title: CEMBA190108_6A_1_CEMBA190108_6A_2_B9_ad001


title: Len +EZH2i

status: Public on Feb 19 2021

type: SRA

city: Aarhus C

first: Theresa

last: Jakobsen

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

library_source: transcriptomic

data_processing:
Sequencing data were quality filtered (Phred score 20) and adapter trimmed using Trim Galore.
Filtered and trimmed sequencing reads were mapped to the human genome (HG19) using TopHat2.
CircRNA expression levels (sequencing reads aligning across particular backsplicing junctions) were quantified based on a stringent version of the find_circ bioinformatics algorithm 33, normalized to the total number of raw reads and communicated as reads per million (RPM).
Host gene expression levels were calculated as the average linear reads corresponding to the splice donor and splice acceptor sites of each circRNA in question, normalized to the total number of raw reads and communicated as reads per million (RPM).
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include Reads Per Million (RPM) and Circular-To-Linear ratio (CTL)

molecule: total RNA

organism: Homo sapiens

source_name: Multiple myeloma cell line

growth_protocol: Cells were grown in suspension at 37ºC and 5% CO2, and was maintained in RPMI-1640 GlutaMAX medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin, 1% sodium pyruvate and 0.05 mmol β-ME.

extract_protocol:
Total RNA were isolated from the cell lines using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s protocol
One microgram total RNA was rRNA depleted using the Ribo-Zero rRNA Removal Kit (Human, Mouse, Rat) (Epicentre Biotechnologies, Madison, WI, USA) according to the manufacturer's instructions followed by a purification step using AMPure XP Beads (Beckman Coulter, Brea, CA, USA). Sequencing libraries were generated using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) according to the manufacturer's instructions using 12 PCR cycles.

treatment_protocol: The Len res and pom res cells were established by continuous culture of NCI-H929 cells in the presence of low-dose lenalidomide or pomalidomide for 4–6 months 32. The pom res and len res cells were treated with different combinations of epi-drugs: the DNA methyl transferase inhibitor (DNMTi), 5-azacytidine, the histone deacetylase inhibitor (HDACi), Panobinostat, the Enhancer of zeste homolog 2 inhibitor (EZH2i), EPZ-6438, and a combination of DNMTi and EZH2i, for 48 hours.

tag: tissue

value: bone marrow

tag: cell type

value: B lymphocyte

tag: cell line

value: Multiple myeloma cell line

tag: treatment

value: treated with low-dose lenalidomide for 6 months + EPZ-6438 for 48h


title: cTEC_Eed_E6

city: Oxford

first: Adam

last: Handel

address: John Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
QC was performed using FastQC and Trimmomatic
RNA-seq reads were aligned using HISAT (version 0.1.6) and ChIP-seq peaks were pre-aligned using BWA (version 0.5.9) and Stampy (--bamkeepgoodreads)
Single cell RNA-seq outliers were identified using robust PCA on alignment proportion, ERCC92 spike-in proportion, number of detectable genes, proportion of reads mapping to protein-coding genes, proportion of mitochondrial transcripts, proportion of ribosomal transcripts, 3’ to 5’ coverage bias, transcriptomic variance, cell-to-mean correlation, the proportion of the library accounted for by the top 500 transcripts and GC content
RNA-seq reads were assigned to genes using HTSeq (intersection non-empty)
ChIP-seq bigWig profiles were generated using MACS2 on deduplicated BAM files with MAPQ >10
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include counts for RNA-seq samples and bigWig files show ChIP/input signal for ChIP-seq samples

molecule: polyA RNA

organism: Mus musculus

source_name: cTEC

extract_protocol:
Thymic lobes were cleaned from fatty tissues and incubated with Liberase and DNaseI (Roche Diagnostics; 200μg/ml and 30μg/ml, respectively; 45min, 37ºC) to obtain a cell suspension which was subsequently filtered through a nylon mesh (100micro pore size, Sefar Nitex) to remove debris. TEC were sorted and then RNA was either isolated from ~1,000 cells or single cells using the SMART-seq2 protocol. TEC for ChIP-seq were treated as detailed in Žuklys S et al. Nature Immunology 2016:17(10):1206-1215
RNA-seq libraries were prepared using the appropriate Illumina kit for SMART-seq2 or HiSeq2500 (ChIP-seq). Nextera adapters were used for single cell RNA-seq and ChIP-seq.

tag: strain

tag: sample type

value: single cell

tag: zsgreen status

value: negative


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B9_ad006

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B9_ad007


title: H929

value: Non-treated


title: Len +pan

value: treated with low-dose lenalidomide for 6 months + panobinostat for 48h


title: cTEC_Eed_E7


title: cTEC_Eed_E8


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B9_ad002


title: cTEC_Eed_E4


title: Calu3_Enriched_HV

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 201 S. University Street

institute: Purdue university

data_processing:
Sequencing reads were aligned as single end to the chimeric genome of human (hg38) and SARS-CoV2 (NC_045512.2) using STAR aligner (v2.7.7a) to get HVC junctions.
The gene expression was calculated by RSEM (v1.3.3).
Genome_build: hg38+SARS-CoV2(NC_045512.2) chimeric genome
Supplementary_files_format_and_content: *.genes.results.txt: Tab-delimited text files; RSEM genes.results files.

source_name: Calu-3 cells infected with SARS-CoV2 (USA-WA1/2020)

growth_protocol: Human adenocarcinomic lung epithelial (Calu-3) cells (ATCC, HTB-55) were cultured in Dulbecco’s Modified Eagle Medium (DMEM, GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, Corning), HEPES, non-essential amino-acids, L-glutamine and 1X Antibiotic-Antimycotic solution (Gibco). All cells were maintained at 37°C and 5% CO2.

extract_protocol:
Infected cells were lysed in TRIzol (Invitrogen) and RNA was extracted using Direct-zol RNA Miniprep kit (Zymo Research) as per manufacturer’s instructions.
The VSP pool contained ~30 oligonucleotides that span all SARS-CoV2 genes (at least one oligo per gene and nearly 1 oligo per 1kb of the genome). Given our goal to additionally enrich for potential HVC events, we used two approaches, enrichment methods 1 (5’->3’ host-virus chimeras) and enrichment method 2 (5’->3’ virus-host chimeras). First strand cDNA synthesis reaction: To capture and enrich for viral, virus-host or host-virus transcripts, we first set up a 20 µl reverse transcription (RT) reaction using 100 ng of mRNA isolated from SARS-CoV2 infected using Superscript III reverse transcriptase. We used 2 pmol T7-P5-VSP oligo pool (for enrichment 1) or 50 pmol of T7-P5-Oligo dT (for enrichment 2) as “gene-specific primer” for RT reaction. After combining all the components as per the recommended protocol (Thermo Fisher, Catalog# 18080044 and 18064014), we incubated the entire reaction mixture at 25°C for 15 minutes followed by 50°C for 30 minutes for SSIII. Next, we inactivated the reaction by heating at 70°C for 15 minutes. To remove RNA/complementary RNA to the cDNA, we added 1 µl of PureLink™ RNase A (20 mg/mL) (Invitrogen Catalog# 12091021) and 1 µl (5 units) of RNase H (abmgood catalog# E018) and incubated at 37°C for 1 hour. We then purified cDNA using 1X Mag-Bind TotalPure NGS (Omega Bio-tek, Catalog# M1378-01) as per manufacturer’s instructions and eluted the cDNA in 15 µl of sterile water. To further remove the excess single-stranded short oligos, we treated the purified RT reaction with 1 µl of Exonuclease I (NEB, Catalog# M0293L) at 37°C for 30 minutes. Next, we added excess sterile water to sample to get a total volume of 40 µl. The reaction was them purified with 1X Mag-Bind TotalPure NGS beads and eluted in 15 ul of sterile water. Second strand cDNA synthesis and In vitro Transcription: Following this, we performed second strand synthesis using the NEBNext Ultra II Non-Directional RNA second strand synthesis module as per the suggested protocol (NEB, Catalog# E6111L). The synthesized DNA was purified via 1X Mag-Bind TotalPure NGS beads and eluted in ~12 ul of sterile water. 10 ul of this was then used as an input for T7 polymerase mediated In vitro Transcription (IVT) using the NEB HiScribe T7 High Yield RNA Synthesis Kit (NEB, # E2040S). Briefly, all the components were mixed as mentioned in the kit protocol and incubated at 37°C (lid at 50°C) for 16 hours. The reaction was eluted in 20 µl of sterile water after a round of 1X Mag-Bind TotalPure NGS bead cleanup. This newly transcribed RNA was quantified using a Nanodrop and to improve the hybridization kinetics and enhance signal, 500ng of the amplified RNA was fragmented by RNA Fragmentation reagent in a total reaction volume of 10 µl as per specifications (Thermo Fisher, Catalog# AM8740). Final reverse transcription and PCR enrichment of the library: Next, to generate final enriched libraries, we performed reverse transcription of the fragmented RNA with 50 pmol of P7-N6 for enrichment (1) and 2 pmol of the P7-VSP primer pool for enrichment (2), respectively, using SSIII reverse transcriptase as per the steps mentioned above. After RT, the reaction mixture was purified using 1X Mag-Bind TotalPure NGS beads and eluted in 20 µl of sterile water. 5 µl of this RT reaction was saved for running on a Bioanalyzer and to perform a qRT-PCR validation assay. The remaining 15 µl was used to PCR amplify the library by using high-fidelity Q5 DNA Polymerase (NEB, Catalog# M0491L) for 16 cycles using Universal primer and unique indices (NEB Catalog# E7335L, E7500L) in a total of in a 50 µl reaction volume. Finally, the amplified and enriched library was purified using the 0.8X Mag-Bind TotalPure NGS beads, quantified by Bioanalyzer/Tape station and then sequenced using Illumina platform.

