title: heart_203s_C16

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the mouse reference genome (GRCm38 / mm10) using TapHat2, Bowtie1 or Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the sample-plates were combined into one expression matrix file
counts data was processed and analyzed using SingleCellExperiment, pagoda2 and monocle packages in R-software
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples


title: heart_203s_C15

status: Public on Jun 18 2020

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: male mouse

extract_protocol:
FACS into 384well plate of single cells from dissociation of mouse heart in Miltenyi's skeletal muscle dissociation kit (supplemented with collagenase IV-S).
RNA libraries were prepared using standard SmartSeq2 protocol

tag: tissue

value: heart

tag: starin

tag: Sex

value: male

tag: age

value: 10-20 weeks

tag: cluster


title: heart_203s_C19


title: heart_203s_C18


title: heart_203s_C17


title: heart_203s_C14


title: heart_203s_C11


title: heart_203s_C13


title: heart_203s_C12


title: Exp2Rep5Day56

city: Boston

first: Volker

last: Hovestadt

state: MA

address: 360 Longwood Avenue

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: DNA-based lineage barcode sequencing for Exp2Rep5Day56

library_source: genomic

data_processing:
Library strategy: Amplicon-seq
Barcode sequencing data was filtered to include only reads that match the expected WSx15 pattern. Error correction and further analysis was performed in R.
For single-cell RNA-seq, identification of cell barcodes, genome alignment and quantification of gene expression levels for each single cell was performed as described in detail in the publication using the splice-aware aligner STAR and the R.
Low-coverage WGS data was aligned to the human reference genome (hg19) using bwa mem. Alignments were coordinate sorted and putative PCR duplicates were removed using samtools. Read coverage in genomic bins of 50kb was calculated using igvtools count and visualized using the IGV browser.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files and bedgraph coverage files. For single-cell RNA-seq experiments, a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns), and an annotation file containing the associated lineage barcode is provided.

molecule: genomic DNA

organism: Homo sapiens

source_name: GSC8 neurosphere culture

growth_protocol: Cells were maintained in stem cell-permissive, serum free, non-adherent spheroid cultures using Neurobasal medium (Gibco) supplemented with N2/B27 (Gibco), penicillin/streptomycin (Gibco), GlutaMAX (Gibco), recombinant human EGF (20 ng/mL, R & D systems), recombinant human FGF2 (20 ng/mL, R&D systems), and heparin (2000 ng/mL, Sigma). Cell dissociation was accomplished with trituration or Accutase (BD Bioscience) treatment.

extract_protocol:
For lineage barcode sequencing, genome DNA (gDNA) was prepared with a QIAmp DNA blood mini Kit (Qiagen). For single-cell transcriptome profiling, accutase-dissociated and filtered GSCs were counted and 10,000 single cells were loaded onto a Seq-Well nanowell array. For low-coverage WGS, gDNA was isolated using DNeasy Blood and Tissue Kit (Qiagen), and then quality and quantity of gDNA was determined by Nanodrop.
For lineage barcode sequencing, gDNA was amplified using primers bearing Illumina adaptor and index sequences. Single-cell transcriptome analysis was performed using the Seq-Well method. For low-coverage WGS, 50ng gDNA was used for tagmentation and sample preparation/amplification was performed using the Nextera DNA kit (Illumina) abd Nextera i7/i5 primers (Illumina).

treatment_protocol: Approximately 1x10E6 GSCs plated in stem cell permissive monolayer culture with laminin were infected with concentrated virus at an MOI of 10% for 24 hours prior to selection of barcode-incorporated GSCs using puromycin for 72 hours. Equivalent numbers (1x10E6) of stably-transduced barcoded cells were plated in replicates and treated with 1 μM dasatinib. Dissociation and passage of cells with renewal of compound-containing cell culture medium was performed at least weekly. Each replicate was passed and treated independently.

tag: gender

value: F


title: Exp2Rep4Day56

description: DNA-based lineage barcode sequencing for Exp2Rep4Day56


title: Blood samples 128073

type: genomic

city: Ningbo

first: cao

last: yuhao

state: Zhejiang Province

address: 818 Fenghua Road, Jiangbei District, Ningbo City, Zhejiang Province

country: China

institute: Medical School of Ningbo University

description:
128073
101035780048_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP167BeadChip

hyb_protocol: Hybridization of DNA and chip: After the DNA sample obtained  is hybridized with the chip, it is placed in a hybridization furnace to fully react.Chip extension and staining: Wash unbound and non-specifically bound DNA with a cleaning solution.Coated chip: Place the above chip in XC4 reagent, apply the coating solution, and place it under vacuum for 1h.

scan_protocol: Chip scanning: Put the chip processed in step (8) into the scanner to perform chip scanning.

data_processing: Genotyping of individual SNPs was performed using the Ovine SNP50BeadChip

label: C-Bio and A-DNP

organism: Ovis aries

label_protocol: (1) Sample standardization: Dilute the DNA concentration to 50ng / µL.2) DNA amplification: add 1N NaOH solution to the sample, and then add the reagents required for genome amplification, and then leave it at room temperature for 12 h.(3) Fragmentation of DNA: Use enzyme preparation to turn DNA into fragments.4) Precipitate DNA: Use anhydrous isopropyl alcohol to deposit DNA on the wall of the tube.(5) Resuspend the DNA: after drying at room temperature, add the corresponding buffer solvent to dissolve it completely.

extract_protocol: Blood samples were collected from the posterior venous plexus of Hu sheep to extract genomic DNA using the standard phenol/chloroform method

value: Famale

tag: g

tag: father

tag: mother

tag: sibling number

tag: birth weight

tag: weaning weight

tag: six-month weight


title: heart_203s_C10


title: Exp2Rep3Day56

description: DNA-based lineage barcode sequencing for Exp2Rep3Day56


title: Blood samples 122126

description:
122126
101035780048_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP165BeadChip


title: Blood samples 122125

description:
122125
101035780048_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP166BeadChip


title: heart_203s_C1


title: heart_203s_B9


title: Blood samples 126110

description:
126110
101035780048_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP164BeadChip


title: heart_203s_B7


title: Exp2Rep1Day56

description: DNA-based lineage barcode sequencing for Exp2Rep1Day56


title: heart_203s_B5


title: heart_203s_B8


title: Exp2Rep6Day42

description: DNA-based lineage barcode sequencing for Exp2Rep6Day42


title: heart_203s_B4


title: heart_203s_B6


title: heart_203s_B3


title: Exp2Rep4Day42

description: DNA-based lineage barcode sequencing for Exp2Rep4Day42


title: heart_203s_B24


title: Exp2Rep2Day56

description: DNA-based lineage barcode sequencing for Exp2Rep2Day56


title: Exp2Rep5Day42

description: DNA-based lineage barcode sequencing for Exp2Rep5Day42


title: heart_203s_B23


title: heart_203s_B22


title: Blood samples 127238

description:
127238
101035780048_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP163BeadChip


title: Blood samples 122062

description:
122062
101035780048_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP161BeadChip


title: Blood samples 122109

description:
122109
101035780048_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP159BeadChip


title: Blood samples 127161

description:
127161
101035780048_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP162BeadChip


title: heart_203s_B21


title: Exp2Rep2Day42

description: DNA-based lineage barcode sequencing for Exp2Rep2Day42


title: heart_203s_B2


title: heart_203s_B19


title: heart_203s_B17


title: heart_203s_B18


title: Exp2Rep1Day42

description: DNA-based lineage barcode sequencing for Exp2Rep1Day42


title: Blood samples 1413116

description:
1413116
200109370106_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP156BeadChip

tag: yearling weight


title: Blood samples 126205

description:
126205
101035780048_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP157BeadChip


title: Blood samples 122004

description:
122004
101035780048_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP160BeadChip


title: Exp2Rep6Day28

description: DNA-based lineage barcode sequencing for Exp2Rep6Day28


title: heart_203s_B20


title: heart_203s_B15


title: Blood samples 1413118

description:
1413118
200109370106_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP155BeadChip


title: heart_203s_B13


title: Exp2Rep5Day28

description: DNA-based lineage barcode sequencing for Exp2Rep5Day28


title: Exp2Rep3Day42

description: DNA-based lineage barcode sequencing for Exp2Rep3Day42


title: Exp2Rep4Day28

description: DNA-based lineage barcode sequencing for Exp2Rep4Day28


title: heart_203s_B12


title: heart_203s_B11


title: Exp2Rep3Day28

description: DNA-based lineage barcode sequencing for Exp2Rep3Day28


title: Blood samples 1211002

description:
1211002
101035780048_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP158BeadChip


title: heart_203s_B14


title: Blood samples 1413111

description:
1413111
200109370106_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP153BeadChip


title: heart_203s_B10


title: heart_203s_A9


title: Blood samples 1413122

description:
1413122
200109370106_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP154BeadChip


title: Blood samples 1414081

description:
1414081
200109370106_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP152BeadChip


title: heart_203s_A5


title: Blood samples 1414080

description:
1414080
200109370106_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP150BeadChip


title: heart_203s_A8


title: heart_203s_A6


title: heart_203s_B16


title: Exp2Rep1Day28

description: DNA-based lineage barcode sequencing for Exp2Rep1Day28


title: Exp2Rep4Day0

description: DNA-based lineage barcode sequencing for Exp2Rep4Day0


title: Blood samples 1413110

description:
1413110
200109370106_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP151BeadChip


title: heart_203s_A7


title: heart_203s_A22


title: heart_203s_A21


title: heart_203s_A19


title: Exp2Rep2Day28

description: DNA-based lineage barcode sequencing for Exp2Rep2Day28


title: heart_203s_A20


title: Exp1Rep4Day70CloneG_WGS

description: Low coverage genome sequencing for Exp1Rep4Day70CloneG

data_processing:
Library strategy: WGS
Barcode sequencing data was filtered to include only reads that match the expected WSx15 pattern. Error correction and further analysis was performed in R.
For single-cell RNA-seq, identification of cell barcodes, genome alignment and quantification of gene expression levels for each single cell was performed as described in detail in the publication using the splice-aware aligner STAR and the R.
Low-coverage WGS data was aligned to the human reference genome (hg19) using bwa mem. Alignments were coordinate sorted and putative PCR duplicates were removed using samtools. Read coverage in genomic bins of 50kb was calculated using igvtools count and visualized using the IGV browser.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data is provided as tab-delimited text files and bedgraph coverage files. For single-cell RNA-seq experiments, a digital expression matrix containing the number of UMIs for each gene (rows) and cell (columns), and an annotation file containing the associated lineage barcode is provided.


