title: 202760950052_R08C01_whole blood healthy control

value: Female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E9_ad007

status: Public on Nov 23 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: RSP

tag: target

value: ACA

tag: gender

value: male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E8_ad012

value: female


title: 48_S29_L005_R1_001

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description:
sample name:
48

library_source: transcriptomic

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. baseline were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38
Supplementary_files_format_and_content: log2-counts per million

molecule: total RNA

organism: Homo sapiens

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.
Next generation sequencing was performed on Illumina Hiseq 4000 with single-ended 100 red cycles. Image analysis and bases calling was conducted in real-time by the Illumina analysis pipeline.

tag: patient diagnosis

value: Atopic Dermatitis

tag: ptid

tag: timepoint

value: Baseline

tag: treatment

value: Placebo

value: skin

tag: tissue disease state

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E7_ad012


title: RNA-P9-WT-2

city: Dallas

first: Andres

last: Ramirez-Martinez

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UTSW Medical Center

data_processing:
Single-end raw reads with more than 30% nucleotide with phred quality scores less than 20 were filtered from further analysis.
Quality-filtered reads were then aligned to the mouse reference genome (version GRCm38.mm10) using the HISAT2 aligner (v2.1.0).
Aligned reads were then counted using featurecount (v 1.6.2) which assign read counts to each annotation gene id.
DESeq2 R Bioconductor package (REFERENCE_22, 23) was used to normalize read counts and identify differentially expressed (DE) genes.
Genome_build: GRCm38.mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for each timepoint

molecule: polyA RNA

source_name: Quadriceps muscle

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was extracted using QIAGEN Rneasy mini kit
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.

tag: genotype

value: WT

value: 9 days old


title: RNA-P9-WT-1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E7_ad008


title: 202796590038_R02C01_whole blood healthy control

type: genomic

city: Brisbane

first: Marta

middle: Filipa

last: Nabais

state: Queensland

address: 306 Carmody Rd, St. Lucia

department: Institute for Molecular Biosciences

country: Australia

institute: University of Queensland

hyb_protocol: Bisulfite conversions were performed in 96-well plates using the EZ-96 DNA Methylation Kit (Zymo Research, Irvine, CA, USA). Prior to conversion, DNA concentrations were determined by the Take3™ Micro-Volume Plate on the Epoch™ Microplate Spectrophotometer (BioTek Instruments, Inc.) and standardized to include 500 ng. DNA recovery after conversion was quantified using the Take3™ Micro-Volume Plate on the Epoch™ Microplate Spectrophotometer (BioTek Instruments, Inc.). Samples that showed incomplete bisulfite conversion (calculated concentration <25 ng/μl) were not taken forward to the assessment of DNA methylation. Bisulfite converted DNA samples were hybridized to the 8 sample, Illumina Infinium HumanMethylation850 Beadchip (Illumina Inc., San Diego, CA), using Infinium HD Methylation protocol and Tecan robotics.

scan_protocol: HiScan reader, using standard recommended Illumina scanner setting

data_processing:
Illumina GenomeStudio sofwtare and Meffil package
Normalized data: Normalized Average Beta (functional normalization, using Meffil)
Raw data includes Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: whole blood

label_protocol: Standard Illumina Protocol

growth_protocol: direct ex-vivo analysis

extract_protocol: genomic DNA was extract from whole blood using a standard buffy coat (EDTA) protocol

value: whole blood

value: Male

tag: disease status

value: healthy control


title: 47_S28_L005_R1_001

description:
sample name:
47

value: Les


title: RNA-P9-KO-3

value: Net39 KO


title: LMNA-P17-KO-3

data_processing:
Raw reads were mapped to the mouse reference genome (GRCh38/mm10) using bowtie2 (version 2.3.4.3) with default parameters. Duplicate reads were removed with ‘mark duplicates’ from Picard tools (v.2.10.3).
To detect lamin-associated domains (LADs), Enriched Domain Detector (v.1.0) was used with a 10Kb bin size, gap penalty of 10 and a FDR-adjusted significance threshold of 0.05.
Gain, loss and overlapping LADs between WT and KO samples were tallied using bedtools (v.2.29.0).
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: bedgraph files with enrichment of ChIP over input

source_name: Hindlimb muscle

extract_protocol:
Frozen hindlimb muscles were crushed to powder and crosslinked in 10mL of PBS with 2% formaldehyde (Sigma, F8775) for 15 minutes at room temperature under rotation. Crosslinking was stopped with 1.5mL of 2.5M glycine. Samples were washed with PBS and incubated on ice for 10 minutes in Farham lysis buffer (5mM PIPES, 85mM KCl, 0.5% N-40, pH 8.0) before bead lysis in Precellys Evolution (3x20s at 6800rpm). Lysates were then incubated on ice for 20min, and the supernatant was removed after centrifugation (1000g, 5 minutes). The remaining pellet was resuspended in TE and 0.2%SDS (10mM Tris-HCl pH 8.0, 1mM EDTA) and nuclei were sonicated on Bioruptor pico (Diagenode) for 10 cycles (30s on, 30s off). 1% of sheared DNA was saved for input and the rest was diluted 1:1 with in 1xTE 0.1% sodium deoxycholate, 1% Triton X-100 and added 8µg of Lamin A/C antibody (Santa Cruz, sc-7292 X) conjugated to 60µl of Protein G Dynabeads (ThermoFisher, 10003D). Lamin A/C immunoprecipitation was performed for 48 hours at 4ºC and beads were subsequently washed twice with RIPA buffer, 360mM NaCl RIPA buffer, LiCl buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0) and TE buffer. DNA was released from the beads by addition of decrosslinking buffer (TE 0.3% SDS, 2mg/mL proteinase K) and incubation at 65ºC for 16 hours under constant mixing. RNA was then removed by incubation with 0.1µg/µl of RNase A and incubation at 37ºC for 1 hour under constant mixing. DNA was purified from the supernatant with Qiagen PCR purification kit (Qiagen, 28104).
Standard Illumina library preparation

value: 17 days old


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E8_ad010

value: brain

value: RSP


title: 46_S27_L005_R1_001

description:
sample name:
46


title: LMNA-P17-KO-2

description: Lamin A/C antibody (Santa Cruz, sc-7292 X)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E7_ad002

value: SSp


title: 202796590019_R05C01_whole blood healthy control

value: Female


title: LMNA-P17-KO-1


title: 202764140044_R02C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E7_ad001

value: male


title: 5_S2_L008_R1_001

description:
sample name:
5

value: Atopic Dermatitis


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E6_ad012

value: ACA

value: female


title: 43_S25_L005_R1_001

description:
sample name:
43

value: skin


title: 202790040131_R08C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E6_ad010


title: 202790040172_R02C01_whole blood healthy control


title: LMNA-P17-WT-2

value: WT


title: 202760950174_R01C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E7_ad007


title: LMNA-P17-WT-3


title: 42_S24_L004_R1_001

description:
sample name:
42

value: Baseline

value: Non-Les


title: 40_S23_L006_R1_001

description:
sample name:
40


title: LMNA-P17-WT-1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E6_ad008


title: 41_S23_L004_R1_001

description:
sample name:
41


title: 202796590014_R01C01_whole blood healthy control

value: whole blood

value: Male


title: 39_S8_L001_R1_001

description:
sample name:
39


title: 45_S26_L005_R1_001

description:
sample name:
45


title: 202772890076_R02C01_whole blood healthy control

value: healthy control


title: Aff4-cko-3

city: Brooklyn

first: Lorin

last: Weiner

address: 450 Clarkson Ave, MSC 5

department: Cell Biology

institute: State University of New York Downstate Health Sciences University

description:
Aff4_KO_vs_Aff4_WT.csv
YKL 12

data_processing:
Raw sequencing data was received in FASTQ format.  Read mapping used Tophat 2.0.9 against the mm10 mouse reference genome.  The resulting BAM alignment files were processed with the HTSeq 0.6.1 python framework and respective mm10 GTF gene annotation (UCSC database).  The Bioconductor package DESeq2 (3.2) was used to identify differentially expressed genes (DEG) and for statistical analysis based on the negative binomial distribution model.  The resulting values were adjusted using the Benjamini-Hochberg method for false discovery rate.  Genes with an adjusted p-value < 0.05 were determined to be differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Differential gene expression analysis

source_name: Skin

extract_protocol:
For each RNA preparation, skin was isolated from the entire back of 1 mouse at age P6.  The skin was washed briefly with cold PBS, the subcutaneous fat was peeled away with forceps, and the skin was cut in half.  Mesenchyme was then largely removed via heat shock so as to enrich for epithelium (epidermis and hair follicles).  In brief, the two skin pieces were plunged into a beaker of PBS at 60°C and incubated for 30 seconds.  The skin pieces were then transferred to a beaker of cold PBS (on ice) and submerged for 1 min with slow, gentle stirring by hand (with forceps).  The skin pieces were next transferred to a dry petri dish, flattened with the dermal sides down, and grasped at the edges of the epithelial and dermal compartments with separate forceps.  The epithelium and mesenchyme were peeled apart, and the epithelial tissue was snap-frozen using liquid nitrogen.  The frozen tissue was ground to a powder using a pre-cooled mortar and pestle.  RNA was then isolated from the powdered tissue using the RNeasy Mini Kit plus QIAshredder (Qiagen).  To eliminate contaminating DNA, the RNA preparations were treated with TURBO DNAse (2 units per 2 µg of RNA prep; Ambion/Invitrogen) at 37°C for 30 min.  The DNAse was then inactivated using EDTA-Na2 (added to a final concentration of 15 mM) and heat (65°C for 10 min).  A 1/10th volume of 0.3 M sodium acetate was added, and the RNA was ethanol precipitated, dried, and resuspended in RNAse-free water.
RNA-seq libraries were prepared using DNAse-treated RNA (1 µg per library) and the Illumina TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold Kit.  Each library underwent ribosomal depletion according to the kit's instructions, was constructed using indexed adapters, was quantified using the KAPA Complete Library Quantification Kit, and was confirmed for quality using an Agilent 2200 TapeStation.
The 12 indexed libraries were pooled and sequenced using 2 lanes of an Illumina HiSeq 2500, V4 chemistry, and 50-bp paired-end reads.