treatment_protocol: SARS coronavirus 2 (SARS-CoV-2), isolate USA-WA1/2020 (NR-52281) was obtained from Bei resources and was propagated in Vero E6 cells in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES. Infectious titers of SARS-CoV-2 were determined using TCID50 method (Reed and Muench). Fifty thousand Calu-3 were seeded in 48 well plate and allowed to form 80% confluent monolayer. SARS-CoV-2 virus was pre-treated with porcine trypsin (10ug/ml) for 15 minutes at 37 degrees. Cells were then infected with the pre-treated virus prep at a multiplicity of infection (MOI) of 10 for 1h in culture media (final concentration of trypsin on cells was 2ug/ml). After absorption, virus inoculum was removed and replaced with fresh culture media. 48hrs post infection, cells were harvested and RNA was isolated.

value: lung adenocarcinoma cells

tag: infection

value: SARS-CoV2 (USA-WA1/2020)

tag: moi

tag: hvc enrichment method

value: 5'->3' host-virus chimeras


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B9_ad004


title: cTEC_Eed_E5


title: Pom +pan

value: treated with low-dose pomalidomide for 6 months + panobinostat for 48h


title: Pom +AZA

value: treated with low-dose pomalidomide for 6 months + 5-azacytidine for 48h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B9_ad008


title: cTEC_Eed_E3


title: Pom +EZH2i +AZA

value: treated with low-dose pomalidomide for 6 months + EPZ-6438 + 5-azacytidine for 48h


title: cTEC_Eed_E24


title: Pom res

value: treated with low-dose pomalidomide for 6 months


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B8_ad010


title: cTEC_Eed_E23


title: cTEC_Eed_E22


title: Len +AZA

value: bone marrow

value: treated with low-dose lenalidomide for 6 months + 5-azacytidine for 48h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B8_ad006


title: cTEC_Eed_E20


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B8_ad002


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B8_ad004


title: Len res

value: B lymphocyte

value: Multiple myeloma cell line

value: treated with low-dose lenalidomide for 6 months


title: IFN siMettl3/14 RNA rep1

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

description:
RNA_M314_IFN_rep1
DEseq_RNA_siCTRLifn_vs_siMettl314ifn.txt
RNAseq_CTRL_IFN_vs_M314_IFN_countMatrix

data_processing:
Reads trimmed with Cutadapt 2.10
Trimmed Reads alignmed to hg38 with STAR 2.7.5
Fragments uniquely mapped to each gene counted with featureCounts
Count matrix was generated from featureCounts output with python script
DEseq was used to caluclate fold change of counts per gene between two conditions
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text files include log2FC

source_name: Huh7 cells

growth_protocol: Huh7 cells were grown at 37C with 5% CO2 in DMEM supplemented with 10% FBS, 1X minimum essential medium non-essential amino acids, and 25 mM HEPES

extract_protocol:
For RNA-seq, cells were harvested in TRIzol and RNA was extracted by manufacturer protocol, after which TURBO DNase treatment was performed and RNA was phenol-chloform precipitated. For Ribo-seq, cells were lysed in polysome lysis buffer and cytoplasmic lysates were clarified by centrifugation, then ribosome protected fragments were generated by micrococcal nuclease treatment. Monosome fractions were isolated by sucrose gradient ultracentrifugation, and RPF RNA was size-selected on TBE urea gels, eluted, T4 PNK treated, and phenol-chloform extracted.
For RNA-seq, libraries were prepared using the KAPA Stranded mRNA-Seq Kit. For Ribo-seq, libraries were prepared using the NEB Next Small RNA Library Prep Kit.

treatment_protocol: siRNAs were transfected for 36 hours using Lipofectamine RNAiMax, after which cells were treated with IFN-β at 50 units/mL or mock treatment

value: Interferon

tag: sirna


title: IFN siMettl3/14 RNA rep2

description:
RNA_M314_IFN_rep2
DEseq_RNA_siCTRLifn_vs_siMettl314ifn.txt
RNAseq_CTRL_IFN_vs_M314_IFN_countMatrix


title: IFN siMettl3/14 RNA rep3

description:
RNA_M314_IFN_rep3
DEseq_RNA_siCTRLifn_vs_siMettl314ifn.txt
RNAseq_CTRL_IFN_vs_M314_IFN_countMatrix


title: cTEC_Eed_E18

value: single cell

value: negative


title: cTEC_Eed_E19


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B8_ad012

value: ACA,PL,ILA

value: male


title: IFN siCTRL RNA rep2

description:
RNA_CTRL_IFN_rep2
DEseq_RNA_siCTRLifn_vs_siMettl314ifn.txt
DEseq_RNA_siCTRLmock_vs_siCTRLifn.txt
RNAseq_CTRL_IFN_vs_M314_IFN_countMatrix
RNAseq_CTRL_MOCK_vs_CTRL_IFN_countMatrix

value: siCTRL


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad001


title: CHD6wt_ChIPSeq_iPSC_Rep2

city: Cologne

first: Yulia

last: Kargapolova

address: Robert-Koch-Straße 21

department: CMMC

country: Germany

institute: Cologne University

data_processing:
ChIP-seq reads were aligned to the hg19 using BWA, reads with mapping quality below 10 were filtered out, duplicates were removed using Picard. Further the ENCODE black listed regions were removed from .bam files prior to peak calling.
peaks were called using MACS2 peak caller with the following arguments: -g hs -B -p 1e-3 --keep-dup 1 --bw=343 --slocal 8000
Genome_build: hg19
Supplementary_files_format_and_content: The Wig file is generated from the bedGraph file, using an in-house script that computes the extended read coverage at a user-defined step size (default: 20 bp). The extended read coverage is normalized to a library size of one million mapped reads, and converted into the TDF format using the toTDF command from the igvtools package (http://www.broadinstitute.org/software/igv/igvtools).

source_name: induced pluripotent stem cells

extract_protocol: For each batch of ChIP experiments ~12 million cells were crosslinked in 2% PFA for 45 min at 4°C. From this point onward, cells were processed via the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions, but using the NEXSON protocol for the isolation of nuclei [1]. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 20-26 cycles of 30s “on” and 30s “off”, at the highest power setting), and immunoprecipitations were carried out by adding 4 μg of the appropriate antiserum (CHD6, A301-221A Bethyl; TF3B, A303-673A Bethyl) to ~30 μg of chromatin and incubating on a rotator overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research) and used in qPCR or sequencing on a HiSeq4000 platform (Illumina).

value: CHD6 wild type

tag: passages


title: cTEC_Eed_E2


title: CHD6m.a.mut_ChIPSeq_iPSC_Rep2

value: CHD6 mutant monoallelic


title: cTEC_Eed_E16


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad006


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad012


title: CHD6het_ChIPSeq_iPSC_Rep2

value: CHD6 heterozyg. Mut


title: cTEC_Eed_E21


title: cTEC_Eed_E15


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B8_ad001


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad004


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad010


title: cTEC_Eed_E14


title: Mock siMettl3/14 rep2

description:
RNA_M314_Mock_rep2
DEseq_RNA_siCTRLmock_vs_siMettl314mock.txt
RNAseq_CTRL_MOCK_vs_M314_MOCK_countMatrix

value: Mock


title: IFN siCTRL RNA rep1

description:
RNA_CTRL_IFN_rep1
DEseq_RNA_siCTRLifn_vs_siMettl314ifn.txt
DEseq_RNA_siCTRLmock_vs_siCTRLifn.txt
RNAseq_CTRL_IFN_vs_M314_IFN_countMatrix
RNAseq_CTRL_MOCK_vs_CTRL_IFN_countMatrix


title: Mock siMettl3/14 rep3

description:
RNA_M314_Mock_rep3
DEseq_RNA_siCTRLmock_vs_siMettl314mock.txt
RNAseq_CTRL_MOCK_vs_M314_MOCK_countMatrix


title: cTEC_Eed_E13


title: cTEC_Eed_E17


title: Mock siMettl3/14 rep1

description:
RNA_M314_Mock_rep1
DEseq_RNA_siCTRLmock_vs_siMettl314mock.txt
RNAseq_CTRL_MOCK_vs_M314_MOCK_countMatrix


title: Mock siCTRL RNA rep3

description:
RNA_CTRL_Mock_rep3
DEseq_RNA_siCTRLmock_vs_siCTRLifn.txt
DEseq_RNA_siCTRLmock_vs_siMettl314mock.txt
RNAseq_CTRL_MOCK_vs_CTRL_IFN_countMatrix
RNAseq_CTRL_MOCK_vs_M314_MOCK_countMatrix


title: IFN siCTRL RNA rep3

description:
RNA_CTRL_IFN_rep3
DEseq_RNA_siCTRLifn_vs_siMettl314ifn.txt
DEseq_RNA_siCTRLmock_vs_siCTRLifn.txt
RNAseq_CTRL_IFN_vs_M314_IFN_countMatrix
RNAseq_CTRL_MOCK_vs_CTRL_IFN_countMatrix


