title: isochronic culture of Young 2

description: isochronic culture of Young 2

value: isochronic culture of Young 2


title: miRNA-seq_heterochronic culture of Aged 2 & Young 1

status: Public on Dec 01 2021

type: SRA

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

country: USA

institute: Rutgers NJ Medical School

description: heterochronic culture: aged donor 2 + young donor 1

library_source: transcriptomic

data_processing:
Raw reads were trimmed and mapped to Hg38 miRNAome
A match score of 1, mismath cost 2, indel linear gap cost 3/gap
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes raw count values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: mobilized peripheral blood

growth_protocol: The cells were cultured up to one month in RPMI 1640 supplemented with 10% FCS, glutamine and 0.5 µM β-mercaptoethanol. 50% percent of media were replaced every 4 days.

extract_protocol:
Total RNA was isolated from exosomes or cells using the miRCURY RNA Isolation Kit; small and large RNAa were fractionated with the RNeasy MinElute Cleanup Kit, both according to manufacturer’s recommended specifications (Qiagen)
Libraries were prepared using NEBNext Multiplex Small RNA Sample Prep Set for Illumina – Set 1 (NEB), according to the following protocol: (1) ligation of the 3´ SR Adaptor, (2) hybridization of the reverse transcription primer, (3) ligation of the 5´ SR Adaptor, (4) reverse transcription for first strand cDNA synthesis and (5) PCR enrichment

treatment_protocol: Mobilized peripheral blood (MPB) from old donors were cultured with MPB from yound donors or cord blood in a non-contact (transwell) system with 0.4 μm membrane (BD Falcon, ThermoFisher)

tag: cellular component

value: cellular

tag: tissue

value: mobilized peripheral blood

tag: culture type

value: heterochronic culture:aged donor 2 + young donor 1

tag: tissue source

value: aged MPB

tag: phenotype

value: restored


title: F0_5NC_T2

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

description: The group information is prefixed with  F0_5NC_T2 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression

organism: Mus musculus

extract_protocol:
F0 mouse testis were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

tag: strain

value: IRC mouse

value: Testis

tag: genotype/variation


title: F0_5NC_T1

description: The group information is prefixed with  F0_5NC_T1 in the column of processed data file


title: F1_3NC_T1

description: The group information is prefixed with F1_3NC_T1 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
F1 mouse testis were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.


title: isochronic culture of Young 1

description: isochronic culture of Young 1

data_processing:
STAR 2.6.1 aligned to HG38
Quantified to Ensembl human genome 92
Normalized via Log2 Counts per million with offset of 1
Lognormal shrinkage was used to remove batch effect between runs
Counts with a maximum of less than 2 were filtered out for a normal distribution
Genome_build: HG38
Supplementary_files_format_and_content: tab-delimited text files, includes RPKM values for each sample

extract_protocol:
Total RNA extraction was performed according to manufacturer’s protocols with the RNeasy Mini Kit (Qiagen). Poly A RNA was purified using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA).
Libraries were prepared using the NEB Ultra II Library Preparation Kit and NEBNext® Multiplex Oligos for Illumina (Dual Index Primers Set 1) (New England BioLabs) following the manufacturer’s protocol.

treatment_protocol: Mobilized peripheral blood (MPB) from old and yound donors were cultured in non-contact (transwell system) with 0.4 μm membrane (BD Falcon, ThermoFisher). The inner wells contained 10e7 young MPB and the same number of old MPBs in the outer wells.

tag: culture method

value: isochronic culture of Young 1

value: young MPB

value: young


title: zl_02_1_4_1

city: Guangzhou

first: Lei

address: Xinzao Road

institute: Guangzhou Medical University

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: GCF_000001635.26_GRCm38.p6
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

source_name: Adult ICR mice (male, 6 to 8 weeks, 20 to 25 g)

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

value: kidney

value: ICR

tag: gender

value: male

tag: age

value: 6 to 8 weeks

tag: group

value: FxUD


title: F0_3NC_T2

description: The group information is prefixed with  F0_3NC_T2 in the column of processed data file


title: R2: heterochronic culture of Aged 3 & Young 4

value: R2:heterochronic culture of Aged 3 & Young 4


title: F0_3NC_T1

description: The group information is prefixed with F0_3NC_T1 in the column of processed data file


title: R4: heterochronic culture of Aged 3 & Young 2

value: R4:heterochronic culture of Aged 3 & Young 2


title: C18_5251OV_1

description: The group information is prefixed with  C18_5251OV_1 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1
Supplementary_files_format_and_content: gene expression

extract_protocol:
C18-4 cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: lncRNA5251 overexpression


title: zl_02_1_3_1


title: zl_02_1_1_1


title: C18_5251OV_3

description: The group information is prefixed with  C18_5251OV_3 in the column of processed data file


title: R3: heterochronic culture of Aged 3 & Young 1

value: R3:heterochronic culture of Aged 3 & Young 1

value: mobilized peripheral blood


title: isochronic culture of Aged 3

description: isochronic culture of Aged 3

value: isochronic culture of Aged 3

value: aged MPB

value: aged


title: zl_02_M_4_1

value: model


title: R1: heterochronic culture of Aged 3 & Young 2

value: R1:heterochronic culture of Aged 3 & Young 2

value: restored


title: isochronic culture of Aged 2

description: isochronic culture of Aged 2

value: isochronic culture of Aged 2


title: C18_5251KD_3

description: The group information is prefixed with  C18_5251KD_3 in the column of processed data file

value: IRC mouse

value: lncRNA5251 knockdown


title: isochronic culture of Aged 1

description: isochronic culture of Aged 1

value: isochronic culture of Aged 1


title: C18_5251KD_2

description: The group information is prefixed with  C18_5251KD_2 in the column of processed data file


title: V5-Hoxa9-AM and V5-ER-Hoxa9-AM samples pooled input

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

library_source: genomic

data_processing:
Reads aligned to genome using Bowtie 2.0 (for histone modification ChIP-seq) or BWA with default settings (for V5-Hoxa9-AM/V5-ER-Hoxa9-AM ChIPs)
Duplicate reads removed
Peaks called with MACS 2.0, with NarrowPeak setting used for H3K27ac ChIP-seq and BroadPeak setting used for H3K27me3 ChIP-seq
Genome_build: mm9 (H3K27ac and H3K27me3 ChIP-seq) and mm10 (H3K4me3, V5-Hoxa9-AM, and V5-ER-Hoxa9-AM ChIP-seq)
Supplementary_files_format_and_content: Peak coordinate bed files

molecule: genomic DNA

source_name: V5-Hoxa9-AM cells and V5-ER-Hoxa9-AM cells

growth_protocol: Cell culturing in RPMI + 10% FBS + 1%SCF conditioned media + 1% pen/strp (+) or (-) E2

extract_protocol:
Formaldehyde fixation, nuclear isolation, probe sonication, ChIP of 500 ug chromatin (for histone modification ChIPs) or 30 ug chromatin (for V5-Hoxa9-AM/V5-ER-Hoxa9-AM ChIPs) with 4-10 ug antibody, cross-link reverasal, proteinase K treatment, and DNA purification via phenol chloroform extraction.
NEBNext ChIP-seq Library Master Mix Set for Illumina kit with AMPure XP beads for purification.

treatment_protocol: (-) E2 treatment: 3X wash in PBS, change to media (-) E2

tag: treatment

value: Mixture of inputs matching all V5-Hoxa9-AM and V5-ER-Hoxa9-AM ChIPs

value: cells cultured in vitro

tag: antibody


title: zl_02_M_2_1

value: kidney

value: ICR

value: male

value: 6 to 8 weeks


title: C18_5NC_3

description: The group information is prefixed with  C18_5NC_3 in the column of processed data file


title: C18_5251KD_1

description: The group information is prefixed with  C18_5251KD_1 in the column of processed data file


title: zl_02_M_1_1


title: F0_3NC_T3

description: The group information is prefixed with F0_3NC_T3 in the column of processed data file

value: Testis


title: C18_5NC_2

description: The group information is prefixed with  C18_5NC_2 in the column of processed data file


title: zl_02_C_3_1

value: sham


title: V5-ER-Hoxa9-AM (-) E2 96h AM ChIP

source_name: V5-ER-Hoxa9-AM cells

value: (-) E2 for 96 hours


title: C18_5NC_1

description: The group information is prefixed with  C18_5NC_1 in the column of processed data file


title: zl_02_C_2_1


title: V5-ER-Hoxa9-AM (+) E2 (untreated) AM ChIP

value: (+) E2 (untreated)


title: NGP_JSK591_rep2

city: Shanghai

first: Xiao-Ou

last: Zhang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

data_processing:
RNA-seq reads from each sample were aligned using STAR against the GRCh38/hg38 human reference genome.
DESeq2 was used to identify differentially expressed genes using raw read counts quantified by htseq-count with GENCODE V29 gene annotation.
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts quantified by htseq-count with GENCODE V29 gene annotation

source_name: NGP cells treated with JSK591 replicate 2

growth_protocol: CHLA-20 cells were cultured in IMEM medium supplemented with 10% fetal bovine serum (FBS), 100 μg/ml streptomycin, and ITS (5 μg/mL insulin, 5 μg/mL transferrin and 5 ng/ml sodium selenite). NGP cells were grown in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS), 100 μg/ml streptomycin.

extract_protocol:
Total RNA was extracted from live cells using Trizol reagent and purified by Direct-zol RNA Purification Kit. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
The mRNA enrichment, mRNA fragmentation, second-strand cDNA synthesis, size selection, PCR amplification, and sequencing were performed by BGI using DNBseq sequencing technology.

treatment_protocol: CHLA-20 and NGP cells were treated with vehicle or IC50 dose of GSK591 for six days.

tag: cell line

value: NGP


title: V5-ER-Hoxa9-AM (-) E2 96h V5 ChIP


title: C18_3NC_2

description: The group information is prefixed with  C18_3NC_2 in the column of processed data file


title: V5-Hoxa9-AM (untreated) AM ChIP

source_name: V5-Hoxa9-AM cells

value: Untreated


title: NGP_DMSO_rep2

source_name: NGP cells treated with DMSO replicate 2

value: DMSO


title: C18_3NC_1

description: The group information is prefixed with C18_3NC_1 in the column of processed data file


title: V5-ER-Hoxa9-AM (-) E2 72h V5 ChIP

value: (-) E2 for 72 hours then +E2 add-back for 48 hours


title: V5-ER-Hoxa9-AM (+) E2 (untreated) V5 ChIP


title: NGP_DMSO_rep1

source_name: NGP cells treated with DMSO replicate 1


title: V5-Hoxa9-AM (untreated) V5 ChIP


title: CHLA_20_JSK591_rep2

source_name: CHLA-20 cells treated with JSK591 replicate 2


title: CHLA_20_DMSO_rep2

source_name: CHLA-20 cells treated with DMSO replicate 2


title: CHLA_20_DMSO_rep1

source_name: CHLA-20 cells treated with DMSO replicate 1


title: C18_3NC_3

description: The group information is prefixed with C18_3NC_3 in the column of processed data file

value: IRC mouse


title: zl_02_C_1_1


title: Aorta, Bcl11b KO_5

city: Boston

first: Francesa

last: Seta

state: MA

address: 650 Albany St Evans Biomed Research Ctr

institute: Boston University

description: Bcl11b KO

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using featureCounts
Differential analysis was performed on raw counts with DESeq2
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Raw_counts.txt contains pre-normalized count values for each sample generated by featureCounts.

source_name: Aorta

extract_protocol:
Aortas were homogenized in Trizol and kept at -80C until RNA extraction with a commercially available column-based RNA purification kit (ZymoResearch, Irvine, CA, USA), following manufacturer’s instructions. RNA quality (18S/28S ribosomal RNA ratio) was analyzed with a Bioanalyzer (Boston University Microarray Core) and samples with a RIN  7 were deemed of good quality and further processed.
RNA was treated with the NEBNext rRNA depletion kit (E6310X, New England Biolabs) to deplete ribosomal RNA, and converted into double-stranded cDNA using NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (E6111L, New England Biolabs). cDNA was subsequently tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit (FC-131, Illumina). Sequencing libraries were analyzed with Qubit and Agilent Bioanalyzer, pooled at a final concentration of 2.2nM, and sequenced on a NextSeq 500 (Illumina).

