title: h1_heat_rep2

city: Uppsala

first: Minerva

middle: Susana

last: Trejo Arellano

state: Uppsala

address: Almas Allé 5

department: Plant Biology

country: Sweden

institute: SLU

description:
10 days old seedlings
h1_heat_MX_CG.txt.gz
h1_heat_MX_CHG.txt.gz
h1_heat_MX_CHH.txt.gz

data_processing:
Quality control was done with an in-house R script
Bisulfite-seq: The 150 bp long pair-end reads were first quality trimmed by removing the first 5 bases from the 5' end and the last 20 bases from the 3' end. Reads were mapped to the reference genome TAIR10 in PE mode (--score_min L,0,-0.6) using Bismark v0.16.3. Mapped reads were deduplicated and cytosine methylation values calculated using the Bismark Methylation Extractor. CX methylation reports were pooled for both replicates for further analyses.
RNA-seq: Untrimmed reads were mapped to the TAIR10 Arabidopsis reference genome using STAR (v2.5.3.a, (Dobin et al., 2012) ). Expression counts were generated using the R function summarizeOverlaps from the package HTSeq in union mode on exons from the reference transcriptome AtRTD2 (Zhang et al., 2017) . Differential expression analyses were performed using the R package DESeq2 [v1.20.0, (Love et al., 2014) ]. Genes with absolute log2FoldChange ≥ 1 and FDR ≤ 0.05 were considered as differentially expressed, using either genotype or unstressed condition and the control. Similarly, expression counts along TEs were generated using the R function summarizeOverlaps from the package HTSeq in union mode along the coordinates of the 31,189 TAIR10 annotated TEs. Differential expression analyses were performed using DESeq2 and the same threshold values as for gene transcripts. Subsequent analysis were performed in R. The gene and transposable element models used were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per condition were created. These reports have the  following format: <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: For the RNA-seq, tables with the values of the differential expression analysis for genes and TEs are presented in text files

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Plants were grown on plates with ½ MS medium including vitamins (Duchefa, Haarlem, The Netherlands) and 1% sucrose. Zebularine treated plants were grown on ½ MS medium supplemented with 40 um zebularine (Abcam). Plates were sealed with micro-pore tape and stratified for two days at 4°C in the dark. The plates were then transferred to a growth chamber with 16 h light (110 µmol m-2 s-1, 22°C) and 8 h dark (20°C) periods. Ten-day-old seedlings were used for RNA extraction.

extract_protocol:
RNA extraction of three biological replicates (50mg plant material per replicate) was performed using an RNeasy Plant Mini Kit (Qiagen).
Genomic DNA was extracted using a MagJET Plant Genomic DNA Kit (K2761).
RNA seq libraries were generated using DNA-free RNA with the TruSeq RNA Library Prep Kit v2 (Illumina) according to manufacturer’s instructions. Sequencing was performed on an Illumina HiSeq2000 in 50-bp single-end mode.
BSeq libraries for two replicates were prepared by Novogene (Hongkong, China) and sequenced on an Illumina HiSeq2000 in 150-bp paired-end mode.

treatment_protocol: For heat stress treatments we incubated 10-day-old seedlings at 4 °C for 1h followed by 37 °C for 24h in the dark, as previously published (Shen et al., 2014).

tag: ecotype

value: Columbia

value: Heat treated

tag: biological replicate


title: GTT89_Fat_Tregs

status: Public on Oct 23 2020

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
Fat Treg Neuropilin-high cells: GTT89 mother (Rank Foxn1 KO)
GTT89_FAT_Treg_S51706

library_source: transcriptomic

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 and 3.3.52 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.3 and 2.7.7.
BCL to BAM file conversion and demultiplexing with Illumina2bam 1.17 (http://wtsi-npg.github.io/illumina2bam/) and custom programmes based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.11 package DESeq2 1.28.1, running under R 4.0.2.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

molecule: total RNA

organism: Mus musculus

source_name: fat

extract_protocol:
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

tag: strain

tag: tissue

value: fat

tag: cell type

value: regulatory T-cell

tag: gender

value: female

tag: genotype

value: Tnfrsf11a (Rank) Foxn1 knock-out

tag: pregnancy status

value: pregnant


title: GTT92_Fat_Tregs

description:
FAT Treg Neuropilin-high cells: GTT92 mother (Rank Foxn1 KO)
GTT92_FAT_Treg_S51709


title: GTT88_Fat_Tregs

description:
Fat Treg Neuropilin-high cells: GTT88 mother (Rank Wt)
GTT88_FAT_Treg_S51701

value: Tnfrsf11a (Rank) Foxn1 wild-type


title: wt_heat_rep2

description:
10 days old seedlings
wt_heat_MX_CG.txt.gz
wt_heat_MX_CHG.txt.gz
wt_heat_MX_CHH.txt.gz

library_source: genomic

molecule: genomic DNA

value: WT

tag: treatment


title: GTT88_Spleen_Tregs

description:
Splenic Treg Neuropilin-high cells: GTT88 mother (Rank wt) duplicate
GTT88_Spl_Treg_2_S51704

source_name: spleen

value: spleen


title: GTT91_Fat_Tregs

description:
FAT Treg Neuropilin-high cells: GTT91 mother (Rank Wt)
GTT91_FAT_Treg_S51710


title: GTT87_Spleen_Tregs

description:
Splenic Treg Neuropilin-high cells: GTT87 mother (Rank wt) duplicate
GTT87_Spl_Treg_2_S51705


title: CNTL-13-01-I

city: Los Angeles

first: Ivette

last: Zelaya

state: CA

address: 695 Young Drive South, Rm 1524 Gonda

country: USA

institute: University of California, Los Angeles

data_processing:
Reads were aligned to the human genome using STAR RNA-seq aligner v2.5.0a with default parameters.
Read counts were generated using HTSeq-count algorithm.
Genome_build: hg19
Supplementary_files_format_and_content: Gene count data in tab-delimited format

organism: Homo sapiens

source_name: Iliopsoas

extract_protocol:
The total RNA was then extracted RNeasy Plus Mini Kit according to manufacturer’s instructions
The RNA-seq libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

value: Iliopsoas

tag: disease state

value: Control


title: CNTL-13-01-D

source_name: Diaphragm

value: Diaphragm


title: CNTL-12-05-I


title: RCM-1_MTA 0 h_rep1

type: RNA

city: Kagoshima

first: Shigehisa

last: Okamoto

address: 1-21-24 Korimoto

department: Food Science and Biotechnology

country: Japan

institute: Kagoshima University

description: Gene expression data from RCM-1 human colorectal cancer cells treated with methylthioacetic acid for 0 h.

hyb_protocol: Following fragmentation, 12.5 µg of cRNA were hybridized for 16 h on Human Genome U133 Plus 2.0 Array. Arrays were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console to summarize the probe set intensity data of all genes on each array and then normalize the average intensity of the experimental array to that of the baseline array.

label: biotin

source_name: Colorectal cancer cells, methylthioacetic acid, 0 h

label_protocol: Biotinylated cRNA were prepared from total RNA with 3’ IVT Express kit.

growth_protocol: RCM-1 human colorectal cancer cells were cultured at 37°C in 5% CO2 atmosphere, in a medium made up of equal volumes of RPMI 1640 and Ham’s F12 containing 10% FBS and 10 μg/mL gentamicin.

extract_protocol: Extraction of total RNA was performed using the SV Total RNA Isolation System according to the manufacturer’s instructions (Promega).

treatment_protocol: RCM-1 human colorectal cancer cells were treated with either 1 mM methylthioacetic acid or vehicle (0.1% acetonitrile) for 0, 6, 12, and 18 h. Then, the medium was replaced with the vehicle medium and further cultured for up to 24 h after chemical application. The chemical-treated RCM-1 cells were directly subjected to RNA extraction.

value: rectum

tag: cell line

value: colorectal cancer cell

tag: grade

value: well-differentiated

tag: agent

value: control

tag: time

value: 0 h


title: CNTL-12-05-D


title: 4ABP treated BC

first: weibo

last: yu

address: Los Angeles

institute: UCLA

hyb_protocol: The Affymetrix WT PLUS Reagent Kit was used to prepare the RNA for hybridization to the HTA.

scan_protocol: Global gene expression profiles of the cells were generated using the Affymetrix GeneChip Human Transcriptome Array (HTA) 2.0 system.

data_processing: Data analysis was performed using the Affymetrix Expression Console software and Transcriptome Analysis Console software. Ingenuity Pathway Analysis (IPA) was followed to compare the changes in gene expression in different signaling pathways.

source_name: uroepithelium

label_protocol: Gene expression profiles of the cells were tested using the Affymetrix GeneChip Human Transcriptome Array 2.0 system. Nucleic acid was labeled with biotin.

growth_protocol: Cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) streptomycin/penicillin (S/P).

extract_protocol: Total RNA was extracted from treated and untreated cells using a TRIzol reagent (Thermo Fisher Scientific). The RNA samples were then applied to a RNeasy Mini spin column for purification (RNeasy Miniprep Kit, Qiagen).

treatment_protocol: Cultured HUC-BC, HUC-PC and MCT-11 cells in 50% confluency were treated with 200 µM 4-ABP. Cells were exposed for 48 hours prior to harvesting for mechanotype analysis.

value: uroepithelial cell line

value: HUC-BC

value: 4ABP treated


title: wt_heat_rep1

value: Columbia

value: Heat treated


title: RCM-1_MTA 12 h_ rep1

description: Gene expression data from RCM-1 human colorectal cancer cells treated with methylthioacetic acid for 12 h.

source_name: Colorectal cancer cells, methylthioacetic acid, 12 h

value: methylthioacetic acid


title: GTT87_Fat_Tregs

description:
Fat Treg Neuropilin-high cells: GTT87 mother (Rank Wt)
GTT87_FAT_Treg_S51702

value: fat

value: regulatory T-cell

value: female

value: Tnfrsf11a (Rank) Foxn1 wild-type

value: pregnant


title: GTT34_T

description:
Thymus Treg Neutropilin-high cells: GTT34 mother (Rank Wt)
GTT34_T_S13937

source_name: thymus

value: thymus

value: non-pregnant


title: RCM-1_MTA 6 h_ rep1

description: Gene expression data from RCM-1 human colorectal cancer cells treated with methylthioacetic acid for 6 h.