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad007


title: Mock siCTRL RNA rep1

description:
RNA_CTRL_Mock_rep1
DEseq_RNA_siCTRLmock_vs_siCTRLifn.txt
DEseq_RNA_siCTRLmock_vs_siMettl314mock.txt
RNAseq_CTRL_MOCK_vs_CTRL_IFN_countMatrix
RNAseq_CTRL_MOCK_vs_M314_MOCK_countMatrix


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad001


title: cTEC_Eed_E11


title: Mock siCTRL RNA rep2

description:
RNA_CTRL_Mock_rep2
DEseq_RNA_siCTRLmock_vs_siCTRLifn.txt
DEseq_RNA_siCTRLmock_vs_siMettl314mock.txt
RNAseq_CTRL_MOCK_vs_CTRL_IFN_countMatrix
RNAseq_CTRL_MOCK_vs_M314_MOCK_countMatrix


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad006


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad002


title: Mock meRIP rep3

data_processing:
Reads trimmed with Trimmomatic
Reads aligned to hg38 with STAR
Counts per gene were counted with feature counts and differential expression calculated with DEseq2
m6A peaks were seperately called with MeTDiff and meRIPPer
Coverage plots were generated uing CovFuzze and motif enrichement was calculated using Homer
Genome_build: hg38
Supplementary_files_format_and_content: Log2FC and peak text files

extract_protocol:
Cells were harvested in TRIzol and RNA was extracted by manufacturer protocol. PolyA-tailed mRNA was selected using the Dynabeads mRNA Purification kit, and MeRIP-seq was performed using the NEB EpiMark m6A-enrichment kit.
Libraries were constructed using the Illumina TruSeq mRNA library prep kit.

treatment_protocol: Cells were treated with IFN-β or Mock treated for 8 hours prior to harvest.

tag: fraction

value: N6-methyladenosine (m6A)


title: cTEC_Eed_E10


title: cTEC_Eed_E12


title: cTEC_Eed_E1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad010


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad002


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad004


title: Mock meRIP rep2


title: cTEC_Eed_D8


title: Mock meRIP rep1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B6_ad008


title: cTEC_Eed_D9


title: cTEC_Eed_D7


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad012


title: Mock input rep3

value: input


title: Mock input rep2


title: cTEC_Eed_D4


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad001


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad007


title: Mock input rep1


title: cTEC_Eed_D3


title: Ifn meRIP rep3

description:
Table_S2.1_meRIPseq
Table_S2.2_meRIPseq_MeTDiff_peaks
Table_S2.3_meRIPseq_meRIPPer_peaks

value: IFN


title: Ifn meRIP rep2


title: cTEC_Eed_D24


title: Ifn meRIP rep1


title: cTEC_Eed_D23


title: cTEC_Eed_D22


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B7_ad008


title: Ifn input rep3


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad008


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad002


title: cTEC_Eed_D21


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B4_ad012


title: Ifn input rep2


title: cTEC_Eed_D20


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B4_ad001


title: Ifn input rep1


title: cTEC_Eed_D6


title: cTEC_Eed_D5


title: input_CM_het

data_processing:
ChIP-seq reads were aligned to the hg19 using BWA, reads with mapping quality below 10 were filtered out, duplicates were removed using Picard.
peaks were called using MACS2 peak caller with the following arguments: -f BAM -g hs -s 100 --keep-dup 1 -q 0.01 (for CHD6)
Genome_build: hg19
Supplementary_files_format_and_content: The Wig file is generated from the bedGraph file, using an in-house script that computes the extended read coverage at a user-defined step size (default: 20 bp). The extended read coverage is normalized to a library size of one million mapped reads, and converted into the TDF format using the toTDF command from the igvtools package (http://www.broadinstitute.org/software/igv/igvtools).

source_name: cardiomyocytes

value: CHD6 heterozygous mutant

tag: chip antibody


title: input_CM_wt


title: cTEC_Eed_D2


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B4_ad010


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B4_ad007


title: CHD6het_ChIPSeq_CM_2

value: A301-221 Bethyl CHD6


title: cTEC_Eed_D19


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad010


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B5_ad006


title: cTEC_Eed_D18


title: CHD6wt_ChIPSeq_CM_2


title: cTEC_Eed_D16


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B4_ad006


title: cTEC_Eed_D17


title: mutant NCC [82742]

description:
polyA-enriched total RNA-Seq
K002000198_82742

data_processing:
Sequenced reads were mapped with STAR v2.2.2a with parameters --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4  --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were mapped to exons were counted by htseq-count using the following parameters: minimum alignment 30
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts (output of htseq-count), bigWig files (strand-specific), raw fastq files.

source_name: iPS derived neural crest cells

extract_protocol:
Cells from different genotypes/differentiations were harvested in Trizol (Life Technologies) and total RNA was isolated and DNase-treated using the Direct-zol RNA miniprep kit as per manufacturer’s instructions (Zymo Research). In the case of cardiomyocytes, cells at D10-D11 of differentiation were used, while in the case of NCCs, cells were obtained by collecting migratory cells from dissected and re-plated rosettes.
polyA-enriched RNA libraries were prepared for sequencing using standard Illumina protocols

value: neural crest cells derived from monoallelic CHD6 mutant iPS cells

value: p 2

tag: genotype

value: monoallelic CHD6 mutant


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B3_ad012


title: mutant NCC [82740]

description:
polyA-enriched total RNA-Seq
K002000198_82740

tag: cell type


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B4_ad004


title: cTEC_Eed_D15

value: single cell


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B3_ad007


title: cTEC_Eed_D14

value: negative


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B3_ad010

value: ACA,PL,ILA


title: cTEC_Eed_D13


title: cTEC_Eed_D12


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B3_ad004

value: male


title: patient NCC [91758]

description:
polyA-enriched total RNA-Seq
K002000258_91758

value: neural crest cells derived from patient iPS cells

value: patient (heterozygously mutated CHD6)


title: WT NCC [82738]

description:
polyA-enriched total RNA-Seq
K002000198_82738

value: neural crest cells derived from wild type iPS cells

value: wild type


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B3_ad002


title: WT NCC [82736]

description:
polyA-enriched total RNA-Seq
K002000198_82736


title: cTEC_Eed_D11


title: cTEC_Eed_D10


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad001


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B3_ad008


title: cTEC_Eed_C9


title: MUT CM [91762]

description:
polyA-enriched total RNA-Seq
K002000258_91762

source_name: iPS derived cardiomyocytes

value: cardiomyocytes derived from monoallelic CHD6 mutant iPS cells


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad010


title: patient CM [94782]

description:
polyA-enriched total RNA-Seq
K002000269_94782

value: cardiomyocytes derived from patient iPS cells


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad006


title: MUT CM [77339]

description:
polyA-enriched total RNA-Seq
K002000171_77339


title: cTEC_Eed_C7


title: WT CM [77329]

description:
polyA-enriched total RNA-Seq
K002000171_77329

value: cardiomyocytes derived from wild type iPS cells


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad004


title: cTEC_Eed_D1


title: patient CM [94781]

description:
polyA-enriched total RNA-Seq
K002000269_94781


title: cTEC_Eed_C6


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad007


title: cTEC_Eed_C5


title: TFEB_iPSC_CHD6m

data_processing:
ChIP-seq reads were aligned to the hg19 using BWA, reads with mapping quality below 10 were filtered out, duplicates were removed using Picard.
peaks were called using MACS2 peak caller with the following arguments: -f BAM -g hs -s 100 --keep-dup 1 -q 0.01 (for CHD6) and -q 0.005 (for TFEB)
Genome_build: hg19
Supplementary_files_format_and_content: The Wig file is generated from the bedGraph file, using an in-house script that computes the extended read coverage at a user-defined step size (default: 20 bp). The extended read coverage is normalized to a library size of one million mapped reads, and converted into the TDF format using the toTDF command from the igvtools package (http://www.broadinstitute.org/software/igv/igvtools).

growth_protocol: iPSCs were cultured in FTDA media

extract_protocol:
For each batch of ChIP experiments ~12 million cells were crosslinked in 2% PFA for 45 min at 4°C. From this point onward, cells were processed via the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions, but using the NEXSON protocol for the isolation of nuclei [1]. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 20-26 cycles of 30s “on” and 30s “off”, at the highest power setting), and immunoprecipitations were carried out by adding 4 μg of the appropriate antiserum (CHD6, A301-221A Bethyl; TF3B, A303-673A Bethyl) to ~30 μg of chromatin and incubating on a rotator overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research) and used in qPCR or sequencing on a HiSeq4000 platform (Illumina).
For each batch of ChIP experiments ~12 million cells were crosslinked in 2% PFA for 45 min at 4°C. From this point onward, cells were processed via the ChIP-IT High Sensitivity kit (Active motif) as per manufacturer’s instructions, but using the NEXSON protocol for the isolation of nuclei [1]. Chromatin was sheared to 200-500 bp fragments on a Bioruptor Plus (Diagenode; 2x 20-26 cycles of 30s “on” and 30s “off”, at the highest power setting), and immunoprecipitations were carried out by adding 4 μg of the appropriate antiserum (CHD6, A301-221A Bethyl; TF3B, A303-673A Bethyl) to ~30 μg of chromatin and incubating on a rotator overnight at 4°C in the presence of protease inhibitors. Following addition of protein A/G agarose beads and washing, DNA was purified using the ChIP DNA Clean & Concentrator kit (Zymo Research) and used in qPCR or sequencing on a HiSeq4000 platform (Illumina).

