title: RNA-Seq PAEC DMSO Replicate 3

data_processing:
Raw reads trimmed using FASTQ groomer.
Aligned to the human genome using BWA-aln
Quality control and read quantification  using SeqMonk
Differentially expressed merged transcripts were quantified using DESeq2 and EdgeR
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text file includes raw transcript counts from SeqMonk quantification

source_name: Lung

growth_protocol: PAEC were cultured in complete EC media (EC basal medium, ECGS and 5% FBS, ScienCell, Carlsbad, CA).

extract_protocol:
After trypsinization, cells were collected by centrifugation and snap-frozen in liquid N2.  Total RNA was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared for sequencing using  ScriptSeq Complete Gold kit (Epicentre, Madison, WI) and standard Illumina protocols

treatment_protocol: PAEC were kept in complete EC media and treated  for 24 h with Doxorubicin (0.5 µg/ml) or PBS vehicle control or Nutlin-3 (10 µM) or DMSO vehicle control before total RNA extraction.

value: PAEC, healthy donor

tag: passages

tag: pharmacological treatment

value: DMSO (10 µL) for 24 h


title: muscle of sedentary aged subject # 4

status: Public on Mar 03 2021

type: SRA

city: Bologna

first: Valentina

last: Indio

state: Bologna

address: via Giuseppe Massarenti,11

country: Italy

institute: University of Bologna

description: 80X2 paired-end sequence reads

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for sequance adapters and low-quality tails, then mapped to hg19 reference using tophat (2.0.9)
Raw count  were computed using the Python package HTSeq-count (0.6.1p1) adopting the gene annotations Ensembl GRCh37.72. Data were normalized as count per million adopting the the R-bioconductor package edgrR (3.8.6)
Genome_build: hg19
Supplementary_files_format_and_content: text file include count per million (cpm) for every gene

molecule: total RNA

organism: Homo sapiens

source_name: muscle  vastus lateralis

extract_protocol:
TRIZOL® (Invitrogen SRL, Milan, Italy)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: male

tag: age (years)

tag: % of resistance training

tag: % of endurance training

tag: average weekly hours of training


title: mRNA_Th17-23_WT_rpt2_OS1417

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

country: USA

institute: NIAMS/NIH

data_processing:
BCL conversion and demultiplexing (Casava 1.8.2 for ChIP, miRNA and mRNA)( Bcl2fastq and CellRanger for scRNA).  scRNA-seq raw files: read1_26/i7index_8/read2_98.
Mapping (Tophat 2.0.8 and Bowtie 2-2.1.0  for mRNA) (Bowtie v0.12.8 for ChIP and miRNA) (CellRanger for scRNA)
peak calling (MACS v1.4.2: default p-value threshold of 1E-5 for ChIP-seq)
BigWig tracks (BEDTOOLS v2.24, UCSC tool bedGraphToBigWig)
Genome_build: mm9 (ChIP, miRNA, mRNA); mm10 (scRNA)
Supplementary_files_format_and_content: BigWig files (ChIP, miRNA, mRNA); Robj, CellRanger output files (scRNA)

organism: Mus musculus

source_name: in vitro cultured CD4+ T cells

growth_protocol: CD4+ T cells were enriched by negative selection (Miltenyi), then purified to naïve population by sorting (CD4+CD62L+CD44-CD25-), then cultured with plate-bound anti-CD3 and anti-CD28 for 3 days with cytokines/antibodies indicated in treatment section.

extract_protocol:
Total RNA was isolated using TRIzol or mirVana miRNA Isolation kit (Thermo Fisher Scientific)
TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) using 200 ng of total RNA

tag: strain

tag: tissue

value: spleen and lymph node

tag: cell type

tag: genotype

value: Wild type

tag: growth condition

value: 3 day in vitro culture

tag: treatment

value: IL-6, IL-23, anti-IFNg, anti-IL4


title: Recovered_rep1

city: Palo Alto

first: Yu

last: Liu

state: CA

address: 1215 Welch Road

department: CVI

institute: Stanford University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore
Trimmed data was mapped to hg38 whole genome using STAR
Read counts of each gene was counted by featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: Raw read counts in TXT format

source_name: Line 1 recovered hiPSC-CM

extract_protocol: hiPSC-CMs RNA was harvested using Trizol reagent

value: hiPSC-CMs

tag: differentiation day

value: Recovered


title: Fresh_rep2

source_name: Line 2 fresh hiPSC-CM

value: Fresh


title: RNA-Seq PAEC DMSO Replicate 2

city: Stanford

first: Jan

middle: K

last: Hennigs

state: California

address: 269 Campus Dr

department: Wall Center for Pulmonary Vascular Diseases, Cardiovascular Institute and Pediatrics - Cardiology


title: RNA-Seq PAEC DMSO Replicate 1


title: mRNA_Th1_WT_rpt1_OS1410

value: IL-12, anti-IL4


title: mRNA_Th17full_KO_rpt2_OS3174

value: Th17 (IL-6, TGFb, IL-23, IL1b)

value: IL-6, TGFb, IL-23, IL1b, anti-IL2, anti-IFNg, anti-IL4


title: Fresh_rep3

source_name: Line 3 fresh hiPSC-CM


title: mRNA_Th1_KO_rpt1_OS1449


title: stage 5 sfGFP-GAF(N) Zld-RNAi GFP IP replicate 2

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
St5_GFPGAFN_zld-RNAi_antiGFP_IP_zscore.bw
St5_GFPGAFN_zld-RNAi_antiGFP_IP_peaks.bed

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the Drosophila melanogaster reference genome (version dm6) using bowtie 2 v2.3.5 with the following non-default parameters: -k 2, --very-sensitive
Aligned reads with a mapping quality < 30 were discarded, as were reads aligning to scaffolds or the mitochondrial genome
peak calling was performed using MACS v2 with the following parameters: -g 1.2e8, --call-summits.
To focus analysis on robust, high-quality peaks, we used 100 bp up- and downstream of peak summits, and retained only peaks that were detected in both replicates and overlapped by at least 100 bp.
DeepTools was used to generate  bigWig files.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files generated using DeepTools; scores represent z-score normalized counts. Replicates are merged into single bigWig file.
Supplementary_files_format_and_content: bed files containing peaks. Contains only peaks that were detected in both replicates

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: All stocks were grown on molasses food at 25ºC

extract_protocol:
ChIP was performed as described previously (Blythe and Wieschaus 2015) on: stage 3 and stage 5 hand selected GAF-sfGFP(C) homozygous embryos, stage 3 and stage 5 hand selected w1118 embryos, 2-2.5 hr AEL hand selected embryos from mat-α-GAL4-VP16/+ (II); sfGFP-GAF(N)/ UAS-shRNA-zld (III) females and mat-α-GAL4-VP16/+ (II); sfGFP-GAF(N)/+ (III) females, 2-2.5hr AEL embryos from nos-degradFP/His2Av-RFP (II); sfGFP-GAF(N) (III) females, and 2-2.5hr AEL embryos from His2Av-RFP (II); sfGFP-GAF(N) (III) females. For each genotype, 2 biological replicates were collected. Briefly, 1000 stage 3 embryos or 400-500 stage 5 embryos were collected, dechorionated in 50% bleach for 3 min, fixed for 15 min in 4% formaldehyde and then lysed in 1 mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl). The fixed chromatin was then sonicated for 20 s 11 times at 20% output and full duty cycle (Branson Sonifier 250). Chromatin was incubated with 6 μg of anti-GFP antibody (Abcam #ab290) or 8μl of anti-Zld antibody (Harrison et al. 2011) overnight at 4°C , and then bound to 50 μl of Protein A magnetic beads (Dynabeads Protein A, Thermo Fisher Scientific). The purified chromatin was then washed, eluted, and treated with 90 μg of RNaseA (37°C, for 30 min) and 100 μg of Proteinase K (65°C, overnight). The DNA was purified using phenol/chloroform extraction and concentrated by ethanol precipitation. Each sample was resuspended in 25 μl of water
Sequencing libraries were made using the NEB Next Ultra II library kit and were sequenced on the Illumina Hi-Seq4000 using 50bp single-end reads or NextSeq500 using 75bp single-end reads. Sequencing was performed at the Northwestern Sequencing Core (NUCore).

value: mat-alpha-GAL4-VP16/+ (II); sfGFP-GAF(N)/ UAS-shRNA-zld (III)

tag: developmental stage

value: stage 5

tag: antibody

value: anti-GFP (Abcam #ab290)


title: RNA-Seq PAEC Nutlin Replicate 3

value: Nutlin-3 (10 µM) for 24 h


title: stage 5 sfGFP-GAF(N) Zld-RNAi GFP input replicate 2

description:
St5_GFPGAFN_zld-RNAi_antiGFP_input_zscore.bw
St5_GFPGAFN_zld-RNAi_antiGFP_IP_peaks.bed

value: none (input)


title: stage 5 sfGFP-GAF(N) Zld-RNAi GFP IP replicate 1


title: CH34_ZnR_2_CH34_2

type: RNA

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Comparison of CH34ZnR with CH34 (replicate 2)

hyb_protocol: Labeled cDNA was re-suspended in the universal hybridization buffer (Pronto kit), mixed and added to the spotted slide for overnight hybridization at 42 C in a Tecan HS4800 Pro hybridization station (Tecan Group Ltd, Switzerland). Afterwards, the slide was washed according to Pronto kit’s protocol.

scan_protocol: Slides were scanned (at 532 and 635 nm) using the GenePix Personal 4100A microarray scanner (Molecular Devices, USA).

data_processing: Micro-array spot-signals were analyzed using the GenePix Pro v.6.0.1 software and flagged according to build-in quality criteria. Raw median intensity data were imported into R version 2.7.0 for statistical analysis using the LIMMA package version 2.15.15 (Smyth 2005) as available from BioConductor. Raw data were background-corrected based on convolution of normal and exponential distributions with an offset of 50 (Ritchie et al. 2007). Data were normalized within each array using the printing-tip loess normalization algorithm (Smyth and Speed 2003). The in-slide replicate correlations were calculated using the Duplicate correlation function in the LIMMA package (Smyth 2005). The log expression values were fitted to al linear model and moderated t-statistics were calculated using empirical Bayes method (Smyth 2004). P-values were corrected for multiple testing using the Benjamin and Hochberg’s method to control the false discovery rate (Benjamini and Hochberg 1995).

organism: Cupriavidus metallidurans

source_name: parental strain CH34

label_protocol: Ten micrograms of RNA were reverse transcribed following the instructions provided with the Pronto kit (Promega, United States). Two color labeling, green for control samples and red for condition (metal challenge) samples, was performed using respectively CyTM3-dCTP and CyTM5-dCTP nucleotides (Amersham BioSciences, United Kingdom).

growth_protocol: The strains were cultivated by inoculating 30 mL MM284 in biological triplicates with 300 µL of an exponential growing C. metallidurans CH34 or CH34ZnR culture at 30 °C. These subcultures were allowed to grow until an OD600 value of around 0.6 was reached. Next, each subculture was immediately subdivided in 15 microcentrifuge tubes of 2 mL and cells were harvested by centrifugation for 2 min at 10000 rpm. Supernatant was removed and the bacterial pellets were flash frozen by immersion into liquid nitrogen.

