title: morc1_H3K36me3_rep2_ChIPseq

city: Beijing

description: ChIPseq data

tag: day post germination

tag: genetic background

value: morc1 mutant carrying SDC:GFP transgene

value: anti-H3K36me3 (abcam #9050)


title: Infected_Donor3_EMB_Infected

status: Public on Apr 29 2020

type: SRA

city: Paris

first: Alexandre

last: Giraud-Gatineau

address: 25-28 rue du docteur roux

department: Microbiology

country: France

institute: Institut Pasteur

library_source: transcriptomic

data_processing:
STAR v2.5.0b was used to map RNA-seq reads to the hg38 reference genome and quantify  gene expression (option--quantMode GeneCounts) by counting the fragments overlapping the Ensembl genes (GRCh38 v. 83).
Genome_build: hg38
Supplementary_files_format_and_content: The raw counts were generated using STAR v2.5.0b for GRCh38 Ensembl genes

molecule: total RNA

organism: Homo sapiens

source_name: Blood mononuclear cells

growth_protocol: Blood mononuclear cells from 4 healthy volunteers (Etablissement Français du Sang, Paris, France) were isolated by Ficoll-Paque (GE Healthcare Life Sciences) centrifugation. CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec). Recovered cells were seeded at 2 × 106 cells/well in six-well plates (Falcon; BD Biosciences) in 3 ml RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated fetal calf serum (Dutscher), L-glutamine, GM-CSF (20 ng/ml; R&D Systems). Cultures were fed every 2 days with complete medium containing full doses of cytokine. Monocytes were allowed to differentiate into macrophages for 6 days at 37°C in 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments.
cDNA libraries were prepared with the Illumina TruSeq RNA Sample Preparation Kit v2 and were sequenced on an llumina HiSeq 2500

treatment_protocol: Mycobacterium tuberculosis H37Rv (MTB) was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Becton Dickinson). Before infection, bacteria were washed three times and re-suspended in 1 ml PBS. Clumps were dissociated by 30 passages through a needle and then allowed to sediment for 5 min. Bacteria in the supernatant were then killed by heating at 90°C during 30min (defined heareafter hk-MTB). The density of bacteria in the supernatant was verified by measuring the OD600 and aliquot volumes defined to allow five bacterium-per two cell infection. Cells were infected in 6-well plates with each well containing 1.3 × 106 cells in 3 ml medium containing GM-CSF (R&D Systems), and treated with 20 µg/mL amikacin (AMK), 20 µg/mL ethambutol (EMB), 10 µg/mL isoniazid (INH), 200 µg/mL pyrazinamide (PZA), or 20 µg/mL rifampicin (RIF) for 18 h.

tag: cell type

value: human monocyte-derived macrophages

tag: infection status

value: infected

tag: agent

value: Mycobacterium tuberculosis

tag: treatment

value: EMB


title: Uninfected_Donor4_Untreated_Uninfected

value: uninfected

value: Untreated


title: Liver NFIL3 KO tunica #1

type: RNA

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

description: Transcriptomic liver of NFIL3 KO mouse treated with tunicamycin

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: RMA and Quantile Normalization with median polish using Partek. The data obtained are log2-transformed.

label: biotin

organism: Mus musculus

source_name: Liver NFIL3 KO tunica

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

extract_protocol: RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: Mice were treated for 8h with 1 µg/g tunicamycin or vehicle (150 mM dextrose).

tag: strain background

tag: genotype/variation

value: NFIL3 KO

tag: age

value: adult

tag: Sex

value: male

tag: tissue

value: liver

value: 1 µg/g tunicamycin for 8hrs


title: Infected_Donor3_RIF_Infected

value: RIF


title: Liver NFIL3 KO vehicle #1

description: Transcriptomic liver of NFIL3 KO mouse treated with vehicle

source_name: Liver NFIL3 KO vehicle

value: vehicle for 8hrs


title: Infected_Donor3_Untreated_Infected


title: Liver WT tunica #5

description: Transcriptomic liver of WT mouse treated with tunicamycin

source_name: Liver WT tunica

value: WT


title: Liver NFIL3 KO tunica #2


title: Liver NFIL3 KO vehicle #2


title: Uninfected_Donor3_AMK_Uninfected

value: AMK


title: MPH Thapsi #1

description: Transcriptomic MPH Thapsi

source_name: MPH Thapsi

treatment_protocol: Mouse primary hepatocytes were prepared as described in Bantubungi K et al, Diabetes 2014. Hepatocytes were grown in serum free William's medium and treated for 4h with 1µM thapsigargin or vehicle (0.04% DMSO).

value: mouse primary hepatocytes (MPH)

value: Thapsi


title: Liver NFIL3 KO vehicle #3


title: Liver WT tunica #3


title: Liver WT tunica #4


title: Uninfected_Donor3_EMB_Uninfected

value: human monocyte-derived macrophages


title: Infected_Donor3_AMK_Infected

value: infected


title: Liver WT vehicle #5

description: Transcriptomic liver of WT mouse treated with vehicle

source_name: Liver WT vehicle


title: Liver WT tunica #2


title: Liver WT tunica #1


title: Infected_Donor3_DMSO_Infected

value: Mycobacterium tuberculosis

value: DMSO


title: Uninfected_Donor3_PZA_Uninfected

value: uninfected

value: PZA


title: Infected_Donor3_INH_Infected

value: INH


title: Uninfected_Donor3_RIF_Uninfected


title: Uninfected_Donor3_Untreated_Uninfected

value: Untreated


title: Uninfected_Donor3_INH_Uninfected


title: RS3_Rnf12_W576Y

city: Santiago

first: Gino

last: Nardocci

address: Av. Mons. Álvaro del Portillo 12.455

country: Chile

institute: Universidad de los Andes

data_processing:
Raw sequencing reads were trimmed by removing Illumina adapters sequences and low-quality bases
Trimmed reads were mapped using STAR software (v2.7.1a)
The number of reads per transcript was counted using HTSeq (v0.11.2)
The differentially expressed genes (DEGs) were estimated using SARTools (v1.6.9) and DESeq2 (v1.24)
Genome_build: mm10
Supplementary_files_format_and_content: .txt files containing normalised counts and differential expression analysis data (DESeq2)

source_name: Embryonic stem cells

growth_protocol: Mouse ESCs were cultured in 0.1% gelatin coated plates in DMEM containing 10% foetal calf serum, 5% Knock-Out serum replacement, 2 mM glutamine, 0.1 mM MEM non-essential amino acids, 1mM sodium pyruvate, and penicillin/streptomycin, 0.1 mM beta-mercaptoethanol, and 100 ng/ml LIF at 5% CO2 and 37°C.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN)
Libraries were prepared using TruSeq Stranded Total RNA Sample Preparation kit (Illumina)

treatment_protocol: Mouse ESCs were transfected with Lipofectamine LTX (Thermo Fisher Scientific)

tag: genotype

value: CRISPR/Cas9 RNF12 KO

tag: plasmid transfected

value: RNF12 W576Y mutant

tag: cell line

value: CCE

value: Embryonic stem cells


title: RS3_Rnf12_WT

value: RNF12 wild type


title: Liver WT vehicle #4

value: WT

value: adult

value: male

value: liver

value: vehicle for 8hrs


title: Liver WT vehicle #2


title: Infected_Donor2_RIF_Infected

value: human monocyte-derived macrophages

value: infected

value: RIF


title: Liver WT vehicle #3


title: RS1_Rnf12_W576Y


title: RS2_Rnf12_W576Y


title: RS3_control

value: empty vector


title: RS1_Rnf12_WT


title: Infected_Donor2_PZA_Infected

value: Mycobacterium tuberculosis

value: PZA


title: Liver WT vehicle #1


title: Infected_Donor2_EMB_Infected

value: EMB


title: RS2_control

value: CRISPR/Cas9 RNF12 KO


title: Infected_Donor2_INH_Infected

value: INH


title: RS1_control

value: CCE


title: Uninfected_Donor2_AMK_Uninfected

value: uninfected

value: AMK


title: Liver NFIL3 KO vehicle #5

value: NFIL3 KO


title: Uninfected_Donor3_DMSO_Uninfected

value: DMSO


title: RS2_Rnf12_WT

value: RNF12 wild type

value: Embryonic stem cells


title: Infected_Donor2_AMK_Infected


title: Beta-cell_enriched_3 [WS8_S8]

city: Jette

first: Willem

last: Staels

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
STAR Version 2.5.2b
STAR –genomeDir path/to/index --sjdbGTFfile /path/to/gtf --runThreadN 24 --readFilesIn /path/to/fastq/files --outFileNamePrefix [sample prefix] --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
rsem-calculate-expression -p 24 --bam –no-bam-output /path/to/bam [rsem index reference] [sample name]
R version 3.5.1
Packages : DESeq2 v1.22.1 -  tximport v1.2.1
Normalization.r
Genome_build: Reference from Ensembl : Mus_musculus GRCm38p6, release 93
Supplementary_files_format_and_content: Count file, Normalized matrix

growth_protocol: Islets were isolated from mouse pancreas, hand-picked for purification and cultured overnight in RPMI 1640 + 10% FBS

extract_protocol:
Islets were dispersed, incubated with antibodies directed against surface markers, sorted by FACS as different subsets into lysis buffer and stored at -80°C until NGS
For library construction 20 ng of high-quality (RIN >7) total RNA was processed using Ovation Solo RNA-seq kit (NuGEN, Leek, The Netherlands) per the manufacturer’s instructions. Briefly, total RNA was treated with DNaseI and reverse-transcribed using random primers. Chemical treatment during second strand synthesis permits to achieve strand specificity. After end-repair, adaptors ligation and library amplification, depletion of rRNA is realized using AnyDeplete technology (NuGEN). Libraries were then quantified with Qubit HS DNA assay (ThermoFisher) and library profiles assessed using the DNA High Sensitivity LabChip kit on an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode.

treatment_protocol: All samples were culture equally

tag: strain

value: Pancreatic islets

tag: surface marker

value: CD24low CD71+


title: Alpha-cell_enriched_3 [WS7_S7]

value: CD24low CD71-


title: Delta-cell_enriched_3 [WS9_S9]


title: Uninfected_Donor2_RIF_Uninfected

value: human monocyte-derived macrophages

value: RIF


title: Delta-cell_enriched_2 [WS6_S6]


title: Infected_Donor2_DMSO_Infected

value: infected

value: Mycobacterium tuberculosis


title: Beta-cell_enriched_2 [WS5_S5]


title: Beta-cell_enriched_1 [WS2_S2]


title: Uninfected_Donor2_EMB_Uninfected

value: EMB


title: Delta-cell_enriched_1 [WS3_S3]


title: Uninfected_Donor2_PZA_Uninfected

value: PZA


title: Infected_Donor1_AMK_Infected


title: Root_Day 3_-Mg, rep2

city: Bunkyo-ku

first: Keitaro

last: Tanoi

state: Tokyo

address: 1-1-1 Yayoi

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

description:
Ogura_Mg_38
Normalized_data_Root_Day3.csv

data_processing:
Real Time Analysis (RTA) v1.18 performed base-calling.
Filtering, alignment and read count were performed on R software version 3.5.0 at the Linux operating system according to Ichihashi et al., Methods in Molecular Biology, 2018. Briefly, sequenced reads were trimmed for the first eight bases and low quality nucleotide at the end of reads, and short or low quality reads were removed. Filtered reads were mapped to the TAIR10 Arabidopsis reference genome sequence, and mapped reads were counted.
The count data were normalised on R software version 3.5.0 based on a trimmed mean of M- values (TMM) method. Normalization was performed for each set of control and Mg deficiency samples.
Genome_build: TAIR10 Arabidopsis reference genome
Supplementary_files_format_and_content: Tab-delimited CSV files contain normalized counts for each biological replicate.