value: CHD6 mutant monoallelic

value: A303-673A Bethyl TFEB


title: Input_CM

value: iPSC-derived cardiomyocytes


title: patient NCC [91760]

description:
polyA-enriched total RNA-Seq
K002000258_91760


title: cTEC_Eed_C4


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad002


title: cTEC_Eed_C3


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B2_ad008


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad012


title: cTEC_Eed_C24


title: cTEC_Eed_C8


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad010


title: cTEC_Eed_C23


title: CHD6m.a.mut_ChIPSeq_CM

value: iPSC-derived cardiomyocytes CHD6 mutant monoallelic

value: A301-221 Bethyl CHD6


title: CHD6wt_ChIPSeq_CM

value: iPSC-derived cardiomyocytes CHD6 wild type


title: WT CM [77331]

description:
polyA-enriched total RNA-Seq
K002000171_77331


title: cTEC_Eed_C22

value: single cell


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad007


title: cTEC_Eed_C21

value: negative


title: CHD6m.a.mut_ChIPSeq_NCC

source_name: neural crest cells

value: iPSC-derived neural crest cells CHD6 mutant monoallelic


title: CHD6pat_ChIPSeq_NCC

value: iPSC-derived neural crest cells CHD6 mutant heterozygous (patient)


title: cTEC_Eed_C20


title: cTEC_Eed_C2


title: CHD6wt_ChIPSeq_NCC

value: iPSC-derived neural crest cells CHD6 wild type


title: Input_NCC

value: iPSC-derived neural crest cells


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad001

value: ACA,PL,ILA

value: male


title: cTEC_Eed_C19


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad007


title: CHD6pat_ChIPSeq_iPSC

value: CHD6 patient


title: CHD6m.a.mut_ChIPSeq_iPSC


title: cTEC_Eed_C17


title: Input_iPSC

value: CHD6 wild type


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad008


title: CHD6wt_ChIPSeq_iPSC


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad010


title: S45

data_processing:
Sequenced reads were mapped with STAR v2.2.2a with parameters --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4  --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were mapped to exons were counted by htseq-count using the following parameters: minimum alignment 30
Genome_build: hg19
Supplementary_files_format_and_content: raw read counts (output of htseq-count), bigWig files (strant-specific)

source_name: iPSCs_heterozygous mutant_etoposide

growth_protocol: iPS cells were grown in FTDA medium as previously described by Frank et al. 2012.

extract_protocol:
Total RNA was isolated using  Direct-Zol RNA purification kit (Zymo Research) as recommended by manufacturer.
3'-endRNA libraries were prepared for sequencing using Lexogen QuantSeq 3' mRNA-Seq kit

treatment_protocol: For starvation cells were treated 2 hour with medium containing DMEM F12, FGF, TGFß,human activin A at the concentration as in FTDA, but lacking insulin, transferin, selenous acid, lipids and human serum albumin. Etoposide treatment was performed for 2 hours with 30 uM etoposide.

value: induced pluripotent stem cells (iPSCs)

tag: passage

value: heterozygous mutant

value: etoposide


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad004


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad008


title: cTEC_Eed_C16


title: cTEC_Eed_C15


title: S43

source_name: iPSCs_heterozygous mutant_starvation

tag: treatment

value: starvation


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B12_ad002

tag: strain


title: S44


title: S42


title: cTEC_Eed_C13

tag: sample type


title: cTEC_Eed_C14

tag: zsgreen status


title: cTEC_Eed_C12


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad004

tag: brain region


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad012

tag: Sex


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad002

tag: age


title: S39

source_name: iPSCs_monoallelic mutant 1_etoposide

value: monoallelic mutant 1


title: cTEC_Eed_C11


title: cTEC_Eed_C18


title: S38


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad010


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad008


title: cTEC_Eed_C10


title: cTEC_Eed_B9


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad007


title: S35

source_name: iPSCs_wild type_etoposide

value: wild type


title: S36

source_name: iPSCs_monoallelic mutant 1_starvation


title: cTEC_Eed_C1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B11_ad006


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad006


title: S34


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad004


title: S32

source_name: iPSCs_wild type_starvation


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad002


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B10_ad001


title: S33


title: cTEC_Eed_B8


title: cTEC_Eed_B6


title: cTEC_Eed_B5


title: S31

source_name: iPSCs_heterozygous mutant_control

value: none (normal condition)


title: S30


title: cTEC_Eed_B24

value: single cell


title: cTEC_Eed_B4

value: negative


title: S28

source_name: iPSCs_monoallelic mutant 2_control

value: monoallelic mutant 2


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad001


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad007


title: S37


title: S27

source_name: iPSCs_monoallelic mutant 1_control


title: cTEC_Eed_B7

source_name: cTEC


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: S26


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad004


title: cTEC_Eed_B23


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad010


title: S25

source_name: iPSCs_wild type_control


title: cTEC_Eed_B21


title: cTEC_Eed_B22


title: cTEC_Eed_B3


title: cTEC_Eed_B2


title: cTEC_Eed_B20


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad008


title: S24


title: S29


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_B1_ad002


title: HOC313-LM si-NC

type: RNA

city: Tokyo

first: Tomoki

last: Muramatsu

address: 1-5-45 Yushima Bunkyo-ku

department: Medical research institute

country: Japan

institute: Tokyo Medical and Dental University

description: Dish culture

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-107) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
processed data files include normalized signal intensity. Two normalizations were performed:1) Pita vs NC in all cell lines, and 2) Pita, si-GGPS1#2, NC, si-NC in HOC313-LM cells.

source_name: HOC313-LM si-NC 72 h after treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HOC313-LM, KYSE150 and KYSE200 were maintained in appropriate media, D-MEM or RPMI-1640 medium supplemented with 10% fetal bovine serum or 10% exosome depleted FBS .

extract_protocol: RNA fractions from whole cell were prepared using TRIsure (BIOLINE,London, UK) following the manufacturer's recommendations. RNAs were quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: HOC313-LM, KYSE150 and KYSE200 cells were treatment of pitavastatin (1 µM) or control solvent (NC) for 72 hours. HOC313-LM cells were transfected with si-NT and si-GGPS1 for 72 hours.

value: Oral squamous cell carcinoma

tag: cell line

value: si-NT control


title: cTEC_Eed_B18


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad001


title: KYSE200 Pitavastatin

description: Dish culture

source_name: KYSE200 Pitavastatin 72 h after treatment

value: Esophageal squamous cell carcinoma

value: Pitavastatin


title: KYSE200 NC

description: Dish culture

source_name: KYSE200 NC 72 h after treatment

value: control solvent


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad007

value: ACA,PL,ILA

value: male


title: KYSE150 Pitavastatin

description: Dish culture

source_name: KYSE150 Pitavastatin 72 h after treatment


title: cTEC_Eed_B16


title: cTEC_Eed_B17


title: HOC313-LM si-GGPS1 #2

description: Dish culture

source_name: HOC313-LM si-GGPS1 #2 72 h after treatment


title: KYSE150 NC

description: Dish culture

source_name: KYSE150 NC 72 h after treatment


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad006


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad008


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad010


title: cTEC_Eed_B15


title: MDCK infection rep1 - 12h total RNA

city: Minneapolis

first: Wei-Shou

last: Hu

state: MN

address: 421 Washington Ave. SE

institute: University of Minnesota

description:
PR8_infection_FPKM.xlsx
PR8_t1_12

data_processing:
All the raw RNA-Seq reads were first trimmed off adapters and removed low-quality bases by Trimmomatic and checked for quality using FASTQC
All the trimmed reads with a minimum read length of 38bp and average quality per base higher than 30 were mapped into the combined genome of host+IAV by STAR v2.5.3a
The expression level of all the genes, including host and viral genes, were quantified by Cufflinks
Genome_build: CanFam3.1 for MDCK cells, GRCh38.p13 for A549 cells, and NCBI Taxon ID 211044 for IAV PR/8/34
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism:
Canis lupus familiaris
Influenza A virus (A/Puerto Rico/8/1934(H1N1))

source_name: MDCK cells

growth_protocol: Madin-Darby canine kidney (MDCK) and Human lung adenocarcinoma epithelial A549 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS. Recombinant A/Puerto Rico/8/34 (H1N1) was rescued by plasmid-based transfection, plaque purified and propagated in embryonic chicken eggs.  The single-cycle virus (Delta-HA and Delta-PB1) were created by replacing the coding sequence of HA and PB1 by mCherry and amplified in MDCK cells engineered to express HA and PB1, respectively. Viral titers were determined by plaque assay in MDCK cells.