extract_protocol: The bacterial pellets were kept frozen at -80 °C until total RNA extraction was performed using the SV Total RNA Isolation system (Promega Corporation). The quantity of extracted RNA was measured using a NanoDropTM 1000 spectrophotometer (Thermo Scientific). The RNA quality was determined with a Bioanalyzer (Agilent 2100 Electrophoresis Bioanalyzer Agilent Technologies).

tag: medium

tag: phenotype

value: susceptible to high zinc levels

source_name: derivative CH34_ZnR

value: resistant to high zinc levels


title: mRNA_Th17full_WT_rpt1_OS3156

value: spleen and lymph node


title: mRNA_Th17full_KO_rpt1_OS3168


title: RNA-Seq PAEC Nutlin Replicate 2

value: PAEC, healthy donor

tag: passages

tag: pharmacological treatment


title: RNA-Seq PAEC PBS Replicate 3

value: PBS (20 µL) for 24 h


title: mRNA_Th1_WT_rpt2_OS1411

value: Wild type

value: 3 day in vitro culture


title: stage 5 sfGFP-GAF(N) Zld-RNAi GFP input replicate 1


title: RNA-Seq PAEC Nutlin Replicate 1


title: PANC1 S-2 RNA

city: Bronx

first: Kamini

last: Singh

state: NY

address: 1300 Morris Park Ave, Golding 203

department: Molecular Pharmacology

institute: Albert Einstein College of Medicine

data_processing:
Sequence Alignment  The human genome sequence GRCh37 was downloaded from Ensembl public database: http:// www.ensembl.org. Ribosome footprint (RF) reads were aligned to reference genome GRCh37 using STAR26. STAR clips the linker sequence (5’- CTGTAGGCACCATCAAT-3’), which is technically introduced during RF library construction, and trims the remaining sequence from the 3’ end while aligning the reads to reference sequence. Briefly, we set the parameters for PALMapper as follows: maximum number of mismatches: 2; minimum aligning length: 15; maximum intron length (splice alignment): 10000. We only use the uniquely aligned reads for further analysis. To remove ribosomal RNA, the footprint reads were also aligned to a ribosome sequence database using STAR with the same parameters except not allowing splice alignment. We retrieved the human ribosome sequences from SILVA30 databases. The FASTA file was used as reference sequence to align against. The rRNA-aligned reads were filtered out from GRCh37-aligned reads.After removing the ribosomal RNA, we still observed a portion of reads that were dominated by linker sequence and Illumina P7 adapter. These reads can also be trimmed during mapping and cause false alignment. Therefore, we searched a string of 1~8 nt from linker sequence around the trimming site (±2 bp) allowing 1 nt mismatch. We removed the read if there was no such linker sequence. Finally, we filtered out reads ≤ 24-bp and ≥ 36-bp, and the remaining reads with aligned length from 25- to 35-bp were used to analyse the translational effects of CR31B.  Total mRNA sequencing reads were aligned to the GRCh37 reference using STAR31. We performed the splice alignment and only use the uniquely aligned reads with maximum 3 mismatches. rRNA contaminating reads were also filtered out using the same strategy described before.
Footprint Profile Analysis using Ribodiff  For each gene, we only counted the number of aligned reads that were mapped within exonic regions. The genome annotation was downloaded from Ensembl database. We used our recently developed tool Ribodiff to analyze the ribosome footprinting data. Ribodiff uses a negative binomial based generalized linear model to detect the significant difference of footprint read counts in two conditions, taking the RNA-Seq transcriptional measurements as the confounding factor. Therefore it is capable of identifying the genes having translational control that is independent of the transcriptional regulation. The statistical test is a chi-squared test on the deviances of the H0 and H1 model fitting. Benjamini–Hochberg procedure was used to obtain the false discovery rate. The ribosomal distribution curves for a single gene were plotted in a similar way but without normalizing the read coverage, and the coverage was smoothed using ‘moving average’ smoothing algorithm.
Motif analysis  The transcripts of each gene were quantified based on the total mRNA-seq data using MISO26,32. The 5’UTR of most abundant transcript was collected for predicting motifs. Both the significant genes with increased or decreased TE and altered ribosomal distribution and the corresponding background gene sets were predicted by DREME26. We considered the predicted consensus sequences with P < 1×10-4 as significant motifs. Motif occurrences were called using FIMO26 with default parameters for strand specific prediction in human and other species using gene orthologs.

source_name: PANC1 cell line

growth_protocol: Pancreatic cancer cell lines were cultured in DMEM media supplemented with 10% fetal bovine serum and Penicillin/Streptomycin and 10mM Glutamine or as per the ATCC recommended medium.

extract_protocol: Human pancreatic cancer cell line PANC1 cells were treated with CR31B (25 nM; 45 minutes) followed by cycloheximide treatment for 10 minutes. Total RNA and ribosome-protected fragments were isolated following published protocol (Ingolia et al 2012). Deep sequencing libraries were generated from these fragments and sequenced on the HiSeq 2000 platform. Genome annotation was from the Ensembl database release 75 (http:// www.ensembl.org).

treatment_protocol: Cells wre treated with DMSO (CT) or CR31B (CR) (25 nM for 45 minutues).

tag: sample type

value: CR31B treated

tag: molecule

value: RNA


title: mRNA_BMC_CD4_T_gut_KO_rpt3_OS2900

source_name: ex vivo CD4+ T cells

value: intestine

value: CD4+ T cells

value: KO cells isolated from bone marrow chimera mice


title: PANC1 S-3 RNA


title: RNA-Seq PAEC PBS Replicate 2


title: stage 5 sfGFP-GAF(N) GFP IP replicate 2

description:
St5_GFPGAFN_control_antiGFP_IP_zscore.bw
St5_GFPGAFN_control_antiGFP_IP_peaks.bed

value: mat-alpha-GAL4-VP16/+ (II); sfGFP-GAF(N)/+ (III)


title: CH34_ZnR_1_CH34_1

description: Comparison of CH34ZnR with CH34 (replicate 1)


title: mRNA_Th17full_WT_rpt2_OS3162

value: Th17 (IL-6, TGFb, IL-23, IL1b)

value: IL-6, TGFb, IL-23, IL1b, anti-IL2, anti-IFNg, anti-IL4


title: PANC1 S-1 RNA


title: RNA-Seq PAEC PBS Replicate 1


title: CH34_ZnR_3_CH34_3

description: Comparison of CH34ZnR with CH34 (replicate 3)


title: mRNA_BMC_CD4_T_gut_KO_rpt1_OS2894


title: stage 5 sfGFP-GAF(N) GFP IP replicate 1

value: stage 5

value: anti-GFP (Abcam #ab290)


title: stage 5 sfGFP-GAF(N) GFP input replicate 2

description:
St5_GFPGAFN_control_antiGFP_input_zscore.bw
St5_GFPGAFN_control_antiGFP_IP_peaks.bed

value: none (input)


title: Fresh_rep1

source_name: Line 1 fresh hiPSC-CM

value: hiPSC-CMs

value: Fresh


title: PANC1 CT-2 RNA

value: control


title: RNA-Seq PAEC Dox Replicate 3

value: PAEC, healthy donor

value: Doxorubicin (0.5 µg/ml) for 24 h


title: mRNA_BMC_CD4_T_gut_WT_rpt3_OS2899

value: Wild type

value: WT cells isolated from bone marrow chimera mice


title: PANC1 CT-1 RNA

value: RNA


title: RNA-Seq PAEC Dox Replicate 2


title: mRNA_BMC_CD4_T_gut_WT_rpt2_OS2895

value: intestine


title: PANC1 S-3 RF

value: CR31B treated

value: Ribosome protected RNA


title: RNA-Seq PAEC Dox Replicate 1


title: mRNA_BMC_CD4_T_gut_WT_rpt1_OS2893

value: CD4+ T cells


title: PANC1 S-2 RF


title: PANC1 S-1 RF


title: mRNA_BMC_CD4_T_gut_KO_rpt2_OS2896

value: KO cells isolated from bone marrow chimera mice


title: PBS input DNA Replicate 2

data_processing:
Raw reads trimmed using FASTQ groomer.
Aligned to the human genome using BWA-aln
Peaks were called using MACS2.
MACS2 narrowPeak files from two biological replicates were submitted into Irreproducible Discovery Rate (IDR) pipeline.
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt files were generated using IDR pipeline.

extract_protocol:
PAEC pellets were treated with hypotonic buffer for 10 min on ice and then were homogenized using a glass homogenizer.  Nuclear pellets were re-suspended in RIPA buffer (Millipore) and incubated for 30 min on ice. Chromatin was sheared with SFX250 Sonifier (Branson, Dunbury, CT).
The ChIP-DNA samples were end-repaired and A-tailed.  Illumina TruSeq adapters (Illumina, San Diego, CA) were ligated and size-selected from the gel before performing PCR amplification.

treatment_protocol: PAEC were kept in complete EC media and treated  for 24 h with Doxorubicin (0.5 µg/ml) or PBS vehicle control before performing p53 ChIP. Cells were then trypsinized and cross-linked with 1% formaldehyde (EMD Millipore), for 10 min at room temperature on a stirrer.  To neutralize formaldehyde, 2M glycine (ThermoFisher Scientific) were added and incubated for five minutes at room temperature while stirring.  The cells were washed with ice cold PBS twice, pelleted, snap-frozen and stored at -80°C.

value: PBS (20 µL) for 24 h

tag: chip antibody


title: stage 5 sfGFP-GAF(N) degradFP ZLD IP replicate 2

description:
processed data file:
degrad_aZLD_IP_cpm.bw
degrad_aZLD_IP_peaks.bed
MG-8_degradFP_2_2-2-5hrs_IP_S8

data_processing:
ChIP-seq data was aligned to the Drosophila melanogaster reference genome (version dm6) using bowtie 2 v2.3.5 with the following non-default parameters: -k 2, --very-sensitive
Aligned reads with a mapping quality < 30 were discarded, as were reads aligning to scaffolds or the mitochondrial genome
peak calling was performed using MACS v2 with the following parameters: -g 1.2e8, --call-summits.
To focus analysis on robust, high-quality peaks, we used 100 bp up- and downstream of peak summits, and retained only peaks that were detected in both replicates and overlapped by at least 100 bp.
DeepTools was used to generate  bigWig files
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files generated using DeepTools; scores represent z-score normalized counts. Replicates are merged into single bigWig file
Supplementary_files_format_and_content: bed files containing peaks. Contains only peaks that were detected in both replicates

source_name: stage 5 sfGFP-GAF(N) degradFP ZLD IP

extract_protocol:
ChIP was performed as described previously (Blythe and Wieschaus 2015) on hand selected embryos: stage 3 and stage 5 GAF-sfGFP (C) homozygous embryos, stage 3 and stage 5 w1118 embryos, stage 5 embryos from mat-α-GAL4-VP16/+ (II); sfGFP-GAF (N)/ UAS-shRNA-zld (III) females, stage 5 embryos from nos-degradFP/His2Av-RFP (II); sfGFP-GAF (N) (III) females, and stage 5 embryos from His2Av-RFP (II); sfGFP-GAF (N) (III) females. Briefly, 1000 stage 3 embryos or 400-500 stage 5 embryos were collected, dechorionated in 50% bleach for 3 min, fixed for 15 min in 4% formaldehyde and then lysed in 1 mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl). The fixed chromatin was then sonicated for 20 s 11 times at 20% output and full duty cycle (Branson Sonifier 250). Chromatin was incubated with 6 μg of anti-GFP antibody (Abcam #ab290) or 8μl of anti-Zld antibody (Harrison et al. 2011) overnight at 4°C , and then bound to 50 μl of Protein A magnetic beads (Dynabeads Protein A, Thermo Scientific). The purified chromatin was then washed, eluted, and treated with 90 μg of RNaseA (37°C, for 30 min) and 100 μg of Proteinase K (65°C, overnight). The DNA was purified using phenol/chloroform extraction and concentrated by ethanol precipitation. Each sample was resuspended in 25 μl of water.
Sequencing libraries were made using the NEB Next Ultra II library kit and were sequenced on the Illumina Hi-Seq4000 using 50bp single-end reads at the Northwestern Sequencing Core (NUCore).