source_name: Colorectal cancer cells, methylthioacetic acid, 6 h

value: rectum

value: colorectal cancer cell

value: 6 h


title: IGROV1-R10 cells, control miRNA transfection

city: Paris

first: Loredana

last: Martignetti

address: 26, rue d'Ulm

country: France

institute: Insitut Curie/ INSERM U900 / Mines Paris Tech

description: human ovarian carcinoma cell line

hyb_protocol: Labeled and fragmented ss-cDNA (5.5 ug) was hybridized to Affymetrix arrays (Genechip HTA human array)

scan_protocol: GC30007G scanner

data_processing: The data obtained for the whole set of samples were normalized by RMA process (Affymetrix Expression Consol). Probe-set annotation, quantitative expressions of all the transcripts and comparisons between the different groups of samples were analyzed using the Affymetrix software TAC.v3

label: biotin-labeled single-strand cDNAs

label_protocol: Sample RNAs (100 ng) were converted to biotin-labeled single-strand cDNAs using the Affymetrix Genechip WT Plus

growth_protocol: IGROV1-R10 25 µM HEPES, 10% Fetal Calf Serum and 33 mM sodium bicarbonate (ThermoFisher Scientific, Illkirch, France)

extract_protocol: Total RNA extracted with Trizol following provider protocol

treatment_protocol: Twenty four hours after seeding, miRNA duplexes were diluted in OptiMEM (Life Technologies, Saint Aubin, France) and cells were transfected using INTERFERin (Polyplus-Transfection, Strasbourg, France) according to manufacturer’s protocol with indicated miRNA to a final concentration of 20 nM

tag: transfection

value: control miRNA transfection


title: h1_rep2

description:
10 days old seedlings
h1_MX_CG.txt.gz
h1_MX_CHG.txt.gz
h1_MX_CHH.txt.gz

value: Not treated


title: IGROV1-R10 cells, miR-491-5p transfection

description: human ovarian carcinoma cell line

value: miR-491-5p transfection


title: CNTL-12-02-I

value: Iliopsoas

value: Control


title: CNTL-12-02-D

value: Diaphragm


title: h1_rep1

value: Columbia


title: GTT28_T

description:
Thymus Treg Neutropilin-high cells: GTT28 mother (Rank Wt)
GTT28_T_S13932


title: GTT27_T

description:
Thymus Treg Neutropilin-high cells: GTT27 mother (Rank Wt)
GTT27_T_S13931


title: GTT26_T

description:
Thymus Treg Neutropilin-high cells: GTT26 mother (Rank KO)
GTT26_T_S13930

value: Tnfrsf11a (Rank) Foxn1 knock-out


title: h1_heat_rep1

description:
10 days old seedlings
h1_heat_MX_CG.txt.gz
h1_heat_MX_CHG.txt.gz
h1_heat_MX_CHH.txt.gz

value: Heat treated


title: SMA-14-04-I

value: SMA case


title: GTT24_T

description:
Thymus Treg Neutropilin-high cells: GTT24 mother (Rank KO)
GTT24_T_S13928

value: regulatory T-cell

value: female


title: GTT25_T

description:
Thymus Treg Neutropilin-high cells: GTT24 mother (Rank KO)
GTT25_T_S13929

value: thymus


title: wt_rep2

description:
10 days old seedlings
wt_MX_CG.txt.gz
wt_MX_CHG.txt.gz
wt_MX_CHH.txt.gz

value: WT


title: SMA-14-04-D


title: GTT23_T

description:
Thymus Treg Neutropilin-high cells: GTT23 mother (Rank Wt)
GTT23_T_S13927

value: Tnfrsf11a (Rank) Foxn1 wild-type

value: non-pregnant


title: GTT33_T

description:
Thymus Treg Neutropilin-high cells: GTT33 mother (Rank KO)
GTT33_T_S13936


title: cmt2_trt_R3

description:
10 days old seedlings
DESeq_cmt2_trt_vs_untrt_df_TE.txt
DESeq_cmt2_vs_Col_trt_df_TEs.txt
DESeq_cmt2_vs_Col_trt_df_genes.txt
DESeq_cmt2_trt_Col_untrt_df_genes.txt
DESeq_cmt2_trt_Col_untrt_df_TEs.txt


title: wt_rep1


title: SMA-12-01-I


title: cmt2_trt_R2


title: cmt2_trt_R1


title: E. coli rpoB(T1037P) rpoB(S508P) + 7.5 μM rifampicin replicate 3

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

description:
SC-78RS-EC-SC-92_S44_L004_R1_001
processed data file: CLC_processed_counts.txt

data_processing:
FastQ files from Illumina HiSeq were processed using CLC genomics workbench (Qiagen), RNA-seq data analysis pipeline. Reads were mapped to the Escherichia coli genome (accession CP009273.1).
Differential expression was further assessed using DESeq2 with the “apeglm” shrinkage estimator yielding log2 fold changes and single-gene p-values.
Genome_build: GenBank accession CP009273.1 (Escherichia coli BW25113)
Supplementary_files_format_and_content: CLC_processed_counts.txt: Tab-delimited text file includes abundance measurements.

organism: Escherichia coli BW25113

source_name: whole bacterial cells

growth_protocol: We isolated RNA for sequencing from both parent strains (pykF(C8Y) and rpoB(T1037P), which grow faster than wild-type in M9-glucose), and their rifampicin-resistant derived strains in triplicate, in both M9G and M9G+Rif; cells were grown and harvested across three separate days. The growth protocol to prepare cultures for RNA isolation was as follows: All strains were cultivated in M9G at 37°C; starter cultures were diluted to OD600 = 0.01 in M9G and grown at 37°C with or without 7.5 mg/ml rifampicin to an OD600 of ~0.18-0.22.

extract_protocol:
RNA was extracted by pelleting cells for 30 seconds and rapidly resuspending the pellets in 1mL Trizol (Invitrogen, Life Technologies). RNA was extracted from the Trizol suspension using the manufacturer’s protocol. The extracted RNA was next treated with Turbo DNase (Ambion, Life Technologies) and further purified using an RNA purification kit (Qiagen). Absence of DNA contamination was confirmed by PCR, where the lack of PCR product (about 100 bp in length) relative to a DNA-containing positive control was interpreted as evidence of DNA removal.
RNA-seq libraries were prepared with an Illumina TruSeq stranded RNA kit according to manufacturer's instructions.

treatment_protocol: We were assessing transcript levels across multiple genetic backgrounds, when cells were cultivated in M9G either with or without rifampicin added.

value: Whole bacterial cells

tag: genotype/variation

value: rpoB(T1037P) rpoB(S508P)

tag: medium

value: M9 + glucose + 7.5 uM rifampicin


title: SMA-12-01-D


title: E. coli rpoB(T1037P) rpoB(S508P) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-91_S43_L004_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(S508P) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-90_S42_L004_R1_001
processed data file: CLC_processed_counts.txt


title: cmt2_untrt_R3

description:
10 days old seedlings
DESeq_cmt2_trt_vs_untrt_df_TE.txt
DESeq_cmt2_vs_Col_untrt_df_TEs.txt
DESeq_cmt2_vs_Col_untrt_df_genes.txt
DESeq_cmt2_vs_Col_trt_df_TEs.txt
DESeq_cmt2_vs_Col_trt_df_genes.txt

tag: ecotype

value: Not treated


title: SMA-10-16-D


title: E. coli rpoB(T1037P) rpoB(S508P) replicate 3

description:
SC-78RS-EC-SC-89_S41_L004_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose


title: cmt2_untrt_R2

tag: biological replicate


title: E. coli rpoB(T1037P) rpoB(I572F) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-110_S62_L005_R1_001
processed data file: CLC_processed_counts.txt

value: rpoB(T1037P) rpoB(I572F)


title: E. coli rpoB(T1037P) rpoB(S508P) replicate 2

description:
SC-78RS-EC-SC-88_S40_L004_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(I572F) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-109_S61_L005_R1_001
processed data file: CLC_processed_counts.txt


title: cmt2_untrt_R1


title: E. coli rpoB(T1037P) rpoB(S508P) replicate 1

description:
SC-78RS-EC-SC-87_S39_L004_R1_001
processed data file: CLC_processed_counts.txt


title: SMA-08-02-I

value: Iliopsoas


title: PlCS.1: WT_Muscle_Smoke_Rep_1

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

data_processing:
Bluebee’s genomics analysis platform
Sequencing targeted mean 7 million 65-nt single-stranded reads per sample, which were mapped to the mouse transcriptome and quantified as transcripts per million mapped reads using the STAR aligner. All sequencing data were uploaded to Illumina’s BaseSpace in real-time for downstream analysis of quality control. Raw Illumina (fastq.gz) sequencing files were downloaded from BaseSpace, and uploaded to Bluebee’s genomics analysis platform (https://www.bluebee.com) to align reads against the mouse genome.
After combining treatment replicate files, a DESeq2 application within Bluebee (Lexogen Quantseq DE 1.2) was used to identify significant treatment-related effects on transcript abundance (relative to controls) based on a false discovery rate (FDR) p-adjusted value <0.1.
Genome_build: mm9
Supplementary_files_format_and_content: csv file contains raw gene counts for every gene and every sample

source_name: Muscle

extract_protocol:
Plantaris muscles were removed, flash frozen, and RNA was harvested using the RNeasy Tissue Mini Kit (Qiagen), according to manufacturer’s instructions. RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
RNA libraries were prepared for sequencing using  manufacturer’s instructions  (Lexogen QuantSeq 3′ FWD)

tag: strain

value: Plantaris muscle

value: wild type

value: Exposed to tobacco smoke for 16 weeks


title: Col_trt_R3

description:
10 days old seedlings
DESeq_Col_trt_vs_untrt_df_TE.txt
DESeq_h1.1h1.2_vs_Col_trt_df_TEs.txt
DESeq_h1.1h1.2_vs_Col_trt_df_genes.txt
DESeq_cmt2_vs_Col_trt_df_TEs.txt
DESeq_cmt2_vs_Col_trt_df_genes.txt

value: Columbia

value: Heat treated


title: E. coli rpoB(T1037P) rpoB(I572F) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-108_S60_L005_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(I572F) replicate 3

description:
SC-78RS-EC-SC-107_S59_L005_R1_001
processed data file: CLC_processed_counts.txt


title: SMA-08-02-D

tag: tissue

value: Diaphragm

value: SMA case


title: E. coli rpoB(T1037P) rpoB(I572F) replicate 2

description:
SC-78RS-EC-SC-106_S58_L005_R1_001
processed data file: CLC_processed_counts.txt

tag: cell type


title: E. coli rpoB(T1037P) rpoB(I572N) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-104_S56_L005_R1_001
processed data file: CLC_processed_counts.txt

value: rpoB(T1037P) rpoB(I572N)


title: Col_trt_R1

value: WT


title: SMA-08-01-I


title: SMA-09-02-I


title: E. coli rpoB(T1037P) rpoB(I572F) replicate 1

description:
SC-78RS-EC-SC-105_S57_L005_R1_001
processed data file: CLC_processed_counts.txt


title: Col_trt_R2


title: SMA-08-01-D


title: A549 ir 72h rep2

city: Guangzhou

first: Mingjian

last: Lu

state: China

address: No.78 Hengzhigang Road, Guangzhou ,P.R.China

country: China

institute: State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center (SYSUCC)

description: A549 cells were exposed to 125I seeds for 72 hours

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: A549 non-small cell lung cancer cells

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The A549 human lung carcinoma cell line was cultured in DMEM supplemented with heat-inactivated fetal calf serum (Gibco, Shanghai, China), penicillin (100 U/ml), and streptomycin (100 mg/ml) in 5% CO2 at 37°C.

extract_protocol: RNA was isolated from A549 cells after irradiation with 125I seeds for 72 h using TRIzol reagent and purified using a PureLink™ RNA Mini Kit (Ambion, USA). RNA was quantified using spectrophotometry and the measurement of the absorbance values at 260 nm and 280 nm, and the 260/280 nm ratio was used to estimate the level of protein contamination. The 260/280 nm ratios of the samples ranged from 1.8 to 2.0. The extracted total RNA from A549 cells was used for cDNA synthesis. The labeled cDNA was purified and hybridized to the microarray, and the arrays were washed and stained following the manufacturer’s instructions.