tag: genotype

value: Bcl11b KO

value: Aorta


title: NGP_JSK591_rep1

source_name: NGP cells treated with JSK591 replicate 1


title: IP-YB1

city: Montreal

first: Brenda

middle: Janice

last: Sanchez

state: QC

address: 3655 promenade Sir-William-Osler, Room 915

department: Bichemistry

country: Canada

institute: McGill University

data_processing:
RNA quantity and quality was assessed using a NanoDrop UV spectrophotometer (Thermo Fisher Scientific Inc), and a Bioanalyser (Agilent Technology Inc).
The 3 RNA-seq libraries were sequenced on the Illumina NextSeq 500 platform. The reads were trimmed for sequencing adapters.
Trimmed reads were aligned to the reference mouse genome version mm10 (GRCm38) using Tophat version 2.0.10.
Gene quantification was performed on the mapped sequences using the htseq-count software version 0.6.1
Differential expression was analyzed using DESeq2 package, log transformation was used to normalize raw read counts and to calculate normalized expression counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Excel files include Log2FoldChange, Log10pvalue, IfcMLE, IfcSE and padj values for each group (IP-IG/IP-YB1/IP-HuR)

source_name: C2C12 cells

growth_protocol: C2C12 cells (ATCC, Manassas, VA, USA) were grown and maintained in Dulbecco's modified eagle medium (DMEM, Invitrogen) containing 20% fetal bovine serum (Invitrogen), and 1% penicillin/streptomycin antibiotics, following the manufacturer's instructions (Invitrogen). Differentiation was induced when the cells reached 100% confluency on plates previously coated with 0.1% gelatin (Day 0). To induce differentiation, growth media was replaced with differentiation media containing DMEM, 2% horse serum, and 1% penicillin/streptomycin antibiotics.

extract_protocol:
RNA was isolated from IP experiments performed on C2C12 total cell extract collected at day 2 of differentiation, using TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fifteen µl of anti-YB1, anti-HuR or IgG antibodies were incubated with 60µl of protein A-Sepharose slurry beads (washed and equilibrated in cell lysis buffer) for 4h at 4°C. Beads were washed three times with cell lysis buffer and incubated with 500µg of cell extracts overnight at 4°C. Beads were then washed again three times with cell lysis buffer and co-immunoprecipitated RNA was then eluted and processed for analysis.

tag: antibodies


title: IP-HuR

value: anti-HuR


title: IP-IgG

value: IgG


title: siLOXL1-3

city: Beijing

first: Wei

last: Chen

state: Beijing

address: No. 95 Yong’an road, Xicheng District

department: Beijing Friendship Hospital

institute: Capital Medical University

data_processing:
The RNA-Seq reads were aligned to human reference genome (hg19) using Tophat (version 2.0.10) with default parameters
Read counts were scaled to fragments per kilobase of exon model per million reads mapped (FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: LX-2 cells

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA). One μg RNA was used to generate cDNA library. We performed RNA-seq by BGISEQ-500.

tag: cell type

value: hepatic stellate cells


title: Aorta, Bcl11b KO_3

description: Bcl11b KO


title: Aorta, Bcl11b KO_4

description: Bcl11b KO


title: siLOXL1-1


title: WT shoot drought_rep2

type: RNA

city: Yokohama-Shi, Tsurumi Ku

first: Khurram

last: Bashir

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: Center for Sustainable Resource Science

country: Japan

institute: RIKEN

hyb_protocol: 600 ng of cRNAs  were hybridized to the microarray (GPL19830) at 65 degree for 17 hours, using Gene Expression Hybridization kit. After hybridization, the microarray was washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer  (Agilent), and then dried immediately by brief centrifugation.

scan_protocol: The microarray was scanned by Agilent DNA Microarray Scanner G2505B and  raw data was extracted using Feature Extraction program ver 9.1.

data_processing: RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R 2.12.1 program.

organism: Arabidopsis thaliana

source_name: Drought shoot of WT

label_protocol: Fluorescent-labeled (Cy3) cRNAs were prepared from 400 ng total RNA from each sample using a Quick Amp labeling kit (Agilent Technologies)

growth_protocol: Seeds of Arabidopsis thaliana (Col-0 ecotype) were grown on MS medium at 22°C under 16-h-light/8-h-dark for 9 days. Plantlets were then transferred to ceramics granular soil (size 2.5L, Sakatanotane, Japan) and grown for 8 days at 22°C.

extract_protocol: RNA was extracted from at least three biological replicates with the mirVana miRNA Isolation Kit (Ambion, USA) according to the manufacturer’s instructions

treatment_protocol: The drought treatment was commenced by removing excess water from the trays and ceasing any subsequent watering. Roots and shoots were harvested separately under control as well as at  5 days after the onset of drought treatment.

value: shoot

tag: protocol

value: drought stress 5 day


title: CHLA_20_JSK591_rep1

source_name: CHLA-20 cells treated with JSK591 replicate 1


title: Aorta, Bcl11b KO_2

description: Bcl11b KO

tag: tissue


title: WT shoot drought_rep1


title: siLOX-3

value: siLOX


title: WT shoot drought_rep3


title: WT root drought_rep1

source_name: Drought root of WT

value: root


title: WT root drought_rep3


title: Aorta, Bcl11b KO_1

description: Bcl11b KO


title: siLOX-2


title: Aorta, Bcl11b WT_5

description: Bcl11b WT

value: Bcl11b WT


title: siLOX-1


title: siLOXL1-2


title: CON-3

value: control

value: TGFβ1+negative control


title: WT shoot control_rep2

source_name: Control shoot of WT

value: unstress condition


title: Aorta, Bcl11b WT_4

description: Bcl11b WT


title: CON-2

value: TGFβ1+negative control siRNA


title: Aorta, Bcl11b WT_3

description: Bcl11b WT


title: Aorta, Bcl11b WT_2

description: Bcl11b WT


title: WT root drought_rep2


title: CON-1


title: WT root control_rep3

source_name: Control root of WT


title: WT shoot control_rep1


title: HFD_AC261066_6

city: New York

first: Xiaohan

last: Tang

address: 1300 York Ave.

institute: Weill Cornell Medicine

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the mouse mm9 reference genome using Tophat2 v2.0.11.
Raw reads counts were extracted using htseq-count v0.6.1.
Differential expression analysis was performed by using DESeq2 package v1.6.3.
Genome_build: mm9
Supplementary_files_format_and_content: excel file including gene name, refseq gene id, normalized read counts (log scale) for each gene in each sample

source_name: Liver

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Qiagen's RNEasy kit
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: chow, high fat diet (HFD), and HFD + AC261066

value: Liver tissue

value: High Fat Diet (HFD) + AC261066


title: Aorta, Bcl11b WT_1

description: Bcl11b WT


title: WT shoot control_rep3


title: WT root control_rep2


title: HFD_AC261066_5


title: TReX_BCBL1_No_IgG_2

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Illimuna next-generation sequencing (2x150bp, paired-end)

data_processing:
Library strategy: CUT&RUN
Base calling and quality scoring were performed with Real-Time Analysis (RTA2) software.
CUT&RUN reads were aligned to the GRCh38 (hg38) human reference genome and KSHV reference genome (Human herpesvirus 8 strain: GQ994935.1) with Bowtie2.
MACS2 was used for detecting peaks following the developer’s manual. The default settings with a minimum FDR (q-value) cut-off of 0.05 were used.
Genome_build: GRCh38/hg38 + KSHV genome (Accession: GQ994935.1)
Supplementary_files_format_and_content: Processed data are in bigWig format.

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: human primary effusion lymphoma

growth_protocol: BCBL-1, (TREx)BCBL-1, and BC-1 cell lines were cultured in RPMI 1640 medium supplemented with 15% FBS. The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v). Mycoplasma contamination was routinely tested by using a PCR-based assay.

extract_protocol:
Cells were washed with PBS and wash buffer (20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine (Sigma, S2626) and proteinase inhibitor (Roche). After removing wash buffer, cells were captured on magnetic ConA beads (Polysciences), in presence of CaCl2. Beads/cells complexes were washed with digitonin wash buffer (0.02% digitonin, 20 mM HEPES-KOH pH 7.5, 150 mM NaCl, 0.5 mM spermidine and 1x proteinase inhibitor) three times, and incubated with specific antibodies in 250 mL volume. After incubation, unbound antibody was washed by digitonin wash buffer 3 times. Beads were then incubated with the recombinant pAG-MNase, in 250 μl digitonin wash buffer (1.0 mg/mL final concentration) for an hour at 4°C with rotation. Unbound pAG-MNase was removed by washing with digitonin wash buffer 3 times. Pre-chilled 2 mM CaCl2 containing digitonin wash buffer (200 mL) was added to beads and incubate on ice for 30 min. The pAG-MNase digestion was halted by the addition of 200 μl 2× STOP solution (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 μg/ml RNase A, 50 mg/ml Glycogens). The beads were incubated/shaked at 37°C for 10 min in tube shaker at 500 rpm to release digested DNA fragments from the insoluble nuclear chromatin. The supernatant was collected after centrifuge (16,000 x g for 5 min at 4°C) and place on magnetic stand. DNA was extracted using the NucleoSpin & PCR kit (Takara Bio, Kusatsu, Shiga, Japan).
Sequencing libraries were prepared from 3 ng of CUT&RUN DNA with the Kapa HyperPrep Kit (Roche) according to the manufacturer’s standard protocol. Libraries were multiplex sequenced (2 x 150bp, paired-end) on an Illumina HiSeq 4000 sequencing system.

value: Stable doxycycline-inducible K-Rta expression and infected with wild-type KSHV BAC16

tag: cut&run antibody


title: NIC3OX shoot drought_rep3

source_name: Drought shoot of NIC3OX

value: drought stress 10 day


title: WT root control_rep1


title: NIC3OX shoot drought_rep2

value: drought stress 9 day


title: HFD_AC261066_4


title: NIC3OX shoot drought_rep1

value: drought stress 8 day


title: HFD_AC261066_3


title: NIC3OX root drought_rep3

source_name: Drought root of NIC3OX

value: drought stress 7 day


title: Veh_2b

city: Vilnius

first: Rapolas

last: Zilionis

state: LT

address: Sauletekis av 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description: Murine KP1.9 lung adenocarcinoma tumor cells were injected into C57BL/6 female mice intravenously (2.5x10^5 cells in 100µl PBS) to develop orthotopic tumors in the lung. The tumor cell line was derived from lung tumor nodules of a C57BL/6 KrasLSL-G12D/WT;p53Flox/Flox (KP) mouse and was kindly provided by Dr. Zippelius (University Hospital Basel, Switzerland).

data_processing:
Basecalling to obtain fastq files.  Software: bcl2fastq v2.17.1.14  Software call: bcl2fastq --use-bases-mask y*,y*,y*,y* --mask-short-adapter-reads 0 --minimum-trimmed-read-length 0
Gene expression counts in single cells were obtained from raw fastq files using the indrop.py pipeline as downloaded  from https://github.com/indrops/indrops on 2019 09 01. Parameters are listed in supplementary yaml files:  h_1_Sep2019.yaml  h_2_Sep2019.yaml  CSF1Ri_Sep2019.yaml
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files in each library consist of:  - a mtx file with raw unfiltered gene counts (cells x genes)  - a tsv file with gene names  - a tsv file with barcode names, as the indrop.py pipeline outputs them

molecule: polyA RNA

source_name: lung tumor

growth_protocol: Murine KP1.9 lung tumor cells were injected into female mice intravenously (2.5x10^5 cells in 100µl phosphate buffered saline (PBS)) to develop orthotopic tumors in the lung. All animals were housed under specific pathogen free conditions at the Massachusetts General Hospital (MGH). Animal experiments were approved by the MGH Institutional Animal Care and Use Committee (IACUC) and were performed in accordance with MGH IACUC regulations.

