title: Ctrl_A11-1_E1

status: Public on Apr 30 2019

type: SRA

city: Zürich

first: Julia

last: Kaiser

address: Winterthurerstrasse 190

country: Switzerland

institute: Brain Research Institute

library_source: transcriptomic

data_processing:
Base-calling was performed using the Illumina HiSeq 4000 software RTA2 (Real Time Analysis)
All statistical analysis was performed using the R environment for statistical computing (R version 3.4.1) with Bioconductor (Huber et al., 2015) and dedicated packages
Reads were aligned to the mouse genome (mm10) using SALMON v0.8.1 followed by quantification with Tximport v1.0.3
Count of reads per million reads of library (CPM) were calculated using edgeR v3.14.0. Reads with counts per million lower than 5 were excluded.
Statistical testing using dispersion estimation (edgeR v3.14.0) identified one sample as an outlier. This sample (20160807.A-4d_A9-3_R1) was excluded from further analysis.
Genome_build: mm10
Supplementary_files_format_and_content: comma seperated text file includes CPM values for all genes over all samples

molecule: total RNA

organism: Mus musculus

source_name: spinal cord tissue

extract_protocol:
Animals were transcardially perfused with ice cold Ringer's solution only. To preserve RNA quality, all following procedures were done rapidly to minimize time between animal sacrifice and tissue collection. Brains and spinal cords were dissected and the intermediate layer of spinal levels C5/C6 was dissected by crude trimming with blades und a dissection microscope. The spinal samples were snap frozen in liquid nitrogen and stored at -80 °C until further processing. Total RNA was prepared from all samples simultaneously by using the NucleoSpin® RNA XS Kit (Macherey-Nagel, Germany) under the protocols of the manufacturer with an additional TRIZol/chloroform extraction step due to the high lipid content of the spinal cord.
The TruSeq RNA Sample Prep Kit v2 (Illumina) was used in the succeeding steps. Briefly, total RNA samples (100 ng) were ribo-depleted using Ribo Zero Gold (Epicentre) and then fragmented. The fragmented samples were reverse transcribed to cDNA, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched by PCR.  Sequencing was performed on the Illumina HiSeq 4000 (single end, 125 bp) using the TruSeq SBS Kit v4-HS.

tag: tissue

value: spinal cord tissue

tag: strain

tag: developmental stage

value: adult


title: 4d_A10-1_E1


title: 4d_A10-4_E1


title: Ctrl_A12-2_E1


title: 4d_A9-2_E1


title: 4d_A9-4_E1


title: Ctrl_A12-3_E1


title: 7d_A7-3_E1


title: 7d_A7-4_E1


title: 14d_A5-1_E1


title: 14d_A6-2_E1


title: 14d_A5-4_E1


title: Ctrl_A12-1_E1


title: 28d_A3-1_E1


title: 28d_A3-3_E1


title: Ctrl_A11-4_E1


title: 4d_A9-3_E1


title: 42d_A1-4_E1


title: in-vitro day14 rep_3

city: Los Angeles

first: Jiwen

last: Li

address: 635 Charles E. Young Dr. S.

country: USA

institute: UCLA

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
14DIV-3

data_processing:
FASTQ files were mapped using STAR, then use the output BAM files do HTSEQ to generate count files. We calculated RPKM by running EdgeR-Limma-Voom in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: cortex

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, 217004) under the protocols of the manufacturer
We used the Ovation RNA-seq system V2 (Nugen 7102) to perform first and second-strand cDNA synthesis. We then used the Next Ultra RNA-seq library prep kit for Illumina (NEB E7530) and NEBNext® multiplex oligos for Illumina (NEB E7710 E7500 E7730) to perform end repair, adaptor ligation, and 10 cycles of PCR enrichment according to manufacturer’s instructions.

treatment_protocol: Astrocyte were immunopanned by HepaCAM antibody and culture in the medium. EGFR or P53 inhibitor was added in the medium on in-vitro day 2. HBEGF was added or withdrawn on the prep day.

value: cortex

tag: cell type

value: astrocyte


title: in-vitro day 2 rep_3

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
2DIV-3


title: 14d_A5-3_E1


title: in-vitro day7 rep_3

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
7DIV-3


title: in-vitro day14 rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
14DIV-1


title: 42d_A1-1_E1


title: 42d_A3-4_E1


title: in-vitro day 2 rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
2DIV-1


title: 42d_A1-3_E1


title: 14d_A6-3_E1


title: 7d_A7-2_E1


title: HBEGF rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
HBEGF-1


title: P53 inhibitor rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
P53i-2


title: HBEGF rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
HBEGF-2


title: 28d_A4-4_E1


title: 28d_A4-1_E1


title: in-vitro day14 rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
14DIV-2


title: EGFR inhibitor rep_3

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
EGFRi-3


title: 7d_A8-3_E1


title: EGFR inhibitor rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
EGFRi-1


title: in-vitro day7 rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
7DIV-2


title: in-vitro day7 rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
7DIV-1


title: 42d_A1-2_E1


title: 28d_A4-3_E1


title: HBEGF withdrawal rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
NoHBEGF-2


title: pl2HFD, 202, Cardia, 12mo

type: RNA

city: München

first: Michael

last: Quante

address: Ismaninger Str 22

department: II Medizinische Klinik

country: Germany

institute: Technische Universität München

description:
Gene expression data from mouse cardia with IL-1b and chow diet
pl2HFD, Cardia
6NS

hyb_protocol: Hybridization of AffymetrixMouse Gene2.1 ST arrays was performed as recommended by the manufacturer

scan_protocol: The microarrays were washed and stained in an Affymetrix Fluidics station and scanned in a GC3000 scanner with G7 update, as recommended by Affymetrix

data_processing: Signal summarization was done in Partek Genomics Suite using the RMA algorithm

label: Biotin

source_name: mouse cardia with IL-1b and chow diet

label_protocol: Total RNA samples (>50ng) were amplified and labelled.

growth_protocol: Mice were maintained up to 12 months age in accordance with the German Animal Welfare and Ethical Guidelines of the Klinikum rechts der Isar, TUM, Munich, Germany up to

extract_protocol: After sacrificing mice, total RNA from cardia and forestomach tissues were extracted by TRIzol Reagen (Inventrogen) according to the manufacture’s protocol.

treatment_protocol: Mice were allowed a standard chow diet from birth until weaning, and water ad libitum. Following weaning and genotyping, between 6 and 8 weeks of age, mice were assigned high fat diet or remained on the chow diet.

value: cardia and forestomach

tag: genotype

value: IL-1b overexpression

tag: timepoint

value: 12 months

tag: diet

value: HFD

tag: concentration (µg/µl)

tag: volume (µl)


title: pl2Chow, 131, Cardia, 12mo

description:
Gene expression data from mouse cardia with IL-1b and HFD
pl2Chow, Cardia
3NS

source_name: mouse cardia with IL-1b and HFD

value: control


title: pl2.IL8, 1891, Cardia, 12 mo

description:
Gene expression data from mouse cardia with IL-1b and IL-8 overexpression
pl2.IL8, Cardia
1CM

value: IL-1b and IL-8 overexpression


title: P53 inhibitor rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
P53i-1


title: Exp3-st19-TP63MO

city: Freiburg

first: Peter

last: Walentek

state: BW

address: Breisacherstr. 113

department: Internal Medicine IV & IMITATE

institute: University Freiburg Medical Center

data_processing:
Quality control was done using FastQC v0.11.5
paired-end reads were mapped to Xenopus laevis genome assembly v9.2 using RNA STAR v2.6.0b-1
featureCounts v1.6.3 was used to count uniquely mapped reads per gene
statistical analysis of differential gene expression was conducted in DEseq2 v1.22.1
Genome_build: X. laevis v9.2 genome assembly
Supplementary_files_format_and_content: tabular results files dervied from DESeq2; raw gene count tables from featurecounts

organism: Xenopus laevis

source_name: animal cap explant

growth_protocol: Explants were cut from the animal portion of stage 8 Xenopus laevis embryos in 1x Modified Barth's Saline (MBS), then they were maintained in the medium for at least 1 hour to heal. After healing of explants, they were transferred to 0.5x MBS containing 0.1% of Gentamycin and cultured in that medium until they reached the indicated stage.

extract_protocol:
Total RNA was extracted using the standard Trizol protocol.
500 ng total RNA per sample was used, poly-A selection and RNA-sequencing library preparation was done using non strand massively-parallel cDNA sequencing (mRNA-Seq) protocol from Illumina, the TruSeq RNA Library Preparation Kit v2, Set A (Illumina #RS-122-2301) according to manufacturer’s recommendation. Quality and integrity of RNA was assessed with the Fragment Analyzer from Advanced Analytical by using the standard sensitivity RNA Analysis Kit (Advanced Analytical #DNF-471). All samples selected for sequencing exhibited an RNA integrity number over 8. For accurate quantitation of cDNA libraries, the QuantiFluor™dsDNA System from Promega was used. The size of final cDNA libraries was determined using the dsDNA 905 Reagent Kit (Advanced Bioanalytical #DNF-905) exhibiting a sizing of 300 bp on average. Libraries were pooled and paired-end 100bp sequencing on a HiSeq2500 was conducted at the Transcriptome and Genome Analysis Laboratory, University of Göttingen.

treatment_protocol: Control embryos remained untreated, while DN-TP63 MO samples were injected 4 times into the animal hemisphere at four-cell stage with 4-6 pmol morpholino oligonucleotide targeting the ATG of DN-tp63 (sequence: 5’-GATACAACATCTTTGCAGTGAGGTT-3’).

value: Xenopus animal cap explant

tag: Stage

tag: treatment

value: deltaN-TP63 MO injected


title: 7d_A8-1_E1


title: Exp3-st19-ctrl


title: P53 DMSO control rep_3

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
P53 CTRL-3


title: P53 inhibitor rep_3

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
P53i-3


title: Exp3-st10.5-TP63MO


title: EGFR DMSO control rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
EGFR CTRL-1


title: Exp3-st10.5-ctrl


title: Exp2-st24-TP63MO


title: P53 DMSO control rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
P53 CTRL-2


title: Exp3-st25-ctrl


title: EGFR DMSO control rep_3

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
EGFR CTRL-3


title: EGFR inhibitor rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
EGFRi-2


title: pl2Chow, 130, Cardia, 12mo

description:
Gene expression data from mouse cardia with IL-1b and HFD
pl2Chow, Cardia
2NS


title: HBEGF withdrawal rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
NoHBEGF-1


title: Exp2-st24-ctrl


title: Exp2-st16-ctrl


title: Exp2-st10.5-ctrl


title: in-vitro day 2 rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
2DIV-2


title: Exp1-st19-ctrl


title: pl2HFD, 199, Cardia, 12mo

description:
Gene expression data from mouse cardia with IL-1b and chow diet
pl2HFD, Cardia
5NS


title: Exp1-st10.5-TP63MO


title: pl2.IL8, 1901, Cardia, 12 mo

description:
Gene expression data from mouse cardia with IL-1b and IL-8 overexpression
pl2.IL8, Cardia
3CM


title: Exp3-st25-TP63MO


title: pl2HFD, 123, Cardia, 12mo

description:
Gene expression data from mouse cardia with IL-1b and chow diet
pl2HFD, Cardia
4NS


title: cSC rep1

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

description:
Isolated cochlea were dissociated with the papain dissociation system. GFP positive cells were FAC sorted directly into lysis buffer for downstream processing.
cSC_P21_Lfng_USC.bigWig

library_source: genomic

data_processing:
ATAC-seq reads were mapped to the mouse genome (mm10) using Bowtie2 with default paired-end settings.
Duplicated reads were removed with the picard MarkDuplicates function, default settings.
Peak calling for differential accessibility analysis was carried out with Macs2 on the merged BAM file, Macs2 callpeak --nomodel –broad.
Blacklisted regions identified by ENCODE from mm9 were lifted over to mm10 and then removed from the comprehensive peak file with the bedtools subtract module.
Genome_build: mm10
Supplementary_files_format_and_content: Files are in BigWig format, and contain merged runs for each experimental group. All BigWigs were generated from bedGraph outputs created in Homer.