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 was grown hydroponically with the MGRL solution (Mg 1.5 mM) at 22ºC under a photoperiod of 16 h light (100 µmol m-2 s-1)/8 h darkness.

extract_protocol:
Mature leaves, expanding leaves and roots (ca. 10 mg) were collected, flash-frozen and lysed with lysis/binding buffer containing Sodium dodecyl sulphate. mRNA was isolated from the lysate by magnetic bead purification.
A strand-specific RNA-Seq library was constructed according to Townsley et al., Frontiers in Plant Science, 2015. Briefly, mRNA was fragmented and primed with 3' primer, cDNA was synthesised, and strand-specific 5’ adapter sequence was added and incorporated. The average fragment length of the constructed library was approximately 400 bp. All the libraries were pooled and subjected to 50 bp single-end sequencing with Illumina HiSeq 2500.

treatment_protocol: Ten days after germination (day 0 of treatment), half of the plants were subjected to Mg deprivation (no Mg added).

tag: ecotype

value: Roots

value: 13 days old (day 3 of Mg deprivation)

value: Magnesium deficiency


title: Root_Day 3_-Mg, rep3

description:
Ogura_Mg_40
Normalized_data_Root_Day3.csv


title: Alpha-cell_enriched_2 [WS4_S4]


title: Infected_Donor2_Untreated_Infected

value: Untreated


title: Uninfected_Donor2_DMSO_Uninfected

value: uninfected


title: Uninfected_Donor2_Untreated_Uninfected


title: Infected_Donor1_PZA_Infected


title: Infected_Donor1_EMB_Infected


title: Root_Day 3_-Mg, rep1

description:
Ogura_Mg_37
Normalized_data_Root_Day3.csv


title: Infected_Donor1_RIF_Infected


title: Root_Day 3_Control, rep6

description:
Ogura_Mg_36
Normalized_data_Root_Day3.csv

value: Control


title: Infected_Donor1_INH_Infected

value: INH


title: Root_Day 3_Control, rep5

description:
Ogura_Mg_35
Normalized_data_Root_Day3.csv


title: Uninfected_Donor2_INH_Uninfected


title: Root_Day 3_Control, rep3

description:
Ogura_Mg_33
Normalized_data_Root_Day3.csv


title: Infected_Donor1_DMSO_Infected

value: DMSO


title: Alpha-cell_enriched_1 [WS1_S1]

value: Pancreatic islets


title: Root_Day 3_Control, rep1

description:
Ogura_Mg_31
Normalized_data_Root_Day3.csv


title: Infected_Donor1_Untreated_Infected


title: Root_Day 3_Control, rep4

description:
Ogura_Mg_34
Normalized_data_Root_Day3.csv


title: Root_Day 3_Control, rep2

description:
Ogura_Mg_32
Normalized_data_Root_Day3.csv


title: Expanding leaves_Day 8_-Mg, rep5

description:
Ogura_Mg_83
Normalized_data_Expanding_leaves_Day8.csv

source_name: Leaf

value: Expanding leaves (the next two leaves)

value: 18 days old (day 8 of Mg deprivation)


title: Uninfected_Donor1_PZA_Uninfected

value: human monocyte-derived macrophages


title: Expanding leaves_Day 8_-Mg, rep3

description:
Ogura_Mg_81
Normalized_data_Expanding_leaves_Day8.csv


title: Uninfected_Donor1_INH_Uninfected


title: Expanding leaves_Day 8_-Mg, rep4

description:
Ogura_Mg_82
Normalized_data_Expanding_leaves_Day8.csv


title: Uninfected_Donor1_DMSO_Uninfected


title: Expanding leaves_Day 8_-Mg, rep2

description:
Ogura_Mg_80
Normalized_data_Expanding_leaves_Day8.csv


title: Expanding leaves_Day 8_-Mg, rep1

description:
Ogura_Mg_79
Normalized_data_Expanding_leaves_Day8.csv


title: 3Dmodel of the human intestine [C2]

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

description:
Cells grown in collagen matrix.
processed data file: AvsC.complete.xls

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11. Only sequences at least 25 nt in length were considered for further analysis.
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome (Human genome Hh38 from Ensembl, release 94).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t exon -g gene_id -s 1)
Count data were analyzed using R version 3.5.1 and the Bioconductor package DESeq2 version 1.20.0. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model including the replicate effect as pairing factor was set in order to test for the differential expression between the two conditions with and without amoeba. Raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: Human genome hg38 from Ensembl, release 94
Supplementary_files_format_and_content: AvsC.complete.xls: DESeq2 output

source_name: Human cells

growth_protocol:
We used four different cell lines. Caco-2/TL7 (ATCC, USA) cell line was added to replicate spatial distribution of epithelial colon. HT29-MTX (ATCC, USA) cells were employed to produces mucin in the epithelial layer. CCD-18Co cell line (ATCC, USA) was used to mimic the intestinal lamina propia. THP-1 cells (ATCC, USA) were differentiated to macrophages and added into lamina propia to replicate the immune response during parasites infection. As extracellular matrix (ECM), was employed Collagen type I from rat tail (Corning, USA). All the cell lines were cultured according with supplier recommended conditions (ATCC, USA). THP-1 cells differentiated to macrophages with phorbol-12-myristate-13-acetate (PMA) (SIGMA-ALDRICH, USA) at 25 ng/ml).
Entamoeba histolytica HM1:IMSS was grown under in vitro conditions using the Diamond medium (Diamond, L. S., et al. (1978). "A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba." Transactions of the Royal Society of Tropical Medicine and Hygiene 72: 431-432).

extract_protocol:
1ml of Trizol reagent (Qiagen) was added to the sample and incubated for 5 min at room temperature, then 200 µl of chloroform were added. After 2 min incubation at room temperature, the samples were spin down at 12000 x g, 15 min at 4°c. The supernatant was complete with 70% ethanol (V/V) and then transferred to a RNeasy Mini spin column (Qiagen) and the RNA was recovered according to the Qiagen' protocol.
DNase treated RNA molecules isolated from - description of conditions - were treated for library preparation using the TruSeq Stranded mRNA sample preparation kit (Illumina, San Diego, California) according to manufacturer’s instructions. An initial poly(A) RNA isolation step (included in the Illumina protocol) is performed on n ng of total RNA to keep only the polyadenylated RNA fraction and remove the ribosomal RNA. A step of fragmentation is then performed on the enriched fraction, by divalent ions at high temperature. The fragmented RNA samples were randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. No end repair step was necessary. An adenine was added to the 3'-end and specific Illumina adapters were ligated. Ligation products were submitted to PCR amplification. The obtained oriented libraries were controlled by Bioanalyzer DNA1000 Chips (Agilent, # 5067-1504) and quantified by spectrofluorimetry (Quant-iT™ High-Sensitivity DNA Assay Kit, #Q33120, Invitrogen).
Sequencing was performed on the Illumina Hiseq2500 platform to generate single-end 65 bp reads bearing strand specificity.

treatment_protocol: Upon 22 days of human cells grown, E. histolytica (8x10 exp5) was added to the apical side of cell cultures and incubated at 37°C for two hours. The all sample was treated for RNA extraction.

tag: human cell line

value: Caco-2, Ht-29, ThP-1, CCD-18Co


title: 3Dmodel of the human intestine [C3]


title: 3Dmodel of the human intestine [C1]


title: MS D48 E+N+H- MS3

city: Los Angeles

first: Haibin

last: Xi

state: CA

address: 615 Charles E Young Dr South, BSRB 257

department: MIMG

country: USA

institute: UCLA

description: PAX7-GFP reporter cells derived from H9 human pluripotent stem cells were used for differentiation

data_processing:
The raw sequencing reads were processed using the Drop-seq_tools-1.13 pipeline from the McCaroll lab (https://github.com/broadinstitute/Drop-seq/releases/tag/v1.13), following the general guidelines from the Drop-seq Alignment Cookbook v1.2 (https://github.com/broadinstitute/Drop-seq/files/2425535/Drop-seqAlignmentCookbookv1.2Jan2016.pdf) (Macosko et al., Cell, 2015). Briefly, the first 20 bp from Read1 were filtered by read quality and used to index the corresponding Read2 fragments. The first 75 bp from the indexed Read2 were trimmed off sequencing adapters and polyA sequences, followed by read quality filtration and further removal of reads fewer than 30 nucleotides of length. Processed reads from Read2 were aligned to the human reference genome (hg19) using Bowtie2 (v2.2.9 with the ‘--very-sensitive’ mode) (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Aligned reads were tagged to gene exons using Bedtools Intersect (v2.26.0) (https://github.com/arq5x/bedtools2).
After read alignment, knee plots of cell-to-read fraction were generated to estimate the number of cell barcodes representing true cells. Digital gene expression matrices (DGEs) were then generated by counting gene transcripts for the number of cell barcodes selected based on the infliction points in the knee plots. To correct for any bead synthesis errors/read errors leading to false barcodes, transcript barcodes (unique molecular identifiers; UMIs) or cell barcodes were merged when they were within 1 Hamming or 2 Levenshtein distances, respectively. Barcodes containing < 2500 reads were excluded from the DGEs.
Downstream computational analyses of scRNA-seq data were mainly performed using the R package Seurat v2.3.3 (https://github.com/satijalab/seurat/releases/tag/v2.3.3) (Butler et al., Nat Biotechnol, 2018) by largely following the standard guidelines from the Satija lab (https://satijalab.org/seurat/). Seurat objects were generated with DGEs constructed as described above. Violin plots of number of expressed genes and unique transcripts (nGene and nUMI, respectively) of each cell were generated and outliers with too high or too low nGene/nUMI were removed to exclude potential cell doublets/aggregates or low quality cells/cell debris, respectively, based on each object/sample.
After the cell filtration step, retained cell barcodes were intersected with the original DGE files for each sample to generate the processed data files for downstream single cell analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files (.tsv) containing filtered cells/barcodes as columns and unique transcript count (nUMI) for each gene in each cell/barcode as rows.

molecule: polyA RNA

source_name: myogenic culture

growth_protocol: The parental H9 human pluripotent stem cells and engineered PAX7-GFP reporter cells were maintained on Matrigel-coated tissue culture plates in mTeSR1 medium. Cells were fed with fresh medium every day and passaged with 0.5 mM of EDTA every 4-6 days. Myogenic differentiations were carried out according to published protocols: HX protocol (Xi et al., Cell Rep, 2017), JC protocol (Chal et al., Nat Biotechnol, 2015) and MS protocol (Shelton et al., Stem Cell Rep, 2014).

extract_protocol:
Prepared single cell solutions were subjected to single cell capture and droplet formation following instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper (Macosko et al., Cell, 2015). Single cells were lysed in oil droplets and polyA-tailed mRNAs were captured by beads coated with barcoded oligonucleotides containing polyT tracks.
After cells were captured and lysed in oil-bead droplets, reverse transcription and library construction were performed according to instructions in the online Drop-seq protocol v.3.1 (http://mccarrolllab.org/download/905/) and those published in the original Drop-seq paper (Macosko et al., Cell, 2015). In brief, after droplets breakdown, cDNAs were made using Thermo Fisher Scientific Maxima H Minus Reverse Transcriptase and amplified using Roche HiFi HotStart ReadyMix. PCR products were made into sequencing-ready libraries with Illumina Nextera XT DNA Library Preparation Kit.