extract_protocol:
MDCK total RNA were extracted using RNeasy Mini Kit (QIAGEN). A549 total RNA were extracted using TRIzol.
MDCK cDNA libraries were prepared using the Clontech Pico SMARTer Stranded Total RNA-Seq kit v2. For the third MDCK infection, the RNA was also prepped by Illumina TruSeq Stranded mRNA Rrep kit to isolate mRNA only. A549 cDNA libraries were prepared using the Stranded Total RNA v2 PicoMammalian kit (Takara).

treatment_protocol: MDCK cells were infected with IAV PR8 (MOI =0.5) and incubated at 4ºC for 30 minutes to allow for the virus to adsorb to the cell surface but not to enter the cytosol. Synchronized IAV infection was initiated by shifting the temperature to 37ºC. Infections with single-cycle viruses (Delta-HA and Delta-PB1) were performed in A549 cells in infection media at an MOI of 1. Infections were also synchronized at 4ºC for 30 minutes then incubated at 37ºC.

value: immortalized kidney epithelial cells

value: MDCK

value: single-cycle infection of IAV PR/8/34, 12h


title: cTEC_Eed_B19


title: HOC313-LM Pitavastatin

description: Dish culture

source_name: HOC313-LM Pitavastatin 72 h after treatment


title: cTEC_Eed_B14


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad004


title: cTEC_Eed_B11


title: MDCK infection rep1 - 6h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t1_6

value: single-cycle infection of IAV PR/8/34, 6h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A9_ad002


title: cTEC_Eed_B12


title: cTEC_Eed_B13


title: cTEC_Eed_B10


title: cTEC_Eed_B1


title: HOC313-LM NC

description: Dish culture

source_name: HOC313-LM NC 72 h after treatment


title: MDCK infection rep1 - 8h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t1_8

value: single-cycle infection of IAV PR/8/34, 8h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad006


title: cTEC_Eed_A9


title: MDCK infection rep1 - 2h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t1_2

value: single-cycle infection of IAV PR/8/34, 2h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad007


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad001


title: MDCK infection rep1 - 0h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t1_0

value: single-cycle infection of IAV PR/8/34, 0h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad002


title: cTEC_Eed_A8

value: single cell


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad004


title: MDCK infection rep1 - 4h total RNA

description:
PR8_infection_FPKM.xlsx
PR8_t1_4

value: single-cycle infection of IAV PR/8/34, 4h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A8_ad008


title: cTEC_Eed_A7

value: negative


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad012


title: cTEC_Eed_A6


title: cTEC_Eed_A5


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad001


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad007


title: cTEC_Eed_A4


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad006


title: cTEC_Eed_A3


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad004


title: cTEC_Eed_A24


title: cTEC_Eed_A23


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad002


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A7_ad008


title: 3D-bioprinted INS-1 cells R2

city: Heidelberg

first: Gabriel

middle: Alexander

last: Salg

address: Im Neuenheimer Feld 420

department: General-, Visceral-, and Transplantation Surgery

institute: University Hospital Heidelberg

data_processing:
Quality control performed with FastQC v0.11.8
Obtained reads were pseudoaligned using the rn4 reference genome in addition with the human insulin gene and quantified by Salmon v1.2 with standard parameters
Genome_build: rn4 + human insulin gene
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Rattus norvegicus

source_name: INS-1 832/3 rat insulinoma cell line

growth_protocol: INS-1 cells and bioprinted INS-1 cells were cultivated in RPMI-1640 (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco), 1% Geneticin (Merck, Darmstadt, Germany), 1% HEPES 1M (Gibco), 1% sodium pyruvate 100 mM (Merck) and 0.1% 2-mercaptoethanol (Merck). Cells were grown at 37 °C and 5% CO2.

extract_protocol:
After 5 days in culture total RNA was isolated from 2D monolayer culture and 3D hydrogel culture group using an RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions (biological replicates, passage 3).  After isolation, the total RNA was treated with the Turbo DNAfree kit according to the manufacturer’s instructions (Thermo Fisher Scientific). The RNA concentration and quality were evaluated by Nanodrop and Agilent2000 Bioanalyzer.
RNAseq libraries were prepared using the TruSeq stranded mRNA kit. The RNAseq libraries were sequenced using an Illumina NextSeq 500 platform, resulting in 75bp single end reads

treatment_protocol: 3D-bioprinting of cells in GelXA LAMININK 411 hydrogel (CellInk, Gothenburg, Sweden) vs. cells seeded for standard 2D-culture as control

tag: hydrogel matrix

value: GelXA LAMININK 411 hydrogel

tag: culture method

value: 3D-bioprinted, 3D-culture


title: 3D-bioprinted INS-1 cells R1


title: 2D-monolayer INS-1 culture R2

value: standard monolayer culture


title: 2D-monolayer INS-1 cells R1


title: cTEC_Eed_A21


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad012


title: cTEC_Eed_A20


title: Aged brain, EMF+AuNPs

city: Seoul

first: Jongpil

last: Kim

address: 30, Pildong-ro 1-gil

country: South Korea

institute: Dongguk university

data_processing:
The 10X Genomics CellRanger v3.0.2 software was used to analyze all datasets.
Fastq files were mapped and aligned to the mouse genome (mm10) with the STAR software using all default options.
Genome_build: mm10
Supplementary_files_format_and_content: barcode.tsv, matrix.mtx, features.tsv

source_name: Hippocampus

growth_protocol: All mice were maintained on a 12h/12h light/dark cycle (lights on at 9:00 am) and a 23±1 °C room temperature with free access to food and water. All experiments were approved by and performed in accordance with the Animal Care Committee of Dongguk University.

extract_protocol:
Tissue dissection and single-cell dissociation were carried out as described by Worthington’s manual protocol. Briefly, mice were euthanized with avertin, after which the hippocampus was isolated. The small pieces of tissue were placed in a papain solution and incubated in a 37 °C water bath for 30 min. The suspension was gently shaken every 15 min during the incubation period. Then, gentle trituration was performed to obtain a single-cell suspension, after which the papain was inactivated with an albumin-ovomucoid inhibitor solution. Single cells dissociated from the hippocampus were suspended in 0.5% BSA/PBS and counted in a LunaTM automated fluorescence cell counter using trypan blue.
The 10X library construction protocol was followed without alteration. Single cell cDNA libraries from individual cells were pooled and sequenced on a HiSeq 4000 sequencer (average depth: 50,000 reads/cells).
single cell RNA-Seq

treatment_protocol: Male C57BL/6 mice were used. For the surgery, the mice were anesthetized with avertin and placed in a stereotaxic frame, after which the AuNPs were injected into the hippocampus at fixed coordinates [anteroposterior (AP): -2.18 mm, mediolateral (ML): ± 1.2 mm, dorsoventral (DV): -2 mm] for 4 min at a 0.5 μl min-1 rate using a 26-gauge 10 μl Hamilton syringe. The mice were then placed in the middle of a pane between two coils at 3 weeks exposure. One pair of Helmholtz coils was used for both the control and AuNPs groups with EMF exposure.

value: 6 month

tag: tissue

value: Brain (Hippocampus)

value: EMF+AuNPs


title: Naïve_ChIP-Seq_WT_noFOXO1Ab_input

first: Stephen

middle: M.

last: Hedrick

address: 9500 Gilman Drive

department: Biology

institute: UC San Diego

description:
FOXO1 ChIP-seq
nCD8.FOXO1.tbp.ucsc.bedGraph.gz

data_processing:
ChIP-seq: Galaxy Server;  FASTQ groomer->Trim-galore->FASTQC->Bowtie2 mapping of reads to mm10->MACS2 peak calling ->HOMER2 nearest gene assignment and peak analysis
RNA-seq: Galaxy server; FASTQ groomer->FASTQC->HISAT2 to refseq mm10 -> Cuffdiff2 to gene expression.
ATAC-seq: Bowtie2->MACS2 peak calling-> HOMER transcription motif finding within peaks.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: Excel file with gene abundances, ATAC-seq & ChIP-seq: bedgraph

source_name: Virus-peptide-specfic CD8 T cell (P14)

growth_protocol: 1x10^4 P14 T cells were adoptively transferred into host mice.

extract_protocol: FOXO1 ChIP-seq was performed as before with minor modifications (Lin et al., 2010). Briefly, 3 x 107 T cells were fixed for 5 to 10 minutes at room temp in 1% formaldehyde then resuspended in lysis buffer. Following adaptor ligation, the DNAs were size selected (200-300bp) by 8% PAGE and index primers added by PCR. Samples were purified by 8% PAGE and precipitated with ethanol.

treatment_protocol: Host mice were infected with LCMV-ARM 2x10^5 pfu ip one day after P14 adoptive transfer. P14 T cells were isolated at indicated day by MACS selection on congenic marker.

