title: thigh; tissue; F83

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79669.gif

tag: reference

source_name: thigh; tissue; F83, 10 ug labeled aRNA

tag: age

value: 83 years

tag: organism part

value: thigh

tag: sample fraction


title: WT-Butyrate3

status: Public on Jan 01 2021

type: SRA

city: Athens

first: Matthew

last: Powers

state: GA

address: 501 DW Brooks Dr

country: USA

institute: University of Georgia

description: Grown in absence of butyrate

library_source: transcriptomic

data_processing:
Reads were trimmed at the 5' and 3' ends to remove ambiguous nucleotides using CLC Genomics Software
Reads were then mapped to Campylobacter jejuni 81-176 using CLC Genomics Software
RPKM values were calculated using CLC Genomics Software
Comparisons were made between relevant genotypes and considered significant if different by a log2 value > |2| with an FDR p-value < 0.05
Genome_build: Campylobacter jejuni 81-176

molecule: total RNA

organism: Campylobacter jejuni

source_name: Bacterial

growth_protocol: Cultures were grown in Campylobacter defined medium as outlined in the manuscript.

extract_protocol:
PureLink Mini RNA (Invitrogen)
Strand-Specific RNAseq

treatment_protocol: Treatment included growth in the presence or absence of 12.5 mM butyrate

tag: strain

tag: genotype/variation

value: wild type

tag: treatment

tag: molecule

value: rRNA-depleted RNA


title: Chicken_Adipose_M1

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Basecalling and demultiplexing were performed using ont-guppy-for-minknow (v3.0.5 for cattle data; v3.2.6 for pig and chicken data), and reads with quality score below 7 were discarded to obtain fastq files.
Demultiplexed fastq files were grouped together for each sample, and processed with Pychopper (v2.4.0) to identify and orient full-length reads.
Full-length strand-oriented reads for each sample were mapped to the respective genome assemblies (ARS-UCD1.2 for cattle; Sscrofa11.1 for pig; GRCg6a for chicken) with minimap2 (v2.16r922) with options “-ax splice -uf -k14” and modifying the maximum allowable intron size by species with option "-G 1000000" for pig and cattle, and "-G 400000" for chicken.
Uniquely mapped reads with a minimum quality score of 10 were extracted with Samtools (v1.7).
Uniquely mapped reads were used to obtain raw gene expression counts, based on the Ensembl v101 annotations for each species, using HTSeq (v0.11.2) with options "-i gene_id --type=exon --stranded=yes --mode=intersection-nonempty."
Genome_build: ARS-UCD1.2 (cattle), Sscrofa11.1 (pig), GRCg6a (chicken)
Supplementary_files_format_and_content: Raw gene counts, based on the Ensembl (v101) annotation for each species

molecule: polyA RNA

organism: Gallus gallus

source_name: Adipose

extract_protocol:
Frozen tissues kept at -80°C were homogenized with a mortar and pestle in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) followed by a column clean-up using the Direct-zol RNA Mini Prep Plus kit (Zymo Research, Irvine, CA) and performing an in-column DNA digestion. Integrity of the DNase-treated RNA was verified on the Experion electrophoresis system (Bio-Rad, Hercules, CA).
For each sample, 50 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9µl with nuclease free water.  Reactions were prepared (9 μl total RNA, 1 μl 10 µM VNP primer , 1 μl 10mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. One μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, and held at 4°C. A round of PCR was used to introduce barcodes to the cDNAs using Oxford Nanopore PCR barcoding expansion 1-96 kit (Cat. No.EXP-PBC096). Barcoding PCR reactions were set up for each cDNA (1 μl PCR barcode, 19 μl first-strand cDNA, 20μl LongAmp Taq 2x master mix), and cycled for [3 min at 95°C]x1, [15 sec at 95°C, 15 sec at 62°C, 7 min at 65°C] x13 cycles, [15 min at 65°C]x1, then held at 4°C. Each barcoded cDNA was purified in 1x Ampure XP Beads, eluted in 20µl of nuclease free water and quantified in the Qubit. Barcoded cDNAs were pooled in a final volume of 47µl and the pool was taken to the DNA Technologies Core and Expression Analysis Laboratory at the University of California Davis where they performed the adapter ligation on the cDNA pool using SQK-DCS109 kit following manufacturer's guidelines. 50 fmol of adapter ligated library was loaded onto PromethION flow cell vR9.4.1.
Long-read Nanopore cDNA sequencing

tag: Sex

value: Male

tag: tissue

value: Adipose


title: Chicken_Duodenum_F1

source_name: Duodenum

value: Female

value: Duodenum


title: YAMATseq, A.thaliana seedling

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

country: China

institute: Tianjin Normal University

description: pretreated RNA

data_processing:
Library strategy: YAMAT-seq
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.

organism: Arabidopsis thaliana

source_name: A.thaliana seedling

growth_protocol: Arabidopsis thaliana, Glycine max, Hordeum vulgare, Setaria italica, Sorghum bicolor, Triticum aestivum, Zea mays plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). The 10-day old seedlings were collected for tRNA-seq or YAMAT-seq analysis.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. tRNA-seq library was constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme). YAMAT-seq was performed as previously described (Shigematsu et al Nucleic Acids Res. 2017) with some modifications. The design of Y-shaped adapters followed previous study. 2 µl of 3’ adaptor (10 µM) and 2 µl of 5’ adaptor mix (10 µM) were incubated at 70ºC for 2 min and cooled at room temperature to allow 5’ and 3’ adaptors to fully anneal. Then, the Y-shaped adaptor was mixed with 2 µg pretreated RNA, 4 unit T4 Rnl2 (New England Biolabs) and 2 µl ligation buffer with total reaction of 20 µl, and incubated at 37 ºC for 2 h. Next, 1 µl RNA RT Primer (RTP, Illumina) was added to the reaction and incubated at 70 ºC for 3 min, and then immediately chilled on ice. Subsequently, reverse transcription and cDNA amplification reactions were performed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). A Universal Primer and RNA PCR Index Primers (Illumina) were used for amplifying cDNAs with 12 PCR cycles. The PCR products were purified using VAHTS DNA Clean Beads (Vazyme).

value: seedling


title: thigh; stromal pellet; F83

type: RNA

city: Stanford

first: Heather

last: Clemons

state: CA

address: Beckman Center

department: Dept of Biochemistry

institute: Stanford School of Medicine

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79731.gif

hyb_protocol: not provided

scan_protocol: Model: GenePix 4000B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Homo sapiens

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

label_protocol: not provided

extract_protocol: not provided

value: Stratagene Human Universal Reference

source_name: thigh; stromal pellet; F83, 10 ug labeled aRNA

extract_protocol:
Adipose Tissue Samples; Specimen Collection Adipose tissue specimens were collected either from the Stanford Tissue Bank, Stanford Dermatology Clinic, Stanford Surgical Pathology or directly from the surgeon at the time of surgery. All surgeries were performed at Stanford Hospital and Clinics. When necessary a trained pathologist dissected the desired adipose specimen from the organ/limb/skin to which it was attached. Samples acquired by Stanford Tissue Bank or Surgical Pathology may have been stored at 4C for up to several hours but were always processed on the same day as the surgery was performed. All samples are considered normal human tissues and were originally collected under the IRB Study of Messenger RNA Expression in Normal Human Tissues ID: 76363, which did not require patient consent as very little patient information (age, gender, procedure) was provided. Subsequently it was determined that our sample collection does not meet the definitions of human subject research under Stanfords Human Research Protection Program and therefore an IRB protocol was no longer required.
Tissue Fractionation - Clemons; Tissue Fractionation Adipose tissue samples were thoroughly rinsed with 70% ethanol to minimize risk of microbial contamination of cell cultures. Tissues were then rinsed with Hanks Balanced Salt Solution (HBSS) and transferred to a clean dish. At this time 1-4 g of tissue were removed and stored at -80C. Additionally a thin slice of each tissue was placed in 10% formalin for paraffin embedding. The remainder of each tissue sample was minced using surgical scissors. Tissue pieces were transferred to 50 ml conical tubes (up to 25 ml tissue per tube), and an equivalent volume of collagenase solution* was added to the tube. Tissue was again minced with scissors until no large pieces remained. Tubes were shaken to mix and incubated at 37C for 30 min to 4 hours, until pieces of tissue were no longer visible. Shin/calf adipose tissue in general took the longest and abdominal and thigh lipoaspirate the shortest time to digest. Digested tissues were then passed through a 180-micron nylon net filter and centrifuged at 100g for 5 minutes to pellet stromal-vascular cells. A 16-gauge needle attached to a 20 ml syringe was passed through the top visible lipid/adipocyte layer and the entire bottom layer containing buffer, cell pellet and blood cells was aspirated from the bottom and transferred to a new conical, tube. This cell suspension (stromal-vascular fraction) was thoroughly mixed by pipetting and divided equally into 2 conical tubes. One of these was set aside for cell culture (see Cell Culture) and the other was centrifuged at 400g for 7 minutes. Buffer was carefully aspirated with a pipette to avoid losing pelleted cells and 15 ml Trizol was added. The remaining lipid/adipocyte layer was washed 1-2 times depending on the amount of visible blood cells: 25 ml HBSS was added to the adipocytes, and gently inverted to mix. Adipocytes were centrifuged at 100g and excess buffer along with contaminating cells was aspirated from the bottom using a needle and syringe as described above. An equal volume of Trizol was added to the washed adipocytes. The stromal-vascular pellet sample and the adipocyte sample were stored in Trizol at -80C.  Collagenase Solution: For stock solution 1000 U/ml Sigma Type II Collagenase (Cat# C6885) was dissolved in HBSS and centrifuged at 1000g for 20 minutes. Resulting liquid fraction was filtered (.22 micron) and stored at -20C and pelleted crystals were discarded. For working solution 1000 U/ml collagenase stock solution was diluted 3x in HBSS containing 5mM CaCl2
Amplification 1 ug of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to manufacturers protocol

value: stromal pellet

value: female


title: Stem rep1

description: pretreated RNA

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by tRanalyzer, a self-designed pipeline for quantifications of tsRNAs and tRNAs.
Genome_build: TAIR10, TIGR7
Supplementary_files_format_and_content: Each excel format file includes four sheets. The tRNAID sheet includes the IDs, genomic coordinates and unique sequences of tRNAs. tRNA_expression sheet shows tRNA abundances. tRFs_from_each_tRNA sheet shows the abundance of tRFs from each tRNA. Each_tRF sheet shows the abundance of each tRF species.