value: Aff4 cko


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E6_ad002


title: 202790040130_R03C01_whole blood healthy control


title: 37_S7_L002_R1_001

description:
sample name:
37

value: Placebo

value: Les


title: 202796590043_R08C01_whole blood healthy control


title: Aff4-cko-2

description:
Aff4_KO_vs_Aff4_WT.csv
YKL 10


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E6_ad001

value: brain

value: RSP


title: 36_S7_L001_R1_001

description:
sample name:
36


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E5_ad012


title: Aff4-wt-2

description:
Aff4_KO_vs_Aff4_WT.csv
YKL 9

value: Wild type


title: 202790040085_R06C01_whole blood healthy control

value: Female


title: 35_S22_L004_R1_001

description:
sample name:
35

value: Atopic Dermatitis


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E6_ad007

value: ACA

value: male


title: 202790040058_R04C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E5_ad008


title: 202796590009_R03C01_whole blood healthy control


title: 34_S21_L004_R1_001

description:
sample name:
34

value: skin


title: 33_S20_L004_R1_001

description:
sample name:
33


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E5_ad006

value: SSp

value: female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E5_ad004


title: Aff4-wt-1

description:
Aff4_KO_vs_Aff4_WT.csv
YKL 7


title: Aff4-wt-3

description:
Aff4_KO_vs_Aff4_WT.csv
YKL 11


title: Aff4-cko-1

description:
Aff4_KO_vs_Aff4_WT.csv
YKL 8


title: 32_S6_L002_R1_001

description:
sample name:
32


title: Foxn1-wt-3

description:
Foxn1_KO_vs_Control.csv
YKL 5


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E5_ad002


title: 31_S19_L004_R1_001

description:
sample name:
31

value: Baseline

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E5_ad001


title: 202796590042_R06C01_whole blood healthy control

value: whole blood

value: Male


title: 30_S6_L001_R1_001

description:
sample name:
30


title: Foxn1-wt-2

description:
Foxn1_KO_vs_Control.csv
YKL 3


title: 202790040179_R03C01_whole blood healthy control

value: healthy control


title: Foxn1-null-3

description:
Foxn1_KO_vs_Control.csv
YKL 6

value: Foxn1 null


title: Foxn1-null-1

description:
Foxn1_KO_vs_Control.csv
YKL 2


title: 202796590005_R02C01_whole blood healthy control


title: Foxn1-null-2

description:
Foxn1_KO_vs_Control.csv
YKL 4


title: 3_S1_L008_R1_001

description:
sample name:
3

value: Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad010

value: brain


title: 28_S5_L002_R1_001

description:
sample name:
28


title: 202796590034_R06C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad008

value: RSP


title: 202796590009_R04C01_whole blood healthy control

value: Female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad007


title: UAB126 2

city: Birmingham

first: Jeonga

last: Kim

state: Alabama

institute: University of Alabama at Birmingham

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore! Version 0.4.1
Trimmed reads were mapped to UCSC mm10 using STAR version 2.5.1b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Transcript abundances were calculated with Cufflinks version 2.2.1 with parameters --library-type fr-firststrand -g
Cuffdiff was used for pairwise differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file containing intensity values in FPKM.

source_name: Liver

extract_protocol:
Livers were collected at the time of mouse sacrifice. The livers were frozen in liquid nitrogen until we prepare total RNA. Total RNA was extracted by Trizol method.Library was constructed with polyA selected
Library construction began with two rounds of polyA selection using oligo dT containing magnetic beads.  The resulting mRNA was randomly fragmented with cations and heat, which was followed by first strand synthesis using random primers with inclusion of Actinomycin D (2.4ng/µL final concentration).  Second strand cDNA production was done with standard techniques and the ends of the resulting cDNA were made blunt, A-tailed and adaptors ligated for indexing to allow for multiplexing during sequencing.
The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for Illumina library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation.  Cluster generation was performed according to the manufacturers recommendations for onboard clustering (Illumina).  Paired end 75bp sequencing runs were completed to allow for better alignment of the sequences to the reference genome.

value: liver

tag: diet

value: high fat diet (60% fat)

tag: Sex


title: 202796590001_R01C01_whole blood healthy control


title: 27_S4_L002_R1_001

description:
sample name:
27

value: Atopic Dermatitis


title: 202790040057_R01C01_whole blood Mild Cognitive Impairment


title: 26_S18_L004_R1_001

description:
sample name:
26

value: skin


title: UAB126 1

value: male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad006

value: SSp

value: female


title: 202796590040_R07C01_whole blood healthy control


title: 25_S17_L004_R1_001

description:
sample name:
25

value: Baseline

value: Non-Les


title: Vehicle 2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad012

value: ACA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad004


title: 24_S16_L003_R1_001

description:
sample name:
24


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad002


title: 202790040089_R03C01_whole blood healthy control

value: whole blood

value: healthy control


title: Vehicle 1


title: 23_S15_L003_R1_001

description:
sample name:
23

value: Les


title: 202760950174_R02C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E4_ad001

value: brain


title: 22_S14_L003_R1_001

description:
sample name:
22


title: 202796590024_R01C01_whole blood healthy control

value: Male


title: Foxn1-wt-1

description:
Foxn1_KO_vs_Control.csv
YKL 1

value: Wild type


title: 202796590028_R05C01_whole blood healthy control


title: 21_S13_L003_R1_001

description:
sample name:
21


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E3_ad008

value: RSP


title: 202796590044_R08C01_whole blood healthy control


title: 2_S10_L003_R1_001

description:
sample name:
2

value: Placebo


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E3_ad007


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E3_ad006


title: 18_S12_L003_R1_001

description:
sample name:
18


title: 202796590024_R08C01_whole blood healthy control


title: 202796590008_R08C01_whole blood healthy control

value: Female


title: 16_S9_L003_R1_001

description:
sample name:
16

value: Atopic Dermatitis


title: 17_S3_L002_R1_001

description:
sample name:
17

value: skin


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E3_ad004

value: male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E3_ad010


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E2_ad010


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E3_ad002

value: SSp


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E2_ad008


title: 202790040048_R04C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 202761400086_R01C01_whole blood healthy control


title: 202760950113_R07C01_whole blood Alzheimer's disease


title: 15_S8_L008_R1_001

description:
sample name:
15

value: Baseline


title: 135_S5_L001_R1_001

description:
sample name:
135

value: Non-Les


title: 202796590035_R04C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: yFR2030_dst1D_Rpb3vsInput_60min-6AU_20161108_rep2

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, dst1D::LEU2
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in dst1Δ cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2030_dst1D_Rpb3vsInput_60min-6AU_20161108_rep1-2__S.cerevisiaeApr11_947396.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in dst1Δ cells treated with 6-azauracil for 60 min.

hyb_protocol: ChIP and control samples were combined and dried by SpeedVac. Combined samples were resuspended in 110 µL of fresh hybridization mix (5 µL 10 mg/mL Salmon Sperm DNA (Thermo Fisher Scientific, 15632011), 5 µL 8 mg/mL Yeast tRNA (Thermo Fisher Scientific, 15401011) and 100 µL DIG Easy Hyb (Roche, 11603558001)) and incubated 5 min at 95˚C followed by 5 min at 45˚C. Samples were hybridized to Agilent microarrays in SureHyb enabled chambers (Agilent, G2534A) with rotation at 42˚C for at least 18 hr. Microarrays were washed on an orbital shaker for 5 min at room temperature with Wash I buffer (6X SSPE, 0.005% N-Lauroylsarcosine), followed by a second wash with pre-warmed (31˚C) Wash II buffer (0.06X SSPE) for 5 min at room temperature. The microarrays used were described before (Jeronimo and Robert, 2014) and were custom designed by Agilent Technologies and contain a total of about 180,000 Tm-adjusted 60-mer probes covering the entire yeast genome with virtually no gaps between probes.

scan_protocol: Microarrays were scanned using an InnoScan900 (Innopsys) at 2 µm resolution.

