title: WT_stage7_rep1

city: University Park

first: Zhao

last: SU

state: PA

address: 354 N. Frear

department: Biology

institute: The Penn State University

description:
replicate1
all_info.xlsx

data_processing:
Raw sequencing reads were examined using FastQC and adapter sequences were trimmed from both ends of the raw reads using Trimmomatic (Bolger, Lohse & Usadel, 2014). Low-quality base calls (Q < 30) were also trimmed from both the 5’ and 3’ ends of the reads. Reads from each of the four libraries were then mapped independently to the rice genome (IRGSP-1.0) using Tophat2, with a GTF (Gene Transfer File) annotation file supplied as an option. Transcript abundance and differential gene expression were calculated using Cufflinks. Gene expression levels were normalized using fragments per kilobase of exon per million mapped reads (FPKM). After confirming high correlation in transcriptome expression levels between biological replicates, data from the replicates were merged using Cuffmerge. Cuffdiff was used to calculate q values (FDR adjusted p-values) to identify differentially expressed (DE) genes between WT and d1. Differentially expressed genes (DE) were defined as those with q value less than 0.05 and with FPKM greater than 1 in either of datasets. DE genes with q values less than 0.05 were further divided into genes up-regulated in d1 as compared to WT control and genes down-regulated in d1 as compared to WT control.
Genome_build: ensemblgenomes_Oryza_sativa_release_45
Supplementary_files_format_and_content: excel file with expression data

organism: Oryza sativa

source_name: Shoot Apical Meristem

growth_protocol: Wild-type (WT) and d1-1 mutant plants were grown in a greenhouse. Plants were grown individually in 2 US gallon pots containing Metro-mix 360 potting mixture (Sun Gro Horticulture Canada Ltd). Growth temperatures averaged 30˚C during the day with peaks of 35˚C at midday; night temperature was 25˚C. The day:night cycle was 16:8 with light supplied as natural daylight supplemented with 1000W metal halide lamps (Philips Lighting Co., Somerset, NJ) for the duration of the light cycle. Light intensity averaged 500 μmol m-2 s-1 PPFD. Plants were grown for 100 days before use in experiments.

extract_protocol:
Total RNA was extracted from each sample using the NucleoSpin RNA Plant kit. After examination of the quality (Bioanalyzer, Agilent) and quantity (NanoDrop 2000, ThermoFisher) of each RNA sample.
Total RNA samples were sent to the Genomics Core Facility at Penn State University for the standard RNA-seq library preparation and next generation sequencing (Hiseq 2500, Illumina).

value: Meristem

value: Panicle initiation


title: WT_stage4_rep2

status: Public on Feb 19 2020

type: SRA

country: USA

description:
replicate2
all_info.xlsx

library_source: transcriptomic

molecule: total RNA

tag: age

tag: tissue

tag: Stage


title: 201148310018_R01C02

type: genomic

city: Langston

first: Yonathan

last: Tilahun

state: OK

address: 100 Success Dr.

department: Extension

institute: Langston University

description: Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping Beadchips (Illumina).

hyb_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.

data_processing:
Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping BeadChips (Illumina).
Image data was analyzed using Genome Studio and further analysis was conducted using PLINK, R, Qlik, and GoldenHelix SNP &Variation Suite

label: Cy3, Cy5

molecule: genomic DNA

organism: Capra hircus

source_name: Milk Somatic Cells

extract_protocol: Norgen Biotek Corp. Milk DNA Preservation and Isolation Kit was used to extract genomic DNA from Bronopol preserved goat milk somatic cells.

treatment_protocol: Goat milk obtained from different sources and different locations throughout the United States were preserved by Bronopol tablet placement in the milk before shipment and downstream procedures.

tag: Sex

value: Female

value: Milk Somatic Cells


title: 201148310018_R02C01

scan_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.


title: WT_stage2_rep2

description:
replicate2
all_info.xlsx


title: WT_stage2_rep1

description:
replicate1
all_info.xlsx


title: 201148310021_R11C01

label_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.


title: 201148310021_R10C01


title: WT_stage4_rep1

description:
replicate1
all_info.xlsx


title: WT_stage1_rep2

description:
replicate2
all_info.xlsx


title: WT_stage1_rep1

description:
replicate1
all_info.xlsx


title: 201148310021_R12C01


title: 201148310021_R09C01


title: d1_stage7_rep1

description:
replicate1
all_info.xlsx


title: d1_stage7_rep2

description:
replicate2
all_info.xlsx


title: 201148310018_R05C01


title: 201148310021_R08C01


title: d1_stage4_rep2

description:
replicate2
all_info.xlsx


title: WT_stage7_rep2

description:
replicate2
all_info.xlsx


title: 201148310021_R07C01


title: d1_stage4_rep1

description:
replicate1
all_info.xlsx


title: 201148310018_R03C01


title: d1_stage2_rep2

description:
replicate2
all_info.xlsx


title: 201148310021_R05C01


title: d1_stage2_rep1

description:
replicate1
all_info.xlsx


title: 201148310021_R04C01


title: d1_stage1_rep2

description:
replicate2
all_info.xlsx


title: 201148310018_R01C01


title: 201148310021_R03C01


title: d1_stage1_rep1

description:
replicate1
all_info.xlsx


title: 201148310015_R12C01


title: 201148310021_R01C01


title: 201148310015_R12C02


title: 201148310015_R11C02


title: SAP rep1

city: Chengdu

first: Yi

last: Yang

state: 四川

address: NO. 270, Rongdu Avenue

country: China

institute: The General Hospital of Western Theater Command

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: mm10
Supplementary_files_format_and_content: Number of raw junction read

organism: Mus musculus

source_name: pancreatic tissues

extract_protocol:
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA).

treatment_protocol: mice were randomly divided into control group and SAP group and anesthetized with 5% isoflurane (via induction box) prior to surgery. The SAP model was induced by a standardized pressure-controlled retrograde infusion of 4% sodium taurocholate into the biliopancreatic duct by using a micro infusion pump. All animals were sacrificed and sampled 24 h after induction of pancreatitis.

value: pancrease

tag: disease

value: Severe acute pancreatitis


title: 201148310015_R11C01


title: SAP rep3


title: SAP rep2


title: 201148310015_R10C02


title: control rep2

value: control


title: 201148310015_R10C01


title: 201148310015_R09C02


title: P19_4-6_Cap

city: New York

first: Hanseul

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: back skin

extract_protocol:
Mouse skin blood endothelial cells and lymphatic endothelial cells were purified from CD1 wildtype mice at postnatal day 19. Each sample was pooled from 3 different mice
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8. Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 machines.

value: back skin

value: pooled male and female

tag: strain

tag: genotype

value: wild type

tag: sorting markers


title: control rep1


title: P19_1-3_Cap


title: P19_4-6_Collect


title: 201148310021_R06C01


title: P19_1-3_Collect


title: 201148310015_R07C02


title: 201148310015_R08C01


title: P19_1-3_BV


title: P19_4-6_BV


title: 201148310015_R08C02


title: 201148310021_R02C01


title: Control_6

city: San Francisco

first: Timothy

last: Marsh

state: California

address: 513 Parnassus Ave, Box 0502, HSW475

department: Pathology

institute: University of California, San Francisco

description: Metastatic PyMT tumor cells isolated from lung

data_processing:
Illumina RTA (v2.0) was used for basecalling.
Transcripts were pseudo-aligned and quantified (TPM) with Kallisto (v0.44.0)
Differential expression of Kallisto output was computed using DeSeq2 (v3.8)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Raw counts of sequencing reads and DESeq2 output

source_name: PyMT tumor cells

extract_protocol:
Qiagen RNeasy Micro was used to extract RNA and DNAseI was used to eliminate residual DNA.
Libraries were prepared using standard Illumina Nextera XT protocols

value: ATG12 F/F

value: 6-week old

value: female

value: Mouse mammary tumor Cells


title: ATG12_knockout_5

value: ATG12 KO


title: 201148310015_R07C01


title: 201148310015_R06C02


title: ATG12_knockout_4


title: control rep3


title: 201148310015_R05C02


title: 201148310015_R06C01


title: Control_5


title: 201148310015_R05C01


title: Control_4


title: ATG12_knockout_2


title: Control_3


title: ATG12_knockout_3


title: 201148310015_R03C02


title: 201148310015_R09C01


title: ATG12_knockout_1


title: 201148310015_R02C02


title: 201148310015_R04C01


title: Control_1


title: Control_2


title: 201148310015_R03C01


title: 201148310015_R01C01


title: 201148310015_R02C01


title: 201148310015_R01C02


title: 30B_Ant

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Mouse back skin

extract_protocol:
Mouse hair follicle stem cells were purified from Krt14-H2BGFP mice along the hair cycle.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8. Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 machines.

value: transgenic for Krt14-H2B-GFP

tag: tissue location

value: anterior

tag: cell type

value: hair follicle stem cells

value: EGFP (high), CD45 (neg) CD31 (neg) CD140a (neg), DAPI (ned), Sca-1 (neg), Alfa 6 integrin  (pos) CD34 (pos)


title: 30A_Ant


title: 201148310008_R12C02

value: Female


title: 201148310008_R11C01

value: Milk Somatic Cells


title: 201148310008_R10C01


title: 201148310008_R11C02


title: 201148310008_R09C01


title: 201148310015_R04C02


title: 201148310008_R12C01


title: 201148310008_R09C02


title: 201148310008_R08C02


title: 201148310008_R10C02


title: M0D055239A_S_B5_TF_NA_NF_FHL

city: Merced

first: Lauren

last: Schiebelhut

state: CA

address: 5200 N. Lake Rd.