source_name: Stem

growth_protocol: Arabidopsis thaliana plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). Oryza sativa seeds were germinated at 30ºC for 2 d. Uniformly germinated seeds were transferred to Yoshida’s nutrient solution and grown at 28ºC under long-day condition (14 hours of light followed by 10 hours of darkness). Yoshida’s solution were replaced every 3 d with pH adjusted to 5.5.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. Pretreated RNAs were subjected to small RNA-seq library construction using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme).
tRNA-seq

treatment_protocol: In salt treatment, Oryza sativa seedlings were transferred to 300 mM NaCl solution for 8 h. In cold treatment, Oryza sativa seedlings were transferred to a cold room at 4ºC under continuous light for 8 h. The control and stress treated seedlings were collected and immediately frozen in liquid nitrogen and stored at -80ºC before RNA extraction.


title: WT-Butyrate2

description: Grown in absence of butyrate


title: pericolonic; tissue; F59

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79620.gif

scan_protocol: Model: GenePix 4000A

source_name: pericolonic; tissue; F59, 10 ug labeled aRNA

value: 59 years

value: pericolonic

value: tissue


title: WT+Butyrate2

description: Grown in presence of 12.5 mM butyrate

value: 12.5 mM butyrate


title: Chicken_Adipose_F2


title: thigh; adipocyte; M84_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80290.gif

source_name: thigh; adipocyte; M84_redo, 10 ug labeled aRNA

value: 84 years

value: adipocyte


title: pericolonic; adipocyte; M52

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79651.gif

source_name: pericolonic; adipocyte; M52, 10 ug labeled aRNA

value: 52 years


title: Silique rep1

description: pretreated RNA

source_name: Silique


title: Chicken_Adipose_F1


title: Silique rep2

description: pretreated RNA


title: WT-Butyrate1

description: Grown in absence of butyrate

value: wild type


title: L27d3

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
Illumina novaseq 6000 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: https://www.ncbi.nlm.nih.gov/genome/?term=Helianthus+annuus
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

organism: Helianthus annuus

source_name: seed

extract_protocol:
RNA was harvested using RNAprep pure Plant Kit
RNA libraries were prepared for sequencing using Illumina novaseq 6000 platform

treatment_protocol: The two cultivars (86-1, L-1-OL-1) in two different seed developmental stages (oleic acid accumulated rapidly at 17 DAF, and kept relatively stable at 27 DAF) for transcriptome sequencing

value: seed

tag: cultivar

value: cultivars "L-1-OL-1"

tag: developmental stage

value: 27d after flowering


title: WT+Butyrate3

description: Grown in presence of 12.5 mM butyrate

value: rRNA-depleted RNA


title: Rosette leaf rep2

description: pretreated RNA

source_name: Rosette leaf


title: pericolonic; tissue; M65_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80285.gif

source_name: pericolonic; tissue; M65_redo, 10 ug labeled aRNA

value: 65 years

value: Male


title: 2ug MBD 30ul beads rep2

city: Tampa

first: Jinyong

last: Huang

state: Florida

address: 12902 USF Magnolia Drive

department: Tumor biology

institute: Moffitt Cancer Center

description:
RaMWAS summary.xlsx
cfMBD_CpG_annotation_coverage_TPM.txt
cfMBD_CpG_annotation_coverage_TPM_sum.txt

library_source: genomic

data_processing:
The sequenced reads were then aligned to the human genome (hg19) using Bowtie-2 (Version 2.4.2) with the default settings.
After the alignment, the generated sam files were converted to bam files, followed by sorting and indexing duplicate read removal, and  read count extractions on chr1 - chr22 using SAMtools (Version 1.11) ‘view’, ‘sort’, ‘index’, and ‘markdup’ command lines.
R (Version 4.0.3 or greater) package RaMWAS (Version 1.12.0) was used for quality control of the overall mapping quality and calculation of average non-CpG/ CpG coverage and coverage by CpG density.
R package MEDIPS (Version 1.40.0) was then applied for saturation analysis and calculation of correlations of genome wide short read coverage profiles between samples.
Normalized data were exported as wiggle file for visualization on the Integrative Genomics Viewer. BEDtools (Version 2.28.0) ‘coverage’ command line was used to call the coverage according to CpG annotations, using hg19 CpG annotations table as a template. TPM (Transcripts Per Kilobase Million) normalization was performed before comparing the CpG annotations coverage between different samples.
Genome_build: hg19
Supplementary_files_format_and_content: RaMWAS summary.xlsx (Output of RaMWAS summary qc)
Supplementary_files_format_and_content: cfMBD_CpG_annotation_coverage_TPM.txt (TPM normalized reads of each CpG annotation feature (cfMBD-seq))
Supplementary_files_format_and_content: cfMBD_CpG_annotation_coverage_TPM_sum.txt (Sum of mapped reads for each CpG annotation feature (cfMBD-seq))
Supplementary_files_format_and_content: MBD_CpG_annotation_coverage_TPM_sum.txt (Sum of mapped reads for each CpG annotation feature (low input MBD-seq))
Supplementary_files_format_and_content: cfMeDIP_CpG_annotation_coverage_TPM_sum.txt (Sum of mapped reads for each CpG annotation feature (cfMeDIP-seq))

molecule: genomic DNA

source_name: Pooled healthy plasma

extract_protocol:
QIAamp Circulating Nucleic Acid Kit and QIAamp DNA Blood Mini Kit
KAPA Hyper Prep Kit

tag: input (ng)

tag: filler dna methylation ratio

tag: filler dna amount (ng)

tag: mbd protein (ug)

tag: mbd-specific beads (ul)

tag: wash

value: Standard

tag: elution fraction

value: Single

tag: elution salt level

value: High


title: breast R; adipocyte; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78498.gif

tag: reference

value: Stratagene Human Universal Reference

source_name: breast R; adipocyte; F52b, 10 ug labeled aRNA

tag: age

tag: organism part

value: breast (right)

tag: sample fraction

value: female


title: shin/calf; stromal pellet; M94

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79649.gif

source_name: shin/calf; stromal pellet; M94, 10 ug labeled aRNA

value: 94 years

value: shin/calf

value: stromal pellet


title: L27d2


title: Rosette leaf rep1

description: pretreated RNA

tag: treatment


title: L27d1


title: Leaf from stem rep2

description: pretreated RNA

source_name: Leaf from stem


title: L17d3

value: 17d after flowering


title: Leaf from stem rep1

description: pretreated RNA


title: WT+Butyrate1

description: Grown in presence of 12.5 mM butyrate

source_name: Bacterial

tag: strain

tag: genotype/variation

value: wild type

value: 12.5 mM butyrate

tag: molecule


title: Stem rep2

description: pretreated RNA


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79639.gif

source_name: perirenal (retroperitoneal); stromal pellet; M58, 10 ug labeled aRNA

value: 58 years

value: perirenal (retroperitoneal)

tag: Sex


title: Control_48h_rep1

city: Shanghai

first: Yu

last: Liang

address: No. 639 Zhizaoju Road, Shanghai 200011, China

institute: Department of Gastroenterology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: control

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: HCT116 cell was cultured in 5% CO2，37℃ with saturated humidity.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: HCT116 cell was treated with different contrations of dichloroacetate (5mM, 10mM, 20mM) for different times (12h, 24h,48h)

tag: cell line

tag: cell type

value: Human coloretal cancer cell line

value: control


title: omentum (colon); stromal pellet; M52

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79653.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: omentum (colon); stromal pellet; M52, 10 ug labeled aRNA

value: 52 years

value: omentum (colon)

value: Male


title: L17d2

tag: tissue

value: seed

tag: cultivar

value: cultivars "L-1-OL-1"

tag: developmental stage


title: Flower rep2

description: pretreated RNA

source_name: Flower


title: Chicken_Cecum_F2

source_name: Cecum

value: Female

value: Cecum


title: Flower rep1

description: pretreated RNA


title: L17d1


title: thigh; stromal pellet; M94

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79642.gif

value: Stratagene Human Universal Reference

source_name: thigh; stromal pellet; M94, 10 ug labeled aRNA

value: 94 years

value: thigh


title: Control_12h_rep1


title: breast L; tissue; F21

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79695.gif

source_name: breast L; tissue; F21, 10 ug labeled aRNA

value: 21 years

value: breast (left)

value: tissue

value: female


title: YAMATseq, T.aestivum seedling

description: pretreated RNA

organism: Triticum aestivum

source_name: T.aestivum seedling

value: seedling


title: D8627d2

source_name: seed

value: cultivars "86-1"

value: 27d after flowering


title: tRNAseq, T.aestivum seedling

description:
pretreated RNA
tRNAseq_tRNA.xlsx

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.