title: Blood samples 1413106

description:
1413106
200109370106_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP149BeadChip


title: Exp2Rep1Day0

description: DNA-based lineage barcode sequencing for Exp2Rep1Day0


title: Exp1Rep4Day70CloneI_WGS

description: Low coverage genome sequencing for Exp1Rep4Day70CloneI


title: Exp2Rep2Day0

description: DNA-based lineage barcode sequencing for Exp2Rep2Day0


title: Blood samples 1413120

description:
1413120
200109370106_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP148BeadChip


title: Blood samples 1413090

description:
1413090
200109370106_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP147BeadChip


title: Blood samples 1414096

description:
1414096
200109370106_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP145BeadChip


title: Exp2Rep3Day0

description: DNA-based lineage barcode sequencing for Exp2Rep3Day0


title: heart_203s_A17


title: heart_203s_A16


title: heart_203s_A3


title: Exp1Rep4Day70

description: DNA-based lineage barcode sequencing for Exp1Rep4Day70


title: Exp1Rep3Day70

description: DNA-based lineage barcode sequencing for Exp1Rep3Day70


title: heart_203s_A23


title: heart_203s_A13


title: heart_203s_A14


title: heart_203s_A12


title: Exp1Rep2Day70

description: DNA-based lineage barcode sequencing for Exp1Rep2Day70


title: Blood samples 1413M06

description:
1413M06
101035780039_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP144BeadChip


title: heart_203s_A18


title: heart_203s_A1


title: Exp1Rep1Day70

description: DNA-based lineage barcode sequencing for Exp1Rep1Day70


title: Exp1Rep4Day56

description: DNA-based lineage barcode sequencing for Exp1Rep4Day56


title: Blood samples 1414N07

description:
1414N07
101035780039_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP143BeadChip


title: Blood samples 1413119

description:
1413119
200109370106_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP146BeadChip


title: Blood samples 125083

description:
125083
101035780039_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP142BeadChip


title: Exp1Rep3Day56

description: DNA-based lineage barcode sequencing for Exp1Rep3Day56


title: Pcp2-TRAP mouse cerebellum P7 TRAP

type: RNA

city: New York

first: Tom

middle: Samuel

last: Carroll

state: New York

address: 1230 York Avenue

department: Bioinformatics

institute: The Rockefeller University

hyb_protocol: 200 μl of hybridization solution containing 5.2 μg of the fragmented and labeled ss-DNA was hybridized to Affymetrix HTA 2.0 arrays (P/N 902662), (or  GeneChip™ Mouse Gene 1.0 ST Array  P/N 902464;  GeneChip™ Mouse Gene 2.0 ST Array P/N 902462) for 16 hours at 45°C. After hybridization, arrays were stained with streptavidin-phycoerythrin, followed by an antibody solution (anti-streptavidin) and a second streptavidin-phycoerythrin solution,( used The GeneChip™ Hybridization, Wash, and Stain Kit P/N 900720)  with all liquid handling performed by a GeneChip Fluidics Station 450. Arrays were then scanned with the Affymetrix GeneChip Scanner 3000 7G.

scan_protocol: Mouse Gene 1.0 ST arrays were scanned using the GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing:
Normalised microarray expression values were acquired with Affymetrix Power Tools’s apt-probeset-summarize tool using rma-sketch normalisation,
MoGene-1_0-st-v1.r3.pgf
MoGene-1_0-st-v1.r3.mps

label: biotin

source_name: Pcp2-TRAP mouse cerebellum P7 TRAP

label_protocol: 300 ng of total RNA was used to synthesize the first strand of cDNA using GeneChip WT Plus Reagent Kit from Affymetrix(P/N 902281). Single-stranded cDNA with T7 promoter sequence at the 5’ end was  synthesized in the reverse transcription reaction. The single-stranded cDNA was then converted into a double-stranded DNA (dsDNA) by DNA polymerase I in the presence of E. coli RNase H and DNA ligase. The dsDNA was then served as a template for amplification with T7 RNA polymerase to create antisense RNA. 15 μg of antisense RNA was used to generate sense-strand cDNA(ss-DNA) by reverse transcription using 2nd-Cycle Primers. The ss-cDNA contains dUTP at a fixed ratio relative to dTTP and 5.5 μg of ss-cDNA was fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues. The fragmented ss-cDNA was labeled with biotin by terminal deoxynucleotidyl transferase (TdT).

growth_protocol: All mice were healthy and were housed with a companion(s) in a specific-pathogen free animal facility in vented cages on a 12 hour light/dark cycle. Food and water were provided ad libitum.

extract_protocol: TRAP-RNA was isolated as previously described (Heiman et al., 2014; Kocabas et al., 2015; Zhu et al., 2016). Briefly, for Tg(Pcp2-L10a-Egfp) mice, pooled cerebella were immediately homogenized with a Teflon-glass homogenizer in ice-cold polysome extraction buffer (10 mM HEPES-KOH [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT (MilliporeSigma, D9779-1G), 100 µg/ml cycloheximide (MilliporeSigma, C7698-1G), Superasin and RNasin RNase inhibitors (ThermoFisher, AM2694, PR-N2515)and complete-EDTAfree protease inhibitor (MilliporeSigma, 11836170001)). Following clearing by centrifugation, supernatants were incubated at 4˚C with end-over-end rotation for 16-18 hours with biotinylated Streptavidin T1 Dynabeads (ThermoFisher, 65601) previously conjugated with GFP antibodies (Sloan Kettering Institute Antibody Core, HtzGFP-19C8 and HtzGFP-19F7). The beads were collected on a magnetic rack, unbound RNA was collected, beads were washed, and resuspended in lysis buffer with β-mercaptoethanol (Agilent, 400753) to extract bound RNA from polysomes. RNA was purified using the Stratagene Absolutely RNA Nanoprep kit (Agilent, 400753). RNA quantity and quality was measured using an Agilent 2100 Bioanalyzer with the 6000 Pico Kit (Agilent, 5067-1513).


title: heart_203s_A15


title: Pcp2-TRAP mouse cerebellum P7 Unbound

source_name: Pcp2-TRAP mouse cerebellum P7 Unbound


title: Blood samples 122053

description:
122053
101035780039_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP141BeadChip


title: Exp1Rep1Day56

description: DNA-based lineage barcode sequencing for Exp1Rep1Day56


title: Blood samples 124049

description:
124049
101035780039_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP139BeadChip


title: Exp1Rep4Day42

description: DNA-based lineage barcode sequencing for Exp1Rep4Day42


title: Pcp2-TRAP mouse cerebellum P56 replicate 2

extract_protocol: TRAP-RNA was isolated as previously described (Heiman et al., 2014; Kocabas et al., 2015; Zhu et al., 2016). Briefly, for Tg(Pcp2-L10a-Egfp) mice, pooled cerebella were immediately homogenized with a Teflon-glass homogenizer in ice-cold polysome extraction buffer (10 mM HEPES-KOH [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT (MilliporeSigma, D9779-1G), 100 µg/ml cycloheximide (MilliporeSigma, C7698-1G), Superasin and RNasin RNase inhibitors (ThermoFisher, AM2694, PR-N2515)and complete-EDTAfree protease inhibitor (MilliporeSigma, 11836170001)). Following clearing by centrifugation, supernatants were incubated at 4˚C with end-over-end rotation for 16-18 hours with biotinylated Streptavidin T1 Dynabeads (ThermoFisher, 65601) previously conjugated with GFP antibodies (Sloan Kettering Institute Antibody Core, HtzGFP-19C8 and HtzGFP-19F7). The beads were collected on a magnetic rack, washed, and resuspended in lysis buffer with β-mercaptoethanol (Agilent, 400753) to extract bound RNA from polysomes. RNA was purified using the Stratagene Absolutely RNA Nanoprep kit (Agilent, 400753). RNA quantity and quality was measured using an Agilent 2100 Bioanalyzer with the 6000 Pico Kit (Agilent, 5067-1513).


title: Exp1Rep3Day42

description: DNA-based lineage barcode sequencing for Exp1Rep3Day42


title: Blood samples 129115

description:
129115
101035780039_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP140BeadChip


title: Exp1Rep2Day42

description: DNA-based lineage barcode sequencing for Exp1Rep2Day42


title: Blood samples 127179

description:
127179
101035780039_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP138BeadChip


title: Pcp2-TRAP mouse cerebellum P56 replicate 3


title: Exp1Rep1Day42

description: DNA-based lineage barcode sequencing for Exp1Rep1Day42


title: Pcp2-TRAP mouse cerebellum P21 replicate 3


title: Pcp2-TRAP mouse cerebellum P21 replicate 1


title: Pcp2-TRAP mouse cerebellum P7 replicate 2


title: Pcp2-TRAP mouse cerebellum P7 replicate 1


title: Pcp2-TRAP mouse cerebellum P15 replicate 3


title: Pcp2-TRAP mouse cerebellum P21 replicate 2


title: Pcp2-TRAP mouse cerebellum P7 replicate 3


title: Blood samples 121114

description:
121114
101035780039_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP136BeadChip


title: Blood samples 124088

description:
124088
101035780039_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP135BeadChip


title: Exp1Rep4Day28

description: DNA-based lineage barcode sequencing for Exp1Rep4Day28


title: Pcp2-TRAP mouse cerebellum P0 replicate 3


title: Pcp2-TRAP mouse cerebellum P0 replicate 1


title: Pcp2-TRAP mouse cerebellum P0 replicate 2


title: Blood samples 127180

description:
127180
101035780039_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP133BeadChip


title: Blood samples 127095

description:
127095
101035780039_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP134BeadChip


title: Blood samples 127208

description:
127208
200109370134_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP132BeadChip