institute: University of California, Merced

data_processing:
Trim Galore v. 0.4.4_dev was used to trim adapters, low quality bases (<Q20), and reads less than 20bp.   Genestack v. 0.72.1 (https://genestack.com/) was used for analyses of trimmed sequences. Trimmed paired-end reads were subsampled to 5 million reads (smallest library size) and aligned to the Pisaster ochraceus nuclear genome using TopHat2 v. 2.0.13 (Kim et al., 2013) allowing 2 mismatches per read and yielding mean 2,599,568 mapped reads per library (range: 2,313,438–2,969,060).  Raw coverage in genes  was quantified using SAMtools v. 0.1.19 (Li et al., 2009). Differential gene expression was tested using EdgeR (McCarthy, Chen, & Smyth, 2012). Given the small sample sizes of individuals included in the asymptomatic (n = 2) compared to symptomatic (n = 2) analyses, a minimum criterion of CPM > 1 in a minimum of two libraries per asymptomatic and/or symptomatic categories was used. Gene enrichment analyses were performed in DAVID for the annotated differentially expressed genes (Huang, Sherman, & Lempicki, 2008, 2009) using the list of Pisaster ochraceus annotated genes as background.
genome annotation on DRYAD https://doi.org/10.6071/M3ND50
Genome_build: NCBI; BioProject PRJNA532896, SUB5448653; genome annotation on DRYAD https://doi.org/10.6071/M3ND50
Supplementary_files_format_and_content: compressed text file with raw counts per gene

organism: Pisaster ochraceus

source_name: Tube feet

extract_protocol:
Qiagen RNeasy Mini Kit
Illumina TruSeq RNA Library Prep Kit v2

tag: batch

tag: color

tag: disease status

value: Symptomatic

tag: feeding status

value: Not feeding

tag: individual id

tag: site

value: Friday Harbor Lab

tag: size

value: Tube feet


title: M0D055239A_A_B5_TF_NA_NF_FHL

value: Asymptomatic


title: M0D055236X_S_B5_DE_MD_NF_LHM

source_name: Dermis

value: Orange

value: Lifeboat House (LHM)

value: medium

value: Dermis


title: M0D055236X_S_B5_TF_MD_NF_LHM


title: 201148310008_R07C01


title: 201148310008_R07C02


title: 201148310008_R08C01


title: M0D055234V_A_B5_PC_LG_NF_LHM

source_name: Pyloric cecum

value: Purple

value: large

value: Pyloric cecum


title: 201148310008_R06C01


title: 201148310008_R05C02


title: 201148310008_R06C02


title: 201148310008_R04C02


title: M0D055233U_S_B2_TF_LG_NF_CCM

value: Brown

value: McClures Beach (CCM)


title: M0D055232T_A_B1_TF_LG_FD_CCM

value: Feeding


title: M0D055232T_A_B1_PC_LG_FD_CCM


title: M0D055234V_A_B5_DE_LG_NF_LHM


title: M0D055233U_S_B2_PC_LG_NF_CCM


title: 201148310008_R04C01

value: Female


title: M0D055236X_S_B5_PC_MD_NF_LHM


title: M0D055232T_A_B1_DE_LG_FD_CCM


title: M0D055231S_A_B5_TF_XL_FD_CCM

value: xlarge


title: 201148310008_R03C02

value: Milk Somatic Cells


title: M0D055234V_A_B5_TF_LG_NF_LHM

value: Not feeding


title: 201148310008_R03C01


title: 201148310008_R02C02


title: 201148310008_R02C01


title: M0D055231S_A_B5_DE_XL_FD_CCM


title: M0D055231S_A_B5_PC_XL_FD_CCM


title: M0D055230R_A_B1_PC_XL_NF_CCM

value: LXL-XL


title: 201148310008_R01C01


title: M0D055233U_S_B2_DE_LG_NF_CCM

value: Symptomatic


title: 201148310004_R12C01


title: M0D055229Q_A_B3_DE_XL_NF_CCM

value: Asymptomatic


title: 201148310004_R12C02


title: 201148310008_R05C01


title: M0D055229Q_A_B4_PC_XL_NF_CCM


title: 201148310004_R11C02


title: M0D055228P_A_B3_DE_XL_NF_CCM

value: Orange


title: 201148310004_R11C01


title: 201148310004_R10C02


title: 201148310004_R10C01


title: M0D055227O_A_B3_PC_LG_NF_CCM


title: 201148310004_R09C02


title: M0D055227O_A_B3_DE_LG_NF_CCM


title: M0D055226N_A_B4_TF_LG_NF_CCM

value: Tube feet


title: 201148310008_R01C02


title: M0D055230R_A_B1_TF_XL_NF_CCM


title: 201148310004_R09C01


title: M0D055226N_A_B2_PC_LG_NF_CCM


title: 201148310004_R07C02


title: M0D055226N_A_B2_DE_LG_NF_CCM


title: 201148310004_R07C01


title: 201148310004_R06C02


title: 201148310004_R08C02


title: M0D055225M_A_B4_PC_LG_NF_CCM


title: M0D055225M_A_B2_TF_LG_NF_CCM


title: M0D055228P_A_B4_PC_XL_NF_CCM


title: 201148310004_R08C01


title: M0D055225M_A_B2_DE_LG_NF_CCM


title: 201148310004_R06C01


title: M0D055224L_A_B3_TF_MD_NF_CCM

value: medium

value: S-SM


title: M0D055228P_A_B3_TF_XL_NF_CCM


title: M0D055227O_A_B4_TF_LG_NF_CCM


title: M0D055224L_A_B3_PC_MD_NF_CCM


title: 201148310004_R05C01


title: M0D055224L_A_B2_DE_MD_NF_CCM

value: Dermis


title: M0D055223K_A_B3_PC_MD_NF_CCM


title: M0D055223K_A_B3_DE_MD_NF_CCM


title: 201148310004_R04C02


title: 201148310004_R04C01


title: 201148310004_R03C02


title: 201148310004_R05C02


title: M0D055223K_A_B2_TF_MD_NF_CCM


title: M0D055222J_A_B4_PC_MD_NF_CCM


title: Grp-4-1

city: Boston

first: Abir

last: Yamak

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description:
RNA from NkxCre.Asb2fl/fl.Flnafl/fl  mice
G4_vs_G1_CPM_log2FC_FDR_complete_table
G4_vs_G2_CPM_log2FC_FDR_complete_table

data_processing:
libraries were sequenced using illumina HiSeq platform.
Splice-aware alignment program STAR was used to map the sample sequencing reads to the Mus musculus mm10 reference genome
Gene expression counts were calculated using HTSeq based on current Ensembl annotation for mm10
The R package “edgeR” was then employed to make differential gene expression calls
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files

source_name: heart

extract_protocol:
RNA extraction was done using the Qiagen RNeasy Micro Kit (Cat No. 74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age


title: Grp-4-3


title: Grp-4-2


title: 201148310004_R03C01

tag: tissue


title: animals with cancer treated with chemotherapy bio rep 4

type: RNA

city: Atlanta

first: Stephen

middle: Nicholas

last: Housley

state: GA

address: 555 14th Street

institute: Georgia Institute of Technology

hyb_protocol: Amplified and labeled RNA was hybridized to Gene Chip Rat Transcriptome Array 2.0 (Affymetrix).

scan_protocol: Scan on Affymetrix GeneChip scanner 3000 7G.

data_processing:
Raw mRNA expression data were processed using Affymetrix Expression Console (EC) software Version 1.4.
Raw data probes were normalized using SST-RMA algorithm. Differentially expressed genes (DEG) were determined through a linear fixed effects model (limma) with a robust empirical Bayes (eBayes) framework to moderate the residual variances (1.4 fold change and FDR <1% for multiple test correction across contrasts).

label: biotin

organism: Rattus norvegicus

source_name: sensory neurons extracted from dorsal root ganglia

label_protocol: Labeling of RNAs was performed with the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, ThermoFisher). Gene expression was determined by microarray analysis on the Affymetrix platform (Rat Transcriptome Array 2.0).

growth_protocol: NA. (Adult rats were used for this study)

extract_protocol: RNAs were isolated and purified from sensory neurons of DRG (L5-S2) using the mRNeasy Micro KIT (Qiagen, Germantown, MD).  Total RNA concentration and integrity was assessed on the Bioanalyzer RNA Pico Chip (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Animals were treated with chemotherapy or vehicle control in vivo with human scaled dose, followed by 5 weeks of experimental coasting

tag: disease state

value: animals with cancer

value: APCPirc/+

tag: treatment

value: chemotherapy

value: sensory neurons of DRG (L5-S2)


title: animals with cancer treated with chemotherapy bio rep 1


title: animals with cancer treated with chemotherapy bio rep 2


title: control treated with chemotherapy bio rep 2

value: control


title: animals with cancer bio rep 1


title: control bio rep 3


title: animals with cancer treated with chemotherapy bio rep 3


title: animals with cancer bio rep 3


title: control bio rep 2


title: control treated with chemotherapy bio rep 3


title: Grp-3-3

description:
RNA from NkxCre.Asb2fl/+.Flnafl/fl  mice
G3_vs_G1_CPM_log2FC_FDR_complete_table


title: control treated with chemotherapy bio rep 1


title: M0D055222J_A_B4_DE_MD_NF_CCM

value: McClures Beach (CCM)


title: control bio rep 1


title: Grp-3-2


title: 201148310004_R02C02

tag: Sex

value: Female


title: M0D055222J_A_B2_TF_MD_NF_CCM


title: 201148310004_R02C01

value: Milk Somatic Cells


title: Grp-3-1

tag: strain


title: Grp-2-3

description:
RNA from NkxCre.Asb2fl/fl  mice
G2_vs_G1_CPM_log2FC_FDR_complete_table
G4_vs_G2_CPM_log2FC_FDR_complete_table

tag: genotype


title: M0D055221I_A_B4_PC_SM_NF_CCM

value: Not feeding

value: small

value: Pyloric cecum


title: animals with cancer bio rep 2


title: 3UTR-3

city: Yangzhou

first: yanqing

last: zhang

address: 136 Jiangyang Road

institute: Yangzhou University

description: Gene expression after LAPTM5 3'UTR overexpression

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours 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), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: 3'UTR overexpression, replicate 3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: 38B9 mouse B-lymphoma cells were grown in  RPMI 1640  culture medium containing 10% fetal bovine serum (FBS) at  37 °C in 5% CO2.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) 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: Infect 38B9 with LAPTM53'UTR or empty vector.48h after infection,The cells were harvested and put into TRIzol reagant

tag: cell line

value: B-lymphoma

tag: overexpression

value: LAPTM5 3'UTR


title: 201148310004_R01C01


title: 3UTR-2

source_name: 3'UTR overexpression, replicate 2

tag: cell type


title: Grp-2-2


title: M0D055221I_A_B2_DE_SM_NF_CCM

tag: batch

value: Orange

value: Asymptomatic


title: 3UTR-1

source_name: 3'UTR overexpression, replicate 1


title: 201148310007_R12C02


title: 201148310007_R12C01


title: Grp-2-1


title: 201148310007_R11C02


title: M0D055219G_A_B3_PC_SM_NF_CCM

tag: color

value: S-SM


title: MSCV-3

description: Gene expression after pMSCV overexpression

source_name: Empty vector, replicate 3

value: empty vector


title: Grp-1-2

description:
RNA from NkxCre.Asb2fl/+  mice
G2_vs_G1_CPM_log2FC_FDR_complete_table


title: 201148310007_R11C01


title: MSCV-2

source_name: Empty vector, replicate 2


title: M0D055219G_A_B1_TF_SM_NF_CCM

tag: disease status

value: Tube feet


title: 201148310007_R10C02


title: MSCV-1

source_name: Empty vector, replicate 1


title: M0D055219G_A_B1_DE_SM_NF_CCM

tag: feeding status

value: Dermis


title: 201148310004_R01C02


title: 201148310007_R10C01


title: O(WT) replicate 2

city: Palo Alto

first: Jamie

middle: O.