data_processing:
BED method: The ChIP-chip data were normalized using the Limma Loess method, and replicates were combined as described previously (Ren et al. 2000, Science 290(5500):2306-9). The data were subjected to one round of smoothing using a Gaussian sliding window with a standard deviation of 100 bp to generate data points in 10-bp intervals (Guillemette et al. 2005, PLoS Biol 3(12):e384).
Correction = Foreground-Background; Normalisation = limma loess (subgrid)

organism: Saccharomyces cerevisiae

label_protocol: The ChIP and Input samples were blunted as follow. 40 µL of ChIP DNA or about 400 ng of Input DNA were added to 70 µL of blunting mix (11 µL 10X NEBuffer 2 (NEB, B7002S), 0.5 µL 10 mg/mL BSA, 0.5 µL 20 mM dNTPs and 0.2 µL (0.6 units) of T4 DNA polymerase (NEB, M0203L)) and incubated at 12˚C for 20 min. Then, the blunted DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) in the presence of 280 mM of NaOAc pH 5.2 and 10 μg of glycogen, precipitated with ethanol and resuspended in 25 µL ddH2O. Blunted DNA was ligated to 100 pmol of annealed linkers (see Table S2) with 2.5 units of T4 DNA ligase (Thermo Fisher Scientific, 15224041) in the supplied buffer, in a final volume of 50 µL, overnight at 16˚C. Samples were precipitated with 6 µL of 3 M NaOAc pH 5.2 and 130 µL ethanol, and resuspended in 25 µL ddH2O. 15 µL of labeling mix (4 µL 10X ThermoPol Reaction buffer (NEB, B9004S), 2 µL of 5 mM aa-dUTP/dNTP mix (5 mM each dATP, dGTP and dCTP, 3 mM dTTP and 2 mM 5-(3-aminoallyl)-dUTP (Thermo Fisher Scientific, AM8439)) and 1.25 µL of 40 µM oligo 1) were added to each sample. Samples were placed in a thermocycler and when temperature reached 55˚C, 10 µL of enzyme mix (1 µL 10X ThermoPol Reaction buffer, 1 µL (5 units) Taq DNA polymerase (Thermo Fisher Scientific, 18038240) and 0.01 µL (0.025 units) Pfu DNA polymerase (Thermo Fisher Scientific, EP0502)) were added and the following program was run. 1) 72˚C, 5 min; 2) 95˚C, 2 min; 3) 32 cycles: 95˚C, 30sec; 55˚C, 30sec; 72˚C, 1 min; 4) 72˚C, 4 min; 5) 4˚C, forever. PCR products were purified using QIAquick PCR Purification kit (QIAGEN, 28106) with few modifications: PE buffer was replaced by Phosphate wash buffer (5 mM KPO4 pH 8.5 and 80% ethanol) and EB buffer was replace by Phosphate elution buffer (4 mM KPO4 pH 8.5). Eluates were dried by SpeedVac and pellets were resuspended in 4.5 µL of freshly prepared 0.1 M Na2CO3 pH 9.0 buffer. 4.5 µL of Cy5 Mono-Reactive NHS Ester Fluorescent Dye (ChIP samples) or Cy3 Mono-Reactive NHS Ester Fluorescent Dye (control samples Input DNA or no-tag ChIP) (GE Healthcare, PA25001 and PA23001) were added. Samples were incubated 1 hr in the dark at room temperature. 35 µL of 0.1 M NaOAc pH 5.2 were added and samples were purified using QIAquick PCR Purification kit according to the manufacturers’ instructions.

growth_protocol: 50 mL of yeast nitrogen-based (YNB) medium lacking uracil (-URA) supplemented with 2% galactose was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow at 30°C to an OD600 of 0.6. Cells were then treated with 100 µg/mL of 6-azauracil (6-AU) for 60 min before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

extract_protocol:
Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation.
Cleanup: Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNase A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 70% ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

treatment_protocol:
100 µg/mL of 6-azauracil for 60 min
IP protocol: Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (Neoclone W0012, 3 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNase A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3, dst1D::LEU2

tag: chip antibody

value: anti-Rpb3 (Neoclone W0012, 3 μL)

treatment_protocol: 100 µg/mL of 6-azauracil for 60 min


title: 202796590026_R07C01_whole blood Mild Cognitive Impairment

value: whole blood


title: 14_S7_L008_R1_001

description:
sample name:
14

value: Les


title: yFR2029_ubp15D-dst1D_Rpb3vsInput_60min-6AU_20161108_rep2

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15D::KanMX4, dst1D::LEU2
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ/dst1Δ cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2029_ubp15D-dst1D_Rpb3vsInput_60min-6AU_20161108_rep1-2_S.cerevisiaeApr11_958933.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ/dst1Δ cells treated with 6-azauracil for 60 min.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3, ubp15D::KanMX4, dst1D::LEU2


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15Δ::KanMX4
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2028_ubp15D_Rpb3vsInput_60min-6AU_20161108_rep1-2_S.cerevisiaeApr11_276104.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ cells treated with 6-azauracil for 60 min.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3, ubp15<delta>::KanMX4


title: yFR2028_ubp15D_Rpb3vsInput_60min-6AU_20161108_rep2

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15Δ::KanMX4
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2028_ubp15D_Rpb3vsInput_60min-6AU_20161108_rep1-2_S.cerevisiaeApr11_276104.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ cells treated with 6-azauracil for 60 min.


title: yFR2014_WT_Rpb3vsInput_60min-6AU_20161108_rep2

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2014_WT_Rpb3vsInput_60min-6AU_20161108_rep1-2_S.cerevisiaeApr11_77664.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells treated with 6-azauracil for 60 min.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E2_ad007

value: brain

value: RSP

value: ACA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E2_ad006

value: female


title: 134_S4_L001_R1_001

description:
sample name:
134

value: Atopic Dermatitis

value: skin


title: 202796590012_R07C01_whole blood Alzheimer's disease

value: Female

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E2_ad002

value: SSp


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, dst1D::LEU2
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in dst1Δ cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2030_dst1D_Rpb3vsInput_60min-6AU_20161108_rep1-2__S.cerevisiaeApr11_947396.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in dst1Δ cells treated with 6-azauracil for 60 min.


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15D::KanMX4, dst1D::LEU2
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ/dst1Δ cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2029_ubp15D-dst1D_Rpb3vsInput_60min-6AU_20161108_rep1-2_S.cerevisiaeApr11_958933.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ/dst1Δ cells treated with 6-azauracil for 60 min.


title: yFR2030_dst1D_Rpb3-IPvsInput_20160713_rep2

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, dst1D::LEU2
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in dst1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2030_dst1D_Rpb3-IPvsInput_20160713_rep1-2_S.cerevisiaeApr11_923412.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in dst1Δ cells.

growth_protocol: 50 mL of yeast nitrogen-based (YNB) medium lacking uracil (-URA) supplemented with 2% galactose was inoculated at OD600 0.1 from an overnight preculture in the same medium and allowed to grow at 30°C to an OD600 of 0.7 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min and quenched with 125 mM glycine. Crosslinked cells were collected by centrifugation and washed twice with 1X TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl). Cell pellets were snap-freezed in liquid nitrogen and stored at -80°C.

treatment_protocol:
none
IP protocol: Cell pellets were resuspended in 700 μL Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and protease inhibitor cocktail (1 mM PMSF, 1 mM Benzamidine, 10 μg/mL Aprotinin, 1 μg/mL Leupeptin, 1 μg/mL Pepstatin)). About the same number of OD600 units was used for all samples. Cells were lysed by bead beating and the lysate was sonicated with a Model 100 Sonic dismembrator equipped with a microprobe (Fisher Scientific), 4 x 20 sec at output 7 Watts, with a 1 min break between sonication cycles. Soluble fragmented chromatin was recovered by centrifugation. 600 μL of the chromatin sample was taken per immunoprecipitation (IP) and, when necessary, 6 μL (1%) were saved as Input sample. The following amount of antibody per IP was used: anti-Rpb3 (Neoclone W0012, 3 μL). 50 μL of Dynabeads coated with Pan Mouse IgG antibodies (Thermo Fisher Scientific, 11042) pre-coupled with the indicated antibody were added to the chromatin sample and incubated overnight at 4°C. Beads were washed twice with Lysis buffer, twice with Lysis buffer 500 (Lysis buffer + 360 mM NaCl), twice with Wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% Na-deoxycholate, 1 mM EDTA) and once with TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Input and immunoprecipitated chromatin were eluted and reverse-crosslinked with 50 μL TE/SDS (TE + 1% SDS) by incubating overnight at 65°C. Samples were treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNase A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % EtOH. Precipitated DNA was resuspended in 50 μL of TE before being used in ChIP-chip experiments.


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells treated with 100 µg/mL of 6-azauracil for 60 min. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2014_WT_Rpb3vsInput_60min-6AU_20161108_rep1-2_S.cerevisiaeApr11_77664.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells treated with 6-azauracil for 60 min.


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E2_ad001

value: male


title: 202790040005_R08C01_whole blood Alzheimer's disease


title: 131_S2_L001_R1_001

description:
sample name:
131

value: Placebo


title: 202796590026_R01C01_whole blood healthy control

value: Male

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E1_ad012


title: 202760950152_R02C01_whole blood healthy control

value: whole blood


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E1_ad008


title: 202790040060_R01C01_whole blood healthy control


title: 13_S6_L008_R1_001

description:
sample name:
13

value: Baseline

value: Non-Les


title: 133_S40_L005_R1_001

description:
sample name:
133


title: 130_S39_L005_R1_001

description:
sample name:
130


title: 129_S38_L005_R1_001

description:
sample name:
129

value: Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E1_ad007

value: brain


title: 202796590027_R01C01_whole blood healthy control


title: 132_S3_L001_R1_001

description:
sample name:
132


title: 202790040108_R01C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E1_ad004

value: RSP


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E1_ad006


title: 127_S37_L005_R1_001

description:
sample name:
127


title: 202764140088_R02C01_whole blood Alzheimer's disease


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15D::KanMX4, dst1D::LEU2
Biological replicate 1 of 1. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ/dst1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2029_ubp15D-dst1D_Rpb3-IPvsInput_20160713_rep2_S.cerevisiaeApr11_563589.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ/dst1Δ cells.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3, ubp15D::KanMX4, dst1D::LEU2

value: anti-Rpb3 (Neoclone W0012, 3 μL)