treatment_protocol: A549 cells were seeded in a 6-well plate and irradiated with seven 125I seeds for 72 h

tag: protocol

value: 125I seeds for 72 hours


title: A549 ir 72h rep1


title: SMA-09-02-D


title: E. coli rpoB(T1037P) rpoB(I572N) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-103_S55_L005_R1_001
processed data file: CLC_processed_counts.txt

value: Whole bacterial cells


title: E. coli rpoB(T1037P) rpoB(I572N) replicate 3

description:
SC-78RS-EC-SC-101_S53_L005_R1_001
processed data file: CLC_processed_counts.txt


title: A549 72h rep2

description: A549 cells were cultured for 72 hours

value: cultured for 72 hours


title: A549 72h rep1

description: A549 cells were cultured for 72 hours


title: E. coli rpoB(T1037P) rpoB(I572N) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-102_S54_L005_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose + 7.5 uM rifampicin


title: Col_untrt_R3

description:
10 days old seedlings
DESeq_cmt2_vs_Col_untrt_df_genes.txt
DESeq_cmt2_vs_Col_untrt_df_TEs.txt
DESeq_Col_trt_vs_untrt_df_TE.txt
DESeq_h1.1h1.2_vs_Col_untrt_df_TEs.txt
DESeq_h1.1h1.2_vs_Col_untrt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_TEs.txt
DESeq_cmt2_trt_Col_untrt_df_genes.txt
DESeq_cmt2_trt_Col_untrt_df_TEs.txt

tag: genotype

value: Not treated


title: SMA14-04-SC

source_name: Spinal Cord

value: Spinal Cord


title: E. coli rpoB(T1037P) rpoB(I572N) replicate 2

description:
SC-78RS-EC-SC-100_S52_L005_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose


title: E. coli rpoB(T1037P) rpoB(I572N) replicate 1

description:
SC-78RS-EC-SC-99_S51_L005_R1_001
processed data file: CLC_processed_counts.txt


title: Col_untrt_R1


title: E. coli rpoB(T1037P) rpoB(L511R) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-98_S50_L005_R1_001
processed data file: CLC_processed_counts.txt

value: rpoB(T1037P) rpoB(L511R)


title: SMA11-01-SC


title: E. coli rpoB(T1037P) rpoB(L511R) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-96_S48_L004_R1_001
processed data file: CLC_processed_counts.txt


title: h1.1 h1.2_trt_R3

description:
10 days old seedlings
DESeq_h1.1h1.2_trt_vs_untrt_df_TE.txt
DESeq_h1.1h1.2_vs_Col_trt_df_TEs.txt
DESeq_h1.1h1.2_vs_Col_trt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_TEs.txt


title: SMA09-02-SC


title: E. coli rpoB(T1037P) rpoB(L511R) replicate 3

description:
SC-78RS-EC-SC-95_S47_L004_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(L511R) replicate 2

description:
SC-78RS-EC-SC-94_S46_L004_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(Q148L) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-44_S12_L003_R1_001
processed data file: CLC_processed_counts.txt

value: rpoB(T1037P) rpoB(Q148L)


title: E. coli rpoB(T1037P) rpoB(L511R) replicate 1

description:
SC-78RS-EC-SC-93_S45_L004_R1_001
processed data file: CLC_processed_counts.txt


title: SMA08-01-SC


title: E. coli rpoB(T1037P) rpoB(Q148L) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-43_S11_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(Q148L) replicate 3

description:
SC-78RS-EC-SC-41_S9_L003_R1_001
processed data file: CLC_processed_counts.txt


title: h1.1 h1.2_trt_R2


title: h1.1 h1.2_untrt_R1

description:
10 days old seedlings
DESeq_h1.1h1.2_trt_vs_untrt_df_TE.txt
DESeq_h1.1h1.2_vs_Col_untrt_df_TEs.txt
DESeq_h1.1h1.2_vs_Col_untrt_df_genes.txt


title: E. coli rpoB(T1037P) rpoB(Q148L) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-42_S10_L003_R1_001
processed data file: CLC_processed_counts.txt


title: h1.1 h1.2_untrt_R2


title: E. coli rpoB(T1037P) rpoB(Q148L) replicate 2

description:
SC-78RS-EC-SC-40_S8_L003_R1_001
processed data file: CLC_processed_counts.txt


title: CNTL95-04-SC

value: Control


title: CNTL93-07-SC


title: E. coli rpoB(T1037P) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-79_S31_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) rpoB(Q148L) replicate 1

description:
SC-78RS-EC-SC-39_S7_L003_R1_001
processed data file: CLC_processed_counts.txt


title: Col_untrt_R2

description:
10 days old seedlings
DESeq_cmt2_vs_Col_untrt_df_genes.txt
DESeq_cmt2_vs_Col_untrt_df_TEs.txt
DESeq_Col_trt_vs_untrt_df_TE.txt
DESeq_h1.1h1.2_vs_Col_untrt_df_TEs.txt
DESeq_h1.1h1.2_vs_Col_untrt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_TEs.txt
DESeq_cmt2_trt_Col_untrt_df_genes.txt
DESeq_cmt2_trt_Col_untrt_df_TEs.txt


title: E. coli rpoB(T1037P) rpoB(L511R) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-97_S49_L005_R1_001
processed data file: CLC_processed_counts.txt


title: SMA10-16-SC


title: E. coli rpoB(T1037P) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-80_S32_L003_R1_001
processed data file: CLC_processed_counts.txt


title: wt-mitoQ_rep4

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
100 cycle single end sequencing on HiSeq2500 system with version 4 reagents
Reads underwent trimming in Skewer version 0.2.2 in order to remove bases with quality less than Phred 20.
Reads were then mapped to Gencode mouse v25 transcripts with kallisto version 0.46.1
Tabular data was read into R version 4.0.2 for downstream analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: mitoGmitoQ_counts.tsv  tabular gene expression count matrix

source_name: renal cortex

growth_protocol: All activities involving the use of animals for research were approved by the Alfred Research Alliance (ARA) Animal Ethics Committee and were conducted according to guidelines of the National Health and Medical Research Council of Australia for animal experimentation. Ins2-Akita mice (C57BL/6J-Ins2Akita) and their wild type (WT) littermates were purchased from the Jackson Laboratory, bred at the ARA Animal Centre and maintained under a 12h light/dark cycle. Animals were housed in groups of three mice per cage in a temperature-controlled environment and ad libitum access to food and water.

extract_protocol:
Renal cortex was harvested from individual animals and underwent RNA isolation with the Direct-zol RNA kit (Zymo).
Approximately 200 ng of total RNA underwent RNA depletion using the NEBNext rRNA Depletion Kit followed by library construction using an NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (both from New England BioLabs Inc.).

treatment_protocol: At 6 weeks of age, male mice of both genotypes were randomly assigned to receive either vehicle (10% ethanol in water), or MitoGamide (10 mg/kg) by daily oral gavage (Figure 1b). Blood glucose (ACCU-CHEK glucometer, Roche) and body weights were recorded on a weekly basis as part of animal monitoring. Mice were placed individually into metabolic cages (Iffa Credo, L’Arbresele, France) and urine was collected for 24 hour at midpoint (12 weeks) and endpoint (21 weeks). Treatment was continued until mice were 22 weeks of age.  At 21 weeks old, mice were transferred to metabolic caging, one week before cull.

value: wild type

value: non-diabetic

tag: drug treatment group

value: MitoQ (water vehicle)


title: CNTL90-08-SC


title: wt-mitoQ_rep5


title: CNTL13-01-SC


title: E. coli rpoB(T1037P) replicate 2

description:
SC-78RS-EC-SC-76_S28_L003_R1_001
processed data file: CLC_processed_counts.txt


title: wt-mitoQ_rep3


title: E. coli rpoB(T1037P) replicate 3

description:
SC-78RS-EC-SC-77_S29_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli rpoB(T1037P) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-78_S30_L003_R1_001
processed data file: CLC_processed_counts.txt


title: h1.1 h1.2_trt_R1

description:
10 days old seedlings
DESeq_h1.1h1.2_trt_vs_untrt_df_TE.txt
DESeq_h1.1h1.2_vs_Col_trt_df_TEs.txt
DESeq_h1.1h1.2_vs_Col_trt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_genes.txt
DESeq_h1.1h1.2_trt_Col_untrt_df_TEs.txt

value: Columbia

tag: treatment

value: Heat treated


title: E. coli pykF(C8Y) rpoB(Q148L) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-74_S26_L003_R1_001
processed data file: CLC_processed_counts.txt

value: pykF(C8Y) rpoB(Q148L)


title: wt-mitoQ_rep2

tag: disease state


title: E. coli rpoB(T1037P) replicate 1

description:
SC-78RS-EC-SC-75_S27_L003_R1_001
processed data file: CLC_processed_counts.txt


title: VLCM-n3

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description:
Flow cytoneter sorted cells
VLCM_ATAC_hg19.bigwig
VLCM_ATAC_peak.bed

data_processing:
Reads were mapped to hg19 build of the mouse genome using BWA (Li et al., 2009) using default settings.
SAMtools was used to merge the replicate BAM files. The BEDTools suite (Quinlan et al., 2010) was used to distribute the genome wide signal into bins of 500bp and subsequently call peaks.
Genome_build: hg19
Supplementary_files_format_and_content: VLCM_ATAC_peaks & SANLPC_ATAC_peaks (BED files with called peaks); VLCM_ATAC_hg19 & SANLPC_ATAC_hg19 (bigWig traces)

source_name: Ventricle-like cells

extract_protocol:
A precise description can be found in: Sinoatrial node cardiomyocytes derived from human pluripotent cells function as a biological pacemaker (Nature Biotechnology 2017)
Tn5 transposase-treated samples were amplified using barcode-labeled primers (Illumina) and sequenced on a HiSeq 2500 system (Illumina) with 125 bp single-end reads

tag: sample type

value: Cell culture


title: VLCM-n1

growth_protocol: A precise description can be found in: Sinoatrial node cardiomyocytes derived from human pluripotent cells function as a biological pacemaker (Nature Biotechnology 2017)


title: SMA08-02-SC

value: SMA case


title: wt-mitoQ_rep1


title: E. coli pykF(C8Y) rpoB(Q148L) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-72_S24_L003_R1_001
processed data file: CLC_processed_counts.txt

value: Whole bacterial cells


title: VLCM-n2

treatment_protocol: A precise description can be found in: Sinoatrial node cardiomyocytes derived from human pluripotent cells function as a biological pacemaker (Nature Biotechnology 2017)


title: E. coli pykF(C8Y) rpoB(Q148L) replicate 3

description:
SC-78RS-EC-SC-71_S23_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) rpoB(Q148L) replicate 1

description:
SC-78RS-EC-SC-69_S21_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) rpoB(Q148L) replicate 2

description:
SC-78RS-EC-SC-70_S22_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) rpoB(I572S) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-67_S19_L003_R1_001
processed data file: CLC_processed_counts.txt

value: pykF(C8Y) rpoB(I572S)


title: Wt-mitoGamide_rep4

value: MitoGamide (ethanol vehicle)


title: Wt-mitoGamide_rep5


title: SANLPC-n2

description:
Flow cytoneter sorted cells
SANLPC_ATAC_hg19.bigwig
SANLPC_ATAC_peaks.bed