molecule: genomic DNA

source_name: Cochlea supporting cells

extract_protocol:
The cell pellet was re-suspended in a transposase-containing reaction mixture complete with 0.05% digitonin prior to tagmentation at 37oC with 1000 rpm agitation for 30 minutes. Next, transposed DNA was purified with a Qiagen PCR MinElute kit (Qiagen 28004).
According to Fast-ATAC protocol, with Illumina Nextera kit transposase and custom Illumina adapters.

value: Cochlea supporting cells

tag: age

tag: virus infection

value: Outbred (ICR)

value: Lfng-GFP (Tg(Lfng-EGFP)HM340Gsat)


title: cSC rep2


title: cHC rep2

description:
Isolated cochlea were dissociated with the papain dissociation system. GFP positive cells were FAC sorted directly into lysis buffer for downstream processing.
P1_cHC.tagdir.ucsc.BigWig

source_name: Cochlea hair cells

value: Cochlea hair cells

value: Atoh1-GFP (Atoh1tm4.1Hzo)


title: cHC rep1


title: EGFR DMSO control rep_2

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
EGFR CTRL-2


title: Control 3 [exon-level]

city: Baltimore

first: Sean

middle: James

last: Miller

state: MD

address: 855 North Wolfe St.

department: Neurology-Neuromuscular Medicine

institute: Johns Hopkins School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

label: biotin

source_name: cerebral cortex

label_protocol: The NuGEN WT-Ovation Exon Module was used according to the manufacturer's protoco in the JHMI Sequencing & Microarray Core facility.

growth_protocol: The care and treatment of animals is in accordance with the NIH Guide for the Care and Use of Laboratory Animals, the Guidelines for the Use of Animals in Neuroscience Research, and the Johns Hopkins University IACUC (protocol M14M089). Mice were housed at standard temperature and in light-controlled environment with ad libitum access to the food and water. No more than 5 mice were kept in a cage, in accordance with Johns Hopkins IACUC.

extract_protocol: Total RNA was isolated from FACS sorted populations using the RNA isolation kit (Qiagen) and the concentrations determined using Nanodrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent Technologies). Only samples with a RNA integrity score greater than 5 were used. Total RNA was lineally amplified and labeled in a NuGEN protocol.

treatment_protocol: SOD1 G93A ALS mice and controls were aged to P120. SOD1 G93A mice that displayed hindleg paralysis at P120 were used for this study. Fluorescent-activated cell sorting (FACS) was performed by first sacrificing mice with an intraperitoneal injection of ketamine xylazine. The entire cortex was immediately dissected and dissociated as previously described (Foo et al. 2011). Single cells were then sorted by using MoFlo high-speed cell sorter and gated based on eGFP fluorescence.

value: cerebral cortex

tag: hind-limb paralysis

value: normal

tag: phenotype

value: Control


title: SOD1 ALS 3 [exon-level]

value: paralyzed

value: ALS


title: pl2.IL8, 1895, Cardia, 12 mo

description:
Gene expression data from mouse cardia with IL-1b and IL-8 overexpression
pl2.IL8, Cardia
2CM

value: cardia and forestomach


title: Atoh1 rep1

description:
Isolated utricle were treated with 0.1mM gentamicin for 24 hours, follow by adenovirus Ad-tdTomato-Atoh1 for 24 hours. The viral infected utricle is then being cultured for additional 9 days.Isolated utricles were dissociated with the papain dissociation system. Dissociated tdTomato positive cells were FAC sorted directly into lysis buffer for downstream processing.
Atoh1.tagdir.ucsc.bedGraph.BigWig

source_name: Utricle supporting cells

value: Utricle supporting cells

value: 4-6 weeks

value: WT


title: SOD1 ALS 1 [exon-level]


title: pl2Chow, 127, Cardia, 12mo

description:
Gene expression data from mouse cardia with IL-1b and HFD
pl2Chow, Cardia
1NS

value: IL-1b overexpression

value: 12 months

value: control


title: Human epimermal keratinocytes, vehicle treated control, biological replicate 1

city: Seoul

first: Minsoo

last: Noh

address: 1 Gwanak-ro, Gwanak-gu

department: Pharmacy

country: South Korea

institute: Seoul National University

description: Control batch1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 oligonucleotide arrays. GeneChips were hybridized and washed using the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Affymetrix Expression Console software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Homo sapiens

source_name: Cultured NHEK_vehicle for 24 hours

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

growth_protocol: Normal human keratinocytes (NHK) from neonatal foreskin were purchased from Lonza (Basel, Switzerland) and cultured in KBM medium with KGM2 growth supplements according to the manufacturer's instuction

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: At passge 2, when NHKs were confluent in culture, 10 microM of avobenzone were treated. After 24 hours in culture, NHKs were harvested for total RNA isolation.

tag: cell line

value: Normal human keratinocytes (NHK)

value: primary epidermal keratinocytes culture

tag: passage

value: passage 2

value: vehicle for 24hrs


title: P53 DMSO control rep_1

description:
mouse brain
rpkm_data.txt
sample name in processed data file:
P53 CTRL-1

tag: tissue

value: cortex

value: astrocyte


title: Exp1-st19-TP63MO

value: Xenopus animal cap explant

value: deltaN-TP63 MO injected


title: ATAC-seq_naive_hESC_dCAS9-KRAB+sgRNA_rep3

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

data_processing:
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned with bowtie2. Mitochondrial reads were removed.
Accessible sites were called using MACS2, only peaks with a score higher than 5 (–log10 p-value) were kept. Then differential analysis between conditions was done using unique reads (filter for MAPQ > 10)
Genome_build: hg19
Supplementary_files_format_and_content: (Peaks tabular File)  A bed file containing the output of the peak called by MACS2

growth_protocol: Conventional (primed) human ESC lines were maintained in mTSER for H1 (Male) and IPS on Matrigel, for WIBR3 (Female) on irradiated inactivated mouse embryonic fibroblast (MEF) feeders in human ESC medium (hESM) and passaged with collagenase and dispase, followed by sequential sedimentation steps in hESM to remove single cells while naïve ES cells, primed H1 and IPS were passaged by Accutase in single cells. hES media composition: DMEM/F12 supplemented with 15% fetalbovine serum, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% nonessential amino acids, 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol and 4 ng/ml FGF2. Naïve media composition: 500 mL of medium was generated by including: 240 mL DMEM/F12, 240 mL Neurobasal, 5 mL N2 supplement, 10 mL B27 supplement, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin-streptomycin, 50 μg/ml BSA. In addition for 4i/LA:  PD0325901 (1 μM), SB590885 (0.5 μM), WH4-023 (1 μM), Activin A (10 ng/mL), 20 ng/ml hLIF, Y-27632 (10 μM) and IM-12 (0-1 μM). In addition for KN/2i media: PD0325901 (1 μM), CHIR99021 (1 μM), 20 ng/ml hLIF and Doxycycline (2 µg/ml). For conversion of primed human ESC lines (WIBR3), we seeded 2-3e105 trypsinized single cells on an MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (10 mM). Two days later, medium was switched to 4i/LA (+/- IM12)-containing naïve hESM (Theunissen et al., 2016). WIBR3dPE cells (OCT4 GFP knock-in depleted for its primed specific Proximal Enhancer (dPE) were converted in naïve with DOX-inducible KLF2 and NANOG transgenes and maintained in 2i/L/DOX (Theunissen et al., 2014).

extract_protocol:
ATAC-seq was performed as in (Buenrostro et al., 2013) on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs
Library were made using Nextera DNA Library Prep Kit (Illumina #FC-121-1030)
Libraries were ligated with Illumina adaptors
Tn5 tagmentation

treatment_protocol: ATAC-seq was performed on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs

tag: source

value: Early Embryo

value: WIBR3dPE hESC

tag: culture media

value: KN/2iL media

tag: status

value: CRISPRi in naive


title: Exp2-st16-TP63MO


title: Human epimermal keratinocytes, avobenzone 10 microM treated, biological replicate 2

description: Avobenzone batch2

source_name: Cultured NHEK_avobenzone 10 microM for 24 hours

tag: cell type

value: 10 microM of avobenzone for 24 h


title: Exp1-st25-ctrl


title: uHC rep1

description:
Isolated utricles were dissociated with the papain dissociation system. GFP positive cells were FAC sorted directly into lysis buffer for downstream processing.
uHC.tagdir.ucsc.BigWig

source_name: Utricle hair cells

value: Utricle hair cells

value: 4-6 weeks

tag: strain

value: Outbred (ICR)

tag: genotype

value: Ai3; Atoh1-CreERT2 (Gt(ROSA)26Sortm3(CAG-EYFP)Hze/J; Tg(Atoh1-cre/Esr1*)14Fsh)


title: ATAC-seq_naive_hESC_dCAS9-KRAB_Empty_rep3


title: Human epimermal keratinocytes, vehicle treated control, biological replicate 2

description: Control batch2

value: Normal human keratinocytes (NHK)


title: tdTomato rep1

description:
Isolated utricle were treated with 0.1mM gentamicin for 24 hours, follow by adenovirus Ad-tdTomato for 24 hours. The viral infected utricle is then being cultured for additional 9 days.Isolated utricles were dissociated with the papain dissociation system. Dissociated tdTomato positive cells were FAC sorted directly into lysis buffer for downstream processing.
TdTomato.tagdir.ucsc.BigWig

value: Utricle supporting cells

value: Ad-tdTomato

value: WT


title: Exp1-st10.5-ctrl

value: control


title: Atoh1 rep2


title: Exp1-st25-TP63MO


title: uSC rep2

description:
Isolated utricles were dissociated with the papain dissociation system. Dissociated cells were stained with anti-CD326 conjugated with Allophycocyanin (APC). GFP negative and APC postive cells were FAC sorted directly into lysis buffer for downstream processing.
uSC.tagdir.ucsc.BigWig


title: BAT-Mcu-KO 4C #4

city: Boston

first: Daniel

last: Flicker

address: Department of Molecular Biology, 185 Cambridge Street, 6th floor

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
2x25bp paired-end reads were aligned to the mouse genome (mm10, with gencode M7 annotations) using STAR 2.4.0j (default parameters).
Counts of reads uniquely mapping within exonic regions of annotated genes (irrespective of strand) were collated using HTSeq.
14,651 genes with at least 8 reads mapping to them in at least 6 of the samples were retained for differential expression analysis. This was performed in R using DESeq2 [115] and the design formula ~Genotype + Temperature + Genotype:Temperature. Where gene expression levels are reported, they represent normalized read counts following application of the estimateSizeFactors function, which implements the median ratio method. Where log2 fold-changes and p-values are reported, they represent the result of the Wald test. P-values are adjusted with the method of Benjamini-Hochberg.
GSEA was performed according to the following parameters. 1000 phenotype permutations, signal to noise ranking metric, weighted enrichment statistic, real sorting mode, descending ordering mode, gene set max 15 and min 5.
Genome_build: mm10
Supplementary_files_format_and_content: flicker_normcounts.csv contains normalized counts for every transcript measured in each sample. flicker_foldchange.csv contains fold change, nominal p-value, and adjusted p-value for each gene in the following comparisons: control RT vs. BAT-Mcu-KO RT, control 4C vs. BAT-Mcu-KO 4C, control RT vs. control 4C, BAT-Mcu-KO RT vs. BAT-Mcu-KO 4C, (control RT vs. control 4C) vs. (BAT-Mcu-KO RT vs. BAT-Mcu-KO 4C).