title: DCA_48h_20mM_rep3

value: Human coloretal cancer cell line

value: dichloroacetate (DCA)_48h_20mM


title: D8627d1


title: D8627d3


title: DCA_48h_20mM_rep1


title: DCA_48h_20mM_rep2


title: DCA_48h_10mM_rep3

value: dichloroacetate (DCA)_48h_10mM


title: D8617d3

value: seed

value: 17d after flowering


title: breast; adipocyte; F52a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79671.gif

source_name: breast; adipocyte; F52a, 10 ug labeled aRNA

value: 52 years

value: breast

value: adipocyte


title: Leaf Plenodomus tracheiphylus treated rep2

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
Sequences putatively belonging to pathogen in inoculated rough lemon samples were removed by filtering out the reads mapped to the fungus genome (https://mycocosm.jgi.doe.gov/Photr1/Photr1.info.html).
In the absence of a reference genome clean reads have been assembled using Trinity software (K 25, Kmer coverage 2). Corset software was used for hierarchical clustering (parameter -m 10)
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS preduction using blast and EST-scan
De novo transcriptome filtered by Corset used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq used for gene expression difference analysis
Genome_build: FASTA of assembled transcripts is available on the series record.
Supplementary_files_format_and_content: Microsoft excell file containing raw readcounts of all unigenes in each sample

organism: Citrus jambhiri

source_name: Leaf

growth_protocol: Seeds of rough lemon (C. jambhiri) were sowed on sterile peat in May 2019. After 6 months of growing in a chamber at 25 °C and 90% humidity, Pt plants were inoculated with the pathogen Plenodomus tracheiphilus PT10 strain

extract_protocol:
Both inoculated and control samples were collected 15 days after inoculation. Leaves were immediately frozen with liquid nitrogen and stored at -80°C until both DNA and RNA extractions were performed. DNA extraction was performed according to Springer 2010. The RNA was extracted using the RNeasy® Plant Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s instructions.
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA from is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.

treatment_protocol: The inoculum was prepared as follows: three pieces of young fungus grown at 21°C ± 2 in Petri dishes containing potato dextrose agar medium (PDA) were placed in 7 different flasks containing 100 mL of carrot broth and incubated for 5 days in a heidolph unimax 2010 shaker at 22 °C. Successively, the growth medium was filtered and centrifugated at 8.000 rpm x 20 min. The pellet was recovered and the phialoconidia were counted with a counting chamber to adjust the inoculum concentration at 106 mL-1. The inoculation of Pt plants was performed by depositing 10 µl on wounds obtained by cutting the midvein of three leaves for each plant with a sharp sterile blade. CK plants were inoculated with sterile water

value: Inoculum containing 10^6 mL-1 phialoconidia of Plenodomus tracheiphilus PT10 strain

value: leaf


title: Leaf Plenodomus tracheiphylus treated rep3


title: DCA_48h_10mM_rep2


title: D8617d2


title: Leaf Plenodomus tracheiphylus treated rep1


title: DCA_48h_10mM_rep1


title: D8617d1


title: omentum (colon); adipocyte; F69

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79658.gif

value: Stratagene Human Universal Reference

source_name: omentum (colon); adipocyte; F69, 10 ug labeled aRNA

value: 69 years

value: omentum (colon)


title: Leaf control rep3

value: Water


title: thigh; tissue; MU

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79646.gif

source_name: thigh; tissue; MU, 10 ug labeled aRNA

value: unknown

value: thigh

value: tissue

value: Male


title: DCA_48h_5mM_rep3

value: Human coloretal cancer cell line

value: dichloroacetate (DCA)_48h_5mM


title: TDdddAC_G_PDO

city: Chongqing

first: Xiao-Ran

last: Jiang

address: No.30 Gaotanyan Main Street, Shapingba District

department: Department of Microbiology

institute: Army Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic).Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05.
Genome_build: ASM21956v1
Supplementary_files_format_and_content: Excel file includes RPKM values

organism: Halomonas bluephagenesis

growth_protocol: Cells were grown in a defined minimal medium supplemented with 30 g L-1 glucose as carbon source.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed usingDNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5μg of total RNA. Shortly, rRNA removal by RiboZero rRNA removal kit(Epicenter) , fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, Paired-end libraries were sequenced by Illumina Novaseq™ 6000 sequencing (150bp*2 )

treatment_protocol: with and without 3HP/PDO treatment

tag: genotype

value: dddA and dddC deleted

value: PDO


title: Leaf control rep2


title: TD_3HP

value: wild type


title: Leaf control rep1


title: DCA_48h_5mM_rep2


title: DCA_48h_5mM_rep1


title: TD_G


title: breast; stromal pellet; F52a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79670.gif

source_name: breast; stromal pellet; F52a, 10 ug labeled aRNA

value: 52 years

value: breast

value: stromal pellet

value: female


title: ∆hpo histone turnover rep2

city: Eugene

first: Eric

middle: U

last: Selker

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using HOMER (Heinz et al., 2010) and tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
H3K9me3 Domain Calling: constitutive heterochromatin domains (delineated by the presence of H3K9me3) were called using SICER (Xu et al., 2014) using the default settings.
Gene Expression Quartiles: RNA-seq data from a wild-type strain was used to rank all genes in order by their total expression level and then divided into quartiles.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC in complete darkness. Cultures were spiked with 100mM hydroxyurea to block DNA replication and incubated for 3hrs. To induce hH3-3xFLAG expression, cultures were exposed to blue light (465 nm; 30 mole photons/m^2/s) for two minutes, and incubated for the indicated time to allow for incorporation into chromatin. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 30 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 20 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, 40µL of 50:50 anti-FLAG conjugated bead slurry was added, and samples were rotated overnight at 4oC. The next day, the beads were washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65˚C.  Samples (IP and input) were decrosslinked at 65˚C overnight.  The next day, samples were proteinase K treated for 2 hours at 50˚C, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μL of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98˚C for 30 sec, 10 cycles at 98˚C for 10 sec, 60˚C for 30 sec and 72˚C for 30 sec and a final extension at 72˚C for 5 min.

tag: chip antibody

value: anti-FLAG conjugated agarose beads (Millipore A2220; lot #SLBW6125

value: mat ? Pvvd::hH3-3xFLAG::his-3+; {delta}hpo::hph

value: germinated conidia


title: Control_24h_rep1

value: control


title: hip lipo; stromal pellet; F62_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80289.gif

value: Stratagene Human Universal Reference

source_name: hip lipo; stromal pellet; F62_redo, 10 ug labeled aRNA

value: 62 years

value: hip lipo


title: arm (upper); tissue; F48

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78538.gif

source_name: arm (upper); tissue; F48, 10 ug labeled aRNA

value: 48 years

value: arm (upper)

value: tissue


title: ∆hpo histone turnover rep1


title: t9_CH_I rep3

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

country: Belgium

institute: Ghent University

data_processing:
Bases were called using the Real Time Analysis 2 software of the HiSeq 3000 machine
Quality of the reads was evaluated with FastQC v0.11.8
Adapters of the reads and low quality sequences were removed using Trimmomatic v0.38. Reads were truncated if the mean quality score dropped below 20 in a window of 5 bases. Remaining reads with a length smaller than 20 bases were removed.
The resulting reads were mapped to the Fragaria ananassa reference genome (Hirakawa et al., 2014) with STAR v2.6.1d
A count table was built by making use of the R package GenomicAlignments. Only those reads overlapping any part of exactly one gene were taking into account.
Differentially expressed genes were analysed using edgeR version 3.4.3 for the RNA sequencing data. After TMM normalization, a NB model with main effects for treatment and infection, as well as treatment x infection interaction was used.Significant differentially expressed genes were obtained by likelihood ratio tests  on the appropriate contrasts.
Genome_build: Fragaria ananassa reference genome (Hirakawa et al., 2014) available at: ftp://ftp.bioinfo.wsu.edu/species/Fragaria_x_ananassa/
Supplementary_files_format_and_content: A count table with raw counts.

organism: Fragaria x ananassa

source_name: Leaves

growth_protocol: Strawberry plants were grown either in peat substrate, peat substrate amended with 3% biochar or with 3% chitin. The peat substrate used in this experiment was NOVOBALT white peat 100% (AVEVE Lammens,Wetteren, Belgium). Biochar was prepared from the pyrolysis of holm oak at 650°C for 12-18 hours (Proininso S.A., Malaga, Spain). Chitin flakes were purified from crab shells (BioLog Hepp Gmbh (lot: 90200705)). Additionally, fertilizer (1,9 g/L potting soil) (PGMix, Peltracom, Ghent, Belgium) and lime (7,7 g/L potting soil) (Dolokal extra, Ankerpoort NV, Maastricht, The Netherlands) were added to the mixtures. For each treatment, 84 plants were grown. The plants were grown in the greenhouse at 20°C.