value: nos-degradFP/His2Av-RFP (II); sfGFP-GAF(N) (III)

value: 2-2.5 hour embryos

value: embryo

value: anti-Zelda (Harrison et al., PLoS Genetics 2011)


title: PBS input DNA Replicate 1


title: PANC1 CT-3 RF


title: stage 5 sfGFP-GAF(N) degradFP ZLD input replicate 1

description:
processed data file:
degrad_aZLD_input_cpm.bw
degrad_aZLD_IP_peaks.bed
MG-5_degradFP_1_2-2-5hrs_Input_S5

source_name: stage 5 sfGFP-GAF(N) degradFP ZLD input

value: none (input)


title: stage 5 sfGFP-GAF(N) degradFP ZLD IP replicate 1

description:
processed data file:
degrad_aZLD_IP_cpm.bw
degrad_aZLD_IP_peaks.bed
MG-6_degradFP_1_2-2-5hrs_IP_S6


title: PANC1 CT-3 RNA

value: control


title: stage 5 sfGFP-GAF(N) degradFP ZLD input replicate 2

description:
processed data file:
degrad_aZLD_input_cpm.bw
degrad_aZLD_IP_peaks.bed
MG-7_degradFP_2_2-2-5hrs_Input_S7


title: Dox input DNA Replicate 2

value: PAEC, healthy donor


title: PANC1 CT-2 RF


title: Mycobacterium abscessus strain GD91 grown to log phase

city: Pittsburgh

first: Rebekah

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.17 using a quality score cutoff of 30
Reads were aligned simultaneously to host and phage genomes using bowtie2 version 2.3.4.2
Reads that did not uniquely map to the reference genomes were removed with the sed command line utility using the "XS:i" flag in the bowtie alignment output
SAM format was converted to BAM format using samtools version 1.9
BAM format was converted to BED format using bedtools version 2.27.1
Expression levels were computed as reads mapped per base pair per strand ("minus" and "plus") using the genomecov tool of bedtools version 2.4.35
Genome_build: various M. abscessus strains that are being submitted to GenBank
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("minus" and "plus" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Mycobacteroides abscessus

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen), rRNA was depleted using QIAseq FastSelect (Qiagen).
Libraries were generated using NEBNext Ultra RNA library kit (NEB)

value: M. abscessus GD91

tag: growth phase

value: log phase


title: stage 5 sfGFP-GAF(N) ZLD IP replicate 2

description:
processed data file:
GFP_GAF_aZLD_IP_cpm.bw
GFP_GAF_aZLD_IP_peaks.bed
MG-4_sfGFPGAF-n-2_2-2-5hrs_IP_S4

source_name: stage 5 sfGFP-GAF(N) ZLD IP

value: His2Av-RFP (II); sfGFP-GAF(N) (III)


title: PANC1 CT-1 RF


title: Dox input DNA Replicate 1

value: Doxorubicin (0.5 µg/ml) for 24 h


title: p53_ChIP_Seq PBS Replicate 2

value: p53 (Cell Signaling Technology, #2425, clone 1C12, lot #10)


title: Mycobacterium abscessus strain GD54 grown to log phase

tag: strain

value: M. abscessus GD54


title: stage 5 sfGFP-GAF(N) GFP input replicate 1

value: mat-alpha-GAL4-VP16/+ (II); sfGFP-GAF(N)/+ (III)

value: stage 5


title: Mycobacterium abscessus strain GD43A grown to log phase

value: M. abscessus GD43A


title: p53_ChIP_Seq PBS Replicate 1

value: PBS (20 µL) for 24 h


title: Mycobacterium abscessus strain GD17 grown to log phase

value: M. abscessus GD17


title: stage 5 sfGFP-GAF(N) ZLD IP replicate 1

description:
processed data file:
GFP_GAF_aZLD_IP_cpm.bw
GFP_GAF_aZLD_IP_peaks.bed
MG-2_sfGFPGAF-n-1_2-2-5hrs_IP_S2

value: 2-2.5 hour embryos

tag: tissue


title: p53_ChIP_Seq Dox Replicate 2

tag: cell type


title: Mycobacterium abscessus strain GD05 grown to log phase

value: M. abscessus GD05


title: B24

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Bovine genome assembly: (ARS-UCD1.2)
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Bos taurus

source_name: Muscle

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA concentration and quality were determined using the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). All samples had RNA integrity number equal or greater than 6.1.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.

value: Muscle

tag: breed

value: Bos taurus x Bos indicus

tag: animal

tag: date collected

tag: year

value: MOLMET


title: B23

tag: treatment


title: B22

value: NOSUP


title: stage 5 sfGFP-GAF(N) ZLD input replicate 1

description:
processed data file:
GFPGAF_aZLD_input_cpm.bw
GFP_GAF_aZLD_IP_peaks.bed
MG-1_sfGFPGAF-n-1_2-2-5hrs_Input_S1

source_name: stage 5 sfGFP-GAF(N) ZLD input

tag: genotype

tag: developmental stage

value: embryo

tag: antibody

value: none (input)


title: stage 5 w1118 GFP IP replicate 2

description:
processed data file:
St5_GAF_IP_w1118_cpm.bw
MG8_Stage_5_W1118_IP_sample_GFP_antibody_S4

source_name: stage 5 w1118 GFP IP

value: anti-GFP (Abcam #ab290)


title: p53_ChIP_Seq Dox Replicate 1

source_name: Lung

value: PAEC, healthy donor

tag: passages

value: Doxorubicin (0.5 µg/ml) for 24 h


title: B20


title: Mycobacterium abscessus strain GD22 grown to log phase

value: M. abscessus GD22

value: log phase


title: B19


title: stage 5 sfGFP-GAF(N) ZLD input replicate 2

description:
processed data file:
GFPGAF_aZLD_input_cpm.bw
GFP_GAF_aZLD_IP_peaks.bed
MG-3_sfGFPGAF-n-2_2-2-5hrs_Input_S3

value: His2Av-RFP (II); sfGFP-GAF(N) (III)


title: Naive #4

city: Kuopio

first: Shalini

last: Das Gupta

address: Neulaniementie 2, P.O.B. 1627

department: A.I.Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Raw sequencing data was analysed with the Qiagen Geneglobe Data analysis center (DAC), a freely available web resource to analyze data from Qiagen’s QIASeq NGS library kits (https://geneglobe.qiagen.com/in/analyze/).
Primary quantification of read counts was performed in the DAC, which involved the following steps: (i) trimming of the 3’-adapter and low-quality bases using cutadapt, (ii) identifying the insert sequences and unique molecular indices (UMIs) (reads with <16 bp insert sequences or < 10 bp UMI sequences were discarded), (iii) alignment of the processed reads to the rat reference genome RGSC Rnor_6.0 with a sequential alignment strategy using bowtie (perfect match to miRBase mature, miRBase hairpin, noncoding RNA, mRNA and other RNA, and ultimately a second mapping to miRBase mature, where up to two mismatches are tolerated). Annotation of the miRNAs in the DAC portal was performed with miRBase v21.
Genome_build: RGSC Rnor_6.0, miRBase v21
Supplementary_files_format_and_content: Compiled matrix table with raw counts for every miRNA in every sample

organism: Rattus norvegicus

source_name: Tail-vein plasma

extract_protocol:
Whole blood was drawn from the lateral tail-vein under isoflurane anesthesia, into Microtainer K2 EDTA-tubes. The blood samples were thoroughly mixed with EDTA and placed on ice. Centrifugation was performed immediately at 1300g for 10 min (+4°C) to obtain plasma. RNA was isolated from 200 µL plasma using the miRNeasy serum/plasma kit.
Small RNA libraries were prepared with QIASeq miRNA library kit for Illumina NGS systems.
Small RNA-Seq. Single-end sequencing of 75 bp reads performed at a depth of 12M, with one sample/lane in the Illumina NextSeq 550.

value: Sprague-Dawley

tag: age

value: Adult

tag: group

value: Naive


title: stage 5 w1118 GFP input replicate 2

description:
processed data file:
St5_GAF_input_w1118_cpm.bw
MG8_Stage_5_W1118_Input_S2

source_name: stage 5 w1118 GFP input

value: stage 5


title: stage 5 w1118 GFP input replicate 1

description:
processed data file:
St5_GAF_input_w1118_cpm.bw
MG7_Stage_5_W1118_Input_S1


title: Severe TBI #5

value: Severe TBI


title: stage 5 w1118 GFP IP replicate 1

description:
processed data file:
St5_GAF_IP_w1118_cpm.bw
MG7_Stage_5_W1118_IP_sample_GFP_antibody_S3


title: miRNA-seq_Root_2

city: Hangzhou

first: Pan

last: Xu

address: 132 Tianmushan Road

country: China

institute: Zhejiang Academy of Traditional Chinese Medicine

description:
Paeonia lactiflora Pall.
small RNA

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Paeonia lactiflora

source_name: Root

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedur
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Root

tag: development stage

value: blossom period


title: stage 5 GAF-sfGFP(C) GFP IP replicate 2

description:
processed data file:
St5_GAF_IP_GFP_GAF_cpm.bw
St5_GAF_IP_GFP_GAF_peaks.bed
MG6_Stage5-GAFGFP_IP_S17

source_name: stage 5 GAF-sfGFP(C) GFP IP

value: homozygous GAF-sfGFP(C)


title: B17

value: Muscle

value: Bos taurus x Bos indicus

value: NOSUP


title: Mild TBI #4

value: Mild TBI


title: miRNA-seq_Root_1

description:
Paeonia lactiflora Pall.
small RNA


title: miRNA-seq_Leaf_1

description:
Paeonia lactiflora Pall.
small RNA

source_name: Leaf

value: Leaf


title: Mycobacterium abscessus strain GD21 grown to log phase

value: M. abscessus GD21


title: miRNA-seq_Fruit_2

description:
Paeonia lactiflora Pall.
small RNA

source_name: Fruit

value: Fruit

value: young fruit period


title: stage 5 GAF-sfGFP(C) GFP input replicate 2

description:
processed data file:
St5_GAF_input_GFP_GAF_cpm.bw
St5_GAF_IP_GFP_GAF_peaks.bed
MG6_Stage5-GAFGFP_Input_S16