extract_protocol:
Mice were perfused with PBS (37C) and lung tumor tissues macroscopically dissected using surgical fine scissors. Small equally sized tissue pieces were digested (RPMI media containing 0.2 mg/mL collagenase type I) for 15 min at 37C while shaking (700 rpm). Digested lung tissue was gently meshed through 70µm cell strainers using a plunger and single cell suspensions stained with a fluorescent conjugated Ab specific to CD45 (clone 30-F11, Biolegend) for 45 min at 4C. The cells were washed with flow cytometry staining buffer (PBS containing 0.5% BSA and 2 mM EDTA) and CD45+ live cells sorted on a FACS Aria cell sorter (BD Biosciences) into FBS containing reaction tubes which were kept on ice until the cells were further processed for single cell RNA sequencing (scRNA-seq). 7AAD was used to exclude dead cells during sorting.
InDrops single cell RNA sequencing was performed as described before [Zilionis et al., 2019, Immunity, 50, 1317-1334.e10; Zilionis et al., 2017, Nat Protoc, 12, 44-73; Klein et al., 2015, Cell, 161, 1187-1201] with changes to DNA primers listed in Table S1 of the publication associated with this GEO record. Single cell transcriptome barcoding was performed by co-encapsulating cells, barcoding reverse transcription (RT) primers attached to polyacrylamide beads, and RT and lysis reagents into 2-3 nl droplets, followed by primer release and RT at 50C. The resulting barcoded cDNA was taken through the following sequencing library preparation steps: i) second strand synthesis; ii) linear amplification by in vitro transcription; iii) fragmentation; iv) RT using random hexamer primers bearing a universal PCR primer annealing site; and v) indexing PCR. The NextSeq Illumina platform was used for sequencing. Read lengths are summarized in Table S1 of the publication associated with this GEO record. All reads, including those for the tumor-free condition which were published previously [Zilionis et al., 2019, Immunity, 50, 1317-1334.e10], were processed with the indrops.py pipeline using the same parameters available at https://github.com/rapolaszilionis/Pfirschke_et_al_2020.

treatment_protocol: Daily vehicle treatment of lung tumor-bearing mice started 4 weeks after tumor cell injection when tumor nodules were macroscopically detectable in the lung and mice were typically euthanized after two weeks (14 drug injections).

value: KP1.9 lung adenocarcinoma tumor cells

value: F

value: vehicle control solution

tag: purification

value: RBC-depletion; CD45+ cells


title: TReX_BCBL1_No_IgG_1


title: Veh_2a


title: Veh_1c


title: TReX_BCBL1_No_SMARCA5_1

value: mouse anti-SMARCA5


title: TReX_BCBL1_No_SMARCA5_2


title: NIC3OX root drought_rep2

value: root

value: drought stress 6 day


title: HFD_AC261066_2


title: NIC3OX root drought_rep1

value: drought stress 5 day


title: HFD_AC261066_1


title: IgG_BC1_2

value: KSHV-positive human B cell lymphoma cells

value: non-specific IgG


title: Veh_1b


title: IgG_BC1_1


title: F1_5251KD_T3

description: The group information is prefixed with  F1_5251KD_T3 in the column of processed data file

value: IRC mouse

value: Testis

value: lncRNA5251 knockdown


title: Veh_1a


title: HFD_6

value: Liver tissue

value: High Fat Diet (HFD)


title: Csf1ri_2c

treatment_protocol: Daily BLZ945 treatment of lung tumor-bearing mice started 4 weeks after tumor cell injection when tumor nodules were macroscopically detectable in the lung and mice were typically euthanized after two weeks (14 drug injections).


title: HFD_5


title: SWI_SNF_BC1_2

value: mouse anti-SMARCC1


title: NIC3OX shoot control_rep3

source_name: Control shoot of NIC3OX

value: shoot

value: unstress condition


title: SWI_SNF_BC1_1


title: HFD_4


title: IgG_BcBL-1_2


title: HFD_3


title: HFD_2


title: Csf1ri_1c

value: KP1.9 lung adenocarcinoma tumor cells

value: F


title: NIC3OX shoot control_rep2


title: Csf1ri_2a

value: RBC-depletion; CD45+ cells


title: IgG_BcBL-1_1


title: wt_input_for_H3K9me2_rep2

city: Norwich

first: Jaemyung

last: Choi

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
Illumina Hiseq basecalls were performed using 'bcl2fq' at the John Innes Centre.
For bisulfite-seq, reads were mapped with bowtie and bs-sequel pipeline (https://zilbermanlab.net/tools/) allowing up to 2 mismatches.
For sRNA-seq libraries, adapter sequences were removed from reads using cutadapt (Martin, 2011). 18-28 bp, 21nt, and 24 nt fragments were isolated using following cutadapt options: -m 18 -M 28, -m 21 -M 21, -m 24 -M 24. Reads were mapped with Bowtie (Langmead et al., 2009) allowing up to 1 mismatch and up to 10 multi-mapped reads. Aligned 21 nt or 24 nt read count were normalized by reads per kilobase per million mapped reads (RPKM) of 18-28 bp fragments.
Native ChIP-seq libraries were mapped with Bowtie (Langmead et al., 2009) allowing up to 2 mismatches and up to 10 multi-mapped reads. To calculate enrichment, ChIP samples were divided by input samples and transformed into log 2 ratio values using deepTools2 bamCompare.
Genome_build: TAIR10
Supplementary_files_format_and_content: For sRNA-seq, gff files contain rpkm normalized read count of 50bp windows.

source_name: leaf

growth_protocol: cmt2 and cmt2 cmt3 (Stroud et al., 2014; Zemach et al., 2013) plants were crossed to h1.1 h1.2 (Zemach et al., 2013) plants to generate h1cmt2 and h1cmt2cmt3 plants. To establish h1cmt2shh1 mutant line, we crossed h1+/-cmt2 heterozygous plants with shh1  (SALK_074540C) plants first, then isolated h1cmt2shh1 homozygous siblings. met1, h1met1, ddm1, h1ddm1 plants were described previously (Choi et al., 2020; Lyons and Zilberman, 2017). Arabidopsis thaliana seedlings were germinated and grown for 4-5 weeks on soil at 20-25℃ in growth chamber (16 hr day/ 8 hr night) for all the experiments performed here.

extract_protocol: MNase digestion of native chromatin was carried out on 0.5g of 4 week old Arabidopsis rosette leaves as described by us previously (Lyons and Zilberman 2017).  Digestion was stopped with  EGTA and chromatin rotated at 4'C for 30 minutes.  The preparation was then centrifuged for 10 minutes at 2000 RPM and solubilized chromatin fragments were isolated by aspirating supernatant immediately.  Chromatin was then diluted to 1ml in wash buffer A (50mM Tris-HCl pH 7.5, 50mM NaCl, 10mM EDTA) and antibody added (Millipore 07-450 for H3K9me1, abcam ab1220 for H3K9me2) to 1ul per 0.1 g of total starting material. Dilute Tween-20 was added to a final concentration of 0.1%, and the mixture was rotated overnight at 4C.  All buffers were supplemented with PMSF and protease inhibitor (Roche).  A standard immunoprecipitation procedure was used the following day.  Briefly, pre-blocked Protein-A and -G dynabeads (Invitrogen) were incubated in the chromatin preparation for 3 hrs. rotating at 4'C, and beads were then washed on ice in Tris-EDTA buffer with increasing concentrations of NaCl, starting at 50mM and ending at 150mM.   DNA was eluted from beads by shaking in 1% SDS and 1% NaHCO3 for 10 minutes at 55'C, and DNA was purified from contaminants with phenol-chloroform extraction. Input and ChIP DNA was converted into sequencing libraries using Celero DNA reagents (Tecan) following manufacturer's instructions.

value: 4-5 week old plants

value: leaf

value: input


title: NIC3OX shoot control_rep1


title: NIC3OX root control_rep3

source_name: Control root of NIC3OX

value: root


title: BCBL1_Pol2

value: KSHV-positive human B cell lymphoma cells

value: mouse anti-RNA polymerase II (Millipore, clone CTD4H8; 1:100)


title: Csf1ri_1b


title: NIC3OX root control_rep2


title: HFD_1


title: Csf1ri_1a


title: chow_6

value: Chow


title: K4me1_BcBL-1_2

value: rabbit monoclonal anti-H3K4me1 (Cell Signaling, D1A9; 1:50)


title: wt_input_for_H3K9me1_rep1


title: chow_5


title: K4me1_BcBL-1_1


title: LV1

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
left ventricle cardiomyocyte nuclei left ventricle
nuclear RNA PCM-1+ nuclei

data_processing:
Library strategy: Cut & Run
The BEDTools suite was used to distribute the genome wide signal into bins of 500 bp. The background read level was determined per sample per 500 bp by taking the average read count in bins with less than 20 tags. The background level of tags was subtracted per bin per sample.
Reads were mapped to mm10 build of the mouse transcriptome using STAR (Dobin et al. 2013).
To allow for differential peak calling between datasets, quantile normalization was applied using the deepTools2 suite (Ramirez et al., 2016).
Differential acetylation was assessed using the DESeq2 package based on a model using the negative binomial distribution (Love et al., 2014). P-values were corrected for multiple testing using the false discovery rate (FDR) method of Benjamini-Hochberg. We have used 0.05 as FDR control level. Continuous bins with differential signal were subsequently merged together using the BEDTools suite
Genome_build: mm10
Supplementary_files_format_and_content: BZ_CUTRUN_BZ_vs_LV_DESEQ2_diff_acetyl_MGU.xlsx

source_name: cardiac tissue left ventricle myocardial infarction

growth_protocol: The border zone or left ventricle was isolated from 8 week old mice, with and without myocardial infarction

extract_protocol:
cardiac nuclei were isolated, stained with PCM1 and sorted by FACS, CUT&RUN-sequencing was performed according to Hainer et al 2019
NEBNext Ultra 2 ( E7645S, E7335S)

treatment_protocol: tissue was snap frozen and stored at -80 degree celcius

value: FVB

value: 8 weeks

value: wildtype


title: NIC3OX root control_rep1


title: wt_H3K9me2_rep2

value: abcam ab1220 (H3K9me2)


title: Healthy_2_2

source_name: lung

growth_protocol: Healthy C57BL/6 mice were grown for ~14 weeks before being euphanized. All animals were housed under specific pathogen free conditions at the Massachusetts General Hospital (MGH). Animal experiments were approved by the MGH Institutional Animal Care and Use Committee (IACUC) and were performed in accordance with MGH IACUC regulations.

value: M

value: untreated


title: Healthy_2_3


title: chow_4

value: Liver tissue


title: 27AC_BcBL-1_2

value: rabbit monoclonal anti-H3K27Ac (Cell Signaling, D5E4; 1:50)


title: Healthy_2_1

value: RBC-depletion; CD45+ cells


title: Csf1ri_2b

value: KP1.9 lung adenocarcinoma tumor cells

value: F


title: chow_3


title: wt_H3K9me2_rep1

value: 4-5 week old plants

value: leaf


title: wt_H3K9me1_rep1

value: Millipore 07-450 (H3K9me1)


title: h1ddm1_input_for_H3K9me2_rep2

value: input


title: wt_input_for_H3K9me2_rep1


title: chow_2

value: Chow


title: 27AC_BcBL-1_1

value: KSHV-positive human B cell lymphoma cells


title: Healthy_1_2


title: Healthy_1_1


title: chow_1


title: h1ddm1_input_for_H3K9me1/2_rep1


title: WT-3T

first: Guan

last: Guiwen

address: 38 Xueyuan Road, Haidian District

institute: Peking University

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer.
Sequenced reads were mapped to GRCm38 and Smart-seq2 and SMARTer sequencing data were aligned with TopHat2
Htseq2  was used to caculate gene expression level, and TPM was used to express expression level.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with TPM for every gene for this sample.