extract_protocol:
RNA was extracted from the plant leaves according to Luypaert et al. (2017) and described in detail in Debode et al. (2018). DNase treatment was done using the DNA-free kit (Ambion, Thermo-Fisher Scientific). For cDNA synthesis, the Tetro cDNA Synthesis kit (Bioline) was used, starting from 1.5 µg of DNA-free RNA.
Samples were first enriched in mRNA by targeting the 3’ polyA-tail using poly-T oligos attached to magnetic beads. The enriched mRNA was converted into cDNA . Samples are multiplexed by using unique barcodes (Kukurba & Montgomery, 2015) and pooled. Sequencing of the library was done using the Illumina HiSeq 3000 platform .

treatment_protocol: Strawberry leaves were inoculated with B. cinerea after 8 weeks of plant growth. Leaves were inoculated using the method described by Meller Harel et al. (2012). B. cinerea was grown on potato dextrose agar and incubated at 20°C for 4 days. Agar disks with mycelium were cut out from the edge of the colony. These agar disks were placed, with the mycelium side down, on the surface of 3 young fully expanded strawberry leaflets. Per leaf, 3-6 disks were placed. As negative control, half of the plants were inoculated with agar disks without mycelium, thus only containing agar. The plants were sprayed with water and each pot was covered with a plastic box for 1 week to create a high humidity level to stimulate the development of B. cinerea.

tag: growth medium

value: peat substrate with chitin

tag: inoculation status

value: inoculated with B. cinerea

value: Leaves

tag: plant age

value: 9 weeks

value: Elsanta

tag: replicate number


title: t9_PS_I rep3

value: peat substrate


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79627.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

tag: reference

source_name: perirenal (retroperitoneal); tissue; M50, 10 ug labeled aRNA

tag: age

value: 50 years

tag: organism part

value: perirenal (retroperitoneal)

tag: sample fraction

value: Male


title: t9_CH rep3

value: mock


title: t9_BC_I rep3

value: peat substrate with biochar


title: t9_BC rep3


title: flank/back lipo; adipocyte; UUa_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80303.gif

value: Stratagene Human Universal Reference

source_name: flank/back lipo; adipocyte; UUa_redo, 10 ug labeled aRNA

value: unknown

value: flank/back lipo

value: adipocyte


title: DCA_24h_5mM_rep3

value: Human coloretal cancer cell line

tag: treatment

value: dichloroacetate (DCA)_24h_5mM


title: DCA_24h_20mM_rep1

value: dichloroacetate (DCA)_24h_20mM


title: DCA_24h_10mM_rep3

value: dichloroacetate (DCA)_24h_10mM


title: DCA_24h_10mM_rep2


title: DCA_24h_10mM_rep1


title: t9_PS rep3

value: Leaves


title: ∆hda-1 histone turnover rep2

value: anti-FLAG conjugated agarose beads (Millipore A2220; lot #SLBW6125

value: mat a Pvvd::hH3-3xFLAG::his-3+; {delta}hda-1::hph

value: germinated conidia


title: DCA_24h_20mM_rep3


title: ∆dim-5 histone turnover rep2

value: mat ? Pvvd::hH3-3xFLAG::his-3+; {delta}dim-5::bar


title: ∆hda-1 histone turnover rep1


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79640.gif

source_name: perirenal (retroperitoneal); tissue; F41, 10 ug labeled aRNA

value: 41 years

value: perirenal (retroperitoneal)

value: tissue

tag: Sex

value: female


title: thigh; adipocyte; M94

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79643.gif

value: Stratagene Human Universal Reference

source_name: thigh; adipocyte; M94, 10 ug labeled aRNA

value: 94 years

value: thigh

value: Male


title: DCA_24h_20mM_rep2

tag: cell line

value: Human coloretal cancer cell line


title: pericolonic; tissue; F75

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78500.gif

source_name: pericolonic; tissue; F75, 10 ug labeled aRNA

value: 75 years

value: pericolonic


title: DCA_24h_5mM_rep2

tag: cell type

value: dichloroacetate (DCA)_24h_5mM


title: shin/calf; tissue; F83

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79648.gif

source_name: shin/calf; tissue; F83, 10 ug labeled aRNA

value: 83 years

value: shin/calf


title: ∆dim-5 histone turnover rep1

value: anti-FLAG conjugated agarose beads (Millipore A2220; lot #SLBW6125

tag: tissue


title: ∆dim-2 histone turnover rep2

value: mat a Pvvd::hH3-3xFLAG::his-3+; {delta}dim-2::hph

value: germinated conidia


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78516.gif

source_name: perirenal (retroperitoneal); adipocyte; M50, 10 ug labeled aRNA

value: 50 years

value: adipocyte


title: t9_CH_I rep2

value: peat substrate with chitin

value: inoculated with B. cinerea

value: Leaves

value: 9 weeks

tag: cultivar

value: Elsanta


title: ∆dim-2 histone turnover rep1


title: thigh; adipocyte; F83

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79732.gif

value: Stratagene Human Universal Reference

source_name: thigh; adipocyte; F83, 10 ug labeled aRNA

value: thigh

value: female


title: t9_BC_I rep2

value: peat substrate with biochar


title: WT histone turnover rep1

description: HOMER_WT_IP_1.bigwig; HOMER_Merged_WT_IP.bigwig

value: mat a Pvvd::hH3-3xFLAG::his-3+


title: t9_PS_I rep2

value: peat substrate


title: t9_CH rep2

value: mock


title: breast R; stromal pellet; F52b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78499.gif

source_name: breast R; stromal pellet; F52b, 10 ug labeled aRNA

value: 52 years

value: breast (right)

value: stromal pellet


title: DCA_24h_5mM_rep1

value: Human coloretal cancer cell line

value: dichloroacetate (DCA)_24h_5mM


title: med8med25-2 H3Ac ChIP

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Basecalls performed using bcl2fastq version 2.16.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2 (v2.2.5) allowing one mismatch.
SAMtools (v1.10) was used to convert the mapped reads into BAM files.
SICER2 was used to identify differentially enriched peaks between wild type and mutant with FDR<0.05 and |log2FC|>0.3.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files were generated using bamCoverage.

source_name: Arabidopsis seedlings

growth_protocol: All plants were grown on MS (Murashige and Skoog) medium plates under 16 h light/8 h dark photoperiod at 22°C.

extract_protocol:
Cross-linked chromatin was fragmented by sonication and then immunoprecipitated by H3Ac antibody. Genomic DNA was extracted from immunoprecipitated sample by phenol/chloroform/isoamy alcohol.
Libraries were built for ChIP-seq (Illumina HiSeq X Ten; 150-bp pair-end sequencing).

value: Seedlings

value: anti-H3Ac (Millipore, 06-599)


title: DCA_12h_20mM_rep3

value: dichloroacetate (DCA)_12h_20mM


title: med8med25-1 H3Ac ChIP


title: DCA_12h_20mM_rep1


title: DCA_12h_20mM_rep2


title: omentum (colon); tissue; M52

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79655.gif

source_name: omentum (colon); tissue; M52, 10 ug labeled aRNA

value: omentum (colon)

value: tissue

value: Male


title: t9_BC rep2

value: Leaves

value: 9 weeks

value: Elsanta


title: t9_PS rep2


title: DCA_12h_10mM_rep3

value: dichloroacetate (DCA)_12h_10mM


title: WT histone turnover rep2

description: HOMER_WT_IP_2.bigwig; HOMER_Merged_WT_IP.bigwig

value: anti-FLAG conjugated agarose beads (Millipore A2220; lot #SLBW6125

value: mat a Pvvd::hH3-3xFLAG::his-3+

value: germinated conidia


title: shin/calf; tissue; M94

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79733.gif

value: Stratagene Human Universal Reference

source_name: shin/calf; tissue; M94, 10 ug labeled aRNA

value: 94 years

value: shin/calf


title: t9_CH_I rep1

value: peat substrate with chitin

value: inoculated with B. cinerea


title: hac1hac5-2 H3Ac ChIP

value: Seedlings

value: anti-H3Ac (Millipore, 06-599)


title: shin/calf; adipocyte; M94

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79650.gif

source_name: shin/calf; adipocyte; M94, 10 ug labeled aRNA

value: adipocyte


title: hac1hac5-1 H3Ac ChIP


title: shin/calf; adipocyte; M17a_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80297.gif

source_name: shin/calf; adipocyte; M17a_redo, 10 ug labeled aRNA

value: 17 years


title: Col-0-2 H3Ac ChIP

value: wild type


title: DCA_12h_10mM_rep2

value: Human coloretal cancer cell line


title: DCA_12h_10mM_rep1


title: t9_BC_I rep1

value: peat substrate with biochar

value: Leaves

value: 9 weeks


title: t9_PS_I rep1

value: peat substrate

value: Elsanta


title: Col-0-1 H3Ac ChIP


title: breast R; adipocyte; F39

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79624.gif

source_name: breast R; adipocyte; F39, 10 ug labeled aRNA

value: 39 years

value: breast (right)

value: female


title: DCA_12h_5mM_rep3

value: dichloroacetate (DCA)_12h_5mM


title: t9_CH rep1

source_name: Leaves

value: peat substrate with chitin

value: mock


title: shin/calf; adipocyte; M55_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80294.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: shin/calf; adipocyte; M55_redo, 10 ug labeled aRNA

value: 55 years

value: shin/calf

value: Male


title: pericolonic; stromal pellet; F85

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79638.gif

source_name: pericolonic; stromal pellet; F85, 10 ug labeled aRNA

value: 85 years

value: pericolonic

value: stromal pellet


title: DCA_12h_5mM_rep1

value: Human coloretal cancer cell line


title: DCA_12h_5mM_rep2


title: t9_PS rep1

value: Leaves

value: 9 weeks


title: t9_BC rep1

value: peat substrate with biochar

value: Elsanta


title: med8med25-2

description:
MGISEQ-2000
gene_expression.txt

data_processing:
Zebracall software used for basecalling.
The qualified data was mapped to the Arabidopsis TAIR10 genome through HISAT2 using the default parameters.
The featureCounts program was used to perform genomic quantification of sequencing data.
In order to identify the differentially expressed genes between the mutant and wild-type in the transcriptome data, we used the |Fold Change| > 2 of R package edgeR and the standard of Pvalue<0.01 for screening.
Genome_build: TAIR10
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file include normalized reads for each sample.