source_name: stage 5 GAF-sfGFP(C) GFP input

value: embryo

value: none (input)


title: Naive #3

value: Sprague-Dawley

value: Adult


title: miRNA-seq_Fruit_1

description:
Paeonia lactiflora Pall.
small RNA


title: Sham #5

value: Sham


title: B15

value: MOL


title: Mild TBI #5


title: Naive #2

value: Naive


title: B18


title: B12


title: B14


title: Severe TBI #4

value: Severe TBI


title: stage 3 w1118 GFP IP replicate 2

description:
processed data file:
St3_GAF_IP_w1118_cpm.bw
MG4_Stage3-W1118_IP_S23

source_name: stage 3 w1118 GFP IP

value: stage 3

value: anti-GFP (Abcam #ab290)


title: miRNA-seq_Leaf_2

description:
Paeonia lactiflora Pall.
small RNA

value: blossom period


title: stage 5 GAF-sfGFP(C) GFP IP replicate 1

description:
processed data file:
St5_GAF_IP_GFP_GAF_cpm.bw
St5_GAF_IP_GFP_GAF_peaks.bed
MG5_Stage_5_C-GAF-GFP_IP_GFP_antibody_S6

value: homozygous GAF-sfGFP(C)

value: stage 5


title: Naive #1


title: B11

value: Muscle

value: Bos taurus x Bos indicus

value: NOSUP


title: Mild TBI #3

value: Mild TBI


title: B9

value: MOLMET


title: B10


title: frog inner ear

city: Shanghai

first: Zhongying

last: Wang

address: No.639, Zhizaoju Road

department: Otolaryngology Head & Neck Surgery

institute: Shanghai Ninth People’s Hospital , School of medicine, Shanghai Jiao Tong University

data_processing:
RNA concentration and purity levels were measured using a NanoDrop 2000 spectrophotometer (Thermo Scientific, MA, USA). Its integrity was confirmed using an Agilent Bioanalyzer 2100 system.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, MA, USA). The generated libraries were assessed for quality using an Agilent 2100 Bioanalyzer and a real-time PCR system, and were sequenced using an Illumina HiSeq 2500 platform (Illumina, CA, USA).
Clean paired reads were mapped to the reference genome.
Trinity (version: v2.8.4) software was used for the de novo assembly of unmapped reads, which has been efficient for the de novo reconstruction of transcriptomes from RNA-Seq data
Genome_build: GCA_002284835.2 RCv2.1
Supplementary_files_format_and_content: fasta file assemblyed by trinity

organism: Aquarana catesbeiana

source_name: inner ear

growth_protocol: frog farm

extract_protocol:
Inner ears of the bullfrogs were dissected and immediately immersed in RNAlater, for subsequent mRNA isolation.
Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, MA, USA).

treatment_protocol: no treatment

tag: tissue type

value: inner ears of frog


title: miRNA-seq_Flower_1

description:
Paeonia lactiflora Pall.
small RNA

source_name: Flower

value: Flower


title: Field Sample M8

city: Madrid

first: Tomas

last: Canto

state: Madrid

address: Ramiro de Maeztu 9

department: Environmental Plant Biology

country: Spain

institute: CSIC

description: sRNA reads 18-50 nt of total RNA samples

data_processing:
Unzip Fasteris files.  Fuse 18 to 50 nt reads and clean (remove no UTF-8 characters and remove bad sequences)
Map against potato genome (potato_dm_v404_all_pm_un.fasta) and transcriptome (PGSC_DM_v3.4_transcript.fasta)
Genome_build: Submit non-plant sRNA reads to VirusDetect to generate contigs of viral sequence.  Further assembling and editing of incomplete viral contigs with Vector NTI (Invitrogen), using as leads known published sequences of isolates of the viruses detected (in our case PYVV)
Split by length viral sRNA reads  and plot their distribution along the three reconstructed PYVV viral genomic RNAs of sample M2
Supplementary_files_format_and_content:   As processed data we have uploaded .txt files showing the distribution of the sRNA reads of viral sequence along the three genomic RNAs (1, 2 and 3) of the PYVV isolates infecting samples M2, M9, M14 and M19, as well as along the PVY genomic RNA of sample M14.

organism: Solanum phureja

source_name: Leaf tissues

growth_protocol: Sampled potato leaves from colombian highlands crops

extract_protocol:
Total RNA extraction from leaf samples
Library source: transcriptomic; Library selection: total RNA samples sent to sequencing company (Fasteris, S.A.) were libraries of the small RNA fraction were created and sequenced (Illumina NextSeq High)

treatment_protocol: Leaf samples kept frozen until extraction

tag: geographycal source

value: Upper leaf


title: stage 3 w1118 GFP input replicate 2

description:
processed data file:
St3_GAF_input_w1118_cpm.bw
MG4_Stage3-W1118_Input_S22

source_name: stage 3 w1118 GFP input

value: embryo

value: none (input)


title: B16

value: MOL


title: Field Sample M2


title: stage 3 w1118 GFP IP replicate 1

description:
processed data file:
St3_GAF_IP_w1118_cpm.bw
MG3_Stage3-W1118_IP_S19


title: stage 3 w1118 GFP input replicate 1

description:
processed data file:
St3_GAF_input_w1118_cpm.bw
MG3_Stage3-W1118_Input_S18


title: DNMT Double Gene Deletion in F. graminearum in preferred nutrient conditions for 24h rep3

city: Ottawa

first: Christopher

middle: Thomas

last: Bonner

state: Ontario

address: 960 Carling

country: Canada

institute: Agriculture Canada

description:
DNMT Double Gene Deletion in F. graminearum in preferred nutrient conditions for 24h
Each sample was performed in triplicate
RNAseqAnalysis_ReadCounts_ProcessedFile_DKO24hPN_Triplicate.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_6hNPMutant vs_24hPNMutant.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPMutant vs_24hPNMutant.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hPN_WTvsMutant.xlsx  CDS_Extracted annotations.fa

data_processing:
Raw read QC and trimming (CLC genomics workbench V12): reads were trimmed of adaptor sequences and for low quality (limit 0.05) bases, and ambiguous bases were trimmed. Reads were filtered based on read length, with minumum length of 15 bases. 5 bases were default trimmed off of both the 5' and 3' ends.
Trimmed reads were aligned to the reference (NRRL29169 CDS - processed files) using the RNAseq Analysis function in CLC genomics workbench V12). Read alignment settings were as follows: Mismatch cost 2, Indel cost 3, length fraction 0.8, similarity fraction 0.8, auto-detect paired distances, both strands and maximum 10 hits per read. RNAseq analysis normalized read counts as per the TMM (trimmed mean of M values) method.
Differential expression analysis was performed in CLC genomics workbench V12 as per the Differential Expression in Two Groups function, which uses multi-factorial statistics based on a negative binomial GLM.
Genome_build: The reference used was the CDS of genes predicted in SPRZ00000000 in the NCBI WGS. The CDS fasta is provided in the processed files.
Supplementary_files_format_and_content: Processed datafiles come in two formats. The first format is the direct RNAseq analysis between two sample groups (eg. WT vs mutant, or environmental condition vs environmental conditions). This data is presented as a table with gene name, location (all beginning at position 1), max group mean, log2 fold change, fold change, P-value, FDR p-value and Bonferroni correction columns. We are interested in the genes which had a Pvalue of less than 0.05 and a fold change of less than or greater than 2. The second format of data is also a table, with columns gene name, transcripts per million, Unique gene reads and total gene reads. This is the processed RNAseq read counts used in the RNAseq comparision (Datafile type 1).

molecule: polyA RNA

organism: Fusarium graminearum

source_name: Fungal mycelia

growth_protocol: 6-well plate growth of fungal mycelia at 28C with shaking of 160RPM in the dark.

extract_protocol:
liquid N2/Trizol extraction followed by RNA cleanup with Stratec RNA clean up kit
mRNA Stranded Illumina HiSeq2500 PE125 or rRNA Depleted Stranded HiSeq4000 PE100 (noted in the characteristics)

tag: strain

tag: environmental condition

value: Preferred Nutrient Growth

tag: timepoint

tag: sequencing

value: Illumina HiSeq2500 PE125 mRNA Stranded Library


title: miRNA-seq_Flower_2

description:
Paeonia lactiflora Pall.
small RNA

tag: tissue


title: stage 5 GAF-sfGFP(C) GFP  input replicate 1

description:
processed data file:
St5_GAF_input_GFP_GAF_cpm.bw
St5_GAF_IP_GFP_GAF_peaks.bed
MG5_Stage_5_C-GAF-GFP_Input_S5

source_name: stage 5 GAF-sfGFP(C) GFP  input


title: stage 3 GAF-sfGFP(C)  GFP IP replicate 2

description:
processed data file:
St3_GAF_IP_GFP_GAF_cpm.bw
St3_GAF_IP_GFP_GAF_peaks.bed
MG2_Stage_3_C-GAF-GFP_IP_GFP_antibody_S14

source_name: stage 3 GAF-sfGFP(C)  GFP IP

value: stage 3

value: anti-GFP (Abcam #ab290)


title: B8

source_name: Muscle

tag: breed

tag: animal

tag: date collected


title: Sham #3

value: Sprague-Dawley

value: Adult

value: Sham


title: DNMT Double Gene Deletion in F. graminearum in preferred nutrient conditions for 24h rep2


title: stage 3 GAF-sfGFP(C) GFP input replicate 2

description:
processed data file:
St3_GAF_input_GFP_GAF_cpm.bw
St3_GAF_IP_GFP_GAF_peaks.bed
MG2_Stage_3_C-GAF-GFP_Input_S13

source_name: stage 3 GAF-sfGFP(C) GFP input

tag: genotype

value: homozygous GAF-sfGFP(C)


title: Mild TBI #2

source_name: Tail-vein plasma


title: B7

value: Muscle

value: Bos taurus x Bos indicus

tag: year

tag: treatment


title: DNMT Double Gene Deletion in F. graminearum in preferred nutrient conditions for 24h rep1


title: B6


title: stage 3 GAF-sfGFP(C)  GFP IP replicate 1

description:
processed data file:
St3_GAF_IP_GFP_GAF_cpm.bw
St3_GAF_IP_GFP_GAF_peaks.bed
MG1_Stage3-GAFGFP_IP_S21

tag: developmental stage

tag: antibody


title: Severe TBI #3

tag: age

tag: group

value: Severe TBI


title: Severe TBI #2


title: Sham #4


title: B5


title: Wt F. graminearum in preferred nutrient conditions for 24h rep2

description:
Wt F. graminearum in preferred nutrient conditions for 24h
Each sample was performed in triplicate
RNAseqAnalysis_ReadCounts_ProcessedFile_WT24hPN_Triplicate.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hPN_WTvsMutant.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_6hNPWT vs_24hPNWT.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hPNWT.xlsx  CDS_Extracted annotations.fa