source_name: C57BL/6 mice

extract_protocol:
300-1000 HBs-specific CD8+ T cells sorted from mice liver was completed by using Clontech-SMART-SeqTM v4 UltraTM Low Input RNA Kit on Illumina Hiseq4000 platform
After the samples pass the test, use the Ribo-zero kit to remove rRNA. Subsequently, high temperature and metal ions are used to achieve RNA fragmentation. Using Ribosomal-depleted RNA as a template, use six-base random primers (random hexamers) to synthesize one-strand cDNA, then add buffer, dNTPs (dUTP, dATP, dGTP and dCTP) and enzymes to synthesize two-strand cDNA, and then use VAHTSTM DNA Clean Beads purify double-stranded cDNA. The purified double-stranded cDNA is first repaired, A-tailed and connected to a sequencing adapter. VAHTSTM DNA Clean Beads are used for fragment size sorting. Then, UDG enzyme is used to degrade the cDNA chain containing U, and finally PCR enrichment is performed, and the PCR product is purified with VAHTSTM DNA Clean Beads to obtain the final chain-specific cDNA library. After the library is constructed, Qubit 3.0 is used to initially determine the concentration, and then the Agilent 2100 Bioanalyzer is used to detect the inserted fragments in the library. After this item meets expectations, the ABI Step One Plus Real-Time PCR system is used to accurately quantify the effective concentration of the library.
Smart-Seq2

value: 4 weeks-old

tag: strain/genotype

value: C57BL/6 WT

value: HBs-specific CD8+ T cells  sorted from liver

value: post 7 day HBsAg stimulation


title: h1ddm1_H3K9me2_rep2

value: h1 ddm1

value: abcam ab1220 (H3K9me2)


title: ICC8261 Genotype sample 1

city: Melbourne

first: Nitin

last: Mantri

state: Victoria

address: 264 Plenty Rd, Bundoora VIC 3083

department: Biosciences and Food Technology

country: Australia

institute: RMIT University

description: ICC8261S1 S4-4_S111

data_processing:
Trimgalore was used for quality trimming  and quality check of the raw sequences
The filtered 150 base pair paired-end reads from each sample were mapped to chickpea genome Cicer arietinum (assembly ASM33114v1) (Varshney, Song et al., 2013) using CLC Workbench 11.0.1 (Qiagen). We used Map Bisulphite Reads to Reference tool using Bisulphite Sequencing plugin 2.1. Which mapped the two versions of bisulphite converted reference sequence (C->T and G->A) to each read and produced mapping reports. The reads that aligned at a particular unique location in the reference genome were retained. A directional bisulphite sequencing protocol was used, which yields reads from both strands of sample DNA. Mapping parameters were set based on desired output.
To obtain the DNA methylation levels and differential DNA methylation context in test and control samples for both genotypes call methylation levels tool was utilized. The read mappings created by Map bisulphite reads to reference tool for both genotypes were used as input for this tool. The base level parameters were set for methylation calling by selecting ignore no specific matched, ignore duplicate matches and ignore broken pairs to get obtain more specific results. To compare the methylation levels in test and control samples Fisher exact test was implied and p value <= 0.01 were considered as differentially methylated. This provided the methylation levels in CpG, CHG and CHH (Where H= A/C/T) context. In our case we looked for methylation calls in restricted target region where a genome digested with MspI enzyme was used for analysis to restrict methylation output to particular regions. The RRBS fragment can be created by RRBS-fragment Track tool described below. The hypermethyled regions in test sample were obtained by analysing sample mapping to control. Whereas, to obtaining hypomethylated regions in test this process was reversed as control was ran against test sample for both geneotypes.
Genome_build: ASM33114v1

organism: Cicer arietinum

source_name: Cicer arietinum L. Chickpea Leaf tissue

growth_protocol: The drought sensitive (ICC283) and drought tolerant (ICC8261) genotypes were used in bisulphite sequencing under drought stress. Chickpea leaf tissues from the shoot apical meristem developmental stage for both ICC8261 and ICC283 genotypes were analysed. The field capacity of soils for control samples was 80% and 20% for drought. Plants for experiments  were grown in 20 cm polypropylene pots containing 4 kg of soil under controlled environmental conditions with air temperature regulated between 23˚C and 28˚C (night/day).

extract_protocol:
The genomic DNA for respective samples was isolated from frozen leaf tissues using Qiagen DNeasy Minikit (Qiagen). The quality check and quantification of the genomic DNA samples was performed by Nanodrop Spectrophotometer (Thermo Scientific) and Qubit Fluorimeter (Life Technologies). Agarose gel electrophoresis was also conducted to determine the quality of respective genomic DNA samples.
The genomic DNA isolated from chickpea leaf tissue at shoot apical meristem stage was further processed for bisulphite sequencing. To perform bisulphite sequencing Ovation® RRBS Methyl-Seq Library System was used for restriction digestion using MspI enzyme according to manusfature’s protocol described briefly below. This approach utilizes the methylation insensi¬tive restriction enzyme MspI, which recognizes CCGG. As a result of partial fragmentation during bisulfite conversion, PCR, and efficiency of cluster generation, only a subset of these fragments, typically under 300 bp in length, are sequenced Ovation® RRBS Methyl-Seq Library System requires 100 ng of DNA for RRBS. The respective genomic DNA samples for both genotypes were fragmented via sonication technique to a smaller size base pairs of approximately 100-300 bp, which were further end repaired and in the end TruSeq-methylated adapters were ligated to the DNA fragments. For bisulphite conversion of unmethylated C’s EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA) used, using approximately 500 ng of adapter-ligated DNA fragments were used according to manufacturer’s protocol. The library quality was analysed after desalting, size selection, and PCR amplification was performed. The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample and processed sequence data (after removal of reads containing adaptor sequences and low-quality reads).  The quality control of the pair end reads was performed by CLC genomics workbench 11.0.1(Qiagen) NGS core tools to remove Illumina adaptors and low quality reads.
RRBS Reduced representation bisulphite sequencing was utilized for this study.The qualified bisulphite converted libraries were sequenced on the HiSeq 3000 system (Illumina Inc) for 150 cycles in the paired-end mode to achieve more than 30X genome coverage for each sample

treatment_protocol: The experiment design was a 3 X 2 X 2 completely randomised block design with leaf tissue from one-time point (Shoot apical meristem), two genotypes (ICC8261 and ICC283), and two treatment conditions (Control/Test). For each genotype, 6 pots were used and randomly designated to one of two treatments as: Well-watered (WW) control and drought-stressed (DS). The drought stress conditions and plant growth conditions were same as mentioned in previous study (Badhan, Kole et al., 2018).

value: Shoot apical meristem stage

value: Drought stressed (DS)

tag: developmental stage


title: ICC8261 Genotype sample 3

description: ICC8261S3 S4-5_S113


title: 20180911_17-ucar-001-run32_FASTQ_NZO-3mo-M-spleen-252_GT18-10914_CAGAGAGG-TCTACTCT_S4

city: Farmington

first: Duygu

last: Ucar

state: Connecticut

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Paired-end ATAC-seq reads were quality trimmed using Trimmomatic.
trimmed reads were aligned to mouse genome (mm10) using BWA
After preprocessing and quality filtering, peaks were called on alignments with MACS2 using the BAMPE option.
For differential accessibility analyses the samples of the same tissue were merged to generate one consensus peak set by using R package DiffBind.
Peaks only present in at least two samples were included in the analysis. Raw read counts were normalized using the cpm function via the log option turned on from edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: Atacseq consensus peaks per tissue/cell type, Normalized Count Files

extract_protocol:
Data is obtained from spleen and peripheral blood lymphocytes (PBLs) of C57BL/6J and NZO/HILtJ mouse strains, hereafter B6 and NZO, respectively, at ages 3, 12, and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq
ATAC-seq libraries were prepared using 50,000 cells, as previously described (Buenrostro et al, 2015), with the following modifications: digitonin was added to the transposition reaction at a final concentration of 0.01%; the transposition reaction was purified using the Genomic DNA Clean & Concentrator-10 kit (Zymo Research Corporation); PCR amplification was carried out using the Nextera DNA Library Prep (Illumina) Index Adapters, Nextera PCR Master Mix, and PCR Primer Cocktail for 10 cycles of PCR; PCR reaction was purified using 1.7x SPRI beads (Agencourt AMPure XP, Beckman Coulter). Libraries were checked for quality and concentration using the DNA High-Sensitivity LabChip assay (Agilent Technologies) and quantitative  PCR (KAPA Biosystems), according to the manufacturer's instructions. Libraries were pooled and sequenced 75 bp paired-end on the NextSeq 500 (Illumina) using NextSeq High Output Kit v2 reagents (Illumina).

tag: strain

value: NZO

tag: Sex

value: Male

value: spleen


title: 20180911_17-ucar-001-run32_FASTQ_NZO-3mo-M-memory-253_GT18-10927_AAGAGGCA-TACTCCTT_S6

value: memory


title: ICC8261 Genotype sample 2

description: ICC8261S2 S4-2_S112


title: ICC8261 Genotype control 3

description: ICC8261C3 S1-1_S107

value: well watered (WW)


title: 20180911_17-ucar-001-run32_FASTQ_NZO-3mo-F-spleen-243_GT18-10910_GCTACGCT-AGAGGATA_S1

value: Female


title: HA10-1

description: The group information is prefixed with  HA10_1 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPHM (Reads Per Hilo bases per Million reads), and then differently expressed genes were identified by the DEGseq pacHage using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: mm10

extract_protocol:
heart tissues were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: IRC mouse

value: Cells


title: WT-1T


title: WT-2T


title: h1ddm1_H3K9me1_rep1

value: 4-5 week old plants

value: leaf

value: Millipore 07-450 (H3K9me1)


title: ICC8261 Genotype control 1

description: ICC8261C1 S1-4_S105


title: h1c2c3_input_for_H3K9me1/2

value: h1 cmt2 cmt3

value: input


title: 20180911_17-ucar-001-run32_FASTQ_NZO-3mo-F-naive-244_GT18-10929_CAGAGAGG-AGGCTTAG_S2

value: naive


title: EXP-2T

source_name: C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice

value: 4 weeks-old

value: HBs-specific CD8+ T cells  sorted from liver

value: post 7 day HBsAg stimulation


title: h1c2c3_H3K9me2_rep2

value: abcam ab1220 (H3K9me2)


title: ICC283 Genotype sample 2

description: ICC283S2 S4-5_S115

value: Shoot apical meristem stage

value: Drought stressed (DS)


title: 20180911_17-ucar-001-run32_FASTQ_NZO-3mo-F-naive-243_GT18-10928_GTAGAGGA-TACTCCTT_S7

value: NZO


title: h1c2c3_H3K9me2_rep1


title: EXP-1T

value: C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic


title: 20180911_17-ucar-001-run32_FASTQ_B6-12mo-M-spleen-218_GT17-14904_GGACTCCT-TATGCAGT_S3

value: Male

value: spleen


title: EXP-3T


title: iHiC_mESC

city: Göttingen

first: Argyris

last: Papantonis

address: Robert-Koch-Straße 40

department: Institut für Pathologie

country: Germany

institute: Universitätsmedizin Göttingen

data_processing:
Raw reads were mapped, annotated, and corrected for biases using the Juicer suite 1.5 with default parameters with the exception of "-r 0" (comprehensive alignment was performed) and "-t 32" (parallelization was performed using 8 processes running in 4 CPUs).
Compartment analysis was performed using the signal of the first principal component of the Pearson's Hi-C contact matrices.
TAD boundaries were identified using rGMAP v.1.4 on contact maps with a resolution of 10 kbp and the following parameters: logt = TRUE, dom_order = 2, maxDistInBin = 80, min_d = 25, max_d = 100, min_dp = 5, max_dp = 10, hthr = 0.99, t1thr = 0.75.
Chromatin contacts (loops) were called using the proposed method Bloom and multiple loop callers (see main manuscript).
Genome_build: NCBI37 (mm9) and GRCh37 (hg19)
Supplementary_files_format_and_content: Juicer suite's .hic contact matrices

source_name: mouse ES cells (mESC)

growth_protocol: mESC were cultured in Knockout-DMEM medium containing 15% FBS and LIF on gelatin-coated plates. hiPSC-CMs were thawed in iCell Cardiomyocyte Plating Medium and plated on a ﬁbronectin-coated plates while after 2nd day they were maintained in iCell Cardiomyocyte Maintenance Medium

extract_protocol:
Standard DNA isolation
Hi-C performed for mESC according to the iHi-C published protocol DOI:10.15252/msb.20167311 and for hiPSC-CM according to the modified iHi-C 2.0 protocol DOI: 10.1016/j.ymeth.2019.07.003

