title: RCC24

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

data_processing:
Sequencing libraries were generated using the TruSeq RNA exome library kit (Illumina, San Diego, CA, USA) according to manufacturer instructions at the Genomics Core Facility (GCF), Norwegian University of Science and Technology (NTNU).
Libraries were normalized to 2.6 pM and subjected to cluster and paired-end read sequencing, performed for 2× 75 cycles on two NextSeq500 HO flowcells (Illumina), according to manufacturer instructions. Base-calling was performed using the NextSeq500 instrument, and RTA 2.4.6.
Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) and Bowtie (http://bowtie-bio.sourceforge.net/index.shtml) were used for assembly of reads and alignment of the contigs to the human genome assembly (GRCh38), respectively
In R LIMMA, genes with at least 1 cpm in at least three samples were used in consecutive analysis.
per progressor sample 2 matched non-progressor samples were used as baseline;
2 SVA (SVA package bioconductor) and Limma´s batch removal function were applied
Differential expression was defined as absolute fold-change (FC) value >2, and adjusted p-value <0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: txt, log2 transformed, normalized counts in cpm

source_name: renal tissue, FFPE

extract_protocol:
Total RNA was extracted from whole FFPE renal biopsy sections (10 μm thickness) using the High Pure FFPE-tissue RNA Isolation kit (catalogue no. 06650775001; Roche Holding AG, Basel, Switzerland)
Sequencing libraries were generated using the TruSeq RNA exome library kit (Illumina, San Diego, CA, USA) according to manufacturer instructions at the Genomics Core Facility (GCF), Norwegian University of Science and Technology (NTNU).

tag: gender

value: Female

tag: pt

tag: fuhrmann

tag: necrosis

value: No

tag: creatinine

tag: leibovich score

tag: group

value: Nonprogr


title: myc ChIP-seq (+SM) Repl. 2 [AGH144_9]

status: Public on Dec 29 2021

type: SRA

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: MD

address: 6 Center Drive, 6/230

country: USA

institute: NIH, NICHD

description:
Biological replicate 2
AGH144_9

library_source: genomic

data_processing:
Paired-end sequences of immunoprecipited DNA were aligned to the yeast genome (SacCer3) using Bowtie2 with parameters -X 1000 --very-sensitive, to map sequences up to 1 kb with maximum accuracy.
Occupancies profiles of Gcn4, TBP, myc-tagged chromatin remoderlers and Rpb3 were created using custom R programs.
The processed data were converted to the bigwig files supplied here: different DNA length exclusion limits were used in the processing (listed with Processed Data Files)
Genome_build: SacCer3
Supplementary_files_format_and_content: bigWig (Lengths used in .bw files; Range: 50 - 300 bp)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 INO80-myc13::HIS3MX6

growth_protocol: All strains were grown to mid-log phase (OD600 about 0.6 to 0.8) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
Sonicated chromatin extracts were immunoprecipitated with anti-Gcn4 (home-made), anti-TBP (from Joseph Reese's lab), anti-myc (Sigma, Cat# 11667203001) and anti-Rpb3 (NeoClone, Cat# W0012). Immunoprecipitated chromatin were treated with proteinase K and DNA were extracted with chloroform and precipitated with iso-propanol.
Libraries were prepared using DNA Library Prep Kit for llumina (Cat# E7370) from New England Biolabs.

treatment_protocol: Cells were fixed with formaldhyde and sonicated with bioruptor. The detail was described previously in Qiu et al., Genome Research 26:211-225 (2006) and Rawal et al., Genes and Development 32:695-710 (2018)

tag: strain

tag: genetic information

tag: treatment

value: Formaldehyde-fixed and sonicated


title: L8 3: Leaves at 8 weeks after planting

type: RNA

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The scanned images were analyzed with GeneSpring GX (Agilent). Percentile normalization (75 percentile) was performed for each chip.

molecule: total RNA

organism: Manihot esculenta

label_protocol: Five mg of total RNA was reverse-transcribed using oligo-dT primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen) in the presence of 100 mCi of [33P]dCTP (Amersham Bioscience, Piscataway, NJ) according to the instructions for the Gene

growth_protocol: Cassava cultivar KU50 stem cuttings were planted in the field at Rayong Field Crop Research Center, Rayong, Thailand. Three independent biological replicates were harvested at 4, 8, and 12 weeks after planting. The roots were classified as fibrous and pre-tuberous (diameter < 2 mm), intermediate storage (diameter = 2–5 mm), and mature storage (diameter > 5 mm) (Sojikul et al. 2015; Teerawanichpan et al. 2008) (Fig. 1a). The cortex and parenchyma region of the intermediate storage and mature storage roots were collected separately. All samples were kept on dry ice during the transport from Thailand to Japan. The samples were frozen with liquid nitrogen and then crushed roughly with a multi-beads shocker (Yasui Kikai Corporation, Osaka, Japan). The in vitro KU50 plantlets obtained from the CIAT germplasm collection were maintained as previously described by Utsumi et al. (2017).

extract_protocol: Total RNA was purified according to manual protocol using RNeasy Plant Mini kit protocol (QIAGEN) followed by Plant RNA reagent protocol (Invitrogen). The total RNA quality was evaluated by electrophoresis with the bioanalyzer system (Agilent, USA). The total RNA was stored at -80ºC until further use.

tag: tag

value: Leaf


title: myc ChIP-seq (no SM) Repl. 2 [AGH144_6]

description:
Biological replicate 2
AGH144_6

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 INO80-myc13::HIS3MX6


title: L8 2: Leaves at 8 weeks after planting


title: LT_HSC_ATF4 KO1

city: Guangzhou

first: Yan

last: Sun

state: Guangdong

address: Zhong shan 2nd Road, Building 74

country: China

institute: Sun Yat-sen University

library_source: transcriptomic

data_processing:
cDNA library construction and sequencing were performed by GENEWIZ using Illumina NovaSeq 6000 platform.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.2.1) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalize  and  differential genes' expression  were performed by  DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files include normalized reads each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: Cells were isolated from mice tibia and femur,long-term HSCs were sorted using FACS

extract_protocol:
Total RNA was extracted from long-term HSCs using TRIzol reagent (Takara) according to manufacturer’s instructions.
The RNA-seq library was prepared  using customized protocol based on Smart-seq2

tag: tissue

value: bone marrow

tag: cell type

value: LT-HSC

tag: genotype

value: ATF4 KO


title: LT_HSC_ATF4-WT2

value: wild-type


title: RCC21

organism: Homo sapiens

value: Male

tag: age


title: L8 1: Leaves at 8 weeks after planting


title: myc ChIP-seq (+SM) Repl. 1 [AGH144_8]

description:
Biological replicate 1
AGH144_8


title: M0 macrophages rep1

city: Xi’an

first: Yangguang

last: Ma

address: Changle West Road No. 127

institute: Department of Orthopedics, The First Affiliated Hospital of Air Force Military Medical University

description: Sample A1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Text file includes FPKM values for each Sample

source_name: M0 macrophages

growth_protocol: The femur and tibia of 6- to 8-week-old C57BL/6 mice were extracted, and their bone marrow cavities were flushed with PBS. The cell-containing pellet was resuspended in pretreated Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS, 1% penicillin/streptomycin solution, and 10 ng/mL macrophage colony-stimulating factor (M-CSF; R&D Systems).  Bone marrow cells were induced to M0 macrophages with M-CSF conditioned medium (10% FBS, 1% penicillin-streptomycin double-antibody, DMEM high-glucose medium, 10 ng/mL M-CSF). Cells were differentiated in fresh conditioned medium for 7 days until the cells matured in culture.

extract_protocol:
Total RNA was isolated from macrophage sample using the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).  Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mature M0 macrophages were polarized to M1 macrophages after the addition of lipopolysaccharide (LPS; Sigma-Aldrich) and interferon-γ (IFN-γ; Sigma-Aldrich) to the medium.

value: femur and tibia

value: M0 mouse bone marrow-derived macrophages

value: 6-8 weeks postpartum

value: wild type

value: non-PBM-treated


title: RCC23


title: S12_Pa 2: Parenchyma of storage tuberous root at 12 weeks after planting

description: Gene expression data from Parenchyma of storage tuberous root at 12 weeks after planting

value: Root


title: RCC22


title: L4 1: Leaves at 4 weeks after planting


title: myc ChIP-seq (no SM) Repl. 1 [AGH144_5]

description:
Biological replicate 1
AGH144_5


title: LT_HSC_ATF4-WT1


title: RCC20


title: S12_Pa 1: Parenchyma of storage tuberous root at 12 weeks after planting


title: L4 3: Leaves at 4 weeks after planting


title: myc ChIP-seq (+SM) Repl. 2 [AGH144_4]

description:
Biological replicate 2
AGH144_4

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: S12_Pa 3: Parenchyma of storage tuberous root at 12 weeks after planting


title: L4 2: Leaves at 4 weeks after planting


title: myc ChIP-seq (+SM) Repl. 1 [AGH144_3]

description:
Biological replicate 1
AGH144_3


title: RCC19

value: No


title: Lit_rep1

city: Norman

first: KAILI

last: LIU

state: Oklahoma

address: 173 Felgar St

institute: The University of Oklahoma

data_processing:
Sequencing reads were processed using the 10× Genomics CellRanger pipeline and further analyzed with the Seurat R package
Genes that were expressed in less than 5 cells or cells that expressed less than 8000 and more than 6000 genes were excluded.
Also, cells that expressed less than 512 and more than 92600 counts or with a mitochondria percentage over 10% were excluded.
Genome_build: mm10
Supplementary_files_format_and_content:
tsv files containing cell barcodes for each sample and features for each cell barcode
Matrix table with raw gene counts for each feature and each cell barcode

source_name: Lit_CD45+ tumor infiltrating cells

extract_protocol:
Tumor tissues were isolated, minced with scalpels, and they digested with Collagenase IV and Dnase I at 37 °C for 20-30 minutes. After enzymatic digestion, immune cells were enriched using lymphocyte separation medium. The enriched cells were then subjected to magnetic bead separation to remove the EpCAM+ cells. The EpCAM-depleted cells were stained with antibodies against CD45 and a viability dye. Live CD45+ cells were sorted using MoFlo and then processed for scRNA-seq via a 10× Genomics platform according to the manufacturer’s instructions (10× Genomics)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: Laser immunotherapy (LIT)

value: CD45+ tumor infiltrating cells

tag: time point

value: 9 days after treatment


title: myc ChIP-seq (no SM) Repl. 2 [AGH144_2]

description:
Biological replicate 2
AGH144_2

value: Formaldehyde-fixed and sonicated


title: RCC18

value: Female

value: Nonprogr


title: myc ChIP-seq (no SM) Repl. 1 [AGH144_1]

description:
Biological replicate 1
AGH144_1


title: myc ChIP-seq (+SM) Repl. 2 [AGH94_12]

description:
Biological replicate 2
AGH94_12

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 STH1-myc13::HIS3MX6


title: RCC17


title: GC_rep1

source_name: GC_CD45+ tumor infiltrating cells

value: N-dihydrogalactochitosan (GC)


title: RCC16

value: Male


title: Lit_rep2


title: RCC15


title: myc ChIP-seq (+SM) Repl. 1 [AGH94_11]

description:
Biological replicate 1
AGH94_11

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 STH1-myc13::HIS3MX6


title: Laser_rep2

source_name: laser_CD45+ tumor infiltrating cells

value: Laser/photothermal therapy (PTT)


title: Rpb3 ChIP-seq (no SM) Repl. 1 [AGH101_13]

description:
Biological replicate 1
AGH101_13

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 snf2∆::kanMX4 HIS3MX6::PTETSTH1