last: Brett

address: 3801 Miranda Avenue, Building 100, Room E4-216

department: Neurology and Neurological Sciences

institute: Stanford University

data_processing:
Reads were adapter- and quality-trimmed with trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adaptor stringency 1, final length filter 50). Trimmed reads were mapped to mm10 (Ensembl release 89, no patches) using transcript annotations from GENCODE with STAR (Dobin et al. 2013) (mismatch cutoff 4% of read length, no non-canonical junction alignments). Exonic reads that mapped uniquely were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014).
Genes lacking an Entrez ID or lacking a raw FPKM value of at least 1.5 in at least 3 samples were filtered out, resulting in ~11,000 genes. Raw count data were then normalized for library preparation and sample collection batch effects using RUVs (Risso et al. 2014) (k=6).
Ccnd1 Pearson correlation coefficients were calculated using log-transformed post-normalization FPKM values, using the weights package in R. To give each replicate group equal contribution to the correlation coefficient, sample weights were assigned to be 1/(group size).
Supplementary_files_format_and_content. Tab-delimited .txt file containing normalized FPKMs and Ccnd1 correlation coefficients for each gene
Genome_build: mm10

molecule: polyA RNA

source_name: Skeletal muscle stem cells

extract_protocol:
FACS-isolated MuSCs were snap-frozen. RNA was extracted using the Nucleospin RNA XS kit (Machery-Nagel)
RNA (10 ng) was reverse-transcribed using oligo(dT) priming with the SMARTer Ultra Low Input system (Takara). The cDNA was then sheared with a Covaris S2 ultrasonicator. End repair, multiplexed adaptor ligation, and 13-15 cycles of library amplification were performed using the Ovation Ultralow Multiplex system (NuGEN). Libraries underwent paired-end 101-bp sequencing at the Stanford Genome Sequencing Service Center with an Illumina HiSeq 2000 to a depth of 20-40 million reads.

tag: gender

value: male

value: 18 months

tag: activity

value: No Exercise

value: WT


title: 201148310007_R09C02

source_name: Milk Somatic Cells

value: Female


title: M0D055220H_A_B3_PC_SM_NF_CCM

tag: individual id

tag: site

value: McClures Beach (CCM)

tag: size


title: RNA-LHSR84-2

city: Beijing

first: li

last: kuan

address: zhongguancun

institute: Tsinghua University

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome using STAR version2.5.3a.
Counting reads in genes with htseq-count version0.9.1.
gene expression was normalized by Deseq2 version1.14.1.
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana

extract_protocol:
RNA extracted by TRIzol reagent
strand-specific RNA library

value: Wild type

tag: ecotype

value: Columbia

tag: tissue

value: seedlings


title: Grp-1-3

tag: age


title: O(WT) replicate 1

tag: strain


title: Y(KO) replicate 5

value: 3 months

value: KO


title: M0D055220H_A_B4_DE_SM_NF_CCM

value: Orange

value: Not feeding

value: small


title: RNA-LHSR12-2

tag: genotype


title: RNA-LHSR84-1


title: O(WT) replicate 3


title: Y(KO) replicate 4


title: 201148310007_R09C01

tag: Sex

value: Milk Somatic Cells


title: RNA-LHSR12-1


title: 201148310007_R08C02


title: 201148310007_R08C01


title: Y(KO) replicate 3


title: INS1E_control_rep2

city: Oslo

first: Mette

middle: Eskild

last: Bornstedt

email: metbo@icloud.com, metbo@ous-hf.no

address: Pb 4959 Nydalen

department: Dep of Medical Biochemistry

country: Norway

institute: Oslo University Hospital

description: Ctr 2

hyb_protocol: The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA, USA). The scanned images were processed using AGCC (AffymetrixGeneChip Command Console) software.

data_processing: For statistical analysis the Affymetrix.CEL files (containing probe intensities) were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). Robust microarray analysis (RMA) yielding normalized log2 transformed signal intensities were applied for normalization (http://bip.weizmann.ac.il/toolbox/overview/Partek_Users_Guide.pdf). Gene transcripts with maximal signal values of less than 5 (Log2 values) across all arrays were removed to filter for low and non-expressed genes, reducing the number of gene transcripts to 17017 (provided in the 'Microarray INS1E Normalized Signal Values Mette Eskild Bornstedt.xlsx'). Differentially expressed genes between groups were identified using one-way ANOVA as implemented in Partek Genomics Suite.

source_name: INS1E cells in RPMI without vitamin D treatment or subsequent glucose stimulation

label_protocol: 150 ng of total RNA from each treatment group with three parallel samples  was subjected to GeneChip HT One-Cycle cDNA Synthesis Kit and GeneChip HT IVT Labeling Kit, following the manufacturer’s protocol for whole genome gene expression analysis (Affymetrix, Santa Clara, CA, USA). Labeled and fragmented single stranded cDNAs were hybridized to GeneChip® Rat Gene 1.0 ST Arrays (Affymetrix) containing approximately 28 000 gene transcripts.

growth_protocol: INS1E cells were grown in monolayer in RPMI medium (Gibco by Life technologies, Paisley, UK) at 11 mM glucose with supplements in a humidified atmosphere at 37°C with 5% CO2 (20).

extract_protocol: Total RNA was extracted from cells cultured in the absence or presence of vitamin D metabolites  and stimulated with or without glucose for 60 minutes using the RNeasy Mini kit (Qiagen, Austin, USA) according to the producer’s instructions.

treatment_protocol: After four passages INS1E cells (105 cells per well) were seeded in RPMI with 10 nM 25(OH)vitamin D (Sigma-Aldrich, Netherlands),  RPMI with 10 nM 1,25(OH)2vitamin D (Sigma-Aldrich, Israel) or RPMI with standard supplements alone (control cells). After 72 hours of preincubation, glucose stimulation was carried out. The cells were first incubated with glucose-free Krebs-Ringer buffer for 60 minutes, and immediately after they were subjected to stimulation with 22 mM glucose in Krebs-Ringer buffer in triplicates for 60 minutes.

tag: cell line

value: beta-cell line

tag: treatment


title: RNA-LHS-2


title: INS1E_control_rep3

description: Ctr 3

tag: cell type

value: without vitamin D treatment or subsequent glucose stimulation


title: INS1E_25-OH VitD+22 mM glucose_rep3

description: 25-OH VitD+ 22 mM glucose 3

source_name: INS1E cells in RPMI with pre-treatment with 25(OH)vitaminD and subsequent glucose stimulation


title: 201148310007_R07C02


title: INS1E_25-OH VitD+22 mM glucose_rep2

description: 25-OH VitD+ 22 mM glucose 2

value: with pre-treatment with 25(OH)vitaminD and subsequent glucose stimulation


title: RNA-LHS-1


title: Y(KO) replicate 1

value: male


title: Y(KO) replicate 2

value: No Exercise


title: 201148310007_R07C01


title: RNA-CTRL-7d-2


title: INS1E_25-OH VitD_rep2

description: 25-OH VitD 2

source_name: INS1E cells in RPMI with pre-treatment with 25(OH)vitaminD without subsequent glucose stimulation


title: INS1E_25-OH VitD+22 mM glucose_rep1

description: 25-OH VitD+ 22 mM glucose 1


title: INS1E_25-OH VitD_rep3

description: 25-OH VitD 3

value: with pre-treatment with 25(OH)vitaminD without subsequent glucose stimulation


title: INS1E_control_rep1

description: Ctr 1


title: RNA-CTRL-7d-1


title: Y(HET) replicate 2

value: HET


title: 201148310007_R06C01

value: Female


title: Y(HET) replicate 3


title: 201148310007_R06C02


title: 201148310007_R05C02


title: LCS-1 7-day old Col-0 seedlings treated by long cold stress

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome with Bowtie 2 using default settings, with all duplicates removed by Picard tools. The total mapped reads (non-strand R-loops) were divided into forward (wR-loops,representing an R-loop formation containing single-strand DNA on the Watson strand and an DNA:RNA hybrid on the Crick strand) and reverse reads(cR-loops) by using samtools.
DESeq2 was used to analyze R-loop differences between samples.The FDR (false discovery rate) method was used to calculate adjusted p value (q value), and the q values and log2FC values were used to determine significant difference. MACS2 was used to identify peaks with default parameters.
For visualization, the aligned reads files (BAM) were converted to normalized coverage files(bigWig) with 1 bp bins using bamCoverage from deepTools. Normalization was performed using bamCoverage from deepTools, with read coverage normalized to 1× sequencing depth (also known as Reads Per Genomic Content) with a re-normalization by shuffled peaks (total R-loop peaks were shuffled randomly, and the 95% mean of R-loop signal from each sample on shuffled peaks was used as denominator) to eliminate the disturbances from abnormally high value regions. Snapshots of the data were constructed using the Integrative Genomics Viewer(IGV).
Genome_build: TAIR10
Supplementary_files_format_and_content: Input_Watson: Watson strand of input DNA; Input_Crick: Crick strand of input DNA

source_name: Wild type

extract_protocol:
Nuclei were isolated from Arabidopsis plants, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments .
The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

tag: sample type

value: DNA:RNA hybird


title: LCS-2 7-day old Col-0 seedlings treated by long cold stress

value: Columbia


title: 201148310007_R05C01


title: Y(HET) replicate 1


title: DK-2 7-day old Col-0 seedlings grown under dark condition

value: seedlings


title: INS1E_22 mM glucose_rep3

description: 22 mM glucose 3

source_name: INS1E cells in RPMI without vitamin D pre-treatment but with subsequent glucose stimulation


title: Y(WT) replicate 3

value: 3 months

value: WT


title: INS1E_25-OH VitD_rep1

description: 25-OH VitD 1


title: INS1E_22 mM glucose_rep2

description: 22 mM glucose 2

value: without vitamin D pre-treatment but with subsequent glucose stimulation


title: 201148310007_R04C02


title: DK-1 7-day old Col-0 seedlings grown under dark condition


title: Y(WT) replicate 2


title: Y(HET) replicate 4


title: INS1E_22 mM glucose_rep1

description: 22 mM glucose 1


title: 201148310007_R04C01


title: 201148310007_R03C02


title: Xpo5_cKO_rep2

city: Chicago

first: Rui

last: Yi

state: Illinois

address: 765 N FAIRBANKS CT

department: Pathology, Feinberg School of Medicine

institute: Northwestern University

description:
Small RNA
Xpo5_normalized_counts.tsv.gz
processed data file sample name:
ko2_41