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, dst1D::LEU2
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in dst1Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2030_dst1D_Rpb3-IPvsInput_20160713_rep1-2_S.cerevisiaeApr11_923412.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in dst1Δ cells.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3, dst1D::LEU2


title: yFR2028_ubp15D_Rpb3-IPvsInput_20160713_rep2

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15Δ::KanMX4
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2028_ubp15D_Rpb3-IPvsInput_20160713_rep1-2_S.cerevisiaeApr11_765568.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ cells.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3, ubp15<delta>::KanMX4


description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3, ubp15Δ::KanMX4
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in ubp15Δ cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_yFR2028_ubp15D_Rpb3-IPvsInput_20160713_rep1-2_S.cerevisiaeApr11_765568.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in ubp15Δ cells.


title: 202790040044_R01C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: yFR2014_WT_Rpb3-IPvsInput_20160713_rep2

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3
Biological replicate 2 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_FR2014_WT_Rpb3-IPvsInput_20160713_rep1-2_S.cerevisiaeApr11_385787.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells.

value: MATa, his3<delta>1, leu2<delta>0, met15<delta>0, ura3<delta>0::URA3


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E1_ad002

value: SSp

value: female


title: 6myc-RIO1

city: Milan

first: Peter

last: De Wulf

address: via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

hyb_protocol: Labelled probes were hybridized to Affymetrix S.cerevisiae whole genome tiling R arrays

scan_protocol: Arrays were scanned on an Affymetrix Scanner

data_processing: Bed files were produced with Tiling Array Suite 1.1 from the command line with these options: tilecore -analysis -bpmap Sc03b_MR_v04.bpmap -type 1 -n 1 -nt 1 -export 1 -output_type 0 -format_type 1 -band 150 -pval_scale 0 -sig_scale 2 -tail_type 1 -nscale 1 -tgt 500 [files]

label: biotin

source_name: 6myc-RIO1 cells were grown in YPD medium (24°C) till an OD=0.3 and then treated for 3h with 5 μg/ml α−factor to arrest them in G1 (>95%).

label_protocol: Synthesis of cDNA, IVT amplification, and labeling were carried out following the Affymetrix GeneChip Expression Anaysis protocol.

growth_protocol: Cells were grown in YPD medium at 24°C.

extract_protocol: Extraction was performed as described in Bermejo R. et al., Meth. Mol. Biol. 582: 103-18 (2009).

treatment_protocol: Cells were synchronised in G1 following treatment with α−factor (3h, 5 μg/ml) in YPD medium at 24°C.

tag: antibody

value: anti-myc 9E10 antibody (Covance, USA)

value: W303, 6myc-RIO1

value: Treatment with α−factor (3h, 5 μg/ml)


title: 126_S35_L005_R1_001

description:
sample name:
126

value: Atopic Dermatitis

value: skin


title: yFR2014_WT_Rpb3-IPvsInput_20160713_rep1

description:
MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0::URA3
Biological replicate 1 of 2. RNAPII (Rpb3) occupancy by ChIP-chip in WT cells. Rpb3 ChIP sample (Cy5-labeled) was performed using a mouse monoclonal antibody against Rpb3 and hybridized against Input DNA (Cy3-labeled).
processed data file: SmtjhBED_FR2014_WT_Rpb3-IPvsInput_20160713_rep1-2_S.cerevisiaeApr11_385787.bed
BED description: A genome browser-ready file for Rpb3 occupancy by ChIP-chip (IP/Input) in WT cells.

tag: strain


title: 202796590023_R05C01_whole blood healthy control

value: whole blood

value: Female

value: healthy control


title: 124_S34_L005_R1_001

description:
sample name:
124

value: Baseline

value: Non-Les


title: 202790040180_R05C01_whole blood healthy control

value: Male


title: 123_S33_L005_R1_001

description:
sample name:
123

value: Les


title: 122_S32_L004_R1_001

description:
sample name:
122


title: 202790040082_R04C01_whole blood healthy control


title: 128_S1_L001_R1_001

description:
sample name:
128


title: 202790040055_R04C01_whole blood healthy control


title: 121_S31_L004_R1_001

description:
sample name:
121


title: Ribo-seq-HBEC-SARS2-highMOI-48hpi

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
Library strategy: Ribo-seq
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots
Supplementary_files_format_and_content: For reads that map to host mRNAs, counts files are provided.

source_name: Primary human bronchial epithelial cells

growth_protocol: Vero E6 cells were grown in DMEM-10%FBS media. Isolation and growth of primary human bronchial epithelial cells is explained elsewhere. Primary CD4+ T-cells were isolated from PBMCs of deidentified blood donors using negative selection kit from StemCell Technologies and grown in RPMI media supplemented with 10%FBS, IL-2 and activated with CD3/CD28 conjugated Dynabeads.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Infected cells were lysed and two aliquots were processed in parallel for ribo-seq and RNA-seq. For RNA-seq, total RNA was isolated using ZymoClean RNA-Clean and Concentrator kit and subjected to Illumina stranded mRNA prep. Ribo-seq libraries were prepared in house following published protocols. Both libraries were sequenced using Illumina NextSeq following the manufacturer's protocols.

treatment_protocol: Cells were infected with SARS-CoV-2 at an MOI of 0.1 pfu/cell (low MOI) and 2 pfu/cell (high MOI) for Vero E6 cells, or MOI of 0.5 pfu/cell (low) and 1 pfu/cell (high) for primary human bronchial epithelial cells. Primary activated CD4+ T-cells were infected with HIV-1 at an MOI of 2

value: Cycloheximide

tag: agent

tag: time point


title: 202761400005_R07C01_whole blood healthy control

tag: tissue


title: 12_S5_L008_R1_001

description:
sample name:
12

value: Placebo


title: RIO1

source_name: Wild-type cells were grown in YPD medium (24°) till an OD=1.0.

value: No treatment


title: 119_S30_L004_R1_001

description:
sample name:
119


title: 202760950105_R01C01_whole blood healthy control


title: Ribo-seq-HBEC-SARS2-highMOI-24hpi


title: 202796590019_R06C01_whole blood healthy control


title: 117_S29_L004_R1_001

description:
sample name:
117


title: Venous blood_d150_MOT_39

type: RNA

city: Bordeaux

first: Aline

last: FOURY

address: 146 rue Léo Saignat

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA were hybridized on the microarray slides following the manufacturer’s instructions.

scan_protocol: Immediately after washing, the slides were scanned on Agilent G2505C Microarray Scanner using Agilent Scan Control A.8.5.1 software.

data_processing:
The fluorescence signal was extracted using Agilent Feature Extraction software v10.10.1.1 with default parameters.
Raw data (median of pixels intensity) were filtered, log2 transformed, corrected for bath effects (washing and labeling serials) and normalized using quantile method.

organism: Ovis aries

source_name: 150 days after birth and feeding with the mother milk in lamb blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of DNase pre-treated (0.2μl DNase 10X, 0.4μl 10X Buffer DNase, 0.4μl RNasin 40U/μl, 3μl total RNA) total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNA clean-up using Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: Total RNA was extracted with the PAXgene Blood RNA kit (Qiagen, Courtaboeuf, France) according to the manufacturer's protocol. Total RNA quality was assessed and its concentration was measured using RNA Nano chips onto a Bioanalyser 2100 (Agilent, Boeblingen, Germany).

treatment_protocol: 5ml venous blood were collected from the 32 lambs 150 days after birth using vacuum tubes which included a reagent that immediately stabilized intracellular RNA (PAXgene blood RNA system, PreAnalytiX GmbH, Hombrechtikon, Switzerland). The samples were kept at room temperature for 8 h as required for stabilizing RNA and then at -20°C until RNA extraction.

tag: age

tag: feeding

value: Natural Rearing


title: Venous blood_d150_LAC_38

source_name: 150 days after birth and feeding with lacaune milk in lamb blood

tag: gender

value: female

value: Lacaune Milk


title: Venous blood_d150_REP_36

source_name: 150 days after birth and feeding with a milk replacer in lamb blood

value: Milk Replacer


title: Venous blood_d150_REP_37


title: 202772890076_R08C01_whole blood healthy control


title: 202790040050_R01C01_whole blood healthy control


title: 115_S28_L004_R1_001

description:
sample name:
115

tag: patient diagnosis

tag: ptid


title: 114_S27_L004_R1_001

description:
sample name:
114

tag: timepoint

tag: treatment


title: Ribo-seq-HBEC-SARS2-lowMOI-72hpi


title: 202796590005_R08C01_whole blood healthy control


title: 113_S26_L004_R1_001

description:
sample name:
113

tag: tissue disease state


title: Ribo-seq-HBEC-SARS2-lowMOI-48hpi


title: Venous blood_d150_REP_35


title: 202760950055_R02C01_whole blood healthy control

tag: disease status


title: Ribo-seq-HBEC-SARS2-lowMOI-24hpi


title: 112_S25_L004_R1_001

description:
sample name:
112


title: Venous blood_d150_REP_34


title: Ribo-seq-HBEC-SARS2-lowMOI-6hpi


title: 202790040117_R05C01_whole blood healthy control


title: Venous blood_d150_LAC_31


title: Ribo-seq-HBEC-SARS2-highMOI-6hpi


title: 111_S24_L003_R1_001

description:
sample name:
111


title: 202796590019_R01C01_whole blood healthy control


title: Venous blood_d150_LAC_32


title: Ribo-seq-HBEC-mock-lowMOI

value: mock-lowMOI


title: 202790040180_R07C01_whole blood healthy control


title: 11_S4_L008_R1_001

description:
sample name:
11

value: Atopic Dermatitis


title: Venous blood_d150_LAC_29

value: male


title: 202796590022_R02C01_whole blood healthy control

value: whole blood


title: 108_S23_L003_R1_001

description:
sample name:
108

value: skin


title: 202790040008_R03C01_whole blood healthy control

value: Female

value: healthy control


title: RNA-seq-HBEC-SARS2-highMOI-48hpi

data_processing:
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots
Supplementary_files_format_and_content: For reads that map to host mRNAs, counts files are provided.