value: P14 T cells

tag: time

tag: condition

value: naive

value: WT

value: no Foxo1 Ab (input control)


title: d12_ChIP-Seq_WT_plusFOXO1Ab

description:
FOXO1 ChIP-seq
d12CD8.FOXO1.tbp.ucsc.bedGraph.gz

value: post-infection

tag: chip antibody

value: with FOXO1 Ab


title: d12_ChIP-Seq_WT_noFOXO1Ab_input

tag: genotype


title: ka120 ndr1_rep3

city: Berkeley

first: Yangnan

last: Gu

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Raw and normalized counts for each sample in .xlsx format

organism: Arabidopsis thaliana

source_name: ka120 ndr1_3 wks_rosette leaves

growth_protocol: Arabidopsis plants were grown in soil at 22C under a 16h light /8h dark cycle

extract_protocol:
Total RNA was extracted from about 50 mg samples of three-week-old rosette leaves using RNAprep pure Plant Kit (TIANGEN Biotech, Cat. # DP432).
mRNA-Seq (Strand-Specific)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: ecotype background

value: ka120 ndr1

value: three-week-old

value: rosette leaves


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad007

value: ACA,PL,ILA

value: male


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad001


title: Aged brain, Control

value: Saline


title: cTEC_Eed_A2

value: single cell

value: negative


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad006


title: ka120 ndr1_rep2


title: SE-14000 stimulated Human Microvascular Endotheilal Cells vs. sham 3

city: bunkyo

first: Masayo

last: Aoki

state: tokyo

address: 1-1-5 Sendagi

department: Plastic Surgery

institute: Nippon Medical School

description: Biological replicate 3 of 3. Control Human Microvascular Endotheilal Cells, sham-treated, harvested after several passages.

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies Microarray Scanner SureScan G4900DA at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 11.5.1.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Human Microvascular Endotheilal Cells

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: cells were kept in medium with 2% Fetal calf serum

extract_protocol: Total RNA extracted using RNeasy Mini Kit following manufacturer's instructions

treatment_protocol: cells were stimulated with 14000V, 90Hz for 6 hours using SE-14000

value: HMEC-1 (ATCC® CRL-3243™)


title: cTEC_Eed_A18

data_processing:
QC was performed using FastQC and Trimmomatic
RNA-seq reads were aligned using HISAT (version 0.1.6) and ChIP-seq peaks were pre-aligned using BWA (version 0.5.9) and Stampy (--bamkeepgoodreads)
Single cell RNA-seq outliers were identified using robust PCA on alignment proportion, ERCC92 spike-in proportion, number of detectable genes, proportion of reads mapping to protein-coding genes, proportion of mitochondrial transcripts, proportion of ribosomal transcripts, 3’ to 5’ coverage bias, transcriptomic variance, cell-to-mean correlation, the proportion of the library accounted for by the top 500 transcripts and GC content
RNA-seq reads were assigned to genes using HTSeq (intersection non-empty)
ChIP-seq bigWig profiles were generated using MACS2 on deduplicated BAM files with MAPQ >10
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include counts for RNA-seq samples and bigWig files show ChIP/input signal for ChIP-seq samples

source_name: cTEC


title: SE-14000 stimulated Human Microvascular Endotheilal Cells vs. sham 2

description: Biological replicate 2 of 3. Control Human Microvascular Endotheilal Cells, sham-treated, harvested after several passages.


title: Naïve_ChIP-Seq_WT_plusFOXO1Ab

tag: cell type


title: cTEC_Eed_A22


title: SE-14000 stimulated Normal Human Dermal Fibroblasts vs. sham 3

description: Biological replicate 3 of 3. Control Normal Human Dermal Fibroblasts, sham-treated, harvested after several passages.

source_name: Normal Human Dermal Fibroblasts

value: Normal Human Dermal Fibroblasts TAKARA C-12302

tag: treatment


title: SE-14000 stimulated Normal Human Dermal Fibroblasts vs. sham 1

description: Biological replicate 1 of 3. Control Normal Human Dermal Fibroblasts, sham-treated, harvested after several passages.


title: SE-14000 stimulated Human Microvascular Endotheilal Cells vs. sham 1

description: Biological replicate 1 of 3. Control Human Microvascular Endotheilal Cells, sham-treated, harvested after several passages.


title: cTEC_Eed_A16

tag: strain


title: ka120 pad4_rep2

source_name: ka120 pad4_3 wks_rosette leaves

value: ka120 pad4


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad004

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain


title: d7klrg1hi_ATAC_FOXO1KO

description:
ATAC-seq
d7.KO.Khi.mm10.ucsc.bedGraph.gz

extract_protocol: Genome-wide measurement of chromatin accessibility and computational alignment of generated data were performed using ATAC-Seq as described (Buenrostro et al., 2013) on 10,000 Naive CD8+ T cells and P14 KLRG1hi or KLRG1low Foxo1 KO and WT at indicated days LCMV-ARM infection.

value: P14 T cells


title: ka120 ndr1_rep1


title: d7klrg1lo_ATAC_FOXO1KO

description:
ATAC-seq
d7.KO.Klo.mm10.ucsc.bedGraph.gz


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad012


title: cTEC_Eed_A17

extract_protocol:
Thymic lobes were cleaned from fatty tissues and incubated with Liberase and DNaseI (Roche Diagnostics; 200μg/ml and 30μg/ml, respectively; 45min, 37ºC) to obtain a cell suspension which was subsequently filtered through a nylon mesh (100micro pore size, Sefar Nitex) to remove debris. TEC were sorted and then RNA was either isolated from ~1,000 cells or single cells using the SMART-seq2 protocol. TEC for ChIP-seq were treated as detailed in Žuklys S et al. Nature Immunology 2016:17(10):1206-1215
RNA-seq libraries were prepared using the appropriate Illumina kit for SMART-seq2 or HiSeq2500 (ChIP-seq). Nextera adapters were used for single cell RNA-seq and ChIP-seq.

tag: sample type


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad002

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: SE-14000 stimulated Normal Human Dermal Fibroblasts vs. sham 2

description: Biological replicate 2 of 3. Control Normal Human Dermal Fibroblasts, sham-treated, harvested after several passages.


title: SE-14000 stimulated Human keratinocyte cells vs. sham 3

description: Biological replicate 3 of 3. Control Human keratinocyte cells, sham-treated, harvested after several passages.

source_name: Human keratinocyte cells

value: HaCaT (Human keratinocyte cell line, cryopreserved in CM-2)


title: Naïve_ATAC_FOXO1KO

description:
ATAC-seq
d0.KO.mm10.ucsc.bedGraph.gz

value: naive


title: ka120 pad4_rep3


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A6_ad008


title: cTEC_Eed_A19

tag: zsgreen status


title: SE-14000 stimulated Human keratinocyte cells vs. sham 2

description: Biological replicate 2 of 3. Control Human keratinocyte cells, sham-treated, harvested after several passages.


title: cTEC_Eed_A13


title: cTEC_Eed_A12


title: d7klrg1lo_ATAC_WT

description:
ATAC-seq
d7.WT.Klo.mm10.ucsc.bedGraph.gz

value: WT


title: cTEC_Eed_A14


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad006

tag: brain region


title: d12klrg1hi_RNA_WT

description:
RNA-seq
WT_FOXO1KO_RNA-seq_gene_expression.xlsx

extract_protocol: Strand-specific RNA-seq libraries were prepared according to Wang et al. with minor modifications: "A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq." PLoS ONE, 2011 CD4+ cells were re-isolated from the culture using the Miltenyi MACS system.


title: d7klrg1hi_ATAC_WT

description:
ATAC-seq
d7.WT.Khi.mm10.ucsc.bedGraph.gz


title: ka120_rep1

source_name: ka120_3 wks_rosette leaves


title: cTEC_Eed_A11


title: ka120_rep3


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad001

tag: Sex


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad004

tag: age


title: cTEC_Eed_A10


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad002


title: d7klrg1hi_RNA_WT


title: cTEC_Eed_A1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad008


title: Naïve_ATAC_WT

description:
ATAC-seq
d0.WT.mm10.ucsc.bedGraph.gz


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A5_ad010


title: SE-14000 stimulated Human keratinocyte cells vs. sham 1

description: Biological replicate 1 of 3. Control Human keratinocyte cells, sham-treated, harvested after several passages.

tag: cell line


title: ka120_rep2


title: d12klrg1hi_RNA_FOXO1KO


title: cTEC_Eed_A15


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad012


title: d7klrg1lo_RNA_WT


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad010


title: Oil plus hypoxia 2

city: Florence

first: Elizabeth

middle: R.

last: Jones

state: SC

address: 4822 E. Palmetto St.

institute: Francis Marion University

data_processing:
Bases Called using Illumina HiSeq Control Software
Initial processing of data was performed using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany).  Adaptor sequences and low quality reads were trimmed, paired ends matched, and reads aligned to the C. variegatus genome
Differentially methylated regions were identified using the MEDIPS R package (v 1.34).
To calculate differential methylation, the C. variegatus genome was divided into consecutive 100 bp windows, and read depth for each window compared between control and treatment samples.
The edgeR Bonferroni adjusted p-value was used to identify differential read coverage between groups; regions were considered differentially methylated at edgeR p adj. of £ 0.1
Genome_build: NCBI genome ID 13078
Supplementary_files_format_and_content: edge R output (CSV files) including TPM for each 100 bp window.