data_processing:
For the XPO5 HITS-CLIP, fastq files were trimmed using cutadapt (v1.8.3). For the miRNAseq, FASTQ files from XPO5cko experiments were trimmed to remove 3’ adapter sequence (TGGAATTCTCGGGTGCCAAGG), 5’ adapter (CTACAGTCCGACGATC) and randomized NN nucleotides introduced by the adapters from both the 5’ and 3’ end. FASTQ files from 293FT cells were trimmed to remove 3’ adapter sequence (TGGAATTCTCGGGTGCCAAGG), 5’ adapter (CTACAGTCCGACGATC) and randomized NN nucleotides introduced by the adapters from both the 5’ and 3’ end
For the XPO5 HITS-CLIP, reads were mapped to the human genome (hg19 build) using novoalign (v3.02.00). ). Reads greater than 25 nt after trimming were aligned with -l 25 -t 85 settings, whereas shorter reads were aligned with -l 20 -t 30 settings. PCR duplicates were removed using UMI-Tools (v. 0.5.3) with the "directional" option and alignments with MAPQ < 10 were discarded. For miRNAseq,  following trimming reads were then aligned with Bowtie2 (v.2.1.0) to the mouse genome (mm10) using local alignment.
For the XPO5 HITS-CLIP, peaks were called by merging all overlapping alignments using bedtools merge (v2.26.0). For the miRNAseq, a custom annotation file was built containing GENCODE annotations, v19 for human, M8 for mouse with Mt_rRNA, lincRNA, misc_RNA, rRNA, sRNA, sm_RNA, snRNA, snoRNA, vaultRNA, and tRNA biotypes, and miRBase microRNA annotations (release 19). Reads overlapping annotations were counted using Htseq-count (v.0.6.0), requiring a minimum MAPQ of 10.
For XPO5 HITS-CLIP, libraries were also independently mapped to a database of pre-microRNA sequences (mirBase release19) using blastn (v.2.2.28) to assess alignments with hairpin sequences.
Genome_build: hg19, Mm10
Supplementary_files_format_and_content: final_peaks_BC3_5reads.bed contains Xpo5 binding sites, read counts per hits-clip library, biological complexity and peak annotation information. Xpo5_normalized_counts.tsv contains normalized counts for small-RNA-Seq libraries from XPO5 cko and controls and log2 fold changes. smrna_293_counts.txt contains read counts for 293 small-RNA-Seq mapped via novoalign and counted via enumerating intersections with a pre-miRNA database from miRbase.

source_name: P2-P4 epidermis

extract_protocol:
For the miRNA-seq, total RNA was extracted by Trizol reagent (Thermo Fisher Scientific) using HEK293Tcells and epidermis cells isolated from XPO5 het and KO animals .
For miRNA-seq, Total RNA samples from p2-p4 back skin epidermis and HEK293T cells were subject to high efficiency 3′ ligation. Products were resolved on 15% PAGE-urea gels and stained with SybrGold (Molecular Probes S-11494 Carlsbad, California, USA). The region corresponding to ligated miRNAs (46 nucleotides) was excised, gel slices were thoroughly minced, and eluted in HSCB (400 mM NaCl, 25 mM Tris-HCl pH 7.5, 0.1% SDS) overnight at 4°C. Nucleic acids were precipitated in the presence of glycogen carrier via 0.1 volumes sodium acetate and 2.5 volumes ethanol. Pellets were washed in 70% ethanol, and dissolved in the 5′ ligation mix without enzyme. Samples were briefly heated to 70°C, snap chilled on ice, and then enzyme was added. Following ligation reactions cDNA was prepared using Superscript III RT (Invitrogen) according to the manufacturer′s recommendation using 3′ linker-specific RT primer. cDNA libraries served as templates for PCR amplification; amplicons were resolved on 8% native acrylamide gels. Bands of the correct molecular weight were isolated and used for high-throughput sequencing on the Illumina HiSeq2000.

value: total epidermis


title: INS1E_1,25 VitD_rep3

description: 1,25 VitD 3

source_name: INS1E cells in RPMI with pre-treatment with 1,25(OH)2vitamin D without subsequent glucose stimulation


title: 201148310007_R03C01


title: INS1E_1,25 VitD_rep2

description: 1,25 VitD 2

value: with pre-treatment with 1,25(OH)2vitamin D without subsequent glucose stimulation


title: INS1E_1,25 VitD_rep1

description: 1,25 VitD 1


title: 201148310007_R02C02

value: Milk Somatic Cells


title: ABA-4h-2 3-day old Col-0 seedlings treated by ABA for 4 hours


title: CTRL-EtOH-4h-1 3-day old Col-0 seedlings treated by EtOH for 4 hours


title: 201148310007_R02C01


title: ABA-4h-1 3-day old Col-0 seedlings treated by ABA for 4 hours


title: Xpo5_cKO_rep1

description:
Small RNA
Xpo5_normalized_counts.tsv.gz
processed data file sample name:
ko1_32


title: Y(WT) replicate 1


title: 201148310007_R01C02


title: XPO5_het_rep1

description:
Small RNA
Xpo5_normalized_counts.tsv.gz
processed data file sample name:
het1_31


title: INS1E_1,25 VitD+22 mM glucose_rep1

description: 1,25 VitD + 22 mM glucose 1

source_name: INS1E cells in RPMI with pre-treatment with 1,25(OH)2vitaminD and subsequent glucose stimulation

value: beta-cell line


title: 201148310007_R01C01


title: Y(+Ex) replicate 3

value: Exercise


title: INS1E_1,25 VitD+22 mM glucose_rep3

description: 1,25 VitD + 22 mM glucose 3

value: with pre-treatment with 1,25(OH)2vitaminD and subsequent glucose stimulation


title: CTRL-EtOH-4h-2 3-day old Col-0 seedlings treated by EtOH for 4 hours


title: UVC-1h-2 14-day old Col-0 seedlings recover 1 hours after UV irradiation


title: Y(+Ex) replicate 2

value: male


title: UVC-1h-1 14-day old Col-0 seedlings recover 1 hours after UV irradiation


title: 201148310010_R12C02


title: N-F

city: Seoul

first: Oh-Chan

last: Kwon

address: 17 Haengdang-dong, Sungdong-gu, Seoul 133-791, Korea

department: Biochemistry and Molecular Biology

country: South Korea

institute: Hanyang University

description: CMV - N+F

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

source_name: mouse brain tissue

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: Microglia and astrocytes were isolated from mixed primary glial cultures that were obtained from the VMs of P3 mouse or rat. Briefly, VMs were dissected in Ca2+- and Mg2+-free HBSS (Thermo Scientific Inc.) and incubated in a 0.125% trypsin solution for 10 min at 37 °C. The resulting cell suspensions were diluted in complete media (DMEM-F12 (Thermo Scientific Inc.) with 10% FBS, 10% horse serum (HyClone), 1 mM L-glutamine (Life Technologies, Carlsbad, CA), and 1% PenStrep (Life Technologies) and cultured for 14 days

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: ICR(CD-1) Outbred Mice

value: postnatal 5 day mice

value: brain


title: XPO5_het_rep2

description:
Small RNA
Xpo5_normalized_counts.tsv.gz
processed data file sample name:
het2_40


title: INS1E_1,25 VitD+22 mM glucose_rep2

description: 1,25 VitD + 22 mM glucose 2


title: foxa2

description: CMV - Foxa2


title: Y(+Ex) replicate 1


title: nurr1

description: CMV - Nurr1


title: R1 scramble total ribo- RNA-seq

city: Shanghai

first: Li

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

description: R1 scramble total

data_processing:
Library strategy: Ribo-seq
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
RNA-seq reads were first processed by using trimmomatic (version 0.35, parameters: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:80) to remove low quality bases and adaptor sequences, and then mapped by using HISAT2 (Kim et al., 2015) (version 2.0.5, parameters: --no-softclip --score-min L,-16,0 --mp 7,7 --rfg 0,7 --rdg 0,7 --dta -k 1 --max-seeds 20) to GRCh37/hg19 human reference genome with the GENCODE gene annotation (version 28lift27) or GRCm38/mm10 mouse reference genome with the GENCODE gene annotation (version M17). The HISAT2-mapped sam files were transferred to bam format by samtools (version 0.1.19).
Bam to Bedgraph using genomeCoverageBed  Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for H9 RNA-seq and mm10 for R1 RNA-seq
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: R1 cells

growth_protocol: H9 hESCs were maintained on irradiated-MEF feeder cells with daily changed hESC cultured medium and passaged weekly;  R1 cells were cultured in DMEM (Gibco, 12430) supplemented with 15% Fetal Bovine Serum (Gibco, 16000-044), 1mM Glutamin, 1% NEAA, 1% Nucleosides (Millipore) and 1% penicillin/streptomycin (Millipore), 0.1mM mercaptoethanol and 1 μM PD0325901, 3 μM CHIR99021 and 1000 units/ ml mouse LIF.

extract_protocol:
Total RNA from each cultured cell line or cultured cells with different treatments was extracted with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol. Fractionation of the cytoplasmic and nuclear RNA in H9 and R1 cells was performed as following. 1 × 106 cells were rinsed twice with ice-cold PBS, and centrifuged at 1,000 rpm for 3 min. Cell pellet was suspended by gentle pipetting in 200 mL lysis buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1.5 mM MgCl2, 0.5% Igepal, 2 mM Ribonucleoside Vanadyl Complex), and incubated on ice for 5 min. During the incubation, one fifth of the lysate was added to 1 mL Trizol for total RNA extraction. The rest of the lysate was centrifuged at 1,000 g for 3 min at 4°C to pellet the nuclei and the supernatant was the cytoplasmic fraction. To obtain pure cytoplasmic RNA, the supernatant fraction was centrifuged at 14,000rpm for 10 min at 4°C and then collected the supernatant carefully to a new tube and extracted the RNA with Trizol. To obtain pure nuclear RNA, nuclear pellets underwent additional wash with 200 µL lysis buffer, one additional wash by adding 0.5% deoxycholic acid into the lysis buffer. Finally, the purified nuclei were resuspended in 200 µL lysis buffer followed by extraction with Trizol. Fractionated RNA from the same amount of cells was used for cDNA production, RT-PCR and RNA-seq analysis.
For RNA-seq samples from H9 and R1 cells, total/cytoplasmic/nuclear RNA was processed with the RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete ribosomal RNAs for sequencing (Ribo– RNA-seq). For hFAST KD total RNA-seq samples, polyadenylated (poly(A)+) RNA preparation was carried out as following. Briefly, total RNAs (8 μg) were incubated with oligo(dT) magnetic beads to isolate poly(A)+ RNAs, which were bound to beads, selection was performed three times to ensure the purity of poly(A)+ RNA populations. Ribo– and poly(A)+ RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA LT Sample Prep Kit. All libraries were size-selected with AmpureXP beads (Agencourt) and quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Size-selected libraries were subjected to deep sequencing with Illumina HiSeq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China. Raw read qualities were evaluated by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).

treatment_protocol: To knock down hFAST,  mPpie, DNA sequences for shRNAs were designed by the GPP Web Portal online tool (https://portals.broadinstitute.org/gpp/public/). DNA oligos of shRNA sequences for targeted RNAs or scramble shRNAs were individually cloned into pLKO.1-TRC vector.  To infect H9 cells with lentivirus, 2 × 105 cells were incubated MEF-CM containing 5 μL concentrated lentivirus, 5 μg/mL polybrene and 10 μM Y-27632 at 37°C for first day. To infect R1 cells with lentivirus, 2 × 105 cells were infected with 5 μL concentrated lentivirus, 5 μg/mL polybrene for first day. Cells were selected by 1mg/ml puromycine for two days, then harvest total RNA or cytoplasm RNA or nucleus RNA.