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen) from 12-day-old seedlings.
Sequencing libraries were built for RNA-seq (the single-ended 50-bp strategy).

value: Seedlings

value: 12 days


title: CD4LAD_rep_3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

hyb_protocol: Labeled RNA was dried and resuspended with Hybridization  Buffer and Blocking Agent, incubated 5 min at 100ºC and transfered to an ice water bath for 5 min. Samples were hybridized in a volume of 45ul to the Mouse miRNA Microarray, Release 21.0, 8x60K (Agilent) for 20 hours at 55°C and 20rpm. Microarrays were then washed at room temperature for 5 min in Gene Expression Wash Buffer 1 and 5 min at 37ºC in Gene Expression Wash Buffer 2 (Agilent Technologies; Palo Alto, CA).

scan_protocol: Arrays were scanned on an Agilent G2565A microarray scanner under default settings recommended by Agilent Technologies for miRNA microarrays with 100% PMT and 3μm resolution. Data was extracted using Agilent Feature Extraction software 10.7.3.1.

data_processing: Raw probe-level data was processed with AgiMicroRna Bioconductor package version 2.28.0, to obtain normalized expression values for each miRNA, using the RMA algorithm with quantile-normalization across samples. To avoid losing information for those miRNAs expressed at the lowest levels, background correction and undetected probe filtering were omitted.

organism: Mus musculus

source_name: draining lymph nodes LAD day 3

label_protocol: 100ng of total RNA from each sample was dephosphorylated with Calf Intestinal Alkaline Phosphatase (CIP) at 37ºC for 30’ following a denaturalization and then a ligation for 2h at 16ºC using Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies; Palo Alto, CA). In this step a molecule of Cyanine3-pCp is incorporated to the 3’ end of RNA molecules.

extract_protocol: MicroRNA were extracted with miRVANA miRNA Isolation kit (Invitrogen) as recommended by the manufacturer. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Draining LN from EAM or LAD were put in single cell suspensions and labelled with biotin-conjugated anti-mouse CD4 (Pharmingen, BD). CD4+ T cells were purified using Streptavidin Microbeads (Miltenyi Biotec) and MS columns (Miltenyi Biotec) designed for positive selection as indicated by manufacturer

tag: mouse model

value: myocardial infarction (LAD) model

value: draining-lymph nodes (dLNs)

value: CD4+ Tcells

tag: day post induction

value: day 3


title: knee; tissue; M24a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78545.gif

value: Stratagene Human Universal Reference

source_name: knee; tissue; M24a, 10 ug labeled aRNA

value: 24 years

value: knee

value: tissue


title: CD4LAD_rep_2


title: pericolonic; adipocyte; F75

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78504.gif

source_name: pericolonic; adipocyte; F75, 10 ug labeled aRNA

value: 75 years

value: pericolonic

value: adipocyte

value: female


title: CD4EAM_rep_4

source_name: draining lymph nodes EAM day 6

value: myocarditis (EAM) model

value: day 6


title: med8med25-1

description:
MGISEQ-2000
gene_expression.txt

tag: genotype


title: hac1hac5-1

description:
MGISEQ-2000
gene_expression.txt


title: shin/calf; adipocyte; F12_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80298.gif

source_name: shin/calf; adipocyte; F12_redo, 10 ug labeled aRNA

value: 12 years

value: shin/calf


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78517.gif

source_name: perirenal (retroperitoneal); stromal pellet; M50, 10 ug labeled aRNA

value: 50 years

value: perirenal (retroperitoneal)

value: stromal pellet

value: Male


title: CD4EAM_rep_3

value: draining-lymph nodes (dLNs)

value: CD4+ Tcells


title: hac1hac5-2

description:
MGISEQ-2000
gene_expression.txt

value: Seedlings

value: 12 days


title: Col-0-2

description:
MGISEQ-2000
gene_expression.txt

value: wild type


title: thigh; tissue; F58a

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78527.gif

value: Stratagene Human Universal Reference

source_name: thigh; tissue; F58a, 10 ug labeled aRNA

value: 58 years

value: thigh

value: tissue


title: CD4LAD_rep_1

value: myocardial infarction (LAD) model

value: day 3


title: pericolonic; tissue; M52

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79652.gif

source_name: pericolonic; tissue; M52, 10 ug labeled aRNA

value: 52 years

value: pericolonic


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80305.gif

source_name: perirenal (retroperitoneal); adipocyte; F67_redo, 10 ug labeled aRNA

value: 67 years

value: adipocyte

value: female


title: Col-0-1

description:
MGISEQ-2000
gene_expression.txt

source_name: Arabidopsis seedlings


title: CD4EAM_rep_2

value: myocarditis (EAM) model

value: day 6


title: CD4EAM_rep_1

value: draining-lymph nodes (dLNs)

value: CD4+ Tcells


title: hypoxia,7 days, biological rep2

status: Public on Dec 31 2020

first: Cuiying

last: Li

address: 30 Fucheng

institute: Air Focre Medical Center, PLA

hyb_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: individuals enter in plateau for 7 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: exposure to plateau in different time

value: Blood


title: hypoxia,30 days, biological rep1

source_name: individuals enter in plateau for 30 days


title: hypoxia,30 days, biological rep2


title: hypoxia,7 days, biological rep1


title: hypoxia,3 days, biological rep2

source_name: individuals enter in plateau for 3 days


title: hypoxia,3 days, biological rep1


title: Plain, biological rep2

source_name: individuals in plain


title: Plain, biological rep1


title: FIP+10

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Relis Catus, Ensembl, 6.2
Supplementary_files_format_and_content: tad-delimited, raw counts

organism: Felis catus

source_name: mesenteric lymph node

extract_protocol:
RNA extracted with Qiagen RNeasy Mini Kit, then remaining DNA removed with ezDNase (Thermo Fisher Scientific).
TruSeq RNA stranded
PolyA, TruSeq RNA Kit

treatment_protocol: NA - all natural infections and clinical cases

tag: breed

value: DSH

tag: fip status

value: Pos

value: mesenteric lymph node


title: FIP+9

value: ESH


title: FIP+8

value: 2 y

value: BSH


title: breast L; tissue; F45

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79635.gif

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: Stratagene Human Universal Reference

source_name: breast L; tissue; F45, 10 ug labeled aRNA

value: 45 years

value: breast (left)

value: tissue


title: FIP+6


title: FIP+2

value: Ragdoll


title: FIP-FCoV+5

value: 8 y

value: Neg

tag: fcov infection

value: FCoV+

tag: disease in non-fip

value: Pleural effusion (FCoV RT-qPCR negative)


title: FIP-FCoV-8

value: 3 y

value: FCoV-

value: Invasive meningioma


title: FIP-FCoV-6

value: 4 y

value: DSH

value: Hepatic encephalopathy


title: FIP+7

value: Oriental

value: Pos

value: mesenteric lymph node


title: FIP-FCoV-5

value: 1 y

value: Poxviral pneumonia


title: FIP-FCoV-4

value: Chronic enteropathy


title: FIP-FCoV+6

value: Chronic kidney disease


title: breast R; adipocyte; F60a_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80282.gif

tag: reference

value: Stratagene Human Universal Reference

source_name: breast R; adipocyte; F60a_redo, 10 ug labeled aRNA

value: 60 years

value: breast (right)

value: adipocyte

value: female


title: FIP-FCoV+4

tag: age

value: Neg

value: FCoV+

value: Lymphoma


title: pericolonic; adipocyte; F51a_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80287.gif

source_name: pericolonic; adipocyte; F51a_redo, 10 ug labeled aRNA

value: 51 years

tag: organism part

value: pericolonic


title: MVR Patient-3

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

description:
MVR patient without diabetes
PER37

data_processing:
Immediately after a run,thresholds were determined and data was analyzed using the QuantStudio™ 6 Flex Software. Spike-in control values were checked to determine the accuracy of RNA isolation and cDNA reaction. If a miRNA is expressed in all donors of a group, it was considered as a valid miRNA for the comparison.
No normalization was performed. Raw Different PF exosomes were compared to check whether they express a certain miRNA or not.  If Ct<40, we consider the miRNA as present in the exosomes.
The files with non-normalized data on the series record include the well ID.