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 snf2{delta}::kanMX4 HIS3MX6::PTETSTH1


title: S12_Co 1: Cortex of storage tuberous root at 12 weeks after planting

description: Gene expression data from Cortex of storage tuberous root at 12 weeks after planting


title: S12_Co 3: Cortex of storage tuberous root at 12 weeks after planting


title: I12_Pa 3: Parenchyma of intermediate tuberous root at 12 weeks after planting

description: Gene expression data from Parenchyma of intermediate tuberous root at 12 weeks after planting


title: RCC14


title: GC_rep2


title: S12_Co 2: Cortex of storage tuberous root at 12 weeks after planting


title: Laser_rep1


title: myc ChIP-seq (no SM) Repl. 2 [AGH94_10]

description:
Biological replicate 2
AGH94_10


title: I12_Pa 1: Parenchyma of intermediate tuberous root at 12 weeks after planting


title: Ctrl_rep2

source_name: Ctrl_CD45+ tumor infiltrating cells

value: CTRL(untreated control)


title: myc ChIP-seq (+SM) Repl. 2 [AGH79_12]

description:
Biological replicate 2
AGH79_12

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 SNF2-myc13::HIS3MX6


title: myc ChIP-seq (no SM) Repl. 1 [AGH94_09]

description:
Biological replicate 1
AGH94_09


title: I12_Pa 2: Parenchyma of intermediate tuberous root at 12 weeks after planting


title: I12_Co 1: Cortex of intermediate tuberous root at 12 weeks after planting

description: Gene expression data from Cortex of intermediate tuberous root at 12 weeks after planting


title: I12_Co 3: Cortex of intermediate tuberous root at 12 weeks after planting


title: RCC13


title: RCC12


title: I12_Co 2: Cortex of intermediate tuberous root at 12 weeks after planting


title: myc ChIP-seq (+SM) Repl. 1 [AGH79_11]

description:
Biological replicate 1
AGH79_11

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 SNF2-myc13::HIS3MX6


title: RCC11

value: Yes

value: Progr


title: RCC10

value: No


title: Ctrl_rep1

value: FVB


title: myc ChIP-seq (no SM) Repl. 2 [AGH79_10]

description:
Biological replicate 2
AGH79_10


title: P12 1: Pretuberous root at 12 weeks after planting

description: Gene expression data from Pretuberous root at 12 weeks after planting

value: Root


title: P12 3: Pretuberous root at 12 weeks after planting


title: myc ChIP-seq (no SM) Repl. 1 [AGH79_09]

description:
Biological replicate 1
AGH79_09


title: RCC09


title: RCC08


title: TBP ChIP-seq (+SM,+dox) Repl. 2 [AGH142_14]

description:
Biological replicate 2
AGH142_14

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: TBP ChIP-seq (+SM,+dox) Repl. 1 [AGH142_13]

description:
Biological replicate 1
AGH142_13


title: RCC06


title: TBP ChIP-seq (+SM,+dox) Repl. 2 [AGH142_12]

description:
Biological replicate 2
AGH142_12

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 HIS3MX6::PTETSTH1


title: RCC05


title: TBP ChIP-seq (no SM,+dox) Repl. 2 [AGH142_10]

description:
Biological replicate 2
AGH142_10

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 HIS3MX6::PTETSTH1


title: S8_Pa 1: Parenchyma of storage tuberous root at 8 weeks after planting

description: Gene expression data from Parenchyma of storage tuberous root at 8 weeks after planting


title: TBP ChIP-seq (+SM,+dox) Repl. 1 [AGH142_11]

description:
Biological replicate 1
AGH142_11

value: Formaldehyde-fixed and sonicated


title: S8_Pa 3: Parenchyma of storage tuberous root at 8 weeks after planting


title: P12 2: Pretuberous root at 12 weeks after planting


title: RCC07


title: Berberine treated A549_biological rep2

city: wuxi

first: jiangan

last: li

address: No 68, Zhongshan Road

institute: Wuxi NO.2 People's Hospital of Nanjing Medical University

description: Gene expression data from Lung adenocarcinoma cells after berberine treatment

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 4.0 with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software12.6.1

label: biotin

organism: Homo

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3' IVT PLUS Reagent Kit

growth_protocol: 500000 lung adenocarcinoma cells were plated and cultured at 37 ° C, 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions

treatment_protocol: After 16 hours, the cells were treated with berberine.

value: Lung adenocarcinoma cells

tag: cell line


title: Berberine treated A549_biological rep3

source_name: Lung adenocarcinoma cells after berberine treatment


title: RCC02

tag: gender


title: S8_Co 2: Cortex of storage tuberous root at 8 weeks after planting

description: Gene expression data from Cortex of storage tuberous root at 8 weeks after planting


title: TBP ChIP-seq (+SM) Repl. 2 [AGH142_8]

description:
Biological replicate 2
AGH142_8

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 snf2∆::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4


title: S8_Co 3: Cortex of storage tuberous root at 8 weeks after planting


title: Berberine treated A549_biological rep1


title: A549_biological rep3

description: Gene expression data from Lung adenocarcinoma cells

source_name: Lung adenocarcinoma cells


title: A549_biological rep1


title: Vsx2:TRAP_22hpf 2

city: Sevilla

first: Jorge

last: Corbacho

address: Universidad Pablo de Olavide. Ctra. de Utrera Km.1

country: Spain

institute: CABD

description: polyribosome-associated RNA

data_processing:
Base calling performed using HiSeq Control Software 2.2.58
Quality of reads was checked using FastQC (v.0.72)
Reads were aligned to Danio rerio GRCz11 genome assembly using Hisat2 with default parameters (v. 2.2.1)
Raw counts of reads were obtained through the featureCounts software using the zebrafish genome GRCz11 annotation from Ensembl
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

extract_protocol:
Tagged ribosomes with mRNA attached to them were purified through inmunoprecipitation. Afterwards, the RNA was isolated.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 22 hours post fertilization

value: Whole embryos (only retina cells tagged)


title: Vsx2:TRAP_22hpf 3

description: polyribosome-associated RNA


title: I8_Pa 2: Parenchyma of intermediate tuberous root at 8 weeks after planting

description: Gene expression data from Parenchyma of intermediate tuberous root at 8 weeks after planting


title: RCC04

value: Male

tag: pt

tag: fuhrmann

value: Nonprogr


title: I8_Co 3: Cortex of intermediate tuberous root at 8 weeks after planting

description: Gene expression data from Cortex of intermediate tuberous root at 8 weeks after planting


title: A549_biological rep2


title: I8_Pa 1: Parenchyma of intermediate tuberous root at 8 weeks after planting


title: TBP ChIP-seq (+SM) Repl. 1 [AGH142_7]

description:
Biological replicate 1
AGH142_7


title: I8_Pa 3: Parenchyma of intermediate tuberous root at 8 weeks after planting


title: TBP ChIP-seq (no SM,+dox) Repl. 1 [AGH142_9]

description:
Biological replicate 1
AGH142_9


title: S8_Co 1: Cortex of storage tuberous root at 8 weeks after planting


title: Vsx2:TRAP_22hpf 1

description: polyribosome-associated RNA


title: RCC03

tag: necrosis

tag: creatinine


title: RCC01

value: Female

tag: leibovich score

tag: group


title: TBP ChIP-seq (no SM) Repl. 2 [AGH142_6]

description:
Biological replicate 2
AGH142_6

tag: strain

tag: genetic information


title: I8_Co 2: Cortex of intermediate tuberous root at 8 weeks after planting

tag: tag


title: M238P Lenti-miR-143/-145_2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Mapping with STAR_2.4.0a versus hg19 folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20". Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M -C" options.
Raw count table was generated with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options.
Genome_build: hg19
Supplementary_files_format_and_content: featurecounts.txt:

source_name: human melanoma M238P cells

extract_protocol:
Total RNA was extracted using the RNA extraction kit (Qiagen, Valencia, CA, USA) according to manufacturer’s instructions.
Truseq Stranded Total RNA  Libraries were generated from 500ng of total RNAs using Truseq Stranded Total RNA kit (Illumina). Libraries were then quantified with Qubit and pooled. 4nM of this pool were loaded on a High Output Flowcell and sequenced on a NextSeq500 platform (Illumina) with 2x75bp paired-end chemistry.

value: human melanoma

tag: genotype/variation


title: TBP ChIP-seq (no SM) Repl. 1 [AGH142_5]

description:
Biological replicate 1
AGH142_5

tag: treatment


title: M238P Lenti-miR-143/-145_1

tag: cell type


title: TBP ChIP-seq (+SM,+dox) Repl. 2 [AGH142_4]

description:
Biological replicate 2
AGH142_4

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 snf2{delta}::kanMX4 HIS3MX6::PTETSTH1


title: TBP ChIP-seq (+SM,+dox) Repl. 1 [AGH142_3]

description:
Biological replicate 1
AGH142_3


title: M238P Lenti-Ctrl_2

description: control vector

value: control vector


title: Glioblastoma multiforme cell line 5522 non-treated control, replicate k3

city: Moscow

first: Irina

middle: A

last: Tarasova

address: Pogodinskaya 10-8

country: Russia

institute: Orekhovich Institute of Biomedical Chemistry

data_processing:
Basecalling with bcl2fastq v2.20.0.422
quality control using FastQC 0.11.5
reads trimming and filtering by Trimmomatic 0.39
read mapping with STAR 2.7
5'-3'-bias analysis using geneBody_coverage.py script (RSeQC package)
reads counting per gene by featureCounts (Subread 1.6.0 package)
Genome_build: GRCh38.80
Supplementary_files_format_and_content: read counts matrix

source_name: glioblastoma multiforme

growth_protocol: Primary cell cultures were derived using surgical material from adult glioblastoma multiforme patients of N.N. Burdenko National Scientific and Practical Center for Neurosurgery (Moscow, Russian Federation). Tissue fragments of 500-1000 mm3 size were taken from intraoperative biopsies and placed in DMEM medium (PanEco, Moscow, Russia) supplemented with 10% fetal bovine serum (Gibco, Thermo Fisher Scientific, Waltham, MA, USA). Stable cell cultures obtained in 8-10 passages were precipitated by centrifugation, washed 3 times with PBS (phosphate buffered solution) and stored at -80C until further use.

extract_protocol:
GBM cells were washed with PBS, followed by lysis using 500 μl of lysis buffer (MagNA Pure Compact RNA Isolation Kit, Roche). Total RNA was extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's protocol. The quality and quantity of RNA was determined using an Agilent 2100 bioanalyzer (Agilent Technologies, USA). All RNA samples had RINs above 9.5.
Total RNA (2 μg) from each sample was used to prepare the mRNA library using the TruSeq RNA Sample Preparation Kit v2 Low Sample (LS) protocol (Illumina, USA) according to the manufacturer's protocol. The cDNA libraries were sequenced (single end reads, 50 bp) using Illumina NextSeq 500 system.