tag: type

value: cDNA

value: scramble


title: 201148310010_R12C01

value: Female


title: control

description: CMV - Control


title: SA-2h-2 14-day old Col-0 seedlings recover 2 hours after SA exposure

value: Columbia

value: seedlings

value: DNA:RNA hybird


title: RNaseH RNase H treated negative control


title: R1 scramble nucleus ribo- RNA-seq

description: R1 scramble nucleus


title: 201148310010_R11C02


title: SA-2h-1 14-day old Col-0 seedlings recover 2 hours after SA exposure


title: R1 scramble cytoplasm ribo- RNA-seq

description: R1 scramble cytoplasm


title: 201148310010_R11C01


title: Y(-Ex) replicate 6

value: 3 months

value: No Exercise

value: WT


title: R1 Ppie KD total ribo- RNA-seq

description: R1 Ppie KD total

value: Ppie shRNA KD


title: CTRL-14d-2 14-day old Col-0 seedlings


title: 201148310010_R10C02

value: Milk Somatic Cells


title: Y(-Ex) replicate 4


title: CTRL-14d-1 14-day old Col-0 seedlings


title: R1 Ppie KD nucleus ribo- RNA-seq

description: R1 Ppie KD nucleus


title: Y(-Ex) replicate 3


title: Germination-2 2-day old Col-0

value: germination


title: R1 Ppie KD cytoplasm ribo- RNA-seq

description: R1 Ppie KD cytoplasm


title: 201148310010_R10C01


title: Germination-1 2-day old Col-0


title: Y(-Ex) replicate 2


title: 201148310010_R09C02


title: 201148310010_R09C01


title: Y(-Ex) replicate 1


title: Youngleaf-2 5-week old Col-0 young leaf

value: young leaf


title: R1 total cell ribo- RNA-seq replicate2

description: R1 total replicate2

value: untreated


title: 201148310010_R08C02


title: R1 total cell ribo- RNA-seq replicate1

description: R1 total replicate1


title: Youngleaf-1 5-week old Col-0 young leaf


title: Y(-Ex) replicate 5

value: male


title: 201148310010_R08C01


title: O(+Ex) replicate 4

value: 18 months

value: Exercise


title: R1 nucleus ribo- RNA-seq replicate1

description: R1 nucleus replicate1

value: cDNA


title: Seedlingleaf-1 7-day old Col-0 seedling leaf

value: seedling leaf


title: Seedlingleaf-2 7-day old Col-0 seedling leaf


title: O(+Ex) replicate 3


title: 201148310010_R07C02

value: Female


title: O(+Ex) replicate 2


title: Root-2 7-day old Col-0 roots

value: Columbia

value: root


title: R1 cytoplasm ribo- RNA-seq replicate2

description: R1 cytoplasm replicate2


title: 201148310010_R07C01


title: R1 cytoplasm ribo- RNA-seq replicate1

description: R1 cytoplasm replicate1


title: 201148310010_R06C02


title: Shh-IUE Cortex  E16.5_RE-4

first: Guoping

last: Liu

address: 138 Yi Xue Yuan Road

description: ShhN IUE brain

data_processing:
cellranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data.
Finally, Seurat (V3) were used for the following dimensionality reduction, clustering, and gene expression.
Genome_build: mm10

source_name: ShhN IUE E16.5 Cortex

extract_protocol:
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C).
The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions.

treatment_protocol: E16.5 wild type and ShhN-IUE (ShhN plasmid were electroporated at E13.5, and the cortex was harvested at E16.5) cortices were carefully dissected under a fluorescent stereoscope, and incubated in 4 ml of papain solution for 20 min at 37℃, The cortical tissues were gently triturated, filtered through a 40 mm strainer, and washed with HBSS to obtain the single cell suspension.

value: Cortex

tag: developmental stage

value: Embryonic day 16.5


title: O(+Ex) replicate 5

tag: gender


title: 201148310010_R06C01

data_processing:
Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping BeadChips (Illumina).
Image data was analyzed using Genome Studio and further analysis was conducted using PLINK, R, Qlik, and GoldenHelix SNP &Variation Suite

extract_protocol: Norgen Biotek Corp. Milk DNA Preservation and Isolation Kit was used to extract genomic DNA from Bronopol preserved goat milk somatic cells.


title: Oldleaf-2 5-week old Col-0 old leaf

value: old leaf

value: DNA:RNA hybird


title: Oldleaf-1 5-week old Col-0 old leaf


title: 201148310010_R05C02


title: R1 nucleus ribo- RNA-seq replicate2

description: R1 nucleus replicate2


title: O(-Ex) replicate 7

tag: activity

value: No Exercise

value: WT


title: Shh-IUE Cortex  E16.5_RE-2

description: ShhN IUE brain


title: Flower-2 5-week old Col-0 flowers

value: flower


title: 201148310010_R05C01

value: Milk Somatic Cells


title: O(+Ex) replicate 1


title: O(-Ex) replicate 5


title: O(-Ex) replicate 6


title: Flower-1 5-week old Col-0 flowers


title: 201148310010_R04C02


title: WT Cortex E16.5_RC-4

description: Wild type littermate

source_name: Wild type E16.5 Cortex


title: 201148310010_R04C01


title: SHS-2 7-day old Col-0 seedlings treated by short heat stress

value: seedlings


title: Root-1 7-day old Col-0 roots


title: O(-Ex) replicate 3

value: male


title: 201148310010_R03C02


title: SCS-2 7-day old Col-0 seedlings treated by short cold stress


title: 201148310010_R03C01


title: SHS-1 7-day old Col-0 seedlings treated by short heat stress


title: O(-Ex) replicate 1

value: 18 months


title: SCS-1 7-day old Col-0 seedlings treated by short cold stress


title: 201148310010_R02C02


title: Grp-1-1

source_name: heart


title: Shh-IUE Cortex  E16.5_RE-3

description: ShhN IUE brain


title: Pbx4-depleted nkx2.5:ZsYellow+ cells 10X Genomics single-cell RNA-Seq

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

data_processing:
Illumina HiSeq2500 used for basecalling
CellRanger software package used for alignment, filtering, barcode reading prior to post processing with ICGS in AltAnalyze.
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes (barcode.tsv), Genes (genes.tsv), and Matrix (matrix.mtx)

organism: Danio rerio

source_name: Pbx4-depleted nkx2.5:ZsYellow+ cells

extract_protocol:
Nkx2.5:ZsYellow+ cells from control and Pbx4-depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by (Stachura and Traver, 2016) with the following modifications, approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank’s Balance Salt Solution (HBSS) containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 µl HBSS and dissociation was initiated by adding 60 µl Liberase (Roche). Embryos were deyolked by pipetting up and down, first with a p1000 tip and subsequently with a p100 tip, as described by (Samsa et al., 2016). Following yolk removal, embryos were incubated at 32.5°C. To facilitate dissociation, embryos were gently homogenized using a handheld pestle homogenizer (5-10 seconds) and returned to 32.5°C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation, cell suspensions were centrifuged for 5 minutes at 13,000 rpm at 4°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum (FBS). Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm nozzle and a gating strategy as described by (Samsa et al., 2016).
The 10X Genomics Chromium Instrument and cDNA synthesis kit (10x Genomics) was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA-sequencing from approximately 4,000 cells. cDNA library quality was determined using an Agilent Bioanalyzer. Using this library, we performed one full lane sequence on two paired-end 75bp Flow Cells using on an Illumina HiSeq2500.
10X Genomics Chromium v2 chemistry

tag: strain background

value: AB/TU

value: 28 hours post-fertilization

tag: genotype/variation

value: cardiac progenitors and cardiomyocytes

value: nkx2.5:ZsYellow+ cells


title: 201148310010_R02C01

value: Female


title: Shh-IUE Cortex  E16.5_RE-1

description: ShhN IUE brain


title: WT Cortex E16.5_RC-2

description: Wild type littermate


title: O(-Ex) replicate 2

source_name: Skeletal muscle stem cells


title: M0D055220H_A_B4_TF_SM_NF_CCM

source_name: Tube feet

tag: batch

tag: color

value: Orange

tag: disease status

value: Asymptomatic

tag: feeding status

value: Not feeding

tag: individual id

tag: site

value: McClures Beach (CCM)

tag: size

value: small

value: S-SM

value: Tube feet


title: control nkx2.5:ZsYellow+ cells 10X Genomics single-cell RNA-Seq

source_name: control nkx2.5:ZsYellow+ cells

tag: age

value: control

tag: tissue


title: WT Cortex E16.5_RC-1

description: Wild type littermate

tag: strain

value: Cortex

value: Embryonic day 16.5


title: 201148310010_R01C02

source_name: Milk Somatic Cells

tag: Sex

value: Milk Somatic Cells


title: LHSR84-1 7-day old Col-0 seedlings recover 84 hours after long heat stress

tag: ecotype

value: Columbia

value: seedlings

tag: sample type

value: DNA:RNA hybird


title: WT Cortex E16.5_RC-3

description: Wild type littermate

tag: developmental stage


title: 201148310010_R01C01


title: D50r3

city: Singapore

first: Swarnaseetha

last: Adusumalli

address: 1 Research Link,  National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

data_processing:
Raw fastq reads were processed and filtered with in-house scripts to remove low quality reads. Adaptor sequences were identified by AdaptorDetect and removed with the trim functional module within IRFinder. Processed reads were aligned to Drosophila reference genome (BDGP6.84) using STAR (v2.5). Intron retention events were computed using the IRFinder algorithm.
Supplementary_files_format_and_content: FPKM

organism: Drosophila melanogaster

source_name: Drosophial head

growth_protocol: Drosophila melanogaster (W1118 strain) were cultured in standard fly media (6% cornmeal, 5% dextrose, 2.4% brewer’s yeast, 0.8% agarose and 0.3% NIPAGIN) at 25◦C with 12-hour light/dark cycle.

extract_protocol:
Fly heads were dissected and frozen by liquid nitrogen. Total RNA was isolated from the pooled fly heads at the age of day 10, 20, 30 or 50 using RNAzol®RT (Sigma).
RNA-sequencing was carried at BGI (Hong Kong) according to company’s protocol. RNA quality was assessed with Agilent 2100 bioanalyzer. Following DNAse I treatment, mRNA enriched by magnetic beads coupled to Oligo-dT was fragmented and used as template for cDNA library construction. Short DNA fragments were then subjected to end-repair, A-tailing, adaptor ligation, size selection and sequenced on Illumina HiSeqTM4000.

treatment_protocol: Twenty flies were housed in one vial (diameter of 2.5 cm, height of 9.5 cm) and the food was changed every two days until the desired age of day 10, 20, 30 and 50.