value: H9 human pluripotent stem cell (hPSC)

tag: differentiation protocol

tag: differentiation length

value: 48 days

tag: sorting/enrichment strategy

value: live and ERBB3+/NGFR+/HNK1-


title: Expanding leaves_Day 8_Control, rep4

description:
Ogura_Mg_72
Normalized_data_Expanding_leaves_Day8.csv


title: Expanding leaves_Day 8_Control, rep2

description:
Ogura_Mg_68
Normalized_data_Expanding_leaves_Day8.csv


title: JC D34 Live JC3

tag: cell type

value: JC protocol (Chal et al., Nat Biotechnol, 2015)

value: 34 days

value: live


title: Uninfected_Donor1_EMB_Uninfected

tag: infection status

tag: treatment

value: EMB


title: Expanding leaves_Day 8_Control, rep1

description:
Ogura_Mg_67
Normalized_data_Expanding_leaves_Day8.csv


title: MS D48 GFP+ MS2

value: MS protocol (Shelton et al., Stem Cell Rep, 2014)

value: live and PAX7-GFP+


title: Uninfected_Donor1_RIF_Uninfected

value: uninfected

value: RIF


title: Expanding leaves_Day 5_-Mg, rep3

description:
Ogura_Mg_60
Normalized_data_Expanding_leaves_Day5.csv

value: 15 days old (day 5 of Mg deprivation)

value: Magnesium deficiency


title: Expanding leaves_Day 8_Control, rep3

description:
Ogura_Mg_71
Normalized_data_Expanding_leaves_Day8.csv

value: Expanding leaves (the next two leaves)

value: Control


title: Uninfected_Donor1_Untreated_Uninfected

value: human monocyte-derived macrophages

value: Untreated


title: JC D34 GFP+ JC1

value: H9 human pluripotent stem cell (hPSC)


title: Uninfected_Donor1_AMK_Uninfected

value: AMK


title: JC D34 E+N+H- JC2

value: live and ERBB3+/NGFR+/HNK1-


title: Expanding leaves_Day 5_-Mg, rep2

description:
Ogura_Mg_58
Normalized_data_Expanding_leaves_Day5.csv


title: Expanding leaves_Day 5_Control, rep3

description:
Ogura_Mg_46
Normalized_data_Expanding_leaves_Day5.csv


title: Expanding leaves_Day 5_Control, rep5

description:
Ogura_Mg_48
Normalized_data_Expanding_leaves_Day5.csv


title: HX D55 Live HX12

value: HX protocol (Xi et al., Cell Rep, 2017)

value: 55 days


title: Expanding leaves_Day 5_Control, rep4

description:
Ogura_Mg_47
Normalized_data_Expanding_leaves_Day5.csv


title: Expanding leaves_Day 5_Control, rep1

description:
Ogura_Mg_43
Normalized_data_Expanding_leaves_Day5.csv


title: HX D35 E+N+H- HX20

value: 35 days


title: HX D35 GFP+ HX19


title: HX D27 Live HX8

value: 27 days

value: live


title: Expanding leaves_Day 3_-Mg, rep3

description:
Ogura_Mg_21
Normalized_data_Expanding_leaves_Day3.csv

value: 13 days old (day 3 of Mg deprivation)


title: Expanding leaves_Day 3_-Mg, rep2

description:
Ogura_Mg_20
Normalized_data_Expanding_leaves_Day3.csv


title: Expanding leaves_Day 5_-Mg, rep1

description:
Ogura_Mg_57
Normalized_data_Expanding_leaves_Day5.csv


title: HX D21 Live HX16

value: 21 days


title: Juv Yr11 AP34

source_name: quadriceps muscle

tag: developmental age

value: juvenile year 11

value: quadriceps muscle

value: live and CD235a-/CD31-/CD45-


title: Expanding leaves_Day 3_-Mg, rep4

description:
Ogura_Mg_24
Normalized_data_Expanding_leaves_Day3.csv

value: Expanding leaves (the next two leaves)

tag: age

value: Magnesium deficiency


title: Adt Yr42 AP28

value: adult year 42


title: Expanding leaves_Day 3_-Mg, rep1

description:
Ogura_Mg_19
Normalized_data_Expanding_leaves_Day3.csv


title: Expanding leaves_Day 3_Control, rep5

description:
Ogura_Mg_12
Normalized_data_Expanding_leaves_Day3.csv

value: Control


title: Expanding leaves_Day 3_Control, rep4

description:
Ogura_Mg_11
Normalized_data_Expanding_leaves_Day3.csv


title: HX D41 Live HX10

description: PAX7-GFP reporter cells derived from H9 human pluripotent stem cells were used for differentiation

value: H9 human pluripotent stem cell (hPSC)

value: 41 days


title: Expanding leaves_Day 3_Control, rep1

description:
Ogura_Mg_07
Normalized_data_Expanding_leaves_Day3.csv


title: Fet Wk14 AP25

source_name: hindlimb skeletal muscles

value: fetal week 14

value: hindlimb skeletal muscles


title: SKM_ERS_mouse #2

description: Transcriptomic gastrocnemius - ER stress

source_name: mix C57Bl6/J-SV129 female mouse

growth_protocol: Female mice (mix C57Bl6/J-SV129) were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use.

treatment_protocol: Intramuscular injection 24h before euthanasia: In the same animal, one gastrocnemius received tunicamycin solution (30µg/30µL) , the other the control saline solution.

value: WT

value: tunicamycin


title: Mature leaves_Day 8_-Mg, rep4

description:
Ogura_Mg_90
Normalized_data_Mature_leaves_Day8.csv

value: Mature leaves (the first two leaves)

value: 18 days old (day 8 of Mg deprivation)


title: Fet Wk9 AP36

source_name: whole hindlimb excluding feet

value: fetal week 9

value: whole hindlimb excluding feet


title: Fet Wk12 AP23

value: fetal week 12


title: Expanding leaves_Day 3_Control, rep3

description:
Ogura_Mg_10
Normalized_data_Expanding_leaves_Day3.csv

value: 13 days old (day 3 of Mg deprivation)


title: Emb Wk7.25 AP29

source_name: whole hindlimb

value: embryonic week 7.26

tag: carnegie stage

value: whole hindlimb


title: Fet Wk9 AP14

tag: tissue


title: Expanding leaves_Day 3_Control, rep2

description:
Ogura_Mg_09
Normalized_data_Expanding_leaves_Day3.csv

value: Expanding leaves (the next two leaves)


title: Mature leaves_Day 8_-Mg, rep2

description:
Ogura_Mg_88
Normalized_data_Mature_leaves_Day8.csv

value: Magnesium deficiency


title: Emb Wk7 AP30

value: embryonic week 7


title: HX D35 Live HX21

value: H9 human pluripotent stem cell (hPSC)

value: HX protocol (Xi et al., Cell Rep, 2017)

value: 35 days

value: live


title: Emb Wk7 AP24


title: Emb Wk7 AP6


title: Expanding leaves_Day 5_Control, rep2

description:
Ogura_Mg_45
Normalized_data_Expanding_leaves_Day5.csv

value: 15 days old (day 5 of Mg deprivation)

value: Control


title: Mature leaves_Day 8_-Mg, rep3

description:
Ogura_Mg_89
Normalized_data_Mature_leaves_Day8.csv

value: Mature leaves (the first two leaves)


title: Mature leaves_Day 8_-Mg, rep1

description:
Ogura_Mg_85
Normalized_data_Mature_leaves_Day8.csv

value: 18 days old (day 8 of Mg deprivation)


title: Emb Wk6 AP13

value: embryonic week 6


title: Emb Wk6.5 AP22

value: embryonic week 6.5


title: Mature leaves_Day 8_Control, rep4

description:
Ogura_Mg_78
Normalized_data_Mature_leaves_Day8.csv


title: Mature leaves_Day 8_Control, rep3

description:
Ogura_Mg_75
Normalized_data_Mature_leaves_Day8.csv


title: Mature leaves_Day 5_-Mg, rep3

description:
Ogura_Mg_64
Normalized_data_Mature_leaves_Day5.csv


title: Mature leaves_Day 8_Control, rep1

description:
Ogura_Mg_73
Normalized_data_Mature_leaves_Day8.csv


title: Emb Wk6 AP5


title: Donor3_Untreated_inactivatedMTB

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque centrifugation (GE Healthcare Life Sciences) from 3 healthy donors. CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec) and allowed to differentiate into Mφs in the presence of granulocyte-macrophage colony-stimulating factor (GM-CSF) (20 ng/mL; R&D Systems) over a six-day period. RPMI medium + GM-CSF was added to the cell cultures every two days.

extract_protocol:
Total RNA was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments.
cDNA libraries were prepared with the Illumina TruSeq RNA Sample Preparation Kit v2 and were sequenced on an llumina HiSeq 4000

treatment_protocol: Mycobacterium tuberculosis H37Rv (MTB) was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Becton Dickinson). Before infection, bacteria were washed three times and re-suspended in 1 ml PBS. Clumps were dissociated by 30 passages through a needle and then allowed to sediment for 5 min. Bacteria in the supernatant were  killed by heating at 90°C during 30min (defined heareafter hk-MTB). The density of bacteria in the supernatant was verified by measuring the OD600. Macrophages were infected with live MTB at a multiplicity of infection 1:1 (one bacterium-per cell), whereas cells were simulated with hk-MTB at a MOI of 5:1. After 18h of stimulation, cells were washed and total RNA was collected. The transcriptome was analyzed by mRNA sequencing.

value: human monocyte-derived macrophages

value: inactivated MTB

tag: donor


title: Emb Wk5 AP32

value: embryonic week 5


title: Mature leaves_Day 8_Control, rep2

description:
Ogura_Mg_74
Normalized_data_Mature_leaves_Day8.csv


title: Donor2_Untreated_inactivatedMTB


title: Mature leaves_Day 5_-Mg, rep2

description:
Ogura_Mg_62
Normalized_data_Mature_leaves_Day5.csv


title: Donor1_Untreated_inactivatedMTB


title: Donor1_Untreated_Infected

value: infected


title: Donor2_Untreated_Infected


title: Donor3_Untreated_Uninfected

value: uninfected


title: Donor3_Untreated_Infected


title: Mature leaves_Day 5_-Mg, rep1

description:
Ogura_Mg_61
Normalized_data_Mature_leaves_Day5.csv

value: Magnesium deficiency


title: Mature leaves_Day 3_-Mg, rep2

description:
Ogura_Mg_28
Normalized_data_Mature_leaves_Day3.csv

value: 13 days old (day 3 of Mg deprivation)


title: Mature leaves_Day 5_Control, rep4

description:
Ogura_Mg_53
Normalized_data_Mature_leaves_Day5.csv


title: Mature leaves_Day 5_Control, rep3

description:
Ogura_Mg_52
Normalized_data_Mature_leaves_Day5.csv


title: Mature leaves_Day 5_Control, rep1

description:
Ogura_Mg_49
Normalized_data_Mature_leaves_Day5.csv


title: Donor2_Untreated_Uninfected


title: Mature leaves_Day 5_Control, rep2

description:
Ogura_Mg_50
Normalized_data_Mature_leaves_Day5.csv


title: Donor1_Untreated_Uninfected


title: Mature leaves_Day 3_-Mg, rep1

description:
Ogura_Mg_27
Normalized_data_Mature_leaves_Day3.csv


title: DFF-Seq of Flavopiridol treated HeLa cells

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

institute: The University of Iowa

library_source: genomic

data_processing:
Adapter trimming using trim_galore v0.4.4.
Alignment of trimmed reads to hg38 using bowtie v1.2.
For NasCap datasets, identical mapped reads with redundant UMIs were collapsed (https://github.com/P-TEFb/dedup), and then bedgraphs were generated using bedtools v2.26. For DFF-Seq data, bedgraphs were generated from aligned reads using bedtools v2.26.
We have described the data processing details and their associated analyses in the manuscript.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated from bedgraph files using the Kent UCSC utility program called bedGraphToBigWig, for display on the UCSC Genome Browser.

molecule: genomic DNA

source_name: Cervical tumor (HeLa cells)

growth_protocol: Adherent HeLa cells were grown in T150 flasks at 37°C and 5% CO2 in 30 ml DMEM (Gibco 11965-092) supplemented with 5% fetal bovine serum (FBS, Gibco 26140-079).