value: E14 mESCs

value: wt

tag: library id


title: h1_input_for_H3K9me2_rep2

tag: age

value: 4-5 week old plants

value: leaf


title: 20180911_17-ucar-001-run31_FASTQ_NZO-3mo-M-PBL-253_GT18-10909_CAGAGAGG-AGAGGATA_S3

value: PBL


title: h1c2c3_H3K9me1_rep1

value: h1 cmt2 cmt3

value: Millipore 07-450 (H3K9me1)


title: NZO-3mo-M-spleen-253_GT18-10968_GTGAAA_S9_L002_R1_001

data_processing:
Libraries were pooled and sequenced 75 bp single-end on the HiSeq 4000 (Illumina) using HiSeq 3000/4000 SBS Kit reagents (Illumina), targeting 40 million reads per sample.
Single-end RNA-seq reads were aligned to the mouse genome (mm10) with Bowtie 2 and counts were generated with RSEM.
To normalize the raw counts count-per-million (cpm) function from edgeR package is used and the genes that are log(cpm)<1 and expressed less than 2 samples were excluded from rest of the analyses.
For differential analysis pipeline, however, raw counts are used with the default options of edgeR package, and via TMM normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Count Files for B6/NZO

extract_protocol:
Data is obtained from spleen and peripheral blood lymphocytes (PBLs) of C57BL/6J and NZO/HILtJ mouse strains, hereafter B6 and NZO, respectively, at ages 3, 12, and 18 months.   Cells were stained with:   CD8 FITC, Clone 53-6.7 BD Bioscience Cat# 553031, used at 1:240 final concentration  CD3e PE, Clone 145-2C11 eBioscience (Now ThermoFisher) cat# 12-0031-85, used at 1:240 final concentration  CD62L PE-Cy7, Clone MEL-14 Tonbo Biosciences Cat# 60-0621-U100, used at 1:480 final concentration  CD44 APC-Cy7, Clone IM7 Tonbo Biosciences Cat# 25-0441-U100, used at 1:240 final concentration  and for 30 minutes at 4 degrees C. Propidium Iodide used for cell viability at 0.5ug/ml.   Then cells were sorted on a FACSAria II (BD Biosciences). Briefly, doublets were gated out, Viable PI- cells were gated, CD3e+, CD8+ cells were gated and subdivided into CD44 Low, CD62L High Naïve cells and CD44 High, CD62L+/- Memory cells. Up to 50,000 cells were sorted for ATAC-seq, remaining cells collected for other RNA preparations.
30 ng of total RNA, with the addition of 6 µl ERCC Spike-In Control Mix 1 (Ambion Thermo Fisher) diluted 1:10,000, was used for library construction. Libraries were prepared by the Genome Technologies core facility at The Jackson Laboratory using the KAPA mRNA HyperPrep Kit (KAPA Biosystems), according to the manufacturer’s instructions. Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  Libraries were checked for quality and concentration using the D5000 assay on the TapeStation (Agilent Technologies) and quantitative PCR (KAPA Biosystems), according to the manufacturer's instructions.

value: male


title: ICC283 Genotype sample 1

description: ICC283S1 S4-1_S109


title: ICC283 Genotype control 3

description: ICC283C3 S4-6_S114

value: well watered (WW)


title: ICC283 Genotype control 2

description: ICC283C2 S4-3_S110


title: ICC8261 Genotype control 2

description: ICC8261C2 S1-3_S106


title: h1ddm1_H3K9me2_rep1

value: h1 ddm1


title: h1_input_for_H3K9me2_rep1

value: input


title: NZO-3mo-M-spleen-251_GT18-10966_CCGTCC_S11_L002_R1_001


title: NZO-3mo-M-spleen-252_GT18-10967_GTCCGC_S13_L002_R1_001


title: h1_input_for_H3K9me1_rep1


title: 20180911_17-ucar-001-run32_FASTQ_NZO-3mo-F-PBL-245_GT18-10906_CGAGGCTG-ATAGAGAG_S5

value: Female


title: NZO-3mo-M-spleen-236_GT18-04604_ATTCCT_S28


title: h1_H3K9me2_rep2

value: abcam ab1220 (H3K9me2)


title: 20180911_17-ucar-001-run31_FASTQ_NZO-3mo-M-memory-252_GT18-10926_CGAGGCTG-TACTCCTT_S5

value: NZO

value: memory


title: 20180911_17-ucar-001-run31_FASTQ_NZO-3mo-F-naive-245_GT18-10930_GCTACGCT-AGGCTTAG_S7

value: naive


title: 20180911_17-ucar-001-run31_FASTQ_NZO-3mo-F-memory-244_GT18-10923_GTAGAGGA-CTCCTTAC_S2


title: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-M-spleen-251_GT18-10913_GTAGAGGA-AGAGGATA_S2

value: Male

value: spleen


title: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-M-naive-252_GT18-10932_AAGAGGCA-AGGCTTAG_S1


title: ICC283 Genotype sample 3

description: ICC283S3 S4-2_S116

value: Shoot apical meristem stage

value: Drought stressed (DS)


title: NZO-3mo-M-spleen-235_GT18-04603_ACTGAT_S20


title: C18_5251OV_2

first: Yong

address: 700 Changcheng Road

institute: Qingdao Agricultural University

description: The group information is prefixed with  C18_5251OV_2 in the column of processed data file

data_processing:
The reads were mapped to reference gene using SOAPaligner (Version 2.20) with a maximum of two nucleotide mismatch allowed at the parameters of “-m 0 -x 1000 -s 40 -l 35 -v 3 -r 2”. The read number of each gene was transformed into RPKM (Reads Per Kilo bases per Million reads), and then differently expressed genes were identified by the DEGseq package using the MARS (MA-plot-based method with Random Sampling model) method. The threshold was set as FDR≤ 0.001 and an absolute value of log2Ratio≥1 to judge the significance of gene expression difference.
Genome_build: ARS1
Supplementary_files_format_and_content: gene expression

extract_protocol:
C18-4 cells were isolated for RNA. Then RNA samples were sequenced.
Total RNA was used for the library.

value: IRC mouse

tag: genotype/variation

value: lncRNA5251 overexpression


title: h1_H3K9me2_rep1

value: 4-5 week old plants

value: leaf


title: h1_H3K9me1_rep1

value: Millipore 07-450 (H3K9me1)


title: NZO-3mo-M-spleen-234_GT18-04602_GAGTGG_S29

value: male


title: 8 days wounded rat bladder 4

first: Clara Ibel

last: Chamorro Jimenez

address: Center for Molecular Medicine (CMM) Karolinska University Hospital L8:02 Sweden

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institute

hyb_protocol: Hybridization  was performed in in GeneTitan Instrument using standard Affymetrix protocol (GeneTitan Instrument user guide for Expression Array Plates  P/N 702933).

scan_protocol: Scanning was performed in a GeneTitan scanner using standard Affymetrix protocol.

data_processing: CEL files were processed in Transcriptome Analysis Console (TAC, v4.0) using the RMA method and including only rat probes.

label: Biotin

organism: Rattus norvegicus

source_name: urinary bladder

label_protocol: Two hundred micrograms of total RNA from bladder samples (collected after 6 hours, 2 days and 8 days post wounding) were biotin-labelled  and polyA taillinged for the Affymetrix GeneChip microRNA array 4.1 using the FlashTag biotin-HSR RNA labeling kit (Thermo Fisher Scientific).

growth_protocol: Animals were aclimatized to the core facility for 1 week previously to the experiments.

extract_protocol: After oh, 6h, 2 days anf  8 days, the anymals are terminated and the urinary bladder is divided into two. One halv of the bladder is placer in RNA later ( Qiagen) . Bladder tissue biopsies were then  homogenized using a Tissue Lyser, (Qiagen, Hilden, Germany)  before RNA extraction. Total RNA was extracted using the Qiazol Lysis Reagent® (Thermo Fisher Scientific, Waltham, MA), following the manufacturer’s instructions. The quantity of RNA was determined using the NanoDrop® ND-1000 Spectrophotometer (NanoDrop Technologies inc, Wilmington, DE). RNA integrity (RIN) was determined using an Agilent 2100 Bioanalyser (RNA 6000 Nano LabChip kit, Agilent Technologies).

treatment_protocol: The animals were anesthetized by inhalation anesthesia with isoflurane. After disinfection of the skin, a 2 cm incision is made in the lower midline with a scalpel down to the free abdominal cavity. By lifting the rectus sheath, the back can be prepared free of abdominal contents with blunt dissection. Then the bladder can be removed from the incisions and a longitudinal incision is made on the bladder from the bladder neck up to the bladder fence, about 1.5 cm long. Then the incision is closed with continuous 7-0 nylon suture.  The tightness of the bladder should be checked by filling the bladder with sterile saline solution which is injected through the wall of the bladder with a 30-gauge injection needle. If a leak is found, this is repaired with suture.  Local anesthesia is applied in the rectus sheath and in the subcutaneous tissue before closing the abdominal wall. The rectus muscle is closed with a continuously resorbable 4-0 suture, then a similar suture is used to close the skin. Anesthesia is terminated and the animal is allowed to wake up in a warm cage.

value: Sprague Dawley

tag: gender

tag: treatment

value: 8 days wounded


title: 8 days wounded rat bladder 3


title: NZO-3mo-M-PBL-253_GT18-10962_CTTGTA_S7_L001_R1_001

value: PBL


title: NZO-3mo-M-PBL-252_GT18-10961_CAGATC_S1_L001_R1_001


title: NZO-3mo-M-PBL-251_GT18-10960_GCCAAT_S4_L001_R1_001


title: ICC283 Genotype control 1

description: ICC283C1 S1-6_S108

value: well watered (WW)


title: 20180911_17-ucar-001-run29_FASTQ_NZO-3mo-M-PBL-252_GT18-10908_GTAGAGGA-ATAGAGAG_S6

value: NZO


title: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-F-memory-243_GT18-10922_AAGAGGCA-CTCCTTAC_S7

value: Female

value: memory


title: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-F-memory-245_GT18-10924_CAGAGAGG-TACTCCTT_S5


title: 8 days wounded rat bladder 1

value: Male


title: 8 days wounded rat bladder 2


title: 2 days wounded rat bladder 3

value: 2 days wounded


title: ddm1_H3K9me2_rep2

tag: antibody

value: abcam ab1220 (H3K9me2)


title: ddm1_input_for_H3K9me1/2_rep1

tag: genotype

value: input


title: ddm1_H3K9me2_rep1


title: 20180911_17-ucar-001-run29_FASTQ_NZO-3mo-M-naive-251_GT18-10931_CGAGGCTG-AGGCTTAG_S2

value: naive


title: 20180911_17-ucar-001-run29_FASTQ_NZO-3mo-M-PBL-251_GT18-10907_AAGAGGCA-ATAGAGAG_S1


title: ddm1_H3K9me1_rep1


title: 2 days wounded rat bladder 1


title: 2 days wounded rat bladder 2


title: NZO-3mo-M-PBL-234_GT18-04596_CCGTCC_S26


title: NZO-3mo-M-PBL-235_GT18-04597_GTCCGC_S18


title: NZO-3mo-M-PBL-236_GT18-04598_GTGAAA_S27


title: 20180904_17-ucar-001-run28_FASTQ_NZO-3mo-M-naive-253_GT18-10933_GTAGAGGA-AGGCTTAG_S7


title: 20180911_17-ucar-001-run30_FASTQ_NZO-3mo-M-memory-251_GT18-10925_GCTACGCT-TACTCCTT_S3


title: NZO-3mo-M-naive-253_GT18-10986_CTTGTA_S29_L004_R1_001


title: 20180904_17-ucar-001-run28_FASTQ_NZO-3mo-F-spleen-245_GT18-10912_AAGAGGCA-AGAGGATA_S4

value: spleen


title: ddm1_input_for_H3K9me2_rep2

value: 4-5 week old plants


title: NZO-3mo-M-naive-252_GT18-10985_CAGATC_S28_L004_R1_001


title: 20180904_17-ucar-001-run28_FASTQ_NZO-3mo-F-spleen-244_GT18-10911_CGAGGCTG-AGAGGATA_S5