value: head


title: LHSR12-2 7-day old Col-0 seedlings recover 12 hours after long heat stress


title: D50r2


title: Rosette leaves, ACN_24h_rep3

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

institute: Norwegian University of Science and Technology

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on 4x44K Arabidipsis thaliana whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327)

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.2.3) and R (version 2.10.1).

source_name: Rosette leaves Col, 21 days old, 2.5 mM ACN, 24h

label_protocol: Total RNA (100 - 200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Seeds of the A. thaliana accession Col-0 and nia1nia2 double mutants were sown on soil (Hasselfors S-soil) and placed in a controlled growth chamber under a 16 hour photoperiod (light intensity: 100 µmol.m-2.sec-1) at 21-23°C.

extract_protocol: The rosette tissue of A. thaliana plants (Col-0 and nia1nia2) from the 24-hour mock and 2.5 mM 3BN treatments were harvested and immediately flash-frozen in liquid N2. The harvested tissue was stored at -80°C until further processing. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen plant tissue, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified using an Agilent BioAnalyzer 2100 and the Plant RNA Nano chip.

treatment_protocol: 3-butenenitrile (3BN, CAS 109-75-1) / allyl cyanide ACN, was purchased from Sigma-Aldrich (122793; 98%). 3BN was freshly diluted in 20 mL of commercial rapeseed oil to 2.5 mM. Exposure to 3BN was obtained by placing plants in plexiglass containers for 24h. The plants were hence exposed to vapors of 3BN in a closed atmosphere. The mock control consisted of rape seed oil.

tag: genotype

value: WT

tag: treatment

value: ACN

value: Rosette leaves


title: D30r3


title: 201148310012_R12C02

city: Langston

first: Yonathan

address: 100 Success Dr.

institute: Langston University

value: Female


title: 201148310012_R10C02


title: D30r2


title: 201148310012_R11C01


title: D50r1


title: AT27-1 7-day old Col-0 seedlings grown under 27°C condition

source_name: Wild type


title: AT17-2 7-day old Col-0 seedlings grown under 17°C condition


title: 201148310012_R12C01


title: AT27-2 7-day old Col-0 seedlings grown under 27°C condition


title: LHS-1 7-day old Col-0 seedlings treated by long heat stress


title: 201148310012_R11C02


title: D20r3


title: LHS-2 7-day old Col-0 seedlings treated by long heat stress


title: 201148310012_R10C01


title: D20r2


title: Rosette leaves, NIA-MockControl_24h_rep3

source_name: Rosette leaves NIA, 21 days old, Mock Control

value: nia1nia2 double mutant


title: Rosette leaves, ACN_24h_rep2


title: Rosette leaves, ACN_24h_rep1


title: Rosette leaves, NIA_ACN_24h_rep2

source_name: Rosette leaves NIA, 21 days old, 2.5 mM ACN, 24h


title: AT17-1 7-day old Col-0 seedlings grown under 17°C condition


title: Rosette leaves, MockControl_24h_rep3

source_name: Rosette leaves Col, 21 days old, Mock Control


title: 201148310012_R09C02


title: D30r1


title: WL-2 7-day old Col-0 seedlings grown under whole day light condition


title: WL-1 7-day old Col-0 seedlings grown under whole day light condition


title: 201148310012_R08C02


title: c.elegans cells (L2 stage) [re-analysis]

city: Philadelphia

first: Junhyong

last: Kim

address: 433 S University Avenue

institute: University of Pennsylvania

description: sciRNAseq with c.elegans cells (during sorting, polyploid c.elegans cells were exlcuded)

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline, mapping to a modified version of the reference transcriptome from WormBase version 260 (WS260). Our modifications to the refrence transcriptome consisted of extending the 3' UTR of transcripts by 0-500 bp (see Methods section of paper).
Genome_build: WS260
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, lineage, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

organism: Caenorhabditis elegans

source_name: whole c.elegans (L2 stage)

growth_protocol: All cultured cell lines were cultured at 37°C with 5% CO2, and were maintained in high glucose DMEM (Gibco cat. no. 11965) supplemented with 10% FBS and 1X Pen/Strep (Gibco cat. no. 15140122; 100U/ml penicillin, 100µg/ml streptomycin).

extract_protocol:
All cell lines were trypsinized, spun down at 300xg for 5 min (4°C). and washed once in 1X PBS. L2 stage worms were disscociated with SDS-DTT solution and pronase to generate single cell suspension. Detailed protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."
library construction protocol was described in "J. Cao et al., Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing. bioRxiv, 104844 (2017)."

treatment_protocol: For c.elegans, a synchronized L2 population was obtained by two cycles of bleaching gravid adults to isolate fertilized eggs allowing the eggs to hatch in the absence of food to generate a population of starved L1 animals.

value: C. elegans strain (RW12139 stIs11435(unc-120::H1-Wcherry;unc-119(+));unc-119(tm4063)) carrying an integrated Punc-120::mCherry gene in a wild type background was used


title: 201148310012_R08C01

last: Tilahun


title: D10r2


title: D10r3


title: Rosette leaves, NIA-MockControl_24h_rep1


title: C3_R3_Mature macrophage_mouse3

city: Perth

first: James

middle: Harvey

last: Steer

state: Western Australia

address: Hospital Avenue, QEII Medical Centre, M Block

country: Australia

institute: University of Western Australia

description:
C3_R3
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt

data_processing:
Torrent Suite Software  5.10  used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence-  returning a fastq file (raw data)
Reads were then mapped to the GRCm38.p6  genome using  the open source  Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)
Ampliseq
Torrent Suite Software  5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.  Returning a fastq file (raw data) of reads associated with each of the 16000 barcoded primer pairs.
Reads were then mapped to the GRCm38.p6  genome using  the open source  Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)
Genome_build: Genome Reference Consortium mouse genome (GRCm39.p6)
Supplementary_files_format_and_content: tab-delimited text files include reads or log2 RPM  for each sample showing all genes or differential expression between conditions.

source_name: bone marrow derived

growth_protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS,  non-adherent cells were incubated for two days in a fresh dish containing 12ng/ml CSF1 in alpha+ MEM /10% FCS and then for 7 days in 120ng/ml CSF1 in alpha+ MEM /10% FCS.

extract_protocol:
mRNA was harvested using RNeasy kit( QIAGEN) with DNase treatment on column.  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols

value: male

value: 8 to 10 weeks


title: SD-1 7-day old Col-0 seedlings grown under short day light condition


title: Rosette leaves, MockControl_24h_rep2


title: Rosette leaves, NIA-MockControl_24h_rep2


title: Rosette leaves, NIA_ACN_24h_rep1


title: Rosette leaves, MockControl_24h_rep1


title: Rosette leaves, NIA_ACN_24h_rep3


title: 201148310012_R07C02


title: D20r1


title: 201148310012_R07C01


title: RL-2 7-day old Col-0 seedlings grown under red light condition


title: C3_R1_Mature macrophage_mouse1

description:
C3_R1
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt


title: SD-2 7-day old Col-0 seedlings grown under short day light condition


title: RL-1 7-day old Col-0 seedlings grown under red light condition


title: 201148310012_R06C02


title: BL-2 7-day old Col-0 seedlings grown under blue light condition


title: Unoperated sciatic nerve 2

city: Austin

first: Tyler

middle: Aaron

last: Smith

state: TX

address: 2415 Speedway

department: Neuroscience

institute: The University of Texas at Austin

description:
UN17R
count_Norm_annotated.txt
res_PEG_vs_Unop_annotated.txt
res_NC_vs_Unop_annotated.txt

data_processing:
Quality control of raw reads was performed using FastQC.
Tophat2 was used for mapping and alignment of reads to the reference genome Rnor 6.0 for Rattus norvegicus.
Read counts were generated with HTSeq-count.
DESeq2 was used to generate normalized read counts (median of ratios normalization method) and perform differential expression analyses.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-delimited text files display normalized read counts (median of ratios method), gene IDs and symbols, and long gene names for each sample.  Differential expression results.

source_name: Unoperated sciatic nerve

extract_protocol:
After sacrificing the animals using potassium chloride under anesthesia, Unoperated Control nerve segments (n=2), 14d PO PEG-fused PNAs (n=3), and 14d PO NC Allografts (n=3) were immediately excised and sliced into 0.5mm pieces with a scalpel blade and stored in RNAlater (Invitrogen) overnight at 4°C to prevent RNA degradation.  The tissue was then placed onto a petri dish with TRIzol (Ambion) and minced into smaller pieces with scissors.  The minced tissue along with the TRIzol was then transferred to a dounce homogenizer and ground until the previously white tissue became nearly transparent.  Chloroform was added to the solution, the solution was centrifuged, and the extracted aqueous layer was then combined with an equal volume of 100% ethanol before transferring it to a RNeasy Mini kit (Qiagen) spin column (including RNase-free DNase I digestion) for RNA extraction.  Total RNA concentration and purity was initially quantified with a Nanodrop 1000 spectrophotometer (Thermo Scientific), and the RNA integrity was determined via BioAnalyzer 2100 (Agilent Technologies).  All RNA used for library preparation and RT-qPCR had RNA Integrity Numbers (RIN) between 7.1 and 8.2.
Libraries for each individual sample (8 total samples) were generated with 0.13-4µg of total RNA per sample using a TruSeq Stranded mRNA Library Prep kit (Illumina), according to instructions specified by the kit manufacturer.

value: Sprague Dawley (Envigo)

value: Unoperated sciatic nerve

value: Postnatal 3-6 months of age


title: Negative Control sciatic nerve allograft 3

description:
I109
count_Norm_annotated.txt
res_PEG_vs_NC_annotated.txt
res_NC_vs_Unop_annotated.txt

source_name: Negative Control sciatic nerve allograft (no PEG) (14d PO)

value: Not treated with PEG


title: C2_R3_Immature macrophage_mouse3

description:
C2_R3
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt

growth_protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS,  non-adherent cells were incubated for a second day in a fresh dish containing 0.6ng/ml CSF1 in alpha+ MEM /15% FCS. Cells were then incubated for a further 4 days in alpha+ MEM /10% FCS containing 12ng/ml CSF1.


title: Unoperated sciatic nerve 1

description:
UN16L
count_Norm_annotated.txt
res_PEG_vs_Unop_annotated.txt
res_NC_vs_Unop_annotated.txt


title: C2_R2_Immature macrophage_mouse2

description:
C2_R2
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt


title: 201148310012_R06C01

description: Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping Beadchips (Illumina).