title: Exp1Rep3Day28

description: DNA-based lineage barcode sequencing for Exp1Rep3Day28


title: Exp1Rep2Day28

description: DNA-based lineage barcode sequencing for Exp1Rep2Day28


title: 8100LU

city: St. Louis

first: Jennifer

middle: Ann

last: McKenzie

state: MO

address: 425 S. Euclid

department: Orthopedics

institute: Washington University in St. Louis

data_processing:
The RNA-seq reads were aligned to the mm10 mouse genome (STAR version 2.4.2a).
Gene counts were derived from the number of uniquely aligned unambiguous reads (Subread:featureCount, version 1.4.6) and annotated (GENCODE v9).Only non-redundant uniquely aligned reads were used to estimate the expression level of genes.
All gene-level transcript counts were then normalized for library size (R/Bioconductor DEseq2). Lowly expressed genes (CPM < 1) in all the samples at any time points were filtered out, and resulted in 17,240 genes for down-stream analysis. To check for outlier samples a correlation analysis was performed (cutoff of r > 0.85).
Differential expression analysis was performed separately for each injury mode and each time point as a comparison of injured samples vs. pooled control samples, with a threshold for differentially expressed genes (DEGs) set as fold-change (FC, Injured/Control) > 2 and Benjamini-Hochberg adjusted p-value <0.05.
Additional characterization was performed by a principle component analysis on stress fracture and full fracture samples separately. For each sample, the reads per kilobase of transcript per million mapped reads (RPKM) values for all 17,240 genes in the data set were used as inputs.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: ulna

extract_protocol:
For stress fracture, a 5 mm section of the ulna was removed surrounding the injury site. Soft tissue was removed, the sample was flash frozen in liquid nitrogen, and stored at −80 °C until RNA extraction. The left ulna was similarly processed to serve as a control. For full fracture, a 7 mm section of the femur was removed surrounding the injury site. Soft tissue was removed and bone marrow was spun out using a centrifuge. The sample was flash frozen in liquid nitrogen and stored at −80 °C until RNA extraction. The left femur was similarly processed to serve as a control.Frozen bone samples were pulverized (Braun Mikrodismembrator), dissolved into TRIzol (Invitrogen), and stored at −80 °C. Later, the TRIzol-sample solution was thawed and processed using an RNA clean-up and concentration kit (Norgen Biotek). RNA concentration was measured (Thermo Scientific Nanodrop ONE) and quality was evaluated (Agilent Technologies Bioanalyzer 2100). Only samples with RINs >6.5, representing acceptable quality, were used in sequencing.
Total RNA was depleted of rRNA (Illumina, Ribo-Zero rRNA Removal Kit) and RNA-seq (Illumina HiSeq 3000) was performed at 1 × 50 bp on 1 μg of RNA by the Washington University Genome Technology Access Center

tag: time point

value: bone

value: female

tag: condition

value: Intact

tag: strain


title: 8096LU


title: 8090LU


title: 8083LU


title: 8092LU


title: 8076LU


title: Exp1Rep1Day28

description: DNA-based lineage barcode sequencing for Exp1Rep1Day28


title: Exp1Rep4Day14

description: DNA-based lineage barcode sequencing for Exp1Rep4Day14


title: 8094LU


title: 8098LU


title: Exp1Rep2Day56

description: DNA-based lineage barcode sequencing for Exp1Rep2Day56


title: 8100RU

value: bone 3d periosteum

value: Stress Fracture


title: 8085LU


title: Blood samples 128168

description:
128168
200109370134_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP130BeadChip


title: Exp1Rep3Day14

description: DNA-based lineage barcode sequencing for Exp1Rep3Day14


title: Blood samples 125086

description:
125086
200109370134_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP129BeadChip


title: Blood samples 122148

description:
122148
200109370134_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP128BeadChip


title: 8080LU


title: 8099RU


title: Pcp2-TRAP mouse cerebellum P56 replicate 1


title: 8098RU

value: bone 7d periosteum


title: Exp1Rep2Day14

description: DNA-based lineage barcode sequencing for Exp1Rep2Day14


title: Blood samples 127239

description:
127239
200109370134_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP131BeadChip


title: Blood samples 133012

description:
133012
200109370134_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP127BeadChip


title: 8097RU

value: bone 5d periosteum


title: 8096RU


title: 8095RU

value: bone 4h periosteum


title: Exp1Rep1Day14

description: DNA-based lineage barcode sequencing for Exp1Rep1Day14


title: 8094RU


title: Exp1Rep4Day0

description: DNA-based lineage barcode sequencing for Exp1Rep4Day0


title: Blood samples 128122

description:
128122
200109370134_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP126BeadChip


title: Exp1Rep3Day0

description: DNA-based lineage barcode sequencing for Exp1Rep3Day0


title: 8090RU


title: 8091RU

value: bone 1d periosteum


title: 8092RU


title: Exp1Rep2Day0

description: DNA-based lineage barcode sequencing for Exp1Rep2Day0


title: Exp1Rep1Day0

description: DNA-based lineage barcode sequencing for Exp1Rep1Day0


title: 8089RU


title: 8086RU


title: 8087RU


title: Blood samples 127162

description:
127162
200109370134_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP123BeadChip


title: PlasmidLibrary

description: DNA-based lineage barcode sequencing for plasmid library


title: 8088RU


title: 8085RU


title: 8083RU


title: Day +95 - 3 TRAPseq

description: co-culture with mouse glia and granule cells

data_processing:
Illumina's bcl2fastq2 Conversion Software v2.19 was used for basecalling.
Salmon quantifications were derived using Salmon (version 0.8.2) from raw FastQ against the hg19 transcriptome sequences retrieved in the Bioconductor TxDb.Hsapiens.UCSC.hg19.knownGene package (version 3.2.2)
Differential expression analysis was performed directly from Salmon quantifications using Tximport (version 1.8.0 ) and DESeq2 (version 1.20.0)
Genome_build: hg19 - (From Bioconductor package - BSgenome.Hsapiens.UCSC.hg19  version 1.4.0)
Supplementary_files_format_and_content: Salmon transcript quantifications against the hg19 transcriptome sequences.

source_name: Purkinje cell

growth_protocol: See manuscript for details of stem cell differentiation protocol

extract_protocol:
Polysomes were stabilized by adding 100 µg/ml cycloheximide to cell culture media for 10 minutes prior to homogenization. Cells were homogenized with a Teflon-glass homogenizer in ice-cold polysome extraction buffer (10 mM HEPES-KOH [pH 7.4], 150 mM KCl, 5 mM MgCl2, 0.5 mM DTT (MilliporeSigma, D9779-1G), 100 µg/ml cycloheximide (MilliporeSigma, C7698-1G), Superasin and RNasin RNase inhibitors (ThermoFisher, AM2694, PR-N2515)and complete-EDTAfree protease inhibitor (MilliporeSigma, 11836170001)). Following clearing by centrifugation, supernatants were incubated at 4˚C with end-over-end rotation for 16-18 hours with biotinylated Streptavidin T1 Dynabeads (ThermoFisher, 65601) previously conjugated with GFP antibodies (Sloan Kettering Institute Antibody Core, HtzGFP-19C8 and HtzGFP-19F7). The beads were collected on a magnetic rack, washed, and resuspended in lysis buffer with β-mercaptoethanol (Agilent, 400753) to extract bound RNA from polysomes. RNA was purified using the RNeasy micro kit (Qiagen, 74004). RNA quantity and quality was measured using an Agilent 2100 Bioanalyzer with the 6000 Pico Kit (Agilent, 5067-1513).
1 ng of total RNA was used to generate full length cDNA using Clontech’s SMART-Seq v4 Ultra Low Input RNA Kit (Cat # 634888).  1 ng of cDNA was then used to prepare libraries using Illumina Nextera XT DNA sample preparation kit (Cat # FC-131-1024).   Libraries with unique barcodes were pooled at equal molar ratios and sequenced on Illumina NextSeq 500 sequencer to generate 75 bp single reads, following manufactures protocol (Cat# 15048776 Rev.E)
cDNA amplification from mRNA followed by library prep

tag: cell type

tag: method

value: Pcp2-TRAP isolation

value: Day +95


title: 8084RU

tag: Sex


title: 8081RU

tag: age


title: 8079RU


title: 8082RU


title: 8080RU


title: Blood samples 125142

description:
125142
101035780063_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP120BeadChip


title: Blood samples 122079

description:
122079
101035780063_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP120BeadChip


title: Blood samples 129075

description:
129075
200109370134_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP122BeadChip


title: Blood samples 127186

description:
127186
200109370134_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP121BeadChip


title: Blood samples 125133

description:
125133
200109370134_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP124BeadChip


title: Day 24 - 3 TRAPseq

value: Day 24


title: Day +95 - 1 TRAPseq


title: Day +95 - 2 TRAPseq


title: Blood samples 126154

description:
126154
101035780063_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP119BeadChip


title: Blood samples 126162

description:
126162
101035780063_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP117BeadChip


title: Day 24 - 2 TRAPseq


title: 8093RU


title: 8076RU


title: 8077RU


title: Blood samples 127199

description:
127199
101035780063_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP115BeadChip


title: Blood samples 126149

description:
126149
101035780063_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP116BeadChip


title: 8078RU


title: Blood samples 126108

description:
126108
101035780063_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP118BeadChip


title: 8027LF

source_name: femur


title: 8005RF

value: bone 7day callus

value: Fracture


title: 8028RF


title: 8002RF


title: 8005LF


title: Day 24 - 1 TRAPseq


title: 8035RF

value: bone 3day periosteum


title: 8024RF


title: 8027RF


title: Blood samples 127228

description:
127228
101035780039_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP137BeadChip


title: 8035LF


title: 10A

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
All analysis steps were done with using docker4seq package (Kulkarni et al. BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):349, Beccuti et al. Bioinformatics. 2018 Mar 1;34(5):871-872).
Demultiplexing was done using bcl2fastq tool (docker.io/repbioinfo/demultiplexing.2017.01)
Adapters removal with skewer (docker.io/repbioinfo/skewer.2017.01)
Expression quantification was done with STAR/RSEM (docker.io/repbioinfo/rsemstar.2017)
Annotation (docker.io/rcaloger/annotate.2017.01) was done using ENSEMBL (hg38) annotation.
Genome_build: hg38
Supplementary_files_format_and_content: counts/TPM/FPKM table generated by RSEM

source_name: podocyte immortalized cell line from podocytes collected from healthy donor urine

growth_protocol: DMEM:F-12  supplemented with 10% FCS (Invitrogen), 50 IU/mL penicillin, 50 g/mL streptomycin, 5mM glutamine, 5 g/mL insulin, 5 g/mL transferrin, 5 mg/mL selenium

extract_protocol:
Total RNA was isolated from samples using RNeasy mini kit (Qiagen). Genomic DNA contaminations were removed from RNA samples with the Ambion® DNA-free kit (Thermo-Fisher Scientific). DNA-free RNA concentration and quality were estimated with NanoVuePlus Spectrophotometer (GE Healthcare) and Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
Libraries for RNA sequencing were generated using TruSeq RNA stranded sample preparation kit v2 (Illumina Inc.) following manufacturer’s instructions, using 1 ug of total RNA as input material. Libraries were pooled and sequenced with NextSeq 500 sequencer (Illumina Inc.) generating 75-bp paired-end sequences.