title: 105_S21_L003_R1_001

description:
sample name:
105


title: RNA-seq-HBEC-SARS2-highMOI-6hpi


title: RNA-seq-HBEC-SARS2-highMOI-24hpi


title: Venous blood_d150_MOT_28


title: 202790040048_R06C01_whole blood healthy control


title: Venous blood_d150_LAC_33


title: RNA-seq-HBEC-SARS2-lowMOI-72hpi


title: 202790040053_R03C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 104_S20_L003_R1_001

description:
sample name:
104

value: Baseline

value: Non-Les


title: 102_S19_L003_R1_001

description:
sample name:
102

value: Les


title: RNA-seq-HBEC-SARS2-lowMOI-48hpi

value: Cycloheximide


title: Venous blood_d150_MOT_26


title: Venous blood_d150_REP_27


title: 101_S18_L003_R1_001

description:
sample name:
101


title: Venous blood_d150_REP_24


title: 202790040004_R08C01_whole blood healthy control

value: Male


title: 106_S22_L003_R1_001

description:
sample name:
106


title: RNA-seq-HBEC-SARS2-lowMOI-24hpi


title: 202796590037_R04C01_whole blood healthy control


title: 10_S3_L008_R1_001

description:
sample name:
10


title: RNA-seq-HBEC-SARS2-lowMOI-6hpi


title: 202796590034_R02C01_whole blood healthy control


title: Venous blood_d150_REP_21


title: 1_S1_L002_R1_001

description:
sample name:
1

value: Placebo


title: 202796590009_R02C01_whole blood healthy control


title: Venous blood_d150_MOT_22

value: Natural Rearing


title: NT3 -Fe Root

city: Nonoichi

first: Takanori

last: Kobayashi

state: Ishikawa

address: 1-308 Suematsu

department: Research Institute for Bioresources and Biotechnology

country: Japan

institute: Ishikawa Prefectural University

description: Sample 9

data_processing:
Preprocessing was performed using trimmomatic version 0.39
Mapping was performed using bowtie version 1.2.3
Quantification of expression was performed using RSEM version 1.2.21
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: Text files including RPM values for each sample.

organism: Oryza sativa

source_name: iron-deficient roots

growth_protocol: Rice (Oryza sativa L.) cultivar Tsukinohikari and its transformants were germinated and cultured hydroponically based on the description in Kobayashi et al. (2019) Plant Mol. Biol. 101:471-486.

extract_protocol:
Total RNA was extracted from hydroponically grown roots and leaves using the RNeasy Plant Mini Kit (QIAGEN), treated with DNase I and reverse-transcribed using ReverTra Ace qRT-PCR RT Master Mix with gDNA Remover (TOYOBO).
RNA libraries were prepared for sequencing using Lasy-Seq v1.1 (Kamitani et al., (2019) Scientific Reports)

treatment_protocol: Iron-sufficiency treatment (which is same as preculture condition) or iron-deficiency treatment for 7 days was imposed after preculture in hydroponics

tag: iron status

value: iron-deficient

tag: cultivar

value: Tsukinohikari

value: roots

tag: genotype

value: non-transformant


title: 202790040086_R02C01_whole blood healthy control


title: NT3 +Fe Root

description: Sample 8 (control for Sample 9)

source_name: iron-sufficient roots

value: iron-sufficient


title: 202790040044_R08C01_whole blood healthy control

value: whole blood


title: Mia PaCa-2 cells, R2

city: Abu Dhabi

first: Mohamed

last: Al-Sayegh

address: Saadiyaat Island - 1st floor ERB, Room 136, P.O. Box 129188

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

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 the Homo sapian (GRCh38/hg38) genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Raw counts of mapped reads of each genes were derived using HTseq count
DESeq2 was used for differential expression analysis.
Genome_build: Homo sapiens (GRCh38/hg38) genome version
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: pancreas - MIA PaCa-2

growth_protocol: DMEM + 10 %FBS

extract_protocol:
Total RNA was extracted using TriZol LS and Rneasy Mini Kit (Qiagen) according to manufacturer protocol.
Total RNA was used for library construction at the Center for Genomics and Systems Biology, New York University Abu Dhabi, using TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: DMEM + 10 %FBS supplemented with ADH-6

tag: cell line

value: Mia PaCa-2

tag: cell type

value: epithelial cell

tag: cell condition

value: adherent, single cells and loosely attached clusters

value: wild-type

value: Positive control


title: Mia PaCa-2 cells, R3


title: IMA2i-3 +Fe Root

description: Sample 7

value: OsIMA2 knockdown line 3


title: Mia PaCa-2 cells, R1


title: Mia PaCa-2 cells, CO-3

value: Negative control


title: 202790040073_R03C01_whole blood healthy control

value: healthy control


title: IMA2OX-2 +Fe Root

description: Sample 6

value: OsIMA2 overexpression line 2


title: 202790040060_R07C01_whole blood healthy control

value: Female


title: Mia PaCa-2 cells, CO-2


title: NT2 +Fe Root

description: Sample 5 (control for Samples 6, 7)


title: 202790040016_R06C01_whole blood healthy control


title: Venous blood_d150_MOT_16

value: female

value: Natural Rearing


title: Mia PaCa-2 cells, C3

value: Control starting timepoint


title: NT1 -Fe Root

description: Sample 4

value: iron-deficient

value: Tsukinohikari

value: roots


title: Venous blood_d150_MOT_18

value: whole blood


title: Venous blood_d150_LAC_20

value: Lacaune Milk


title: 202790040060_R06C01_whole blood healthy control

value: Male


title: IMA1i-2 +Fe Root

description: Sample 3

value: iron-sufficient

value: OsIMA1 knockdown line 2


title: 202761400022_R06C01_whole blood healthy control


title: IMA1OX-4 +Fe Root

description: Sample 2

value: OsIMA1 overexpression line 4


title: Venous blood_d150_MOT_17


title: Mia PaCa-2 cells, C2

value: Mia PaCa-2

value: epithelial cell

value: adherent, single cells and loosely attached clusters

value: wild-type


title: Venous blood_d150_REP_14

value: Milk Replacer


title: Mia PaCa-2 cells, C1


title: 202796590038_R07C01_whole blood healthy control

value: Female

value: healthy control


title: NT1 +Fe Root

description: Sample 1 (control for Samples 2-4)

value: non-transformant


title: Mia PaCa-2 cells, CO-1

value: Negative control


title: Venous blood_d150_LAC_13

value: female


title: Venous blood_d150_REP_7

value: male


title: t(14;18) neg Follicular Lymphoma 27

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

description:
FL27
Hybridized to Affymetrix OncoScan FFPE Assay

hyb_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602

scan_protocol: Affymetrix® GeneChip® Scanner 3000G to detect target bound to Oncoscan array after staining with Biotin.

data_processing:
Nexus biodiscovery software
Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: t(14;18) neg Follicular Lymphoma 27

extract_protocol: DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted after dewaxing and proteinase K digestion applying standard phenol/chloroform purification procedures

tag: lymph node

value: Axillary LN

tag: type of sample

value: t(14;18)-neg/BCL2-neg FL

value: FFPE


title: Venous blood_d150_MOT_15

tag: age

value: Natural Rearing

tag: tissue

value: whole blood


title: Venous blood_d150_REP_6

tag: gender

tag: feeding


title: Venous blood_d150_REP_8


title: Venous blood_d150_LAC_11

value: Lacaune Milk


title: Venous blood_d150_MOT_5


title: Mia PaCa-2 cells, A6-2

value: Mia PaCa-2

value: Treated cell lines with ADH-6


title: t(14;18) neg Follicular Lymphoma 25

description:
FL25
Hybridized to Affymetrix OncoScan FFPE Assay

source_name: t(14;18) neg Follicular Lymphoma 25

label_protocol: Affymetrix OncoScan™ FFPE Assay kit /GPL18602

value: Inguinal LN


title: Mia PaCa-2 cells, A6-1

value: epithelial cell

value: adherent, single cells and loosely attached clusters

value: wild-type


title: 202790040075_R06C01_whole blood healthy control

value: Male

value: healthy control


title: 202796590022_R05C01_whole blood healthy control


title: t(14;18) neg Follicular Lymphoma 23

description:
FL23
Hybridized to Affymetrix OncoScan FFPE Assay

source_name: t(14;18) neg Follicular Lymphoma 23

value: LN left groin


title: Mia PaCa-2 cells, A1-3

value: Treated negative control


title: Venous blood_d150_LAC_4

value: male


title: 202790040045_R08C01_whole blood healthy control

value: Female


title: Mia PaCa-2 cells, A1-2


title: RNA-seq-HBEC-mock-lowMOI

value: Cycloheximide

tag: agent

value: mock-lowMOI


title: Mia PaCa-2 cells, A6-3


title: Venous blood_d150_LAC_3


title: 202760950117_R01C01_whole blood healthy control


title: t(14;18) neg Follicular Lymphoma 22

description:
FL22
Hybridized to Affymetrix OncoScan FFPE Assay

source_name: t(14;18) neg Follicular Lymphoma 22

value: Cervical LN (left lower jugular)