value: Milk Somatic Cells


title: Negative Control sciatic nerve allograft 2

description:
I108
count_Norm_annotated.txt
res_PEG_vs_NC_annotated.txt
res_NC_vs_Unop_annotated.txt

value: Negative Control sciatic nerve allograft (no PEG) (14d PO)


title: BL-1 7-day old Col-0 seedlings grown under blue light condition

value: Columbia

value: seedlings


title: C2_R1_Immature macrophage_mouse1

description:
C2_R1
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt


title: Negative Control sciatic nerve allograft 1

description:
I106
count_Norm_annotated.txt
res_PEG_vs_NC_annotated.txt
res_NC_vs_Unop_annotated.txt


title: C1_R3_Non-adherent precursors_mouse3

description:
C1_R3
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt

growth_protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS,  non-adherent cells were incubated for a second day in a fresh dish containing 0.6ng/ml CSF1 in alpha+ MEM /15% FCS


title: C1_R2_Non-adherent precursors_mouse2

description:
C1_R2
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt


title: PEG-fused sciatic nerve allograft 3

description:
G193
count_Norm_annotated.txt
res_PEG_vs_NC_annotated.txt
res_PEG_vs_Unop_annotated.txt

source_name: PEG-fused sciatic nerve allograft (14d PO)

value: Treated with PEG-fusion protocol


title: 201148310012_R05C01


title: FRL-1 7-day old Col-0 seedlings grown under infrared light condition

value: DNA:RNA hybird


title: 201148310012_R04C02


title: PEG-fused sciatic nerve allograft 2

description:
G187
count_Norm_annotated.txt
res_PEG_vs_NC_annotated.txt
res_PEG_vs_Unop_annotated.txt

value: PEG-fused sciatic nerve allograft (14d PO)


title: O(-Ex) replicate 4

tag: gender

value: 18 months

tag: activity

value: No Exercise

value: WT


title: C1_R1_Non-adherent precursors_mouse1

description:
C1_R1
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt


title: C3_R2_Mature macrophage_mouse2

description:
C3_R2
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt


title: 201148310012_R04C01

value: Female


title: D10r1

value: head


title: 201148310012_R03C02


title: PEG-fused sciatic nerve allograft 1

description:
G186
count_Norm_annotated.txt
res_PEG_vs_NC_annotated.txt
res_PEG_vs_Unop_annotated.txt


title: FRL-2 7-day old Col-0 seedlings grown under infrared light condition


title: C3_R3_48h_IL4_Mature macrophage_mouse3

description:
IL4_48h_M26_BMM
Wt_vs_IL4_allprobes_reads.txt
Wt_vs_IL4_allprobes_log2_RPM.txt

growth_protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS,  non-adherent cells were incubated for two days in a fresh dish containing 12ng/ml CSF1 in alpha+ MEM /10% FCS and then for 7 days in 120ng/ml CSF1 in alpha+ MEM /10% FCS. Cells were incubated for a further two days in fresh alpha+ MEM /10% FCS containing 120ng/ml CSF1 and 20ng/ml IL4.

value: male

value: 8 to 10 weeks


title: 201148310012_R05C02


title: 201148310012_R03C01


title: C3_R2_48h_IL4_Mature macrophage_mouse2

description:
IL4_48h_M25_BMM
Wt_vs_IL4_allprobes_reads.txt
Wt_vs_IL4_allprobes_log2_RPM.txt


title: C3_R1_48h_IL4_Mature macrophage_mouse1

description:
IL4_48h_M10_BMM
Wt_vs_IL4_allprobes_reads.txt
Wt_vs_IL4_allprobes_log2_RPM.txt


title: Adult_SVZ_Ependymal_CTR_3

first: Qin

last: Shen

address: 1239 Siping Road

department: School of Life Sciences and Technology

institute: Tongji University

description: cytoplasmic RNA

data_processing:
Basecalls performed using CASAVA version 1.8
Paired-end reads were first pre-processed using Cutadapt (version 1.11) to remove adaptors and trim low-quality bases from 5’ and/or 3’ ends. Reads shorter than 30bp were discarded.
Abandances are quantified with Kallisto (version 0.42.5) quantification algorithm (kallisto quant).
Expected read counts and TPM of each transcript from the same gene were combined with a customized Perl script.
Genome_build: Gencode M9
Supplementary_files_format_and_content: Tab-delimited text files include estimated read count and TPM values for each Sample

source_name: Adult SVZ

extract_protocol: none provided by the submitter

tag: cell

value: Ependymal


title: Adult_SVZ_Ependymal_CTR_2

description: cytoplasmic RNA


title: 201148310012_R02C02


title: 201148310012_R02C01


title: C3_R3_48h_unstim_Mature macrophage_mouse3

description:
Wt_48h_M24_BMM
Wt_vs_IL4_allprobes_reads.txt
Wt_vs_IL4_allprobes_log2_RPM.txt

growth_protocol: After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS,  non-adherent cells were incubated for two days in a fresh dish containing 12ng/ml CSF1 in alpha+ MEM /10% FCS and then for 7 days in 120ng/ml CSF1 in alpha+ MEM /10% FCS. Cells were incubated for a further two days in fresh alpha+ MEM /10% FCS containing 120ng/ml CSF1.


title: Epcam-derived HCC with CLC_rep2

city: Suita

first: Tomonori

last: Matsumoto

state: Osaka

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

description: HCC in an Epcam-AID mouse after 8-month DDC administration

hyb_protocol: 0.6 ug of Cy3-labeled complementary RNA was fragmented and hybridized to SurePrint G3 Mouse Gene Expression 8x60K v2 (Agilent Technologies) according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned with the Agilent SureScan G2600D Microarray Scanner (Agilent Technologies) using the one-color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies).

source_name: HCC with CLC, Epcam-derived, replicate 2

label_protocol: Cy3-labeled complementary RNA was prepared from 0.1 ug total RNA using the Low Input Quick Amy Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: Alb-AID mice were sacrificed at 90 weeks age. Tamoxifen-adeministered Epcam-AID mice were fed with 0.1% DDC diet for 8 months to develop DPC-derived HCCs.

extract_protocol: RNA was extracted from frozen samples using Sepasol RNA-I Super G (Nacalai Tesque, Kyoto, Japan).

tag: group

value: Epcam-AID

tag: tumor

value: HCC with CLC


title: C3_R2_48h_unstim_Mature macrophage_mouse2

description:
Wt_48h_M23_BMM
Wt_vs_IL4_allprobes_reads.txt
Wt_vs_IL4_allprobes_log2_RPM.txt


title: Adult_SVZ_Ependymal_CKO_3

description: cytoplasmic RNA


title: Epcam-derived HCC with CLC_rep1

source_name: HCC with CLC, Epcam-derived, replicate 1


title: 201148310012_R01C02

description: Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping Beadchips (Illumina).

value: Milk Somatic Cells


title: CTRL-7d-1 7-day old Col-0 seedlings grown under normal condition


title: Adult_SVZ_Ependymal_CKO_2

description: cytoplasmic RNA


title: C3_R1_48h_unstim_Mature macrophage_mouse1

description:
Wt_48h_M7_BMM
Wt_vs_IL4_allprobes_reads.txt
Wt_vs_IL4_allprobes_log2_RPM.txt


title: 201148310012_R01C01


title: Adult_SVZ_Ependymal_CKO_1

description: cytoplasmic RNA


title: HNF4a KO RNA-Seq replicate 1

status: Public on Feb 18 2020

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer as well as standard Illumina base callers (bcl2fastq).
The RNA-Seq FASTQ files were mapped on the UCSC mm9 reference genome using tophat2 , with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The ChIP-Seq FASTQ files were also mapped to the mm9 genome using bwa  with standard parameters. The resulting BAM files were visualized in the UCSC Genome Browser using bedtools  and tools provided by the UCSC Genome Browser toolkit. Prior to any alignment or further analysis, the quality all the FASTQ files and the reads contained therein was inspected with the FastQC package.
The raw bam files were summarized to an exon read counts table and the exon read counts were filtered for artifacts as follows: if an annotated gene had up to 5 exons, read presence was required in at least 2 of the exons, else if an annotated gene had more than 5 exons, then read presence was required in at least 0.2x⌈E⌉ exons, where ⌈.⌉ is the ceiling mathematical function. After exon filtering, the final read counts for each gene model were calculated as the sums of their exon reads, creating a gene counts table where each row corresponded to an Ensembl gene model and each column corresponded to an RNA-Seq sample. The gene counts table was normalized using the Bioconductor package DESeq after removing genes that had zero counts over all samples. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500, ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp, iii) genes with read counts below the median read counts of the total normalized count distribution. The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq. Differentially expressed genes were identified with an FDR threshold of 0.05 and a fold change threshold of -1 and 1 (log2) scale for up and down regulated genes respectively. All the analyses and reporting  were performed within the Bioconductor package metaseqR.  For the transcription factor data (CEBPα, HNF4α), the two biological replicates for each developmental stage and their respective DNA input samples were subjected to peak calling using MACS 1.4  with the default settings for mouse genome. Prior to peak calling and in order to compensate for differences in library sizes between ChIP and Input DNA sequencing samples, the total number of reads of each sample was equalized by uniformly downsampling reads relatively to the sample with the lower number of reads. The putative binding sites returned by MACS were further filtered for artifacts by i) imposing an additional MACS FDR threshold of 0.1%, ii) excluding peaks demonstrating a fold enrichment less than 1 in log2 scale (where fold enrichment is the ratio of reads under a peak area in the ChIP sample to the respective number of reads in the Input DNA sample).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. BED files with peak coordinates for ChIP-Seq data. BigWig signal files for ChIP-Seq data.

source_name: HNF4a KO RNA-Seq

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) or High Fat Diet (34% crude Fat, 23% crude Protein, 5% crude fiber by Mucedola s.r.l.) and water ad libitum. All animal experiments were approved by the Prefecture of Attica and were performed in accordance with the respective national and European Union regulations. All the experiments were performed in randomly chosen age-matched male mice. No blinding was used in this study.