label: SYBR Green

source_name: Pericardial fluid exosome

label_protocol: A synthetic analog of the non-human Caenorhabditis elegans microRNA-39 (cel-miR-39; Qiagen, Hilden, Germany) was spiked in (10 μl of a 5 fmol/μl stock) to normalize RNA extraction efficiency. cDNA synthesis and real-time qPCR was performed using the miRCURY LNA™ Universal RT microRNA PCR system (Exiqon, Denmark). The cDNA products were transferred to the microRNA PCR Human Panels (I + II; version 4) and run using QuantStudio 6 Flex Real-Time PCR System (Applied Biosystems, Foster City, CA, USA).

growth_protocol: Exosomes were isolated from the pericardial fluid of the patients undergoing AVR (aortic valve replacement), and CABG (coronary artery bypass graft) surgeries (n=4 in each group) using Exo-SpinTM columns from Cell Guidance Systems (Cambridge, UK). Briefly, 200 µL pericardial fluid was filtered through a sterile 0.22 μm filter (Merck Millipore, Burlington, MA, USA) into a fresh tube. Then, the filtered pericardial fluid was applied onto the Exo-SpinTM columns and exosome separation was performed as described by the manufacturer.

extract_protocol: Total RNA was extracted from isolated exosomes using the miRNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

treatment_protocol: Samples were used without any further treatment.

value: Pericardial fluid

tag: cell compartment

value: exosome

tag: gender

tag: nhya class


title: MVR Patient-1

description:
MVR patient without diabetes
PER29


title: AVR Patient-4

description:
AVR patient without diabetes
PER95

value: Male


title: omentum (colon); adipocyte; M17

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79689.gif

source_name: omentum (colon); adipocyte; M17, 10 ug labeled aRNA

value: 17 years

value: omentum (colon)

tag: sample fraction

tag: Sex


title: AVR Patient-3

description:
AVR patient without diabetes
PER109

tag: tissue


title: MVR Patient-4

description:
MVR patient without diabetes
PER38


title: AVR Patient-2

description:
AVR patient without diabetes
PER132


title: arm (lower); tissue; F48

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78537.gif

source_name: arm (lower); tissue; F48, 10 ug labeled aRNA

value: 48 years

value: arm (lower)

value: tissue


title: AVR Patient-1

description:
AVR patient without diabetes
PER150


description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79626.gif

value: Stratagene Human Universal Reference

source_name: perirenal (retroperitoneal); tissue; M58, 10 ug labeled aRNA

value: 58 years

value: perirenal (retroperitoneal)


title: pelvic; adipocyte; F51b_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80302.gif

source_name: pelvic; adipocyte; F51b_redo, 10 ug labeled aRNA

value: pelvic

value: adipocyte

value: female


title: CABG Patient-4

description:
CABG patient without diabetes
PER120


title: CABG Patient-3

description:
CABG patient without diabetes
PER101


title: breast R; tissue; F62b

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79694.gif

source_name: breast R; tissue; F62b, 10 ug labeled aRNA

value: 62 years

value: breast (right)


title: CABG Patient-2

description:
CABG patient without diabetes
PER93


title: heel; tissue; M77

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-04/79641.gif

source_name: heel; tissue; M77, 10 ug labeled aRNA

value: 77 years

value: heel


title: CABG Patient-1

description:
CABG patient without diabetes
PER87

value: Pericardial fluid

value: exosome


title: shin/calf; adipocyte; M23_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80293.gif

source_name: shin/calf; adipocyte; M23_redo, 10 ug labeled aRNA

value: 23 years

value: shin/calf

value: Male


title: Diabetic CABG Patient-4

description:
CABG patient with diabetes
PER129


title: Diabetic CABG Patient-3

description:
CABG patient with diabetes
PER128


title: Diabetic CABG Patient-2

description:
CABG patient with diabetes
PER108


title: thigh; stromal pellet; M84_redo

description:
Simple annotation: Normal tissue, fat
image: http://smd.stanford.edu/MicroArray/gifs/2008-06/80291.gif

source_name: thigh; stromal pellet; M84_redo, 10 ug labeled aRNA

value: 84 years

value: thigh

value: stromal pellet


title: MVR Patient-2

description:
MVR patient without diabetes
PER36


title: Diabetic CABG Patient-1

description:
CABG patient with diabetes
A50CR


title: Hem1_KO_Mac_2

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

hyb_protocol: 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ (MTA-1_0) for 17 hours at 45°C. Steps for washing and staining were processed on the fluidics station 450 using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix; Santa Clara, CA).

scan_protocol: Image Analysis was performed on GCOS3000 Scanner and GCOS1.2 Software Suite (Affymetrix; Santa Clara, CA).

data_processing: Signal intensities (raw data) were log2 transformed and normalized using RMA summarization method.

source_name: Macrophage

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix).

growth_protocol: Bone marrow cells were harvested from femurs of mice and differentiated in vitro into macrophages using L929 conditioned medium (RPMI+20%L929cM+10%FCS). Cells were harvested after 8 days differentiation.

extract_protocol: RNAeasy (Qiagen). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: not applicable

value: Hem1 KO


title: FIP-FCoV-7

value: unknown

value: DSH

value: Neg

value: FCoV-

value: Behavioural

value: mesenteric lymph node


title: Hem1_WT_Mac_2

value: WT


title: FIP+5

value: 1 y

value: BSH

value: Pos


title: 1_N_TF_spleen_CD8

data_processing: Signal intensities (raw data) were background corrected, log2 transformed and normalized using RMA summarization method.

source_name: spleen

growth_protocol: All animal experiments have been approved by the German legal authorities, Niedersächsisches Landesamt für Verbraucherschutz und Lebensmittelsicherheit (LAVES). Experimental animals were housed and maintained under specific pathogen-free conditions in individually ventilated cages (IVCs) in accordance with the institutional guidelines of the Hannover Medical School.

treatment_protocol: We made use of the well established hydrodynamic tail vein injection for the induction of hepatocellular carcinoma.

tag: cell type

tag: sample type

value: C1 (control):N_TF


title: 3_N_TF_spleen_CD4


title: Hem1_KO_Mac_1


title: 3_N_TF_spleen_CD8


title: 1_N_TF_spleen_CD4


title: 3_N_TF_relLN_CD4

source_name: lymphnode


title: 1_N_TF_liver_CD8

source_name: liver


title: Hem1_WT_Mac_1


title: 1_N_TF_liver_CD4


title: 3_N_TF_relLN_CD8


title: 1_N_TF_relLN_CD8


title: 3_N_TF_irrLN_CD8


title: 3_N_TF_liver_CD8


title: 3_CN_TB_spleen_CD8

value: T (Tumor):CN_TB


title: 1_CN_TB_spleen_CD8


title: 1_N_TF_relLN_CD4


title: 1_N_TF_irrLN_CD8


title: 1_CN_TB_spleen_CD4


title: 3_N_TF_liver_CD4


title: 3_CN_TB_spleen_CD4


title: 3_N_TF_irrLN_CD4


title: 3_CN_TB_relLN_CD4


title: 1_CN_TB_relLN_CD8


title: 1_N_TF_irrLN_CD4


title: 3_CN_TB_relLN_CD8


title: 1_CN_TB_relLN_CD4


title: 3_CN_TB_liver_CD8


title: 3_CN_TB_irrLN_CD8


title: 1_CN_TB_liver_CD8


title: 1_CN_TB_irrLN_CD8


title: 1_CN_TB_liver_CD4 (E)


title: 1_CN_TB_irrLN_CD4


title: 3_CN_TB_liver_CD4


title: 6x-HCPro from PVX vector input tissue

first: Tomas

last: Canto

address: Ramiro de Maeztu 9

department: Environmental Plant Biology

institute: CSIC

description:
Sample 9
sRNA reads 18-30 nt of total RNA samples

data_processing:
Raw files uploaded as received from FASTERIS SA
Processed files trimmed from adaptors, cleaned from reads with erroneous characters, and analyzed for sRNA abundance
Supplementary files linked to the Series record contain quantitative data from our analysis that was used for making figures of the manuscript.
Genome_build: The genomic sequence of A. tumefaciens used was that of Wood et al., (2001; GenBank accession number AE007869.2).
Genome_build: The genomic sequence of N. benthamiana (version 0.5), obtained from the University of Sydney (http://sydney.edu.au/; Naim et al., 2012).
Genome_build: The genomic sequence of Potato virus X (construct pgR107; GenBank accession number: AY297842.1)
Supplementary_files_format_and_content: sRNAabundance18to30nt

organism: Nicotiana benthamiana

source_name: infected tissue

growth_protocol: Plant leaf tissue was agroinfiltrated with binary vectors expressing HCPro variants or mRFP (samples 1-8) or infected with a PVX vector expressing 6x-HCPro

extract_protocol:
Libraries were constructed by FASTERIS SA
Illumina Version NextSeq HighBase; Calling pipeline: - NextSeq Control Software 2.2.0.4 - RTA 2.4.11