value: WT NRRL29169


title: stage 3 GAF-sfGFP(C)  GFP input replicate 1

description:
processed data file:
St3_GAF_input_GFP_GAF_cpm.bw
St3_GAF_IP_GFP_GAF_peaks.bed
MG1_Stage3-GAFGFP_Input_S20

source_name: stage 3 GAF-sfGFP(C)  GFP input


title: B4


title: Wt F. graminearum in preferred nutrient conditions for 24h rep3


title: B2


title: A24


title: Mild TBI #1

value: Mild TBI


title: Human brain microvascular pericytes_RNAi-notch1

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

country: Australia

institute: University of Sydney

description:
bg_table_GEO.csv
B4

data_processing:
RNA-seq reads were mapped to H. sapiens GRCh38 reference transcriptome using Hisat2
StringTie was utilized to assemble and quantify expressed transcripts.
The transcript abundance and differential expression tables were generated using Ballgown.
The statistical analysis of between-group differences was performed using EdgeR package
Gene ontology (GO) enrichment analysis was done using the NetworkAnalyst platform and the Reactome database as reference for transcripts with p<0.001
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited csv files generated using EdgeR: scores represent log2fold change and FDR

source_name: Human brain microvascular pericytes

growth_protocol: Human primary neural pericytes were purchased from ScienCell (Carlsbad, CA; #1200) and were cultured in Dulbecco's Modified Eagle Medium/F12 (DMEM/F12) supplemented with 10% fetal calf serum, recombinant human FGF‐2 20 ng/ml (R&D Systems, 233‐FB), and Antibiotic‐Antimycotic (100×, Life Technologies).

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent).
After enrichment of Poly-A+ mRNA, the libraries were constructed using NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: For small interfering RNA (siRNA)-mediated knockdown of antisense and sense notch-1, cells were electroporated with 200 nM of the targeting or control siRNA.

tag: cell type

value: Primary adult brain pericytes

value: brain


title: Sham #2


title: Wt F. graminearum in preferred nutrient conditions for 24h rep1


title: Human brain microvascular pericytes_RNAi_antisense

description:
bg_table_GEO.csv
B3


title: Severe TBI #1


title: Human brain microvascular pericytes_Ct

description:
bg_table_GEO.csv
B1

value: Control


title: L1_N2_Rep2

city: Atlanta

first: Brandon

middle: S.

last: Carpenter

state: Georgia

address: 615 Michael St., SOM: Cell Biology Dept.

department: Cell Biology

institute: Emory University

description: Replicate 2

data_processing:
Raw RNAseq reads were checked for quality using FastQC (Andrews 2010), filtered using Trimmomatic (Bolger et al. 2014)
Reads were and aligned to genome WS220/ce10 using  (Kim et al 2015)
Read count by gene was obtained by FeatureCounts (Yang liao et al 2014)
Differentially expressed transcripts were determined using DESEQ2 (v.2.11.40.2) (Love et al 2014)
Genome_build: ce10
Supplementary_files_format_and_content: Processed files from DESEQ2 analysis are in tabular format and contain a list of differentially expressed genes compared to N2

organism: Caenorhabditis elegans

source_name: L1 larvae

growth_protocol: Animals were cultured with OP50 on 10-cm NGM agar plates at 20C.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) from 500-750 starved L1 larvae born at room temperature (21° C - 22° C) overnight in M9 Buffer.
Libraries were prepared by HAIB-GSL (for Illumina NovaSeq).

value: whole animal

tag: Stage

value: L1 larvae


title: L1_met-2; spr-1_Rep2

description: Replicate 2


title: L1_spr-1_Rep2

description: Replicate 2


title: L1_met-2_Rep2

description: Replicate 2


title: A22

value: MOLMET


title: A23

value: MOL


title: L1_met-2; spr-1_Rep1

description: Replicate 1


title: DNMT Double Gene Deletion in F. graminearum in NON preferred nutrient conditions for 24h rep3

description:
DNMT Double Gene Deletion in F. graminearum in NON preferred nutrient conditions for 24h
Each sample was performed in triplicate
RNAseqAnalysis_ReadCounts_ProcessedFile_DKO24hNP_Triplicate.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPMutant vs_6hNPMutant.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPMutant vs_24hPNMutant.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hNPMutant.xlsx  CDS_Extracted annotations.fa

tag: strain

value: NON Preferred Nutrient Growth

value: Illumina HiSeq4000 PE100 rRNA depleted mRNA Stranded Library


title: A21


title: L1_met-2_Rep1

description: Replicate 1


title: DNMT Double Gene Deletion in F. graminearum in NON preferred nutrient conditions for 24h rep1

tag: environmental condition


title: L1_spr-1_Rep1

description: Replicate 1


title: DNMT Double Gene Deletion in F. graminearum in NON preferred nutrient conditions for 24h rep2

tag: timepoint


title: Wt F. graminearum in NON preferred nutrient conditions for 24h rep2

description:
Wt F. graminearum in NON preferred nutrient conditions for 24h
Each sample was performed in triplicate
RNAseqAnalysis_ReadCounts_ProcessedFile_WT24hNP_Triplicate.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_6hNPWT.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hNPMutant.xlsx  RNAseqAnalysis_ComparisonTwoSampleGroups_ProcessedFile_24hNPWT vs_24hPNWT.xlsx  CDS_Extracted annotations.fa

tag: sequencing


title: Wt F. graminearum in NON preferred nutrient conditions for 24h rep3


title: L1_N2_Rep1

description: Replicate 1

tag: tissue


title: A18

tag: breed


title: A17

tag: animal


title: A19

tag: date collected


title: Wt F. graminearum in NON preferred nutrient conditions for 24h rep1


title: Sham #1

value: Sprague-Dawley

value: Adult


title: A16


title: A15


title: A14

value: NOSUP


title: A13

value: Muscle


title: A12

value: Bos taurus x Bos indicus


title: Propionate 2

city: München

first: Gemma

last: Llovera

address: Feodor-Lynen-Straße 17

country: Germany

institute: Institut für Schlaganfall- und Demenzforschung (ISD)

hyb_protocol: The final hybridization reaction will contain the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet. Incubate hybridization assays for at least 12 hours at 65°C. Hybridizations should be left at 65°C until ready  for processing.

scan_protocol: nCounter® SPRINT Profiler

data_processing: For both experiments, we use the advanced analysis tool, included in the nSolver data analysis software.     Pairwise Variance during HK Selection  Displays the geNorm pairwise variation statistic after successive genes are removed. This statistic cannot be computed for the final two genes, which are therefore not displayed. The ideal normalization gene set will minimize the pairwise variation statistic.    Normalization Summary: mRNA  The lower the MSE of the reference profile the higher quality of normalization. The more positive the normalization factor, the higher counts were registered for the sample and vice versa.

label: codeset probes

source_name: Microglia culture

growth_protocol: DMEM F12 with 10% fetal bovine serum and 1% PenStrep (Gibco)

extract_protocol: cells were lysed in Qiazol Lysis Reagent and RNA extraction was performed using the RNeasy Mini Kit (all Qiagen)

treatment_protocol: At 5DIV culturing medium was replaced with fresh medium containing single SCFA (Acetate, Butyrate or Propionate, Sigma Aldrich) or an equimolar combination of them (final concentration 250 µM for all conditions). NaCl was used as control in equimolar concentration.

tag: Sex

value: Male

tag: agent

value: Propionate


title: Propionate 3


title: Propionate 1


title: A20

tag: year

tag: treatment


title: Butyrate 3

value: Butyrate


title: Butyrate 1


title: Acetate 3

value: Acetate


title: A7


title: A10


title: A9


title: A8


title: Acetate 2


title: Butyrate 2


title: Acetate 1


title: A6


title: aorta_A+B_rep3

city: BeiJing

last: Tan

address: No. 38 Xue Yuan Road

institute: Peking University Health Science Center

description: Gene expression in aortae of AngⅡ-infused mice with berberine

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with the Gene Spring GX v12.1 software package (Agilent Technologies).

source_name: aorta, AngⅡ+berberine,  replicate 3

label_protocol: The mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: After mice were sacrificed, aortae were removed, cleaned of adhering tissue in sterilized PBS, and then stored in liquid nitrogen for total RNA extraction. Total RNA from each sample was extracted using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA quantity and quality were measured by NanoDrop ND-1000 to make sure the high purity of the isolated RNA.

treatment_protocol: Under ketamine/xylazine anesthesia (75 and 6 mg/kg), Ang Ⅱ- or PBS-loaded osmotic pumps were implanted in Male C57BL/6J mice (8-10 weeks old). Then the mice received berberine administration (100 mg/kg/day) or vehicle for 2 weeks.

value: aorta

tag: gender

value: male

value: 8-10 weeks old


title: aorta_AngⅡ_rep3

description: Gene expression in aortae of AngⅡ-infused mice without berberine

source_name: aorta, AngⅡ-infusion,  replicate 3

tag: age


title: A11


title: aorta_AngⅡ_rep1

source_name: aorta, AngⅡ-infusion,  replicate 1


title: A5


title: NaCl 3

value: NaCl


title: muscle of well endurance trained aged subject #4

city: Bologna

first: Valentina

last: Indio

address: via Giuseppe Massarenti,11

institute: University of Bologna

description: gene expression data from miRNA-4_0 Affymetrix chip

hyb_protocol: Standard GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: miRNA-4_0 chips were scanned at the “Giorgio Prodi” Cancer Research Center, Bologna, Italy.

data_processing: Data were processed by Robust Multichip Average method (R-bioconductor, package oligo, function rma) to perform background subtraction and quantile normalization at single probe level

label: biotin

source_name: muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: TRIZOL® (Invitrogen SRL, Milan, Italy)

tag: age (years)

tag: % of resistance training

tag: % of endurance training

tag: average weekly hours of training


title: aorta_AngⅡ_rep2

source_name: aorta, AngⅡ-infusion,  replicate 2

tag: strain


title: muscle of well endurance trained aged subject #3


title: A4


title: aorta_A+B_rep1

source_name: aorta, AngⅡ+berberine,  replicate 1


title: NaCl 1


title: aorta_Veh_rep2

description: Gene expression in aortae of Vehicle mice

source_name: aorta, Vehicle,  replicate 2


title: aorta_A+B_rep2

source_name: aorta, AngⅡ+berberine,  replicate 2


title: muscle of well endurance trained aged subject #5


title: aorta_Veh_rep3

source_name: aorta, Vehicle,  replicate 3


title: aorta_Veh_rep1

source_name: aorta, Vehicle,  replicate 1


title: A2

source_name: Muscle


title: YLQ MUT+ SARS060

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description:
tetramer-positive CD8+ T cells from patient SARS060 exposed to mutant YLQ peptide of SARS-CoV2
features060.tsv
barcodes060.tsv
QC060rep.csv
Covid_060_hash.csv
matrix060.mtx

data_processing:
Hashtag oligos were identified using CITE-seq, demultiplexed with a custom script and sequences aligned using 10X CellRanger (v1.3.0).
Pre-processed data were loaded into R and analyzed using Seurat (v3.9.9.9038).
Genome_build: GRCh38
Supplementary_files_format_and_content: CellRanger sparse matrix mtx file with UMI counts per barcode and gene

growth_protocol: CD8+ T cells were purified from blood samples and incubated with a YLQ bound tetramer for 10-12 days.