extract_protocol:
RNA preparation: Total RNA was prepared by homogenizing liver pieces in 10 volumes of Trizol reagent followed by the addition of 2 volumes of chlorophorm and centrifugation at 12000 g for 15 minutes. The aqueous phases were precipitated with isopropanol. Following resuspension in water RNAs were subjected to additional precipitation with ethanol. The RNA samples were digested with 10 units of DNase I for 10 min at 37 0C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation. Chromatin immunoprecipitation: Liver tissue was minced to small pieces in PBS and after addition of formaldehyde to a 1% final concentration immediately was subjected to 10 strokes of dounce homogenization. Cross-linking was continued for 10 min and stopped by the addition of glycine at 0.125 M final concentration. Cross-linked cells were treated with a buffer containing 50 mM HEPES pH 7.5, 0.14 M NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40 and 0.25% Triton-X100, for 10 minutes and then with a buffer containing 0.2 M NaCl, 1 mM EDTA, 0.5 mM EGTA and 10 mM Tris-HCl pH 8.0 for 5 minutes. The nuclei were resuspended up to 4 ml with sonication buffer containing 10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate and 0.5% N-lauroylsarcosine and sonicated for 12 minutes in Covaris Sonicator instrument. After sonication, samples were supplemented with 400 μl of 10% Triton X-100 and centrifuged for 10 minutes at 20.000 rcf. After centrifugation, the extracted chromatin was incubated overnight with Dynabeads Protein G, that were prebound by 10 ug of the respective antibodies. The beads were washed six times with a buffer containing 50 mM Hepes pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-deoxycholate, and then once with a buffer containing 20 mM Tris-HCl pH 7.6 and 150 mM NaCl. Immunoprecipitated chromatin was eluted from the beads and reverse crosslinked by overnight incubation with a buffer containing 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1 % SDS, at 65 0C. Following incubation, samples were diluted by addition of one volume of TE. RNAs and proteins were removed by incubation with 20 ug/ml RNAse A for 30 minutes at 37 C, followed by incubation with 20 ug/ml Proteinase-K for 2 hours at 55 0C. DNA was extracted by phenol/chlorophorm and precipitated with ethanol. About 10 ng of the immunoprecipitated DNA and input DNA was used for library preparation.
Libraries were prepared using TruSeq or NEBNext Adaptors, depending on whether less or more than 6 indexes were included. In all cases, 25 μl of immunoprecipitated DNA was purified using the MinElute columns (Qiagen, 28604) and eluted with 10 ul elution buffer. The concentration of the eluted DNA was measured in Qubit using the dsDNA HS Assay Kit (Invitrogen Q32851). Subsequently, ten ng of ChIP or input DNA were subject to end repair, in a mix containing T4 DNA polymerase (NEB M0203L), Klenow fragment (NEB M0210L), T4 DNA PNK (NEB M0201L) and dNTPs in T4 DNA Ligase Buffer (NEB, B02025) at 20 °C for 30 min. Following end repair, samples were purified using the Agentcourt AMPURE XP system (Agentcourt A63881) and subject to A addition by incubation with dATP and Klenow 3’-->5’ exo- 37 °C for 30 min. Another AMPURE XP purification was performed and then Truseq or NEBNext adaptors were ligated using Quick Ligase in Quick Ligase Buffer. Following adaptor ligation, samples were incubated with 1.5 ul USER enzyme at 37 °C for 15 minutes, to cleave the adaptor hairpin loop. Purification and size selection was performed again by AMPURE XP and PCR amplification was performed using Truseq or NEBnext Primers in Kapa Hifi Hotstart mix. A final purification was performed and libraries were ready for Bioanalyzer assessment and sequencing.

treatment_protocol: The mice were not treated.

value: F1 mice (C57Bl6/CBA)

value: 60 days postnatal

value: HNF4a lox/lox / Alfp-Cre mice

value: liver


title: CEBPa KO RNA-Seq replicate 3

source_name: CEBPa KO RNA-Seq

value: C/EBPa lox/lox / Alfp-Cre mice


title: CEBPa KO RNA-Seq replicate 2


title: HNF4a KO RNA-Seq replicate 2


title: Adult_SVZ_Ependymal_CTR_1

description: cytoplasmic RNA


title: DM12.DNMT3B-amp.BRAF-OIS.Rep3

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description:
FPKM_Matrix.csv
DNMT3B-BRAF_vs_vector-vector.gene_exp.diff

data_processing:
Paired-end reads were aligned to the human genome (hg19) using a splicing-aware aligner (TopHat2) (Kim et al., 2013)
Only unique reads were retained. Reference splice junctions were provided by a reference transcriptome (Ensembl build 73) and novel splicing junctions defined by the detection of reads that spanned exons not in the reference annotation.
True read abundance at each transcript isoform was assessed using HTSeq (Python) before determination of differential expression using CuffDiff, from which differential expression and splicing can be derived (Trapnell et al., 2013). Significance was determined using an FDR corrected p-value of <0.05. Heatmaps were created in R using the ggplots package.
Genome_build: hg19
Supplementary_files_format_and_content: CuffDiff results files and FPKM matrix

organism: Homo sapiens

growth_protocol: Human fetal lung fibroblasts (IMR-90) were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 10units/mL Penicillin G and 10μg/ml streptomycin. Cells were cultured in 10cm plates in a humidified atmosphere with 3% O2 and 5% CO2. Passaging of cells was performed at 70-80% confluency. Culture media were aspirated, and the cells lavaged twice with sterile phosphate-buffered saline to remove remaining traces of culture media. Trypsinisation was then performed with 1mL of 1% trypsin in phosphate-buffered EDTA solution for 3 minutes at 37°C. With cell detachment confirmed by visual inspection with a microscope, the trypsin solution was neutralised by the addition of fresh culture media (supplemented with FBS) to the plate. Cells were then resuspended in culture media, passaged to fresh plates, and returned to the incubator.

extract_protocol:
RNA was extracted from adherent cells using the RNeasy Mini Kit according to the manufacturer’s protocol. In summary, cell pellets were lysed on ice into buffer RLT supplemented with β-mercaptoethanol. Cell lysates were then homogenised by centrifugation in QiaShredder columns. RNA isolation was then performed using RNeasy mini kit columns, with residual DNA removed by on-column treatment with DNaseI. Following wash steps, RNA was eluted into RNase-free distilled water, and stored at -80°C prior to subsequent analysis.
Prior to sequencing, RNA quantification was performed using the Qubit RNA HS assay kit, and qualitative assessment performed using the Agilent RNA ScreenTape assay according to the manufacturer’s instructions. RNA-sequencing was performed in the sequencing facility at the Beatson Institute for Cancer Research, Glasgow. RNA was prepared for sequencing using the TruSeq RNA sample preparation kit. RNA is first purified, fragmented and reverse transcribed to produce cDNA. Following the removal of any remaining RNA, single stranded cDNA is converted to double stranded cDNA. Blunt-end DNA fragments are then generated. The subsequent addition of an “A” base to blunt ends prepares them for ligation to the sequencing adapters, which possess a “T” base overhang at the 3’ end, thus providing a complementary overhang for adapter ligation. Adapters possess sequencing primer hybridisation sites for single, paired-end and multiplex reads. PCR is then employed to selectively enrich for those DNA fragments in possession of an adapter molecule on both ends (12 cycles only to prevent skewed representation in the library) and then libraries validated using the Agilent DNA 1000 kit. Libraries were then sequenced using the Illumina GAIIX sequencer at the Beatson Institute for Cancer Research, Glasgow.

treatment_protocol: 12x106 HEK-293T cells were seeded in 25 mL of culture medium to TC175 flasks 20 hours prior to transfection. Cells were approximately 70% confluent for transfection. Immediately prior to transfection, 13mL of culture medium was aspirated from flasks, and the cells returned to the incubator. Lipofectamine 2000 was selected as a transfection agent for all lentivirus production. 120μL of transfection agent were added dropwise to 1.5mL of sterile DMEM in a 15mL centrifuge tube, gently agitated and incubated for five minutes at room temperature. Concurrently, packaging plasmids (5μg plpVSVG and 8μg psPAX2) were combined with 20μg of vector genome in 1.5mL of sterile DMEM in a separate 15mL centrifuge tube. Thereafter the DNA and transfection reagent solutions were combined, gently agitated and incubated for 20 minutes at room temperature. The transfection solution was then added to the prepared HEK-293T flasks to yield a total final transfection volume of 15mL. Following transfection, HEK-293T cells were returned to the incubator for six hours, following which the transfection solution was aspirated, and a fresh 15mL of culture medium added to the flask. For all transfections, a separate green fluorescent protein (GFP) control transfection was performed in parallel to confirm transfection efficiency. After a period of twenty hours following transfection, GFP controls were examined to confirm transfection efficiency. Lentiviral supernatant was then aspirated from transfected HEK-293T cells, reserved and stored at 4°C. A further 15mL of culture medium was added to the HEK-293T cells and returned to the incubator for a further twenty hours. The second lentiviral supernatant fraction was then combined with the first, centrifuged at 3000RPM in a table-top centrifuge, and filtered through a 0.45μM low-protein binding PVDF filter prior to concentration. Filtered viral supernatants were transferred to sterile 38.5mL polypropylene centrifuge tubes (Beckman 326823) and weights equalised by the addition of sterile PBS. Ultracentrifugation was performed at 47,000 x g in an SW-28 Beckman- Coulter ultracentrifuge for two hours at 10°C. Following centrifugation, the supernatant was discarded by gentle inversion, and the viral pellet resuspended in 100μL of sterile PBS overnight at 4°C, prior to being aliquoted and stored at -80°C. The multiplicity of infection (MOI) for lentiviral preparations was calculated empirically by seeding cells to a 6-well plate twenty-four hours prior to transduction. Culture medium was then aspirated from each well, replaced with 1mL of fresh culture medium supplemented with polybrene at a final concentration of 8μg/mL, and the cells returned to the incubator for four hours prior to transduction. Concentrated lentivirus was then added to each well at 0, 1, 2, 4, 8 and 16 μL/mL, and returned to the incubator for sixteen hours. Following transduction, the infection medium was removed from each well, and replenished with 2mL of fresh culture medium supplemented with the appropriate drug selection as determined by the construct design. The minimum volume of lentiviral construct required to yield 100% cell survival following drug-selection was then employed for all subsequent experiments. All experiments involving lentivirus were performed in their entirety under drug selection.

tag: cell type

value: Human Fetal Lung Fibroblasts

tag: passages

value: Ectopically expressed DNMT3B / BRAF OIS


title: Wild type RNA-Seq replicate 3

source_name: Wild type RNA-Seq

value: Wild type


title: DM10.DNMT3B-amp.BRAF-OIS.Rep1


title: Albumin-derived HCC without CLC_rep2

description: HCC in an Alb-AID mouse at 90 weeks age

source_name: HCC without CLC, Albumin-derived, replicate 2

value: Alb-AID

value: HCC without CLC


title: Epcam-derived HCC without CLC_rep2

source_name: HCC without CLC, Epcam-derived, replicate 2


title: Epcam-derived HCC without CLC_rep1

source_name: HCC without CLC, Epcam-derived, replicate 1


title: DM9.vector.BRAF-OIS.Rep3

description:
FPKM_Matrix.csv
vector-BRAF_vs_vector-vector.gene_exp.diff

value: BRAF OIS


title: DM8.vector.BRAF-OIS.Rep2


title: DM7.vector.BRAF-OIS.Rep1


title: DM6.DNMT3B-amp.vector.Rep3

description:
FPKM_Matrix.csv
DNMT3B-vector_vs_vector-vector.gene_exp.diff

value: Ectopically expressed DNMT3B


title: DM4.DNMT3B-amp.vector.Rep1


title: DM1.vector.vector.Rep1

value: Empty vector control


title: CEBPa KO RNA-Seq replicate 1


title: DM3.vector.vector.Rep3


title: DM2.vector.vector.Rep2


title: DM5.DNMT3B-amp.vector.Rep2


title: LHSR84-2 7-day old Col-0 seedlings recover 84 hours after long heat stress

first: li

address: zhongguancun

source_name: Wild type

value: Columbia

value: seedlings

value: DNA:RNA hybird


title: Wild type RNA-Seq replicate 1