title: c2c3_input_for_H3K9me1_rep1

value: leaf

value: cmt2 cmt3


title: 20180904_17-ucar-001-run28_FASTQ_NZO-3mo-F-PBL-244_GT18-10905_GCTACGCT-ATAGAGAG_S1


title: c2c3_H3K9me2_rep2


title: c2c3_H3K9me2_rep1


title: 20180904_17-ucar-001-run28_FASTQ_NZO-3mo-F-PBL-243_GT18-10904_CAGAGAGG-ATAGAGAG_S6


title: 6 hours wounded rat bladder 3

value: 6 hours wounded


title: NZO-3mo-M-memory-252_GT18-10979_GTCCGC_S19_L003_R1_001

value: male


title: Control not wounded rat bladder 4

value: Sprague Dawley

value: control


title: 6 hours wounded rat bladder 2


title: 6 hours wounded rat bladder 1


title: c2c3_H3K9me1_rep1

value: Millipore 07-450 (H3K9me1)


title: NZO-3mo-M-memory-251_GT18-10978_CCGTCC_S23_L003_R1_001

value: NZO


title: Control not wounded rat bladder 3


title: NZO-3mo-F-spleen-245_GT18-10965_ATGTCA_S15_L002_R1_001

value: female


title: 20180524_17-ucar-001-run25_FASTQ_B6-3mo-F-spleen-5_GT18-04664_CGTACTAG-AGAGGATA_S5

value: Female


title: c2c3_input_for_H3K9me2_rep2


title: 6 hours wounded rat bladder 4

value: Male


title: c2c3_input_for_H3K9me2_rep1


title: wt_srna_rep2

description: small RNA

extract_protocol: We extracted total RNA from rosette leaves of 4-5-week-old plants using Trizol (Invitrogen, cat. No. 15596026) according to manufacturer’s manual. To remove DNA from samples, 5 ug of RNA was treated with DNA-free DNA removal kit (Thermo, AM1907). 1 ug of DNA-free total RNA was subjected to sRNA library construction according to manufacturer’s protocol (Illumina, RS-200-0012 and RS-200-0024).


title: 20180524_17-ucar-001-run25_FASTQ_B6-3mo-F-memory-4_GT18-04668_TAAGGCGA-TCTACTCT_S4

value: memory


title: 20180524_17-ucar-001-run24_FASTQ_B6-3mo-M-memory-2_GT18-04671_TCCTGAGC-TCTACTCT_S4


title: NZO-3mo-F-spleen-244_GT18-10964_AGTTCC_S5_L001_R1_001


title: NZO-3mo-F-spleen-243_GT18-10963_AGTCAA_S8_L001_R1_001


title: 20180524_17-ucar-001-run24_FASTQ_B6-3mo-F-spleen-4_GT18-04663_TAAGGCGA-AGAGGATA_S2


title: NZO-3mo-M-naive-251_GT18-10984_GCCAAT_S27_L004_R1_001


title: NZO-3mo-M-memory-253_GT18-10980_GTGAAA_S30_L004_R1_001


title: h1ddm1_srna_rep3

description: small RNA

value: h1 ddm1


title: wt_srna_rep1

description: small RNA


title: 20180524_17-ucar-001-run24_FASTQ_B6-3mo-F-naive-5_GT18-04674_CGTACTAG-CTCCTTAC_S1


title: h1ddm1_srna_rep2

description: small RNA


title: 20180524_17-ucar-001-run25_FASTQ_B6-3mo-M-PBL-1_GT18-04660_AGGCAGAA-ATAGAGAG_S3

value: PBL


title: 20180524_17-ucar-001-run23_FASTQ_B6-3mo-M-naive-2_GT18-04676_TCCTGAGC-CTCCTTAC_S5

value: naive


title: NZO-3mo-F-spleen-231_GT18-04599_GTGGCC_S24

value: spleen


title: h1cmt2cmt3_srna_rep3

description: small RNA

value: 4-5 week old plants

value: h1 cmt2 cmt3


title: wt_srna_rep3

description: small RNA

value: leaf


title: 2 days wounded rat bladder 4

value: 2 days wounded


title: 20180524_17-ucar-001-run23_FASTQ_B6-3mo-M-naive-1_GT18-04675_AGGCAGAA-CTCCTTAC_S2


title: Control not wounded rat bladder 2


title: h1cmt2cmt3_srna_rep2

description: small RNA


title: NZO-3mo-F-PBL-245_GT18-10959_ACAGTG_S2_L001_R1_001


title: 20180524_17-ucar-001-run22_FASTQ_B6-3mo-M-PBL-3_GT18-04662_TAGGCATG-ATAGAGAG_S4


title: Control not wounded rat bladder 1


title: NZO-3mo-F-PBL-244_GT18-10958_TGACCA_S6_L001_R1_001


title: NZO-3mo-F-spleen-232_GT18-04600_GTTTCG_S22


title: 20180524_17-ucar-001-run22_FASTQ_B6-3mo-M-PBL-2_GT18-04661_TCCTGAGC-ATAGAGAG_S3


title: NZO-3mo-F-spleen-233_GT18-04601_CGTACG_S32


title: NZO-3mo-F-PBL-243_GT18-10957_CGATGT_S3_L001_R1_001


title: 20180524_17-ucar-001-run22_FASTQ_B6-3mo-M-memory-1_GT18-04670_AGGCAGAA-TCTACTCT_S1


title: HL_young_10

city: Gainesville

first: Stephan

last: Jahn

state: FL

institute: University of Florida

hyb_protocol: The labeled sample was hybridized to miRNA array at 48°C and 60 rpm for 16 to 18 hours on an Affymetrix Fluidics Station 450.

scan_protocol: Samples were scanned on a Genechip® 7G Scanner.

data_processing: RMA

label: biotin

source_name: liver

label_protocol: miRNA labeling was performed using FlashTag Biotin HSR Labeling for miRNA kit from Affymetrix. Basically, 500ng of total RNA was used for poly A tailing, then followed by FlashTag Biotin HSR ligation.

extract_protocol: Total RNA was isolated from each sample using the miRNeasy kit from Qiagen.

value: 28 days

value: M

tag: race

value: White


title: HL_young_7

value: 31 days

value: F


title: NZO-3mo-F-PBL-233_GT18-04595_ATGTCA_S21

value: NZO

value: female


title: HL_young_9

value: 11 days


title: h1_srna_rep3

description: small RNA


title: h1_srna_rep2

description: small RNA


title: h1ddm1_srna_rep1

description: small RNA


title: NZO-3mo-F-PBL-232_GT18-04594_AGTTCC_S30


title: 20180524_17-ucar-001-run22_FASTQ_B6-3mo-F-memory-5_GT18-04669_CGTACTAG-TCTACTCT_S2

value: Female

value: memory


title: h1_srna_rep1

description: small RNA


title: 20180524_17-ucar-001-run21_FASTQ_B6-3mo-M-spleen-2_GT18-04666_TCCTGAGC-AGAGGATA_S3

value: Male


title: HL_young_6

value: 39 days

value: Black


title: ddm1_srna_rep3

description: small RNA

value: 4-5 week old plants


title: HL_young_5

value: 70 days

value: unknown


title: NZO-3mo-F-PBL-231_GT18-04593_AGTCAA_S19

value: PBL


title: HL_young_3


title: HL_young_4

value: 303 days


title: 20180524_17-ucar-001-run21_FASTQ_B6-3mo-M-spleen-1_GT18-04665_AGGCAGAA-AGAGGATA_S6

value: spleen


title: NZO-3mo-F-naive-245_GT18-10983_ACAGTG_S25_L004_R1_001

value: naive


title: HL_young_8

value: 1 day

value: M

value: Hispanic


title: h1cmt2cmt3_srna_rep1

description: small RNA

value: leaf

value: h1 cmt2 cmt3


title: HL_young_2

value: 120 days

value: White


title: 20180524_17-ucar-001-run21_FASTQ_B6-3mo-M-memory-3_GT18-04672_TAGGCATG-TCTACTCT_S2

value: Male

value: memory


title: NZO-3mo-F-naive-244_GT18-10982_TGACCA_S24_L004_R1_001

value: NZO

value: female


title: HL_adult_10

value: 32 years

value: F


title: 20180524_17-ucar-001-run21_FASTQ_B6-3mo-F-PBL-5_GT18-04659_CGTACTAG-ATAGAGAG_S1

value: Female

value: PBL


title: ddm1_srna_rep1

description: small RNA

value: 4-5 week old plants


title: ddm1_srna_rep2

description: small RNA


title: NZO-3mo-F-naive-243_GT18-10981_CGATGT_S26_L004_R1_001

value: naive


title: cmt2cmt3_srna_rep3

description: small RNA

value: cmt2 cmt3


title: HL_adult_9

value: 43 years


title: 20180524_17-ucar-001-run21_FASTQ_B6-3mo-F-PBL-4_GT18-04658_TAAGGCGA-ATAGAGAG_S4


title: 20180406_17-ucar-001-run15_FASTQ_NZO-18mo-M-spleen-40_GT18-03791_CAGAGAGG-TCTACTCT_S2

value: spleen


title: cmt2cmt3_srna_rep1

description: small RNA

value: leaf


title: cmt2cmt3_srna_rep2

description: small RNA


title: NZO-3mo-F-memory-244_GT18-10976_AGTTCC_S18_L003_R1_001


title: NZO-3mo-F-memory-245_GT18-10977_ATGTCA_S21_L003_R1_001


title: NZO-3mo-F-memory-243_GT18-10975_AGTCAA_S17_L003_R1_001


title: h1cmt2shh1_bisulfite_rep2

extract_protocol: gDNA for bisulfite sequencing was extracted with Dneasy plant mini kit according to manufacturer's protocol. 500 ng total gDNA was sheared to 100-1000bp DNA using Bioruptor Pico (Diagenode), then purified with 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was ligated to NEBNext Adaptor for Illumina using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, ca. No. E7645). We performed bisulfite conversion twice with ligated libraries (QIAGEN, cat. No. 59104) to prevent imperfect conversion (<99% conversion) of unmethylated cytosines. Converted libraries were subjected to SPRI beads purification with 0.8X volume of beads. We amplified bisulfite-converted libraries with NEB next indexing primers (New England Biolabs Inc. cat. No. E7335S).

value: h1 cmt2 shh1


title: 20180406_17-ucar-001-run15_FASTQ_NZO-18mo-M-spleen-39_GT18-03790_CTCTCTAC-TCTACTCT_S6


title: 20180406_17-ucar-001-run15_FASTQ_NZO-18mo-M-memory-39_GT18-03796_CAGAGAGG-CTCCTTAC_S5


title: HL_adult_8

value: 48 years


title: NZO-18mo-M-spleen-40_GT18-03826_GTGAAA_S1

value: male


title: h1cmt2shh1_bisulfite_rep1


title: 20180406_17-ucar-001-run14_FASTQ_NZO-18mo-M-naive-40_GT18-03803_CGAGGCTG-TACTCCTT_S5

value: Male


title: h1cmt2cmt3_bisulfite

value: h1 cmt2 cmt3


title: 20180406_17-ucar-001-run14_FASTQ_NZO-18mo-M-memory-38_GT18-03795_CTCTCTAC-CTCCTTAC_S1

value: NZO

value: memory


title: HL_adult_5

value: 76 years

value: M

value: White


title: HL_adult_6

value: 54 years

value: F


title: NZO-18mo-M-spleen-38_GT18-03824_CCGTCC_S41


title: h1cmt2_bisulfite_rep1

value: 4-5 week old plants

value: h1 cmt2


title: NZO-18mo-M-spleen-39_GT18-03825_GTCCGC_S9


title: 20180406_17-ucar-001-run14_FASTQ_NZO-18mo-F-PBL-42_GT18-03782_GCTACGCT-ATAGAGAG_S6

value: Female

value: PBL


title: NZO-18mo-F-spleen-36_GT18-03822_AGTTCC_S43

value: female

value: spleen


title: HL_adult_7

value: 53 years


title: cmt2cmt3_bisulfite

value: leaf

value: cmt2 cmt3


title: HL_adult_4

value: 77 years


title: 20180406_17-ucar-001-run13_FASTQ_NZO-18mo-M-PBL-39_GT18-03784_AAGAGGCA-ATAGAGAG_S3

value: NZO

value: Male


title: HL_adult_3

value: 78 years


title: eDRG_8HPI_Rep3

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

institute: Washington University in St. Louis

hyb_protocol: 500 ng of RNA was hybridized for 16 hours at 60 rpm at 48°C on Affymetrix GeneChip miRNA 4.0 Array.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner G3000 7G

data_processing: The data were analyzed with Affymetrix Expression Console (v1.4) using default analysis settings. The signal values were background-corrected with Robust Multi-Array Averaging (RMA) method, quanitle-normalized, and median-polish summarized.