source_name: Brown adipose tissue

extract_protocol:
Animals were sacrificed by CO2 asphyxiation followed by cervical dislocation, and tissues were immediately harvested and snap frozen in liquid N2. Frozen BAT samples were homogenized in 1mL Qiazol per 100mg tissue using the Qiagen TissueRuptor II. The homogenate was mixed thoroughly with chloroform (1:5 chloroform:homogenate), incubated for 3 mins at room temperature, and centrifuged at 12,000g for 15 mins at 4C, and 100uL of the resulting aqueous phase was added to 350uL Qiagen buffer RLT plus 250uL of 100% ethanol. The resulting mixture was transferred to a column from the Qiagen RNeasy Mini Kit, and RNA was purified according to the manufacturer’s protocol.
RNA-sequencing libraries were prepared by the Broad Technology Labs at the Broad Institute based on the Smart-seq2 protocol (S. Picelli, O. R. Faridani, Å. K. Björklund, G. Winberg, S. Sagasser, and R. Sandberg, “Full-length RNA-seq from single cells using Smart-seq2,” Nat. Protoc., vol. 9, no. 1, pp. 171–181, 2014.)

treatment_protocol: Age and sex-matched animals were individually housed at 4C for up to six hours in pre-cooled cages without bedding, with ad libitum access to pre-cooled water. Animals at 4C did not have access to food unless otherwise indicated; if food was provided, it was pre-cooled to 4C overnight. Body temperature was measured rectally at indicated time points using a Physitemp BAT-12 thermometer outfitted with a RET-3 probe. All animals used for cold tolerance and RNA-seq experiments were males at 8-12 weeks of age.

value: Brown adipose tissue

value: 8-12 weeks

tag: Sex

value: Male

tag: temperature


title: SOD1 ALS 4 [exon-level]

value: cerebral cortex

value: paralyzed

value: ALS


title: BAT-Mcu-KO 4C #6


title: ATAC-seq_naive_hESC_dCAS9-KRAB+sgRNA_rep2

value: Early Embryo

value: WIBR3dPE hESC

value: KN/2iL media

value: CRISPRi in naive


title: Exp2-st10.5-TP63MO

value: Xenopus animal cap explant

tag: Stage

value: deltaN-TP63 MO injected


title: BAT-Mcu-KO 4C #3


title: uHC rep2

value: Utricle hair cells

value: 4-6 weeks

value: Outbred (ICR)

value: Ai3; Atoh1-CreERT2 (Gt(ROSA)26Sortm3(CAG-EYFP)Hze/J; Tg(Atoh1-cre/Esr1*)14Fsh)


title: Control 2 [exon-level]

value: normal

value: Control


title: ATAC-seq_naive_hESC_dCAS9-KRAB_Empty_rep2


title: tdTomato rep3

value: Utricle supporting cells

value: WT


title: tdTomato rep2

value: Ad-tdTomato


title: ATAC-seq_naive_hESC_dCAS9-KRAB+sgRNA_rep1


title: BAT-Mcu-KO RT #6

value: Brown adipose tissue

value: 8-12 weeks

value: Male

value: RT


title: KLF4_HAP1+OKS

data_processing:
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned with bowtie2
Peak calling for ChIP-seqs were done using MACS for single-end data and MACS2 for paired-end data
Genome_build: hg19
Supplementary_files_format_and_content: A bed file containing the output of the peak called by MACS or MACS2 is provided.

extract_protocol:
Cells were cross-linked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution to the PBS followed by quenching with glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was conserved in -80°C. Pellets were lysed, resuspended in 1mL of LB1 on ice for 10 min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10 min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) for histone marks and SDS shearing buffer (10 mM Tris pH8, EDTA 1mM, SDS 0.15% and protease inhibitors) for transcription factor and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 20 min), yielding genomic DNA fragments with a bulk size of 100-300bp. Coating of the beads with the specific antibody and carried out during the day at 4°C, then chromatin was added overnight at 4°C for histone marks while antibody for transcription factor is incubated with chromatin first with 1% Triton and 150mM NaCl. Subsequently, washes were performed with 2x Low Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 150mM NaCl, 0.15% SDS), 1x High Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 0.15% SDS), 1x LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% NaDOC) and 1 with TE buffer. Final DNA was purified with Qiagen Elute Column. Up to 10 nanograms of ChIPed DNA or input DNA (Input) were prepared for sequencing. Library was quality checked by DNA high sensitivity chip (Agilent). Quality controlled samples were then quantified by picogreen (Qubit® 2.0 Fluorometer, Invitrogen). Cluster amplification and following sequencing steps strictly followed the Illumina standard protocol.
Libraries were ligated with Illumina adaptors

treatment_protocol: Primed H1 were transduced with GFP, KLF4 or KLF17-containing lentiviral vectors and split after 48h then selected using blasticydin for the 3 following days. Naïve WIBR3dPE hESC cells in KN/2iL media were transduced with GFP or ZNF611-containing lentiviral vectors, split after 96h, then selected for a couple of passages with blasticydin on irradiated Mouse Embryonic Blasticidin-resistant (MMMbz).

value: chronic myeloid leukemia

value: DMEM+FBS

value: Overexpression in HAP1

tag: chip antibody

value: R&D Systems RRID:AB_2130224


title: uSC rep1

tag: age


title: SOD1 ALS 2 [exon-level]

value: cerebral cortex

value: paralyzed

value: ALS


title: Control 1 [exon-level]


title: Human epimermal keratinocytes, avobenzone 10 microM treated, biological replicate 1

description: Avobenzone batch1

value: Normal human keratinocytes (NHK)

value: primary epidermal keratinocytes culture

value: passage 2

tag: treatment

value: 10 microM of avobenzone for 24 h


title: KLF4_naive_hESC

value: Early Embryo

value: naive


title: H3K27ac_iNeuron

value: tissue culture

value: induced Neurons


title: H3K27ac_naive_hESC

value: Abcam Cat# ab4729, RRID:AB_2118291


title: BAT-Mcu-KO RT #4

value: Brown adipose tissue

value: 8-12 weeks

value: Male

value: RT


title: uSC rep3

value: Utricle supporting cells

value: 4-6 weeks

tag: virus infection

value: Outbred (ICR)


title: BAT-Mcu-KO RT #5


title: H3K9me3_naive_hESC_dCAS9-KRAB+sgRNA_rep2

value: WIBR3dPE hESC

value: KN/2iL media

value: CRISPRi in naive

value: Diagenode Cat# pAb-056-050, RRID:AB_2616051


title: BAT-Mcu-KO RT #2


title: Input_naive_hESC_dCAS9-KRAB+sgRNA_rep1


title: BAT-Mcu-KO RT #1


title: H3K9me3_naive_hESC_dCAS9-KRAB+sgRNA_rep1


title: BAT-Mcu-KO 4C #5


title: uHC rep3

value: Utricle hair cells

value: Ai3; Atoh1-CreERT2 (Gt(ROSA)26Sortm3(CAG-EYFP)Hze/J; Tg(Atoh1-cre/Esr1*)14Fsh)


title: Ctrl 4C #4

value: Mcu[fl/fl]


title: Ctrl 4C #2


title: Ctrl 4C #3


title: Ctrl RT #6


title: Input_+-KLFs_primed_hESC

value: Early Embryo

value: H1 hESC

value: mTSER

value: Overexpression in primed


title: H3K27ac_primed_hESC+KLF4_rep2

value: Abcam Cat# ab4729, RRID:AB_2118291


title: Ctrl RT #5

value: Brown adipose tissue

value: 8-12 weeks

value: Male


title: BAT-Mcu-KO 4C #1


title: Ctrl RT #4

value: RT


title: Ctrl RT #3


title: Ctrl RT #1


title: ATAC-seq_naive_hESC_dCAS9-KRAB_Empty_rep1


title: H3K9me3_primed_hESC+KLF17_rep2


title: H3K27ac_primed_hESC+KLF17_rep2


title: H3K9me3_primed_hESC+KLF17_rep1


title: H3K27ac_primed_hESC+KLF17_rep1


title: Input_naive_hESC_dCAS9-KRAB_Empty_rep2


title: Ctrl 4C #1


title: Input_naive_hESC_dCAS9-KRAB+sgRNA_rep2


title: H3K27ac_primed_hESC+GFP_rep1


title: H3K9me3_primed_hESC+GFP_rep2


title: H3K9me3_naive_hESC_dCAS9-KRAB_Empty_rep1


title: H3K27ac_primed_hESC+KLF4_rep1


title: BAT-Mcu-KO 4C #2


title: H3K9me3_primed_hESC+KLF4_rep2


title: BAT-Mcu-KO RT #3


title: Input_+-611_naive_hESC

value: Overexpression in naive


title: Input_naive_hESC_dCAS9-KRAB_Empty_rep1

value: WIBR3dPE hESC


title: Ctrl 4C #5


title: H3K9me3_naive_hESC+ZNF611_rep1

value: KN/2iL media


title: donor 983, omentum, rosiglitazone tech rep1

first: Mi-Jeong

last: Lee

address: 650 Albany St 810

department: Medicine

institute: Boston University

description: Gene expression data from omental adipose tissue explant treated with BRL-37344.