treatment_protocol: At 4 days after infiltration or a 7 days after infection, leaf tissues were collected and total RNAs extracted (input samples 1,3,5,7,9).  Histidine-tagged HCPro variants were purified under non-denaturing conditions and the associated RNAs were then isolated (samples 2,4,6,8,10)

value: leaf

tag: infected with

value: PVX vector expressing 6x-HCPro

tag: viral suppressor activity

value: suppression of silencing active

value: plant leaf tissue (input)


title: 6x-HCPro from PVX vector purified protein

description:
Sample 10
sRNA reads 18-30 nt of total RNA samples

source_name: purified protein prep

value: purified protein prep


title: 3_CN_TB_irrLN_CD4


title: 1_C_TF_spleen_CD8

value: C2 (control):C_TF


title: 3_C_TF_spleen_CD8


title: 3_C_TF_relLN_CD8


title: 3_C_TF_spleen_CD4


title: 3_C_TF_relLN_CD4


title: 1_C_TF_relLN_CD4


title: mRFP from T-DNA purified protein

description:
Sample 8
sRNA reads 18-30 nt of total RNA samples

tag: agroinfiltrated with

value: binary vector expressing mRFP

value: suppression of silencing inactive


title: 1_C_TF_liver_CD8


title: 6x-HCPro mutD from T-DNA purified protein

description:
Sample 6
sRNA reads 18-30 nt of total RNA samples

value: binary vector expressing 6x-HCPro mutD


title: 6x-HCPro mutD from T-DNA input tissue

description:
Sample 5
sRNA reads 18-30 nt of total RNA samples

source_name: infiltrated tissue


title: 3_C_TF_liver_CD4


title: 3_C_TF_liver_CD8


title: 6x-HCPro mutB from T-DNA input tissue

description:
Sample 3
sRNA reads 18-30 nt of total RNA samples

value: binary vector expressing 6x-HCPro mutB


title: 3_C_TF_irrLN_CD8


title: mRFP from T-DNA input tissue

description:
Sample 7
sRNA reads 18-30 nt of total RNA samples


title: 1_C_TF_irLN_CD8


title: 1_C_TF_relLN_CD8


title: 1_C_TF_liver_CD4


title: 1_C_TF_spleen_CD4


title: 3_C_TF_irrLN_CD4


title: 1_C_TF_irLN_CD4


title: 6x-HCPro mutB from T-DNA purified protein

description:
Sample 4
sRNA reads 18-30 nt of total RNA samples


title: BGC823 cells, control

city: Jinan

first: Yujing

last: Sun

state: Shandong

address: 44 Wen Hua Xi Road

department: Department of pathology

institute: School of Basic Medical Sciences, Shandong University

data_processing:
Perl script was used to  filter the original data and to get the clean data. Steps are:1.Trim Smart-seq2 public primer sequence from the Reads ; 2. Remove the contaminated reads for adapters ;3. Remove the low quality reads; 4.Remove the reads whose N base more than 5% for total bases .
Reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample
Genome_build: GRCh38.94.chr
Supplementary_files_format_and_content: FPKMs

source_name: gastric cancer cell lines, siNC

growth_protocol: BGC823 cells were cultured in RPMI-1640 medium (HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (Gibco) and were incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
Total RNA were extracted using Trizol reagent (TaKaRa, Dalian, China) according to the manufacturer's instruction. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations a

treatment_protocol: BGC823 cells were transfected with siNC or siZBTB7A in X-tremegene 48h before harvest

tag: cell line

value: BGC823 Human Gastric Cancer Cells

tag: passage

tag: genotype

value: control


title: 6x-HCPro from T-DNA purified protein

description:
Sample 2
sRNA reads 18-30 nt of total RNA samples

value: binary vector expressing 6x-HCPro


title: BGC823 cells, ZBTB7A-knockdown

source_name: gastric cancer cell lines, siZBTB7A

value: ZBTB7A knockdown


title: ΔCSP2

first: Hong

last: Zheng

address: 30 Gaotanyan Street

institute: Army Medical University (Third Military Medical University)

description: ΔCSP stable expressing HepG2 cells

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b). Principal Component Analysis (PCA) and Principal co-ordinates analysis (PCoA) were performed to reflect the distance and difference between samples. The TPM (Transcripts Per Million), eliminates the influence of gene lengths and sequencing discrepancies to enable direct comparison of gene expression between samples. DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significant differentially expressed if q-value <0.001 and |FoldChange| >2. When the normalized expression of a gene was zero between two samples, its expression value was adjusted to 0.01 (as 0 cannot be plotted on a log plot). If the normalized expression of a certain gene in two libraries was all lower than 1, further differential expression analysis was conducted without this gene. Gene expression differences were visualized by scatter plot, MA plot and volcano plot.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample …

source_name: HepG2 cells

growth_protocol: HepG2 cells were infected with overexpression ΔCSP and control lentivirus for 48h, then the ΔCSP stably transfected and control cells were screened by 5mg/mL puromycin (Gibco) and sorted by flow cytometry, finally cloned by limited dilution method continually in 96-well and 3mg/mL puromycin was used to maintain the resistance of stable transfected cells.

extract_protocol:
Total RNAs of ΔCSP stable expressing or control HepG2  cells were extracted using TRIzol (Invitrogen), following the manufacturer's instructions.
Sequencing libraries were generated using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech, Nanjing, China) following manufacturer's recommendations.

value: overexpressing {delta}CSP


title: Control2

description: Control HepG2 cells

value: Control


title: Control3

description: Control HepG2 cells


title: ΔCSP3

description: ΔCSP stable expressing HepG2 cells


title: MJ-sh2

first: Yumei

last: Gao

state: Beijing

address: No.8 Xishiku Street, Xi Cheng District

department: Department of Dermatology and Venereology

institute: Peking University First Hospital

data_processing:
Illumina bcl2fastq v2.19.0.316 software used for basecalling.
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads. Hisat2 version:2.0.4）[1] was used to map the cleaned reads to the human hg38 reference genome with two mismatches.
After genome mapping, Stringtie（version:1.3.0）[2,3] was run with a reference annotation to generate FPKM values for known gene models. Differentially expressed genes were identified using edgeR [4].
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MJ cells

extract_protocol:
Total RNA was extracted from control MJ cells and MJ cells with SATB1 silencing using EZNA total RNA kit II(Omega Bio, USA). Total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MJ cells were subjected with infection of lentivirus expressing SATB1-shRNA1(sh1) and SATB1-shRNA2(sh2) or scrambled shRNA(sh0), and then cultured  to produce stable SATB1 knockdown cell line.

value: MJ cells

tag: treatment

value: lentivirus expressing SATB1-shRNA2


title: Control1

description: Control HepG2 cells


title: MJ-sh0

value: lentivirus expressing scrambled shRNA


title: MJ-sh1

value: lentivirus expressing SATB1-shRNA1


title: SW480_KOEMT cells (PTEN knockout)  RNA-seq

city: Haining

first: Wei

last: Guo

state: Zhejiang

address: 718 South Tan Road

department: ZJU-UoE Institute

institute: Zhejiang University

data_processing:
RNA-seq reads were mapped to the hg19 reference genome using Tophat (version 2.0.11). The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for RNA seq including FPKM values for individual genes

source_name: colon cancer cells

growth_protocol: 2-3 × 10^6 SW480 and derivative cells in a 10cm dish were routinely cultured in DMEM medium (thermo, MA, USA)

extract_protocol:
RNA was extracted using Trizol.
The Smart-Seq2 protocol

value: colon cancer cells

tag: genotype/variation

value: KOEMT cells (PTEN knockout)


title: DIO-2

first: huimin

last: liu

address: 38 Xueyuan Rd , Haidian District

department: Peking University Health Science Center

institute: Peking University

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: submandibular gland

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The submandibular glands of mice are preserved at -80 degrees Celsius.

extract_protocol: Total RNA was extracted using Trizol reagentaccording to the manufacturer’s instructions.

value: submandibular gland

tag: diet

value: high-fat diet

value: male

tag: age

value: 20-week-old male


title: DIO-1

tag: gender


title: DIO-4


title: Ctrl-1

value: normal chow


title: SW480_KOEMT cells reconstituted with nuclear PTEN (C124S)

data_processing:
ChIP-seq reads were mapped to the hg19 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files including number of reads in 100bp bin in the genome for each ChIP-seq sample

extract_protocol:
Lysates were sonicated and the SMAD3-DNA complexes were isolated via immunoprecipitation with a SMAD3 antibody.
Illumina's DNA smart ChIP-seq

tag: antibody

value: SMAD3 ( Abcam, catalog:ab28379, lot:GR321957-3)


title: Ctrl-4


title: DIO-3


title: Ctrl-3


title: Ctrl-2


title: SW480


title: SW480 RNA-seq


title: SW480_KOEMT cells (PTEN knockout)


title: SW480_KOEMT cells reconstituted with nuclear PTEN (C124S)  RNA-seq


title: ΔCSP1

description: ΔCSP stable expressing HepG2 cells


title: IFN2

city: Tel Aviv

first: Amit

last: Gutwillig

address: 35 klachkin st.