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (Nilson et al. 2017; Ball et al. 2019).
DFF-seq used genomic DNA fragments resulting from digestion of nuclei from flavopiridol treated HeLa cells with the DNA fragmentation factor (DFF). Standard Y adaptors were ligated onto the polished ends and sequenced without amplification.

treatment_protocol: 1 h prior to harvest, when cells were at 80-90% confluence, 10 ml of media was removed from each flask and either 30 µl of DMSO or 1 µM flavopiridol in DMSO was added before the mixture was returned to the flask (final concentrations 0.1% DMSO or 1 µM flavopiridol and 0.1% DMSO). In DFF-Seq, cells treated with 1 µM flavopiridol for 1 hr were digested with 5 µg of DFF for 30 minutes to generate mononucleosomes.

value: HeLa

value: 1 µM flavopiridol for 1 h and DFF for 30 minutes

tag: library prep

value: DFF-Seq


title: NasCap capped w/o m7 Flavopiridol treated Hela

extract_protocol:
Rapid nuclei isolation steps were performed on wet ice using ice-cold buffers as previously described (Nilson et al. 2017; Ball et al. 2019).
A PRO-Seq protocol like that in Mahat, et al. 2016 (10.1038/nprot.2016.086) and Nilson, et al. 2017 (10.1093/nar/gkx724) was followed except that an antibody to mRNA cap was used to select m7G capped nascent transcripts. The protocol is called NasCap and details are in the manuscript.

tag: cell line

value: 0.1% DMSO and 1 µM flavopiridol for 1 h

value: NasCap

tag: molecule subtype

value: nascent nuclear transcripts


title: Mature leaves_Day 5_Control, rep5

description:
Ogura_Mg_54
Normalized_data_Mature_leaves_Day5.csv

value: Mature leaves (the first two leaves)

value: 15 days old (day 5 of Mg deprivation)

value: Control


title: Mature leaves_Day 3_Control, rep4

description:
Ogura_Mg_17
Normalized_data_Mature_leaves_Day3.csv


title: NasCap capped w/o m7 Control Hela

description: HeLa_capped_w/o_ m7_control

value: 0.1% for DMSO 1 h


title: KO-R-head-4

city: Tsukuba

first: Ki-Hyeon

last: Seong

state: Ibaraki

address: 3-1-1 Koyadai

institute: RIKEN

description: KO-RS-head

data_processing:
Basecalls performed using CASAVA
Sequenced reads (fastq files) were mapped to dm3 whole genome derived from iGenomes (illumina) using tophat2 V２.0.12.
FPKM were calculated using the Cufflinks suite (cuffnorm).
All parameters were left at the default value.
Genome_build: dm3(Drosophila melanogaster)

organism: Drosophila melanogaster

source_name: KO-R-Head

growth_protocol: flies were reared in an incubator at 25°C and 60% humidity using Drosophila satandard diet under 12L:12D light cycle.

extract_protocol:
mRNA were prepared from 50 F1 males using ISOGENII(nippon gene) and  OligotexTM-dT30<Super> mRNA purification kit (TAKARA)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Father flies were exposed restraint stres for 10 hours three times and crossed with females. The F1 males (5-6-days old) were used for RNA-seq analysis.

value: Head

tag: father's genotype

tag: paternal restraint stress

value: Yes


title: KO-R-head-3

description: KO-RS-head


title: NasCap m7G capped Control Hela

value: 0.1% DMSO 1 h


title: Mature leaves_Day 3_Control, rep2

description:
Ogura_Mg_15
Normalized_data_Mature_leaves_Day3.csv

tag: ecotype


title: KO-R-head-2

description: KO-RS-head


title: KO-R-head-5

description: KO-RS-head


title: Mature leaves_Day 3_Control, rep3

description:
Ogura_Mg_16
Normalized_data_Mature_leaves_Day3.csv


title: KO-F-head-4

description: KO-RS-head

source_name: KO-F-Head

value: No


title: KO-F-head-3

description: KO-RS-head


title: Mature leaves_Day 3_Control, rep1

description:
Ogura_Mg_13
Normalized_data_Mature_leaves_Day3.csv


title: Arabidopsis_RH_120min_decay3

city: Riverside

first: Maureen

last: Hummel

state: California

address: 900 University Avenue

department: Botany and Plant Sciences

institute: University of California

description:
rh decay 120 min replicate 3
AllThanincounts.txt

data_processing:
Processing of RNA-seq data was performed using the package systemPipeR
Alignment to TAIR10 with bowtie2 2.2.5 and tophat 2.0.14
Aligned reads were counted against the Araport11 genome release 201606 using the summarizeOverlaps function in ôunionö mode
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: Col-0 5 days old seedling

extract_protocol: rRNA depleted; Illumina TruSeq Total RNA Sample Prep Kit with Ribo-Zero (Plant)

value: 5-days-old seedling

tag: developmental stage

value: seedling

tag: genotype

tag: time point

value: 120 min

tag: agent

value: Cordycepin


title: Arabidopsis_RH_000min_decay3

description:
rh decay 0 min replicate 3
AllThanincounts.txt

value: 0 min


title: Arabidopsis_WT_060min_decay3

description:
wt decay 60 min replicate 3
AllThanincounts.txt

value: 60 min


title: Arabidopsis_WT_030min_decay3

description:
wt decay 30 min replicate 3
AllThanincounts.txt

value: 30 min


title: Arabidopsis_RH_060min_decay3

description:
rh decay 60 min replicate 3
AllThanincounts.txt


title: NasCap m7G capped Flavopiridol treated HeLa

value: HeLa

value: 0.1% DMSO and 1 µM flavopiridol for 1 h

value: NasCap


title: Arabidopsis_WT_000min_decay3

description:
wt decay 0 min replicate 3
AllThanincounts.txt


title: Arabidopsis_RH_120min_decay2

description:
rh decay 120 min replicate 2
AllThanincounts.txt


title: Arabidopsis_RH_060min_decay2

description:
rh decay 60 min replicate 2
AllThanincounts.txt


title: Mature leaves_Day 3_-Mg, rep3

description:
Ogura_Mg_30
Normalized_data_Mature_leaves_Day3.csv

value: Mature leaves (the first two leaves)

value: 13 days old (day 3 of Mg deprivation)

value: Magnesium deficiency


title: KO-R-head-1

description: KO-RS-head

value: Head


title: Arabidopsis_RH_030min_decay3

description:
rh decay 30 min replicate 3
AllThanincounts.txt


title: Arabidopsis_WT_120min_decay2

description:
wt decay 120 min replicate 2
AllThanincounts.txt


title: Arabidopsis_RH_015min_decay3

description:
rh decay 15 min replicate 3
AllThanincounts.txt

value: 15 min


title: Arabidopsis_WT_015min_decay2

description:
wt decay 15 min replicate 2
AllThanincounts.txt


title: KO-F-head-5

description: KO-RS-head


title: Arabidopsis_WT_120min_decay3

description:
wt decay 120 min replicate 3
AllThanincounts.txt


title: w-R-head-5

description: w-RS-head

source_name: w-R-Head

value: Yes


title: KO-F-head-2

description: KO-RS-head

value: No


title: KO-F-head-1

description: KO-RS-head


title: Arabidopsis_WT_000min_decay2

description:
wt decay 0 min replicate 2
AllThanincounts.txt

value: 5-days-old seedling


title: w-R-head-4

description: w-RS-head


title: Arabidopsis_WT_015min_decay3

description:
wt decay 15 min replicate 3
AllThanincounts.txt

value: seedling


title: KO-R-OP-5

description: KO-RS-OP

source_name: KO-R-OP

value: Body without head


title: KO-R-OP-3

description: KO-RS-OP


title: KO-R-OP-2

description: KO-RS-OP


title: Arabidopsis_RH_030min_decay2

description:
rh decay 30 min replicate 2
AllThanincounts.txt

value: Cordycepin


title: KO-R-OP-4

description: KO-RS-OP


title: KO-R-OP-1

description: KO-RS-OP


title: Arabidopsis_RH_060min_decay1

description:
rh decay 60 min replicate 1
AllThanincounts.txt


title: w-R-head-2

description: w-RS-head


title: Arabidopsis_RH_015min_decay2

description:
rh decay 15 min replicate 2
AllThanincounts.txt


title: Arabidopsis_RH_000min_decay2

description:
rh decay 0 min replicate 2
AllThanincounts.txt

value: 0 min


title: KO-F-OP-5

description: KO-RS-OP

source_name: KO-F-OP


title: KO-F-OP-4

description: KO-RS-OP


title: Arabidopsis_RH_015min_decay1

description:
rh decay 15 min replicate 1
AllThanincounts.txt


title: w-F-head-5

description: w-RS-head

source_name: w-F-Head


title: Arabidopsis_RH_000min_decay1

description:
rh decay 0 min replicate 1
AllThanincounts.txt


title: KO-F-OP-3

description: KO-RS-OP


title: Arabidopsis_WT_060min_decay2

description:
wt decay 60 min replicate 2
AllThanincounts.txt

value: 60 min


title: Arabidopsis_WT_030min_decay2

description:
wt decay 30 min replicate 2
AllThanincounts.txt

value: 30 min


title: Arabidopsis_WT_060min_decay1

description:
wt decay 60 min replicate 1
AllThanincounts.txt


title: Arabidopsis_RH_120min_decay1

description:
rh decay 120 min replicate 1
AllThanincounts.txt

value: 120 min


title: w-F-head-3

description: w-RS-head


title: KO-F-OP-2

description: KO-RS-OP


title: KO-F-OP-1

description: KO-RS-OP


title: Arabidopsis_WT_030min_decay1

description:
wt decay 30 min replicate 1
AllThanincounts.txt


title: Arabidopsis_WT_000min_decay1

description:
wt decay 0 min replicate 1
AllThanincounts.txt


title: w-R-head-3

description: w-RS-head


title: Arabidopsis_RH_030min_decay1

description:
rh decay 30 min replicate 1
AllThanincounts.txt


title: w-F-head-4

description: w-RS-head


title: Arabidopsis_WT_120min_decay1

description:
wt decay 120 min replicate 1
AllThanincounts.txt


title: w-R-head-1

description: w-RS-head


title: w-F-head-1

description: w-RS-head


title: Arabidopsis_WT_015min_decay1

description:
wt decay 15 min replicate 1
AllThanincounts.txt


title: w-R-OP-1

description: w-RS-OP

source_name: w-R-OP


title: w-R-OP-3

description: w-RS-OP


title: w-R-OP-5

description: w-RS-OP


title: w-R-OP-4

description: w-RS-OP


title: w-R-OP-6

description: w-RS-OP


title: w-R-OP-2

description: w-RS-OP


title: w-F-OP-6

description: w-RS-OP

source_name: w-F-OP


title: w-F-OP-5

description: w-RS-OP


title: w-F-OP-3

description: w-RS-OP


title: w-F-head-2

description: w-RS-head


title: w-F-OP-4

description: w-RS-OP


title: w-F-OP-2

description: w-RS-OP


title: w-F-OP-1

description: w-RS-OP


title: qHSC rep1

city: Guangzhou

first: Chen

last: Qu

state: Guangdong

address: #601 West Huangpu Road

country: China

institute: Jinan University

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 mm10 whole genome using Hisat2 with default parameters.
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.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: primary hepatic stellate cells

extract_protocol:
Hepatic stellate cells were isolated from control and CCl4-treated mice, The total RNA was immediately isolated from the cells using Trizol Reagent (Invitrogen, Waltham, MA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using the standard Illumina protocols

tag: strain

tag: cell type

value: hepatic stellate cells isolated from control mouse


title: qHSC rep3


title: qHSC rep2


title: endometrial biopsy using control_Sample no: 3440

city: San Francisco

first: Deepak

last: Srivastava

address: 1650 Owens St

institute: J David Gladstone Institutes

hyb_protocol: The labeled cDNA was hybridized to Human (or Mouse) Gene 1.0 or 2.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: The signal intensity fluorescent images produced during the Affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: The raw cel files were read using the read.celfiles function that is part of the oligo package in biocondutor.  The expression of all genes were normalized across all the samples in the chosen contraceptive and control group using the Robust Multi-array Average (RMA) procedure.

source_name: endometrial biopsy using control

label_protocol: Purified RNA was analyzed for quality using chip-based capillary electrophoresis (Bioanalyzer, Agilent, Inc) and quantity and purity was determined with a NanoDrop Spectrometer.  The NuGen Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation and biotinabelling.

growth_protocol: samples were collected directly from female participants; no growth step was performed

extract_protocol: frozen samples were minced and then extracted with NuceloSpin RNA II Kit (Marcherey-Nagel Inc, Bethlehem, PA)

treatment_protocol: the particpants were users of contraceptives hence no treatment was performed

tag: sample no.