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Human Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 15.1) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.

source_name: omental adipose tissue explant

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Omental human adipose tissue fragements were cultured in explants culture system with serum free M199 with 0.7 nM + 10 nM Dexamethasone for 7 days.  Tissues were refed every 2 days and one day prior to the harvest on day 7.

extract_protocol: Total RNA was extracted with Trizol followed and cleaned with RNA-easy mini cleanup kits from Qiagen.

treatment_protocol: Tissues were treated with vehical control or 1 μM rosiglitazone for 7 days.

tag: donor

value: donor 983, female, 33yrs old, BMI=43.0 kg/m2

value: rosiglitazone

tag: depot

value: omentum


title: H3K27ac_naive_hESC+GFP_rep1


title: H3K9me3_primed_hESC+KLF4_rep1

value: Diagenode Cat# pAb-056-050, RRID:AB_2616051


title: H3K9me3_primed_hESC+GFP_rep1


title: H3K27ac_naive_hESC+GFP_rep2


title: H3K27ac_primed_hESC

value: hESM

value: primed


title: donor 983, omentum, vehicle control tech rep1

description: Gene expression data from omental adipose tissue explant treated with vehicle control.

value: vehicle control


title: H3K27ac_primed_hESC+GFP_rep2

value: Early Embryo

value: H1 hESC

value: mTSER


title: H3K27ac_naive_hESC+ZNF611_rep1

value: Abcam Cat# ab4729, RRID:AB_2118291


title: H3K9me3_naive_hESC+GFP_rep2


title: H3K9me3_naive_hESC+ZNF611_rep2


title: H3K9me3_naive_hESC+GFP_rep1


title: H3K27ac_naive_hESC+ZNF611_rep2


title: H2AZ replicate 1 (tiling1)

type: genomic

city: Bronx

first: Kami

last: Kim

state: New York

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

hyb_protocol: Cy3/5 labelled DNA (input/Experiment) were precipitated with 0.1 vol of 5M NaCl and 0.9 vol Isopropanol. Using NimbleGen Hybridization Kit, manufacturer's instructions were followed for hybridization reaction

scan_protocol: Arrays were scanned at wavelengths (532=cy3, 635=Cy5) with pixel size 5_m at 100% power using Agilent's DNA Microarray Scanner using Agilent scanner software

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction. Following this a custom R-script was used to convert T. gondii genome version 4 data to version 11 and combine tiling 1 and 2 arrays. Processed files (_ratio.gff and ratio_peaks.gff) are in T. gondii version 11.

organism: Toxoplasma gondii RH

source_name: H2AZ ChIP DNA from T. gondii

label_protocol: 1.2_g of Input and Experimental DNA sample were labelled with Cy3 and Cy5 dye respectively (NimbleGen Dual-Color DNA Labelling Kit) using Klenow Fragment 3->5 exo- (NEB) following manufacturer's instructions

growth_protocol: Normal pH7 growth conditions

extract_protocol: Nuclei extracted with high salt buffer and chromatin digested with micrococcal nuclease and digested DNA was incubated with antibodies against H3K4me3, H2AZ, H2AX or anti-Myc followed by protein G Dynabeads (Invitrogen). Immunoprecipitated DNA was amplified using Complete Whole Genome Amplification Kit (SIGMA ALDRICH)

treatment_protocol: Mnase-digestion

value: Tachyzoite

value: Wild type

source_name: Input Mnase-digested DNA

treatment_protocol: Input DNA


title: H2AZ replicate 2 (tiling1)


title: H2AX replicate 1 (tiling1)

source_name: H2AX ChIP DNA from T. gondii


title: H2AX replicate 2 (tiling1)


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_B_rep3

data_processing:
Reads were mapped to the human (hg19) genome using TopHat v2.0.11
Counts of reads on genes were computed using HTseq-count v0.6.1 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: .pileup files contain counts on genes.

extract_protocol:
SMARTer Stranded Total RNA-seq sample
Truseq mRNA-seq protocol

treatment_protocol: WIBR3dPE in KN/2iL media or in Induced Neurons were transduced dCAS9-KRAB overexpression containing or not a guide RNA targeting LTR7YB or SVA/LTR5Hs or overexpressing. Primed H1 were transduced with GFP, KLF4 or KLF17-containing lentiviral vectors and split after 48h then selected using blasticydin for the 3 following days. Naïve WIBR3dPE hESC cells in KN/2iL media were transduced with GFP or ZNF611-containing lentiviral vectors, split after 96h, then selected for a couple of passages with blasticydin on irradiated Mouse Embryonic Blasticidin-resistant (MMMbz).

tag: cell line

value: CRISPRi in naive

tag: culture


title: Ctrl RT #2

tag: tissue

value: Brown adipose tissue

value: 8-12 weeks

value: Male

value: Mcu[fl/fl]

value: RT


title: H3K9me3_naive_hESC_dCAS9-KRAB_Empty_rep2

tag: source

value: WIBR3dPE hESC

tag: culture media

value: KN/2iL media


title: donor 983, omentum, vehicle control tech rep2

value: donor 983, female, 33yrs old, BMI=43.0 kg/m2

value: omentum


title: RNA-seq_iNeurons_hESC_dCAS9-KRAB_Empty_rep1

extract_protocol:
TruSeq stranded RNA sample preparation kit (Illumina).
Truseq mRNA-seq protocol

value: IPS

tag: status

value: CRISPRi in induced Neurons

value: N2B27 + Doxycyclin


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_B_rep2

value: Early Embryo


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_A_rep4


title: RNA-seq_iNeurons_hESC_dCAS9-KRAB+sgRNA_rep1


title: RNA-seq_iNeurons_hESC_dCAS9-KRAB+sgRNA_rep2


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_B_rep1


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_A_rep3


title: donor 983, omentum, rosiglitazone tech rep2

value: rosiglitazone


title: RNA-seq_iNeurons_hESC_dCAS9-KRAB_Empty_rep2


title: H3K4me3 replicate 1 (tiling1)

source_name: H3K4me3 ChIP DNA from T. gondii

value: Tachyzoite


title: RPE1_hTERT_deltaP53_Cas9_s1_T18A

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

description:
Cas9 CRISPR guide sequences
RPE1_dP53_T18A
T18 replicate A

data_processing:
Library strategy: CRISPR dropout screen
Where necessary, raw reads were trimmed and/or reverse complemented to extract the CRISPR guide sequence using a custom PERL script.  11nt of flanking sequence was used to locate the guide, allowing up to 2 mismatches.
Reads were aligned to one of two CRISPR library files (TKOv1 or TKOv3) using bowtie (v0.12.7) with the following command:  bowtie -v 2 -m 1 -p 6 --sam-nohead <CRISPR_lib_file> <readsFile> > output.sam
Alignments were summarized to count reads mapping to each guide using a custom PERL script, and merged into a read count matrix.
Genome_build: TKOv1 (library-90k), TKOv2, or TKOv3 CRISPR libraries
Supplementary_files_format_and_content: Tab-delimited text of read counts; Tab-delimited inventory of CRISPR library

growth_protocol: Modified McCoy’s 5A medium (Gibco/Thermo Fisher) supplemented with 10% FBS and Pen/Strep

extract_protocol:
Genomic DNA was extracted from cell pellets using the QIAamp Blood Maxi Kit (Qiagen). Genomic DNA was precipitated using ethanol and sodium chloride, and resuspended in Buffer EB (10 mM Tris-HCl, pH 7.5).
gRNA inserts were amplified via PCR using primers harboring Illumina TruSeq adapters with i5 and i7 barcodes (primers listed below), and the resulting libraries were sequenced.

treatment_protocol: Cells stably expressing SpCas9 were transduced with either the TKOv1, TKOv2, or TKOv3 genome-wide CRISPR library at an MOI of approximately 0.3.  Following puromycin selection, an aliquot was saved as a representative T0, and cells were passaged and/or sampled at the indicated number of days (ie: T#) until the end-point

tag: cell type

value: retinal pigment epithelial cells (RPE1)

tag: p53 status

tag: transduction

tag: time


title: RPE1_hTERT_Cas9_s4_T3B

description:
Cas9 CRISPR guide sequences
Durocher_RPE1_hTERT_WT_T3B
T3 replicate B

growth_protocol: Dulbecco’s Modified Eagle Medium (DMEM; Gibco/Thermo Fisher) supplemented with 10% fetal bovine serum (FBS; Wisent), 200 mM GlutaMAX, 1× non-essential amino acids (both Gibco/Thermo Fisher), 100 U ml−1 penicillin and 100 μg ml−1 streptomycin (Pen/Strep; Wisent)

value: wild-type


title: RPE1_hTERT_deltaP53_Cas9_s1_T0

description:
Cas9 CRISPR guide sequences
RPE1_dP53_T0
T0


title: RPE1_hTERT_deltaP53_Cas9_s1_T18B

description:
Cas9 CRISPR guide sequences
RPE1_dP53_T18B
T18 replicate B


title: donor 136, omentum, vehicle control

value: donor 136,  female, 62 yrs old, BMI=31.4 kg/m2

value: vehicle control


title: RPE1_hTERT_Cas9_s4_T3A

description:
Cas9 CRISPR guide sequences
Durocher_RPE1_hTERT_WT_T3A
T3 replicate A


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_A_rep2

value: CRISPRi in naive


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_B_rep4


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgRNA_LTR5HS/SVA_A_rep1


title: RNA-seq_naive_hESC+dCAS9-KRAB_Empty_rep4


title: RPE1_hTERT_Cas9_s4_T0

description:
Cas9 CRISPR guide sequences
Durocher_RPE1_hTERT_WT_T0
T0


title: RNA-seq_naive_hESC+dCAS9-KRAB_Empty_rep2


title: RNA-seq_naive_hESC+dCAS9-KRAB_Empty_rep1


title: RNA-seq_naive_hESC+dCAS9-KRAB_Empty_rep3


title: RPE1_hTERT_Cas9_s2_T25A

description:
Cas9 CRISPR guide sequences
PACE006_T25A
T25 replicate A

growth_protocol: F-12 + 15 mM HEPES + 2.5 mM L-Glutamine @ 2.4 g/L sodium bicarbonate


title: donor 136, omentum, rosiglitazone


title: RNA-seq_primed_hESC+KLF17_rep2

molecule: polyA RNA

value: H1 hESC

value: Overexpression in primed

value: mTSER


title: RNA-seq_primed_hESC+KLF17_rep1


title: Rh30_siNR4A2/3_rep1

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A2, 25nM siRNA against NR4A3, and 25nM non-targeting siRNA, biological replicate 1

hyb_protocol: Microarray hybridization was performed at 65°C for 18 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 3μm resolution, and the array data was extracted with Agilent feature extraction software using the GE1_107_Sep09 protocol

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used along with LOWESS normalization

label_protocol: 100ng of total RNA were labeled (Cy3) according to Agilent's labeling protocol

growth_protocol: Rh30 rhabdomyosarcoma cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum at 37°C, 5% CO2

extract_protocol: Total RNA was extracted using Promega simplyRNA kit and Maxwell-16 following manufacturer's instructions

treatment_protocol: Rh30 rhabdomyosarcoma cells were transfected for 48 hours with 25 nM of Dharmacon ON-TARGETplus SMARTpool NR4A-specific siRNA or non-targeting siRNA alone or in combination (total of 75nM siRNA) using 6μL Lipofectamine RNAiMAX per well of a 6-well plate

value: Rhabdomyosarcoma


title: Rh30_siNR4A1/2/3_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A2, and 25nM siRNA against NR4A3, biological replicate 2


title: RNA-seq_primed_hESC+KLF4_rep3


title: Rh30_siNR4A1/2/3_rep1

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A2, and 25nM siRNA against NR4A3, biological replicate 1


title: Rh30_siNR4A1/3_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A3, and 25nM non-targeting siRNA, biological replicate 3


title: Rh30_siNR4A1/2/3_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A2, and 25nM siRNA against NR4A3, biological replicate 3


title: RNA-seq_primed_hESC+KLF4_rep1


title: Rh30_siNR4A1/3_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A3, and 25nM non-targeting siRNA, biological replicate 2


title: RPE1_hTERT_Cas9_s2_T25B

description:
Cas9 CRISPR guide sequences
PACE006_T25B
T25 replicate B


title: Rh30_siNR4A2/3_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A2, 25nM siRNA against NR4A3, and 25nM non-targeting siRNA, biological replicate 3


title: Rh30_siNR4A2/3_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A2, 25nM siRNA against NR4A3, and 25nM non-targeting siRNA, biological replicate 2


title: RPE1_hTERT_Cas9_s1_T30B

description:
Cas9 CRISPR guide sequences
PACE002_T30B
T30 replicate B

growth_protocol: DMEM+ 10% FBS


title: RPE1_hTERT_Cas9_s1_T30C

description:
Cas9 CRISPR guide sequences
PACE002_T30C
T30 replicate C


title: RPE1_hTERT_Cas9_s1_T30A

description:
Cas9 CRISPR guide sequences
PACE002_T30A
T30 replicate A


title: Rh30_siNR4A1/3_rep1

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A3, and 25nM non-targeting siRNA, biological replicate 1