organism: Cyprinodon variegatus

source_name: whole body; n = 5 larvae

growth_protocol: C. variegatus brood stock were maintained at the University of Southern Mississippi’s Toxicology Lab in Ocean Springs, MS.  Fish were kept in 300 L circulating raceways containing 15 ppt artificial sea water at 25°C and 15 ppt salinity on a 16:8 light/dark cycle and fed commercial flake food daily.  Breeding was initiated by the placement of breeding nets in raceways.  After 12 hours embryos were collected and examined for fertilization.  Embryos were rolled on mesh mats to remove external villi, and incubated in 15 ppt sea water at 30°C with agitation to prevent clumping.  After hatching, embryos were reared until yolk-sacks were absorbed and larvae began free-feeding (4 days post-hatch).  Upon initiation of feeding, larvae were fed Artemia nauplii once daily.  Feeding continued throughout experiments.

extract_protocol:
DNA was extracted and RNAse treated using DNeasy Blood and Tissue kit.
To fragment DNA for immunoprecipitation, 8µg of DNA per sample was digested using MseI and DraI restriction.  Resulting fragments were end repaired using the large (Klenow) fragment of DNA polymerase. Purified, fragmented DNA (3 µg) was diluted in 450 µL of ultra-pure water, and heat denatured at 95°C for 10 minutes.  Samples were then immediately placed on ice to prevent re-annealing of fragments.  Following cooling, 50 µL of 10x immunoprecipitation (IP) buffer and 4µL of 5-methyl cytosine (5meC) antibody. Samples were then incubated overnight with rotation at 4°C. For each sample, 50 µL of MagnaBind Goat Anti-Mouse IgG magnetic beads were added to each sample and incubated with rotation for 2 h at room temperature.  Following incubation, beads were collected using a magnetic rack, and supernatent discarded.  Beads were then washed three times in 1X IP buffer, and resuspended in in 500μL of proteinase K digestion buffer containing 5μL/mL proteinase K solution (stock concentration 20 mg/mL).  Proteinase K reactions were incubated with rotation for 2 h at 50°C.  After incubation, beads were collected using a magnetic rack and the supernatant collected.  To purify immunoprecipitated DNA, the supernatant from each reaction was PCI purified according to published protocols.
Libraries were prepared using ACCEL-NGS® 1S Plus & Methyl-SEQ kit (Swift Biosciences, Ann Arbor, MI.) and sequenced on an Illumina NovaSeq to generate 2 x 150 bp reads.

treatment_protocol: Larvae were exposed to one of four conditions: control, hypoxia, oil, or oil plus hypoxia.  Larvae (n =20) were placed in mesh cups, with three replicate cups per treatment.  All larvae were exposed for 48 h and depurated in clean, normoxic water for an additional 48 h to allow stabilization of any treatment induced effects to methylation patterns.  Exposures were conducted in flow through systems delivering test solutions at a rate of 2L/h.  Hypoxic conditions were achieved via bubbling of nitrogen gas through test solutions until dissolved oxygen reached  £ 2 mg/L O2.  Environmental conditions were held at 15 ppt and 30°C across treatments and tanks were monitored daily for temperature and salinity.  Dissolved oxygen was monitored every six hours to ensure maintenance of oxic regimes.  Following 48h of depuration, larvae were sampled and stored in RNA later at -80°C until further analysis.

value: 8 days post-hatch

tag: oil concentration (tpah50, ug/l)

tag: salinity (ppt)

tag: oxygen concentration

value: less than or equal to 2 mg/ml


title: Oil plus hypoxia 3


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad006


title: ka120 pad4_rep1

tag: tissue


title: PFNF54-Pfs16-GFP-LUC late stage (stageIV-V) gametocytes 48 h after experiment initiation- compound MMV674850

city: University Park

first: Riette

last: van Biljon

address: W122 Millenium Science Complex

institute: Pennsylvania State University

hyb_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

scan_protocol: Agilent G2600D Microarray Scanner. Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1).

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction.

organism: Plasmodium falciparum

source_name: PFNF54-Pfs16-GFP-LUC LG 850 48 RNA

growth_protocol: P. falciparum NF54-Pfs16-GFP-LUC were induced by culturing in glucose-deficient media to produce gametocytes, before removing asexual parasites from the population by daily 5% D-sorbitol treatments from day 1-4 and thereafter culturing the parasites in glucose positive media and grown under stationary conditions for the entire experiment.

extract_protocol: Early gametocyte samples were harvested from culture by 0.01%(w/v) saponin addition  and late-stage samples were harvested via density centrifugation using Nycoprep 1.077 cushions and stored at -80˚C until RNA isolation using TRIZOL reagent along with on-column extraction using the Qiagen RNeasy kit (Qiagen, Germany).

treatment_protocol: Samples were grown until the desired stage of development and treated with 10x their previously determined IC50 values for 24 h  or 48 h respectively or left untreated.

tag: sample treatment and stage

value: Late stage (stageIV-V) gametocytes 48 h after experiment initiation- compound MMV674850

source_name: 3D7 Mixed Stage asexual + NF54-Pfs16-GFP-LUC Mixed Stage gametocyte Reference Pool

value: 3D7 + NF54-Pfs16-GFP-LUC

value: Mixed Stage gametocyte Reference Pool


title: Hypoxia 2


title: d7klrg1hi_RNA_FOXO1KO

tag: time

tag: condition

tag: chip antibody


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad002

value: ACA,PL,ILA


title: Cnot4-WT-LZ-rep2

city: Hangzhou

first: Xingxing

last: Dai

address: YuHangTang 866

country: China

institute: Life Sciences Institute

data_processing:
RNA-seq analysis was performed in duplicate using biological replicates for all samples. Raw reads were trimmed to 50 bp reads and mapped to the mouse genome (mm9) using TopHat (v2.1.1) with default parameters. Uniquely mapped reads were subsequently assembled into transcripts by using reference annotation (University of California at Santa Cruz [UCSC] gene models) and Cufflinks (v2.2.1). The expression level of each gene was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) and FPKM values of replicates were averaged. Only the expressed genes (FPKM > 1 in at least one sample) were considered in all analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values of different stage samples.

source_name: LZ (leptotene and zygotene)

extract_protocol:
Spermatocytes were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: Male

tag: cell type

value: Spermatocytes

tag: Stage

value: LZ (leptotene and zygotene)


title: Col-0_rep3

source_name: Col-0_3 wks_rosette leaves

tag: ecotype background

value: wild type

value: three-week-old

value: rosette leaves


title: Cnot4-WT-PD-rep1

source_name: PD (pachytene and diplotene)

tag: strain

value: PD (pachytene and diplotene)


title: Hypoxia 1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad008

tag: brain region

value: male


title: PFNF54-Pfs16-GFP-LUC late stage (stageIV-V) gametocytes 24 h after experiment initiation- compound MMV674850

source_name: PFNF54-Pfs16-GFP-LUC LG 850 24 RNA

label_protocol: Painter, H. J., Altenhofen, L. M., Kafsack, B. F. C. & Llinás, M. Whole-genome analysis of Plasmodium spp. Utilizing a new agilent technologies DNA microarray platform. Methods Mol. Biol. 923, 213–219 (2013).

value: Late stage (stageIV-V) gametocytes 24 h after experiment initiation- compound MMV674850

tag: sample type


title: PFNF54-Pfs16-GFP-LUC late stage (stageIV-V) gametocytes 48 h after experiment initiation- untreated

source_name: PFNF54-Pfs16-GFP-LUC LG UT 48 RNA

value: Late stage (stageIV-V) gametocytes 48 h after experiment initiation- untreated


title: Col-0_rep2

tag: age


title: PFNF54-Pfs16-GFP-LUC late stage (stageIV-V) gametocytes 24 h after experiment initiation- compound MMV666810

source_name: PFNF54-Pfs16-GFP-LUC LG 810 24 RNA

value: Late stage (stageIV-V) gametocytes 24 h after experiment initiation- compound MMV666810


title: Col-0_rep1


title: Hypoxia 3

value: 8 days post-hatch


title: Cnot4-WT-PD-rep2

tag: Sex


title: PFNF54-Pfs16-GFP-LUC late stage (stageIV-V) gametocytes 24 h after experiment initiation- untreated

source_name: PFNF54-Pfs16-GFP-LUC LG UT 24 RNA

value: Late stage (stageIV-V) gametocytes 24 h after experiment initiation- untreated


title: d7klrg1lo_RNA_FOXO1KO

source_name: Virus-peptide-specfic CD8 T cell (P14)

value: P14 T cells


title: Naïve_RNA_FOXO1KO

value: naive


title: Oil plus hypoxia 1

tag: oil concentration (tpah50, ug/l)

value: less than or equal to 2 mg/ml


title: Normoxic Control 1

description: Hypoxia_dif_meth.csv.gz; Oilhypoxia_dif_meth.csv.gz

tag: salinity (ppt)

value: greater than or equal to  5 mg/ml


title: Cnot4-KO-PD-rep1

value: Male


title: Cnot4-KO-LZ-rep2

value: Spermatocytes


title: Oil 3

tag: oxygen concentration


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad010

value: ACA,PL,ILA


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad004


title: Cnot4-KO-LZ-rep1

value: LZ (leptotene and zygotene)