value: t(14;18)-neg/BCL2-neg FL

value: female

value: FFPE


title: Mia PaCa-2 cells, A1-1

value: Mia PaCa-2


title: t(14;18) neg Follicular Lymphoma 21

description:
FL21
Hybridized to Affymetrix OncoScan FFPE Assay

source_name: t(14;18) neg Follicular Lymphoma 21

value: LN


title: 202764140144_R05C01_whole blood healthy control

source_name: whole blood

value: whole blood


title: 202760950170_R01C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: ets5 sample2

first: Mary

last: Rossillo

state: ny

address: 550 1st ave

institute: NYU Langone

data_processing:
Fastq files were aligned to ws243 using STAR.
Quantification was performed using HTSeq.
Differential expression analysis was performed using DESeq2.
Genome_build: ws243
Supplementary_files_format_and_content: bigwig files including coverage data for wt and ets-5 averaged between two biological samples each

organism: Caenorhabditis elegans

source_name: BAG

growth_protocol: C elegans grown on E Coli OP50

extract_protocol:
Embryos were extracted from gravid adult worms, dissociated into cells, and plated. They were then FACS sorted to isolate BAG cells. RNA was prepped, and a cDNA library was made and sequenced.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: BAG

value: embryonic

value: wzIs135[Pglb-34{delta}ets-5::gfp] I; ets-5(tm1734) X


title: t(14;18) neg Follicular Lymphoma 24

description:
FL24
Hybridized to Affymetrix OncoScan FFPE Assay

source_name: t(14;18) neg Follicular Lymphoma 24

value: Axillary LN


title: ets5 sample1


title: 202790040050_R04C01_whole blood healthy control

value: healthy control


title: Venous blood_d150_MOT_1

value: male

value: Natural Rearing


title: WT sample2

value: wzIs135[Pglb-34{delta}ets-5::gfp] I


title: 202796590038_R01C01_whole blood healthy control

value: Female


title: Venous blood_d150_LAC_2

value: Lacaune Milk


title: 202796590031_R03C01_whole blood healthy control


title: ets5 IP sample3

data_processing:
ChIP-seq reads were aligned to the ws220 genome assembly using Bowtie2
peaks were called using MACS2.1.1
Genome_build: ws220
Supplementary_files_format_and_content: wig files were generated by subtracting control from ets5-gfp signal for each replicate
Supplementary_files_format_and_content: text files containing 200 bp intervals around each peak

source_name: whole worm extract

extract_protocol:
Lysates were flash frozen, ground, cross-linked with formaldehyde, and sonicated. TF-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: whole worm extract

tag: chip antibody

value: GFP (ab290 abcam)


title: Tissue_Seronegative_rep3

city: Leioa

first: Begoña

middle: M

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

institute: University of the Basque Country (UPV/EHU)

description:
P15
Gene expression in lung of seronegative animal

hyb_protocol: Samples were analysed using Agilent Sheep Gene Expression microarrays, 8x15K (Design ID 019921) (Agilent Technologies), with 15,208 sheep features represented.  600 ng of labeled cRNA samples were hybridized at 65 ºC for 17 h in a SureHyb hybridization chamber (Agilent Technologies).

scan_protocol: The arrays were scanned immediately after washing on a G2565CA DNA microarray scanner, with ozone-barrier slide covers (Agilent Technologies) using one-color AgilentHD_GX_1color scanner protocol for HD microarray formats (scanner settings Dye channel: Green, Scan Region: Agilent HD (61x21.6 mm), Scan resolution 5 um, Tiff file dynamic range 20 bit, Green PMT gain 100 %)

data_processing:
The scanned images were analyzed with Feature Extraction Software v 10.7.3.1.  (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 019921_D_F_20130125) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data from Feature Extraction software was subsequently processed on GeneSpring GX 12.6 (Agilent Technologies). Data were normalized by quantile normalization and centered by mean. After normalization and mean centering of the data, Features flagged in Feature Extraction as Feature Non-uniform outliers, population outliers or features with intensities not significantly above background signal in 100 % of samples in 1 out of any 3 conditions (Seronegative, Asymptomatic, Lesions) were excluded.
For the identification of differentially expressed genes with statistical significance between groups, LIMMA package was used.

source_name: Lung tissue_Seronegative

label_protocol: RNA samples were labeled and hybridized following standard Agilent Protocol One-Color Microarray-Based Gene Expression analysis (Low Input Quick Amp Labeling) v 6.5. Briefly, 50 ng of total RNA were retrotranscribed and labeled using Low imput Quick Amp Labeling kit one color (Agilent Technologies) following manufacturer instructions. First, total RNA was retrotranscribed with AffinityScript Reverse Transcriptase (Agilent Technologies), using Oligo dT primers coupled to T7 promoter. Double stranded cDNA synthesized by AffinityScript RT was in vitro transcribed by T7 RNA pol in the presence of Cy3-CTP to generate amplified and labeled cRNA. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen, Hilden, Germany). After labeling and purification, cRNA was quantified with NanoDrop 1000 spectrophotometer in order to determine the yield and specific activity of each reaction.

growth_protocol: Animals were sacrificed under controlled conditions as approved by the Ethics Committee of the University of Zaragoza.

extract_protocol: Total RNA was isolated from lung tissue using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA). 60-70 mg tissue samples were homogenized in 1 ml of TRIzol Reagent using Precellys®24 homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) combined with 1.4 and 2.8 mm ceramic beads mix lysing tubes (Bertin Technologies). RNA isolation was performed following manufacturer instructions and RNA was suspended in RNase free water and stored at −80 ⁰C. RNA quantity and purity was assessed with NanoDrop 1000 Spectrophotometer (Thermo Scientific Inc, Bremen, Germany). RNA integrity was assessed on a Agilent 2100 Bioanalyzer with Agilent RNA 6000 Nano chips (Agilent Technologies, Santa Clara, CA, USA), which estimates the 28S/18S (ribosomic RNAs) ratio and the RNA integrity number (RIN value).

treatment_protocol: A sample from lung was aseptically taken from each animal and tissue sections were preserved in RNAlater solution (Ambion, Austin, TX, USA) at −80 ⁰C until used.

tag: breed

value: Rasa sheep

tag: status

value: Seronegative

value: Lung


title: 202760950123_R04C01_whole blood healthy control

value: whole blood

tag: disease status


title: ets5 IP sample2


title: Tissue_Seronegative_rep2

description:
P14
Gene expression in lung of seronegative animal


title: Tissue_Seronegative_rep4

description:
P16
Gene expression in lung of seronegative animal


title: 202790040179_R04C01_whole blood healthy control

value: Male


title: Tissue_Pulmonary lesions_rep6

description:
10P
Gene expression in lung of animal with lesions

source_name: Lung tissue_Pulmonary lesions

tag: infected with

value: Visna-Maedi virus (VMV)

value: Pulmonary lesions


title: Tissue_Seronegative_rep1

description:
P13
Gene expression in lung of seronegative animal


title: 202790040112_R07C01_whole blood healthy control


title: Tissue_Pulmonary lesions_rep4

description:
7P
Gene expression in lung of animal with lesions


title: Tissue_Pulmonary lesions_rep5

description:
9P
Gene expression in lung of animal with lesions


title: SOLPg4

city: Tokyo

first: Sayaka

last: Katagiri

institute: Tokyo Medical and Dental University

description: Gene expression in skeletal muscle after 6 weeks oral administration

hyb_protocol: 0.825 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Microarrays (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 11.1 (Agilent) using default parameters

source_name: soleus muscle, Pg4

label_protocol: The Agilent Low Input Quick Amp Labeling kit was used to generate cRNA with a sample input of 200 ng total RNA for single-color microarray (Cy3) analysis according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from muscle tissue using the NucleoSpin® RNA kit (TaKaRa Bio, Shiga, Japan) and quantifed by measuring absorbance at 260 and 280 nm.

treatment_protocol: C57BL/6J mice (8-weeks-old; Sankyo Laboratory, Tokyo, Japan) were allowed free access to water and food throughout the experimental period.  All mice were fed High-fat diet 32.  Mice were randomly divided into two group.A total of Porphyromonas gingivalis cells suspended in 100μL of physiological saline solution were given to  Pg mice via a feeding needl. Co mice were recieved only saline solution.

tag: diet

value: high fat

value: skeletal muscle

tag: Sex


title: 202790040089_R02C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: WT sample1

value: BAG

value: embryonic

tag: genotype


title: SOLPg3

source_name: soleus muscle, Pg3

value: male


title: 202772890012_R07C01_whole blood healthy control

value: Female

value: healthy control


title: Tissue_Pulmonary lesions_rep3

description:
4P
Gene expression in lung of animal with lesions


title: ets5 input sample3

tag: cell type

value: whole worm extract


title: 202760950174_R06C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: SOLCo4

source_name: soleus muscle, Co4


title: ets5 input sample2

value: GFP (ab290 abcam)


title: SOLPg2

source_name: soleus muscle, Pg2


title: ets5 input sample1


title: Tissue_Pulmonary lesions_rep2

description:
2P
Gene expression in lung of animal with lesions

value: Rasa sheep


title: SOLCo3

source_name: soleus muscle, Co3


title: SOLCo1

source_name: soleus muscle, Co1


title: Tissue_Pulmonary lesions_rep1

description:
1P
Gene expression in lung of animal with lesions

value: Lung


title: SOLPg1

source_name: soleus muscle, Pg1


title: SOLCo2

source_name: soleus muscle, Co2


title: Tissue_Seropositive asymptomatic_rep5

description:
P19
Gene expression in lung of seropositive and asymptomatic animal

source_name: Lung tissue_Seropositive asymptomatic

value: Seropositive asymptomatic


title: wt IP sample3


title: TAPg4

source_name: tibialis anterior muscle, Pg4

extract_protocol: Total RNA was extracted from muscle using the NucleoSpin® RNA kit (TaKaRa Bio, Shiga, Japan) and quantifed by measuring absorbance at 260 and 280 nm.