extract_protocol:
Cells were loaded onto a 10X Genomics Chromium Controller following manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.
Per manufacturer instructions, droplet emulsions were broken, cDNA was amplified, and libraries were generated using enzymatic fragmentation folowed by enrihment PCR and sequencing on Illumina NovaSeq Platform.

treatment_protocol: Cryopreserved PBMCs were thawed in pre-warmed RPMI-1640 medium containing 10% FBS, 10 mM Hepes, 2 mM Glutamax, 50 IU/ml PenStrep and 50 IU interleukin-2 at a concentration of 1×106 cells/ml. PBMCs were pulsed with peptides (1 µg/ml) and cultured for 10-12d adding 100 IU interleukin-2 on day 5

tag: donor id

tag: cell type

value: purified CD8+ T lymphocytes

tag: disease state

tag: qc name

tag: peptide genotype

value: MUT

tag: response

value: YLQ+


title: A3

tag: tissue

tag: breed

tag: animal

tag: date collected

value: MOL


title: muscle of well endurance trained aged subject #1

tag: gender


title: YLQ MUT- SARS060

description:
tetramer-negative CD8+ T cells from patient SARS060 exposed to mutant YLQ peptide of SARS-CoV2
features060.tsv
barcodes060.tsv
QC060rep.csv
Covid_060_hash.csv
matrix060.mtx

value: YLQ-


title: SCFA 3

tag: Sex

tag: agent

value: SCFA


title: A1

tag: year

tag: treatment

value: NOSUP


title: SCFA 1


title: Control 3

value: Control


title: YLQ WT+ SARS060

description:
tetramer-positive CD8+ T cells from patient SARS060 exposed to wildtype YLQ peptide of SARS-CoV2
features060.tsv
barcodes060.tsv
QC060rep.csv
Covid_060_hash.csv
matrix060.mtx

value: WT


title: Control 2

value: Male


title: YLQ MUT+ SARS042

description:
tetramer-positive CD8+ T cells from patient SARS042 exposed to mutant YLQ peptide of SARS-CoV2
features042.tsv
barcodes042.tsv
QC042rep.csv
Covid_042_hash.csv
matrix042.mtx


title: SCFA 2


title: Control 1


title: GF+SCFA 3

source_name: Brain

tag: protocol

value: SCFA supplemented GF


title: YLQ MUT- SARS042

description:
tetramer-negative CD8+ T cells from patient SARS042 exposed to mutant YLQ peptide of SARS-CoV2
features042.tsv
barcodes042.tsv
QC042rep.csv
Covid_042_hash.csv
matrix042.mtx


title: GF+SCFA 2


title: sfGFP-GAF(N) degradFP replicate 5

description:
GAF_degradFP_accessble_zscore.bw
GAF_ATAC_peaks.bed

data_processing:
Adapter sequences were removed from raw sequence reads using NGMerge
ATAC-seq reads were aligned to the Drosophila melanogaster (dm6) genome using bowtie2 with the following parameters: --very-sensitive, --no-mixed, --no-discordant, -X 5000, -k 2
Reads with a mapping quality score < 30 were discarded, as were reads aligning to scaffolds or the mitochondrial genome
Aligned fragments were further filtered to include only fragments < 100 bp, which are most likely to originate from nucleosome-free regions.
To maximize the sensitivity of peak calling, accessible fragments from all replicates of GAFdeGradFP and control embryos were combined. Peak calling was performed on combined reads using MACS2 with parameters -f BAMPE --keep-dup all -g 1.2e8 --call-summits. Peaks were filtered to include only those with a fold enrichment over background > 2.5.
Reads aligning within 201 bp peak regions (100 bp on either side of peak summit) were quantified using featureCounts.
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files were generated using deepTools; scores represent z-score normalized read depth.
Supplementary_files_format_and_content: BED file contains peaks used for analysis.

source_name: embryo

growth_protocol: All stocks were grown on molasses food at 25ºC.

extract_protocol:
Embryos from His2Av-RFP/nos-degradFP (II); sfGFP-GAF(N) (III) and His2Av-RFP (II); sfGFP-GAF(N) (III) females were collected from a half hour lay and aged for 2 hours. Embryos were dechorionated in bleach, mounted in halocarbon 700 oil, and imaged on a Nikon Ti-2e Epifluorescent microscope using 60x magnification. Embryos with nuclei that were not grossly disordered as determined by the His2Av-RFP marker were selected for single embryo ATAC-seq. 6 replicates were collected for each genotype. Single embryos were homogenized under a dissecting microscope.
Nuclei were  pelleted for 10 minutes at 1000g at 4ºC and resuspended in 5 µl of buffer TD (Illumina 15027866), 2.5 µl water, and 2.5 µl Tn5 transposase (Tagment DNA Enzyme, Illumina).  Reactions were incubated for 30 min at 37ºC then immediately purified with the MinElute Cleanup Kit (Qiagen) and eluted in 10 µL buffer EB. Libraries were amplified for 12 PCR cycles with unique dual index primers using the NEBNext Hi-Fi 2X PCR Master Mix (NEB M0541).

tag: genotype

value: His2Av-RFP/nos-degradFP (II); sfGFP-GAF (N) (III)

tag: developmental stage

value: 2-2.5 hour embryos


title: YLQ WT+ SARS042

description:
tetramer-positive CD8+ T cells from patient SARS042 exposed to wildtype YLQ peptide of SARS-CoV2
features042.tsv
barcodes042.tsv
QC042rep.csv
Covid_042_hash.csv
matrix042.mtx

tag: donor id

tag: cell type


title: GF+SCFA 1


title: sfGFP-GAF(N) degradFP replicate 6


title: YLQ WT- SARS060

description:
tetramer-negative CD8+ T cells from patient SARS060 exposed to wildtype YLQ peptide of SARS-CoV2
features060.tsv
barcodes060.tsv
QC060rep.csv
Covid_060_hash.csv
matrix060.mtx

tag: disease state

tag: qc name


title: YLQ WT- SARS042

description:
tetramer-negative CD8+ T cells from patient SARS042 exposed to wildtype YLQ peptide of SARS-CoV2
features042.tsv
barcodes042.tsv
QC042rep.csv
Covid_042_hash.csv
matrix042.mtx

tag: peptide genotype

tag: response


title: sfGFP-GAF(N) degradFP RNA-seq replicate 3

description:
Degrad_HisRFP_AB_3_S6
GFPGAF_degrad_3

data_processing:
RNA-seq data was aligned using HISAT v2.1.0.
Reads with a mapping quality score < 30 were discarded.
The number of reads aligning to each gene was quantified using featureCounts.
Genome_build: dm6
Supplementary_files_format_and_content: read count table was generated using featureCounts; contains the number of reads mapping to each gene.

source_name: sfGFP-GAF(N) degradFP

extract_protocol:
150-200 embryos from His2Av-RFP/nos-degradFP (II); sfGFP-GAF (N) (III) and His2Av-RFP (II); sfGFP-GAF (N) (III) females were collected from a half hour lay and aged for 2 hours. Embryos were then picked into Trizol (Invitrogen) with 200 μg/ml glycogen (Invitrogen). RNA was extracted using the Universal RNA-Seq with NuQuant, Drosophila AnyDeplete Universal kit (Tecan).
Libraries were prepared using the Universal RNA-Seq with NuQuant, Drosophila AnyDeplete Universal kit (Tecan).

tag: developmental stage/tissue


title: GF 3

value: control


title: muscle of well resistance trained aged subject #4

value: male

tag: age (years)

tag: % of resistance training

tag: % of endurance training

tag: average weekly hours of training


title: muscle of sedentary aged subject # 5

tag: gender


title: GF 2

tag: Sex


title: muscle of well resistance trained aged subject #2


title: sfGFP-GAF(N) degradFP RNA-seq replicate 1

description:
Degrad_HisRFP_AB_1_S4
GFPGAF_degrad_1


title: muscle of well endurance trained aged subject #2


title: sfGFP-GAF(N) degradFP replicate 3


title: B. animalis subsp. animalis CNCM I-4602 grown in modified MRS with glucose vs. grown in RSM with cysteine

city: Cork

first: Francesca

last: Bottacini

address: Western Road

department: APC Microbiome Institute & School of Microbiology

country: Ireland

institute: University College Cork

description: Gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium animalis subsp. animalis CNCM I-4602 was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing 0.5% to an OD of 0.5 glucose or in reconsituted skimmed milk containing 0.5 % glucose to a pH of 5.3.

extract_protocol: Bifidobacterial cells were isolated from milk-based medium (RSM) according to a previously described method (de Jong et al., 2013). Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: wild type

source_name: B. animalis subsp. animalis CNCM I-4602 grown in RSM with cysteine


title: muscle of sedentary aged subject # 4


title: 3907_normal_sub

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
Raw sequences were ran within a Singularity container (https://hub.docker.com/r/ramiremars/star_dropest), and the outputs from STAR read alignment and dropEst were used to generate a droplet count matrix through an R script packaged with the container.
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - 3' end
Genome_build: Ensembl 85 (GRCh38.p7)
Supplementary_files_format_and_content: unfiltered counts matrix

source_name: subsampled from GSE158636_S1

growth_protocol: primary cells

extract_protocol:
Human epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of using TruDrop library structure (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2x150 paired-end kit standard run

tag: tissue type

value: adjacent normal


title: sfGFP-GAF(N) control RNA-seq replicate 3

city: Madison

first: Melissa

last: Harrison

address: 420 Henry Mall

institute: University of Wisconsin Madison

description:
HisRFP_AB_3_S3
GFPGAF_control_3

source_name: sfGFP-GAF(N) control

value: His2Av-RFP (II); sfGFP-GAF (N) (III)


title: B. animalis subsp. animalis CNCM I-4602 grown in modified MRS with glucose vs. grown in RSM

description: Gene expression array

organism: Bifidobacterium animalis subsp. animalis

source_name: B. animalis subsp. animalis CNCM I-4602 grown in RSM


title: sfGFP-GAF(N) degradFP replicate 4


title: B. animalis subsp. animalis CNCM I-4602 grown in RSM with cysteine vs. grown in modified MRS with glucose

description: Gene expression array

source_name: B. animalis subsp. animalis CNCM I-4602 grown in modified MRS with glucose


title: muscle of well resistance trained aged subject #1


title: GF 1

tag: protocol


title: muscle of well resistance trained aged subject #3


title: muscle of sedentary aged subject # 1


title: MM099 ChIP-seq JunB

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

institute: VIB

data_processing:
Reads for each ChIP-seq and ATAC-seq sample were aligned to the hg38 genome assembly using Bowtie2 version 2.3.4.1 with default parameters for paired-end read mapping.
The resulting BAM file for each sample was deduplicated with Picard 2.21.8.
The deduplicated BAM file for each sample was filtered with SAMtools 1.9 to remove reads with mapping quality lower than 30 or reads in chrM.
Peaks were called with MACS2 version 2.2.7.1 callpeak subcommand with parameters -q 0.05 -g hs --keep-dup all.
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak files

source_name: MM099 ChIP-seq JunB

growth_protocol: MM047 and MM099 were cultured in Ham's F10 nutrient mix (ThermoFisher Scientific) supplemented with 10% fetal bovine serum (Invitrogen) and 100 µg ml-1 penicillin/streptomycin (ThermoFisher Scientific). The A375 cell line was maintained in Dulbecco’s Modified Eagle’s Medium with high glucose and glutamax (ThermoFisher Scientific), supplemented with 10% fetal bovine serum (Invitrogen) and penicillin-streptomycin (ThermoFisher Scientific). Cell cultures were kept at 37°C, with 5% CO2 and were regularly tested for mycoplasma contamination, and were found negative.