treatment_protocol: Four GBM cultures treated with IFN α-2b (Farmaclon, Moscow, Russia) at concentrations of 1000 units/ml for 24 hours, as well as their untreated controls were subjected to high throughput transcriptomics analyses. Three biological replicates of glioblastoma cultures, treated with IFN α-2b, and the untreated controls, were used for evaluation of IFN type 1 response specific for each cell culture. The sub-confluent cell cultures were grown and treated in 6 cm culture plates. The cells were scraped from the surface, washed 3 times with cold PBS, pelletized by low speed centrifugation and stored in liquid nitrogen until further use.

tag: disease state

value: Glioblastoma multiforme

tag: age

value: adult

tag: ethnicity

value: caucasian

tag: race

value: white

value: non treated

tag: population

value: Russian

tag: replicate


title: M238P Lenti-Ctrl_1

description: control vector

tag: cell line


title: Glioblastoma multiforme cell line 5522 non-treated control, replicate k2


title: I8_Co 1: Cortex of intermediate tuberous root at 8 weeks after planting

value: Root


title: Glioblastoma multiforme cell line 5522 non-treated control, replicate k1


title: Gcn4 ChIP-seq (+SM) Repl. 1 [AGH113_13]

description:
Biological replicate 1
AGH113_13

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 ino80∆::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 ino80{delta}::kanMX4

value: Formaldehyde-fixed and sonicated


title: TBP ChIP-seq (no SM,+dox) Repl. 1 [AGH142_1]

description:
Biological replicate 1
AGH142_1


title: MGC-803_DDP_rep1

first: Shu-Zhong

last: Cui

address: hengzhigang road NO78, yuexiu region

department: Department of Gastrointestinal Surgery II

institute: Affiliated Cancer Hospital & Institute of Guangzhou Medical University

description: mRNA and lncRNA

data_processing:
Data generated from Illumina HiSeq TM were transformed into sequence reads by base calling.
The raw sequencing reads were filtered and cleaned by Cutadapt, whereas FastQC was conducted to verify the sequence quality. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) for transcripts and Bowite (v2.2.5) for miRNA as described.
The lncRNA and mRNA expression levels of each sample are calculated by StringTie (v.2.1.2) with the fragments per kilobase of exon model per million mapped fragments (FPKM) values. The small RNA expression level is calculated by FeatureCounts (v1.6.1) with transcripts per kilobase million (TPM).
Genome_build: Hg38
Supplementary_files_format_and_content: text file including FPKM for every lncRNA and every mRNA expression of each sample.
Supplementary_files_format_and_content: text file including TPM for every miRNA expression of each sample.

source_name: Stomach

growth_protocol: The human GC cell line MGC-803 was cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) at 37℃ with an atmosphere of 5% CO2.

extract_protocol:
Total RNA from MGC-803 and MGC-803/DDP cells was isolated using TRIzol reagent. RNA purity and concentration were measured by the NanoPhotometer spectrophotometer and Qubit RNA Assay Kit in Qubit® 2.0 Flurometer. Approximately 3 μg total RNA was treated by Epicentre Ribo-ZeroTM rRNA Removal Kit (Epicentre, USA) to remove ribosomal RNA, then sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA libarary Prep Kit for Illumina® (NEB, USA). Total RNA (1 μg) was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA) following manufacture’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MGC-803/DDP cells were continuously exposed to increasing concentrations of cisplatin and cultured in drug free madia for at least two passages before each experiment.

value: gastric cancer cell

tag: phenotype

value: Cisplatin resistant


title: P8 3: Pretuberous root at 8 weeks after planting

description: Gene expression data from Pretuberous root at 8 weeks after planting


title: Gcn4 ChIP-seq (+SM) Repl. 2 [AGH113_10]

description:
Biological replicate 2
AGH113_10

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: P8 2: Pretuberous root at 8 weeks after planting


title: TBP ChIP-seq (no SM,+dox) Repl. 2 [AGH142_2]

description:
Biological replicate 2
AGH142_2


title: MGC-803_DDP_rep2

description: mRNA and lncRNA


title: Gcn4 ChIP-seq (+SM) Repl. 2 [AGH113_14]

description:
Biological replicate 2
AGH113_14


title: Glioblastoma multiforme cell line 5522 treated with IFN α-2b, replicate a2

value: IFN α-2b 1000 units/ml for 24 hours


title: F4 2: Fibrous root at 4 weeks after planting

description: Gene expression data from Fibrous root at 4 weeks after planting


title: Gcn4 ChIP-seq (+SM) Repl. 1 [AGH113_09]

description:
Biological replicate 1
AGH113_09


title: F4 1: Fibrous root at 4 weeks after planting


title: P8 1: Pretuberous root at 8 weeks after planting


title: Glioblastoma multiforme cell line 5522 treated with IFN α-2b, replicate a1


title: MGC-803_rep2

description: mRNA and lncRNA

value: Cisplatin sensitive


title: MGC-803_rep1

description: mRNA and lncRNA


title: F4 3: Fibrous root at 4 weeks after planting


title: Gcn4 ChIP-seq (no SM) Repl. 2 [AGH113_08]

description:
Biological replicate 2
AGH113_08


title: Glioblastoma multiforme cell line 4446 non-treated control, replicate k3


title: Gcn4 ChIP-seq (no SM) Repl. 1 [AGH113_07]

description:
Biological replicate 1
AGH113_07


title: Gcn4 ChIP-seq (+SM) Repl. 4 [AGH66_06]

description:
Biological replicate 4
AGH66_06


title: HL60_ADR_1_IP

city: Beijing

first: Shu

last: Fang

address: 28 Fuxing Road, Haidian District

institute: Chinese PLA general hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Genome_build: homo sapiens Ensembl release-101
Supplementary_files_format_and_content: .xlsx files include gene expression and methylation level

growth_protocol: HL60 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 100 μg/ml penicillin and 100 μg/ml streptomycin at 37 ℃ in a humidified 5% CO2 atmosphere. HL60/ADR cells were cultured in the same condition.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to create the final cDNA library in accordance with the protocol for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, cat.e7530L, USA).
MeRIP-seq

treatment_protocol: HL60 in 100-mm dish were treated with a low dose of ADR to remove the drug-sensitive cells until its growth rate was similar to the untreated counterpart. Then, the concentration of ADR was increased stepwise to 0.5 μg/ml.

tag: experiment

value: m6A antibody IP


title: HL60_ADR_2_IP


title: Glioblastoma multiforme cell line 4446 non-treated control, replicate k2


title: HL60_2_IP


title: Glioblastoma multiforme cell line 4446 non-treated control, replicate k1


title: Gcn4 ChIP-seq (+SM) Repl. 3 [AGH66_05]

description:
Biological replicate 3
AGH66_05

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 snf2{delta}::kanMX4 HIS3MX6::PTETSTH1


title: Glioblastoma multiforme cell line 4446 treated with IFN α-2b, replicate a3


title: Glioblastoma multiforme cell line 4446 treated with IFN α-2b, replicate a2


title: Gcn4 ChIP-seq (+SM) Repl. 2 [AGH96_12]

description:
Biological replicate 2
AGH96_12


title: HL60_ADR_2_input

value: non


title: HL60_1_IP


title: genomic DNA from PBMC 33

type: genomic

city: Little Rock

first: Michael

middle: Anton

last: Bauer

state: United States

address: 4301 W Markham  Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: abnormalPBMC sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

source_name: PBMC sample 33

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from PBMCs using QIAamp DNA Blood Mini Kit  according to standard instructions

tag: timepoint

tag: gender

value: Female

value: W

value: abnormal

tag: tissue

value: PBMC


title: Gcn4 ChIP-seq (+SM) Repl. 1 [AGH96_11]

description:
Biological replicate 1
AGH96_11

tag: strain

tag: genetic information


title: Glioblastoma multiforme cell line 4446 treated with IFN α-2b, replicate a1

value: Glioblastoma multiforme

value: adult

value: caucasian

value: white


title: genomic DNA from PBMC 34

description: normalPBMC sample

source_name: PBMC sample 34

value: baseline

value: B

value: normal


title: genomic DNA from PBMC 35

description: normalPBMC sample

source_name: PBMC sample 35


title: S8_Pa 2: Parenchyma of storage tuberous root at 8 weeks after planting

tag: tag

value: Root


title: Gcn4 ChIP-seq (+SM) Repl. 4 [AGH66_04]

description:
Biological replicate 4
AGH66_04

value: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 HIS3MX6::PTETSTH1

tag: treatment

value: Formaldehyde-fixed and sonicated


title: Glioblastoma multiforme cell line 4114 non-treated control, replicate k3

value: non treated

value: Russian


title: HL60_ADR_1_input

value: non


title: Gcn4 ChIP-seq (+SM) Repl. 3 [AGH66_03]

description:
Biological replicate 3
AGH66_03


title: genomic DNA from PBMC 36

description: abnormalPBMC sample

source_name: PBMC sample 36

value: Female


title: genomic DNA from PBMC 30

description: abnormalPBMC sample

source_name: PBMC sample 30

value: W


title: genomic DNA from PBMC 29

description: normalPBMC sample

source_name: PBMC sample 29


title: HL60_1_input


title: genomic DNA from PBMC 28

description: normalPBMC sample

source_name: PBMC sample 28


title: Gcn4 ChIP-seq (+SM) Repl. 2 [AGH96_10]

description:
Biological replicate 2
AGH96_10


title: HL60_2_input


title: Glioblastoma multiforme cell line 4114 non-treated control, replicate k1


title: genomic DNA from PBMC 37

description: abnormalPBMC sample

source_name: PBMC sample 37

value: abnormal


title: genomic DNA from PBMC 32

description: abnormalPBMC sample

source_name: PBMC sample 32

value: PBMC


title: IPIKID134.T1

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

data_processing:
Alignement in human genome
Cell ranger processing
Geneation of Seurat object using Seurat V3
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files

source_name: Kidney

extract_protocol:
10x genomics 3 prime v2
scRNA-seq

value: tumor lesion

tag: cell type

value: Myeloid cells sorted from tumor tissue


title: Gcn4 ChIP-seq (+SM) Repl. 1 [AGH96_09]

description:
Biological replicate 1
AGH96_09

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 HIS3MX6::PTETSTH1


title: Glioblastoma multiforme cell line 4114 treated with IFN α-2b, replicate a3

tag: disease state

value: Glioblastoma multiforme

value: adult

value: caucasian

value: IFN α-2b 1000 units/ml for 24 hours


title: IPIMEL460.T1

source_name: Melanoma

value: Melanoma


title: Gcn4 ChIP-seq (+SM) Repl. 2 [AGH95_12]

description:
Biological replicate 2
AGH95_12

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 snf2∆::kanMX4

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 snf2{delta}::kanMX4


title: genomic DNA from PBMC 27

description: normalPBMC sample

source_name: PBMC sample 27

tag: age

value: normal


title: Glioblastoma multiforme cell line 4114 treated with IFN α-2b, replicate a2

source_name: glioblastoma multiforme

tag: ethnicity

value: white


title: IPIMEL456.T2


title: Gcn4 ChIP-seq (+SM) Repl. 1 [AGH95_11]