treatment_protocol: C57BL/6J mice (8-weeks-old; Sankyo Laboratory, Tokyo, Japan) were allowed free access to water and food throughout the experimental period.  Mice were randomly divided into two group. Mice were fed High-fat diet 32. A total of Porphyromonas gingivalis cells suspended in 100μL of physiological saline solution were given to NCAa and HFAa mice via a feeding needl.

tag: treatment

value: Porphyromonas gingivalis (6 weeks oral administration)

value: tibialis anterior muscle


title: TAPg3

source_name: tibialis anterior muscle, Pg3


title: 202796590033_R02C01_whole blood Alzheimer's disease

source_name: whole blood

value: whole blood


title: ets5 IP sample1


title: wt IP sample2


title: 202790040040_R06C01_whole blood healthy control

value: Male


title: wt IP sample1


title: Tissue_Seropositive asymptomatic_rep4

description:
P17
Gene expression in lung of seropositive and asymptomatic animal

value: Visna-Maedi virus (VMV)


title: 202796590010_R02C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: Tissue_Seropositive asymptomatic_rep2

description:
11P
Gene expression in lung of seropositive and asymptomatic animal


title: 202796590008_R01C01_whole blood healthy control


title: 202760950119_R05C01_whole blood Alzheimer's disease


title: 202796590033_R03C01_whole blood healthy control


title: Tissue_Seropositive asymptomatic_rep3

description:
12P
Gene expression in lung of seropositive and asymptomatic animal


title: 202796590039_R03C01_whole blood healthy control


title: wt input sample2


title: wt input sample1


title: ATAC-P17-KO-3

description: ATAC-seq

data_processing:
Paired-end raw reads were mapped to the mouse reference genome (GRCh38/mm10) using bowtie2 (version 2.3.4.3) with parameter ‘–very-sensitive’ enabled.
Read duplication and reads that mapped to chrM were removed from downstream analysis
Peaks were called using findpeaks command from HOMER software package version 4.9, with parameter ‘–style dnase’, and the FDR threshold (for Poisson p-value cutoff) was set to 0.001.
Called peaks were merged from all samples and annotatePeaks.pl command was used to produce raw count matrix
Differential peaks were identified using R package DEseq version 3.8. Peaks with > 2-fold change were designated as DE peaks.
Genome_build: GRCh38/mm10
Supplementary_files_format_and_content: bigwig files for each ATAC-seq replicate

source_name: Quadriceps muscle

extract_protocol:
Flash-frozen quadriceps muscle samples from post-natal day 17 mice were added 1 mL of homogenization buffer (5mM CaCl2, 3mM Mg Acetate, 10mM Tris pH 7.8, 320mM Sucrose, 200uM EDTA, 0.1% NP-40, 0.05% BME, with Complete protease inhibitor cocktail (Sigma, 11697498001)) and disrupted with beads in Precellys Evolution (3x20s at 6800rpm). Lysate was sequentially filtered through 70um and 40um cell strainers, laid on top of sucrose buffer (1M sucrose, 3mM Mg acetate, 10mM Tris pH 7.8) and centrifuged at 1000g for 10min. Nuclei in the pellet were permeabilized in 0.5mL of 0.3% Triton in PBS for 30 minutes and washed twice with resuspension buffer (10mM NaCl, 3mM Mg Acetate, 10mM Tris pH 7.8).
Omni ATAC-seq PMID: 28846090 and Illumina Nextera DNA Library Prep Kit (#15028212)

value: Net39 KO

value: 17 days old


title: ATAC-P17-KO-2

description: ATAC-seq


title: TAPg1

source_name: tibialis anterior muscle, Pg1

value: male


title: 4CRE

city: Boston

first: Qian

last: Cong

state: MA

address: 188 Longwood Ave

department: Harvard School of dental medicine

institute: Harvard University

data_processing:
Illumina Casava1.7 software used for basecalling.
All sequencing reads from ATAC-seq were trimmed by Cutadapt to remove adapter sequence.
Trimmed reads were aligned to the mouse genome (Mm9, Genome Reference Consortium GRCm38) using Bowtie2
Peak-calling were performed using Genrich with ATAC-seq mode
ATAC-seq signal tracks were generated using ‘bamcoverage’ function in Deep tools and presented by Integrative Genomics Viewer (IGV) software
Genome_build: mm9
Supplementary_files_format_and_content: bw files were generated using bamcoverage

source_name: subcutaneous progenitor cells

growth_protocol: The infected SMPs were cultured in osteogenic medium for 7 days

extract_protocol:
Subcutaneous tissue was isolated and adipose deposits was removed under sterile conditions and washed in PBS supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin on ice. Tissue was minced and digested with 1 mg/ml collagenase type I and 0.5%Trypsin in 0.1% BSA, for 70 minutes at 37 °C. Digested tissue was centrifuged at 500 g for 10 min and the pellet was carefully collected after aspirating off the floating fat depots. After a second centrifugation at 500 g for 10 min, the cellular pellet was filtered through a 100-μm mesh filter to remove debris.
Nuclei were isolated from 50,000 cells for transposition reaction with Tn5 Trnsposase (Illumina, catalog # FC-121-1030). DNA were purified by using PCR purification kit (Qiagen).
To generate sequencing libraries, purified DNA was amplified with NEBNext high-fidelity 2X PCR Master Mix (New England Biolabs). Sequencing libraries was sequenced using Illumina Nextseq 550 sequencer to obtain 150bp paired-end reads.

treatment_protocol: The Gnas flox SMPs were infected with AdCre/GFP

value: Primary subcutaneous progenitor cells

value: Gnas-/-

value: Ad-Cre


title: 1GFP

value: wild type

value: Ad-GFP


title: Tissue_Seropositive asymptomatic_rep1

description:
8P
Gene expression in lung of seropositive and asymptomatic animal

value: Rasa sheep


title: anaerobically grown cells rep 3

city: Brno

first: Jiri

last: Kucera

address: Kamenice 753/5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
Quality control of reads was performed using R package ShortRead.
Subsequently, reads were aligned to the genome sequence of the At. ferrooxidans CCM 4253 (GCA_003233765.1) using the software BBmap.
R package DeSeq2 was used for differential analysis of count data. Transcripts with a |log2 fold change| > 1 and q < 0.05 (FDR-adjusted P-values) were considered as significantly change.
Genome_build: GCA_003233765.1
Supplementary_files_format_and_content: Tab-delimited text file includes gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for every gene and every sample

organism: Acidithiobacillus ferrooxidans

source_name: Bacterial culture

growth_protocol: Acidithiobacillus ferrooxidans strain CCM 4253 was grown aerobically (electron acceptor O2) and anaerobically (electron acceptor Fe3+) in the atmosphere enriched by H2 (electron donor) and CO2 (carbon source) in sealed jars at 30 °C and agitated.

extract_protocol:
The total RNA was extracted with a TRI reagent (Sigma-Aldrich) and was treated with a TURBO DNA-free kit (Ambion) to remove the contaminating DNA.
The cDNA libraries were constructed using the ScriptSeq™ Complete Kits (Bacteria) (Illumina), including Ribo-ZeroTM technology for ribosomal RNA removing and ScriptSeq v2 RNA-Seq Library Preparation Kit.
Sequencing was performed on the Illumina MiSeq platform with MiSeq Reagent Kit v2 (500-cycles), which generated 250-bp paired-end reads.

tag: growth

value: anaerobic

tag: electron donor

value: hydrogen

tag: electron acceptor

value: ferric iron


title: anaerobically grown cells rep 2


title: wt input sample3

source_name: whole worm extract

value: whole worm extract

value: GFP (ab290 abcam)


title: TAPg2

source_name: tibialis anterior muscle, Pg2

value: Porphyromonas gingivalis (6 weeks oral administration)

tag: tissue

value: tibialis anterior muscle

tag: age


title: anaerobically grown cells rep 1


title: ATAC-P17-KO-1

description: ATAC-seq


title: IMA2OX-5 +Fe Leaf

description: Sample 10

source_name: iron-sufficient leaves

treatment_protocol: Iron-sufficiency treatment (which is same as preculture condition) was imposed after preculture in hydroponics

tag: iron status

value: iron-sufficient

tag: cultivar

value: Tsukinohikari

value: leaves

value: OsIMA2 overexpression line 5


title: TACo2

source_name: tibialis anterior muscle, Co2

tag: strain

value: male

value: control


title: TACo3

source_name: tibialis anterior muscle, Co3


title: ATAC-P17-WT-3

description: ATAC-seq

value: WT

value: 17 days old


title: IMA2OX-2 +Fe Leaf

description: Sample 9

value: OsIMA2 overexpression line 2


title: TACo4

source_name: tibialis anterior muscle, Co4


title: aerobically grown cells rep 3

value: aerobic

value: oxygen


title: SAMPLE 16: WT_IR

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using the Illumina iScan

data_processing: The Data where normalized using quantile normalisation strategies  improved with a batch controlling Combat algorithm, PMID 20181233

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit ( Applied Biosystems)

extract_protocol: RNA was extracted with TriReagent ( Sigma). Quality control ( RQI) was performed with  Biorad Experion.