title: Rh30_siNR4A1/2_rep1

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A2, and 25nM non-targeting siRNA, biological replicate 1


title: RPE1_hTERT_Cas9_s2_T0

description:
Cas9 CRISPR guide sequences
PACE006_T0
T0


title: RNA-seq_primed_hESC+KLF4_rep2


title: RPE1_hTERT_Cas9_s1_T0

description:
Cas9 CRISPR guide sequences
PACE002_T0
T0


title: RPE1_hTERT_Cas9_s1_T18B

description:
Cas9 CRISPR guide sequences
PACE002_T18B
T18 replicate B


title: Rh30_siNR4A1/2_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A2, and 25nM non-targeting siRNA, biological replicate 3


title: RPE1_hTERT_Cas9_s1_T18C

description:
Cas9 CRISPR guide sequences
PACE002_T18C
T18 replicate C


title: RNA-seq_primed_hESC+GFP_rep1


title: RNA-seq_naive_hESC+ZNF611_rep1

value: WIBR3dPE hESC

value: KN/2iL media


title: RNA-seq_primed_hESC+GFP_rep2


title: Rh30_siNR4A1/2_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1, 25nM siRNA against NR4A2, and 25nM non-targeting siRNA, biological replicate 2


title: P4_Normal

city: Winston-Salem

first: Qianqian

last: Song

state: NC

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

description: 26 bp Read1, 8 bp i7 Index, 0 bp i5 Index and 98 bp Read2

data_processing:
Run cellranger mkfastq on the Illumina BCL output folder to generate FASTQ files.
Run cellranger count on each library that was demultiplexed by cellranger mkfastq.
Run cellranger aggr to aggregate multiple libraries from a single experiment that were analyzed by cellranger count.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each Sample ...

source_name: Adjacent normal

extract_protocol:
Cellular suspensions were loaded on a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs. Single-cell RNA-Seq libraries were prepared using Chromium™ Single Cell 3’ Library & Gel Bead Kit (10x Genomics, P/N-120237).  GEM-RT was performed in a Biometra Thermal cycler with TempAssure PCR 8-tube strip (USA Scientific, P/N 1402-4700): 53 °C for 45 min, 85 °C for 5 min; held at 4 °C.
Constructed using the reagents in the Chromium™ Single Cell 3’ Library & Gel Bead Kit, following these steps: (1) end repair and A-tailing; (2) adapter ligation; (3) post-ligation cleanup with SPRIselect; (4) sample index PCR and cleanup.  The barcode sequencing libraries were quantified using the Qubit 3.0 (Thermo Fisher, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: treatment-naïve

tag: diagnosis

value: Lung adenocarcinoma

tag: tnm status

value: pT1a pN0

tag: Sex

value: Female

tag: race

value: Caucasian

tag: smoking status

value: unknown

value: Adjacent normal


title: P4_Tumor

source_name: tumor

value: tumor


title: RNA-seq_primed_hESC+GFP_rep3

value: Early Embryo


title: RNA-seq_naive_hESC+GFP_rep2


title: RNA-seq_naive_hESC+ZNF611_rep2


title: P3_Normal

value: pT2a pNx

value: former smoker


title: Rh30_siNR4A3_rep1

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A3 and 50nM non-targeting siRNA, biological replicate 1


title: Rh30_siNR4A3_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A3 and 50nM non-targeting siRNA, biological replicate 2


title: SPD-/-_168h post Af /12h post Ozone_6

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

description: Gene expression data

hyb_protocol: The GeneChip HT MG-430 PM 24 Array Plate consists of 24 single MG-430 PM arrays arranged into standard 96 well plate format. Array hybridization, washing and scanning were performed according to the manufacturer's recommendations on a GeneTitan Instrument.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Data was processed in ArrayStudio and quality was assessed via Almac QC ToolBox. Differential expression of genes with false discovery rate (FDR) adjusted to p<0.05 was included for downstream pathway analysis. Pathway analysis was performed using Metacore and pathways with FDR adjusted p<0.05 were reported.

label: Matrix lysis D fast prep

source_name: whole lung homogenate

label_protocol: Expression profiling was performed using the NuGEN cDNA RNA Amplification system along with GeneChip HT Mouse430PM 96 Array Plate.

extract_protocol: Animals were sacrificed using a 30G needle, loaded with 200 uL 1:1 Ketamine:Xylazine (100/20 mg/kg). The lungs were perfused with Ca++/Mg++ free PBS. The left lung lobe was collected for RNA extraction in a Matrix lysis D fast prep tube and frozen immediately after collection.

treatment_protocol: Mice received treatment as described for each sample. Ozone exposure (3 ppm) is performed for 2 hours and mice are sacrificed 12 hours later. Control mice received air exposure for 2 hours and are sacrificed 12 hours later. Af sensitization was performed by intraperitoneal injection on day 0 and day 7. Af challenge was performed by intranasal instillation on day 13. Timepoints for each sample indicate the time of euthanasia following Af challenge and/or ozone exposure.

tag: strain

value: male

tag: age

value: 7-8 weeks

value: whole lung homogenate

tag: treatment

value: 168 hours after Af and 12 hours after ozone exposure


title: Rh30_siNR4A3_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A3 and 50nM non-targeting siRNA, biological replicate 3

tag: cell line

value: Rhabdomyosarcoma


title: SPD-/-_168h post Af /12h post Ozone_4

description: Gene expression data

tag: tissue


title: Rh30_siNR4A2_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A2 and 50nM non-targeting siRNA, biological replicate 3


title: Rh30_siNR4A2_rep1

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A2 and 50nM non-targeting siRNA, biological replicate 1


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgLTR7YB_B_rep2

tag: source

value: WIBR3dPE hESC

value: CRISPRi in naive

tag: culture


title: RPE1_hTERT_Cas9_s1_T18A

description:
Cas9 CRISPR guide sequences
PACE002_T18A
T18 replicate A

value: retinal pigment epithelial cells (RPE1)

value: wild-type


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgLTR7YB_B_rep1

tag: status

value: KN/2iL media


title: P1_Normal

value: Lung adenocarcinoma

value: pT1b pN1

value: Male

value: Caucasian

value: former smoker, quit date:1993


title: Rh30_siNR4A2_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A2 and 50nM non-targeting siRNA, biological replicate 2

tag: cell type


title: P3_Tumor

source_name: Tumor

value: pT2a pNx

value: Female

value: Tumor


title: SPD-/-_168h post Af /12h post Ozone_1

description: Gene expression data

value: male

value: 7-8 weeks


title: SPD-/-_168h post Af /12h post Ozone_3

description: Gene expression data

value: whole lung homogenate

value: 168 hours after Af and 12 hours after ozone exposure


title: Rh30_siNR4A1_rep3

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1 and 50nM non-targeting siRNA, biological replicate 3

value: Rhabdomyosarcoma


title: SPD-/-_168h post Af /12h post air_6

description: Gene expression data

value: 168 hours after Af and 12 hours after air exposure


title: Rh30_siNR4A1_rep2

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1 and 50nM non-targeting siRNA, biological replicate 2


title: SPD-/-_168h post Af /12h post air_3

description: Gene expression data


title: P2_Normal

value: Lung squamous cell carcinoma

value: pT2a pN0

value: former smoker, quit date:Oct. 2017

value: Adjacent normal


title: P1_Tumor

value: Lung adenocarcinoma

value: pT1b pN1


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgLTR7YB_A_rep2

value: Early Embryo

value: WIBR3dPE hESC

value: CRISPRi in naive

value: KN/2iL media


title: RNA-seq_naive_hESC+GFP_rep1


title: RNA-seq_naive_hESC+dCAS9-KRAB_sgLTR7YB_A_rep1


title: RNA-seq_naive_hESC+dCAS9-KRAB_without_sgLTR7YB_rep2


title: Rh30_non-targ_rep3

description: Gene expression after 48hr transfection with 75nM non-targeting siRNA, biological replicate 3


title: SPD-/-_168h post Af /12h post air_2

description: Gene expression data


title: RNA-seq_naive_hESC+dCAS9-KRAB_without_sgLTR7YB_rep1


title: SPD-/-_168h post Af /12h post air_4

description: Gene expression data


title: DMSO day 14 replicate [S2DMSOB3]

city: Portland

first: Olga

last: Nikolova

state: OR

address: 2720 SW Moody Ave

department: Computational Biology

institute: OHSU

description:
PCR library sequencing
LIB170321JT_S2DMSOB3_S9_L002

data_processing:
Sequences were trimmed using cutadapt version 1.10 called with parameters "cutadapt -n 2 -g {adapter5} -a {adapter3}" where adapter3 = GTTTTAGAGCTA and adapter5 = CGAAACACCG
Trimmed reads were aligned using bowtie2 called with parameters "bowtie2 -p 8 --norc -U"
Formatting was done using samtools called as "samtools view -bS"
Filtering was performed using samtools called as "samtools view -bq 10"
MAGeCK( version 0.5.6) count command was executed.
Genome_build: custom reference created from CRISPR library (brunello4bowtie2.fasta) PMID: 26780180
Supplementary_files_format_and_content: Raw read counts sgRNA x sample matrix .tsv format

source_name: MOLM13 cells infected with library

growth_protocol: MOLM13 cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone.

extract_protocol:
10e6 cells were collected for DMSO day 0, 30 miln cells were collected for Venetoclax/DMSO days 7,14. DNA was extracted by desalting method
50 microgramms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/ml concentration for 5 days. Venetoclax (1microMolar) or DMSO were applied to 30 million cells in single flask

tag: genotype/variation

value: infected with CRISPR/Cas9 library

value: day 14post puromycin selection, DMSO


title: DMSO day 0 [S2DMSOD3A6]

description:
PCR library sequencing
LIB170321JT_S2DMSOD3A6_S7_L002

value: day 0 post puromycin selection


title: Brunello Plasmid Library  [Brunlibrep]

description:
PCR library sequencing
LIB170321JT_Brunlibrep_S1_L001

source_name: Library plasmid sequencing

tag: sample type

value: Library plasmid sequencing


title: Rh30_siNR4A1_rep1

description: Gene expression after 48hr cotransfection with 25nM siRNA against NR4A1 and 50nM non-targeting siRNA, biological replicate 1


title: Venetoclax day 14 [S2ABTA5]

description:
PCR library sequencing
LIB170321JT_S2ABTA5_S10_L002

value: day 14 post puromycin selection, Venetoclax


title: P2_Tumor

value: Female

value: Caucasian

value: Tumor


title: Rh30_non-targ_rep2

description: Gene expression after 48hr transfection with 75nM non-targeting siRNA, biological replicate 2

value: Rhabdomyosarcoma


title: Rh30_non-targ_rep1

description: Gene expression after 48hr transfection with 75nM non-targeting siRNA, biological replicate 1


title: SPD-/-_96h post Af/12h post Ozone_2

description: Gene expression data

value: male

value: 7-8 weeks

value: whole lung homogenate

value: 96 hours after Af and 12 hours after ozone exposure


title: SPD-/-_96h post Af/12h post Ozone_3

description: Gene expression data


title: SPD-/-_24h post Af/12h post air_6

description: Gene expression data

value: 24 hours after Af and 12 hours after air exposure


title: SPD-/-_24h post Af/12h post air_3

description: Gene expression data


title: SPD-/-_96h post Af/12h post Ozone_4

description: Gene expression data


title: SPD-/-_24h post Af/12h post air_1

description: Gene expression data


title: SPD-/-_12 hr Ozone_5

description: Gene expression data

value: 12 hours after ozone exposure


title: SPD-/-_24h post Af/12h post air_2

description: Gene expression data


title: SPD-/-_96h post Af/12h post Ozone_6

description: Gene expression data


title: SPD-/-_24h post Af/12h post air_4

description: Gene expression data


title: RPE1_hTERT_Cas9_s3_T18A

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T18A
T18 replicate A

growth_protocol: DMEM with high glucose and pyruvate (Life Technologies) supplemented with 10% FBS (Life Technologies) and 1% Penicillin/Streptomycin