tag: source subject status

value: healthy donor

tag: source tissue

value: urine

value: podocyte immortalized cell line

tag: passage

value: passage 11


title: Blood samples 125151

description:
125151
101035780063_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP113BeadChip

tag: gender

value: Famale

tag: g

tag: father


title: 10C

value: passage 15


title: 10B

value: passage 12


title: Blood samples 127200

description:
127200
101035780063_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP114BeadChip

tag: mother

tag: sibling number

tag: birth weight


title: 710P3

source_name: podocyte immortalized cell line clone from AS patient

value: Alport syndrome (AS) patient

tag: subject id/genotype

value: AS patient 3 (col4a5 mutation)

value: passage 10


title: Blood samples 127204

description:
127204
101035780063_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP111BeadChip

tag: weaning weight

tag: six-month weight


title: 8032RF

tag: time point

value: female

tag: condition

tag: strain


title: 8030RF

tag: Sex


title: 8007RF

tag: age


title: 8007LF

value: bone

value: Intact


title: 8022RF

value: bone 14day callus


title: 8034RF


title: 8016RF


title: 72P3

tag: source subject status

tag: cell type


title: 71P3

tag: passage


title: Blood samples 127164

description:
127164
101035780063_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP110BeadChip

tag: gender


title: Blood samples 1212019

description:
1212019
101035780063_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP112BeadChip

tag: g


title: Blood samples 123116

description:
123116
200109370135_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP109BeadChip

tag: father


title: AS212P1

value: AS patient 1 (col4a3 mutation)

value: passage 13


title: AS213P1


title: Pcp2-TRAP mouse cerebellum P15 replicate 1


title: 8016LF


title: 8014RF

value: Fracture


title: Pcp2-TRAP mouse cerebellum P15 replicate 2


title: 8011RF


title: Blood samples 123086

description:
123086
200109370135_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP108BeadChip

tag: mother


title: 8033RF


title: 8019RF

value: bone 1day periosteum


title: 8025RF


title: AS611P2

value: AS patient 2 (col4a5 mutation)

value: passage 14


title: Blood samples 126109

description:
126109
200109370135_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP107BeadChip

tag: sibling number


title: 8029RF


title: AS216P1

value: podocyte immortalized cell line


title: 8033LF


title: 8026RF

value: bone 4hour periosteum


title: AS610P2


title: Blood samples 122146

description:
122146
200109370135_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP104BeadChip

value: Famale

tag: birth weight


title: Blood samples 127166

description:
127166
200109370135_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP106BeadChip


title: 8021RF


title: 8019LF


title: 8006RF


title: AS612P2

tag: subject id/genotype

value: passage 12


title: TT-seq_NM_30min_rep1

city: Göttingen

first: Eusra

last: Mohammad

address: Am Faßberg 11

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
Library strategy: TT-Seq
TT-seq data preprocessing and global normalization parameters. Paired-end 75 base reads with additional 6 base reads of barcodes were obtained for each of the samples.  Reads were demultiplexed and mapped with STAR 2.5.2b (Dobin and Gingeras 2015) to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium). Samtools (Li, Handsaker et al. 2009) was used to quality filter SAM files, whereby alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. We used a spike-in (RNAs) normalization strategy essentially as described (Schwalb, Michel et al. 2016) to allow observation of global shifts (sequencing depth), cross-contamination rate (proportion of unlabeled reads purified in the TT-seq samples) and antisense bias ratio (ratio of spurious reads originating from the opposite strand introduced by the reverse transcription reaction). Read counts (kij) for spike-ins were calculated using HTSeq (Anders, Pyl et al. 2015).
Calculation of the number of transcribed bases. Of all fragments, only those were kept that exhibited a positive inner mate distance. The number of transcribed bases (tbj) for all samples was calculated as the sum of the coverage of evident (sequenced) fragment parts (read pairs only) for all fragments with an inner mate interval not entirely overlapping a Refseq annotated intron (UCSC RefSeq GRCh38, ~ 98.5% of all fragments) in addition to the sum of the coverage of non-evident fragment parts (entire fragment). Definition of transcription units based on the UCSC RefSeq genome assembly GRCh38 (RefSeq-TUs). For each annotated gene, transcription units were defined as the union of all existing inherent transcript isoforms (UCSC RefSeq GRCh38). Number of transcribed bases (coverage). Coverages were calculated upon antisense bias corrected number of transcribed bases (tbj) falling into the region of a RefSeq-TU. Read counts per kilobase (RPK). RPKs were calculated upon antisense bias corrected read counts (kj) falling into the region of a RefSeq-TU divided by its length in kilobases.
TT-seq normalization. For a robust normalization, we first identified a subgroup of RefSeq-TU’s as non-Differentially Expressed (non-DE) for both 15 minutes and 30 minutes time point over the response of NM-PP1(CDK12as inhibitor) using DESeq2 package. Based on the antisense bias corrected RPKs, a group of expressed TUs was defined to comprise all TUs with an RPK of 100 or higher in two summarized replicates of TT-seq 15 minutes samples without inhibitor treatment. An RPK of 100 corresponds to approximately a coverage of 10 per sample due to an average fragment size of 200. Within this group, a subset of TUs having a length greater than 50 kb was used to identify the non-Differentially Expressed (non-DE) TU’s. The antisense bias corrected coverage sij of transcribed unit i in sample j was normalized for sequencing depth σj where σj was balanced between replicates via classical size factor normalization to gain statistical power in the differential expression analysis. On the resulting 140 non-differentially expressed RefSeq-TUs, size factors for each sample were then estimated as described by Equation (5) in DESeq package (Anders and Huber) to correct for library size and sequencing depth variations.
Biological replicates were merged using "samtools merge" and processed as described for the individual replicates.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigWig coverage files for both individual replicates and merged replicates.

source_name: HEK293 Human embryonic kidney cells

growth_protocol: CRISPR/Cas9 genome engineering was used to mutate F813 (TTT) to G (GGT) of CDK12 gene loci in HEK293 to generate asCDK12 HEK293 cells.  HEK293 WT and asCDK12 HEK293 cells were grown in DMEM medium supplemented with 10% heat-inactivated fetal calf serum, 2 mM L-glutamine at 37ºC and 5% CO2. Cells were routinely verified to be free of mycoplasma contamination. Biological replicates were cultured independently.

extract_protocol:
TT-seq (Schwalb et al., 2016).
Ovation Universal RNA-Seq System (NuGEN).

treatment_protocol: 6 x 107 cells from two biological replicates were treated for 15 min and 30 min with solvent (DMSO) or 7.5mM 1-NM-PP1 (NM) at 37 °C and 5 % CO2. For the 15 min treatment, cells were exposed to 10 min 500 µM of 4-thiouracil (4sU, Carbosynth, NT06186) after 5 min of DMSO or NM treatment (15 min total treatment). For the 30 min treatment, cells were exposed to 10 min 500 µM of 4-thiouracil (4sU, Carbosynth, NT06186) after 20 min of DMSO or NM treatment (30 min total treatment).

tag: tissue

value: HEK293 Human embryonic kidney cells

tag: treatment conditions

value: 37 °C, 7.5mM 1-NM-PP1 for 30min, 500mM 4sU (Carbosynth) labeling during the last 10 minutes.

tag: molecule subtype

value: 4sU-labeled RNA


title: Blood samples 124001

description:
124001
200109370135_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP105BeadChip

tag: weaning weight

tag: six-month weight


title: 8029LF

tag: time point

tag: Sex

value: female

tag: condition

tag: strain


title: 8012RF

tag: age


title: 8004RF


title: 8023RF


title: TT-seq_NM_30min_rep2


title: TT-seq_NM_15min_rep2

value: 37 °C, 7.5mM 1-NM-PP1 for 15min, 500mM 4sU (Carbosynth) labeling during the last 10 minutes.


title: Blood samples 127004

description:
127004
200109370135_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP103BeadChip

tag: gender


title: Blood samples 127206

description:
127206
200109370134_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP125BeadChip

tag: g


title: TT-seq_NM_15min_rep1


title: 8001RF


title: 8026LF

value: bone

value: Intact


title: M6_G6RBF2

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

description: Ribosome footprint RNA

data_processing:
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcodes were separated using Novobarcode
Sequences were aligned to mm10 genome using Bowtie2
Normalized abundance was generated by RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet includes FPKM for all genes per sample

source_name: Mouse Embryonic Stem Cells

growth_protocol: mESCs were grow n in standard 2i+Lif condition

extract_protocol:
For RBF libraries, cell extract was incubated with Rnase A+T1, separated on a sucrose gradient to obtain 80S ribosomes, RNA was isolated by phenol-chloroform and ran on a gel to acquire 26-32nt RNAs. RNAseq libraries were made from RNA isolated using Trizol + isopropanol precipitation.
Libraries were prepared using protocol described in Heyer et al. 2015 NAR
RNAseq, Ribosome profiling

treatment_protocol: Cells were treated with cycloheximide for 10min prior to lysis

tag: genotype

value: METTL6 KO G6


title: M6_WTRBF2

description: Ribosome footprint RNA

value: wild type


title: Blood samples 125113

description:
125113
200109370135_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP101BeadChip

tag: father

tag: mother


title: Blood samples 127234

description:
127234
200109370135_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP99BeadChip

tag: sibling number

tag: birth weight


title: Blood samples 125125

description:
125125
200109370135_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP100BeadChip


title: M6_WTRBF1

description: Ribosome footprint RNA


title: 8006LF


title: M6_G6RBF1

description: Ribosome footprint RNA


title: TT-seq_DMSO_30min_rep2

tag: tissue

value: 37 °C, DMSO for 30min, 500mM 4sU (Carbosynth) labeling during the last 10 minutes.