extract_protocol:
For Omni-ATAC-seq, cells were detached by trypsinization, counted and processed according to downstream protocols. For ChIP-seq, cells were grown and processed 15-cm dishes. A total of 20 million cells per ChIP sample were collected. ChIP samples were prepared following the ‘Myers Lab ChIP-seq Protocol v011014’.
OmniATAC-seq was performed as described previously [Corces et al., 2017]. 50,000 cells were pelleted at 500 RCF at 4°C for 5 min, medium was carefully aspirated and the cells were washed and lysed using 50 uL of cold ATAC-Resupension Buffer (RSB) (see Corces et al., 2017 for composition) containing 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin by pipetting up and down three times and incubating the cells for 3 min on ice. The lysis was washed out by adding 1 mL of cold ATAC-RSB containing 0.1% Tween-20 and inverting the tube three times. Nuclei were pelleted at 500 RCF for 10 min at 4°C, the supernatant was carrefully removed and nuclei were resuspended in 50 uL of transposition mixture (25 uL 2x TD buffer (see Corces et al., 2017 for composition), 2.5 uL transposase (100 nM), 16.5 uL DPBS, 0.5 uL 1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O) by pipetting six times up and down, followed by 30 minutes incubation at 37°C at 1000 RPM mixing rate. Samples were cleaned-up by MinElute.  After MinElute clean-up and elution in 21 uL elution buffer, the transposed fragments were pre-amplified with Nextera primers by mixing 20 uL of transposed sample, 2.5 uL of both forward and reverse primers (25 uM) and 25 uL of 2x NEBNext Master Mix (program: 72°C for 5 min, 98°C for 30 sec and 5 cycles of [98°C for 10 sec, 63 °C for 30 sec, 72°C for 1 min] and hold at 4°C). To determine the required number of additional PCR cycles, a qPCR was performed [see Bruenrostro et al., 2015 for the determination of the number of cycles to be added]. The final amplification was done with the additional number of cycles, samples were cleaned-up by MinElute and libraries were further prepped using the KAPA Library Quantificaton Kit as previously described [Corces et al., 2017]. For ChIP-seq, 5-20 ng of precipitated DNA was used per sample to perform library preparation according to the Illumina Truseq DNA sample preparation guide. In brief, the immunoprecipitated DNA was end-repaired, A-tailed and ligated to diluted sequencing adapters (1/100). After PCR amplification (15 cycles) and bead purification (Agencourt AmpureXP, Analis).

treatment_protocol: No treatment

tag: cell line

value: melanoma cell line

tag: chip antibody

value: Jun B antibody (sc-8051 X, Santa Cruz Biotechnology)


title: Field Sample M19

description: sRNA reads 18-50 nt of total RNA samples

organism: Solanum tuberosum

source_name: Leaf tissues

tag: geographycal source

tag: tissue

value: Upper leaf


title: sfGFP-GAF(N) control RNA-seq replicate 2

description:
HisRFP_AB_2_S2
GFPGAF_control_2

tag: genotype


title: B. animalis subsp. animalis CNCM I-4602 grown in RSM vs. grown in modified MRS with glucose

description: Gene expression array


title: muscle of sedentary aged subject # 3

source_name: muscle


title: sfGFP-GAF(N) degradFP replicate 1

tag: developmental stage


title: muscle of sedentary aged subject # 2


title: MM099 ChIP-seq Fra-1

source_name: MM099 ChIP-seq Fra-1

tag: cell type

value: Fra-1 antibody (sc-376148, Santa Cruz Biotechnology)


title: Field Sample M14


title: P3_MUT rep2

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description:
linearly amplified mRNA
Paired-end RNA-Seq libraries constructed using standard Illumina protocols (Illumina)

data_processing:
Bowtie v1.1.2 was used to map sRNA-Seq reads; Tophat was used to map RNA-seq reads
Sequence reads were trimmed using Cutadapt version 1.13 (Martin, 2011) and trimmed reads, 18-26 nucleotides in length, aligned to the maize B73 RefGen_v3 genome (release 5a.57) using Bowtie version 1.1.2 (Langmead et al., 2009), allowing no mismatches and a maximum of 20 alignments per read; For RNA-seq, reads were trimmed using trimmomatic verstion 0.36. Trimmed RNA-Seq reads were aligned to the B73 RefGen_V3 using tophat, and uniquely mapped reads were used for subsequent analyses
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: SAM_datamatrix.txt.gz includes bulk RNA-seq tab-delimited text file includes RPM values for each Sample
Supplementary_files_format_and_content: miRNA_info.txt includes name, sequence, raw reads count and normalized data (reads per million)

organism: Zea mays

growth_protocol: maize B73 seedlings were grown in growth-chambers at 16 hour 25 oC/light and 8 hour 21 oC/dark cycles

extract_protocol:
For small RNA-seq, total RNA was extracted using TRIzol reagent (Invitrogen) followed by treatment with DNase I (Promega). For bulk RNA-seq, RNA was extracted with the PicoPure RNA isolation kit (Arcturus), treated with DNaseI (Qiagen) and linearly amplified with the TargetAmp 2-Round aRNA Amplification kit 2.0 (Epicentre Biotechnologies).
sRNA-Seq libries were prepared from 1.2 𝝁g total RNA using TruSeq small RNA sample preparation kit (Illumina). Libraries were quantified with the KAPA Illumina library Quantification Kit (KAPABIOSYSTEMS) and sequenced on the Illumina HiSeq2000 platform; RNA-Seq Libraries were constructed from linearly amplified RNA using the TruSeq RNA Library Kit from Illumina following the recommended protocols.

treatment_protocol: Cells of interest were captured by LCM from 2-week-old B73 apices as described (Knauer et al., 2019).

tag: strain

value: leaf primordia P3

tag: age

value: 14-day-old seedlings

value: dc1-2 introgressed into the B73 inbred


title: sfGFP-GAF(N) control RNA-seq replicate 1

description:
HisRFP_AB_1_S1
GFPGAF_control_1

tag: developmental stage/tissue


title: Field Sample M9


title: MM099 ChIP-seq cFos

source_name: MM099 ChIP-seq cFos

value: c-Fos antibody (sc-166940 X, Santa Cruz Biotechnology)


title: MM099 ChIP-seq cJun

source_name: MM099 ChIP-seq cJun

value: c-Jun antibody (sc-74543 X, Santa Cruz Biotechnology)


title: MM047 ATAC-seq B

source_name: MM047 ATAC-seq


title: sfGFP-GAF(N) degradFP replicate 2


title: sfGFP-GAF(N) degradFP RNA-seq replicate 2

description:
Degrad_HisRFP_AB_2_S5
GFPGAF_degrad_2


title: P3_MUT rep1


title: Root_2_Root

description: Paeonia lactiflora Pall.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
De novo assembly of the transcriptome was performed with Trinity 2.4.0 ( Grabherr, M. G., et al. 2011). Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample and De novo assembly of the transcriptome
Supplementary_files_format_and_content: tab-delimited text files De novo assembly of the transcriptome

source_name: Root

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an IlluminaHiseq2000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Root

tag: developemental stage

value: blossom period


title: sfGFP-GAF(N) control replicate 4

description:
GAF_control_accessble_zscore.bw
GAF_ATAC_peaks.bed

value: 2-2.5 hour embryos


title: sfGFP-GAF(N) control replicate 6


title: Root_1_Root

description: Paeonia lactiflora Pall.


title: Leaf_2_Leaf

description: Paeonia lactiflora Pall.

source_name: Leaf

value: Leaf


title: sfGFP-GAF(N) control replicate 3


title: sfGFP-GAF(N) control replicate 2


title: Fruit_2_Fruit

description: Paeonia lactiflora Pall.

source_name: Fruit

value: Fruit

value: young fruit period


title: A375 ATAC-seq B

source_name: A375 ATAC-seq


title: Leaf_1_Leaf

description: Paeonia lactiflora Pall.


title: SAM_MUT rep2

description:
linearly amplified mRNA
Single-end RNA-Seq libraries constructed using standard Illumina protocols (Illumina)

value: SAM Center Zone


title: P3_WT rep1

value: wild type


title: sfGFP-GAF(N) control replicate 5

source_name: embryo

value: His2Av-RFP (II); sfGFP-GAF (N) (III)


title: P3_WT rep2


title: MM047 ATAC-seq A

value: melanoma cell line


title: sfGFP-GAF(N) control replicate 1


title: A375 ATAC-seq A


title: SAM_MUT rep1


title: 3907_crc

description: unfiltered and filtered h5ad

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table.
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - 3' end
Genome_build: Ensembl 85 (GRCh38.p7)
Supplementary_files_format_and_content: Delimited tables in h5ad format - unfiltered barcodes

source_name: colon cancer

value: colon

tag: disease state

value: CRC


title: Fruit_1_Fruit

description: Paeonia lactiflora Pall.


title: 3907_normal

description: unfiltered and filtered h5ad

source_name: adjacent normal

value: normal


title: SAM_WT rep2

value: 14-day-old seedlings


title: SAM_WT rep1


title: Flower_2_Flower

description: Paeonia lactiflora Pall.

source_name: Flower

value: Flower


title: ARP1_KD-SRD5A1+Dox

city: Nanjing

first: Ye

last: Yang

address: 138 Xianlin Road

institute: Nanjing University of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Read alignment software,software HISAT ,version 2.1.0 ,parameters -l --no-mixed --no-discordant --rna-strandness
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.4d,parameters -p 4 -f 0.2 -j 2 -c 4.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include FPKM values for each Sample

source_name: multiple myeloma cell line

extract_protocol:
ARP1 cells were pelleted and total RNAs was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were checked and ~10 ug of total RNA was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads. Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces and reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.
Illumina NovaSeq 6000 platform was utilized for PE150 sequencing

value: Lentivirus-expressing shRNA-SRD5A2

tag: treatment

value: treated with doxycycline (Dox)


title: Flower_1_Flower

description: Paeonia lactiflora Pall.