source_name: Spot cultures were axotomized with a blade on DIV 7 then collected 8 hours post injury

label_protocol: Probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from samples using the miRNeasy Micro Kit as per the manufacturers protocol. RNA was quantified using a Synergy H1 Hybrid Reader and quality was analyzed using an Agilent Bioanalyzer 2100.

value: Embryonic day 13

value: Dorsal Root Ganglia


title: HL_young_1

value: 266 days

value: M

value: Black


title: HL_adult_2

value: 86 years

value: White


title: NZO-18mo-F-spleen-42_GT18-03823_ATGTCA_S46


title: 20180406_17-ucar-001-run13_FASTQ_NZO-18mo-M-PBL-38_GT18-03783_CGAGGCTG-ATAGAGAG_S4

value: PBL


title: eDRG_8HPI_Rep2

treatment_protocol: Spot cultures were axotomized with a blade on DIV 7 then collected 8 hours post injury


title: A-N Ang II+NaBu 28 day 3

city: Chongqing

first: Yaowen

last: Wang

state: Chongqing

address: No. 74 Linjiang Road, Yuzhong District

department: Cardiology

institute: the Second Affiliated Hospital of Chongqing Medical University, Chongqing Cardiac Arrhythmias Therapeutic Service Center

description: Transcript Expression Sample A-N.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rnor6
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Rat left ventricle

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with TruSeq RNA sample Preparation kit V2 in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyzer
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley rats

value: heart

value: 8 weeks + 28 day

value: Ang II+NaBu


title: NZO-18mo-F-PBL-42_GT18-03817_GATCAG_S45

value: female


title: NZO-18mo-M-PBL-39_GT18-03819_GGCTAC_S33

value: male


title: 20180406_17-ucar-001-run13_FASTQ_NZO-18mo-M-naive-39_GT18-03802_GCTACGCT-TACTCCTT_S5

value: NZO

value: naive


title: A-N Ang II+NaBu 28 day 1

description: Transcript Expression Sample A-N.txt


title: 20180406_17-ucar-001-run13_FASTQ_NZO-18mo-M-spleen-38_GT18-03789_AAGAGGCA-AGAGGATA_S1

value: Male

value: spleen


title: h1cmt2_bisulfite_rep2

value: 4-5 week old plants

value: leaf

value: h1 cmt2


title: NZO-18mo-M-PBL-40_GT18-03820_CTTGTA_S44


title: A-N Ang II+NaBu 28 day 2

description: Transcript Expression Sample A-N.txt


title: 20180406_17-ucar-001-run13_FASTQ_NZO-18mo-F-naive-42_GT18-03800_CTCTCTAC-TACTCCTT_S6

value: Female


title: NZO-18mo-F-spleen-35_GT18-03821_AGTCAA_S32


title: eDRG_8HPI_Rep1

value: Embryonic day 13

value: Dorsal Root Ganglia


title: eDRG_3HPI_Rep2

source_name: Spot cultures were axotomized with a blade on DIV 7 then collected 3 hours post injury


title: eDRG_3HPI_Rep1

treatment_protocol: Spot cultures were axotomized with a blade on DIV 7 then collected 3 hours post injury


title: NZO-18mo-M-PBL-38_GT18-03818_TAGCTT_S35

value: PBL


title: HL_adult_1

value: 77 years

value: M

value: White


title: cmt2_bisulfite


title: A Ang II 28 day 3

description: Transcript Expression Sample A.txt

value: Sprague-Dawley rats

value: heart

value: 8 weeks + 28 day

value: Ang II


title: eDRG_1HPI_Rep3

source_name: Spot cultures were axotomized with a blade on DIV 7 then collected 1 hour post injury


title: A Ang II 28 day 2

description: Transcript Expression Sample A.txt


title: NZO-18mo-F-PBL-35_GT18-03815_CAGATC_S34

value: NZO

value: female


title: NZO-18mo-F-PBL-36_GT18-03816_ACTTGA_S36


title: eDRG_1HPI_Rep2

treatment_protocol: Spot cultures were axotomized with a blade on DIV 7 then collected 1 hour post injury


title: 20180406_17-ucar-001-run12_FASTQ_NZO-18mo-F-spleen-35_GT18-03786_CAGAGAGG-AGAGGATA_S5

value: spleen


title: 20180406_17-ucar-001-run12_FASTQ_NZO-18mo-M-memory-40_GT18-03797_GCTACGCT-CTCCTTAC_S2

value: Male

value: memory


title: 20180406_17-ucar-001-run13_FASTQ_NZO-18mo-M-naive-38_GT18-03801_CAGAGAGG-TACTCCTT_S2

value: naive


title: NZO-18mo-F-naive-42_GT18-03835_TTAGGC_S13


title: eDRG_Control_Rep3

source_name: Spot cultures were collected at DIV7

treatment_protocol: Spot cultures were collected at DIV7


title: eDRG_1HPI_Rep1


title: 20180406_17-ucar-001-run12_FASTQ_NZO-18mo-F-naive-36_GT18-03799_AAGAGGCA-CTCCTTAC_S6

value: Female


title: C saline 28 day  3

description: Transcript Expression Sample C.txt

value: saline


title: A Ang II 28 day 1

description: Transcript Expression Sample A.txt


title: eDRG_Control_Rep2

value: Embryonic day 13

value: Dorsal Root Ganglia


title: 9-108: Colon tumor from patient 108

type: genomic

city: Barcelona

first: Sara

last: Lahoz

address: Carrer del Rosselló, 149

country: Spain

institute: Institut D'Investigacions Sanitàries August Pi i Sunyer

description: Hybridized to Affymetrix Oncoscan SNP array for profiling copy-number alterations in tumor samples

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
raw SNP-array fluorescence intensity data (CEL files) were processed using SNP-FASST2 segmentation algorithm from Nexus  Copy  Number  software  version  9.0 (BioDiscovery,  El  Segundo,  CA,  USA) , achieving an estimate of the mean log2-ratio and B-allele frequency (BAF) values for each genome region. Major and minor allele numbers of each segment were inferred utilizing ASCAT R package version 2.5. For a chromosome region to be considered as carrying a CN gain or loss, log2-ratio cut-offs  were  set  on  0.18  and -0.18,  respectively;  and  to  be  considered  to  have  a  loss  of heterozygosity (LOH), BAF threshold was set on 0.3. Chromosomal regions showing a non-altered log2-ratio and BAF <0.3 were classified as copy-number neutral LOH (CNN-LOH).
Probe set values in OSCHP files include intensity values (column ‘Log2Ratio’) and frequency of the alternative allele (BAF) for each array-probe.

source_name: FFPE tumor

label_protocol: Affymetrix OncoScan FFPE Assay kit for staining with Biotin.

extract_protocol: DNA was extracted from each formalin-fixed paraffin-embedded (FFPE) tumor samples using the QIAmp DNA FFPE kit (Qiagen, Hilden, Germany) and then quantified using Qubit fluorometer assay (Thermo Fisher Scientific, MA, USA)

treatment_protocol: All patients were first-line treated with surgery, and none of them received adjuvant chemotherapy.

tag: disease state

value: Colon cancer

value: FFPE tumor


title: 20180406_17-ucar-001-run12_FASTQ_NZO-18mo-M-PBL-40_GT18-03785_CTCTCTAC-AGAGGATA_S1

value: PBL


title: C saline 28 day  2

description: Transcript Expression Sample C.txt

value: Sprague-Dawley rats


title: 8-107: Colon tumor from patient 107


title: NZO-18mo-M-naive-40_GT18-03838_GCCAAT_S4

value: male


title: eDRG_Control_Rep1


title: 20180406_17-ucar-001-run12_FASTQ_NZO-18mo-F-memory-35_GT18-03792_GCTACGCT-TCTACTCT_S3


title: C saline 28 day  1

description: Transcript Expression Sample C.txt

value: heart

value: 8 weeks + 28 day


title: 20180406_17-ucar-001-run12_FASTQ_NZO-18mo-F-naive-35_GT18-03798_CGAGGCTG-CTCCTTAC_S4

value: NZO


title: 7-106: Colon tumor from patient 106


title: 6-105: Colon tumor from patient 105


title: NZO-18mo-M-naive-39_GT18-03837_ACAGTG_S11


title: NZO-18mo-F-naive-36_GT18-03834_CGATGT_S8

value: female


title: NZO-18mo-M-naive-38_GT18-03836_TGACCA_S15


title: Limb Bud Vehicle control

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

country: India

institute: SciGenom Labs Pvt. Ltd.

data_processing:
Illumina bcl2fastq Conversion Software v1.8.4 used for basecalling.
Alignment performed using STAR (2.4.2a) program to the Ensembl Release 81 Gallus gallus reference genome and genemodel
cuffllinks (version 2.2.1) used for gene and isoform expression estimation
cuffdiff program of cufflinks (version 2.2.1) used for differential expression  analysis
Genome_build: Galgal4 - Ensembl Release 81 database
Supplementary_files_format_and_content: Gene expression of the samples in excel format

organism: Gallus gallus

source_name: limb bud

growth_protocol: The chick embryos were grown upto HH22(4rth day) stage in a hatching incubator.

extract_protocol:
Tissue was harvested in RNA later and shipped to SciGenom Labs, Cochin, India. for RNA isolation and further processing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embryos of HH22 stage were removed from eggshell and washed with 1X PBS. Limb buds were removed surgically and were cut into small pieces. These pieces were divided into two groups i.e. vehicle control (5% DMSO) & thalidomide(40ug/ml) and treated accordingly and then incubated at 37°C for 4h. After incubation, limb bud tissue was homogenized and processed for total RNA isolation.

value: limb bud

value: DMSO


title: Limb Bud Thalidomide

value: Thalidomide (40µg /ml)


title: 20180406_17-ucar-001-run11_FASTQ_NZO-18mo-F-spleen-42_GT18-03788_CGAGGCTG-AGAGGATA_S2

value: spleen


title: 20180406_17-ucar-001-run11_FASTQ_NZO-18mo-F-spleen-36_GT18-03787_GCTACGCT-AGAGGATA_S3

value: Female


title: 5-104: Colon tumor from patient 104


title: NZO-18mo-F-naive-35_GT18-03833_ATCACG_S7

value: naive


title: NZO-18mo-F-memory-42_GT18-03829_CGTACG_S16

value: memory


title: Heart Control

data_processing:
Illumina bcl2fastq Conversion Software v1.8.4 used for basecalling.
Alignment performed using STAR (2.4.2a) program to the Ensembl Release 81 Gallus gallus reference genome and genemodel
cuffllinks (version 2.2.1) used for gene and isoform expression estimation
cuffdiff program of cufflinks (version 2.2.1) used for differential expression  analysis
Genome_build: Galgal4 - Ensembl Release 81 database
Supplementary_files_format_and_content: Gene Expression of the samples in Excel format

source_name: Heart

growth_protocol: Fertilized brown leg horn eggs were incubated in a sterile humidified incubator at 37°C for 24h.

extract_protocol:
Total RNA was isolated using Trizol reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 2% agarose gel. RNA  samples, free of DNA and protein contamination was resuspended in in nuclease free water. 1ug of RNA sample for each stage was given for Next Generation Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All eggs were grouped into two, vehicle control and Nitric oxide (NO). Eggs of vehicle control group were treated with 20 ul of 1X PBS while eggs of NO group were treated with 20ul of 10uMAfter 45 h of incubation, eggs were opened and embryos were isolated. Then heart was removed surgically and 10 samples of each group were pooled. The samples were processed for RNA isolation. SpNO(NO donor) drug as a single dose by making small aperture in the air sac using sterile needle. All the eggs were sealed with mediplast tape and incubated further upto 45 h.