description:
Biological replicate 1
AGH95_11

value: Formaldehyde-fixed and sonicated


title: genomic DNA from PBMC 26

description: normalPBMC sample

source_name: PBMC sample 26

value: baseline

tag: race


title: Glioblastoma multiforme cell line 4114 non-treated control, replicate k2

value: non treated

tag: population

value: Russian


title: genomic DNA from PBMC 24

description: abnormalPBMC sample

source_name: PBMC sample 24

value: Female

value: W


title: genomic DNA from PBMC 23

description: normalPBMC sample

source_name: PBMC sample 23

value: PBMC


title: genomic DNA from PBMC 21

description: abnormalPBMC sample

source_name: PBMC sample 21

value: B

value: abnormal


title: genomic DNA from PBMC 25

description: abnormalPBMC sample

source_name: PBMC sample 25


title: Glioblastoma multiforme cell line 4114 treated with IFN α-2b, replicate a1

value: Glioblastoma multiforme

tag: replicate


title: genomic DNA from PBMC 20

description: abnormalPBMC sample

source_name: PBMC sample 20


title: Gcn4 ChIP-seq (+SM) Repl. 4 [AGH66_02]

description:
Biological replicate 4
AGH66_02

source_name: MATa his3∆1 leu2∆0 met15∆0 ura3∆0

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0


title: Glioblastoma multiforme cell line 3821 non-treated control, replicate k3

tag: cell line

value: adult

value: caucasian


title: genomic DNA from PBMC 22

description: normalPBMC sample

source_name: PBMC sample 22


title: Glioblastoma multiforme cell line 5522 treated with IFN α-2b, replicate a3

value: IFN α-2b 1000 units/ml for 24 hours


title: genomic DNA from PBMC 18

description: abnormalPBMC sample

source_name: PBMC sample 18


title: IPIMEL456.T1

value: tumor lesion

value: Myeloid cells sorted from tumor tissue

value: Melanoma


title: Glioblastoma multiforme cell line 3821 non-treated control, replicate k2

value: white


title: genomic DNA from PBMC 17

description: normalPBMC sample

source_name: PBMC sample 17

value: normal


title: Gcn4 ChIP-seq (+SM) Repl. 3 [AGH66_01]

description:
Biological replicate 3
AGH66_01

value: Formaldehyde-fixed and sonicated


title: IPIMEL445.T2


title: genomic DNA from PBMC 19

description: abnormalPBMC sample

source_name: PBMC sample 19


title: genomic DNA from PBMC 16

description: normalPBMC sample

source_name: PBMC sample 16

value: baseline


title: IPIMEL444.T2


title: genomic DNA from PBMC 15

description: normalPBMC sample

source_name: PBMC sample 15

value: Female


title: Gcn4 ChIP-seq (+SM) Repl. 1 [AGH95_09]

description:
Biological replicate 1
AGH95_09


title: IPIMEL435.T2

source_name: Melanoma

value: involved Lymph Node


title: Gcn4 ChIP-seq (+SM) Repl. 2 [AGH95_10]

description:
Biological replicate 2
AGH95_10


title: Dab2 KO clone set 3

city: Pittsburgh

first: B. Rhodes

last: Ford

state: PA

address: 4401 Penn Ave.

department: Department of Pediatrics

institute: University of Pittsburgh

data_processing:
trimmed high quality reads were aligned to genome using TopHat2
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000002295.2/
Supplementary_files_format_and_content: raw counts and normalized counts

organism: Didelphis virginiana

source_name: OK_Dab2 KO clone

growth_protocol: Control, Cubn KO, Lrp2 KO, and Dab2 KO cells were plated at superconfluence on 12 mm permeable supports in 0.5 mL apical and 1.5 mL basolateral DMEM/F12 medium (Sigma D6421) with 10% FBS (Atlanta Biologicals) and 5 mM GlutaMAX (Gibco). After 18 h (t = 0 h), the filters were transferred to an orbital platform shaker rotating at 146 rpm and the incubation continued for 72 h with daily medium changes.

extract_protocol:
Cells were collected using Accutase (BD Biosciences) and RNA was extracted using the Ambion PureLink RNA mini kit (Thermo Fisher Scientific). RNA from three independent experiments was sequenced for each clone.
Library preparation and RNA Seq was performed by the University of Pittsburgh School of Medicine Genomics Analysis Core

tag: model

value: proximal tubule cell model

tag: genotype

value: Dab2 knockout

value: opossum kidney (OK) cells


title: IPIHNSC109.T2

source_name: Head & Neck cancer

value: Head & Neck cancer


title: Dab2 KO clone set 2


title: Glioblastoma multiforme cell line 3821 non-treated control, replicate k1

source_name: glioblastoma multiforme

value: Glioblastoma multiforme

value: non treated

value: Russian


title: Glioblastoma multiforme cell line 3821 treated with IFN α-2b, replicate a1

value: adult

value: caucasian

value: IFN α-2b 1000 units/ml for 24 hours


title: IPIHNSC109.T1

value: tumor lesion

value: Myeloid cells sorted from tumor tissue


title: genomic DNA from PBMC 14

description: normalPBMC sample

source_name: PBMC sample 14

tag: timepoint

value: B

value: normal

value: PBMC


title: Dab2 KO clone set 1


title: Glioblastoma multiforme cell line 3821 treated with IFN α-2b, replicate a2

value: white


title: IPIHNSC099.T1


title: Lrp2 KO clone set 3

source_name: OK_Lrp2 KO clone

value: megalin knockout


title: Glioblastoma multiforme cell line 3821 treated with IFN α-2b, replicate a3


title: WT_PVM-2

first: Helene

middle: F.

last: Rosenberg

address: 50 South Drive

institute: NIAID

description: PVM treated, replicate 2

data_processing:
Raw fastq files were trimmed for quality and adapter contamination using Cutadapt v2.10
Trimmed reads were mapped to the mm10 mouse reference genome and Gencode M25 transcriptome using STAR v2.5.3
Gene-level expression quantification was performed using RSEM v1.3.0
Differential expression analysis was performed using the R package limma with voom normalization
Genome_build: mm10

source_name: lung

growth_protocol: Wild-type BALB/c mice (6 – 10 weeks old) were purchased from Charles River Laboratories. Mice and maintained on-site in the 14BS vivarium at the National Institutes of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health. All mice were maintained under pathogen-free conditions at an American Association for the Accreditation of Laboratory Animal Care accredited animal facility at the NIAID and housed in accordance with the procedures outlined in the Guide for the Care and Use of Laboratory Animals under an animal study proposal approved by the NIAID Animal Care and Use Committee.

extract_protocol:
Lungs were removed from the body cavity, washed, and homogenized immediately in 3 mL TRIzol reagent (Invitrogen), followed by chloroform extraction and precipitation with 70% ethanol. RNA was isolated and purified using an RNeasy Mini or RNeasy MinElute cleanup kit (Qiagen).
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit  following the manufacturer’s instructions.

treatment_protocol: Pneumonia virus of mice (PVM) strain J3666 was prepared from clarified mouse-passaged stocks stored in liquid nitrogen. Mice under isoflurane anesthesia were inoculated intranasally on day 0 with 50 µL PVM diluted to 27 virus copies/mL (as determined by qPCR) in phosphate-buffered saline (PBS) with 0.1% bovine serum albumin (BSA) or diluent control. L. plantarum NCIMB 8826 (BAA-793; ATCC) was grown overnight in De Man Rogosa Sharp (MRS) medium, heat-inactivated (70°C for 30 min), washed once in sterile PBS and stored at 1011/mL (see conversion from OD to cells / mL in reference xx) in sterile PBS with 0.1% BSA at -20°C. L. plantarum (108 cells in 50 µL PBS with 0.1% BSA or diluent control) was administered to the respiratory tract on days 1 and 2.

value: BALB/c

value: Lung

value: Pneumonia virus of mice (PVM) treatment


title: WT_PVM-3

description: PVM treated, replicate 3


title: genomic DNA from PBMC 12

description: normalPBMC sample

source_name: PBMC sample 12

tag: gender

value: Female

value: W


title: Lrp2 KO clone set 1

value: proximal tubule cell model

value: opossum kidney (OK) cells


title: WT_PVM-1

description: PVM treated, replicate 1

tag: tissue


title: Cubilin KO clone set 3

source_name: OK_Cubn KO clone

value: cubilin knockout


title: WT_RNASeq_replicate1

city: Stanford

first: Ashby

middle: J

last: Morrison

address: 371 Serra Mall Gilbert Bldg, Room 326

department: Biology

institute: Stanford University

data_processing:
Raw sequencing read was aligned to GrCh37 with gencode.v19.annotation.GTF using STAR 2.7.2b
Genome_build: GrCh37v19
Supplementary_files_format_and_content: bigwig file was generated using ENCODE pipeline; score represents log2FC(IP/Input)

source_name: Human fetal lung fibroblast

growth_protocol: Cells were grown in 37°C and 5% CO2 in DMEM with high glucose, 15%(v/v) FBS and 1% Pen/Strep.

extract_protocol:
RNA was isolated using Zymo Research Quick-RNA miniprep kit (cat. no. R1054).
rRNA was depleted using Ribo-Zero Plus rRNA Depetion Kit (cat. no. 20040526), followed by library preparation with NEBNext Ultra II Directional RNA library prep kit for illumina (cat. No. NEB#E7765)

treatment_protocol: RB1 was knocked out with CRISPR-Cas9.

value: wild type


title: genomic DNA from PBMC 13

description: normalPBMC sample

source_name: PBMC sample 13

value: baseline


title: RbKO_RNASeq_replicate2

value: RB1 knockout


title: Cubilin KO clone set 2


title: WT-4

description: Control, replicate 4

tag: strain

value: Untreated


title: WT-3

description: Control, replicate 3


title: Cubilin KO clone set 1


title: WT_RNASeq_replicate2


title: Molm13_PP_100nM_6h

city: Taipei

first: Yu-Hsuan

last: Fu

address: No.1, Chang-Te St

department: Department of Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

data_processing:
Sequencing was sequenced on Illumina NovaSeq 6000 platform.
Paired-end sequencing alignment toward hg19 and reads mapping to known genes (feature counts)were performed by Rsubread.
Differentially expressed genes (DEGs) identification between groups were conducted with EBSeq, with a threshold of fold change ≥ 2 or ≤ 0.5 and p-value of ≤ 0.05.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *csvt: comma-separated values of row and normalized counts for each known gene (EntrezID, and HGNC symbol) in columns and sample in rows.

source_name: Asynchronous cells

growth_protocol: Cancer cells were cultured in RPMI medium suppled with 10% FBS

extract_protocol:
Total RNAs were isolated with NucleoSpin® RNA kit (Macherey-Nagel); The final library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.
Strand-specific RNA library were built by TruSeq stranded protocols from Illumina

treatment_protocol: Cells were exposure for 6h to 50nM or 100M pyrvinium or to the vehicle control (DMSO).