source_name: Sinoatrial node-like pacemaker cells


title: E. coli pykF(C8Y) rpoB(I572S) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-66_S18_L003_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose + 7.5 uM rifampicin


title: Wt-mitoGamide_rep3


title: SANLPC-n1


title: E. coli pykF(C8Y) rpoB(I572S) replicate 3

description:
SC-78RS-EC-SC-65_S17_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) rpoB(I572S) replicate 1

description:
SC-78RS-EC-SC-63_S15_L002_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) rpoB(I572S) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-68_S20_L003_R1_001
processed data file: CLC_processed_counts.txt


title: CT4

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

description:
Per2-dLuc trough, DMSO treat 4 h
all_fpkm.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using TopHat v2.0.10 with default parameters
Reads which mapped to intron region were used to calculate relative quantitation of nascent genes expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Human osteosarcoma U2OS cells

growth_protocol: U2OS cells (passage 15-20) were routinely grown till confluence (10% FBS with 1% Pen+Str antibiotics in DMEM), released to serum-free DMEM medium and continued for 36 - 48 h

extract_protocol:
Cells were washed twice with cold PBS, trypsinized and normalized cell numbers; extract total RNA and normalize to 1ug/ul. Goat anti-Mouse IgG beads (50ul) were incubated with anti-BrU (2ug), wash with PBS+0.1% BSA, and resuspend in 200ul. 200ul prepaired RNA were heated at 80C for 10min to open secondary structure, and incubate with 200ul antibody-bound beads for 1 h at room temperature. Wash 3 times with PBS+0.1% BSA. Extract beads captured RNA with RNeasy MiniElute Cleanup kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When Per2-dLuc reached exact time (peak or trough, as indicated), cells were treated with DRB (10uM) or DMSO control. BrU (250uM) were added 0.5 h before harvesting the cells

tag: labeling compound

tag: antibody

value: Anti-BrU (BD Biosci #555627)


title: Wt-mitoGamide_rep2


title: E. coli pykF(C8Y) rpoB(I572S) replicate 2

description:
SC-78RS-EC-SC-64_S16_L002_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose


title: E. coli pykF(C8Y) rpoB(Q148L) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-73_S25_L003_R1_001
processed data file: CLC_processed_counts.txt


title: Wt-mitoGamide_rep1


title: human microvascular endothelial cells-TNF-a treatment 2

city: St. Louis

first: Joanna

last: Kim

state: MO

address: 660 S Euclid Ave

institute: Washington University

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52.
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
Genome_build: Ensembl release 76 primary assembly
Supplementary_files_format_and_content: tab-delimited text files of raw accounts

growth_protocol: human primary microvascular endothelial cells were grown in EGM-2 MV media from Lonza Bioscience, 5% CO2 and 37C

extract_protocol:
total RNA was isolated using Qiagen Rneasy mini kit
RNA-polyA

treatment_protocol: For knocking down septin 2 expression, cellls were incubated for 3~4 days incubation with shSeptin 2. For TNF-a treatment, cells were incubated with 20 ng/mL TNF-a overnight

value: Primary cells

value: TNF-a treated


title: SANLPC-n3


title: E. coli pykF(C8Y) rpoB(L511R) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-62_S14_L002_R1_001
processed data file: CLC_processed_counts.txt

value: pykF(C8Y) rpoB(L511R)


title: human microvascular endothelial cells-TNF-a treatment 1

source_name: human primary microvascular endothelial cells


title: T4

description:
Per2-dLuc trough, DRB treat 4 h
all_fpkm.txt

value: DRB (Sigma #D1916)


title: CP4

description:
Per2-dLuc peak, DMSO treat 4 h
all_fpkm.txt


title: human microvascular endothelial cells-Untreated 1

value: Untreated


title: E. coli pykF(C8Y) rpoB(L511R) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-61_S13_L002_R1_001
processed data file: CLC_processed_counts.txt


title: wt-h2o_rep4

value: wild type

value: non-diabetic

value: water vehicle


title: P4

description:
Per2-dLuc peak, DRB treat 4 h
all_fpkm.txt


title: wt-h2o_rep5


title: human microvascular endothelial cells-Untreated 2


title: E. coli pykF(C8Y) rpoB(L511R) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-60_S12_L002_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) rpoB(L511R) replicate 2

description:
SC-78RS-EC-SC-58_S10_L002_R1_001
processed data file: CLC_processed_counts.txt


title: CP2

description:
Per2-dLuc peak, DMSO treat 2 h
all_fpkm.txt


title: E. coli pykF(C8Y) rpoB(L511R) replicate 3

description:
SC-78RS-EC-SC-59_S11_L002_R1_001
processed data file: CLC_processed_counts.txt


title: wt-h2o_rep3


title: CT2

description:
Per2-dLuc trough, DMSO treat 2 h
all_fpkm.txt


title: wt-etoh_rep4

value: ethanol vehicle


title: wt-h2o_rep1


title: T2

description:
Per2-dLuc trough, DRB treat 2 h
all_fpkm.txt


title: wt-h2o_rep2


title: human microvascular endothelial cells-Control 2

value: shControl shRNA expressed


title: human microvascular endothelial cells-Septin 2 suppression 1

value: shSeptin 2 shRNA expressed


title: human microvascular endothelial cells-Control 1


title: E. coli pykF(C8Y) rpoB(D516G) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-56_S8_L002_R1_001
processed data file: CLC_processed_counts.txt

value: Whole bacterial cells

value: pykF(C8Y) rpoB(D516G)


title: wt-etoh_rep5


title: P2

description:
Per2-dLuc peak, DRB treat 2 h
all_fpkm.txt


title: E. coli pykF(C8Y) rpoB(D516G) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-55_S7_L002_R1_001
processed data file: CLC_processed_counts.txt


title: CT1

description:
Per2-dLuc trough, DMSO treat 1 h
all_fpkm.txt


title: GIGYF1/2-null replicate 2 for Ribo-seq

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

country: Switzerland

institute: University of Zurich

description:
small RNA
GIGYF-2_Ribo

data_processing:
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translation efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimited file for translation efficiency analysis

growth_protocol: 6.4x10^6 cells of HEK293T WT or 4EHP-null or GIGYF1/2-null cells were plated on 15 cm dishes 24 hrs before harvesting.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). For Ribo-seq, the original procedure of Ingolia et al (2012) Nature Protocols was followed with modifications from Calviello et al (2016) Nature Methods.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: strategy

value: Ribo-Seq


title: E. coli pykF(C8Y) rpoB(L511R) replicate 1

description:
SC-78RS-EC-SC-57_S9_L002_R1_001
processed data file: CLC_processed_counts.txt

tag: genotype/variation


title: wt-etoh_rep3


title: T1

description:
Per2-dLuc trough, DRB treat 1 h
all_fpkm.txt


title: 4EHP-null replicate 2 for Ribo-seq

description:
small RNA
4EHP-2_Ribo


title: E. coli pykF(C8Y) rpoB(D516G) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-54_S6_L002_R1_001
processed data file: CLC_processed_counts.txt

tag: medium

value: M9 + glucose + 7.5 uM rifampicin


title: E. coli pykF(C8Y) rpoB(D516G) replicate 2

description:
SC-78RS-EC-SC-52_S4_L002_R1_001
processed data file: CLC_processed_counts.txt


title: GIGYF1/2-null replicate 1 for Ribo-seq

description:
small RNA
GIGYF-1_Ribo


title: 4EHP-null replicate 1 for Ribo-seq

description:
small RNA
4EHP-1_Ribo


title: E. coli pykF(C8Y) rpoB(H526Y) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-50_S2_L002_R1_001
processed data file: CLC_processed_counts.txt

value: pykF(C8Y) rpoB(H526Y)


title: E. coli pykF(C8Y) rpoB(D516G) replicate 3

description:
SC-78RS-EC-SC-53_S5_L002_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose


title: CP1

description:
Per2-dLuc peak, DMSO treat 1 h
all_fpkm.txt

value: Anti-BrU (BD Biosci #555627)


title: E. coli pykF(C8Y) rpoB(D516G) replicate 1

description:
SC-78RS-EC-SC-51_S3_L002_R1_001
processed data file: CLC_processed_counts.txt


title: Wild-type replicate 2 for Ribo-seq

description:
small RNA
control-2_Ribo

value: Wild-type


title: P1

description:
Per2-dLuc peak, DRB treat 1 h
all_fpkm.txt


title: het-mitoQ_rep5

value: Ins2-Akita heterozygous

value: diabetic

value: MitoQ (water vehicle)


title: Liver_KCZ_High_Day14_rep2

city: Jefferson

first: Dongying

last: Li

state: AR

address: 3900 NCTR Rd

department: NCTR

institute: FDA

data_processing:
Alignment, annotation and quantification by miRDeep2
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was extracted from rat liver tissues using RNeasy Plus Universal Mini kits according to the manufacturer's protocol
Small RNA libraries were constructed using Illumina TruSeq Small RNA Library Preparation kits according to the manufacturer's protocol

value: Liver

value: Sprague-Dawley

value: 100 mg/kg ketoconazole for 14 days


title: E. coli pykF(C8Y) rpoB(H526Y) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-49_S1_L002_R1_001
processed data file: CLC_processed_counts.txt


title: Liver_KCZ_High_Day14_rep3


title: het-mitoQ_rep3


title: Wild-type replicate 1 for Ribo-seq

description:
small RNA
control-1_Ribo


title: het-mitoQ_rep2


title: het-mitoQ_rep1


title: E. coli pykF(C8Y) rpoB(H526Y) replicate 3

description:
SC-78RS-EC-SC-47_S15_L003_R1_001
processed data file: CLC_processed_counts.txt


title: GIGYF1/2-null replicate 1 for RNA-seq

description:
messenger RNA
GIGYF-1_RNA

value: RNA-Seq


title: Liver_KCZ_High_Day14_rep1


title: wt-etoh_rep2

value: wild type

value: non-diabetic

value: ethanol vehicle


title: GIGYF1/2-null replicate 2 for RNA-seq

description:
messenger RNA
GIGYF-2_RNA


title: wt-etoh_rep1


title: 4EHP-null replicate 2 for RNA-seq

description:
messenger RNA
4EHP-2_RNA


title: het-mitoQ_rep4


title: Liver_KCZ_High_Day7_rep1

value: 100 mg/kg ketoconazole for 7 days


title: Liver_KCZ_High_Day7_rep2


title: E. coli pykF(C8Y) rpoB(H526Y) replicate 2

description:
SC-78RS-EC-SC-46_S14_L003_R1_001
processed data file: CLC_processed_counts.txt

value: Whole bacterial cells


title: 4EHP-null replicate 1 for RNA-seq

description:
messenger RNA
4EHP-1_RNA


title: Het-mitoGamide_rep4

value: MitoGamide (ethanol vehicle)


title: E. coli pykF(C8Y) rpoB(H526Y) replicate 1

description:
SC-78RS-EC-SC-45_S13_L003_R1_001
processed data file: CLC_processed_counts.txt

value: pykF(C8Y) rpoB(H526Y)


title: Liver_KCZ_High_Day3_rep3

value: 100 mg/kg ketoconazole for 3 days


title: Wild-type replicate 2 for RNA-seq

description:
messenger RNA
control-2_RNA


title: E. coli pykF(C8Y) rpoB(H526Y) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-48_S16_L003_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose + 7.5 uM rifampicin