value: 1X PBS


title: Heart Spermine NONOate

value: Spermine NONOate (10 µM)


title: 20180406_17-ucar-001-run11_FASTQ_NZO-18mo-F-PBL-35_GT18-03780_CTCTCTAC-ATAGAGAG_S5


title: 4-103: Colon tumor from patient 103

value: Colon cancer

value: FFPE tumor


title: NZO-18mo-M-memory-40_GT18-03832_ATTCCT_S2


title: 20180406_17-ucar-001-run11_FASTQ_NZO-18mo-F-memory-36_GT18-03793_CGAGGCTG-TCTACTCT_S4


title: 20180406_17-ucar-001-run11_FASTQ_NZO-18mo-F-memory-42_GT18-03794_AAGAGGCA-TCTACTCT_S1


title: 3-102: Colon tumor from patient 102


title: 20180301_17-ucar-001-run9_FASTQ_B6-18mo-M-PBL-45_GT18-01757_TCCTGAGC-ATAGAGAG_S2

value: Male

value: PBL


title: 2-101: Colon tumor from patient 101


title: NZO-18mo-M-memory-39_GT18-03831_ACTGAT_S6

value: male


title: NZO-18mo-M-memory-38_GT18-03830_GAGTGG_S14


title: 20180301_17-ucar-001-run9_FASTQ_B6-18mo-M-memory-47_GT18-01771_CTCTCTAC-TCTACTCT_S3


title: NZO-18mo-F-memory-36_GT18-03828_GTTTCG_S3


title: 20180301_17-ucar-001-run9_FASTQ_B6-18mo-F-spleen-41_GT18-01761_CGTACTAG-AGAGGATA_S4


title: NZO-18mo-F-memory-35_GT18-03827_GTGGCC_S5


title: 11-110: Colon tumor from patient 110


title: 13-112: Colon tumor from patient 112


title: 20180301_17-ucar-001-run9_FASTQ_B6-18mo-F-PBL-42_GT18-01756_AGGCAGAA-ATAGAGAG_S5


title: 20180301_17-ucar-001-run9_FASTQ_B6-18mo-F-naive-40_GT18-01772_TAAGGCGA-CTCCTTAC_S1


title: 1-100: Colon tumor from patient 100


title: 12-111: Colon tumor from patient 111


title: 10-109: Colon tumor from patient 109


title: NZO-12mo-M-spleen-97_GT18-00084_ATTCCT_S48


title: NZO-12mo-M-spleen-95_GT18-00082_GAGTGG_S36


title: T98: Colon tumor from patient 98


title: NZO-12mo-M-spleen-96_GT18-00083_ACTGAT_S34


title: K5 +SP 3h rep3

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 3h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of SP (200 nM).

hyb_protocol: Microarray hybridization and washing were performed using reagents and instruments (hybridization chambers and rotating oven) as indicated by the manufacturer (Agilent Technologies, Palo Alto, CA).

scan_protocol: Arrays were then scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System (Agilent Technologies, Palo Alto, CA).

data_processing: Raw microarray data were acquired and analyzed using Agilent’s Feature Extraction v.12.1 software to assess the array spot quality, as well as to check signal and background intensity statistics in the default setting. Raw signal values were thresholded to 1, log2 transformed, normalized to the 75th percentile, and baselined to the median of all samples using GeneSpringGX v.14.9 (Agilent Technologies). Then, to identify genes with significant temporal expression changes and evaluate trend differences in CGNs undergoing apoptosis (K5 vs K25) and exposed to SP, PACAP or IGF1 treatment with respect to untreated (K5), pre-processed normalized array data were analyzed by using the R package maSigPro (microarray Significant Profiles). Genes whose expression levels varied in a statistically significant way along time were detected using the linear step-up Benjamini-Hochberg false discovery rate (FDR) procedure setting a corrected p-value ≤ 0.05.

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 3h, replicate 3

label_protocol: Aliquots (750 ng) of Cy3‐labeled cRNA targets were hybridized on arrays using the SurePrint G3 Rat Gene Expression 8x60K microarray kit (Agilent Technologies, Palo Alto, CA).

growth_protocol: Primary cultures of CGNs were prepared from 8-day-old Wistar rats (Charles River, Calco, Italy) and were cultured as previously described (ins ref). In brief, cerebella were sliced and tissue was dissociated through trypsinization in 0.025% trypsin solution (15 min at 37 °C) and trituration in presence of DNase (0.01%) and trypsin inhibitor (0.05%). Dissociated cells were collected through centrifugation and resuspended in basal Eagle’s medium supplemented with 10% fetal calf serum, 25 mm KCl, 2 mm glutamine and 100 μg/ml gentamycin. Cytosine arabinofuranoside (10 μM) was added after 18 h of culture to inhibit the growth of non-neuronal cells. After 6 days ‘in vitro’, extracellular KCl was shifted from 25 to 5 mm for neuronal apoptotic death induction. After two washes with serum-free BME containing 5 mm KCl, neurons were incubated with the same medium up to 48 h (K5), whereas control neurons were incubated with a serum-free medium supplemented with 25 mm KCl (K25).

extract_protocol: Total RNA was extracted with Trizol (Life Technologies, Monza, Italy) from four biological replicates for each experimental condition (K25, K5, K5+SP, K5+Pacap, K5+Igf1). RNA quantity and quality were assessed using a NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific, MA, USA) and a 2100 Bioanalyzer microfluidic electrophoresis platform (Agilent Technologies, Palo Alto, CA), respectively, according to the manufacturer's instructions. Complementary RNAs (cRNAs) labeled with Cy3-CTP were synthesized from 1 μg of total RNA of each sample using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Palo Alto, CA), following the manufacturer's protocol.

treatment_protocol: K5 neurons were also treated with a maximal effective dose of SP (200 nM), Pacap (100 nM) or Igf1 (3.26 pM). All the substances were obtained from Sigma-Aldrich (Milano, Italy), unless otherwise specified.

value: Wistar

value: Cerebella

tag: cell type

value: Cerebellar Granule Neurons (CGNs) primary culture

value: 8-day-old (P8)


title: 20180301_17-ucar-001-run10_FASTQ_B6-18mo-M-spleen-47_GT18-01765_CTCTCTAC-AGAGGATA_S2

tag: tissue


title: 20180301_17-ucar-001-run10_FASTQ_B6-18mo-M-naive-45_GT18-01775_TCCTGAGC-CTCCTTAC_S5


title: NZO-12mo-F-spleen-94_GT18-00081_CGTACG_S44

value: NZO

value: female


title: 20180227_17-ucar-001-run8_FASTQ_B6-18mo-M-PBL-47_GT18-01759_CTCTCTAC-ATAGAGAG_S4


title: 20180301_17-ucar-001-run10_FASTQ_B6-18mo-F-naive-42_GT18-01774_AGGCAGAA-CTCCTTAC_S4


title: T94: Colon tumor from patient 94


title: NZO-12mo-F-spleen-90_GT18-00080_GTTTCG_S40

value: spleen


title: K5 +SP 3h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 3h, replicate 2


title: T96: Colon tumor from patient 96


title: K5 +SP 3h rep4

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 3h, replicate 4


title: K5 + SP 1h rep2

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 1h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of SP (200 nM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 1h, replicate 2


title: K5 +SP 3h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 3h, replicate 1


title: K5 + SP 1h rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 1h, replicate 1


title: 20180227_17-ucar-001-run8_FASTQ_B6-18mo-F-memory-40_GT18-01766_TAAGGCGA-TCTACTCT_S5

value: Female


title: B6-3mo-M-spleen-3_GT18-04695_CCGTCC_S59


title: K5 + SP 1h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 1h, replicate 3


title: 20180227_17-ucar-001-run7_FASTQ_B6-18mo-F-spleen-40_GT18-01760_TAAGGCGA-AGAGGATA_S3


title: K5 + SP 1h rep4

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 1h, replicate 4


title: K5+SP 30' rep2

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 0.5h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of SP (200 nM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 0.5h, replicate 2


title: K5+SP 30' rep4

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 0.5h, replicate 4


title: K5+SP 30' rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 0.5h, replicate 3


title: B6-3mo-M-spleen-2_GT18-04694_ATGTCA_S49


title: K5 +Igf1 3h rep4

description: Gene expression in serum-deprived cerebellar granule neurons (CGNs) after 3h switch from 25 mM (K25) to 5 mM KCl (K5) and treated with a maximal effective dose of Igf1 (3.26 pM).

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 3h, replicate 4


title: T86: Colon tumor from patient 86


title: 20180227_17-ucar-001-run8_FASTQ_B6-18mo-F-naive-41_GT18-01773_CGTACTAG-CTCCTTAC_S1

value: naive


title: T95: Colon tumor from patient 95


title: NZO-12mo-F-spleen-89_GT18-00079_GTGGCC_S33


title: T92: Colon tumor from patient 92


title: B6-3mo-F-spleen-5_GT18-04692_AGTCAA_S54


title: B6-3mo-F-spleen-4_GT18-04691_CTTGTA_S60


title: 20180227_17-ucar-001-run7_FASTQ_B6-18mo-M-memory-45_GT18-01769_TCCTGAGC-TCTACTCT_S1

value: memory


title: K5 +Igf1 3h rep3

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 3h, replicate 3


title: T84: Colon tumor from patient 84


title: T89: Colon tumor from patient 89


title: B6-3mo-F-PBL-5_GT18-04687_ACTTGA_S51


title: T88: Colon tumor from patient 88


title: B6-3mo-M-spleen-1_GT18-04693_AGTTCC_S55


title: 20180227_17-ucar-001-run7_FASTQ_B6-18mo-F-memory-41_GT18-01767_CGTACTAG-TCTACTCT_S2


title: 20180227_17-ucar-001-run7_FASTQ_B6-18mo-F-memory-42_GT18-01768_AGGCAGAA-TCTACTCT_S5


title: 20180227_17-ucar-001-run6_FASTQ_B6-18mo-M-spleen-45_GT18-01763_TCCTGAGC-AGAGGATA_S4


title: B6-3mo-F-PBL-4_GT18-04686_CAGATC_S48


title: T83: Colon tumor from patient 83


title: 20180227_17-ucar-001-run6_FASTQ_B6-18mo-M-naive-47_GT18-01777_CTCTCTAC-CTCCTTAC_S3


title: T80: Colon tumor from patient 80


title: B6-3mo-M-PBL-3_GT18-04690_GGCTAC_S61


title: 20180227_17-ucar-001-run6_FASTQ_B6-18mo-F-spleen-42_GT18-01762_AGGCAGAA-AGAGGATA_S5


title: B6-3mo-M-PBL-2_GT18-04689_TAGCTT_S50


title: B6-3mo-M-PBL-1_GT18-04688_GATCAG_S63


title: K5+ SP 30' rep1

source_name: CGNs_medium aspirated_K5 + 0% FCS + SP 200 nM, 0.5h, replicate 1


title: T79: Colon tumor from patient 79

source_name: FFPE tumor


title: 20180227_17-ucar-001-run6_FASTQ_B6-18mo-F-PBL-41_GT18-01755_CGTACTAG-ATAGAGAG_S6


title: T78: Colon tumor from patient 78


title: 20180227_17-ucar-001-run6_FASTQ_B6-18mo-F-PBL-40_GT18-01754_TAAGGCGA-ATAGAGAG_S2


title: B6-3mo-F-naive-5_GT18-04702_ACTGAT_S3


title: 20180125_17-ucar-001-run4_FASTQ_NZO-12mo-M-spleen-96_GT18-00078_TAGGCATG-AGGCTTAG_S1


title: T77: Colon tumor from patient 77


title: B6-3mo-F-naive-4_GT18-04701_GAGTGG_S10


title: T76: Colon tumor from patient 76


title: K5 +Igf1 3h rep2

source_name: CGNs_medium aspirated_K5 + 0% FCS + IGF 3.26 pM, 3h, replicate 2


title: T74: Colon tumor from patient 74