tag: contraceptive used

value: control

value: endometrial biopsy


title: aHSC rep3

value: hepatic stellate cells isolated from mouse with CCl4-induced liver fibrosis


title: endometrial biopsy using COC_Sample no: 3622

source_name: endometrial biopsy using COC

value: COC

tag: age


title: endometrial biopsy using cu-IUD_Sample no: 3216

source_name: endometrial biopsy using cu-IUD

value: cu-IUD

tag: tissue


title: cervical biopsy using cu-IUD_Sample no: 3589

source_name: cervical biopsy using cu-IUD

value: cervical biopsy


title: cervical biopsy using cu-IUD_Sample no: 3527


title: endometrial biopsy using LNG-IUD_Sample no: 3404

source_name: endometrial biopsy using LNG-IUD

value: LNG-IUD


title: endometrial biopsy using cu-IUD_Sample no: 3700


title: endometrial biopsy using control_Sample no: 2910


title: endometrial biopsy using control_Sample no: 2821


title: endometrial biopsy using LNG-IUD_Sample no: 3306


title: cervical biopsy using COC_Sample no: 3526

source_name: cervical biopsy using COC


title: cervical biopsy using control_Sample no: 2960

source_name: cervical biopsy using control


title: endometrial biopsy using cu-IUD_Sample no: 2519


title: endometrial biopsy using LNG-IUD_Sample no: 3412


title: aHSC rep2


title: cervical biopsy using cu-IUD_Sample no: 3618


title: cervical biopsy using control_Sample no: 3225


title: endometrial biopsy using LNG-IUD_Sample no: 3169


title: endometrial biopsy using control_Sample no: 2946


title: endometrial biopsy using LNG-IUD_Sample no: 3304


title: aHSC rep1


title: cervical biopsy using cu-IUD_Sample no: 3216


title: tKO-3

city: Hong Kong

first: Yin

last: Xia

address: LKIBSB

institute: The Chinese University of Hong Kong

data_processing:
The original image data were analyzed using Bcl2fastq (v2.17.1.14) for base calling and preliminary quality analysis.
Sequencing was carried out using a 2x150bp paired-end (PE) configuration
Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution. After adjusted by Benjamini and Hochberg’s approach for controlling the false discovery rate, P-value of genes were setted <0.05 to detect differential expressed ones.
Supplementary_files_format_and_content: Tab-delimited txt files include FPKM values for each Sample.

source_name: Initial Segements of Epididymis

extract_protocol:
Total RNA was extracted from WT, dKO and tKO initial segments of epididymis at 4 weeks of age using RNA extraction kit (Takara, Cat#9767) with DNase I treatment. Then mRNAs are isolated from total RNA with oligo(dT) method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Initial Segements of Epididymis

value: 4 weeks of age


title: endometrial biopsy using cu-IUD_Sample no: 3408


title: cervical biopsy using control_Sample no: 3300


title: endometrial biopsy using LNG-IUD_Sample no: 3345


title: endometrial biopsy using COC_Sample no: 2546


title: tKO-1


title: dKO-3


title: cervical biopsy using cu-IUD_Sample no: 3264


title: endometrial biopsy using cu-IUD_Sample no: 3293


title: dKO-2


title: dKO-1


title: WT-3


title: endometrial biopsy using cu-IUD_Sample no: 3527


title: endometrial biopsy using LNG-IUD_Sample no: 2853


title: endometrial biopsy using control_Sample no: 2705


title: tKO-2


title: endometrial biopsy using control_Sample no: 3300


title: endometrial biopsy using cu-IUD_Sample no: 3264


title: WT-2


title: endometrial biopsy using control_Sample no: 2960


title: cervical biopsy using LNG-IUD_Sample no: 3404

source_name: cervical biopsy using LNG-IUD


title: WT-1


title: cervical biopsy using cu-IUD_Sample no: 3571


title: 6M-WT5: 6 Month Wildtype, Regular activity, rep. 5

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Samples were trimmed with trimGalore!, followed by alignment to the mm10 genone using HISAT2.
Features were quantified using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file

source_name: Cardiac myocytes

extract_protocol:
Total RNA was isolated from cardiac myocytes using  miRNAeasy mini kit (Qiagen, Cat#217004)
Ribosome depleted, strand specific paired end libraries were prepared using TruSeq RNA Library Prep Kit v2 from Illumina

value: Cardiac myocytes

tag: genotype/variation

value: Wildtype

tag: exercise

value: no


title: cervical biopsy using COC_Sample no: 3611


title: endometrial biopsy using COC_Sample no: 3689


title: cervical biopsy using control_Sample no: 2946


title: cervical biopsy using LNG-IUD_Sample no: 3412


title: endometrial biopsy using control_Sample no: 3623


title: cervical biopsy using LNG-IUD_Sample no: 3265


title: cervical biopsy using LNG-IUD_Sample no: 3304


title: endometrial biopsy using COC_Sample no: 3198


title: endometrial biopsy using cu-IUD_Sample no: 3364


title: cervical biopsy using COC_Sample no: 3689


title: endometrial biopsy using cu-IUD_Sample no: 3276


title: cervical biopsy using cu-IUD_Sample no: 3364


title: 6M-Het8: 6 Month Myh6-Cre:DspW/F, Regular activity, rep.5


title: 6M-WT3: 6 Month Wildtype, Regular activity, rep.3


title: cervical biopsy using control_Sample no: 2821


title: 6M-WT2: 6 Month Wildtype, Regular activity, rep. 2


title: cervical biopsy using LNG-IUD_Sample no: 3294


title: endometrial biopsy using COC_Sample no: 3593


title: cervical biopsy using LNG-IUD_Sample no: 2853


title: cervical biopsy using COC_Sample no: 2546


title: cervical biopsy using COC_Sample no: 3622


title: cervical biopsy using LNG-IUD_Sample no: 2947


title: 6M-WT1: 6 Month Wildtype, Regular activity, rep. 1


title: 6M-Het7: 6 Month Myh6-Cre:DspW/F, Regular activity, rep. 4


title: endometrial biopsy using COC_Sample no: 3600


title: 6M-Het6: 6 Month Myh6-Cre:DspW/F, Regular activity, rep. 3


title: cervical biopsy using control_Sample no: 2545


title: 6M-WT4: 6 Month Wildtype, Regular activity, rep. 4


title: 6M-Het2: 6 Month Myh6-Cre:DspW/F, Regular activity, rep. 2


title: endometrial biopsy using COC_Sample no: 3607


title: endometrial biopsy using cu-IUD_Sample no: 2562


title: cervical biopsy using cu-IUD_Sample no: 3700


title: cervical biopsy using LNG-IUD_Sample no: 3169


title: cervical biopsy using COC_Sample no: 3593


title: endometrial biopsy using COC_Sample no: 3596


title: cervical biopsy using COC_Sample no: 3612


title: 3M-Het3: 3 Month Myh6-Cre:DspW/F, Regular activity, rep. 3


title: 3M-WT8: 3 Month Wildtype, Regular activity, rep. 4


title: 6M-Het1: 6 Month Myh6-Cre:DspW/F, Regular activity, rep. 1


title: 3M-Het1: 3 Month Myh6-Cre:DspW/F, Regular activity, rep. 1


title: cervical biopsy using COC_Sample no: 3607


title: endometrial biopsy using COC_Sample no: 3612


title: 3M-WT9: 3 Month Wildtype, Regular activity, rep. 5


title: 3M-Het5: 3 Month Myh6-Cre:DspW/F, Regular activity, rep. 4


title: endometrial biopsy using LNG-IUD_Sample no: 2947


title: 3M-Het2: 3 Month Myh6-Cre:DspW/F, Regular activity, rep. 2


title: cervical biopsy using control_Sample no: 3440


title: cervical biopsy using COC_Sample no: 3198


title: endometrial biopsy using control_Sample no: 3079


title: cervical biopsy using cu-IUD_Sample no: 3435


title: cervical biopsy using COC_Sample no: 3588


title: cervical biopsy using COC_Sample no: 3600


title: cervical biopsy using COC_Sample no: 3499


title: cervical biopsy using control_Sample no: 2910


title: cervical biopsy using cu-IUD_Sample no: 3719


title: 3M-Het6: 3 Month Myh6-Cre:DspW/F, Regular activity, rep. 5


title: 3M-WT6: 3 Month Wildtype, Regular activity, rep. 3


title: 3M-WT2: 3 Month Wildtype, Regular activity, rep. 1


title: cervical biopsy using LNG-IUD_Sample no: 3466


title: 3M-WT4: 3 Month Wildtype, Regular activity, rep. 2


title: endometrial biopsy using COC_Sample no: 3557


title: endometrial biopsy using control_Sample no: 3225


title: 6M-EX-DH2: 6 Month Myh6-Cre:DspW/F, exercised, rep. 2

value: yes


title: cervical biopsy using control_Sample no: 3079


title: endometrial biopsy using cu-IUD_Sample no: 3590


title: endometrial biopsy using cu-IUD_Sample no: 3707


title: endometrial biopsy using cu-IUD_Sample no: 3719


title: cervical biopsy using COC_Sample no: 3485


title: endometrial biopsy using control_Sample no: 3730


title: cervical biopsy using cu-IUD_Sample no: 3293


title: 6M-EX-WT4: 6 Month Wildtype, exercised, rep. 4


title: cervical biopsy using LNG-IUD_Sample no: 3345


title: 6M-EX-WT1: 6 Month Wildtype, exercised, rep. 1


title: 6M-EX-DH3: 6 Month Myh6-Cre:DspW/F, exercised, rep. 3


title: 6M-EX-DH5: 6 Month Myh6-Cre:DspW/F, exercised, rep. 5


title: 6M-EX-WT3: 6 Month Wildtype, exercised, rep. 3


title: cervical biopsy using control_Sample no: 3730


title: endometrial biopsy using COC_Sample no: 3174


title: 6M-EX-DH1: 6 Month Myh6-Cre:DspW/F, exercised, rep. 1


title: cervical biopsy using cu-IUD_Sample no: 3707


title: endometrial biopsy using LNG-IUD_Sample no: 3437


title: endometrial biopsy using COC_Sample no: 3485


title: endometrial biopsy using LNG-IUD_Sample no: 3466


title: cervical biopsy using control_Sample no: 3052


title: Butyrate_input

first: Qianhong

last: Ye

address: Malianwa

institute: China Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.7.
ChIP-seq reads were aligned to the hg19 genome assembly using EasyAlign version 3.2 with the following configurations.
Data were filtered using the following specifications: Individual reads mapping to the plus or minus strand and present significant enrich, and strand cross-correlation of tag density providing a quick assessment of IP-seq data set quality and binding characteristics.
Peaks finding used MACS2 version 2.1.0 with a q value threshold of enrichment of 0.05. Then, the distribute of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: NarrowPeaks tables were generated for each sample.

source_name: human ovarian granulosa KGN cells

growth_protocol: KGN cells were cultured in a RPMI1640 medium supplemented with 10% FBS, and maintained at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
We used ChIP-seq kit (CST, Cat# 9003) to extract chromatins following the manufacturer instructions.
Libraries were prepared according to Illumina's protocols. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: KGN cells were treated without or with 1mM butyrate for 6 hours at 37 °C in a humidified 5% CO2 incubator.