title: Het-mitoGamide_rep3


title: Liver_KCZ_High_Day7_rep3


title: Liver_KCZ_High_Day3_rep2


title: E. coli pykF(C8Y) + 7.5 μM rifampicin replicate 3

description:
SC-78RS-EC-SC-38_S6_L003_R1_001
processed data file: CLC_processed_counts.txt


title: Het-mitoGamide_rep2


title: E. coli pykF(C8Y) + 7.5 μM rifampicin replicate 2

description:
SC-78RS-EC-SC-37_S5_L003_R1_001
processed data file: CLC_processed_counts.txt


title: het-mitoGamide_rep1


title: Wild-type replicate 1 for RNA-seq

description:
messenger RNA
control-1_RNA

value: Wild-type


title: E. coli pykF(C8Y) + 7.5 μM rifampicin replicate 1

description:
SC-78RS-EC-SC-36_S4_L003_R1_001
processed data file: CLC_processed_counts.txt


title: E. coli pykF(C8Y) replicate 3

description:
SC-78RS-EC-SC-35_S3_L003_R1_001
processed data file: CLC_processed_counts.txt

value: M9 + glucose


title: Liver_KCZ_Middle_Day14_rep2

value: 30 mg/kg ketoconazole for 14 days


title: het-h20_rep5

value: Ins2-Akita heterozygous

value: diabetic

value: water vehicle


title: het-h20_rep4


title: Liver_KCZ_Middle_Day14_rep3

value: Liver

value: Sprague-Dawley


title: Liver_KCZ_Middle_Day14_rep1


title: E. coli pykF(C8Y) replicate 2

description:
SC-78RS-EC-SC-34_S2_L003_R1_001
processed data file: CLC_processed_counts.txt


title: D10_resident_infiltrating_m2

city: Cambridge

first: Regan

last: Hamel

address: Cambridge Biosciences Campus, Hills Rd

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

data_processing:
Libraries were sequenced via the Illumina Novaseq 6000 platform with the default real-time analysis software.
Using the Cell Ranger 3.1.0  pipeline (10x Genomics), reads were demultiplexed, aligned to the GRCm38 (mm10) genome, reads were grouped by cell barcode, and gene counts were calculated based on unique molecular identifiers (UMI).
Quality controls, including low-quality cell exclusion and normalisation, were applied as described here (https://github.com/regan-hamel/SCI_2020)
Genome_build: mm10
Supplementary_files_format_and_content: A table of ensembl gene IDs (rows) x cell barcodes (columns) containing raw counts after quality control excludding normalisation (scripts 1-3 on GitHub)
Supplementary_files_format_and_content: A table of ensembl gene IDs (rows) x cell barcodes (columns) containing either the raw or normalised counts of the merged data from all samples.
Supplementary_files_format_and_content: Cell annotations, such as time collected post-SCI, sex, cluster ID. Can be added to the colData of a SingleCellExperiment object

molecule: polyA RNA

source_name: CNS myeloid cells

extract_protocol:
Spinal cord injury lesions (5 mm) were extracted and mechanically homogenized, myelin was removed using a percoll gradient, we enriched for myeloid cells via FACS and isolated single cells via the 10x Genomics Single Cell 3' Droplet-based single cell solution.
10x Genomics Single Cell 3' Droplet-based single cell solution, 10x Genomics Single Cell 3' library construction

tag: days post-sci

tag: Sex

value: Male

tag: facs label

value: YFP+


title: D10_resident_infiltrating_m

tag: strain


title: Het-mitoGamide_rep5


title: D21_resident_infiltrating_f

value: Female


title: Znion-2

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

institute: University of Queensland

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Acinetobacter baylyi ADP1

source_name: Acinetobacter baylyi ADP1 bacteria

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acinetobacter baylyi ADP1 was cultured in 10 mL PBS (plus 40 mg/L COD) containing 0, 1 mg/L AgNPs or Ag ions, 1 mg/L CuO NPs or Cu ions, 10 mg/L ZnO NPs or Zn ions for 2 h, in triplicate, at 30 °C, without shaking

tag: tissue

value: liquid LB culture


title: het-h20_rep3


title: Liver_KCZ_Middle_Day7_rep3

value: 30 mg/kg ketoconazole for 7 days


title: Liver_KCZ_High_Day3_rep1


title: het-h20_rep2


title: D10_resident_f

value: RFP+/YFP+


title: D10_infiltrating_m

value: RFP-/YFP+


title: Liver_KCZ_Middle_Day7_rep2


title: het-h20_rep1


title: Liver_KCZ_Middle_Day7_rep1


title: het-etoh_rep5

value: ethanol vehicle


title: D21_infiltrating_m


title: D10_infiltrating_f


title: D3_resident_infiltrating_m3


title: het-etoh_rep4


title: Liver_KCZ_Middle_Day3_rep2

value: 30 mg/kg ketoconazole for 3 days


title: Liver_KCZ_Middle_Day3_rep1


title: D3_resident _infiltrating_m


title: het-etoh_rep3


title: E. coli pykF(C8Y) replicate 1

description:
SC-78RS-EC-SC-33_S1_L003_R1_001
processed data file: CLC_processed_counts.txt

tag: cell type

value: Whole bacterial cells


title: D3_resident_m


title: D3_resident_infiltrating_m2


title: Liver_KCZ_Low_Day14_rep3

value: 10 mg/kg ketoconazole for 14 days


title: het-etoh_rep2

tag: genotype


title: normal keratinocytes biological replicate 3

city: SINGAPORE

last: Tan

address: BLK 652 YISHUN AVE 4

country: Singapore

institute: NTU

description: Normal migrating keratinocytes day 3 post wounding

hyb_protocol: Hybridization was carried out on GeneChip™ Mouse Gene 1.0 ST Assay in accordance to the manufacturer's protocol (GeneChip® WT Pico Reagent Kit) using GeneChip® Hybridization Oven 645. Gene chips were washed and stained in the GeneChip® Fluidics Station 450.

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

data_processing: Data was analyzed using Partek® Genomics Suite®. The data was analyzed by contrasting the diabetic samples against the normal samples. A fold change cutoff of 1.2 was used.

label_protocol: Biotinylated cRNA was prepared using GeneChip® WT Pico Reagent Kit according to manufacturer's protocol.

growth_protocol: Mice aged 8 weeks were induced with diabetes through a high fat high fructose diet for a period of 16 weeks, with the controls having a control diet for the same duration of time. Wounds were made on the mice and harvested 3 days post wounding.

extract_protocol: Ambion's RecoverAll™ Total Nucleic Acid Isolation Kit was used according to manufacturer's protocol.

treatment_protocol: Samples were fixed and dehydrated. Laser capture microdissection of migrating keratinocytes at the tip of the epithelial tongue was carried out and cells from sections of the same sample was accumulated into a single tube.

value: skin

value: keratinocytes

value: normal


title: normal keratinocytes biological replicate 2

source_name: Normal migrating keratinocytes day 3 post wounding


title: D3_resident_f


title: Liver_KCZ_Low_Day14_rep2


title: diabetic keratinocytes biological replicate 3

description: Diabetic migrating keratinocytes day 3 post wounding

value: diabetic


title: Liver_KCZ_Middle_Day3_rep3

value: Liver


title: normal keratinocytes biological replicate 1


title: Liver_KCZ_Low_Day7_rep3

value: Sprague-Dawley

value: 10 mg/kg ketoconazole for 7 days


title: Liver_KCZ_Low_Day14_rep1


title: Untreated_3

city: Cincinnati

first: Soma

last: Sengupta

state: OH

address: 3125 Eden Avenue

department: Neurology

institute: University of Cincinnati

data_processing:
Aligned to the mm10 human reference genome using STAR (v 2.4.1a)
FeatureCounts tool was used to count the reads of the mapped bam files (featureCounts -p -a mm10.gtf -o counts.txt *.bam).
Differential expression analysis between different samples was performed based on the negative-binomial statistical model of read counts as implemented in the edgeR Bioconductor package and p-values adjusted using False Discovery Rates.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts data

source_name: B16F10-GP cells_Untreated

growth_protocol: B16F10-GP cells (5 x 105) were implanted in matrigel (25%) on right/left-flanks of 6-8 week old female C57BL/6 mice.

extract_protocol:
RNA extracted from tumors met the following requirements: ≥750 ng RNA, a preferred concentration 10 ng/μL, DV200>0.3 (where DC200 is fraction of RNA fragments whose length is >200 nucleotides).
RNA was processed and sequenced at the Broad Institute by the Transcriptome Capture method using Illumina HiSeq2500.

treatment_protocol: Mice received either: (i) vehicle alone control; (ii) radiation alone (5 Gy, right-flank only); (iii) QH-II-066 beginning Day 10; (iv) radiation (5 Gy, right-flank only) on Day 10 (morning), followed by QH-II-066 (evening). Palpable tumors (10 days) were irradiated right-side with a Superflab bolus (0.5 cm tissue equivalent material) placed over tumor and thereafter tumor measurements taken as indicated. The Superflab bolus allows for a maximum surface to the tumor and reduces penetration of the rays to the internal body organs Irradiation was done using an X-RAD 320 irradiation unit, a self-contained X-ray system for delivering a precise radiation dosage. In groups receiving QH-II-066, 10 mg/kg was injected i.p. daily for 7 days.

tag: strain background

tag: tumor type

value: Melanoma

value: Untreated


title: diabetic keratinocytes biological replicate 1

source_name: Diabetic migrating keratinocytes day 3 post wounding

tag: disease state


title: Untreated_4

tag: treatment


title: D3_infiltrating_f

value: Female


title: diabetic keratinocytes biological replicate 2


title: Untreated_2


title: D2_resident_infiltrating_m

value: Male

value: YFP+


title: Liver_KCZ_Low_Day7_rep2


title: Untreated_1


title: het-etoh_rep1

value: Ins2-Akita heterozygous

tag: drug treatment group


title: Tumor M-MDSC, rep 2

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

description:
Tu_M-MDSC_2
gene expression data from Tumor M-MDSC

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix chip scanning protocol

data_processing: RMAExpress for RMA normalization and QC; Significance Analysis for Microarray analysis for differential gene expression using BRBArrayTools