title: TT-seq_DMSO_30min_rep1

tag: treatment conditions

value: 37 °C, DMSO for 30min, 500mM 4sU Carbosynth) labeling during the last 10 minutes.


title: Blood samples 126161

description:
126161
200109370135_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP98BeadChip


title: TT-seq_DMSO_15min_rep2

value: 37 °C, DMSO for 15min, 500mM 4sU (Carbosynth) labeling during the last 10 minutes.

tag: molecule subtype


title: G6_RNA2

description: Total RNA


title: G6_RNA1

description: Total RNA


title: TT-seq_DMSO_15min_rep1


title: mES Dnmt-WT_RNAseq_Hypoxia_r2

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

data_processing:
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using tophat (version 2.0.10).
Counrs were called byHTSeq (version 0.5.3p3)
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain raw read counts for each sample

source_name: Dnmt-WT Hypoxia

extract_protocol:
RiboMinus Eukaryote System (Life technologies)
Briefly, total RNA was extracted using TRIzol (Invitrogen), and remaining DNA contaminants in 17-20ug of RNA was removed using Turbo DNase (Ambion) according to the manufacturers instruction. RNA was repurified using RNeasy Mini Kit (Qiagen).
Strand specific library preparation

value: inner cell mass

tag: cell line

value: mES Dnmt-WT

tag: cell type

value: Embryonic Stem cells

tag: treatment

tag: growth protocol

value: cultured feeder-free in fibroblast-conditioned medium


title: mES Dnmt-WT_RNAseq_Normoxia_r2

source_name: Dnmt-WT Normoxia


title: 82

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from  the Populus genome (version3.0,https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: abundance measurements

organism: Populus ussuriensis

source_name: basal ends of stem cuttings_96 h after cutting

growth_protocol: Plantlets cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Media used in experiments were adjusted to pH 5.8 before adding 3 g l-1 Gelrite (Duchefa). Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

extract_protocol:
Basal ends of in vitro stem cuttings (0.5 cm) were harvested, flash frozen on dry ice, and RNA was isolated using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: two week-old seedlings were cutting

value: basal ends of stem cuttings

value: 2-week-old in vitro plant

tag: time point

value: 96 h after cutting


title: WT1RNA_new

description: Total RNA

tag: strain


title: Blood samples 127160

description:
127160
200109370135_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP102BeadChip

value: Famale

tag: weaning weight

tag: six-month weight


title: Blood samples 125106

description:
125106
200109370013_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP97BeadChip

tag: gender

tag: g


title: Blood samples 125105

description:
125105
200109370013_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP96BeadChip

tag: father


title: 81

tag: age


title: WT2RNA_new

description: Total RNA

tag: genotype


title: mES Dnmt-TKO_RNAseq_Hypoxia_r5

source_name: Dnmt-TKO Hypoxia

value: mES Dnmt-TKO

value: cultured in 0.1% Gelatin Solution in DMEM 4,500 mg /L glucose, 1% sodium pyruvate, 15% FBS, 1% Pen Strep, 0.1 mM of non-essential amino acids (EmbryoMax), 50 μM β-mercaptoethanol, 103 U LIF ESGRO (Millipore).


title: mES Dnmt-WT_RNAseq_Hypoxia_r1


title: 72

source_name: basal ends of stem cuttings_48 h after cutting

value: 48 h after cutting


title: mES Dnmt-WT_RNAseq_Normoxia_r1


title: mES Dnmt-TKO_RNAseq_Normoxia_r5

source_name: Dnmt-TKO Normoxia


title: mES Dnmt-TKO_RNAseq_Normoxia_r4


title: mES Dnmt-TKO_RNAseq_Hypoxia_r4


title: Blood samples 122103

description:
122103
200109370013_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP95BeadChip

tag: mother

tag: sibling number

tag: birth weight


title: 71

tag: tissue


title: 61

source_name: basal ends of stem cuttings_24 h after cutting

value: 24 h after cutting


title: mES Dnmt-WT_RNAseq_Normoxia_r3

tag: cell line


title: Blood samples 126159

description:
126159
200109370013_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP93BeadChip


title: mES Dnmt-WT_RNAseq_Hypoxia_r3

tag: cell type


title: Blood samples 124073

description:
124073
200109370013_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP92BeadChip


title: Blood samples 120011

description:
120011
200109370013_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP94BeadChip


title: 52

source_name: basal ends of stem cuttings_12 h after cutting

value: 12 h after cutting


title: E_BITC2

city: Dalian

first: Ke

last: Zhang

address: NO.1 Light-Industry Garden, Ganjingzi Borough, Dalian 116034, China

institute: Dalian polytechnic university

data_processing:
Illumina Casava 1.8 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=Vibrio+parahaemolyticus%5Borgn%5D+
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Vibrio parahaemolyticus

source_name: Food-borne microorganism

extract_protocol:
Extracting RNA from cultured bacteria under different conditions (presence and absence of BITC). A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: 1/8MIC BITC


title: E_BITC3


title: mES Dnmt-TKO_RNAseq_Normoxia_r3

tag: growth protocol


title: mES Dnmt-TKO_RNAseq_Hypoxia_r3


title: Toledo_DMSO_2

city: Houston

first: Margarida

last: Almeida Santos

state: Texas

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the human genome (hg38) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENECODE Release 27 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.18.0).
Genome_build: hg38
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq) for all the samples.

molecule: polyA RNA

growth_protocol: Cells were grown in suspension in T75 flasks with RPMI 1640 media and corresponding treatment for 6 days

extract_protocol:
RNA was purified using a QIAGEN Rneasy mini kit
Libraries were made using an Illumina TruSeq stranded mRNA kit

treatment_protocol: Cells were treated for 6 days before harvest. CARM1 inhibitor was used at 5uM concentrations.

value: Toledo lymphoma cell line

value: DMSO


title: C2

value: Control


title: Toledo_DMSO_3


title: 41

source_name: basal ends of stem cuttings_6 h after cutting

tag: time point

value: 6 h after cutting


title: Blood samples 128019

description:
128019
200109370013_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP91BeadChip


title: 32

source_name: basal ends of stem cuttings_2 h after cutting

value: 2 h after cutting


title: Blood samples 128115

description:
128115
200109370013_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP90BeadChip


title: Blood samples 123095

description:
123095
200109370013_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP89BeadChip


title: C1

tag: strain


title: Blood samples 128160

description:
128160
200109370001_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP85BeadChip

tag: weaning weight


title: Blood samples 127191

description:
127191
200109370013_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP88BeadChip

tag: six-month weight


title: Toledo_CARM1i_2

value: CARM1 inhibitor TP-064


title: 51


title: E_BITC1


title: Blood samples 126116

description:
126116
200109370013_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP87BeadChip

tag: gender


title: 31


title: mpk1rrp6_45-REP_C

city: Los Angeles

first: Guillaume

middle: Francois

last: Chanfreau

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

data_processing:
RNA-Seq reads were aligned to S. cerevisiae reference (assembly 64-1-1) using HISAT2 (version 2.1.0)
Read counts were obtained using htseq-count2 (with the option -s reverse) with the S. cerevisiae genome annotation (release 97)
Genome_build: R64-1-1
Supplementary_files_format_and_content: Processed data files are tab searated files representing read counts

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast strains were grown to mid-log phase in standard YPD medium at 25ºC

extract_protocol:
RNAs were extracted using a standard acid phenol-chloroform based protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pre-warmed YPD medium was added to cultures to rapidly elevate its temperature to 42ºC. Heat shocked samples were harvested and flash frozen in liquid nitrogen after 45 minutes

tag: duration of 42ºc heat shock

tag: deleted gene(s)


title: 62

tag: age


title: 42


title: Toledo_DMSO_1


title: 22

source_name: basal ends of stem cuttings_1 h after cutting

value: 1 h after cutting


title: mpk1rrp6_10-REP_C


title: Toledo_CARM1i_1


title: Toledo_CARM1i_3


title: C3


title: mpk1rrp6_0-REP_C


title: Input_DMSO_2

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
Reads were mapped to the human genome (hg38) using Bowtie (version 1.1.2) and only the reads that were mapped to unique position were retained.
To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
The peaks in each ChIP sample were detected by MACS (version 1.4.2) by comparing to the corresponding input sample. The window size was set as 500 bp and the p-value cutoff was 1e-5. Then the peaks that overlapped ENCODE blacklisted regions were removed.
Genome_build: hg38
Supplementary_files_format_and_content: Peak locations in bed format

extract_protocol:
Sonicated chromatin was immunoprecipitated using the ChIP antibodies indicated
Libraries were made using the NEBNext Ultra II DNA library prep kit

tag: chip antibody


title: Blood samples 127203

description:
127203
200109370013_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP86BeadChip

tag: g

tag: father

tag: mother


title: 21

tag: tissue

value: basal ends of stem cuttings


title: Blood samples 123093

description:
123093
200109370001_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP82BeadChip

tag: sibling number

tag: birth weight


title: Input_CARM1i_1

tag: cell line

tag: treatment


title: Blood samples 127075

description:
127075
200109370001_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP84BeadChip


title: Input_DMSO_1


title: rrp6_0-REP_C


title: 01

source_name: basal ends of stem cuttings_0 h after cutting

value: 2-week-old in vitro plant

tag: time point

value: 0 h after cutting


title: Blood samples 128101

description:
128101
200109370001_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP83BeadChip

value: Famale


title: Blood samples 1413M03

description:
1413M03
200109370001_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP80BeadChip

value: male

tag: yearling weight


title: H3K4me3_DMSO_2

value: H3K4me3 (abcam ab8580)


title: H3K4me1_DMSO_2

value: H3K4me1 (abcam ab8895)


title: Blood samples 127181

description:
127181
200109370001_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP81BeadChip

tag: weaning weight


title: Mpk1_10-REP_C

tag: strain


title: Blood samples 1414N05

description:
1414N05
200109370001_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP77BeadChip

tag: gender

tag: six-month weight


title: Mpk1_45-REP_C

tag: duration of 42ºc heat shock

tag: deleted gene(s)


title: Blood samples 123139

description:
123139
200109370001_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP78BeadChip


title: 12

source_name: basal ends of stem cuttings_0.5 h after cutting

tag: age

value: 0.5 h after cutting


title: Blood samples 128021

description:
128021
200109370001_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP79BeadChip

tag: g


title: Blood samples 128133

description:
128133
200109370001_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP76BeadChip

tag: father


title: Blood samples 123133

description:
123133
200109370001_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP75BeadChip

tag: mother


title: Input_CARM1i_2

tag: chip antibody


title: rrp6_10-REP_C


title: H3K27ac_DMSO_2

value: H3K27ac (abcam ab4729)


title: 11

tag: tissue


title: Mpk1_0-REP_C


title: H3K4me3_DMSO_1


title: rrp6_45-REP_C


title: T20

description: PuHox52-OE 96h after cutting

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The RNA-seq reads were aligned to the Populus genome (version 3.0, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa) using TopHat (version 2.1.1) .
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: processed file with phytozome Populus trichocarpa gene model name and the read counts. The gene information provided in our processed data file correspond to Popgenie Transcript name.