title: ARP1_KD-SRD5A1

value: Lentivirus-expressing shRNA-SRD5A1

value: untreated


title: pit-38: low growth rate, pituitary

status: Public on Mar 02 2021

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

data_processing:
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (Sscrofa11.1) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
The de novo alignment using Trinity
Annotation and counting using Blast/Kallisto/Salmon
Genome_build: GCA_002592135.1
Genome_build: GCA_002166845.1
Supplementary_files_format_and_content: raw.genes.ab.csv.gz: compressed gzip file containing raw genes counts for GCA_002592135.1
Supplementary_files_format_and_content: raw.genes.ac.csv.gz: compressed gzip file containing raw genes counts for GCA_002166845.1
Supplementary_files_format_and_content: raw.genes.ad.kallisto.csv.gz: compressed gzip file containing raw genes counts for de novo experiment and kallisto
Supplementary_files_format_and_content: raw.genes.ad.salmon.csv.gz: compressed gzip file containing raw genes counts for de novo experiment and salmon
Supplementary_files_format_and_content: results.genes.ab.hypothalamus.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002592135.1
Supplementary_files_format_and_content: results.genes.ab.pituitary.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002592135.1
Supplementary_files_format_and_content: results.genes.ac.hypothalamus.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002166845.1
Supplementary_files_format_and_content: results.genes.ac.pituitary.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis and GCA_002166845.1
Supplementary_files_format_and_content: results.genes.ad.kallisto.hypothalamus.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo kallisto experiment and hypothalamus
Supplementary_files_format_and_content: results.genes.ad.kallisto.pituitary.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo kallisto experiment and pituitary
Supplementary_files_format_and_content: results.genes.ad.salmon.hypothalamus.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo salmon experiment and hypothalamus
Supplementary_files_format_and_content: results.genes.ad.salmon.pituitary.tsv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis,de novo salmon experiment and pituitary

organism: Anser anser

source_name: Kołudzka White Geese

growth_protocol: Sixty 1-day-old male strain W33 of White Kołuda® geese were individually weighed and randomly allocated in 4 pens of 15 birds each on deep litter. During the first 4 weeks of the rearing birds were kept indoors, under controlled temperature and humidity environment and then, up to week 15.5 they had access to free range. All birds were kept in semi-intensive rearing system according to the oat-fattening technology

extract_protocol:
RNA was isolated by RNA was isolated by the PureLink™ RNA Mini Kit (Ambion, Cambridge, UK) according to the manufacturer’s recommendations. The RIN values were over 7 what was estimated by TapeStation2200 and RNA tapes (Agilent, Palo Alto, USA).
The cDNA libraries were prepared by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the supplied protocol.

tag: day

value: male

tag: growth rate

value: low

tag: replicant

value: pituitary


title: hyp-54: high growth rate, hypothalamus

tag: Sex

value: high

value: hypothalamus


title: hyp-52: high growth rate, hypothalamus


title: hyp-50: high growth rate, hypothalamus


title: pit-54: high growth rate, pituitary


title: pit-52: high growth rate, pituitary


title: pit-37: low growth rate, pituitary


title: pit-49: high growth rate, pituitary


title: hyp-37: low growth rate, hypothalamus


title: hyp-38: low growth rate, hypothalamus


title: pit-33: low growth rate, pituitary


title: hyp-40: low growth rate, hypothalamus


title: pit-40: low growth rate, pituitary


title: hyp-49: high growth rate, hypothalamus


title: UT_6

city: Beijing

first: Bo

last: He

state: Beijing

address: Yiheyuan Road 5th.

department: School of Life Science

institute: Peking University

data_processing:
Library strategy: CATCH-Seq
Low-quality bases (trim_galore v.0.4.1,using options: -q 30, --stringency 3) , adaptor (cutadapt v.1.16, using options: -a CCCCCCCCCCCCCCCCCCCCCCCCCC -g GATCTGGGGGGGGG -m 40) and PCR duplicates(FASTX Toolkit v 0.0.13) were removed.
Unique reads were trimmed for the poly-C sequence at the 3’ end of reads. Reads with minimum length of 40 bp were mapped to the human (hg38) reference genome by bismark(v.0.15.0) using options –bowtie2 -N 1 -L 30.
Read visualization was done with IGV(v.2.3.90).
The identification of 5hmC-enriched regions (peaks) in each sample was performed using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: Mismatch rate file in tab-delimited format; containing the mutation number for every nucleotide in the genome.

source_name: Uterus

extract_protocol:
Genomic DNA was isolated from frozen tissues by TIANamp Genomic DNA Kit(TIANGEN).
The AI-labeled ssDNA was used directly for library preparation with the TELP protocol except PCR amplification. Click chemistry was performed by adding the DBCO-S-S-PEG3-Biotin (Click Chemistry Tools, Cat. No. A112-10) to a final concentration of 400 mM, and incubated in the thermomixer (Eppendorf) for 1 h at 37°C (800 rpm). Purification steps were performed with DNA Clean & Concentrator 5 (Vistech) with the help of carrier RNA (Thermo Fisher Scientific).

treatment_protocol:
block endogenous 5fC using O-ethylhydroxylamine
oxidation reaction using K2RuO4
labeling of the newly generated 5fC

value: Uterus


title: TR_3

source_name: Thyroid

value: Thyroid


title: TC_3

source_name: Trachea

value: Trachea


title: AtmsKO-LT-HSC

city: Tokyo

first: Noriko

last: Sorimachi

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biophysics and Biochemistry

country: Japan

institute: Graduate School of Science, The University of Tokyo

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used according to the manufacturer's instruction

scan_protocol: DNA Microarray Scanner (Agilent SureScan G4900DA) was used according to the manufacturer's instruction

data_processing: The scanned images were analyzed with Feature Extraction Ver.11.5.1.1 (Agilent). Normalization method was 75 percentile shift for each sample.

source_name: HSC

label_protocol: Gene Expression Hybridization Kit (5188-5242 : Agilent) was used according to the manufacturer's instruction

extract_protocol: Fresh WT, AtmsKO, or Atmp38dKO HSCs were sorted into SF-O3 medium and then centrifuged at 340 x g for 5 minutes at 4℃. Cell pellets were lysed in 75uL of RLT buffer plus 1% 2-ME, followed by RNA extraction using Qiagen RNeasy micro kit (74004 : Qiagen) according to the manufacturer's instruction.

value: 11 weeks old

value: Bone marrow

value: CD150+CD48-Flt3-CD34- LSK

tag: genotype/variation

value: AtmsKO


title: TC_2


title: Atmp38dKO-LT-HSC


title: SX_1

source_name: Spleen

value: Spleen


title: SX_5


title: SK_6

source_name: Skin

value: Skin


title: ST_5

source_name: Stomach

value: Stomach


title: WT-LT-HSC

value: wild-type


title: hyp-33: low growth rate, hypothalamus


title: pit-50: high growth rate, pituitary


title: Input_LE_2_RE

data_processing:
Library strategy: CATCH-Seq
Low-quality bases (trim_galore v.0.4.1,using options: -q 30, --stringency 3) , adaptor (cutadapt v.1.16, using options: -a CCCCCCCCCCCCCCCCCCCCCCCCCC -g GATCTGGGGGGGGG -m 40) and PCR duplicates(FASTX Toolkit v 0.0.13) were removed.
Unique reads were trimmed for the poly-C sequence at the 3’ end of reads. Reads with minimum length of 40 bp were mapped to the human (hg38) reference genome by bismark(v.0.15.0) using options –bowtie2 -N 1 -L 30.
Read visualization was done with IGV(v.2.3.90).
The identification of 5hmC-enriched regions (peaks) in each sample was performed using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: Large intestine

treatment_protocol:
block endogenous 37fC using O-ethylhydroxylamine
oxidation reaction using K2RuO36
labeling of the newly generated 37fC

value: Large intestine


title: SK_3


title: OV_5

source_name: Ovary

value: Ovary


title: LN_1

source_name: Lung

value: Lung


title: LN_5


title: UT_5


title: SE_5

source_name: Small intestine

value: Small intestine


title: SE_6


title: HR_1

source_name: Heart

value: Heart


title: LI_1

source_name: Liver

value: Liver


title: HR_6_LV


title: SK_1


title: BR_3_CE

source_name: Brian

value: Brian


title: LE_6


title: BR_3_BS


title: LI_6


title: AO_1

source_name: Aorta

value: Aorta


title: LE_2_RE

source_name: Rectum

value: Rectum


title: ST_4

data_processing:
Library strategy: CATCH-Seq
Low-quality bases (trim_galore v.0.4.1,using options: -q 30, --stringency 3) , adaptor (cutadapt v.1.16, using options: -a CCCCCCCCCCCCCCCCCCCCCCCCCC -g GATCTGGGGGGGGG -m 40) and PCR duplicates(FASTX Toolkit v 0.0.13) were removed.
Unique reads were trimmed for the poly-C sequence at the 3’ end of reads. Reads with minimum length of 40 bp were mapped to the human (hg38) reference genome by bismark(v.0.15.0) using options –bowtie2 -N 1 -L 30.
Read visualization was done with IGV(v.2.3.90).
The identification of 5hmC-enriched regions (peaks) in each sample was performed using MACS.
Genome_build: hg38
Supplementary_files_format_and_content: bw files contain genome-wide read coverage data.

source_name: stomach

value: stomach


title: SE_3_IE

source_name: Ileum

value: Ileum


title: SE_4


title: SX_4

source_name: spleen

value: spleen


title: NaCl 2

data_processing: For both experiments, we use the advanced analysis tool, included in the nSolver data analysis software.     Pairwise Variance during HK Selection  Displays the geNorm pairwise variation statistic after successive genes are removed. This statistic cannot be computed for the final two genes, which are therefore not displayed. The ideal normalization gene set will minimize the pairwise variation statistic.    Normalization Summary: mRNA  The lower the MSE of the reference profile the higher quality of normalization. The more positive the normalization factor, the higher counts were registered for the sample and vice versa.

source_name: Microglia culture

value: Male

tag: agent

value: NaCl


title: UT_4

source_name: uterus

value: uterus


title: SE_3_JE

source_name: jejunum

value: jejunum


title: ST_3


title: SE_2_JE


title: SE_2_IE


title: OV_6


title: PA_4

source_name: pancreas

value: pancreas


title: PA_3


title: LE_3_CL

source_name: colon

value: colon


title: LE_4

source_name: large intestine

value: large intestine


title: LE_3_AP

source_name: appendix

value: appendix


title: KD_4

source_name: kidney

value: kidney


title: LE_3_RE

source_name: rectum

value: rectum


title: ES_5

source_name: esophagus

value: esophagus


title: LE_2_AP


title: BR_4_BF

source_name: Brain frontal lobe

value: Brain frontal lobe


title: AG_1

source_name: Adrenal gland

value: Adrenal gland


title: KD_5


title: BR_5_BF


title: BR_3_SC

source_name: spinalcord

value: spinalcord


title: BR_3_HT

source_name: hypothalamus

value: hypothalamus


title: BD_3

source_name: bladder

value: bladder


title: BR_3

source_name: brian

value: brian