department: Pathology

country: Israel

institute: Tel Aviv University

data_processing:
reads were aligned using Kallisto(Bray et al., 2016) to mouse genome version mm10, followed by further processing using the Bioconductor package DESeq2 1.24.0(Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: IFNg activated Rep.2

growth_protocol: CD8 positive T cells were isolated from the spleen of six weeks old mice by magnetic beads (MojoSort), then cultured for six hours with or without treatment.

extract_protocol:
RNA was extracted from cells using NucleoSpin® RNA (MACHEREY-NAGEL), according to manufacturer instructions.
Sequencing Libraries were prepared using INCPM mRNA Seq.

treatment_protocol: T cells were supplied in culture with aCD3 (1 mg/ml), IFNg (70 ng/ml), LPS (1 mg/ml) or left untreated.

tag: strain

value: Spleen

value: CD8 T cells

value: 6 weeks

value: 70 ng/ml IFNgamma for 6 hours


title: N1

source_name: Naïve Rep.1

value: untreated


title: LPS2

source_name: LPS activated Rep.2

value: 1 ug/ml LPS for 6 hours


title: LPS3

source_name: LPS activated Rep.3


title: CD3_3

source_name: CD3 activated Rep.3

value: 1 ug/ml alphaCD3 for 6 hours


title: N2

source_name: Naïve Rep.2


title: IFN3

source_name: IFNg activated Rep.3


title: CD3_2

source_name: CD3 activated Rep.2


title: StyloCSC_1

city: Serdang

first: Gayathri

middle: Thevi

last: Selvarajah

state: Selangor

address: University Putra Malaysia

department: Faculty of Veterinary Medicine

country: Malaysia

institute: University Putra Malaysia

description: Cancer stem cells (CSC) isolated from CMT-Stylo cells which are CD44+, CD24-/low and ALDH+.

hyb_protocol: Dried labelled cRNA were resuspended with 17 ul nuclease free water and fragmented at 100°C for 5 minutes in a reaction volume of 45 ul containing 25 ul of 2x Hi-RPM Agilent hybridization buffer and 10x Agilent blocking agent following the manufacturers instructions. Samples are then hybridized to Agilent Custom miRNA Microarray (V2:084492) for 20 hours at 55Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) with 5 μm resolution at wavelengths of 532 nm (Cy3) using the extended dynamic range (10–100 %) setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters with protocol miRNA_1200_Jun14 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Canis lupus familiaris

source_name: Cells sorted from CMT-Stylo through flow cytometry, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) and then dried using vacuum concentrators according to the manufacturer's instructions.

growth_protocol: Cells were maintained in DMEM with 10% FBS in 5% CO2 at 37 degrees Celcius.

extract_protocol: Total RNA was extracted from CMT-Stylo cells, CMT-Star cells and their respective cancer stem cells using the RNeasy Plus Mini Kit (Qiagen®) according to manufacturer’s instructions. To ensure DNA-free extracted RNA, a two-step genomic DNA removal was employed which included the manufacturer’s recommendation using the gDNA column spin and additional incubation with RNase-free DNase (Qiagen®) to digest genomic DNA. The concentration and purity of the RNA was determined using nano-spectrophotometer. RNA integrity number (RNA) was determined using a Bioanalyzer, and samples with RIN 7 and above were used for one color microarray hybridization using Agilent platform.

treatment_protocol: To develop CMT-Star cells from CMT-Stylo, the cells were exposed to increasing concentration of doxorubicin in complete growth media, until the cells became resistant at the level of 100 nM doxorubicin exposure over several months. To isolate cancer stem cells (CSC) from CMT-Stylo and CMT-Star cell respectively, Phycoerythrin (PE) conjugated CD24 antibody (clone M1/69, BD Pharmingen) and Allophycocyanin (APC) conjugated CD44 antibody (clone IM7, BD Pharmingen) were used.

value: sorted cells from cell line

value: non treated


title: StyloParent_1

description: CMT-Stylo cells grown in culture

source_name: Cell line CMT-Stylo, replicate 1

value: cell line


title: StyloCSC_2

source_name: Cells sorted from CMT-Stylo through flow cytometry, replicate 2


title: StyloParent_2

description: CMT-Stylo cells grown in culture

source_name: Cell line CMT-Stylo, replicate 2


title: StarParent_1

description: CMT-Star cells grown in culture

source_name: Cell line CMT-Star, replicate 1

value: doxorubicin treated


title: StarCSC_2

description: Cancer stem cells (CSC) isolated from CMT-Star cells which are CD44+, CD24-/low and ALDH+.

source_name: Cells sorted from CMT-Star through flow cytometry, replicate 2


title: StarParent_2

description: CMT-Star cells grown in culture

source_name: Cell line CMT-Star, replicate 2


title: Lyso3

data_processing:
sequencing adaptors were trimmed using fastp 0.19.6(Chen et al., 2018) and aligned to the GRCm38 mouse assembly using STAR 2.7.1a(Dobin et al., 2012). Gene count matrix was analyzed for differential expression using DESeq2 1.24.0(Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: B16F10 incubated with T cell derived lysosomes for 48 hours

growth_protocol: Cultured B16F10 were grown in complete DMEM medium, tumor B16 were injected S.C. to the back of 6 weeks old mice and isolated by FACS.

treatment_protocol: WT B16F10 remained untreated. ITM, ITF1 and Rel were injected to mice S.C. and left to grow for several days before injection of immunotherapy. B16 cells were sorted from the relapsed tumors and were cultured to confluency before RNA extraction. Tumor1, Tumor2 and Tumor3 were injected to mice S.C. and left to grow for several days before injection of immunotherapy. B16 cells were sorted from the relapsed tumors and RNA was extracted immediately. Lyso1, Lyso2 and Lyso3 were incubated with T cell drived lysosomes for 48 hours.

value: B16F10 tumor cells


title: StarCSC_1

source_name: Cells sorted from CMT-Star through flow cytometry, replicate 1


title: Lyso2

value: incubated with T cell derived lysosomes for 48 hours


title: Lyso1


title: LPS1

source_name: LPS activated Rep.1


title: ITM

source_name: cultured B16F10, isolated from relapsed tumor following immunotherapy

value: isolated from relapsed tumor following immunotherapy. Were grown in culture before RNA extraction


title: CD3_1

source_name: CD3 activated Rep.1


title: IFN1

source_name: IFNg activated Rep.1


title: Tumor4

source_name: B16F10, isolated directly from relapsed tumor following immunotherapy

value: isolated directly from relapsed tumor following immunotherapy. RNA was extracted immediately after isolation


title: Tumor3


title: N3

source_name: Naïve Rep.3


title: Tumor1


title: ITF1


title: Rel


title: WT3

source_name: WT B16F10


title: WT1


title: WT2


title: OKS+FoxO6_D1

city: guangzhou

first: huan

last: chen

address: Huangpu District

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

data_processing:
Sequenced reads were aligned to a transcriptome index generated from the GENCODE annotations transcriptome (M13), using RSEM, bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MEF

extract_protocol:
Cells were collected at different time points in reprogramming and lysed with TRIzol reagent. VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing according to standard Illumina protocols

treatment_protocol: MEFs were plated for OKS+DR or OKS+Foxo6, infected with retrovirus generated from PlatE cells and then cultured in iCD1 medium.

value: CBA/CaJ X C57BL/6J

tag: developmental stage

value: Embryos

value: MEF


title: OKS+FoxO6_D3

tag: tissue


title: OKS+DR_D5

tag: cell type


title: EZH2i_rep6

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
read quality was assessed using FastQC v0.11.7.
adaptors and low-quality bases (Q < 20) were trimmed using Trimmomatic v0.38 (minimum read length: 35 base pairs)
fastq files were aligned to the mouse reference genome (GRCm38 / mm10) using TopHat 2.1.1 with the following parameters:  -p 10 --library-type=fr-firststrand --no-novel-juncs -G genes.gtf --transcriptome-index=transcriptome_data/known genome.
bam files were sorted using samtools v1.9
gene level expression counts based on known gene annotation were quantified using featureCounts
genes with at least 1 CPM in a minimum of 6 libraries were retained for further analysis.
filtered counts were TMM normalized to correct for compositional bias.
Genome_build: GRCm38 / mm10
Supplementary_files_format_and_content: tab-delimited text file of gene level counts for each sample

source_name: CD8+ T cells_EZH2 inhibitor

extract_protocol: cDNA libraries were prepared from 500 ng of total RNA using Illumina’s (San Diego, CA) TruSeq stranded mRNA Sample Preparation Kit v2 following the manufacturer’s protocol. Library fragment sizes were validated using a Fragment Analyzer and quantified by a Qubit fluorometer. Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75bp SE reads per sample.

treatment_protocol: We performed RNA-seq on DMSO control and EZH2 inhibited CD8+ T cells.

value: spleenocytes

tag: cell subtype

value: CD8+ T cells

value: EZH2 inhibitor


title: OKS+FoxO6_D5


title: EZH2i_rep3


title: OKS+DR_D7


title: OKS+FoxO6_D0


title: OKS+FoxO6_D7


title: OKS+DR_D3


title: EZH2i_rep1


title: OKS+DR_D0


title: EZH2i_rep2


title: OKS+DR_D1


title: CON_rep6

source_name: CD8+ T cells_DMSO control

value: DMSO control


title: CON_rep5


title: CON_rep4


title: CON_rep3


title: CON_rep1


title: CON_rep2