value: ischemia / reperfusion (I/R) injury

value: WT-Littermate

value: Cardiac tissue


title: TACo1

source_name: tibialis anterior muscle, Co1


title: ATAC-P17-WT-2

first: Andres

last: Ramirez-Martinez

institute: UTSW Medical Center

description: ATAC-seq


title: SAMPLE 14: TG_Sham

value: SHAM


title: SAMPLE 15: TG_Sham


title: SAMPLE 12: TG_IR


title: SAMPLE 11: WT_Sham


title: IMA1OX-9 +Fe Leaf

description: Sample 8

value: OsIMA1 overexpression line 9


title: SAMPLE 13: TG_IR


title: ATAC-P17-WT-1

description: ATAC-seq


title: SAMPLE 10: WT_Sham


title: aerobically grown cells rep 1

value: hydrogen


title: SAMPLE 9: WT_IR


title: IMA1OX-7 +Fe Leaf

description: Sample 7

value: iron-sufficient

value: OsIMA1 overexpression line 7


title: Rhes KO 3

city: Jupiter

first: Srinivasa

last: Subramaniam

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

data_processing:
Libraries were sequenced on the NextSeq 500 with paired-end 40bp reads. Base-calling was performed with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2
RNAseq reads were trimmed for adapter sequence and low quality.
Reads were mapped to the mouse genome mm10 (mouse-UCSC -mm10) using star v2.5.2a and gene abundance was estimated with puthon v2.7.11 and htseq v0.8.0.
Differential gene expression analysis was performed using Deseq2.
Genome_build: mm10
Supplementary_files_format_and_content: The raw data files are in the fastq format untrimmed. Illumina adapter sequences need to be trimmed; Read 1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, Read 2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Supplementary_files_format_and_content: comma-separated file includes the raw gene count data for all genes and all samples.
Supplementary_files_format_and_content: comma-separated file includes the TPM (transcripts per million) normalized gene count data for all genes and all samples.

source_name: Striatum

extract_protocol:
Total RNA extracted from 1 male and 1 female pooled striatum per sample. Qiagen miRNAeasy kit (#217004) was used for total RNA extraction and Dnase-treatment done on-column.
Libraries were generated using the Illumina TruSeq stranded total RNA kit following manufacturer's protocol. 500ng of total RNA was rRNA-depleted, cDNA generated, end repaired, adapter-ligated and PCR amplified with 9 PCR cycles.

value: Homozygous Rhes knock out


title: RBMX_overexpression_3

city: guangzhou

first: jizhong

last: wang

address: 63 Duobao Road

country: China

institute: Guangzhou Medical University

description:
A3SS.MATS.JCEC.txt
A5SS.MATS.JCEC.txt
MXE.MATS.JCEC.txt
RI.MATS.JCEC.txt
SE.MATS.JCEC.txt

data_processing:
Basecalls performed using CASAVA version 1.4
Raw fastq files were processed using fastp 0.20.0 with default parameters
RNA-seq reads were mapped to GRCh38 human reference genome using hisat2 2.1.0
Alternative Splicing was analysised using rmats 4.0.2. Human genecode v29 annotation gtf was used for finding splicing events, no novo splicing events are included.
Genome_build: GRCh38: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
Supplementary_files_format_and_content: rmats output format: http://rnaseq-mats.sourceforge.net/user_guide.htm

source_name: T24 Cells

extract_protocol:
The RNAs from T24 cells over-exprssing RBMX or control were isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: T24 cells were seeded in 6-well plates the day before transfection and infected with PCDNA3.1-RBMX plasmid (2ug per well) or a PCDNA3.1 plasmid (Control) using lipofectamine 3000 (Invitrogen) for 48h.

value: bladder

tag: transfection

value: over-exprssing RBMX


title: NT +Fe Leaf

description: Sample 6 (control for Samples 7-10)

value: Tsukinohikari

value: leaves

value: non-transformant


title: Rhes KO 2


title: RBMX_overexpression_2


title: IMA2OX-5 +Fe Root

description: Sample 5

source_name: iron-sufficient roots

value: roots

value: OsIMA2 overexpression line 5


title: aerobically grown cells rep 2

value: aerobic

value: oxygen


title: SAMPLE 8: TG_IR

value: ischemia / reperfusion (I/R) injury


title: Rhes KO 1


title: IMA2OX-2 +Fe Root

description: Sample 4

value: OsIMA2 overexpression line 2


title: RBMX_overexpression_1


title: WT 3

value: Wild Type


title: control sample 3

value: control


title: SAMPLE 7: WT_Sham

value: SHAM

value: WT-Littermate

value: Cardiac tissue


title: IMA1OX-9 +Fe Root

description: Sample 3

value: iron-sufficient

value: OsIMA1 overexpression line 9


title: SAMPLE 6: WT_Sham


title: control sample 2

value: bladder


title: IMA1OX-7 +Fe Root

description: Sample 2

value: Tsukinohikari

value: OsIMA1 overexpression line 7


title: control sample 1


title: WT 2


title: SAMPLE 4: WT_IR


title: WT 1


title: NT +Fe Root

description: Sample 1 (control for Samples 2-5)

value: non-transformant


title: DFFDA_L.2

status: Public on Nov 22 2020

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

institute: Universitat de Valencia

data_processing:
Read file QC: Total reads were analysed with FastQC and visually inspected to make sure each sequenced sample met the adequate quality standards.
Adapter clipping, quality trimming and filtering: Cutadapt and Trimmomatic were used to remove Illumina adapters, filter reads shorter than 20 bases, and discard the ones with more than 30 Ns.
Genome alignment: Filtered reads were mapped to the mouse genome with HISAT2 using the Mus musculus GRCm38 (mm10) genome as reference
Read count extraction: Raw read counts were extracted with the featureCounts tool from the R package Rsubread using the mouse genome version M16 (Ensembl 91) annotation as a reference.
Filtering by expression and normalization: Genes with less than 1 count per million (CPM) in at least 4 of the samples were filtered out and remaining genes were normalised with Voom.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text file containing the filtered and Voom-normalised read count matrix

source_name: in vitro NSC culture

growth_protocol: Neurosphere cells derived form adult SEZ samples were cultured and mantained under non-adherent conditions and mitogenic stimulaton (EGF and FGF). Cells were passaged every 4-5 days and seeded at 1,25 x 10e5 cells/cm2

extract_protocol:
Mouse total RNA was extracted from eight FACS-separated SEZ populations, obtaining 3-4 biological replicates for each of them (total of 28 samples) and subjected to poly(A) selection. The same procedure was used to extract the RNA from the two DFFDA samples FACS-separated from NSC in vitro cultures (4 biological replicates per population).
The poly(A) enriched fraction was used to construct libraries for sequencing with the SMARTer Ultra Low RNA Kit for Illumina (Clontech/Takara), using the Dual index Nextera XT v2 Set A Adapters (Illumina). Libraries were sequenced in a NextSeq 500 system (Ilumina).

treatment_protocol: Cells were loaded with 2 ug/ml DFFDA and then cultured during 4 days before FACS.

value: brain subependymal zone

value: 8 weeks

tag: isolation

value: FACS from passage 4 neurospheres

tag: cell population


title: DFFDA_L.3


title: DFFDA_H.4


title: DFFDA_L.1


title: SAMPLE 2: TG_Sham


title: DFFDA_H.3


title: DFFDA_H.2


title: SAMPLE 3: TG_Sham


title: SAMPLE 1: TG_IR


title: Other.2

source_name: mouse brain SEZ

value: FACS from tissue homogenate

value: Other


title: SAMPLE 5: WT_IR

value: ischemia / reperfusion (I/R) injury


title: NB1.3


title: NB2.1


title: Other.3


title: NB2.3


title: Other.1


title: NPC2.2


title: NPC2.1


title: NPC1.1


title: NPC1.2


title: DFFDA_L.4


title: DFFDA_H.1


title: NPC1.3


title: aNSC.4

value: aNSC


title: NB1.2


title: pNSC.4

value: pNSC


title: aNSC.3


title: aNSC.1


title: NPC1.4


title: pNSC.3


title: NB2.2


title: qNSC.3

value: qNSC


title: pNSC.1


title: qNSC.4


title: NB1.1


title: pNSC.2


title: qNSC.2


title: qNSC.1


title: NPC2.3


title: aNSC.2


title: OM_063

city: Perth

first: Kyle

last: Mincham

address: Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands

institute: Telethon Kids Institute

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68  and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA  performs real-time base calling on the HiSeq instrument computer. Then the Illumina  bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Sequencing data quality control (QC) was performed with the Bioconductor package Rqc (de Souza et al. J Statistical Software. 2018). Sequencing reads were aligned to the reference murine genome (mm10) using Subread and summarised at the gene level using featureCounts (Liao et al. Genome Biol. 2014). Sample QC was performed by analysing the distribution of the raw read counts to check for sample outliers using boxplots, relative log-transformed expression (RLE) plots and principal component analysis (PCA), before and after global-scale median normalisation.
Genome_build: mm10
Supplementary_files_format_and_content: OM_counts_mm10.csv

source_name: Bone marrow

extract_protocol:
Fetal bone marrow and thymus samples were homogenised using a rotor-star homogeniser (Qiagen) and total RNA extracted via TRIzol (Ambion), followed by RNA elution using RNeasy MinElute (Qiagen). RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies; RIN: 10 ± 0 (mean ± SD)).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Maternal OM-85 from GD9.5-17.5

value: BALB/c

value: Bone marrow

value: Gestation day 18.5

tag: maternal treatment

tag: fetal gender

value: Male


title: OM_062

source_name: Thymus

value: Thymus

value: Female


title: OM_064


title: OM_061


title: OM_058

value: Naïve


title: OM_059


title: OM_060