value: retinal pigment epithelial cells (RPE1)

tag: p53 status

value: wild-type

tag: transduction

tag: time


title: SPD-/-_96h post Af/12h post Ozone_5

description: Gene expression data

tag: Sex


title: SPD-/-_96h post Af/12h post Ozone_1

description: Gene expression data


title: SPD-/-_12 hr Ozone_2

description: Gene expression data


title: SPD-/-_12 hr Ozone_3

description: Gene expression data


title: SPD-/-_168h post Af /12h post air_5

description: Gene expression data

value: 168 hours after Af and 12 hours after air exposure


title: RPE1_hTERT_Cas9_s3_T9B

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T9B
T9 replicate B


title: DMSO day 14 [S2DMSOA9]

description:
PCR library sequencing
LIB170321JT_S2DMSOA9_S8_L002

value: infected with CRISPR/Cas9 library

value: day 14post puromycin selection, DMSO


title: RPE1_hTERT_Cas9_s3_T9A

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T9A
T9 replicate A


title: SPD-/-_12 hr Forced Air_2

description: Gene expression data

value: 12 hours after air exposure


title: SPD-/-_12 hr Forced Air_4

description: Gene expression data


title: RPE1_hTERT_Cas9_s3_T0

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T0
T0


title: RPE1_hTERT_Cas9_s3_T15B

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T15B
T15 replicate B


title: H3K27ac_Nr5a2_with_4OHT

city: Nijmegen

first: Hendrik

middle: G

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 and reads with mapping quality less than 15 were discarded. PCR duplicates were removed from mapped BAM files and in case of pair-end sequencing, paired fragments were kept only when both reads were mapped uniquely to the same genomic region (unique and concordant alignments). Fragment size modeling was then applied on filtered BAM files (http://code.google.com/p/phantompeakqual-tools/) and peaks were called using MACS2  (http://github.com/taoliu/MACS/) and with default (narrow) settings. For allele-specific analysis, reads were mapped to cast or 129 alleles using described polymorphic sites
Genome_build: mm9
Supplementary_files_format_and_content: BigWig tracks, data are not normalized for sequencing depth. BedGraph files show the SNP-read counts in 129 and cast alleles for each sample

source_name: Mouse Embryonic Stem Cells

growth_protocol:
E14Tg2a or F1 ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were transfered from serum-medium to   NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) for 72h.
For CRE-recombination, cells were treated with 4-hydroxy tamoxifen (0.5 μM) for 2 days.

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) in ES-medium. Fixed cells were sonicated using a Diagenode Bioruptor UCD-300 for 4x1 minutes (30 seconds on; 30 seconds off). 50µl of chromatin (500,000 cells) were used with 0.5-1µg of H3K27ac antibody (Diagenode) and incubated overnight at 4ºC with rotation. For TF-ChiP-seq, 15-million cells were used per ChIP together with 15 μg anti-GFP antibody (ab290, Abcam) and 3 ChIP-samples were pooled to yield chromatin equal to 30-million cells per transcription factor. Antibody-chromatin complexes were incubated with protein-A/G magnetic beads, eluted, Supernatant was collected, 8µl 5M NaCl, 3µl proteinase K were added and samples were incubated for 4 hours at 65°C. Finally samples were purified using Qiagen; Qiaquick MinElute PCR purification Kit and eluted in 20µl EB. De-crosslinked DNA was used for library construction using KAPA Hifi kit according to manufacturer’s instruction.
Illumina library preparation was done using the Kapa Hyper Prep Kit. For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 minutes at 20°C and then for 30 minutes at 65°C.Subsequently adapters were  ligated  by adding 30µl ligation buffer, 10 Kapa l DNA  ligase, 5µl diluted adaptor  in a total volume of 110µl and incubated for 15 minutes at 15°C.Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20µl elution buffer. Libraries were amplified by adding 25µl 2x KAPA HiFi Hotstart ReadyMix and 5µl 10x Library Amplification Primer Mix and PCR, 10 cycles. Samples were purified using the QIAquick MinElute PCR purification kit and 300bp fragments selected using E-gel. Correct size selection was confirmed by BioAnalyzer analysis.   Sequencing was performed using Illumina HiSeq 2000 machines and generated 43bp single end reads.

tag: background strain

value: Mouse Embryonic Stem Cells

tag: chip antibody


title: H3K27ac_ChIP_F1_ESCs

growth_protocol: E14Tg2a or F1 ESCs were cultured in standard culture medium without feeder and on gelatin coated-dishes. Serum supplemented medium contains Dulbecco's Modified Eagle's Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, Gibco), L-glutamine (2 nM, Gibco), Na-Pyruvate (1 mM, Gibco), non-essential amino acids (0.1 mM each, Gibco), Penicillin Streptomycin (Gibco), 2-mercaptoethanol (55 µM, Gibco) and LIF (1000 U/ml, Milipore). For serum free culture, cells were transfered from serum-medium to   NDiff 227 (StemCells, Inc.) supplemented with MEK inhibitor PD0325901 (1 μM) and GSK3 inhibitor CHIR99021 (3 μM) and LIF (1000 U/ml, Milipore) for 72h.


title: SPD-/-_24h post Af/12h post air_5

description: Gene expression data

tag: strain


title: Esrrb_ChIP_CRISPR_ESCs

value: Esrrb


title: C57_168h post Af /12h post Ozone_2

description: Gene expression data

tag: age

value: 168 hours after Af and 12 hours after ozone exposure


title: Spermatogonia_Input_16

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

institute: McGill University

data_processing:
Basecalling was performed with RTA 1.18.64.
Sequenced reads were trimmed for adaptor sequence and were then aligned to the mm10 genome assembly using Bowtie2 (Version: 2.2.9). Aligned reads were then filterd to allow for a maximum of 3 mismatches.
Duplicates were marked using Picard tools.
Genomic regions enriched in H3K4me2 (peaks) were identified using the software MACS2 with the parameters --broad --broad-cutoff 0.05 --mfold 5 50 --nomodel over input files.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated form the bedgraphs files generated by MACS2 using the bedGraphToBigWig utility (UCSC)

source_name: Testis of GOF/deltaPE-Oct4/GFP mice

extract_protocol:
Testes were removed and decapsulated. They were then digested with collagenase B (2mg/mL) for 10 minutes at 37°C. After rinsing in PBS, another digestion with 0.25% trypsin-EDTA for 5 minutes at 37°C was performed. The resulting cell suspension was washed twice, resuspended in sterile phosphate buffer solution (PBS) with DNase (50μg/mL) and filtered (40μm). Spermatogonia were isolated by fluorescence-activated cell sorting of Oct4-GFP positive germ cells with a FACSAria III laser sorter.
ChIP-seq libraries were prepared using the Kapa HTP Library Preparation Kit (Roche) as per the manufacturer's recommendations except that adapters and PCR primers were diluted 100-fold and the size selection step was done after the PCR step.

value: testis

value: spermatogonia


title: RPE1_hTERT_Cas9_s3_T12A

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T12A
T12 replicate A


title: C57_168h post Af /12h post air_3

description: Gene expression data

value: male

tag: treatment


title: Spermatogonia_Input_15


title: RPE1_hTERT_Cas9_s3_T18B

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T18B
T18 replicate B


title: SPD-/-_12 hr Forced Air_6

description: Gene expression data

value: 7-8 weeks


title: C57_168h post Af /12h post air_2

description: Gene expression data

value: whole lung homogenate


title: C57_168h post Af /12h post Ozone_3

description: Gene expression data


title: C57_168h post Af /12h post Ozone_6

description: Gene expression data


title: C57_168h post Af /12h post Ozone_5

description: Gene expression data


title: RPE1_hTERT_Cas9_s3_T12B

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T12B
T12 replicate B


title: SPD-/-_12 hr Forced Air_3

description: Gene expression data


title: C57_96h post Af/12h post Ozone_6

description: Gene expression data

value: 96 hours after Af and 12 hours after ozone exposure


title: C57_168h post Af /12h post air_4

description: Gene expression data


title: H3K27ac_Esrrb_Flox_No_4OHT


title: SPD-/-_12 hr Forced Air_5

description: Gene expression data


title: H3K27ac_ChIP_CRISPR_ESCs


title: RPE1_hTERT_Cas9_s3_T15A

description:
Cas9 CRISPR guide sequences
Hart_Cell2015_RPE1_T15A
T15 replicate A


title: H3K27ac_Nr5a2_NO_4OHT


title: MGH119-d1-veh2_S8

first: Sana

last: Raoof

address: 175 Cambridge St

data_processing:
RNA-seq reads were aligned to the hg19genome assembly using STAR with default parameter
Counted with htseq-0.6.1 based on UCSC gene annotations
Genome_build: hg19
Supplementary_files_format_and_content: read count abundance measurements were generated using htseq

source_name: MGH119 Cell line

growth_protocol: cells were grown in RPMI supplemented with 10% FBS at 37 degrees C and 5% CO2

extract_protocol:
Total cellular RNA using Qiagen RNEasy kit
Strand-specific RNA-seq library preparation using the Ovation Universal RNA-Seq System 1-96; For PC9 and MGH119 - Illumina Poly-A kit followed by NEB's Ultra Directional Library Prep

treatment_protocol: Cells were treated with vehicle or the indicated concentrations of Gefitinib/WZ4002 for 2-3 weeks

value: vehicle

tag: dose

tag: cell line


title: C57_96h post Af/12h post Ozone_3

description: Gene expression data

tag: tissue


title: MGH119-d14-gef2_S12

value: Gefitinib


title: PC9-d14-gef2_S6

source_name: PC9 Cell line


title: E14_Esrrb_2iD3


title: E14_Esrrb_serum

value: serum


title: C57_24h post Af/12h post air_3

description: Gene expression data

value: 24 hours after Af and 12 hours after air exposure


title: PC9-d14-gef1_S5


title: Esrrb_ChIP_F1_ESCs


title: MGH119-d1-gef1_S9


title: SPD-/-_12 hr Ozone_4

description: Gene expression data

value: 12 hours after ozone exposure


title: H3K27ac_Esrrb_Flox_with_4OHT

value: 2i_Day3, Tamoxifen(4OHT)


title: C57_168h post Af /12h post Ozone_4

description: Gene expression data


title: C57_168h post Af /12h post air_6

description: Gene expression data

value: 168 hours after Af and 12 hours after air exposure


title: C57_24h post Af/12h post air_1

description: Gene expression data


title: C57_12 hr Ozone_4

description: Gene expression data


title: PC9-d1-gef2_S4


title: MGH119-d1-gef2_S10


title: MGH119-d14-gef1_S11


title: C57_12 hr Ozone_6

description: Gene expression data


title: C57_24h post Af/12h post air_4

description: Gene expression data


title: C57_12 hr Ozone_5

description: Gene expression data


title: right_IRI_reperfused_30min_rep2

city: Chapel Hill

first: Thomas

middle: Michael

last: Egan

address: Med Schol Wing C Room 354

department: Surgery

institute: University of North Carolina

description: rat lung right IRI reperfused 30min rep2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on RAE 230A Affymetrix arrays in the GeneChip Fluidics Station 400 and washed and scanned with a Hewlett Packard GeneArray Scanner.  During the washing, the cRNA probe was labeled with R-Phycoerythrin streptavidin.