source_name: PuHox52-OE 96h after cutting

growth_protocol: Approximately 3 cm stem segments were excised from 4-week-old in vitro plants and cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Media used in experiments were adjusted to pH 5.8 before adding 3 g l-1 Gelrite (Duchefa). Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

tag: genotype

tag: hours after cutting


title: WT_45-REP_C


title: 02


title: T18

description: WT 96h after cutting

source_name: WT 96h after cutting

value: WT


title: T19

description: PuHox52-OE 96h after cutting


title: H3K27ac_DMSO_1

tag: cell line

value: Toledo lymphoma cell line

tag: treatment


title: T17

description: WT 96h after cutting


title: T16

description: PuHox52-OE 48h after cutting

source_name: PuHox52-OE 48h after cutting


title: H3K4me3_CARM1i_2


title: H3K4me1_DMSO_1

value: DMSO


title: WT_0-REP_C


title: WT_10-REP_C


title: H3K4me1_CARM1i_2


title: Blood samples 127125

description:
127125
200109370001_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP74BeadChip

tag: sibling number

tag: birth weight


title: mpk1rrp6_10-REP_B

tag: strain


title: H3K27ac_CARM1i_2


title: Blood samples 1414149

description:
1414149
101035780074_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP73BeadChip

tag: gender

tag: weaning weight

tag: yearling weight


title: T15

description: PuHox52-OE 48h after cutting


title: Blood samples 1414154

description:
1414154
101035780074_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP71BeadChip

tag: six-month weight


title: mpk1rrp6_0-REP_B

tag: duration of 42ºc heat shock

tag: deleted gene(s)


title: mpk1rrp6_45-REP_B


title: Blood samples 1414151

description:
1414151
101035780074_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP72BeadChip

tag: g

tag: father


title: rrp6_45-REP_B


title: rrp6_10-REP_B


title: T14

description: WT 48h after cutting

source_name: WT 48h after cutting


title: T10

description: WT 24h after cutting

source_name: WT 24h after cutting


title: T13

description: WT 48h after cutting


title: T11

description: PuHox52-OE 24h after cutting

source_name: PuHox52-OE 24h after cutting


title: T12

description: PuHox52-OE 24h after cutting


title: H3K4me1_CARM1i_1

tag: chip antibody


title: H3K27ac_CARM1i_1


title: rrp6_0-REP_B


title: H3K4me3_CARM1i_1


title: T09

description: WT 24h after cutting

tag: tissue


title: Mpk1_10-REP_B


title: T08

description: PuHox52-OE 12h after cutting

source_name: PuHox52-OE 12h after cutting

tag: genotype


title: Mpk1_45-REP_B


title: T07

description: PuHox52-OE 12h after cutting

tag: hours after cutting


title: Blood samples 1414147

description:
1414147
101035780074_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP70BeadChip

tag: mother


title: Mpk1_0-REP_B


title: T06

description: WT 12h after cutting

source_name: WT 12h after cutting


title: hsp70- 5h-3

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Short read trimming (Trimmomatic)
alignment of Illumina short reads with STAR_2.5.0a
Read counting with featureCounts (v1.5.0-p1)
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: Tab-delimeted text file with FlyBase gene identifyer (1 column) and read counts per gene (2 column)

organism: Drosophila melanogaster

source_name: Drosophila adult head

extract_protocol:
For each behavioural experiment, four biological replicates of approximately 100 flies were collected and frozen. Naive or trained males snap-frozen in liquid nitrogen at the appropriate time point after training were manually decapitated. The heads were collected on a dry ice-cooled surface. Total RNA extraction was performed with RNAzol reagent (Molecular Research Center, USA) according to the manufacturer’s protocol
Libraries for RNA-seq were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s guidelines. The 75-bp single-end sequencing was conducted on an Illumina NextSeq 500 platform

tag: time point

value: 5 hours (short-term)

value: adult head


title: hsp70- control-3

value: 0 hours (naive)


title: hsp70- 5h-2


title: WT_45-REP_B


title: Blood samples 1413140

description:
1413140
101035780074_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP67BeadChip

tag: sibling number


title: T05

description: WT 12h after cutting


title: Blood samples 1414146

description:
1414146
101035780074_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP68BeadChip

tag: birth weight


title: hsp70- control-2


title: Blood samples 1414153

description:
1414153
101035780074_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP69BeadChip


title: Blood samples 1414144

description:
1414144
101035780074_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP66BeadChip


title: Blood samples 1414141

description:
1414141
101035780074_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP64BeadChip


title: T04

description: PuHox52-OE 6h after cutting

source_name: PuHox52-OE 6h after cutting


title: Blood samples 1414140

description:
1414140
101035780074_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP62BeadChip


title: Blood samples 1413139

description:
1413139
101035780074_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP65BeadChip


title: Blood samples 1414049

description:
1414049
101035780074_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP63BeadChip


title: WT_10-REP_B

tag: strain


title: hsp70- 5h-1


title: WT_0-REP_B


title: w+hsp70- - 5h-3


title: Blood samples 1414105

description:
1414105
101035780003_R06C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP60BeadChip

tag: gender


title: Blood samples 1414128

description:
1414128
101035780003_R06C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP61BeadChip

tag: weaning weight


title: mpk1rrp6_45-REP_A


title: T03

description: PuHox52-OE 6h after cutting


title: hsp70- control-1


title: w+hsp70- - 5h-2


title: w+hsp70- - 5h-1


title: mpk1rrp6_0-REP_A


title: T02

description: WT 6h after cutting

source_name: WT 6h after cutting


title: T01

description: WT 6h after cutting


title: mpk1rrp6_10-REP_A


title: rrp6_45-REP_A


title: H3K9me2_tas3D_25

city: Wuxi

first: Li

last: Sun

state: Jiangsu

address: No. 1800, Lihu Avenue

institute: Jiangnan University

data_processing:
Quality control performed using FASTX-Toolkit.
ChIP-seq reads were trimmed to ensure uniformity using FASTX-Toolkit.
ChIP-seq reads were aligned to the S. pombe genome assembly ASM294v.2.22 using Burrows-Wheeler Aligner (BWA)’s default parameters, which randomly assigned the ChIP-seq reads to the repetitive DNA sequences.
Model-based Analysis of ChIP-seq (MACS) was used for peak calling. Briefly, the mapped reads were filtered to keep one tag at the same location (--keep-dup) and were normalized by sequencing depth in million reads (-B --SPMR).
The mapped reads were extended to the size of 146 bp to define the nucleosome positions (--shift 73 --extsize 146). Others were set as the default parameters.
Genome_build: S. pombe genome ASM294v.2.22
Supplementary_files_format_and_content: bdg files were generated using MACS.

organism: Schizosaccharomyces pombe

source_name: fission yeast haploid cells

growth_protocol: Strains wt, ago1D and tas3D growing at 25℃. swo1-26 mutant cells are cultured under permissive condition (25℃) and non-permissive condition (25℃ shifted to 37℃ for 4 h).

extract_protocol:
Cells were digested with Zymolase and lysed, the chromatin lysates were treated with micrococcal nuclease to digest chromatin into mononucleosomes. The histone-DNA complexes were isolated with antibody.
Libraries of DNA were prepared using KAPA library preparation kit following the accompanied instructions.

value: H3K9me2(Abcam, ab1220)


title: H3K9me2_ago1D_25


title: rrp6_0-REP_A


title: w+hsp70- - control-1


title: H3K9me2_swo1-26_ts_37


title: w+hsp70- - control-2


title: rrp6_10-REP_A


title: Blood samples 1414125

description:
1414125
101035780003_R04C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP57BeadChip

data_processing: Genotyping of individual SNPs was performed using the Ovine SNP50BeadChip

tag: yearling weight


title: Blood samples 1414098

description:
1414098
101035780003_R05C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP58BeadChip

tag: six-month weight


title: Blood samples 1414127

description:
1414127
101035780003_R05C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP59BeadChip


title: Blood samples 1414097

description:
1414097
101035780003_R04C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP56BeadChip


title: Blood samples 1414077

description:
1414077
101035780003_R03C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP54BeadChip


title: hsp70-4c-5h-control-4


title: H3K9me2_swo1-26_ts_25


title: hsp70-4c-5h-control-3


title: Blood samples 1414124

description:
1414124
101035780003_R03C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP55BeadChip


title: Mpk1_10-REP_A

tag: duration of 42ºc heat shock


title: H3K9me2_wt_25

value: wt


title: hsp70-4c-5h-control-1


title: hsp70-4c-5h-control-2


title: Mpk1_0-REP_A

tag: deleted gene(s)


title: WT_45-REP_A


title: Blood samples 1414121

description:
1414121
101035780003_R02C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP53BeadChip

tag: g


title: hsp70-4c-5h-3


title: WT_10-REP_A


title: w+hsp70- - control-3


title: Rph1_del_Pol II_rapa_ChipSeq_rep2

city: Wuhan

first: shu

last: Wenjie

address: East Lake South Road

department: College of Life Sciences

institute: Wuhan University

data_processing:
Low quality reads and adaptor contamination were removed by Trimmomatic v0.38
For RNA-Seq, the filtered reads were mapped to SacCer3 using STAR v2.5.3a. For ChIP-Seq, the filtered reads were aligned against SacCer3 genome using Bowtie2 v2.3.4.3  with default parameters.
For RNA-Seq, the mapped reads was quantified using featureCounts v1.6.3. Reads count normalization and differential gene expression analysis was performed using DESeq2 v1.24.0. For ChIP-Seq, MACS2 v2.2.1 with a P value threshold of 1e -5 was used to call ChIP peaks.
Genome_build: SacCer3
Supplementary_files_format_and_content: reads were quantified using featureCounts v1.6.3

source_name: yeast cells

extract_protocol:
After beads beating, chromatin was sonicated. Then cell lysates were centrifuged to pellet debris. Immunoprecipitation was performed overnight with antibody.
The ChIP-seq libraries were prepared using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme). The quality and quantity of constructed libraries were determined using Fragment Analyzer (Advanced Analytical).