value: acute myeloid leukemia Molm13

value: peripheral blood

tag: cell phenotype

value: Asynchronous cells


title: Control clone set 3

source_name: OK_Control clone

value: control cells


title: WT-1

description: Control, replicate 1


title: Molm13_PP_50nM_6h


title: WT_PVM_LP-3

description: PVM and LP treated, replicate 3

value: Pneumonia virus of mice (PVM) treatment + Lactobaccilus plantarum treatment


title: IPIMEL449.T2

value: tumor lesion

value: Myeloid cells sorted from tumor tissue

value: Melanoma


title: RbKO_RNASeq_replicate1


title: Control clone set 1


title: WT_PVM-4

description: PVM treated, replicate 4

value: BALB/c

value: Lung

value: Pneumonia virus of mice (PVM) treatment


title: SFN_47B_RaGene-1 0-st-v1).CEL

city: Wallace Wurth Building, Sydney

first: Margaret

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Rat Gene ST 1.0 GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: male_High Fat Diet (HFD)

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

growth_protocol: With the exception of animals killed at P1, the remaining cohort were weighed every third day from P1 to P16.

extract_protocol: Total RNA from islet were extracted using Trizol method according to manufacturer's instructions

value: Sprague Dawley

value: male

tag: diet

value: High Fat Diet (HFD)

value: islet


title: genomic DNA from PBMC 11

description: normalPBMC sample

source_name: PBMC sample 11

value: baseline

value: Female

value: W

value: normal

value: PBMC


title: Control clone set 2

value: proximal tubule cell model

value: control cells

value: opossum kidney (OK) cells


title: genomic DNA from PBMC 9

description: normalPBMC sample

source_name: PBMC sample 9


title: genomic DNA from PBMC 10

description: normalPBMC sample

source_name: PBMC sample 10


title: Molm13_DMSO_6h

value: acute myeloid leukemia Molm13

value: peripheral blood

value: Asynchronous cells


title: WT_PVM_LP-2

description: PVM and LP treated, replicate 2

value: BALB/c

value: Lung

tag: treatment

value: Pneumonia virus of mice (PVM) treatment + Lactobaccilus plantarum treatment


title: WT-2

description: Control, replicate 2

value: Untreated


title: WT_PVM_LP-1

description: PVM and LP treated, replicate 1


title: SFN_35B_RaGene-1 0-st-v1).CEL

value: Sprague Dawley

value: male

value: High Fat Diet (HFD)


title: FOP hiPSC-derived (FOP3-2)

first: Emilie

last: Barruet

state: California

address: 513 Parnassus Av

institute: UCSF

data_processing:
Sequencing reads were processed with Cell Ranger version 2.0.0. using the human reference transcriptome GRCh38 or hg19 (used for the merged analysis with the human vastus lateralis).
Output files (filtered_gene_bc_matrices) were generated with Cell Ranger version 2.0.0.
Genome_build: GRCh18 or hg19
Supplementary_files_format_and_content: filtered_gene_bc_matrices (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: hiPSC-derived muscle stem/progenitor cells

growth_protocol: Cells were seeded at 7.5x105 cells per well of a 12-well plate on Matrigel two days before the differentiation medium was added. Cells were cultured with differentiation medium made from E6 medium, supplemented with with 3µM CHIR99021 and 0.5µM LDN193189 for six days. Cells were then grown in un-supplemented E6 media until day 12. At Day 12 E6 was replaced by StemPro-34 media supplemented with 10ng/ml bFGF until day 20. The medium was then replaced by E6 medium until day 35. At day 35, DMEM/F12 supplemented with N2 (Gibco) and Insulin-Transferrin-Selenium (ITS-A, 100X Gibco) was added. Media was changed every day until cells were harvested at day 50.

extract_protocol:
Control (1323-2) and FOP (FOP3-2) HNK1-CD45-CD31-CXCR4+CD29+CD56dim cells were sorted from skeletal muscle differentiation of control and FOP hiPSCs. The Chromium Single Cell 3' Reagent Version 2 Kit from 10X Genomics was used to produce Gel Bead-in-Emulsion from single cells.
Libraries were prepared with the Chromium Single Cell 3' Reagent Version 2 Kit.
single cell RNA seq

tag: cell type

value: hiPSC FOP3-2


title: genomic DNA from PBMC 3

description: abnormalPBMC sample

source_name: PBMC sample 3

value: baseline

value: Female

value: W

tag: disease state

value: abnormal


title: genomic DNA from PBMC 31

description: abnormalPBMC sample

source_name: PBMC sample 31

tag: age

value: PBMC


title: Control hiPSC-derived (1323-2)

value: hiPSC-derived muscle stem/progenitor cells

value: WT


title: pSRKb

city: Bloomington

first: Clay

last: Fuqua

state: IN

address: 1001 E. Third Street

institute: Indiana University

description: Illumina sequenced using adaptor-specific primers

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.33 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the Agrobacterium tumefaciens C58 genome reference, AE007869.2, AE007870.2, AE007871.2 and AE007872.2 using bowtie2 (version 2.3.2) (Langmead et al. 2012).
Individual gene expression was quantified by counting the number reads mapping to each of the annotated genes using htseq-count tool (version 0.11.1) . Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s reverse -m union)
Genome_build: Agrobacterium tumefaciens C58 genome reference, AE007869.2, AE007870.2, AE007871.2 and AE007872.2
Supplementary_files_format_and_content: Text files with counts of reads aligned to each annotated gene

organism: Agrobacterium fabrum str. C58

source_name: Vector Control

growth_protocol: Cultures of the strains for comparison were grown in ATGN minimal medium at 30 C with agitation to an OD600 of ~0.6.

extract_protocol:
Total RNA was prepared using Qiagen RNEasy kit, and contaminating DNA was removed with the Turbo RNAse-free DNAse kit for 1 hr at 37 ⁰C
Integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. 1ug of total RNA was used for ribosomal RNA depletion with the Illumina Ribo-Zero kit bacteria.  After rRNA depletion, the libraries were prepared following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads. Finally, the demultiplexing of the reads was performed with bcl2fastq version 2.20.0 pipeline.

treatment_protocol: Cells were collected by centrifugation

value: pSRKGM vector control


title: SFN_23B_RaGene-1 0-st-v1).CEL

value: islet


title: SFN_39B_RaGene-1 0-st-v1).CEL


title: genomic DNA from PBMC 6

description: normalPBMC sample

source_name: PBMC sample 6

value: normal


title: genomic DNA from PBMC 5

description: abnormalPBMC sample

source_name: PBMC sample 5


title: WT_LP-4

city: Bethesda

description: LP treated, replicate 4

source_name: lung

value: BALB/c

value: Lung

value: Lactobaccilus plantarum treatment


title: genomic DNA from PBMC 7

description: normalPBMC sample

source_name: PBMC sample 7


title: pSRKa


title: WT_LP-3

description: LP treated, replicate 3


title: mirAc

source_name: MirA Expression - Plasmid-borne ectopic

value: pSRKGm::PmirA::mirA (pMAT14)


title: genomic DNA from PBMC 8

description: normalPBMC sample

source_name: PBMC sample 8


title: WT_LP-2

description: LP treated, replicate 2


title: mirAb


title: SFN_13B_RaGene-1 0-st-v1).CEL

value: Sprague Dawley

value: male


title: WT_LP-1

description: LP treated, replicate 1


title: genomic DNA from PBMC 4

description: abnormalPBMC sample

source_name: PBMC sample 4


title: genomic DNA from PBMC 2

description: abnormalPBMC sample

source_name: PBMC sample 2


title: SFN_48B_RaGene-1 0-st-v1).CEL

value: control


title: Vitrified follicle_Vitrified_5

city: Piscataway

first: Yingzheng

last: Wang

state: New Jersey

address: 170 Frelinghuysen Rd, Rm 406

department: Pharmacology and Toxicology

institute: Rutgers University

data_processing:
Bowtie 2 was used to remove potential rDNA and mtDNA
Filtered reads were aligned to the whole mouse genome assembly-mm10 using the HISAT 2 aligner
Raw read counts were obtained by quantifying aligned reads to Ensembl Transcripts release 99 using Partek EM algorithm
Differential expression analysis was performed using the DESeq2(R)
Genome_build: mm10

source_name: day 8 follicle

growth_protocol: Follicles were individually encapsulated in 0.5% alginate hydrogel and alginate beads were placed into maintenance media containing minimum essential medium (αMEM Glutamax) with 1% FBS for 30 min at 37°C in 5% CO2 incubator. Then, encapsulated follicles were placed individually in 96-well plate, with each well containing 100 µl growth media (50% αMEM Glutamax and 50% F-12 Glutamax supplemented with 3 mg/mL bovine serum albumin (BSA), 10 mIU/mL recombinant follicle-stimulating hormone (rFSH), 1 mg/mL bovine fetuin, 5 µg/mL insulin, 5 µg/mL transferrin, and 5 ng/mL selenium (ITS). Follicles were cultured at 37°C in 5% CO2 for 8 days and half of the culture media (50 µl) was exchanged every other day.

extract_protocol:
Total RNA was extracted from single-follicle lysate using SPRI beads based method.
Libraries were prepared according to Smart-seq RNA-seq protocol

tag: follicle type

value: Vitrified follicle

tag: mouse strain


title: mirAa


title: normothermic (NT) hamster EH03-36 (no torpor on day of sampling)

city: Ulm

first: Annika

last: Herwig

address: Albert-Einstein-Allee 11

department: Institute of Neurobiology

country: Germany

institute: Ulm University

data_processing:
FastQC 0.11.9
trim-galore 0.6.6
Trinity 2.8.5
Genome_build: GRCm39, Mus musculus and trinity assembled transcripts. The file Trinity-Hypothalamus-Phodopus-ZT04_aftermapping.fasta is a reduced assembly performed using two RUBY scripts, which will be provided at SourceForge.
blastx 2.5.0+
extract_hits_from_fasta.rb
hits_to_genemap.rb
bowtie 1.3.0
rsem 1.3.1
Supplementary_files_format_and_content: .genes.results.txt, non-normalized gene expression

organism: Phodopus sungorus

source_name: hypothalamus

growth_protocol: indoor breeding colony of Ulm University, Ulm, Germany

extract_protocol:
Hypothalamic tissue was disrupted and homogenized in 100 µL buffer RLT with beta-ME using prefilled 2 mL beadbug tubes containing Zirconium beads (Biozym Scientific GmbH, Oldendorf, Germany) on a microtube homogenizer (D1030-E, Benchmark Scientific Inc., Sayreville, NJ, USA). Purification of total RNA was performed using the RNeasy Midi Kit (Qiagen GmbH, Hilden, Germany).
The mRNA was isolated, and the library prepared (NEBNext® Ultra™ II directional, dual index RNA). mRNA-Seq was performed in 2020 on an Illumina NextSeq 500 (1 lane, 50 mio paired end reads, 2x25 mio reads, 2 x 150 nt, 7.5 gb).