tag: cell line

value: KGN

value: Ovarian granulosa cells

tag: passages

tag: treatment

value: Butyrate

tag: chip antibody


title: Butyrate_H3K9ac

value: H3K9ac (CST, Cat# C5B11)


title: Butyrate_IgG

value: IgG (CST, Cat# 9003)


title: Butyrate_H4K16ac

value: H4K16ac (CST, Cat# E2B8W)


title: 6M-EX-WT2: 6 Month Wildtype, exercised, rep. 2


title: cervical biopsy using cu-IUD_Sample no: 2519


title: CON_input

value: Control


title: CON_IgG


title: CON_H4K16ac


title: cervical biopsy using control_Sample no: 3540

value: control


title: cervical biopsy using cu-IUD_Sample no: 2562

value: cu-IUD


title: cervical biopsy using LNG-IUD_Sample no: 3437

value: cervical biopsy


title: CON_H3K9ac


title: Input DNA from MPH Thapsi

data_processing:
Reads were mapped to the mouse genome (mm10) using Bowtie 1
Mapped reads were filtered to remove duplicates and reads mapping to ENCODE blacklisted regions (Encode_Project_Consortium 2012) or mouse ChIP-seq false-positives regions (Dubois-Chevalier et al. 2017)
Regions with significant changes in H3K27ac ChIP-seq signals induced by Thapsy were identified using csaw 1.6.1 (Lun and Smyth 2014; Lun and Smyth 2016). The genome was binned and reads counted before normalization using a loess regression. Finally, after dispersion estimation with the function estimateDisp, a paired-differential analysis was performed on this filtered and normalized data using glmQLFit. Bins overlapping H3K27ac peaks (broad regions called with MACS2 using a pool of all H3K27ac ChIP-seq datasets and inputs as control - parameters : q-val narrow = 0.001 et q-val broad = 0.01) were identified using findOverlaps from GenomicRanges 1.24.3 (Lawrence et al. 2013) (parameters : minoverlap=75, maxgap=0). Bins overlapping a single H3K27ac peak were combined using combineOverlaps and only merged bins with FDR < 0.05 and > two-fold enrichment in bins with similar change were considered.
Genome_build: mm10
Supplementary_files_format_and_content: Bed files reporting H3K27ac regions UP, DOWN or unchanged regions upon Thapsy treatment identified using csaw

source_name: Input DNA from MPH Thapsi

extract_protocol:
ChIP was performed as described in Flajollet S., Lefebvre B., Rachez C., and Lefebvre P. 2006. Distinct Roles of the Steroid Receptor Coactivator 1 and of MED1 in Retinoid-induced Transcription and Cellular Differentiation. J. Biol. Chem. 281:20338-20348.
Diagenode MicroPlex Library Preparation kit v2

treatment_protocol: Mouse primary hepatocytes were prepared as described in Bantubungi K et al, Diabetes 2014. Hepatocytes were grown in serum free William's medium and  treated for 4h with 1µM thapsigargin or vehicle (0.04% DMSO). ChIP-seq was performed using an H3K27ac antibody (Active Motif ref 39685).

tag: strain background

value: WT

value: adult

tag: Sex

value: male

value: mouse primary hepatocytes (MPH)

value: 1µM thapsigargin for 4hrs


title: 6M-EX-WT5: 6 Month Wildtype, exercised, rep. 5

value: Cardiac myocytes

value: Wildtype


title: cervical biopsy using LNG-IUD_Sample no: 3306

value: LNG-IUD


title: cervical biopsy using COC_Sample no: 3557

value: COC


title: scRNA_seq_B+A0_Intestine

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

description: The group information is prefixed with B+A0 in the column of processed data file

data_processing:
We used CellRanger count pipeline 2.2.0 to analyze the sequencing data and generated the single cell information. To generate same number of total cells for downstream analysis, we used augments ‘--force-cells=5000 \’.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files stores normalized and log-transformed single cell expression value

extract_protocol:
Intestine samples were isolated and washed with PBS solution supplemented with 0.04% bovine serum albumin. Then, the intestine was digested with 1X TrypLE™ Express (Cat# 12605010) for 3 min to obtain single cell pellets. The single-cell Gel-Bead in Emulsions (GEMs) were then generated with Chromium 10x Genomics single-cell system by using single-cell 3’ Library and Gel Bead Kit V2 (10x Genomics, Cat#120237). Captured cells were then lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

value: ICR

value: Intestine

value: busulfan alone


title: endometrial biopsy using LNG-IUD_Sample no: 3265

value: endometrial biopsy


title: scRNA_seq_AOS0_Intestine

description: The group information is prefixed with AOS0 in the column of processed data file


title: Input DNA from MPH DMSO

source_name: Input DNA from MPH DMSO

value: vehicle (0.04% DMSO) for 4hrs


title: H3K27ac ChIP-seq MPH Thapsi #3

source_name: H3K27ac ChIP-seq MPH Thapsi

value: H3K27ac (Active Motif, Cat. # 39685)


title: 6M-EX-DH4: 6 Month Myh6-Cre:DspW/F, exercised, rep. 4

value: yes


title: KW_1

city: Jerusalem

first: Hadar

last: Benyamini

address: Ein Karem

country: Israel

institute: The Hebrew University

data_processing:
Quality trimming with q=32 threshold and adapter trimming with Trim Galore!, version 0.3.7, using parameters --stringency 1 -e 0.1 --length 15. Filtering low quality reads with the fastq_quality_filter program of the FASTX package, version 0.0.14, using parameters -q 20 and -p 90.
Alignment with TopHat2, version 2.0.11, using parameters -G genes.gtf -N 3 --read-gap-length 5 --read-edit-dist 8 --segment-length 18 --read-realign-edit-dist 3 --b2-i S,1,0.75 --b2-mp 3,1 --b2-score-min L,-0.5,-0.5 genome processed.fastq.
Quantification with Cufflinks (cuffquant), version 2.2.1, using parameters -b and -u.
Normalization and differential expression with DESeq2, version 1.12.4, testing for lfc > 0.5 (lfcThreshold parameter), with default significance threshold, padj < 0.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file. First line is a header line. First 3 columns have general gene details (accession, symbol and biotype), the next 12 columns are for raw counts, then 12 columns of normalized counts, then the average expression (baseMean), then 5 columns of DESeq2 results for each comparison.

source_name: kidney

growth_protocol: Standard animal care of the Hebrew University Hadassah Medical Center

extract_protocol:
RNA was extracted from mouse tissues using the miRvana Ambion kit and subsequently treated with DNase
Libraries were prepared using Trueseq

treatment_protocol: GNE M743T/M743T knock in mice or wild-type mice

tag: genotype

value: Wild-type

tag: phenotype

value: healthy

value: kidney


title: KS_4

value: GNE M743T/M743T knock in

value: Sick


title: 5-D2AS

city: Melbourne

first: Zheng

last: Fan

state: Victoria

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
HISAT2 (Galaxy Version 2.1.0) was used to map paired FASTQ file to Human Genome (hg19; stranded information was not considered).
Reads mapped to exons were counted using featureCounts (Galaxy Version 1.6.2)
Limma-Voom (Galaxy Version 3.36.5) was used to generate normalized counts.
Genome_build: hg19
Supplementary_files_format_and_content: Normalised count matrix  in tab-delimited flie

source_name: MV4;11 cells

growth_protocol: Cells were cultured in RPMI- 1640 supplemented with 10% v/v heat-inactivated fetal bovine serum, 100U/mL penicillin and 100μg/mL streptomycin 2mM GlutaMAX  and 1mM sodium pyruvate at 37 degree Celsius and 5% carbon dioxide.

extract_protocol:
Cells were lysed in TRIzol, then RNA was extrated using Direct-Zol RNA MiniPrep kit (Zymo Research)
poly-dT enrichment (New England BioLabs, Ipswich MA USA, E7490) sequencing libraries were prepared from 500ng RNA using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina. 75 paired-end base-pair reads were sequenced using the Illumina NEXTseq 500 (Illumina, San Diego CA USA).
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: No treatment

tag: analog sensetive muntants

value: #2CDK12AS/NULL;CDK13AS/AS Clone


title: 3-CDK13AS

value: CDK13AS/AS Clone


title: KS_3


title: KW_4


title: 2-CDK12AS


title: H3K27ac ChIP-seq MPH Thapsi #2

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

value: WT

value: adult

value: male

value: mouse primary hepatocytes (MPH)

value: 1µM thapsigargin for 4hrs


title: H3K27ac ChIP-seq MPH DMSO #2

source_name: H3K27ac ChIP-seq MPH DMSO


title: KS_2


title: 1-WT

value: WT Clone


title: KH_4


title: H3K27ac ChIP-seq MPH Thapsi #1


title: KW_2


title: KH_3


title: KH_2


title: KS_1


title: KH_1


title: ru-wyf-rm-4

city: Morgantown

first: Apoorva

last: Ravi Shankar

state: WV

address: 53 Campus Drive

department: Biology

institute: West Virginia University

data_processing:
Basecalls performed with Illumina’s FASTQ Generation (v1.0.0) available in BaseSpace.
Transcripts quantification was done with salmon (v0.13.1) vs the transcript files of S288c and RM11 respectively from SGD
Supplementary_files_format_and_content: Salmon’s quantification file

organism: Saccharomyces cerevisiae

source_name: RM11_YM +  WYF_treated (0.25% Cr41)

growth_protocol: Yeast were grown in YM with or without WYF and grown to mid-log phase

extract_protocol:
Hot-phenol extraction (Short protocols in molecular biology, 1995)
library built using Epicenre's ScriptSeq complete gold Yeast kit

treatment_protocol: 0.25% glyphosate in Cr41 was added to cultures and grown for 90 minutes before harvest, washed once with water and flash frozen

tag: strain

tag: medium

value: YM +  WYF

value: treated (0.25% Cr41)


title: ru-wyf-rm-3


title: ru-wyf-rm-5


title: 4-D1AS

value: #1CDK12AS/NULL;CDK13AS/NULL Clone


title: ru-wyf-rm-2


title: KW_3


title: ru-wyf-rm-1


title: H3K27ac ChIP-seq MPH DMSO #3

institute: CNRS

tag: cell type

value: vehicle (0.04% DMSO) for 4hrs

value: H3K27ac (Active Motif, Cat. # 39685)


title: wyf-rm-4

source_name: RM11_YM +  WYF_untreated

value: untreated


title: wyf-rm-2


title: wyf-rm-3


title: ru-wyf-gsy-2

source_name: GSY147_YM +  WYF_treated (0.25% Cr41)


title: wyf-rm-1


title: ru-wyf-gsy-4


title: H3K27ac ChIP-seq MPH DMSO #1


title: ru-wyf-gsy-5


title: wyf-gsy-3

source_name: GSY147_YM +  WYF_untreated


title: wyf-gsy-5


title: ru-rm-5

source_name: RM11_YM_treated (0.25% Cr41)

value: YM


title: wyf-gsy-4


title: ru-rm-4


title: ru-rm-2


title: ym-rm-4


title: ym-rm-5


title: wyf-gsy-2


title: ym-rm-2


title: ru-rm-1


title: ym-rm-3


title: ru-rm-3


title: wyf-rm-5


title: ru-gsy-5

source_name: GSY147_YM_treated (0.25% Cr41)


title: ym-rm-1


title: ru-gsy-4


title: ru-wyf-gsy-3


title: ru-wyf-gsy-1


title: ru-gsy-3


title: ru-gsy-2


title: ym-gsy-5


title: wyf-gsy-1


title: ym-gsy-1


title: ym-gsy-4


title: ru-gsy-1


title: ym-gsy-3


title: ym-gsy-2


title: Unprecipitated-DNA-C2C12-Background

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: To identify DNA regions interacting with Pvt1 it was searched for peacks produced by the alignement of precipitated DNA against non precipitated DNA.

data_processing:
Library strategy: ChIRP-Seq
Raw reads were aligned using TMAP from Ion Torrent Server. TMAP was used with default parameters.
Pvt1 DNA binding regions were computed using macs2 (version 2.1). Each sample versus against the input (macs2 call: macs2 callpeak -t <sample> -c <input> -B --nomodel --extsize 147 -SPMR -g  ce -n <name>)
Genome_build: Mouse GRCm38/mm10
Supplementary_files_format_and_content: macs2 output in Tab Separated Value file. After description, columns are chr, start, end, length, abs_summit, pileup, -log10(pvalue), fold_enrichment, -log10(qvalue), name.

source_name: DNA-unprecipitated

growth_protocol: C2C12 myoblasts were cultured on Tissue Culture Dishes (Thermo Fisher Scientific). Myoblasts were maintained in proliferation medium (DMEM, 10% FBS, 1 unit/ml Penicillin, 100 µg/ml Streptomycin), detached when reaching ~80% confluence using Trypsin-EDTA (Thermo Fisher Scientific) and re-seeded at a lower density. Cell cultures were maintained in a humid environment with controlled temperature and carbon dioxide levels (37°C, 5% v/v CO2).