source_name: Ascites from mice 7 days after being injected i.p. with RM-1 cells

label_protocol: Standard Affymetrix biotin labeling protocol

extract_protocol: Qiagen RNAeasy kit

tag: host strain

tag: gender

value: male

tag: age

value: 12 weeks

value: tumor


title: Liver_KCZ_Low_Day7_rep1


title: D3_infiltrating_m

value: RFP-/YFP+


title: QHII_4

source_name: B16F10-GP cells_Drug

value: Drug


title: Liver_KCZ_Low_Day3_rep3

value: 10 mg/kg ketoconazole for 3 days


title: Tumor M-MDSC, rep 4

description:
Tu_M-MDSC_4
gene expression data from Tumor M-MDSC


title: D2_resident_m

value: RFP+/YFP+


title: D2_resident_infiltrating_f


title: QHII_3


title: Tumor M-MDSC, rep 1

description:
Tu_M-MDSC_1
gene expression data from Tumor M-MDSC


title: D2_infiltrating_f


title: QHII_2


title: Tumor M-MDSC, rep 3

description:
Tu_M-MDSC_3
gene expression data from Tumor M-MDSC


title: Liver_KCZ_Low_Day3_rep2


title: human microvascular endothelial cells-Septin 2 suppression 2

value: Primary cells

value: shSeptin 2 shRNA expressed


title: D1_resident_infiltrating_m3


title: Tumor G-MDSC, rep 4

description:
Tu_G-MDSC_4
gene expression data from Tumor G-MDSC


title: QHII_1


title: Liver_Control_Day14_rep2

value: Liver

value: Sprague-Dawley

value: Control (0.5% methylcellulose) for 14 days


title: D1_resident_infiltrating_m2


title: 5Gy_QHII_4

source_name: B16F10-GP cells_5 Gy radiation + Drug

value: Melanoma

value: 5 Gy radiation + Drug


title: Tumor G-MDSC, rep 3

description:
Tu_G-MDSC_3
gene expression data from Tumor G-MDSC


title: D1_resident_infiltrating_m

value: Male


title: Liver_Control_Day14_rep1


title: 5Gy_QHII_3


title: 5Gy_QHII_2


title: Liver_Control_Day7_rep2

value: Control (0.5% methylcellulose) for 7 days


title: 5Gy_QHII_1


title: Liver_Control_Day7_rep3


title: D1_infiltrating_m


title: Liver_KCZ_Low_Day3_rep1


title: Spleen M-MDSC, rep 4

description:
Sp_M-MDSC_4
gene expression data from spleen M-MDSC

source_name: Spleen of POET mice with prostatic inflammation

value: spleen


title: Spleen M-MDSC, rep 3

description:
Sp_M-MDSC_3
gene expression data from spleen M-MDSC

value: male


title: Tumor G-MDSC, rep 2

description:
Tu_G-MDSC_2
gene expression data from Tumor G-MDSC

value: 12 weeks


title: Tumor G-MDSC, rep 1

description:
Tu_G-MDSC_1
gene expression data from Tumor G-MDSC

value: tumor


title: Ctrl_resident_m

value: Ctrl


title: 5Gy_4

source_name: B16F10-GP cells_5 Gy radiation

value: 5 Gy radiation


title: Liver_Control_Day3_rep3

value: Control (0.5% methylcellulose) for 3 days


title: Liver_Control_Day7_rep1


title: Ctrl_resident_infiltrating_f

value: Female

value: YFP+


title: Spleen M-MDSC, rep 2

description:
Sp_M-MDSC_2
gene expression data from spleen M-MDSC


title: 5Gy_2


title: mm_ret_M1_C57OS

city: Bethesda

first: Zachary

middle: A

last: Batz

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

data_processing:
Data was processed through cellranger suite v3.1.0.
Fastq files were generated from raw BCL files using "cellranger mkfastq" with default settings.
Expression matrix were generated using "cellranger count" with default settings.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: filtered output in HSF format containing gene expression matrix in single-cell resolution.

source_name: Retina

extract_protocol:
Mouse retinae were dissociated using papain.
Cell suspension was passed through 10x Genomics' protocol for "Chromium Single Cell 3' v2" following manufacturers instructions.

value: 1 month

value: WT

tag: preparation

value: fresh tissue


title: 5Gy_1


title: mm_ret_M2_NRLGFP

value: 2 month

value: Nrl-L-EGFP


title: Spleen G-MDSC, rep 4

description:
Sp_G-MDSC_4
gene expression data from spleen G-MDSC


title: Spleen M-MDSC, rep 1

description:
Sp_M-MDSC_1
gene expression data from spleen M-MDSC


title: D1_infiltrating_f

value: RFP-/YFP+


title: Liver_Control_Day3_rep2

value: Liver

value: Sprague-Dawley


title: mm_ret_M1_C57OD


title: mm_ret_M1_MeOH_rep2

value: methanol fixation


title: S29_SD

city: Taipei

first: Roger

last: Shen

address: 128 Sec. 2, Academia Rd. Nankang

country: Taiwan

institute: Academia Sinica

description: SLC29A2-expressing SK-hep1 received sorafenib and dipyridamole

data_processing:
Raw data (raw reads) of fastq format were firstly processed through Novogene in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC contentthe clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Qualified reads after filtering low-quality data were analyzed using   TopHat  v2.0.  12. and HTSeq v0.6.1 for gene expression estimation.
The gene expression level was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression
The reference genome and gene annotations were retrieved from Ensembl database.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text file includes readcounts and FPKM values for each Sample

growth_protocol: SK-hep1 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 1% L-glutamine (Invitrogen) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA was extracted from cancer cell lines by NucleoSpin RNA XS (Macherey Nagel, Duren, Germany).
A total amount of 3 μg RNA per sample was used as in put material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out. using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H. Second strandcDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: cell line

value: sorafenib and dipyridamole


title: 5Gy_3

value: Melanoma


title: mm_ret_M1_D8C_rep2


title: Liver_Control_Day3_rep1


title: scrambled rep2

city: Bangalore

first: Manchanahalli

middle: Rangaswamy

last: Satyanarayana Rao

state: Karnataka

address: Jakkur, Bengaluru, Karnataka

department: Molecular Biology and Genetics Unit (MBGU)

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)

data_processing:
Raw reads were aligned with Tophat2 against mm10 mouse genome
Readcounts were normalized with Cufflink
DE genes were identified using CuffDiff
Genome_build: mm10 (Mus musculus)
Supplementary_files_format_and_content: xlsx

source_name: mouse ES cells

growth_protocol: E14tg2a cells were maintained on 0.2% gelatine coated dishes in mESC medium containing DMEM (Dulbecco’s modified Eagle’s medium), high glucose, 15% FBS, 1X non-essential amino acids, 0.1 mM β mercaptoethanol and 1X pencillin-streptomycin.

extract_protocol:
Total RNA was isolated from cell pellets using Trizol regent and treated with DNaseI.
Library preparation was using Illumina TruSeq RNA Sample Prep Kit.

treatment_protocol: mES cells were transiently transfected with either scrambled shRNA or shRNA 4 (against Mrhl) for 48 hours using Mirus TransIT-X2® Transfection Reagent

value: mouse ES cells

value: embryo

tag: lentivirus

value: scrambled


title: sh-Mrhl rep1

value: sh-Mrhl


title: sh-Mrhl rep2


title: Spleen G-MDSC, rep 2

description:
Sp_G-MDSC_2
gene expression data from spleen G-MDSC

value: male

value: 12 weeks

value: spleen


title: S29_D

description: SLC29A2-expressing SK-hep1 received dipyridamole

value: dipyridamole


title: STING_2

city: Seongnam-si

first: Hannah

last: Yang

address: CHA Bundang Medical Center

country: South Korea

institute: CHA Bundang Medical Center

hyb_protocol: According to the manufacturer's protocol.

data_processing: See manufacturer's website (http://www.nanostring.com). The data were normalized against internal reference genes.

source_name: Wild-type, colon

growth_protocol: We implanted 5 × 10^5 MC38 cells into peritoneum of C57BL/6 mice.

extract_protocol: Total RNA from the whole tumor tissues using TRIzol.

treatment_protocol: After 7 days, we performed intraperitoneal injections of the STING agonist. Mice in the control group were intraperitoneally injected with the same volume of PBS.

value: Male

value: Wild-type

value: Colon

tag: growth protocol

value: implanted MC38 cells into peritoneum of C57BL/6 mice

value: STING agonist


title: scrambled rep1


title: STING_3

scan_protocol: According to the manufacturer's protocol.


title: STING_4

label_protocol: According to the manufacturer's protocol.


title: Spleen G-MDSC, rep 1

description:
Sp_G-MDSC_1
gene expression data from spleen G-MDSC


title: S29_S

description: SLC29A2-expressing SK-hep1 received sorafenib

value: sorafenib


title: Spleen G-MDSC, rep 3

description:
Sp_G-MDSC_3
gene expression data from spleen G-MDSC


title: OSN6 Cel-Seq2 scRNA-Seq

city: Plainsboro

first: Patrick

last: Pfister

state: New Jersey

address: 250 Plainsboro Road

department: Corporate R&D

institute: Firmenich Inc.

description: Paired-end sequencing but only R2 reads submitted, as R1 only have barcode and UMI sequence (which is transferred to read names in R2), followed by polyA stretch. Alignment is done using R2 reads only.

data_processing:
Basecalling and filtering of reads was performed by Illumina CASAVA.
Reads were demultiplexed and adapter, cell-specific barcode and UMI sequences were trimmed. Barcode and UMI sequences from R1 mates were appended to the read names of R2 mates (only R2 reads have transcript sequence).
R2 reads were mapped as single reads on the mouse genome (mm10) using Bowtie2 v2.3.4 with default parameters.
Reads mapping to gene exons were counted using HTSeq-count; reads sharing the same UMI were discounted.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file contains UMI counts per gene in each cell

source_name: Olfactory epithelium

extract_protocol:
After physiological recordings, individual cells were flash frozen in solution containing barcoded primers.
Barcoded cell-specific libraries with unique molecular identifiers (UMI) were made as described in the Cel-Seq2 paper (Hashimshony et al., Genome Biology, 2016).

value: Olfactory sensory neuron

value: 6 weeks


title: OSN5 Cel-Seq2 scRNA-Seq


title: V_SD

description: SK-hep1 received sorafenib and dipyridamole treatment

value: control

value: sorafenib and dipyridamole


title: OSN4 Cel-Seq2 scRNA-Seq


title: V_D

description: SK-hep1 received dipyridamole treatment


title: Control_2


title: Control_3


title: B6N_DMC1 ChIP Rep 2

city: Bar Harbor

first: Natalie

middle: R

last: Powers

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description:
B6_DMC1_ChIP_merge_mm10_RPM.bedgraph
B6_DMC1_merge_DMC1Peaks.bed
B6_DMC1_merge_DMC1Peaks_DefaultSites.bed
B6_DMC1_merge_DMC1Peaks_Hotspots.bed

data_processing:
Fastq files for paired-end sequenced DMC1 samples were trimmed using Trimmomatic (v0.32) and subsequently parsed for detection and selection of paired reads having homology at the 5’ and 3’ ends as established by protocols for single strand DNA enrichment.
These selected paired-end reads represent the detectable single stranded DNA reads. Selected reads were aligned to mm10 genome using BWA (0.5.10-tpx) and bam files were parsed for detection and subsequent selection of single ended reads containing true genomic sequence versus fill-in sequence at the homologous region.
Fastq files were created containing only the single ended, single stranded DNA reads for subsequent alignments. Peaks were called utilizing MACS 2.0 with the read extension parameter set to 800 in order to force pileups.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome_build: mm10
Supplementary_files_format_and_content: MACS callpeak

source_name: Anti-DMC1 B6N_testis_SSDS_2

growth_protocol: Germ cells were extracted from 8 weeks old testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol:
To determine the sites and frequencies of double-stranded breaks in mouse spermatocytes ChIP was performed on 2-month old testis samples using anti-DMC1 antibody which specifically recognizes single-stranded end protruding from germ cell-specific double-stranded ends as per Brick et. al. 2012. Germ cells were isolated from the desired genotypes using Dounce Homogenizer, crosslinked, sonicated and immunoprecipitated with anti-DMC1(C-20) antibody.
The libraries were prepared using adapters from TruSeq DNA LT sample prep kit. Libraries were prepared according to the prescribed protocols and amplified for 12 cycles. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation. The amount of DNA after PCR is low to reduce background. Important comments:  The samples were run on Bioanalyzer for quality control. Libraries were sequenced on an Illumina® HiSeq 2500, with 75 bp paired-end reads.