value: rph1 deletion

tag: treatment

value: rapamycin treatment

value: Pol II (Santa Cruz, 56767, lot AB_C1017


title: Blood samples 1414060

description:
1414060
101035780003_R02C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP52BeadChip

extract_protocol: Blood samples were collected from the posterior venous plexus of Hu sheep to extract genomic DNA using the standard phenol/chloroform method

value: Famale

tag: father


title: Blood samples 1414055

description:
1414055
101035780003_R01C01
Genomic DNA extracted from blood was genotyped using the Ovine SNP50BeadChip


title: Blood samples 1414120

description:
1414120
101035780003_R01C02
Genomic DNA extracted from blood was genotyped using the Ovine SNP51BeadChip


title: WT_0-REP_A

source_name: Yeast


title: Rph1_del_Pol II_rapa_ChipSeq_rep1

tag: chip antibody


title: Rph1_del_Pol II_rapa_ChipSeq_rep2_Input

tag: genotype


title: hsp70-4c-5h-2

tag: tissue


title: hsp70-4c-5h-1


title: Rph1_del_Pol II_rapa_ChipSeq_rep1_Input


title: Mpk1_45-REP_A


title: F374

city: Kiel

first: Felix

middle: Hans

last: Mittermayer

address: Düsternbrooker Weg 20

department: Evolutionary Ecology of Marine Fishes

institute: GEOMAR Helmholtz Centre for Ocean Research

data_processing:
[Adaptor trim and quality filter] java -Xmx16G -jar trimmomatic-0.36.jar PE -threads 8 -phred33 R1.fastq.gz R2.fastq.gz -baseout sample.fq ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:4:true
[QC] FastQC using MultiQC
[Bedtools getfasta] create fasta transcriptome from genome annotation file
[Kallisto index] kallisto index -i kallisto_index_gadMor2 gadMor2_predicted_transcripts_filtered.fasta
[Kallisto abundance] kallisto quant -i  -o out  R1.fastq.gz R2.fastq.gz
Genome_build: Genome and transcriptome information available at https://figshare.com/articles/Transcript_and_genome_assemblies_of_Atlantic_cod/3408247
Genome_build: Genome build: gadMor2.fasta; Annotations gadMor2_annotation_filtered.gff; Transcriptome gadMor2_transcripts_filtered.fasta
Supplementary_files_format_and_content: .tsv transcript abundance data for each sample

organism: Gadus morhua

source_name: Whole larvae

extract_protocol:
Larvae preserved in RNALater, were extracted using Rneasy kit( Qiagen), applying a modified protocol( please consult publication for details)
Libraries were consctructed according to manufacturers instructions: IlluminaTruSeq Stranded mRNAseq Sample Prep kit

value: Ambient pCO2

tag: age (dph)

tag: tank

value: Whole larvae


title: Brain

city: Calgary

first: Steven

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

data_processing:
Raw FASTQ files were generated using Illumina MiSeq Control software (version 2.02)
Reads were mapped such that the entire length of the read aligned with no less than 80% similarity to the GRCh37 reference genome. Therefore, all non-specific reads and broken pairs were discarded.
Methylation levels were determined for each individual CpG site within each of the DMRs on chromosome 9 and 12 using the methylation caller of the bisulfite sequencing plugin in the CLC genomics workbench (Qiagen).
Genome_build: GRCh37
Supplementary_files_format_and_content: csv

source_name: Brain

extract_protocol:
Consented heart transplant recipients provided 8-10 mL of whole blood, which was extracted from the right jugular vein, the same point of entry for the biopsy, and centrifuged at 1900 x g at room temperature for 10 minutes to fractionate the blood. The entire plasma layer was transferred into 2-3 2.0 mL Eppendorf tubes and centrifuged at maximum speed (13,000 RPM) for 16 minutes at 4oC. The resulting supernatant was then used to isolate cell free DNA using the semi-automated MagNA Pure 24 System (Roche).The extracted cell free DNA was then bisulfite coverted using the Epitect Bisulfite Kit (Qiagen).
Libraries were prepared using the Illumina MiSeq library preparation kit. Libraries were then sequenced using the v3 MiSeq reagent kit v3 (150 cycles) to produce 2x75 bp paired-end reads

tag: disease state

value: Healthy Control


title: F375


title: Colon

source_name: Colon


title: hsp70-4c-24h-1

tag: time point

value: 24 hours (long-term)


title: F372


title: WT_Pol II_rapa_ChipSeq_rep2

tag: strain

value: wild type


title: hsp70-4c-24h-3


title: WT_Pol II_rapa_ChipSeq_rep2_Input


title: Intestine

source_name: Intestine


title: F369

value: High pCO2


title: hsp70-4c-24h-2


title: WT_Pol II_rapa_ChipSeq_rep1


title: F366


title: Esophagus

source_name: Esophagus


title: hsp70-1c-control-3


title: Liver

source_name: Liver


title: Rph1_rapa_ChipSeq_rep2

value: FLAG (Sigma-Aldrich, A2220)


title: F371


title: hsp70-1c-control-1


title: F362


title: F361


title: hsp70-1c-control-4


title: Kidney

source_name: Kidney


title: WT_Pol II_rapa_ChipSeq_rep1_Input


title: hsp70-1c-control-2


title: Rph1_ChipSeq_rep2


title: Lung

source_name: Lung


title: Pancreas

source_name: Pancreas


title: hsp70-1c-5h-1


title: Stomach

source_name: Stomach


title: Rph1_rapa_ChipSeq_rep2_Input


title: Rph1_rapa_ChipSeq_rep1_Input


title: hsp70-1c-24h-3


title: F363


title: F357


title: Skin

source_name: Skin


title: F359


title: hsp70-1c-5h-2

source_name: Drosophila adult head


title: Spinal Chord

source_name: Spinal Chord


title: Rph1_ChipSeq_rep1_Input


title: Rph1_ChipSeq_rep1


title: F358


title: hsp70-1c-24h-1


title: Rph1_ChipSeq_rep2_Input


title: Rph1_rapa_ChipSeq_rep1


title: Skeletal Muscle

source_name: Skeletal Muscle


title: Rph1_del_rapamycin_rep2

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols


title: hsp70-1c-5h-3


title: Patient 1025-9

source_name: Patient 1025 Routine EMB

value: Heart Transplant Recipient


title: F351


title: Rph1_del_rapamycin_rep1

source_name: yeast cells


title: F353


title: pNaKtide-4

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

data_processing:
Reads were trimmed to remove adapters and low-quality base calls using Trimmomatic v0.38
Reads were aligned to the reference genome GRCm38 using HISAT2 v2.1.0
Count tables were generated using GenomicAlignments v1.16.0
Data were analyzed using DESeq2 v1.20.0. Raw and normalized count tables, and FPKM values as computed by DESeq2, were exported as CSV files
Genome_build: GRCm38
Supplementary_files_format_and_content: raw_counts.csv: raw read counts per gene per sample
Supplementary_files_format_and_content: normalized_counts.csv: read counts per gene per sample, normalized by library size by DESeq2
Supplementary_files_format_and_content: fpkm.csv: FPKM values per gene per samples as computed by the DESeq2 function fpkm()

growth_protocol: Frozen mouse pre-adipocytes (3T3-L1) were purchased from ATCC (ATCC, Manassas, VA, USA) and re-suspended in Dulbecco’s Modified Eagle Media (DMEM). 3T3-L1 cells were then supplemented with 10% heat-inactivated fetal bovine serum and 1% antibiotic/antimycotic solution. The cells were plated at a density of 1–5 x 106 cells per 25 cm2 dish. The cultures were maintained at 37οC in a 5% CO2 incubator and the medium was changed after 48 h and every 3–4 days thereafter. When the 3T3-L1 cells were confluent, the cells were recovered by the addition of trypsin. The 3T3-L1 cells (Passage 2–3) were plated in a 6- and 24-well plates at a density of 10,000 cells/cm2 and cultured in DMEM to achieve at least 80% confluency. The medium was replaced with adipogenic medium and the cells were cultured for an additional five days. The adipogenic media consisted of complete culture medium supplemented with DMEM-high glucose, 10% (v/v) FBS, 10 _g/mL insulin, 0.5 mM dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 0.5 mM isobutylmethylxanthine (Sigma-Aldrich, St. Louis, MO, USA) and 0.1 mM indomethacin (Sigma-Aldrich, St. Louis, MO, USA)

extract_protocol:
Total RNA was extracted from adipose tissue using RNeasy Protect Mini Kit (QIAGEN, Maryland)
Libraries were prepared from 1 ug total RNA per sample using the Truseq strand mRNA kit (Illumina , San Diego, CA) according to the manufacturers’ instructions.