extract_protocol:
RNA was extracted with Tizol solution and Pvt1 quantized by qRT-PCR. DNA was extracted by Phenol-chloroform and isoamyl alcohol in the ratio of 25:24:1 (v/v), pH 8.0 (Sigma Aldrich).
DNA libraries were produced by the Accel-NGS DNA library kit (Swift Bioscience). We used this approach because the technology underlying Accel NGS does not require intact double stranded DNA (dsDNA), making it compatible with single stranded, denatured, or nicked samples. In fact, using sonication to produce fragmented DNA it is highly probable to have all DNA structures described before. Briefly, following are described principal steps for library production. ssDNA is the starting material to link the first adapter by Adaptase step. For this reason before starting DNA was denaturated. The Adaptase step is a highly efficient, proprietary reaction that simultaneously performs end repair, tailing of 3’ ends, and ligation of the first adapter to 3’ ends. A second adapter was incorportaed to the sequence by an Extension step. The synthesized strand lacks full length adapters and does not get sequenced. To remove unincorporated adapters DNA was purified using Agencourt Ampure beads. A Ligation reaction was used to add the second adapter to the 5’ ends. Prepared dsDNA was purified by Agencourt Ampure beads and user for library quantization using the Lib Quant Kit Ion/Rox Low (Roches). DNA was used for emulsion PCR in One Touch instrument as suggested by manufacturer (Thermo Fisher Scientific) to produce covered beads to load on PGM sequencing chip.

treatment_protocol: ChIRP experiements were performed on C2C12 cells. About 40 x 10^6 cells were washed in PBS 1x and fixed in PBS 1x, 1% glutaraldehyde for 15 minutes at room temperature. The cross-linking reaction was quenched at RT for 5 min. by adding 10% volume of a 1.25 M glycine solution. Cells were then spin and washed in PBS 1x twice. After removing the excess of PBS cells were flash frozen in liquid nitrogen and stored at -80°C. Cells lysis was performed using 100 μl of lysis buffer for every 10 mg of pellet (Water, 50 mM Tris HCl pH 7.6, 10 mM EDTA, 1% SDS, 1 mM DTT, 1 mM PMSF, 1X Protease inhibitor, 0.1 units/µl RNase OUT). The content of lysis solution was split in two falcon tubes (600 µl each) and then sonicated with the bioruptor UCD-200 (Diagenode) using the following settings: 60 sec. ON + 90 sec. OFF high setting. The solution was sonicated until the content of the tube was clear. To analyze the quality of the sonication, 10 µl of the solution were separated with gel electrophoresis, lysis step was repeated until the size of the fragments was between ~50 and ~130 base pairs for samples used for the Pvt1 precipitation and around 400 bp for unprecipitated saple. After lysis, 150 µl of lysate were recovered from each tube for RNA input, and 100 µl for DNA input and stored at -20°C for later use. Hybridization step was performed adding to each tube 2 volumes of hybridization buffer (Water, 750 mM NaCl, 1% SDS, 50 mM Tris HCl pH 7.6, 1 mM EDTA, 3% Formammide, 1 mM DTT, 1 mM PMSF, 1X protease inibitor, 0.1 units/µl RNase OUT). After adding hybridization buffer and 400 pmol of biotinylated probes (in one experiment odd and in the replicated even probes) the solution was incubated 5-6 h at 30°C. Hybridization with odd or even probes was performed in two different biological replicates. In the meantime, C1 dynabeads magnetic beads covered with streptavidin (Life Technologies) were washed three times in lysis buffer. Washed beads were then resuspended in 200 µl of lysis buffer and added to each sample to complete hybridization. After 40 min. of further incubation at 26°C on a tube rotator, magnetic beads were isolated using a magnet and washed twice with 800 µl of wash buffer (Water, 3X SSC, 0.5% SDS, 1 mM DTT, 1 mM PMSF). After the second wash, the beads were resuspended in 1 ml of wash buffer, split in two micro centrifuge tubes (800 µl for DNA analysis and 200 µl for RNA analysis) and precipitated one last time using the magnet. Magnetic beads for RNA analysis were resuspended in 190 µl of Proteinase K buffer (100 mM NaCl, 10 mM Tris HCl pH 7.5, 1 mM EDTA, 0.5% SDS) plus 10 µl of Proteinase K (20 mg/ml). The solution was heated to 50°C for 45 min. on a termoblock (Eppendorf) continuously shaking at 600 rpm. To inactivate proteinase K the solution was incubated at 70°C for 15 min. RNA was extracted with Tizol solution and Pvt1 quantized by qRT-PCR. DNA was extracted by Phenol-chloroform and isoamyl alcohol in the ratio of 25:24:1 (v/v), pH 8.0 (Sigma Aldrich).

value: myoblasts

tag: probe sequences


title: C2C12 (Biol. Repl. 1; Even probes)

description: ChIRP technique allows the identification of RNA binding sites on the genomic DNA. It is based on the precipitation of RNA for the identification of crosslinked molecules. In this work we evaluated co-precipitated DNA because we evidenced tha the long non-coding RNA Pvt1 is localized inside the nuclei of C2C12 cells. To corroborate results we performed Pvt1 precipitation in two separated biological samples. Each biological replicate was precipitated with different biotinilated probes (Odd or Even) spanning Pvt1 RNA sequence.

source_name: Even probes for Pvt1

value: TTCAGGAAGTCTCCAGAGAG, ACTCGGCTCTATTTTAGAGG, CCTTCTGGAACGCTTAAAGG, TCTTAGGGTCAGTATCATGG, TGCTTAAAGACCACAGAGGC, ATTCTAGAGCCTTCAGGAAG, AATGTCTACTTGTTGGCCAA, AGAATTTCAGAGGGCACTCG, TAAAGCATCCAGGGCAGAAC

tag: molecule subtype

value: nuclear DNA linked to lncRNA Pvt1


title: C2C12 (Biol. Repl. 1; Odd probes)

source_name: Odd probes for Pvt1

value: TCTGGGAATGCTAAGTTCGT, GGCATCCAGGCTGAAGAATC, CTTGAATTCTCAATGGCCAC, AGACTTCCATCTTTGCTATT, AGTATTCTAGCTTGGAGCTA, TTTTTCACAAGCCAGCATTC, GTCCCTCACTACACAGAAAG, TAGCAGAGTGGTTCAAAGGC, AGACTTAGGGCATACAGGTA


title: Simvastatin 4

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

description:
S4
Donor 4

data_processing:
TrimGalore
STAR
RSEM
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression values (TPM and FPKM) generated by RSEM

source_name: iPSC-CM

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol: Total RNA was isolated using Direct-zol RNA MiniPrep Plus (Zymo Research) in accordance to manufacturer’s instructions, followed by DNAse treatment.

treatment_protocol: iPSC-CMs were treated with statins or DMSO as a vehicle for a period of 7 days. Each statin was applied at its serum peak concentration.

value: Simvastatin

value: iPSC-CM

tag: cell origin

value: Human


title: Lovastatin 4

description:
L4
Donor 4

value: Lovastatin


title: Fluvastatin 4

description:
F4
Donor 4

value: Fluvastatin


title: Atorvastatin 4

description:
A4
Donor 4

value: Atorvastatin


title: Fluvastatin 3

description:
F3
Donor 3


title: Vehicle 4

description:
D4
Donor 4

value: Control


title: PSI_2

city: Blacksburg

first: Honglin

last: Jiang

state: VA

address: 3130 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Polytechnic Institute and State University

data_processing:
Raw reads were processed to generate clean reads through in-house perl scripts. Clean reads were mapped to the porcine genome (Sscrofa11.1, Ensemble release 93) using TopHat v2.0.12. Gene expression level was quantified as expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) using HTSeq v0.6.1. A gene was considered to be expressed if it had a FPKM value of at least 0.5.
Genome_build: Sscrofa11.1, Ensemble release 93
Supplementary_files_format_and_content: Txt file for FPKM value per gene from each library

organism: Sus scrofa

source_name: smooth muscle cells

growth_protocol: cells were cultured in growth medium consisting of DMEM and 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted using TRIzol
RNA-seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina.

tag: tissue

value: ileum


title: PSI_1


title: Lovastatin 3

description:
L3
Donor 3


title: Atorvastatin 3

description:
A3
Donor 3


title: Vehicle 3

description:
D3
Donor 3


title: Fluvastatin 2

description:
F2
Donor 2


title: P4-2.HiC

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

state: NC

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

data_processing:
The HiC reads were processed with the Juicer platform (v1.5.6).  The ~.hic files were generated with juicer.sh, using the mm10 reference genome (canonical chromosomes only) and restriction sites provided by Arima.
Chromatin loop calls were made with the Juicer hiccups tool at default parameters based on HiC contacts with MAPQ>30.
Genome_build: mm10
Supplementary_files_format_and_content: HiC chromatin loops in tab-delimited text format; HiC contact matrix in ~.hic format

source_name: uterus

extract_protocol:
Arima Hi-C kit
Illumina-compatible sequencing libraries were prepared by first shearing purified Arima-HiC proximally-ligated DNA and then size-selecting DNA fragments from ~200-600bp using solid phase reversible immobilization (SPRI) magnetic beads. The size-selected fragments were then enriched for biotin and converted into Illumina-compatible sequencing libraries using the KAPA Biosystems Hyper Prep kit (Wilmington, MA). After adapter ligation, DNA was PCR amplified and purified using SPRI beads.

treatment_protocol: >10 week old female mice were ovariectomized, and rested for 10-14 days to allow endogenous hormones to clear. Mice were given a single intraperitoneal injection of 100 ul saline vehicle (V) or a subcutaneous injection of 1 mg of progesterone (P4) dissolved in 100 ul of sesame oil. Uterine tissue was collected 1 hour later and frozen

value: uterus

value: WT


title: ERaKO_V.HiC


title: V-3.HiC


title: Simvastatin 3

description:
S3
Donor 3


title: Simvastatin 2

description:
S2
Donor 2


title: V-2.HiC


title: Lovastatin 2

description:
L2
Donor 2


title: 21 days old ERa KO uterus V, 24h-rep2

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

description: Gene expression from uterus from 21 day old ERa knockout mouse that was treated for 24h with saline vehicle

hyb_protocol: Five and one half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

label: Biotin

label_protocol: Three hundred nanograms (300 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: pre-pubertal 21-days old female WT and ERa KO mice

extract_protocol: RNA was extracted using Trizol reagent followed by Rneasy clean up protocol

treatment_protocol: for saline vehicle: 100 ul of sailne injected intraperitoneally, tissue collected 24 hours later. For estradiol (E2) 250 ng of E2 dissolved in 100 ul of saline injected intraperitoneally, tissue collected after 2 hours or 24 hours. For IGF1 samples, 50 ug of IGF1 dissolved in PBS was injected intraperitoneally, and tissue collected after 2h, or 50 ug of IGF1 dissolved in PBS injected intraperitoneally 3 times (0, 8 and 16 hours after first injection), and tissue was collected 24h after the first injection


title: 21 days old ERa KO uterus IGF1, 24h-rep1

description: Gene expression from uterus from 21 day old ERa knockout mouse that was treated for 24h with IGF1


title: Ischemia_Drp1 flox/+_4

city: Chongqing

first: Chenyang

last: Duan

state: Chongqing

address: Changjiang Road, Yuzhong District

department: Second Department of Research Institute of Surgery, Daping Hospital

institute: Third Military Medical University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Ischemia_Drp1 flox/+