value: Testis

value: Wildtype

tag: chip antibody

value: Anti-DMC1 (C-20); vendor:Santa Cruz; sc-8973


title: mm_ret_M1_D8C_rep1

value: 1 month

value: WT

value: fresh tissue


title: B6N_DMC1 ChIP Rep 3

source_name: Anti-DMC1 B6N_testis_SSDS_3

tag: strain


title: OSN3 Cel-Seq2 scRNA-Seq


title: B6N_DMC1 ChIP Rep 1

source_name: Anti-DMC1 B6N_testis_SSDS_1

tag: tissue


title: V_S

description: SK-hep1 received sorafenib treatment


title: OSN2 Cel-Seq2 scRNA-Seq

tag: cell type


title: OSN1 Cel-Seq2 scRNA-Seq


title: Control_4

tag: genotype


title: S29_DM

description: Ectopic expression of SLC29A2 in SK-hep1


title: STING_1


title: RPE-1 aphidicolin treated_rep2

city: Leiden

first: Marten

last: Hornsveld

address: Einthovenweg 20

institute: Leiden University Medical Center

data_processing:
RNA-seq alignment using TopHat 2.1.1
Differentially expressed genes were called with DEseq2
Genome_build: hg19
Supplementary_files_format_and_content: Individual samples were downsampled to 10 million reads, subsequently diferentially expressed genes were indentified by DEseq2

source_name: retinal Pigment Epithelial Cells

growth_protocol: RPE-1 cells were cultured in DMEM-F12 (Lonza) containing 10% FBS (Bodinco), 100U/ml penicillin and 100mg/ml streptomycin (Lonza)

extract_protocol:
RNA from cultured cells was extracted using TRIzol reagent (Invitrogen)
Strand-specific libraries were generated using the TruSeq PolyA Stranded mRNA sample preparation kit (iIlumina)

treatment_protocol: Cells were treated with 400nM aphidicolin for 7 hours

tag: protocol

value: hTERT immortalized

value: Retinal Pigment Epithelium

value: Aphidicolin 400nM 7 hours


title: V_DM

description: Control from SK-hep1


title: SSD1_4_42_CRAC

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

institute: University of Edinburgh

description: CRAC: sequencing of RNA UV-crosslinked to proteins and pulled down with a tandem HTP-tag

data_processing:
Library strategy: CRAC
pyFastDuplicateRemover.py: Removes PCR duplicates by collapsing the data in fasta format
novoalign and samtools: Aligns reads to the Saccharomyces cerevisiae genome and can output to .novo files for downstream analysis with pyReadCounters.py or to SAM files which can then be converted to BAM and indexed BAM files using samtools.
pyReadCounters.py: Generates hit tables with number of reads mapped to gene/transcript features in a gtf file as well as text files containing information about the complexity of the sequencing data and a hit table text file showing the number of intervals mapping sense or antisense to each genomic feature.
pyCalculateFDRs: Calculates the minimum coverage height required to obtain a FDR lower or equal to a threshold and outputs the genomic regions with an FDR below that threshold (set here at 0.01)
Genome_build: Saccharomyces_cerevisiae.EF4.74 (SacCer3)
Supplementary_files_format_and_content: Bedgraph of aligned reads on minus and plaus strands
Supplementary_files_format_and_content: Counts on full-length messenger RNA (coding) transcripts for all 5 samples, in gff-style tab format including transcript chromosome position, start, end, and id. Output by bedtools (multiBamCov).

organism: Saccharomyces cerevisiae BY4741

source_name: Yeast cells

growth_protocol: 100ml starter cultures of yeast strains in SMM-Trp Medium were grown overnight at 30C from freshly isolated single colonies on YPDA plates,  then diluted to around 0.070 x 10^7 cells/ml in 2.86l of SMM-Trp pre-warmed to 30oC and grown at 30oC to a density of 0.7-0.85 x 10^7cells/ml. We grew two biological replicates (independent clones) samples to exponential phase at 30C, and two identically before transferring to pre-warmed media at 42C for 16 minutes.

extract_protocol:
The full protocol for extraction of RNAs bound to SSD1 is available on protocols.io: http://dx.doi.org/10.17504/protocols.io.5ppg5mn. Briefly, total cell lysates were extracted from the frozen cell pellets using Zirconia beads, cleared of cell debris and then incubated with IgG Sepahrose beads to pull down the ProteinA moiety of the HTP-tagged SSD1 and its cross-linked RNAs. After sufficient washes to remove non-specific protein, etc, the bound protein was released from the beads using HALO-TEV protease and then collected by passing through SnapCap columns.The cross-linked RNA was partially digested with a 1:100 dilution of RNace-IT (Promega) at 37oC for 5 min and stopped by the addition of Guanidine HCl. NaCl and Imidazole were added to 300mM and 10mM respectively  and the protein/RNA mixtures bound to Nickel beads at 4oC overnight. The beads were transferred to fresh SnapCap columns, washed extensively and the cross-linked RNAs treated with Alkaline Phosphatase to remove 3' phosphates left after RNase-cleavage. After extensive washing and removal of Guanidinium, a miRCat-33 linker (activated 5' and blocked 3') was ligated to the 3'-end for 5h at 25oC. After further washing, the 5'ends of the bound RNAs were phosphorylated using T4 Polynucleotide Kinase and gamma-32P-ATP, adding cold ATP to ensure almost all of the 5' ends were phosphorylated, and the columns extensively washed again. 5' SOLEXA linkers (mixed DNA:RNA oligos with inverted ddT at the 5’ end to prevent degradation, a barcode sequence at the 3’ end  and a random 3mer to reveal PCR duplicates plus constant 3 nucleotide 3’ termini to ensure all linkers ligate with equal efficiency) were ligated on-bead and incubated at 18oC overnight. The beads were washed 3x and the tagged protein-RNA samples eluted by increasing the Imidazole concetration to 150mM. 30 and 42oC samples from the same biological replicate were pooled at this stage and the mixture was precipitated with 5V acetone, in the presence of 40ug GlycoBlue to help visualise the pellets, by incubation at -20oC for 2 hours.The pellets were resuspended in 1x NuPAGE Sample Buffer, heated to 65oC for 10 mins and loaded and run on a 10 well NuPAGE 4-12% gradient gel alongside SeeBlue Plus 2 Markers in 1x MOPS Buffer which was then blotted onto Hybond C Extra Nitrocellulose membrane in 1x NuPAGE Transfer Buffer (without methanol as SSD1-HTP is a big protein). The membrane was briefly dried and placed between 2 acetate sheets and exposed for autoradiography with intensifying screens at -80oC overnight. After developing the film, strong bands with smears above of protein:RNA complexes of the expected sizes (around 145kDa) in the SSD1-HTP sample lanes but only a faint smear in the BY4741 sample were detected. The film was used to identify the location of the smears on the membrane and cut through to remove the relevant fragments of nitrocellulose which were placed in Eppendorf SafeLock tubes and then digested with Proteinase K for 2h at 55oC before Phenol/Chloroform/Isoamyl alcohol extraction, ethanol precipitation in the presence of 20ug of Glycoblue, washed in 70% ethanol and resuspended in Reverse Transcription (RT) Reaction Mix containing miRCat oligo and dNTPs, heated at 80oC for 3 min and Superscript IV Reverse Transcriptase, RNasin and DTT added to the reactions which were incubated at 50oC for  1 hour. The enzyme was heat inactivated andthe samples digested with RNase H for 30 mins at 37oC before storing at -20oC overnight.
3x 50ul PCR Reactions for each of the 3 RT reactions were prepared with PCRFwd and Rev primers, LA Taq Buffer, dNTPS and LA Taq Polymerase and amplified  for 22 cycles to yield 5-50ng  of DNA from each sample. After pooling the PCR reactions, ethanol precipitation and resuspending  in 1x Purple Loading Dye (NEB), the amplified samples were run in alternating lanes on a 3% Metaphor agarose gel in 1x TBE Buffer with 50bp ladders run on either side and staining with SYBRSafe. The gel was then scanned on a PhosphorImager using the '1 laser option' and the negative image printed at 100% magnification and used as a template to determine the areas of the gel containing the amplified library samples  (larger than primer dimers and <180bp fragments) which were then excised by careful cutting with a scalpel, extracted from the gel using a Qiagen Gel Extraction Kit, washing an extra time to ensure complete removal of Guanidine HCl.  20ul of nuclease-free water was added to each column and left on the membrane for 5 mins before elution. Individual library samples (+/- HS) were quantified on the Qubit and, assuming an average DNA Fragment size of 150nt (including linkers) diluted to 10nM before mixing 1ul of each library sample, making up to 5ul with nuclease-free water, adding 5ul of 0.1M NaoH and denaturing the combined library for 5 mins at room temperature, neutralising with 5ul of 200mM Tris.HCl, ph6.8, vortexing and spinning down before mixing with 985ul of of Illumina Hybridization Buffer, vortexing and spinning again. 500ul of this pooled library  was then loaded on the Illumina MiniSeq following the manufacturer's instructions.

treatment_protocol: Samples at 30oC were transferred directly to the Megatron and cross-linked with uvC light for 100s before rapid filtration and collection of the cells on Millipore 0.45um MF-membrane filters which were then transferred to pre-chilled 50ml tubes containing 50ml PBS on ice. After removal of the filters, the cells were split between 3 pre-chilled tubes and were spun at 3000rpm for 5 mins at 4oC, the supernatent removed and the cell pellets (~1ml per tube) snap frozen on dry ice before transfer to storage at -80oC. Samples for Heat Shock at 42oC were grown as for 30oC samples, collected by filtration on Millipore filters which were immediately transferred to 2.86l of SMM-Trp medium pre-warmed to 42oC and incubated at 42oC for a total of 16 mins, including the time required to pour into the Megatron, and then uv cross-linked, collected and aliquoted as for the 30oC samples.

tag: background strain

tag: submission date

value: 16min heat shock at 42C

tag: genotype/variation


title: BY4741_Ctrl_CRAC

tag: treatment

value: Exponential phase 30C

value: Control


title: SSD1_4_30_CRAC


title: SSD1_3_42_CRAC


title: post_SM6

city: Kyoto

first: Takayuki

last: Nakagawa

state: Kyoto

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of Otolaryngology Head and Neck Surgery

institute: Kyoto University Hospital

description: Before hair cell regeneration

data_processing:
RTA3.4.4 (real time analysis) is used for the initial image analysis and base calling.
BCL -> FASTQ conversion process: bcl2fastq v2.16
The senescence data was mapped to the genome sequence with STAR ver. 2.7.1a.
RNA-seq reads derived from rRNAs were searched with Bowtie2 ver. 2.1.0, and removed.
Genome_build: GRCg6a/galgal6
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. RSEM-1.3.0.

organism: Gallus gallus

source_name: Basilar papilla

growth_protocol: Explant cultures of basilar papillae dissected out from post-hatched day 1 chicks

extract_protocol:
Total RNA was extracted for every 50 cultured basilar papillae per each sample using an RNeasy Plus Micro kit (Qiagen)
0.8 μg of total RNA was subjected to library synthesis using the NEB Next Ultra RNA Library Prep Kit for Illumina.  mRNA from eukaryotic organisms is enriched using oligo(dT) beads and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR.