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

data_processing: Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Analysis of microarray data was performed using GeneSpring software 7.2.  A cross gene error model was employed to set a cut off value for normalization.  Analysis of variance (ANOVA) was performed with Benjamini and Hochberg false discovery rate (FDR) of 5%.

organism: Rattus norvegicus

source_name: rat lung tissue, right, after 2 hours of in situ warm left lung ischemia via left hilar clamp, and 30 minutes reperfusion

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction.

extract_protocol: Trizol extraction of total RNA from frozen lung specimens was performed according to the manufacturer's instructions

treatment_protocol: Anesthetized ventilated male Sprague-Dawley rats underwent tracheotomy for mechanical ventilation, then left thoracotomy and left lung hilar clamping for two hours, then the left lungs were reperfused and ventilated for 30 minutes (n=3) or 3 hours (n=3).  Both the right and left lungs were retrieved for RNA extraction.  RNA retrieved from lungs of six rats retrieved immediately after sacrifice served as controls.

tag: Sprague-Dawley rat, male


title: PC9-d1-gef1_S3


title: C57_168h post Af /12h post Ozone_1

description: Gene expression data


title: right_IRI_reperfused_30min_rep3

description: rat lung right IRI reperfused 30min rep3


title: PC9-d1-veh2_S2


title: PC9-d1-veh1_S1


title: C57_96h post Af/12h post Ozone_4

description: Gene expression data


title: right_IRI_reperfused_3hours_rep3

description: rat lung right IRI reperfused 3hours rep3

source_name: rat lung tissue, right, after 2 hours of in situ warm left lung ischemia via left hilar clamp, and 3 hours reperfusion


title: C57_96h post Af/12h post Ozone_2

description: Gene expression data


title: C57_24h post Af/12h post air_6

description: Gene expression data


title: C57_12 hr Ozone_3

description: Gene expression data


title: MGH119-d1-veh1_S7


title: right_IRI_reperfused_30min_rep1

description: rat lung right IRI reperfused 30min rep1


title: C57_96h post Af/12h post Ozone_1

description: Gene expression data


title: C57_12 hr Ozone_2

description: Gene expression data


title: C57_12 hr Forced Air_6

description: Gene expression data

value: 12 hours after air exposure


title: right_IRI_reperfused_3hours_rep2

description: rat lung right IRI reperfused 3hours rep2


title: H1975_TKI_b

source_name: H1975 Cell line


title: right_IRI_reperfused_3hours_rep1

description: rat lung right IRI reperfused 3hours rep1


title: C57_12 hr Ozone_1

description: Gene expression data


title: left_IRI_reperfused_30min_rep3

description: rat lung left IRI reperfused 30min rep3

source_name: rat lung tissue, left, after 2 hours of in situ warm ischemia via left hilar clamp, and 30 minutes reperfusion


title: H1975_TKI_c


title: H1975_TKI_a


title: HCC4006_TKI_b

source_name: HCC4006 Cell line


title: HCC4006_TKI_c


title: HCC4006_TKI_a


title: C57_12 hr Forced Air_5

description: Gene expression data


title: H1975_par_c


title: H1975_par_b


title: left_IRI_reperfused_30min_rep1

description: rat lung left IRI reperfused 30min rep1


title: BALB/c_168h post Af /12h post Ozone_4

description: Gene expression data

value: Balb/c


title: left_IRI_reperfused_3hours_rep1

description: rat lung left IRI reperfused 3hours rep1

source_name: rat lung tissue, left, after 2 hours of in situ warm ischemia via left hilar clamp, and 3 hours reperfusion


title: C57_12 hr Forced Air_1

description: Gene expression data


title: left_IRI_reperfused_30min_rep2

description: rat lung left IRI reperfused 30min rep2


title: C57_12 hr Forced Air_4

description: Gene expression data


title: control_rep6

description: rat lung control rep6

source_name: rat lung tissue, retrieved immediately after anesthesia and sacrifice


title: HCC827_TKI_b

source_name: HCC827 Cell line


title: H1975_par_a


title: HCC827_TKI_a


title: left_IRI_reperfused_3hours_rep3

description: rat lung left IRI reperfused 3hours rep3


title: BALB/c_168h post Af /12h post Ozone_6

description: Gene expression data


title: OtB9338

city: Terre Haute

first: Steven

last: Templeton

state: IN

address: 620 Chestnut St. HH135

institute: Indiana University School of Medicine - Terre Haute

data_processing:
Illumina library prep/QC; PE100-125 and HiSeq2500 sequencing
20M reads. DNAnexus Platform RNAseq analysis: comparative expression analysis
The data has been mapped and filtered against the m. mucus reference genome (mm10) with STAR 2.5.1j, Qualimap 2, Picard (A-C).
Supplementary_files_format_and_content: FPKM measurements were calculated using cufflinks (D).  HTSeq (E) was used to calculate raw counts of gene expression. Comparison of expression level between samples was conducted using the DESeq2 package (F) in an R computational environment (G) using the HTSeq raw count data.

source_name: lung

extract_protocol:
Lungs tissue was removed, flash frozen in liquid nitrogen. Frozen lungs were freeze dried and total RNA was extracted using Trizol extraction followed by Qiagen column purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were depeleted neutrophils with anti-Ly6G antibody 1 day before and after infection and infected with 10 million A.fumigatus (Af293)

value: Adipo-/-

value: lung

value: post natal day 32

tag: genotype


title: left_IRI_reperfused_3hours_rep2

description: rat lung left IRI reperfused 3hours rep2


title: C57_12 hr Forced Air_2

description: Gene expression data

source_name: whole lung homogenate


title: control_rep5

description: rat lung control rep5


title: control_rep4

description: rat lung control rep4


title: control_rep2

description: rat lung control rep2


title: BALB/c_168h post Af /12h post Ozone_3

description: Gene expression data

value: 168 hours after Af and 12 hours after ozone exposure


title: C57_12 hr Forced Air_3

description: Gene expression data

value: male


title: control_rep3

description: rat lung control rep3


title: BALB/c_168h post Af /12h post Ozone_5

description: Gene expression data

value: 7-8 weeks


title: HCC4006_par_c


title: BALB/c_168h post Af /12h post air_6

description: Gene expression data

value: whole lung homogenate


title: control_rep1

description: rat lung control rep1


title: HCC827_TKI_c


title: BALB/c_168h post Af /12h post air_4

description: Gene expression data


title: HCC4006_par_b


title: BALB/c_168h post Af /12h post air_1

description: Gene expression data


title: OtB9334

value: wild type


title: HCC4006_par_a

value: vehicle


title: BALB/c_168h post Af /12h post air_3

description: Gene expression data


title: OtB9336


title: OtB9335


title: OtB9333


title: BALB/c_168h post Af /12h post air_2

description: Gene expression data


title: UF-dFBS-2

city: Helsinki

first: Sippy

last: Kaur

address: PO Box 63

department: Oral and Maxillofacial Diseases

country: Finland

institute: University of Helsinki

description:
miRNA_raw.txt
smRNA_raw.txt
miRNA_spikein_normalized.txt
smRNA_spikein_normalized.txt

data_processing:
Raw data was demultiplexed and FASTQ files for each sample were generated using the bcl2fastq software (Illumina inc.).
To correct PCR bias with UMI information, raw reads were processed as follows: First, cutadapt 1.11  was used on each raw read with the adapter sequence to acquire information about the presence of adapter. Only reads that fulfilled the following criteria were kept: 1) read contained adapters, 2) read had at least 16nt insert sequence length, and 3) read had at least 10nt-long UMI sequence. Second, insert sequences with incomplete UMI sequence were extracted as partial-UMI reads. Third, all unique insert+UMI combinations were identified from reads with full-length UMI and collapsed into a single read. Fourth, collapsed full-length UMI reads and partial-UMI reads were combined.
After UMI-correction, reads were trimmed using cutadapt output and an in-house script.
Reads were mapped using Bowtie 2 (2.2.2) as follows: First, reads mapped to spike-ins or outmapped (mapped to adapter sequences, polyA and polyC homopolymers, or abundant ribosomal or mitochondrial RNA sequences) were filtered out. Perfect match to the reference sequence was required. Second, reads were aligned to mature sequences of miRBase 20, requiring perfect matches. Third, unmapped reads were mapped to either to human GRCh37 or bovine UMD3 reference genome, allowing one mismatch in the first 32 bases of the read. Reads aligned to known miRNA loci in the genome were combined with the miRBase-mapped reads and reads aligned to smallRNA reqions in the Exiqon smallRNA database were classified as smallRNA. Reads mapping to the reference genome outside the miRNA or smallRNA regions were classified as genome-mapped. No indels were allowed in any of the mapping steps.
Read counts were normalized using the external spike-ins (UniSp100-UniSp151) that were present in three relative concentrations of 0.1 (low), 1 (moderate) and 5 (high), reflecting the expected range of miRNAs in the samples. Linear functions with intercept fixed at zero were fitted to the spike-in concentration versus observed counts in each sample. The linear fit was used calculate an estimated relative concentration for each RNA.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt files contain results of mapping to miRBase 20 and GRCh37 reference genome. miRNA_raw.txt: miRNA raw counts for all samples, smRNA_raw.txt: other smRNA raw counts for all samples, miRNA_spikein_normalized.txt: spike-in normalized miRNA counts for all samples, smRNA_spikein_normalized.txt: spike-in normalized counts for other smRNA for all samples.

organism: Bos taurus

source_name: Ultrafiltrated EV-depleted fetal bovine serum extracellular vesicles

extract_protocol:
Two supernatant removal steps were used on 3 ml of culture media to get rid of the un-precipitated material. EV lysis and RNA isolation was performed on 500 µl of media using exoRNeasy Serum/Plasma Maxi Kit (QIAGEN).
Library preparation was done using the QIAseq miRNA Library Kit (QIAGEN). Out of 12µl of isolated RNA, 5µl was converted into microRNA NGS libraries. Adapters containing 12nt-long unique molecular indices (UMIs) were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR the samples were purified. Library preparation quality control was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent). Based on the quality of the inserts and the concentration measurements the libraries were pooled in equimolar ratios. The library pools were quantified using the qPCR ExiSEQ LNA™ Quant kit (Exiqon). The library pools were then sequenced on a NextSeq500 sequencing instrument according to the manufacturer instructions using 1x75bp reads.

value: EV

tag: medium

tag: supplier

value: Gibco


title: HCC827_par_a


title: Lung_YFP_Negative_2

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

data_processing:
Base calling performed using CASAVA 1.8
Quality control on fastq files was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment and junction mapping to mouse genome mm10 performed using Tophat2 and Bowtie2 (Trapnell et. Al. Genome Biology, 2013)
Transcript quantitation, normalization and differential expression testing performed using Cufflinks ((Trapnell et. al. 2012 Nature Protocols)
Data analysis and visualization performed in R, using packages cummeRbund (http://compbio.mit.edu/cummeRbund/) and pheatmap (https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf).
Genome_build: mm10
Supplementary_files_format_and_content: [Gene_Expression_Mca34.txt]  file of normalized FPKM between samples
[Mus_Musculus_GRCm38_genes.gtf]  GTF file from Ensembl used for transcript and gene identification

source_name: YFP Negative TRM Cells

growth_protocol: Mice were immunized intranasally with heat-killed klebsiella pneumoniae 35 days prior to cell extraction.