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: Drp1 flox/+

tag: age

value: ischemia treatment

value: superior mesenteric artery


title: 21 days old WT uterus IGF1, 24h-rep3

description: Gene expression from uterus from 21 day old WT mouse that was treated for 24h with IGF1


title: 21 days old WT uterus E2, 24h-rep3

description: Gene expression from uterus from 21 day old WT mouse that was treated for 24h with E2


title: 21 days old ERa KO uterus V, 24h-rep1

source_name: uterus from 21 day old ERa knockout mouse that was treated for 24h with saline vehicle


title: 21 days old ERa KO uterus IGF1, 24h-rep3

source_name: uterus from 21 day old ERa knockout mouse that was treated for 24h with IGF1


title: 21 days old ERa KO uterus IGF1, 24h-rep2


title: 21 days old ERa KO uterus E2, 24h-rep1

description: Gene expression from uterus from 21 day old ERa knockout mouse that was treated for 24h with E2


title: 21 days old WT uterus V, 24h-rep2

description: Gene expression from uterus from 21 day old WT mouse that was treated for 24h with saline vehicle


title: 21 days old WT uterus V, 24h-rep3

source_name: uterus from 21 day old WT mouse that was treated for 24h with saline vehicle


title: 21 days old WT uterus E2, 24h-rep2

source_name: uterus from 21 day old WT mouse that was treated for 24h with E2


title: 21 days old ERa KO uterus V, 24h-rep3


title: Ischemia_Drp1 flox/+_3


title: 21 days old WT uterus E2, 24h-rep1


title: 21 days old ERa KO uterus E2, 24h-rep2

source_name: uterus from 21 day old ERa knockout mouse that was treated for 24h with E2


title: 21 days old ERa KO uterus E2, 24h-rep3


title: 21 days old ERa KO uterus IGF1, 2h-rep3

description: Gene expression from uterus from 21 day old ERa knockout mouse that was treated for 2h with IGF1


title: 21 days old WT uterus IGF1, 24h-rep1

source_name: uterus from 21 day old WT mouse that was treated for 24h with IGF1


title: Vehicle 2

description:
D2
Donor 2


title: Ischemia_Drp1 flox/+_1


title: Atorvastatin 2

description:
A2
Donor 2


title: Fluvastatin 1

description:
F1
Donor 1


title: scRNA_seq_B+A10_Intestine

description: The group information is prefixed with B+A10 in the column of processed data file

value: ICR

value: Intestine

value: busulfan plus AOS 10 mg/kg Body Weight


title: Ischemia_Drp1 +/+_3

source_name: Ischemia_Drp1 +/+


title: Ischemia_Drp1 +/+_2


title: Simvastatin 1

description:
S1
Donor 1


title: Ischemia_Drp1 flox/+_2


title: 21 days old WT uterus IGF1, 24h-rep2


title: PplusS2-Pooled-Input

data_processing:
The sequenced reads were demultiplexed using bcl2fastq (v2.17.1.14) and basic QC was performed on the resulting FASTQ files using FASTQC (v0.11.5).
FASTQ reads were mapped to combined hg19/dm3 genome using Bowtie2 (v2.3.3) using the standard settings.
The resulting SAM files were converted to BAM files using Samtools (v 1.4.1) using the view command, after which the BAM files were sorted, indexed and potential PCR duplicates removed using the rmdup function.
Reads were mapped to a combined hg19/dm3 genome after which the reads mapping to fly and human genomes were calculated using FeatureCounts from the Subread package (v1.5.0).
The scaleFactor subquently determined by calculating the reads mapping to the fly genome relative to total mapped reads (combined hg19/dm3 reference) and applied in the BamCoverage command (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor (as calculated)).
Genome_build: hg19 & dm3
Supplementary_files_format_and_content: bigWig files of Pol II and normalised PolII Ser2 reads coverage across the genome in CPM.

organism:
Drosophila melanogaster
Homo sapiens

source_name: MV4;11 cells & Schneider 2 cells

extract_protocol:
Cells were crossed-linked with formaldehylde solution. Then nuclear extracts were isolated, and sonicated. Chromatin bound to phospho Ser2 Pol II was isolated using RNA polymerase II (phospho CTD Ser-2), clone 3E10, rat monoclonal, and chromatin bound to total Pol II was isolated uisng RNA polymerase II, clone CTD4H8, mouse monoclonal.
ChIP-Seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645). Fragments between 200 and 500 base pairs were selected using a Pippin Prep 1.5% agarose cassette (Sage Science, Beverly MA US), pooled and 75 single-end base pair reads were sequenced using the Illumina NEXTseq 500.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, E7645)

treatment_protocol: Cells were treated with 10 μM of  1-NM-PP1/DMSO for 4 hours,

tag: antibody

value: WT, CDK12AS/NULL, CDK13AS/AS, #1CDK12AS/NULL;CDK13AS/NULL


title: Ischemia_Drp1 +/+_1

tag: treatment


title: 9123

city: Bloomington

first: Alexandra

middle: B

last: Moussa-Tooks

state: Indiana

department: Psychological and Brain Sciences

institute: Indiana University

data_processing:
FASTQ files were aligned with STAR v.2.5.2b using parameter “--outSAMmapqUnique 60”
Aligned reads in BAM files were counted with featureCounts from the subread package v.1.5.1 with parameters “-s 2 –p –Q 10”
Genome_build: UCSC rn6
Supplementary_files_format_and_content: A tab-separated text file containing gene annotation information and RAW unfiltered read counts for each sample

organism: Rattus norvegicus

source_name: Cerebellar Interpositus Nucleus

extract_protocol:
Whole brains were removed and flash frozen, then sliced into 1mm sections. 2mm round punches across 3 consecutive sections were take to extract the cerebellar interpositus nucleus. Punches were homogenized in Trizol and RNA Isolation, extraction, and purification using Qiagen RNeasy Plus Mini Kit.
KAPA mRNA Hyperprep Kit

value: Long-Evans

value: brain

value: postnatal day 70

value: Male

value: Limited Bedding (postnatal day 2-9)


title: Lovastatin 1

description:
L1
Donor 1

value: Lovastatin

value: iPSC-CM

value: Human


title: 9122


title: 9121


title: 21 days old ERa KO uterus IGF1, 2h-rep2

source_name: uterus from 21 day old ERa knockout mouse that was treated for 2h with IGF1


title: 21 days old ERa KO uterus E2, 2h-rep3

description: Gene expression from uterus from 21 day old ERa knockout mouse that was treated for 2h with E2


title: 21 days old ERa KO uterus IGF1, 2h-rep1


title: 21 days old ERa KO uterus E2, 2h-rep2

source_name: uterus from 21 day old ERa knockout mouse that was treated for 2h with E2


title: 8024

value: Female


title: TS4

data_processing:
Quality and adapter trimming with cutadapt 1.18, using parameters -q28,28, -O 1, --match-read-wildcards and -m 15. Remaining reads were filtered by overall quality, with fastq_quality_filter (FASTX, 0.0.14), using -q 20 and -p 90.
Alignment with TopHat 2.1.1, using parameters -G genes.gtf, -N 3, --read-gap-length 5, --read-edit-dist 8, --segment-length 23, --read-realign-edit-dist 3, --no-coverage-search.
Counting with htseq-count 0.6.0, using parameter -s no, and masking for short genes (miRNA, piRNA, etc.).
Differential expression with DESeq2 1.22.1, after discarding genes with less than 10 reads, using default parametes (except not using independentFiltering), testing either the disease state (sick vs. healthy) or the combined factor of tissue, genotype and phenotype.
Filtering significant genes, taking only genes with absolute log2FoldChange > 5/baseMean^0.5 + 0.6.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file with expression data. The first row is a header line. Columns include general gene details, raw counts, normalized counts, the baseMean, and the DESeq2 analysis results for each comparison. For each muscle type ('Ga' for Gastrocnemius; 'Q' for Quadriceps; 'T' for Tibialis), the first letter is for the numerator and the second for the denominator ('W' for wild type; 'H' for GNE M743T/M743T healthy; 'S' for GNE M743T/M743T sick). 'YN' denotes the phenotype comparison, sick as numerator and healthy as denominator. 'best' column for each comparison shows the results for the additional filtering of significant genes, 'FALSE' are non-significant, 'TRUE' are significant but below filtering threshold, 'THR' for significant genes that passed the further filtering threshold. '?' denotes missing data. Missing raw counts is due to masking genes at the counting step; missing normalized counts (but with raw counts) is due to having too few reads.

source_name: Tibialis

extract_protocol: none provided by the submitter

value: GNE M743T/M743T knock in

value: sick


title: Vehicle 1

description:
D1
Donor 1

value: Control


title: Normal_Drp1 flox/+_2

source_name: Normal_Drp1 flox/+

value: Drp1 flox/+

value: superior mesenteric artery


title: TS2


title: 21 days old ERa KO uterus E2, 2h-rep1


title: 21 days old WT uterus IGF1, 2h-rep3

description: Gene expression from uterus from 21 day old WT mouse that was treated for 2h with IGF1

value: WT


title: 8023


title: Normal_Drp1 flox/+_1


title: 8022


title: TS1


title: Atorvastatin 1

description:
A1
Donor 1

source_name: iPSC-CM

value: Atorvastatin


title: TH4

value: healthy


title: 8021

value: Long-Evans


title: Normal_Drp1 +/+_2

source_name: Normal_Drp1 +/+


title: Normal_Drp1 flox/+_4


title: Normal_Drp1 flox/+_3


title: TH3


title: 21 days old WT uterus E2, 2h-rep2

description: Gene expression from uterus from 21 day old WT mouse that was treated for 2h with E2


title: 21 days old WT uterus IGF1, 2h-rep1

source_name: uterus from 21 day old WT mouse that was treated for 2h with IGF1


title: Arabidopsis_RH_Total3

first: Maureen

last: Hummel

address: 900 University Avenue

institute: University of California

description:
Total mRNA rh replicate 3
AllThanincounts.txt

data_processing:
Processing of RNA-seq data was performed using the package systemPipeR
Alignment to TAIR10 with bowtie2 2.2.5 and tophat 2.0.14
Aligned reads were counted against the Araport11 genome release 201606 using the summarizeOverlaps function in ôunionö mode
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: Col-0 5 days old seedling

extract_protocol: poly(A)+ selected; library construction method based on Townsley et al., Front. Plant Sci. 6, 366 (2015)  and Kumar et al., Front. Plant Sci. 3, 202 (2012)

tag: ecotype

value: 5-days-old seedling

tag: developmental stage

value: seedling

tag: agent


title: TH2

tag: genotype


title: Normal_Drp1 +/+_1

tag: strain background


title: 7122

value: brain

value: postnatal day 70

tag: Sex

value: Male


title: 21 days old WT uterus E2, 2h-rep3

source_name: uterus from 21 day old WT mouse that was treated for 2h with E2


title: Arabidopsis_RH_Total2

description:
Total mRNA rh replicate 2
AllThanincounts.txt


title: TH1

tag: phenotype


title: 7121

tag: strain

value: Limited Bedding (postnatal day 2-9)


title: Arabidopsis_RH_Total1

description:
Total mRNA rh replicate 1
AllThanincounts.txt


title: Arabidopsis_WT_Total3

description:
Total mRNA wt replicate 3
AllThanincounts.txt


title: TW4

value: Wild-type


title: TW3


title: 6111

value: Normal Rearing


title: 5023

value: Female


title: Arabidopsis_WT_Total2

description:
Total mRNA wt replicate 2
AllThanincounts.txt


title: 1K_2

city: Houston

first: Janani

last: Kumar

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: MCF7 cells stably expressing 1K fragment_2

data_processing:
Basecalling was done by Illumina HiSeq Control Software (version 3.3.76).
The reads were mapped to the human genome (hg38) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release 32 (83) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genome_build: hg38
Supplementary_files_format_and_content: Number of fragments in each gene
Supplementary_files_format_and_content: raw counts

growth_protocol: Stable gene expression Cells

extract_protocol:
Qiagen mRNA kit
Illumina TruSeq Stranded total RNA kit according to the manufacturer’s protocol. The libraries were sequenced using 2x76 bases paired end protocol on Illumina HiSeq 3000 instrument. Two biological replicates per condition were sequenced, generating 45-58 million pairs of reads per sample. Each pair of reads represents a cDNA fragment from the library.

tag: cell line

tag: origin

value: Breast Cancer ER +ve

tag: shRNA

value: 1K fragment


title: 21 days old WT uterus E2, 2h-rep1


title: 1K_1

description: MCF7 cells stably expressing 1K fragment_1


title: 5022


title: 21 days old WT uterus V, 24h-rep1


title: TW2


title: Arabidopsis_WT_Total1

city: Riverside

description:
Total mRNA wt replicate 1
AllThanincounts.txt