treatment_protocol: Thermolysin treatment was performed to remove the surrounding tissues from the sensory epithelium

value: basilar papilla explant culture

value: 6-h culture after 48-h damage

value: supporting cells


title: RPE-1 Untreated_rep2

value: DMSO


title: RPE-1 Untreated_rep1


title: SM24

description: Total hair cell loss

value: 24-h damage


title: SM48

description: End of damaging

value: 48-h damage


title: Teosinte_DroughtSubmergence

city: Tuxtepec

first: Blanca

middle: Estela

last: Barrera-Figueroa

state: Oaxaca

address: Av. Circuito Central 200

department: Instituto de Biotecnología

country: Mexico

institute: Universidad del Papaloapan

description: Plants were water-deprived by interrupting water supply until half their initial weight (water deficit). Then, water was added in small amounts daily to maintain a regular water deficit condition for 6 days. Immediately after this, plants were treated in empty 32 cm depth submergence tanks that were added with filtered tap water to increase the water column by 6 cm every 2 h for 10h until the maximum capacity was reached and plants were fully submerged. The plants were maintained in this treatment for 48h.

data_processing:
Base calling was performed with the Illumina in-house software (Bustard)
Quality control, adapter trimming, removal of sequences smaller than 18nt and longer than 35nt, mapping to the B73 RefGen-v5, and normalization of counts, were carried out using CLC Genomics Workbench 12.
Filtered sequences were compared to conserved and known miRNA sequences from maize and other plants registered in the MiRBASE, with CLC Genomics Workbench 12.
Genome_build: B73 RefGen_v5
Supplementary_files_format_and_content: Text (txt) files with raw counts for every sequence in the corresponding library and matrix (xlsx) file with normalized counts for plant miRNAs.

organism: Zea mays subsp. parviglumis

source_name: Shoot

growth_protocol: Maize seeds (Zea mays ssp. mays) of tropical homozygous line CML496, and teosinte (Zea mays ssp. parviglumis) were germinated directly in pots with Sunshine Mix 3, three seeds per pot. Maize and teosinte plantlets were maintained in a growth room at 23°C and 16h/8h light/dark cycle.

extract_protocol:
The shoots were removed, frozen in liquid nitrogen and processed with TRIzol to extract total RNA. The small RNA fraction of 20-30 nt was size-purified from total RNA on denaturing polyacrylamide gels.
Small RNA fractions purified from 12µg of total RNA were ligated to a preadenylated adapter in the 3'end. Next,  the 5' RNA Illumina adapter was ligated to the 5'end of small RNAs. The products with adapters in both ends were used in cDNA synthesis reactions followed by a 15 cycle PCR with primers compatible with Illumina. The products were purified, quantified, and sequenced on the Illumina HiSEQ2500.

tag: subspecies

value: parviglumis

tag: developmental stage

value: 28 days after sowing

value: Drouht for 6 days followed by submergence for 48 h

tag: rna fraction

value: Small RNAs


title: SSD1_3_30_CRAC


title: SM0

description: No hair cell loss

value: before damage

value: hair cells and supporting cells


title: Teosinte_SubmergenceDrought

description: Plants were treated in empty 32 cm depth submergence tanks that were added with filtered tap water to increase the water column by 6 cm every 2 h for 10h until the maximum capacity was reached and plants were fully submerged. The plants were maintained in this treatment for 48h. Following, these plants were water-deprived by interrupting water supply until half their initial weight (water deficit). Then, water was added in small amounts daily to maintain a regular water deficit condition for 6 days.

value: Submergence for 48 h followed by drought for 6 days


title: Control_1

tag: gender

value: Male

value: Wild-type

value: Colon

value: implanted MC38 cells into peritoneum of C57BL/6 mice

value: control


title: RPE-1 aphidicolin treated_rep1

value: hTERT immortalized

value: Retinal Pigment Epithelium

value: Aphidicolin 400nM 7 hours


title: whole gut total RNA- st95 mut2

city: Chapel Hill

first: Celia

middle: E

last: Shiau

state: NC

address: 4344 Genome Sciences Building

institute: UNC Chapel Hill

data_processing:
Alignment of reads to the UCSC GRCz10/danRer10 genome build using BBmap v37.99 (assigning ambiguous reads randomly)
Calculating gene counts using the featureCounts tool in the Subread suite v1.5.2 with UCSC annotations
Analysis of differential gene expressions with DESeq2 (R v3.3.1)
Genome_build: GRCz10/danRer10
Supplementary_files_format_and_content: gene counts using featureCounts tool; genes short list from analysis using CLC Genomics Workbench 9

organism: Danio rerio

source_name: whole gut total RNA- st95 mut

growth_protocol: for details see Earley et al., 2018 Cell Reports

extract_protocol:
Toal RNA extracted by using the RNAqueous-Micro Total RNA Isolation Kit (Ambion).
Total RNA was used to create cDNA libraries with adapters using the KAPA stranded mRNA-seq kit. Magnetic oligo-dT beads were used to capture mRNAs. Amplification of libraries was conducted using high fidelity, low bias PCR.

treatment_protocol: no treatment

tag: age

value: adult

value: irf8 homozygous mutant

value: intestine


title: Teosinte_Drought

description: Plants were water-deprived by interrupting water supply until half their initial weight (water deficit). Then, water was added in small amounts daily to maintain a regular water deficit condition for 6 days.

value: parviglumis

value: 28 days after sowing

value: Drought for 6 days


title: whole gut total RNA- st95 mut1


title: Teosinte_Submergence

description: Plants were treated in empty 32 cm depth submergence tanks that were added with filtered tap water to increase the water column by 6 cm every 2 h for 10h, until the maximum capacity was reached and plants were fully submerged. The plants were maintained in this treatment for 48h.

value: Submergence for 48 h

value: Small RNAs


title: Ctrl LSK cells 5FU

city: BRONX

first: Shuxian

last: Dong

state: NY

address: 1300 morris park ave., Chanin 504

institute: albert einstein college of medicine

description: gene expression data from Ctrl bone marrow LSK cells 8 days post 5FU injection

hyb_protocol: 5.5 micrograms of cDNA from each sample was hybridized to ThermoFisher Scientific (Affymetrix) GeneChip Mouse Gene 2.0 ST Array (902118). Hybridization cocktail was made using the hybridization kit (ThermoFisher Scientific, 900454)

scan_protocol: array scans were performed according to the manufacturer's instructions using the high-resolution GeneArray Scanner 3000 7G (ThermoFisher Scientific, Santa Clara, CA,) (Affymetrix).

data_processing: The data were analyzed with the GeneChip Command Console Software from ThermoFisher Scientific (Affymetrix) default analysis settings.

source_name: LSK cells from Ctrl mice bone marrow at day8 after 5FU

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: LSK cells were freshly isolated from bone marrow by cell sorter acording to the surface marker (Lin-Scal+Ckit+) staining, cell pellete were flash frozen in liquid nitrogen and stored in -80 until RNA extraction

extract_protocol: Extraction was performed by RNeasy Micro kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: mice were injected with/without 150mg/kg 5FU and sacrificed at day8 after the injection.

tag: sample type

value: mice (male, 4m) bone marrow LSK


title: whole gut total RNA- st95 het2

source_name: whole gut total RNA- st95 het

value: irf8 heterozyous mutant


title: Teosinte_Control

description: Untreated

value: Untreated


title: whole gut total RNA- st95 het1


title: THP-1 control2

city: Guangzhou

first: Ran

last: Wei

state: Guangdong

address: Dongfengdong Road 651, Guangzhou

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina 1.9 used for basecalling.
The obtained sequence reads were filtered by using the SeqPrep and Sickle to delete some low quality reads.
The final clean data was mapped to the human reference genome (GRCh38) using Tophat and gene expression changes were analyzed using Cufflinks.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with FPKM values for differentially expressed genes (FC≥2&FDR≤0.05) between sample1 and sample3 (THP1-THP1gongG2_gene_DEG.anno.xls) or between sample2 and sample4 (THP-THP1-gong-97.DEG.xls).

source_name: periphery blood

growth_protocol: MHCC-97H and HepG2 cells were maintained in DMEM (Hyclone) with 10% fetal bovine serum (FBS, Gibco), and THP-1 cells were cultured in RPMI 1640 medium (Hyclone) with 10% FBS.

extract_protocol:
Total RNA was prepared from THP-1 derived macrophages and THP-1 derived TAMs (THP-1 derived macrophages co-cultured with MHCC-97H or HepG2 cells) using the TRIzol reagent.
The libraries were generated by using the Illumina TruseqTM RNA sample prep Kit (Illumina, USA). Then, the prepared libraries were sequenced using an Illumina HiSeq 4000 sequencer (Biomarker Technologies, China). The obtained sequence reads were filtered by using the SeqPrep and Sickle to delete some low quality reads. The final clean data was mapped to the human reference genome (GRCh38) using Tophat and gene expression changes were analyzed using Cufflinks.

treatment_protocol: THP-1 cells were polarized into macrophages using PMA (Sigma, 100ng/ml) treatment for 24 hours. As for THP-1 derived TAM, THP-1 cells (2×106 cells) treated with PMA were placed on the lower chamber of a 6-well transwell plate. Meanwhile, HepG2 or MHCC-97H cells were placed on the 0.4μm porous membrane of upper chamber. After 24 hours, we co-cultured HepG2 or MHCC-97H cells with THP-1 derived macrophages. Then 48 hours later, macrophages were collected for RNA extraction.

value: human leukemia monocytic cell line

value: periphery blood

value: untreated


title: THP-1 co-cultured with MHCC-97H

value: co-cultured with MHCC-97H for 48h


title: THP-1 co-cultured with HepG2

value: co-cultured with HepG2 for 48h


title: CD8+ biological replicate 2

city: Naples

first: Mario

last: Galgani

address: via S. Pansini, 5

country: Italy

institute: IEOS Istituto per l'endocrinologia e l'oncologia sperimentale

description: Gene expression data from human lymphocytes

hyb_protocol: Hybridization is an integral part of the GeneChip Pico protocol (Cartridge Array Hybridization on the GeneChip¨ Instrument)

scan_protocol: The arrays were scanned on a GeneChip scanner 3000 7G

data_processing: Data was analyzed using the the Affymetrix Expression Console software. Normalization was done by RMA normalization

source_name: CD8+ lymphocyte subset flow sorted by PBMCs

label_protocol: The RNA was labeled using 2 ng and the GeneChip Pico Reagent kit and according to AffymetrixÕs protocol

growth_protocol: Cells were flow sorted and frozen immediately upon isolation

extract_protocol: The RNA was extracted according the RNNeasy Plus Micro Handbook 12/2014 and eluted using 20µl H2O

treatment_protocol: Cells were not treated in any way

value: T cell

tag: cell subset


title: AMKO LSK cells Basal

description: gene expression data from AMKO bone marrow LSK cells

source_name: LSK cells from AMKO mice bone marrow at day0 after 5FU


title: CD3+CD56- biological replicate 2

source_name: CD3+CD56- lymphocyte subset flow sorted by PBMCs


title: THP-1 control1


title: CD8+ biological replicate 3