treatment_protocol: 3T3-L1 cells were treated with IS (100μM) or oxLDL (50μg/mL) with or without pNaKtide (0.7μM), for five days

tag: cell line

value: 3T3 cells

tag: indoxyl sulphate treatment

tag: oxidative ldl treatment

tag: pnaktide treatment


title: F360


title: Thymus

source_name: Thymus


title: pNaKtide-5


title: hsp70-1c-24h-2

value: adult head


title: WT_rapamycin_rep2


title: Patient 1025-7


title: F349

source_name: Whole larvae


title: pNaKtide-3


title: WT_rapamycin_rep1


title: Patient 1025-6


title: Spleen

source_name: Spleen


title: pNaKtide-2


title: Patient 1025-5


title: F345


title: pNaKtide-1


title: Patient 1025-4


title: Rph1_del_rep2


title: F352


title: F340


title: Patient 1025-1


title: Ox-LDL-pNaKtide-4


title: F336


title: Ox-LDL-pNaKtide-5


title: F315


title: WT_rep1


title: Ox-LDL-pNaKtide-3


title: F314


title: Rph1_del_rep1


title: Patient 1021-7

source_name: Patient 1021 Routine EMB


title: Ox-LDL-pNaKtide-2


title: WT_rep2


title: Patient 1021-6


title: Patient 1021-8


title: Ox-LDL-5


title: Ox-LDL-pNaKtide-1


title: Patient 1021-3


title: TC276T

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

data_processing:
initial QC with fastQC 0.11.5 and multiQC 0.9
alignment using STAR 2.6.0c
post alignment QC with QoRTs 1.3.6
quantification of reads mapping to gene exons with featureCounts in Subread package 1.6.1
normalization in DESeq2 package in R
Genome_build: Oar_rambouillet_v1.0
Supplementary_files_format_and_content: normalized_counts.csv: normalized gene counts in csv file

source_name: theca cells

extract_protocol:
Ovaries cryopreserved in OCT medium were sectioned at 14µm thickness using a Leica CM1950 cryotome on to polyethylene naphthalate (PEN) membrane glass slide (Leica Microsystems, Buffalo Grove, IL). Granulosa and theca cells were microdissected from multiple antral follicles from each animal and pooled in RLT buffer (Qiagen, Valencia, CA, USA) and stored at −80C. RNA extraction was performed using the RNeasy Micro (Qiagen, Germantown, MD) isolation kit.
Ribosomes were depleted and libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit (Takara, Mountain View, CA).

treatment_protocol: Prenatal testosterone treated animals were generated by intramuscular administration of 100mg T propionate (1.2mg / kg; Sigma-Aldrich St. Louis, MO) to pregnant ewes twice weekly from days 30 to 90 of gestation . Control animals were generated by administration of vehicle for the same duration. Ovaries were collected from control and prenatal testosterone treated animals at 21 months-of-age (end of second breeding season). Estrus was synchronized with prostaglandin F2α (10mg, intramuscular; Lutalyse, Pfizer, Florham Park, NJ) administered twice, 11 days apart and ovaries were collected 18 hours post the second injection. RNA extraction was performed using the RNeasy Micro (Qiagen, Germantown, MD) isolation kit.

tag: sheepid

value: prenatal testosterone

tag: cell type

value: theca

tag: sample id


title: F311

tag: treatment


title: TC210T


title: Ox-LDL-4


title: TC315T


title: F309


title: TC230T


title: F308


title: TC209T


title: Ox-LDL-3


title: F303


title: Patient 1017-15

source_name: Patient 1017 Routine EMB


title: TC224C

value: control


title: Patient 1017-13


title: Ox-LDL-2


title: Patient 1017-11


title: TC268C


title: F298


title: Ox-LDL-1


title: Patient 1017-10


title: TC246C


title: Indoxyl-Sulphate-pNaKtide-5


title: F295


title: F294


title: Patient 1021-1


title: F310


title: Patient 1017-9


title: TC244C


title: Indoxyl-Sulphate-pNaKtide-4


title: F293


title: Indoxyl-Sulphate-pNaKtide-3


title: F291


title: Patient 1017-8


title: TC139C


title: Patient 1017-7


title: Indoxyl-Sulphate-pNaKtide-2


title: Patient 1017-6


title: F290


title: F288


title: Patient 1002-15

source_name: Patient 1002 Routine EMB


title: F287


title: Indoxyl-Sulphate-5


title: GC230T

source_name: granulosa cells

value: granulosa


title: Patient 1002-14


title: GC315T


title: GC210T


title: Indoxyl-Sulphate-4


title: F286


title: GC209T


title: F284


title: Patient 1002-13


title: GC224C


title: Patient 1002-12


title: Indoxyl-Sulphate-3


title: F283


title: Patient 1002-11


title: GC276T


title: Indoxyl-Sulphate-pNaKtide-1


title: F282


title: Indoxyl-Sulphate-1


title: T3-rep3 [mRNA]

city: Taian

first: Huicui

last: Wang

state: Shandong

address: No. 61 Daizong Street

department: College of Animal Science and Technology

institute: Shandong Agricultural University

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N (with the ratio of ‘N’ greater than 10%) and low quality reads (Qphred <= 20) from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean sequences were calculated. All the downstream analyses were based on the high quality clean reads with high quality.
The left files (read1 files) from all libraries were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity r20140413p1 with min_kmer_cov set to 2 by default and all other parameters set default as described for de novo transcriptome assembly without a reference genome.
The expression level of each transcript was calculated by the number of clean reads mapped to the assembled transcriptome. Readcount for each gene was obtained from the mapping results. The mapped clean read number was calculated and normalized to FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) with RSEM v1.2.15. DESeq R package (1.10.1) was utilized to perform differential expression analysis of genes between two groups (three biological replicates per group).
Genome_build: The transcriptome assembled from the six transcriptome libraries was used as the reference genome because Litopenaeus vannamei did not have a reference genome till date.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Penaeus vannamei

source_name: hepatopancreas

extract_protocol:
Hepatopancreas were removed, immediately snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq PE Cluster Kit v3-cBot-HS was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: injected with Vibrio parahaemolyticus

value: hepatopancreas

tag: Stage

value: intermolt


title: Control-5


title: GC246C


title: F280


title: Control-4


title: T2-rep2 [mRNA]


title: F279

value: Ambient pCO2


title: GC139C


title: T1-rep1 [mRNA]


title: Control-3


title: Indoxyl-Sulphate-2


title: F278

value: Whole larvae


title: C3-rep3 [mRNA]


title: GC268C


title: F277


title: WT-IP-2

description:
WT 96h after cutting.
processed data file: WT-IP-2_WT-Input-2.pval.signal.bigwig

data_processing:
bigWig
Genome_build: Ptrichocarpa_444_v3.0
Supplementary_files_format_and_content: bigWig

source_name: basal ends of stem cuttings

growth_protocol: 4-week-old in vitro plants cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose and 3 g l-1 Gelrite (Duchefa) (pH 5.8). Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 46 µmol m−2 s−1.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The DNA is combined with End Repair Mix, and incubate at 20℃ for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen)，then add A-Tailing Mix, incubate at 37℃ for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20℃ for 15 min. Purify the Adapter-ligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected (about 100 - 300bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). The final library is quantitated in two ways: Determine the average molecule length and sample integrity as well as purity using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and quantify the library by real-time quantitative PCR (QPCR). The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit. The sequencing will be performed with the BGISEQ-500 sequencing system, featuring combinatorial probe-anchor synthesis (cPAS) and DNA Nanoballs (DNB) technology for superior data quality (BGI-Shenzhen, China).

treatment_protocol: The basal ends of stem cuttings (0.5 cm) of 96 h after being excised from 2-week-old in vitro plantlets.

tag: genotype/variation

value: WT

value: Basal ends of stem cuttings

tag: age

value: Post cutting 96h

tag: chip antibody

value: Anti-H3K9ac (Abcam, ab10812)


title: WT-Input-2

tag: tissue


title: C2-rep2 [mRNA]


title: C1-rep1 [mRNA]


title: Control-1


title: WT-IP-1

description:
WT 96h after cutting.
processed data file: WT-IP-1_WT-Input-1.pval.signal.bigwig


title: F276

value: High pCO2

tag: age (dph)

tag: tank


title: WT_M_hippocampus

city: New York

first: David

last: Goldstein

state: NY

department: Institute for Genomic Medicine

institute: Columbia University Med Center

data_processing:
Reads were aligned using the 10X Cell Ranger pipeline with default parameters to generate the feature-barcode matrix.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *barcodes.tsv: Barcodes
Supplementary_files_format_and_content: *genes.tsv: List of Ensembl genes.
Supplementary_files_format_and_content: *matrix.mtxt: Gene expression matrix (10X Chromium output).

source_name: hippocampus

extract_protocol:
Single cell suspensions were prepared on dissected tissue using a papain/DNase digestion followed by titration and filtration through a 40um cell strainer.
Libraries were constructed using 10X Chromium Single Cell 3′ Reagent Kits v2 according to manufacturer descriptions.

tag: genotype

value: Hnrnpu+/+

tag: Sex

value: Male

tag: developmental stage

value: postnatal day 0

value: hippocampus


title: GC244C


title: WT-Input-1


title: Hox52-IP-2

description:
PuHox52-OE 96h after cutting.
processed data file: Hox52-IP-2_Hox52-Input-2.pval.signal.bigwig


title: HET_F_hippocampus

tag: strain

value: Hnrnpu+/-

value: Female


title: T2-rep2 [miRNA]

data_processing:
Raw data of fastq format were firstly processed through custom perl and python scripts. In this step, clean reads were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, we chose a certain range of lengths from clean reads to do all the subsequent analyses.
The small RNA tags were mapped to the reference sequence by Bowtie (Langmead et al., 2009) without mismatches to analyze their expression and distribution on the reference.
In order to compare miRNA expression between control group and treatment group, miRNA expression levels were normalized by TPM (transcripts per million) values using the following formula for normalized expression: mapped read count/total number of reads × 1000000.
Differential expression analysis of two groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default.
Genome_build: The small RNA tags were mapped to the reference sequence by Bowtie (Langmead et al., 2009) without mismatches to analyze their expression and distribution on the reference.
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample

extract_protocol:
Hepatopancreas were removed, immediately snap frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. The library preparations were sequenced at the Novogene Bioinformatics Institute (Beijing, China) on an Illumina HiSeq 2500 platform and 50 bp single-end reads were generated after the clustering of the index-coded samples, performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: F267


title: T3-rep3 [miRNA]


title: Control-2

tag: cell line

value: 3T3 cells

tag: indoxyl sulphate treatment

tag: oxidative ldl treatment


title: T1-rep1 [miRNA]

value: injected with Vibrio parahaemolyticus


title: Hox52-IP-1

description:
PuHox52-OE 96h after cutting.
processed data file: Hox52-IP-1_Hox52-Input-1.pval.signal.bigwig


title: F265


title: HET_M_hippocampus


title: C3-rep3 [miRNA]

value: control

value: hepatopancreas


title: Hox52-Input-2


title: F274


title: WT_F_cortex

source_name: neocortex

value: neocortex


title: C1-rep1 [miRNA]

value: intermolt


title: WT_M_cortex


title: Hox52-Input-1


title: WT_F_hippocampus


title: HET_M_cortex