treatment_protocol: long or short photoperiod

value: hypothalamus

value: adult

tag: photoperiod

value: adapted to short photoperiod (LD 8:16)

tag: Sex

value: female


title: Vitrified follicle_Vitrified_6


title: normothermic (NT) hamster EH03-37 (no torpor on day of sampling)


title: Vitrified follicle_Vitrified_3


title: SFN_36B_RaGene-1 0-st-v1).CEL


title: genomic DNA from PBMC 1

description: abnormalPBMC sample

source_name: PBMC sample 1

value: baseline

value: Female

tag: race

value: W

value: abnormal

value: PBMC


title: Vitrified follicle_Vitrified_2


title: normothermic (NT) hamster EH03-19 (no torpor on day of sampling)


title: normothermic (NT) hamster EH03-38 (no torpor on day of sampling)


title: hypothermic (HT) hamster EH03-33 in spontaneous daily torpor


title: hypothermic (HT) hamster EH03-26 in spontaneous daily torpor


title: Fresh follicle_Fresh_6

value: Fresh follicle


title: Vitrified follicle_Vitrified_1


title: hypothermic (HT) hamster EH03-10 in spontaneous daily torpor


title: Lrp2 KO clone set 2

source_name: OK_Lrp2 KO clone

tag: model

value: proximal tubule cell model

value: megalin knockout

value: opossum kidney (OK) cells


title: Vitrified follicle_Vitrified_4


title: IPIHNSC098.T1

source_name: Head & Neck cancer

value: tumor lesion

value: Myeloid cells sorted from tumor tissue

value: Head & Neck cancer


title: Fresh follicle_Fresh_5


title: hypothermic (HT) hamster EH03-02 in spontaneous daily torpor


title: Fresh follicle_Fresh_4


title: SFN_46B_RaGene-1 0-st-v1).CEL

value: Sprague Dawley

value: male

value: control

value: islet


title: hamster EH03-LP05

value: hypothalamus

value: adult

value: remained in long photoperiod (LD 16:8)

value: female


title: SFN_26A_RaGene-1 0-st-v1).CEL

source_name: female_High Fat Diet (HFD)

value: High Fat Diet (HFD)


title: Fresh follicle_Fresh_3


title: SFN_22A_RaGene-1 0-st-v1).CEL


title: hamster EH03-LP03


title: SFN_34B_RaGene-1 0-st-v1).CEL


title: Fresh follicle_Fresh_2


title: SFN_20A_RaGene-1 0-st-v1).CEL


title: hamster EH03-LP02


title: hamster EH03-LP01


title: Fresh follicle_Fresh_1


title: SFN_24B_RaGene-1 0-st-v1).CEL


title: SFN_31A_RaGene-1 0-st-v1).CEL


title: SFN_50A_RaGene-1 0-st-v1).CEL


title: replicate 6-3

status: Public on Dec 28 2021

city: Nashville

first: Pius

middle: N

last: Nde

state: TN

address: 1005 Dr. D.B. Todd Jr. Blvd

department: Microbiology and Immunology

institute: Meharry Medical College

data_processing:
BGISEQ-500 plattform used for basecalling
Trimmed adapters and filtered low-quality reads
Mappeed to reference genome using Bowtiw2
Transcripts per million (TPM) were calculated using RSEM v1.2.12
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts and TPM for each gene and sample

source_name: primary human cardiac myocytes

growth_protocol: PHCMs cultured according to manufactuerer's recommendations (PromoCell). Invasive T. cruzi trypomastigotes were purified from  heart myoblasts monolayers cultured in complete DMEM.

extract_protocol:
Parasite challenged and control PHMC were lysed in QIAzol, extracted with chloroform. The aqueous phase of the extract was mixed with an equal volume of 70% ethanol and passed through the RNeasy Mini spin column. The eluate containing small RNA species was mixed with 0.65 volumes of pure ethanol and passed through an RNeasy MiniElute spin column. Bound small RNA species were eluted with RNase-free water as described by the manufacturer (Qiagen).
Libraries were constructed using the BGISeq-500 library construction protocol.

treatment_protocol: PHCM monolayers were starved with HBSS containing 30nM HEPES followed by the addition of  T. cruzi trypomastigotes in PHCM basal growth media at an MOI of 10 parasites per cell.

value: Heart

value: challenged with T. cruzi for 6 hours

tag: molecule subtype small non-coding RNA


title: replicate 3-3

value: challenged with T. cruzi for 3 hours


title: replicate 2-3

value: challenged with T. cruzi for 2 hours


title: replicate 3-1


title: replicate 3-2


title: replicate 6-2


title: SFN_17A_RaGene-1 0-st-v1).CEL


title: SFN_43A_RaGene-1 0-st-v1).CEL


title: SFN_45A_RaGene-1 0-st-v1).CEL


title: repliicate 1-1

value: challenged with T. cruzi for 1 hour


title: replicate 1-3


title: replicate 0-2

value: untreated


title: replicate 0-3


title: replicate 0-1


title: SFN_19A_RaGene-1 0-st-v1).CEL


title: DKO-C2-R3

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

institute: Hudson Institute of Medical Research

data_processing:
Basecalling using BGI
Alignment using STAR 2.5.2
Using Featurecounts function (Subread 1.6.3) to generate counts file based on Gencode v90 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Gene level counts

source_name: Colon carcinoma

growth_protocol: Cells were cultured as adherent monolayers in Dulbecco’s Modified Eagle’s Medium (DMEM) (Sigma-Aldrich #D5796) supplemented with 10% (v/v) fetal bovine serum (Bovogen #SFBS-AU), 2mM L-glutamine (Life technologies #25030081), 100 units/mL penicillin and 0.1% (w/v) streptomycin (Life technologies #15140122) (complete DMEM, C-DMEM). Cells were grown at 37°C in a 5% CO2 humidified incubator, and passaged every 2-3 days (30-80% confluency).

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen,#74106) following manufacturer’s instructions.
100bp Paired end

tag: cell line

value: CDK8/19 KO HCT116 cells

tag: crispr knockout

value: CDK8/19KO cells

tag: ercc spike in control

value: ERCC Spike in control


title: DKO-C2-R2


title: DKO-C2-R1


title: DKO-C1+JQ1-R1


title: DKO-C1+JQ1-R2


title: DKO-C1-R3


title: replicate 6-1

tag: tissue


title: DKO-C1-R1


title: DKO-C1-R2


title: SFN_41A_RaGene-1 0-st-v1).CEL

tag: strain

value: Sprague Dawley

tag: gender


title: replicate 2-2

tag: treatment


title: HCT116+JQ1-R3

value: HCT116 control cells

value: Control cells


title: HCT116+JQ1-R2


title: HCT116-R2


title: CDK19KO-C2-R2

value: CDK19KO HCT116 cells

value: CDK19KO cells


title: HCT116-R1


title: CDK19KO-C1-R3


title: replicate 1-2


title: HCT116+JQ1-R1


title: replicate 2-1


title: CDK19KO-C2-R1


title: CDK8KO-C2-R1

value: CDK8KO HCT116 cells

value: CDK8KO cells


title: CDK8KO-C1-R3


title: CDK19KO-C1-R1


title: CDK8KO-C1-R1


title: CDK19KO-C1-R2


title: CDK8KO-C1-R2


title: mESCs_E518K#15+dox

city: Saarbrücken

first: Tim

last: Kehl

address: Campus E2.1, P.O. box 151150

department: Center for Bioinformatics

institute: Saarland University

data_processing:
The paired fastq files were aligned using the STAR aligner (Version 020201).
The mRNA (GENCODE vM18) counts of every protein coding gene and every sample were extracted using bedtools (Version v2.29.2).
The raw counts of every gene were normalized by gene length and library size to create TPM values.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: Embryonic stem cells

growth_protocol: DGCR8 mESC lines were cultured in ES cell medium (DMEM high glucose, 10% FCS, 1% penicillin/streptomycin, 1% MEM non-essential amino acids, 2 mM glutamine, 100 µM β-mercaptoethanol and 1,000 U/mL leukemia inhibitory factor (LIF)) at 37°C with 5% CO2. ES cells were grown under feeder-free conditions in 2i medium (ES cell medium supplemented with 3 µM CHIR99021 and 1 µM PD0325901) on porcine skin gelatin (0.1%) coated cell culture dishes.

extract_protocol:
Total RNA was isolated using peqGold TriFastTM. Quality of the RNA samples was assessed using a Bioanalyzer 2100 (Agilent).
mRNA-sequencing was done by BGI NGS Lab (Hong Kong) on a BGISEQ-500 platform (hexamer-primed oligo-dT selected RNA, 100 bp paired end, ~70 million reads per sample).

treatment_protocol: Cells were treated with 300 ng/mL doxycyline for 48h

value: NBA1-19349, Novus Biochemicals

tag: transfection

value: transfected with pSB ET iE-FlagDGCR8-E518K and pCMV(CAT)-SB100X

value: treated with 300 ng/mL doxycycline for 48h

tag: genotype

value: DGCR8 E518K/E518K


title: pSRKc

source_name: Vector Control

value: pSRKGM vector control


title: mESCs_E518K#8+dox


title: CDK8KO-C2-R3


title: CiSCs1

city: Guangzhou

first: Quan

last: Li

address: West Huangpu Avenue

institute: Jinan University

data_processing:
BGISEQ software used for basecalling.
The raw data for sequencing contains low-quality, linker contamination, and high reads with unknown base N content. These reads need to be removed before data analysis to ensure the reliability of the results.
After getting clean reads, we used HISAT to align clean reads to the reference genome sequence.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample.

source_name: Embryonic Fibroblasts

growth_protocol: MEFs were prepared from 12.5 days or 13.5 days post coitum embryos and MSCs were prepared from testicular tissues. The cells were plated on 90-mm dishes and cultured at a 37°C, 5% CO2 incubator.

extract_protocol:
The Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Then 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using BGISEQ-500 RNASeq(Quantification).

treatment_protocol: The passaged MEFs were seeded onto a 6-well plate and induced by some small molecule compounds after 24 h.

tag: cell type

value: Mouse Embryonic Fibroblasts-indused Sertoli Cells

value: KM mice

tag: age

value: 13.5 days post coitum embryos


title: HCT116-R3


title: CDK19KO-C2-R3


title: MSCs1

source_name: Sertoli Cells

value: Mouse Sertoli Cells

value: post natal day 60


title: MEFs1

value: Mouse Embryonic Fibroblasts


title: CiSCs2

value: Mouse Embryonic Fibroblasts-induced Sertoli Cells


title: mESCs_wt#16+dox

value: transfected with pSB ET iE-FlagDGCR8-wt and pCMV(CAT)-SB100X

value: DGCR8 wt/wt


title: mESCs_wt#12+dox


title: mESCs_KO#261+dox_3

value: non-transfected

value: DGCR8 -/-


title: MEFs2


title: mESCs_KO#261+dox_1


title: CDK8KO-C2-R2

value: CDK8KO HCT116 cells

value: CDK8KO cells


title: MSCs2


title: mch33_2

city: New York

first: Yariv

last: Houvras

state: NY

address: 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Reads were then aligned to the zebrafish genome (GRCz10) using Star v2.3
The Ensemble transcriptome was used to identify genes
Differential gene expression was analyzed using DESeq2
Genome_build: GRCz10
Supplementary_files_format_and_content: DESeq2 was used to normalize gene expression and to identify differentially regulated genes

source_name: melanoma

growth_protocol: Transgenic zebrafish were created by injecting MiniCoopR transposon vectors into Tg(mitfa:BRAF(V600E);p53(M214K;nacre) zebrafish.

extract_protocol:
Total RNA was isolated using Qiagen RNAeasy extraction kit
RNA-seq libraries were prepared according to the Illumina TruSeq RNA protocol. cDNA libraries were then run on the HiSeq platform to obtain 50 bp paired-end reads.

