (Agilent Technologies, USA)

organism: Rattus norvegicus

source_name: DIV7 cultured corticial neurons

label_protocol: Total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA).

growth_protocol: Rat cortical neurons were prepared from E18.5 embryos and cultured in neurobasal medium until the designated days for experiments.

extract_protocol: Neurons were rinsed once with PBS and then extracted with TriZol to prepare total RNAs.

treatment_protocol: Cultured neurons were infected with lentiviruses expressing control or Cmtr1 shRNA at DIV2 and harvested at DIV7.

value: both genders

tag: strain

value: Sprague Dawley

tag: embrayonic stage

tag: organ

value: cortices

value: primary cultured neurons

tag: shRNA

value: shCM1 lentivirus


title: HCEC 1CT_WT-2


title: siCM1_sample2


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B4_ad004

institute: HHMI-Salk-Institute


title: stage4 rep5


title: siCTL_sample1

description: control

value: shCTL


title: siCTL_sample2

description: control


title: stage3 rep8

description: rims of carpel primordia elevated

value: Kiragami

value: developmental stage3


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B3_ad007


title: stage3 rep6

description: rims of carpel primordia elevated

value: floral meristems


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B3_ad006


title: stage3 rep7

description: rims of carpel primordia elevated

value: wild-type


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B3_ad002

value: male


title: stage3 rep5

description: rims of carpel primordia elevated


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B3_ad008


title: S24M-3

city: Wuhan

first: Ying

last: He

address: 1095 Jiefan Avenue

institute: Institute of Organ Transplantation

description:
S24M_3_NS
Liver tissue were obtained from different ages 24M Lewis rats

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 9.5.3 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 10.0 (Agilent technologies, Santa Clara, CA, US).

source_name: 24 months-old male rat liver

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: All animals were housed under specific pathogen-free conditions with a 12-h light/dark cycle and all animals had free access to food and water

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: Liver tissue were obtained from different ages(3M ,9M ,12M ,18M, 24M) Lewis rats , placed in liquid nitrogen to freeze and then transferred to the -80℃ to save until to be used.

value: Lewis rat

value: 24 months

value: liver


title: S18M-3

description:
S18M_3_NS
Liver tissue were obtained from different ages 18M Lewis rats

source_name: 18 months-old male rat liver

value: 18 months


title: S24M-4

description:
S24M_4_NS
Liver tissue were obtained from different ages 24M Lewis rats


title: S12M-3

description:
S12M_3_NS
Liver tissue were obtained from different ages 12M Lewis rats

source_name: 12 months-old male rat liver

value: 12 months


title: S24M-1

description:
S24M_1_NS
Liver tissue were obtained from different ages 24M Lewis rats


title: S18M-1

description:
S18M_1_NS
Liver tissue were obtained from different ages 18M Lewis rats


title: S18M-4

description:
S18M_4_NS
Liver tissue were obtained from different ages 18M Lewis rats


title: S12M-4

description:
S12M_4_NS
Liver tissue were obtained from different ages 12M Lewis rats


title: S24M-2

description:
S24M_2_NS
Liver tissue were obtained from different ages 24M Lewis rats


title: stage3 rep4

description: rims of carpel primordia elevated


title: S12M-2

description:
S12M_2_NS
Liver tissue were obtained from different ages 12M Lewis rats


title: S9M-3

description:
S9M_3_NS
Liver tissue were obtained from different ages 9M Lewis rats

source_name: 9 months-old male rat liver

value: 9 months


title: S9M-2

description:
S9M_2_NS
Liver tissue were obtained from different ages 9M Lewis rats


title: S9M-1

description:
S9M_1_NS
Liver tissue were obtained from different ages 9M Lewis rats


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad007

value: SSs


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad001


title: Primary myoblasts H3K4me3

city: Ottawa

first: Theodore

last: Perkins

state: Ontario

address: 501 Smyth Rd.

department: Regenerative Medicine Program

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Reads mapped to genome by bowtie version 1.1.0: bowtie -l 32 --strata --best -y --chunkmbs 3072 -n 2 -m 1 -p 4
Mapped reads sorted: samtools sort
Mapped reads deduplicated: samtools rmdup
Read intervals converted to bed: bedtools bamtobed
Read intervals extended to 200bp: bedtools slop -s -l 0 -r 200
Read intervals sorted: bedtools sort
Clip read intervals to stay within chromosome bounds: bedClip
Compute coverage from read intervals: bedtools genomecov -bg
Convert bedgraph to bigwig: bedGraphToBigWig
Genome_build: GRCm38
Supplementary_files_format_and_content: Bigwig coverage files

source_name: Primary myoblasts

growth_protocol: Ham's F10 supplements with 20% FBS and 2.5 ng/ml of bFGF

extract_protocol:
DNA/protein complexes were cross-linked by 1% formaldehyde in PBS followed by ChIP as described previously (Soleimani et al. 2018 Nucleic Acids Research)
Libraries were prepared according to Illumina library preparation protocol as described previously (Soleimani et al. 2012 Molecular Cell)

value: Mouse primary myoblasts

tag: antibody

value: ChIP antibody Cat # 8580 Abcam


title: stage3 rep2

description: rims of carpel primordia elevated


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad012


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad010


title: Primary myoblasts H3K4me1

tag: cell type

value: ChIP antibody Cat # 5326, Cell Signaling


title: stage3 rep1

description: rims of carpel primordia elevated


title: stage2 rep8

description: staminode primordia finish initiating

value: developmental stage2


title: stage3 rep3

description: rims of carpel primordia elevated


title: stage2 rep7

description: staminode primordia finish initiating


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad006


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad004


title: stage2 rep6

description: staminode primordia finish initiating


title: S3M-3

description:
S3M_3_NS
Liver tissue were obtained from different ages 3M Lewis rats

source_name: 3 months-old male rat liver

value: 3 months


title: S3M-2

description:
S3M_2_NS
Liver tissue were obtained from different ages 3M Lewis rats


title: stage2 rep5

description: staminode primordia finish initiating

value: Kiragami


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B2_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: S3M-1

description:
S3M_1_NS
Liver tissue were obtained from different ages 3M Lewis rats


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_ad012


title: stage2 rep4

description: staminode primordia finish initiating


title: stage2 rep3

description: staminode primordia finish initiating


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_ad007


title: CEMBA181210_5C_1_CEMBA181210_5C_2_B12_ad008


title: Retina from C3H WT mice, PN35, biological rep 1

city: Paris

first: Frederic

last: Blond

address: 17 rue Moreau

country: France

institute: Institut de la Vision

description:
Sample name: wtwt_d35_1
retina from WT C3H mouse aged 35 days

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2007, Affymetrix).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner

data_processing: Normalization: RMA, data analysis: R/Bioconductor

source_name: Retinal RNA from C3H WT mice

label_protocol: The cDNA was transcribed in vitro using RNA Transcript Labeling kit (ENZO Diagnostics, Farmingdale, NY) to form biotin-labeled cRNA

extract_protocol: Neural retinas from wild-type control (C3Hwt/wt) and rd1 (C3Hrd1/rd1) mice were dissected at different post-natal days. Total RNA was purified onto cesium gradient.

tag: genotype/variation

value: WT

value: retina


title: Retina from C3H WT mice, PN28, biological rep 1

description:
Sample name: wtwt_d28_1
retina from WT C3H mouse aged 28 days