extract_protocol:
RNA was extracted from sorted cells as described in methods section.
Libraries were constructed using Illumina TruSeq mRNA-Seq Sample Prep Kits, library quality and concentration assayed using a Bioanalyzer.

treatment_protocol: Cells were extracted from mouse lymph nodes using a cell strainer, or from lung tissue via collagenase digestion and percoll gradient separation. Cells were stained with the indicated antibodies and sorted on a BD FACSAria.

value: Lung

tag: cell type

value: YFP Negative TRM Cells

value: Immunization (Kp) 35 days prior


title: HCC827_par_c


title: UF-dFBS-1

tag: sample type

value: Ultrafiltrated EV-depleted fetal bovine serum

value: Sigma-Aldrich


title: HCC827_par_b


title: LN_Memory_2

source_name: Memory CD4 T-Cells

value: Lymph Node

value: Memory CD4 T-Cells


title: BALB/c_96h post Af/12h post Ozone_4

description: Gene expression data

value: Balb/c

value: 96 hours after Af and 12 hours after ozone exposure


title: UC-dFBS-2

source_name: Ultracentrifugated EV-depleted fetal bovine serum extracellular vesicles


title: LN_Naive_1

source_name: Naive CD4 T-Cells

value: Na CD4 T-Cells


title: Lung_exTh17_3

source_name: ex-Th17 TRM Cells

value: ex-Th17 TRM Cells


title: SBI-dFBS-1

source_name: Commercial exosome-depleted fetal bovine serum extracellular vesicles

value: System Biosciences


title: BALB/c_96h post Af/12h post Ozone_6

description: Gene expression data

value: male

value: 7-8 weeks

value: whole lung homogenate


title: SBI-dFBS-2

value: EV

value: Commercial exosome-depleted fetal bovine serum


title: LN_Naive_2

value: Naive CD4 T-Cells


title: UC-dFBS-1

value: Ultracentrifugated EV-depleted fetal bovine serum


title: Lung_Th17_1

source_name: Th17 TRM Cells

value: Lung

value: Th17 TRM Cells

value: Immunization (Kp) 35 days prior


title: Lung_exTh17_2


title: BALB/c_96h post Af/12h post Ozone_5

description: Gene expression data


title: BALB/c_96h post Af/12h post Ozone_3

description: Gene expression data


title: Lung_YFP_Negative_1

value: YFP Negative TRM Cells


title: Lung_exTh17_1


title: RNAseq_ann_M_pd2_T

city: Ithaca

first: Karin

middle: Revka Loek

last: van der Burg

state: NY

address: 215 Tower Road, Corson Hall

department: EEB

institute: Cornell University

description: This RNA library was used solely for annotation purposes, so no quantitative analyses were done.

data_processing:
Alignment to junonia coenia genome using tophat.
Read counts overlapping genes were calculated with bedtools
Differential expression analysis was performed using DESeq2
Genome_build: jc.gen.v1
Supplementary_files_format_and_content: normalized bigwig files were produced using ucsc script
Read counts file (Gene IDs can be found online at lepbase.org)

organism: Junonia coenia

source_name: thorax

growth_protocol: Caterpillars and pupae were raised at ~27C

extract_protocol:
RNA was isolated from whole wing tissue and poly-A selected using NEB poly-A selection beads
Libraries were prepared using the NEB RNA library prep kit

tag: developmental stage

value: 2 days after pupation

value: thorax

tag: gender


title: FBS-2

source_name: Fetal bovine serum extracellular vesicles

value: Fetal bovine serum

value: Gibco


title: BALB/c_96h post Af/12h post Ozone_1

description: Gene expression data

value: Balb/c

tag: Sex

value: 96 hours after Af and 12 hours after ozone exposure


title: BALB/c_24h post Af/12h post air_3

description: Gene expression data

value: male

value: 24 hours after Af and 12 hours after air exposure


title: RNAseq_ann_F_pd2_T

value: female


title: BALB/c_24h post Af/12h post air_1

description: Gene expression data

value: 7-8 weeks

value: whole lung homogenate


title: OtB9337

value: Adipo-/-

value: lung

value: post natal day 32


title: BALB/c_12 hr Forced Air_4

description: Gene expression data

value: 12 hours after air exposure


title: BALB/c_24h post Af/12h post air_4

description: Gene expression data


title: BALB/c_12 hr Forced Air_6

description: Gene expression data


title: LN_Memory_1

value: Lymph Node

value: Memory CD4 T-Cells

value: Immunization (Kp) 35 days prior


title: FBS-1

value: EV

value: Sigma-Aldrich


title: RNAseq_ann_M_pd2_H

source_name: abdomen

value: 2 days after pupation

value: abdomen


title: RNAseq_ann_F_mel_A

value: melanin stage


title: BALB/c_12 hr Forced Air_3

description: Gene expression data

value: Balb/c

value: male


title: RNAseq_ann_M_mel_A

source_name: head

value: head


title: BALB/c_96h post Af/12h post Ozone_2

description: Gene expression data

value: 7-8 weeks

value: 96 hours after Af and 12 hours after ozone exposure


title: Control 3 [transcript-level]

city: Baltimore

first: Sean

last: Miller

address: 855 North Wolfe St.

institute: Johns Hopkins School of Medicine

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: cerebral cortex

growth_protocol: The care and treatment of animals is in accordance with the NIH Guide for the Care and Use of Laboratory Animals, the Guidelines for the Use of Animals in Neuroscience Research, and the Johns Hopkins University IACUC (protocol M14M089). Mice were housed at standard temperature and in light-controlled environment with ad libitum access to the food and water. No more than 5 mice were kept in a cage, in accordance with Johns Hopkins IACUC.

extract_protocol: Total RNA was isolated from FACS sorted populations using the RNA isolation kit (Qiagen) and the concentrations determined using Nanodrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent Technologies). Only samples with a RNA integrity score greater than 5 were used. Total RNA was lineally amplified and labeled in a NuGEN protocol.

treatment_protocol: SOD1 G93A ALS mice and controls were aged to P120. SOD1 G93A mice that displayed hindleg paralysis at P120 were used for this study. Fluorescent-activated cell sorting (FACS) was performed by first sacrificing mice with an intraperitoneal injection of ketamine xylazine. The entire cortex was immediately dissected and dissociated as previously described (Foo et al. 2011). Single cells were then sorted by using MoFlo high-speed cell sorter and gated based on eGFP fluorescence.

value: cerebral cortex

tag: hind-limb paralysis

value: normal

tag: phenotype

value: Control


title: RNAseq_ann_F_pd2_A

value: female


title: RNAseq_ann_M_mel_H


title: Control 2 [transcript-level]


title: RNAseq_ann_F_mel_H


title: BALB/c_24h post Af/12h post air_5

description: Gene expression data

tag: strain

value: whole lung homogenate

value: 24 hours after Af and 12 hours after air exposure


title: RNAseq_ann_eggs

source_name: embryos

value: RNA pooled from 2, 5, 12, 32 hours after oviposition

value: embryos


title: RNAseq_ann_F_mel_T

value: thorax


title: SOD1 ALS 3 [transcript-level]

tag: age

value: paralyzed

value: ALS


title: RNAseq_ann_F_pd2_H

value: 2 days after pupation


title: BALB/c_12 hr Ozone_3

description: Gene expression data

value: Balb/c

tag: treatment

value: 12 hours after ozone exposure


title: RNAseq_ann_M_mel_T

value: melanin stage

value: male


title: RNAseq_d7_HW_S1

source_name: whole wing tissue

value: 6 days after pupation

value: hindwing


title: RNAseq_d7_FW_S3

value: forewing


title: BALB/c_12 hr Forced Air_2

description: Gene expression data

value: 7-8 weeks

value: 12 hours after air exposure


title: RNAseq_d7_FW_S2


title: Control 1 [transcript-level]

value: cerebral cortex

value: normal

value: Control


title: 11752X6

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: 15 N Medical Dr.

institute: University of Utah

data_processing:
Reads were aligned to mm10 + splice junctions
Spliced alignments were converted back to genomic coordinates using USeq_8.8.8 SamTranscriptomeParser
Reads mapping uniquely to features were counted using USeq_8.8.8 DefinedRegionDifferentialSeq (DRDS)
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCm38 (mm10 from UCSC)
Supplementary_files_format_and_content: raw count table from DRDS

source_name: IFNγR KO 3

growth_protocol: 1x10^6 B16f10 tumor cells were injected into the flank of the indicated mice and after 12 days tumors were isolated, digested in accumax solution to obtain a single cell suspension and flow sorted based on the expression of CD11b and F480

extract_protocol: RNA was isolated with miRneasy mini kit, library was prepped.

treatment_protocol: Cells from 3 to 4 mice were pooled per sample, thus each indvidual sample is representative of cells aquired from 3 to 4 individual mice

value: tumor-associated macrophages (TAMs)

value: IFNgR KO

tag: cell markers


title: BALB/c_12 hr Forced Air_1

description: Gene expression data

source_name: whole lung homogenate

value: whole lung homogenate


title: RNAseq_d7_HW_S3


title: RNAseq_ann_larvae

source_name: whole larvae tissue

value: third instar

value: whole larvae tissue


title: SOD1 ALS 2 [transcript-level]

value: paralyzed

value: ALS


title: CH34S2_CH34_Ag_3

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Comparison of CH34S2 with CH34 in the presence of 1 µM AgNO3

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

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

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

organism: Cupriavidus metallidurans

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

growth_protocol: The strains were cultivated by inoculating 30 ml of MM284 in biological triplicates with 300 μL of a stationary phase culture at 30 °C. These subcultures were allowed to grow until an OD600 value of around 0.6 was reached. Next, cells were exposed to 1 µM AgNO3 for 30 min, harvested by centrifugation for 2 min at 10000 rpm and the bacterial pellets were flash frozen by immersion into liquid nitrogen.

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

treatment_protocol: 1 µM AgN03 for 30 min.

value: strain CH34 exposed to 1 microM AgNO3

value: wildtype

value: strain CH34S2 exposed to 1 microM AgNO3

value: CH34-derived evolved strain


title: RNAseq_d7_FW_S1

value: 6 days after pupation

value: forewing


title: CH34S1_CH34_Ag_2

description: Comparison of CH34S1 with CH34 in the presence of 1 µM AgNO3

value: strain CH34S1 exposed to 1 microM AgNO3


title: CH34S1_CH34_Ag_1


title: RNAseq_d7_HW_S2

value: hindwing


title: 11752X5

source_name: IFNγR KO 2


title: CH34S2_CH34_Ag_2


title: 11752X3

source_name: Wt 3

value: WT


title: 11752X4

source_name: IFNγR KO 1


title: CH34S2_CH34_Ag_1


title: RNAseq_72h_HW_S2

value: 72 hours after pupation


title: CH34S1_CH34_Ag_3


title: SOD1 ALS 4 [transcript-level]

value: cerebral cortex


title: BALB/c_168h post Af /12h post air_5

description: Gene expression data

value: Balb/c

value: male

value: 7-8 weeks

value: 168 hours after Af and 12 hours after air exposure


title: RNAseq_72h_FW_S3


title: RNAseq_72h_HW_S3


title: RNAseq_72h_HW_S1