treatment_protocol: Zebrafish were raised until melanomas were identified as visible raised lesions. Melanomas were harvested and RNA was extracted

value: Melanoma

tag: genotype/variation

value: H3 wild type


title: mck9m_3


title: mch33_1


title: mck9m_1


title: K27M_2

value: histone 3 (K27M)


title: K27M_3


title: K27M_1


title: H3_3_4

value: H3 wildtype


title: H3_3_3


title: H3_3_1


title: H3_3_2


title: K27M_4


title: klf15LKO_atac_r1

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: processed data file: klf15LKO_atac.bed

data_processing:
Read Alignment: RNA-seq was aligned to the mm10 genome using STAR (version STAR_2.5.1b) with default parameters. ChIP-seq and ATAC-seq fastq files were aligned to the mm10 genome using BWA with default pipeline parameters.
Read Counting : RNA-seq transcript expression quantification was performed using featureCounts (version 1.6.3) with default parameters to generate gene expression values in units of RPKM. ChIP-seq and ATAC-seq normalized read density in any genomic region was calculated using the Bamliquidator (version 1.0) read density calculator (https://github.com/BradnerLab/pipeline/wiki/bamliquidator). Briefly, ChIP-seq/ATAC-seq reads aligning to the region were extended by 200bp and the density of reads per base pair (bp) was calculated. The density of reads in each region was normalized to the total number of million mapped reads producing read density in units of reads per million mapped reads per bp (rpm/bp).
Peak Calling: Following alignment low quality, improperly paired, and multi-mapped reads were removed using SAMtools (v. 1.7) (samtools view -F 1804 -f 2 -q 30). PCR duplicates were removed using Picard's (v.1.126) MarkDuplicates. Bam files were converted to tagAlign file, ATAC-seq reads were Tn5 shifted, and peaks were called using Peaks calls were done with the MACS2 peak finding algorithm (56) at a significance level of (P< 0.01) and irreproducibility discovery rate (IDR) (5%) (https://projecteuclid.org/euclid.aoas/1318514284) thresholded peaks were used as the final peak set.
Genome_build: mm10
Supplementary_files_format_and_content: final peak bed files (peaks passing IDR threshold of 5%)
Supplementary_files_format_and_content: text file of counts for gene expression

growth_protocol: Mice were housed in a temperature- and humidity-controlled pathogen-free facility with 12-hour light/dark cycle and libitum access to water and standard laboratory rodent chow

extract_protocol:
ChIP-Seq: Liver tissue (∼300 mg) was freshly excised from adult male KLF153xFLAG/WT mice. The ChIP-seq replicates reported in our study are derived from two separate pieces of liver tissue which came from the same mouse.  Liver tissue was minced, crushed, and fixed with 1.1% (wt/vol) formaldehyde for 10 min.  For chromatin preparation, fixed tissue was homogenized in lysis buffer 1 (50mM Hepes pH 7.5, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitor cocktail) using a Dounce homogenizer, then rotated at 4°C for 10 min. Pellet was spun down and resuspended in lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1 mM EDTA, 0.5mM EGTA, protease inhibitor cocktail) for 10 min at 4°C. The pellet was spun down and resuspend pellet in 1 ml sonication buffer (50mM Hepes pH 7.5, 140mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, protease inhibitor cocktail). The sonication buffer with chromatin was then sheared on a BioRuptor (Diagenode, Bioruptor® Plus, UCD-300) with samples continuously cooled at 4°C. The BioRuptor settings used were 30 sec on, 30 sec off with output setting on “high” for a total of 12 cycles. The sonicated chromatin was immunoprecipitated overnight at 4°C using 5g anti-FLAG (Sigma F1804) monoclonal antibody bound Dynabeads (Invitrogen 10004D) followed by extensive washing and elution. Input and immunoprecipitated chromatin were then reverse-cross-linked followed by purification of genomic DNA, which was then subject to library preparation and next generation sequencing. RNA-Seq: For RNA isolation from mouse tissues, tissue samples were disrupted/homogenized in TRIzol (Thermo Fisher) in a TissueLyser (Qiagen) using stainless steel beads (QIAGEN) at 30 Hz for a total of 4 min. Total RNA was isolated using Aurum Total RNA Fatty and Fibrous Tissue kit (Bio-Rad, 7326870). ATAC-seq: Primary hepatocytes were isolated from liver tissues of KLF15-LKO mice and Klf15flox/flox control mice. For each sample, 50,000 cells were pelleted after washing once with 1ml PBS. Cell pellets were then resuspended in 50mL cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) and incubated on ice for 3 min. 1ml cold wash buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20) was then added to the lysis. The sample was centrifuged at 500g for 10 min at 4°C. The pelleted nuclei were resuspended in 50mL transposition mixture [25mL 2X Tagment DNA buffer, 5mL of Tagment DNA Enzyme (Nextera Sample Prep Kit from Illumina, FC-121-1030, 16.5ml PBS, 0.5ml 0.1% digitonin, 0.5ml 10% Tween-20, 2.5ml H2O], and incubated at 37°C for 2hr in a thermomixer with 1000 rpm mixing. Transposed DNA was purified with MinElute Reaction Cleanup Kit (Qiagen, 28204) and eluted in 21mL water
ChIP-Seq: Purified DNA were quantified using Qubit fluorometric analysis and assessed for quality using Agilent Bioanalyzer Nano DNA Chip. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit from Illumina (NEB, E7645). Libraries were sequenced on a NextSeq 500/550 at the Genomics Core of The Gladstone Institutes (paired-end, 75 base pairs, >40M reads per sample). RNA-Seq: RNA-seq libraries were prepared with the Ovation Solo RNA-Seq kit (NuGEN). The final libraries were analyzed by Agilent Bioanalyzer Nano RNA Chip and quantified by KAPA qPCR. The library was then sequenced on an Illumina HiSeq 2500 at the Genomics Core of Gladstone Institutes. ATAC-Seq: Purified DNA was amplified using 25mL of NEBNext High Fidelity 2x PCR Master Mix, 1.25 mM Nextera custom primers with unique barcodes, and nuclease-free water. Samples were amplified using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and cycled at 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. Half of each sample was amplified for 12 cycles, purified, and assessed by Bioanalyzer (Agilent) for library quality. Sample concentration was quantified by Qubit (Invitrogen) prior to pooling. Pooled samples were sequenced on a NextSeq 500/550 at the Genomics Core of Gladstone Institutes (paired-end, 75 base pairs, >80 M reads per sample)

tag: strain background

value: 14-20 weeks

value: Alb1-Cre / KLF15flox/flox

value: liver


title: klf15LKO_atac_r2

description: processed data file: klf15LKO_atac.bed


title: control_atac_r2

description: processed data file: control_atac.bed


title: mESCs_E518K#15+dox

data_processing:
The paired fastq files were aligned using the STAR aligner (Version 020201).
The miRNA (miRBase v22) and piRNA (piRNAdb v1_7_5) counts of all samples were extracted using bedtools (Version v2.29.2).
Since the miRNA content in the cells varies due to the mutation and knock-out of the DCGR8 gene, a cusom normalization procedure was used that scales RPM values based on the piRNA content of the cells (see manuscript).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw counts for every miRNA and every sample
Supplementary_files_format_and_content: Matrix table with raw counts for every piRNA and every sample
Supplementary_files_format_and_content: Matrix table with normalized expression values (proportional RPM values - pRPM) for every miRNA and every sample.

extract_protocol:
Total RNA was isolated using peqGold TriFastTM. Quality of the RNA samples was assessed using a Bioanalyzer 2100 (Agilent).
Sequencing libraries were generated using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® according to the manufacturer’s protocol.

value: NBA1-19349, Novus Biochemicals

value: transfected with pSB ET iE-FlagDGCR8-E518K and pCMV(CAT)-SB100X

value: treated with 300 ng/mL doxycycline for 48h

value: DGCR8 E518K/E518K


title: mESCs_E518K#13+dox


title: control_atac_r1

description: processed data file: control_atac.bed


title: Muscle-Rbx1-deficient-rep2

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

description: Gene expression data from Rbx1-deficient Treg cells in mice

hyb_protocol: Samples were hybridized to Clariom S Arrays, mouse (Affymetrix, 902931).

data_processing: Microarray data sets were analyzed with Applied Biosystems Expression Console Software 1.4.

source_name: peripheral lymph nodes and spleens of mice (8-12 weeks old)

label_protocol: RNA samples were reverse transcribed, amplified, labeled (Affymetrix GeneChip pico kit, 703308).

growth_protocol: Mice were maitain in SPF condition until they were killed.

extract_protocol: RNA samples were prepared with the miRNeasy Mini Kit (Qiagen, 21704).

treatment_protocol: Peripheral lymph nodes and spleens were harvested from mice with indicated genotypes, and grinded into single cells, followed by treatment with Dynabeads™ Untouched™ Mouse CD4 Cells Kit (Invitrogen, 11415D) to isolate the CD4+ T cells. The FACS sorting (SONY Cell Sorter, SH800S) was used to isolate the CD4+YFP+ Treg cells with purities > 99%.

tag: treg cells

value: peripheral lymph nodes and spleens


title: mESCs_E518K#8+dox


title: shr replicate 3

city: Seoul

first: Souvik

last: Dhar

state: Gwanak gu

address: 1, Gwanak ro

country: South Korea

institute: Seoul National University

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix Arabidopsis ATH1 Genome Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Microarray Suite version 5.0 (MAS 5.0) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called Present by the MAS5 detection call in 100% of the samples were selected.  Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label: Biotin

organism: Arabidopsis thaliana

source_name: shr mutant

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® 3’ IVT Express Kit User Manual P/N 702646 Rev. 1, Affymetrix).

growth_protocol: Seedlings were plated on half MS medium and allowed for germination for 24 hours.Then they were grown in dark for 5 days on half MS medium. The hypocotyl part were excised from the seedlings and were used for RNA isolation.

extract_protocol: RNeasy plant mini kit (Qiagen), according to manufacturer protocol.

value: hypocotyl

tag: ecotype

value: Columbia


title: Muscle-Ube2m-deficient-rep2

description: Gene expression data from Ube2m-deficient Treg cells in mice


title: shr replicate 2


title: mESCs_wt#12+dox

value: transfected with pSB ET iE-FlagDGCR8-wt and pCMV(CAT)-SB100X

value: DGCR8 wt/wt


title: mESCs_wt#16+dox


title: Col-0 replicate 2

source_name: wild type

value: Wild type


title: Muscle-Ube2m-deficient-rep1


title: Muscle-Rbx1-deficient-rep1


title: Muscle-wt-rep1

description: Gene expression data from Treg cells in mice

value: WT


title: Muscle-Rbx1-deficient-rep3


title: Col-0 replicate 3


title: Col-0 replicate 1


title: Muscle-wt-rep3


title: Muscle-wt-rep2


title: input_ChIP_r1


title: klf15_ChIP_r1

description: processed data file: klf15_ChIP_peaks.bed


title: klf15_ChIP_r2


title: mESCs_E518K#8

value: untreated


title: shr replicate 1


title: input_ChIP_r2


title: Muscle-Ube2m-deficient-rep3


title: mESCs_KO#261+dox_2

value: non-transfected

value: DGCR8 -/-


title: mESCs_KO#261+dox_3


title: mESCs_wt#10


title: mESCs_wt#10+dox


title: mESCs_KO#261+dox_1


title: Tex15ko-d2_2

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Sequenced reads were mapped to reference genome either in unique or multiple mapping mode.
The alignments in the unique mapping mode were used to evaluate expression of protein coding genes and individual repeats. For this, we used STAR for alignment with the default parameters. The annotation of genes and individual repeats were acquired from UCSC RefSeq annotation and RepeatMasker, separately. Number of reads mapping to genes and repeats were determined by using FeatureCount. Differential gene and repeat expression was determined by using edgeR, with a FDR cutoff of 5%.
The alignments in the multiple mapping mode were used to evaluate repeat families. Before alignment, adapters were trimmed and reads mapping to ribosomal RNA (GenBank identifiers: 18S NR_003278.3, 28S NR_003279.1, 5S D14832.1, 5.8S K01367.1) by up to three mismatches were discarded. We used Bowtie for alignment, keeping reads that map up to 10,000 sites. Each mapping read was assigned a score of 1/N, where N is the number of sites in the genome the read mapped to. Expression values for each repeat family was calculated by adding the scores contained within the repeat body, divided by the total million reads mapped and average length of repeats (kb) within the family. Differential expression for each repeat family was determined by simple t-test and FDR correction.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample ...

source_name: male germ cells

growth_protocol: Male germ cells were flow-sorted based on green fluorescence (GFP).

extract_protocol:
RNA extraction by PicoPure RNA Isolation Kit (Cat# KIT0202) from ARCTURS
RNA-seq libraries were made by using Ovation RNA-Seq System V2 (Part No.7102) and Ovation Ultralow System V2 1-16 (Part No.0344) from NuGEN

value: mixed

value: postnatal day 2 (d2)

tag: isolation

value: GFP flow sorting

value: male

value: germ cells


title: Tex15ko-d2_3


title: Tex15ko-d2_1


title: Tex15ht-d2_1


title: Tex15ht-d2_2


title: Tex15ko-e18.5_1

value: embryonic day 18.5 (e18.5)


title: Tex15ko-e18.5_3


title: Tex15ko-d2_4


title: Tex15ht-e18.5_2


title: Tex15ht-e18.5_3


title: Tex15ko-e18.5_2


title: Tex15ht-d2_4


title: Tex15ko-e16.5_3

value: embryonic day 16.5 (e16.5)


title: Tex15ko-e16.5_1


title: Tex15ko-e16.5_2


title: Tex15ht-e16.5_3


title: Tex15ht-e18.5_1


title: Tex15ht-e16.5_1


title: Tex15ht-e16.5_2


title: HCT116 BRD4

description: HCT116 -WT

data_processing:
Basecalls performed using BWA algorithm with default settings
ChIP-seq reads were aligned to the human genome (hg38) using the BWA algorithm.
The tags are extended in silico at their 3 ́- ends to a length of 200bp. To identify the density of fragments  along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.
Peaks were callled using Model-based Analysis of ChIP-Seq (MACS) to identify significant enrichments in the ChIP/IP data file when compared to the Input data file.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files contains the density of fragments in every 32-nt bin of the genome.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on a NexSeq 500 (100 bp, single end reads).

value: Parental

tag: chip antibody

value: BRD4; 91301 (Active motif)


title: DKO-C2 BRD4

tag: cell line

value: CDK8/19 KO-C1


title: Pooled Input

tag: crispr knockout

value: Parental-CDK8/19 KO-C1-CDK8/19 KO-C2


title: DKO-C1 RNAPOLII

value: RNA pol II; 39097 ( Active motif)


title: DKO-C1 MED12

value: MED12; A300-774A - M  (Bethyl Laboratories)


title: DKO-C2 RNAPOLII

value: CDK8/19 KO-C2


title: HCT116 RNAPOLII

description: HCT116 -WT


title: HCT116 MED12

description: HCT116 -WT


title: Tex15ht-d2_3


title: DKO-CL2 H3K27AC

value: H3K27Ac; 39685 (Active motif)


title: HCT116 H3K27AC

description: HCT116 -WT


title: miR-6126 transfected-1

city: Takamatsu

first: Koji

last: Fujita

state: Kagawa

address: Saiwai 1-1

institute: Kagawa University

data_processing:
Gene expression level was calculated using CLC Genomics Workbench version 12.0.4 (CLC bio, Aarhus, Denmark) based on the hg19 reference sequences. After the quality control based on the default parameters of base calling, the reads were trimmed and analyzed for the differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: Genes expressed in all samples, including samples transfected by miR-6126 and their negative control, were quantified as transcripts per million values.

source_name: HepG2-NTCP cell line

growth_protocol: HepG2-NTCP cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Life Technologies, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS, 100 U/mL penicillin, 100 µg⁄mL streptomycin and 100 U/mL nonessential amino acids; Life Technologies).

extract_protocol:
RNA was extracted using RNeasy Mini kit (Qiagen, Venlo, the Netherlands).
Gene expression was evaluated using the AmpliSeq™ Transcriptome Human Gene Expression Kit (ThermoFisher Scientific). Complementary DNA (cDNA) was generated with SuperScript® VILO™ cDNA Synthesis Kit using 4 ng of total RNA followed by library preparation using Ion AmpliSeq technology and the human gene expression core panel to generate barcoded libraries.

treatment_protocol: MiRNA mimics (Thermo Fisher Scientific, Waltham, Massachusetts) were transfected using Lipofectamine RNAiMAX® Reagent (Thermo Fisher Scientific, Waltham, Massachusetts) and Opti-MEM® (Thermo Fisher Scientific, Waltham, Massachusetts) according to the manufacturer’s protocol. MiRNA mimics were used at a final concentration of 50 nM.

value: NTCP-transgenic hepatoma cell line

value: miR-6126 transfection


title: DKO-C2 MED12


title: Negative control-2

value: MOC


title: sRNA uvr8 30K III

city: Saint Paul

first: Stefanie

last: Dukowic-Schulze

state: Minnesota

address: 1970 Folwell Avenue

department: Horticultural Science

institute: University of Minnesota

data_processing:
FastQC for quality control
Cutadapt for trimming
ShortStack for alignment, with annotation file extracted from Gramene BIOMART (www.gramene.org) and reduced from 2643 to 2071 total entries by removing duplicates
Genome_build: Arabidopsis_thaliana.TAIR.10.35.gtf
Supplementary_files_format_and_content: Tables with raw and normalized read counts for all samples (RPM for all sRNAs or just miRNAs), plus means and standard errors of replicates.

source_name: etiolated hypocotyl

growth_protocol: Arabidopsis seeds were sterilized, sowed onto filter paper with 0.5x MS medium with 100 µM GA4, then kept in the absolute dark. After 2.5 days, seeds germinated and were exposed to UV-B, and then put back into the dark.

extract_protocol:
6 hours after UV-B exposure, hypocotyls were excised and put into Trizol reagent. Zymoresearch DirectZol RNA MicroPrep kit was used for extraction of total RNA.
Clontech SMARter smRNA

treatment_protocol: Germinating seeds were exposed to UV-B for different duration (~5min or ~45min) to achieve the desired UV-B dosage

value: 30K µmol m-2 UV-B

value: etiolated hypocotyl


title: DKO-C1 H3K27AC


title: klf15LKO_rna_r4

description: processed data file: rna_counts.txt

value: 14-20 weeks

value: Alb1-Cre / KLF15flox/flox

value: liver


title: control_rna_r3

description: processed data file: rna_counts.txt


title: klf15LKO_rna_r3

description: processed data file: rna_counts.txt


title: Negative control-3


title: control_rna_r1

description: processed data file: rna_counts.txt


title: miR-6126 transfected-3


title: control_rna_r4

description: processed data file: rna_counts.txt


title: sRNA uvr8 3K II

value: 3K µmol m-2 UV-B


title: control_rna_r2

description: processed data file: rna_counts.txt


title: sRNA uvr8 3K III


title: klf15LKO_rna_r1

description: processed data file: rna_counts.txt


title: sRNA uvr8 0K III

value: dark control


title: sRNA uvr8 3K I


title: Negative control-1


title: klf15LKO_rna_r2

description: processed data file: rna_counts.txt


title: sRNA uvr8 30K II


title: sRNA uvr8 0K II


title: sRNA uvr8 30K I


title: sRNA xpf 30K II


title: sRNA xpf 3K III


title: sRNA xpf 30K I


title: sRNA xpf 30K III


title: miR-6126 transfected-2


title: sRNA xpf 3K II


title: sRNA xpf 3K I


title: sRNA xpf 0K III


title: sRNA xpf 0K II


title: sRNA uvr8 0K I


title: sRNA xpf 0K I


title: sRNA WT 30K III

value: WT (Columbia-0)


title: sRNA WT 3K II


title: sRNA WT 3K III


title: mRNA uvr8 30K I

data_processing:
A University of Minnesota Genomics Center pipeline ("Gopher-Pipeline") was used, including:
FastQC for quality control (v0.11.5)
Trimmomatic for quality trimming (v0.33)
HiSat2 for alignment
Genome_build: Arabidopsis_thaliana.TAIR.10.35.gtf
Supplementary_files_format_and_content: Table with raw read counts
Supplementary_files_format_and_content: Table with normalized read counts for all samples (TMM normalization by DEseq2), plus means and standard errors of replicates.

extract_protocol:
6 hours after UV-B exposure, hypocotyls were excised and put into Trizol reagent. Zymoresearch DirectZol RNA MicroPrep kit was used for extraction of total RNA.
Illumina TruSeq stranded RNA libraries


title: sRNA WT 0K III


title: mRNA uvr8 30K II


title: sRNA WT 0K II


title: sRNA WT 30K I


title: sRNA WT 30K II


title: mRNA uvr8 30K III


title: mRNA uvr8 3K II


title: mRNA uvr8 0K I


title: mRNA uvr8 3K I


title: mRNA xpf 30K III


title: mRNA uvr8 0K III


title: mRNA xpf 30K II


title: mRNA xpf 3K II


title: sRNA WT 0K I


title: sRNA WT 3K I


title: mRNA xpf 3K III


title: mRNA uvr8 3K III


title: mRNA uvr8 0K II


title: mRNA xpf 3K I


title: mRNA xpf 0K III


title: mRNA xpf 0K II


title: mRNA xpf 0K I


title: mRNA WT 3K III


title: mRNA WT 30K I


title: mRNA WT 30K II


title: mRNA WT 3K I


title: mRNA WT 3K II


title: mRNA WT 0K III


title: mRNA WT 30K III


title: mRNA xpf 30K I


title: mRNA WT 0K II


title: mRNA WT 0K I


title: Patient3 normal ovarian tissues

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

institute: The Affiliated Cancer Hospital of Nanjing Medical University

data_processing:
nonr provided by the submitter
Genome_build: hg38

source_name: ovary

extract_protocol: none provided by the submitter

value: normal ovarian tissues

tag: age (years)

tag: Stage

value: FIGO III


title: Patient1 ovarian cancer tissue

tag: tissue

value: ovarian tumors


title: Patient2 ovarian cancer tissue