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad004


title: Normoxic Control 3


title: Naïve_RNA_WT

value: WT


title: IP-Rbbp4 FF+WT-Cre

city: Nanjing

first: Su

last: Ting

address: No. 12, Xuefu Road, Pukou District

department: Model Animal Research Center

institute: Nanjing University

data_processing:
ChIP-seq reads were aligned to the reference genome using the bowtie2 software
The reads coverage and depth were caculated by samtools. And deeptools was used to generate the correlation plot for all samples including input samples.
Signal track files in BigWig format were generated using the MACS2 pileup function and were normalized to 1 million reads for visualization.
Differential analysis between treat and control samples was conducted using bedtools
Genome_build: GRCm38.91
Supplementary_files_format_and_content: Bigwig files were generated using the MACS2; The bigWig format is useful for dense, continuous data that will be displayed in the Genome Browser as a graph.

source_name: Embryonic stem cells

extract_protocol:
Lysates were clarified from sonicated nuclei and then  protein-DNA complexes  were isolated with specific antibody.
Adjust the volume of the combined DNA sample to a total volume of 41 μl using 1x TE buffer and fragment the DNA to 300 bp using the Biorupter.Blunt-ended fragments were end repaired and then went through A-Tailing. Adaptor containing sequences required downstream in the sequencing workflow were ligated to the dA-tailed fragment. Finally, the KAPA HiFi DNA Polymerase has been inactivated, enabling amplification of DNA.

tag: strain background

tag: genotype/variation

value: Rbbp4 FF+WT-cre

value: Embryonic stem cells

value: Protein A/G Plus-Agarose(Santa Cruz,sc-2003)


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A4_ad001

value: male


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad012


title: PFNF54-Pfs16-GFP-LUC early stage (stageII-III) gametocytes 48 h after experiment initiation- compound MMV674850

source_name: PFNF54-Pfs16-GFP-LUC EG 850 48 RNA

tag: sample treatment and stage

value: Early stage (stageII-III) gametocytes 48 h after experiment initiation- compound MMV674850

value: 3D7 + NF54-Pfs16-GFP-LUC

value: Mixed Stage gametocyte Reference Pool


title: Dog 4, Sample 2, Insulin stimulated

city: Nashville

first: Justin

last: Gregory

state: TN

address: 1211 Medical Center Drive

department: Dept of Pediatrics

institute: Vanderbilt University Medical Center

description:
processed data header: 4537-JG-13
Raw_Normalzed_Gene_Counts_Matrix.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CanFam3.1 whole genome using bowtie v0.12.2 with default parameters
tab-delimited text files include FPKM values for each Sample ...
Genome_build: CanFam3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Canis lupus familiaris

source_name: Skeletal Muscle

extract_protocol:
A <1 cm scalpel incision was made over the biceps femoris muscle and a small muscle biopsy was collected under local anesthesia using sterile technique. Muscle samples were immediately flash frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted and purified using Qiagen’s All prep kit.
Sequencing ready libraries were prepared using Takara SMARTseq v4 for cDNA synthesis kit and addition of sequencing ready adaptors with Nextera XT prep kits respectively.  Libraries were sequenced on an Illumina NovaSeq 6000 to an approximate sequencing depth of 40 million total reads.

value: 9-10 months

value: wild type

tag: stimulation

value: insulin


title: Normoxic Control 2

value: 8 days post-hatch


title: PFNF54-Pfs16-GFP-LUC late stage (stageIV-V) gametocytes 48 h after experiment initiation- compound MMV666810

source_name: PFNF54-Pfs16-GFP-LUC LG 810 48 RNA

value: Late stage (stageIV-V) gametocytes 48 h after experiment initiation- compound MMV666810


title: PFNF54-Pfs16-GFP-LUC early stage (stageII-III) gametocytes 48 h after experiment initiation- untreated

source_name: PFNF54-Pfs16-GFP-LUC EG UT 48 RNA

value: Early stage (stageII-III) gametocytes 48 h after experiment initiation- untreated


title: Cnot4-KO-PD-rep2

value: Male

value: Spermatocytes

value: PD (pachytene and diplotene)


title: PFNF54-Pfs16-GFP-LUC early stage (stageII-III) gametocytes 24 h after experiment initiation- compound MMV666810

source_name: PFNF54-Pfs16-GFP-LUC EG 810 24 RNA

value: Early stage (stageII-III) gametocytes 24 h after experiment initiation- compound MMV666810


title: Input-Rbbp4 FF+WT-Cre

value: Rbbp4 FF+WT-cre

tag: chip antibody


title: Control 3

source_name: whole body; n = 5 larvae

value: greater than or equal to  5 mg/ml


title: PFNF54-Pfs16-GFP-LUC early stage (stageII-III) gametocytes 24 h after experiment initiation- compound MMV674850

source_name: PFNF54-Pfs16-GFP-LUC EG 850 24 RNA

value: Early stage (stageII-III) gametocytes 24 h after experiment initiation- compound MMV674850


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad007

source_name: C57BL/6J Male P56 Mouse Brain

value: ACA,PL,ILA

value: male


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad008


title: Control 2


title: Cnot4-WT-LZ-rep1

source_name: LZ (leptotene and zygotene)

tag: genotype

value: LZ (leptotene and zygotene)


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad012


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad006


title: Dog 4, Sample 0, Basal insulin

description:
processed data header: 4537-JG-11
Raw_Normalzed_Gene_Counts_Matrix.txt

value: basal


title: Control 1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad001


title: PFNF54-Pfs16-GFP-LUC early stage (stageII-III) gametocytes 48 h after experiment initiation- compound MMV666810

source_name: PFNF54-Pfs16-GFP-LUC EG 810 48 RNA

value: Early stage (stageII-III) gametocytes 48 h after experiment initiation- compound MMV666810

source_name: 3D7 Mixed Stage asexual + NF54-Pfs16-GFP-LUC Mixed Stage gametocyte Reference Pool

value: 3D7 + NF54-Pfs16-GFP-LUC

value: Mixed Stage gametocyte Reference Pool


title: Oil 2

value: 8 days post-hatch


title: Oil 1


title: Ground Infected-2

city: Tempe

first: Jennifer

last: Barrila

state: AZ

address: 1001 S McAllister Ave

department: Biodesign Center for Fundamental and Applied Microbiomics

institute: Arizona State University

description:
Groud control-cultured HT-29 cells infected for 6 hr with WT S. Typhimurium; Space Shuttle mission STS-131
CN11_S22_L003_R1_001

data_processing:
bcl2fastq v2.17.1.14 used for basecalling
STAR v2.5.1b used for alignment
Cufflinks v2.2.1 was used to report FPKM values (Fragments Per Kilobase of transcript per Million mapped reads) and read counts. TPM (Transcripts Per Million) was calculated by an in-house R script.
Differential expression (DE) analysis was performed with EdgeR package from Bioconductor v3.2 in R 3.2.3.
Genome_build: Human: GRCh38.p7 primary assembly; Bacteria: S. Typhimurium LT2 genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values

organism:
Homo sapiens
Salmonella enterica subsp. enterica serovar Typhimurium

source_name: In vitro human colonic epithelial cells (HT-29)

growth_protocol: HT-29 cells were seeded into collagen-coated hollow fiber bioreactors at Kennedy Space Center at a concentration of 1x10^6 CFU. Cells were cultured using GTSF-2 medium. Wild Type Salmonella Typhimurium strain Chi-3339 (an animal-passaged derivative of wild type SL1344) was prepared from overnight cultures in Dulbecco's Phosphate Buffered Saline (DPBS) stasis buffer at a final concentration of ~1x10^7 CFU/mL. Prepared S. Typhimurium was loaded in to gas permeable FEP bags designated for a subset of the bioreactors. The RNA fixative RNAlater II (40 mL) was separately loaded into FEP bags (one per bioreactor). All bioreactors, bacteria bags and fixative bags were integrated into the Cell Culture Module (CCM) flight hardware, which was then sealed, powered and set to 37 °C and 5% CO2. The CCM was turned over to the KSC integration team at L-18 hours. STL-IMMUNE launched aboard Space Shuttle Discovery (STS-131) on April 5, 2010 at 6:21 am. At approximately L+3 hours, astronauts activated the on orbit programming of the CCM.

extract_protocol:
RNA was extracted from duplicate samples using the miRNeasy kit (Qiagen).  All samples were analyzed in biological duplicate (two separate bioreactors), except for the infected spaceflight sample which was analyzed in technical duplicate from the same bioreactor. Samples were lysed with 700 µl Qiazol (Qiagen), vortexed extensively and passed several times through a 25G needle. After a 5-minute static incubation at room temperature with intermittent vortexing, samples were added to MaXtract High Density tubes (Qiagen) together with 100 µl RNase-free water (Qiagen) and 200 µl chloroform (Sigma-Aldrich). Samples were then processed (including on-column DNase-treatment) according to the manufacturer’s instructions. RNA was quantified using a Nanodrop spectrophotometer and the integrity validated using an Agilent Bioanalyzer 2100 to confirm a RIN of 7 or greater for all samples. One of the uninfected ground control samples (CN122) had a RIN of 6.4.
RNA was fragmented with heat and magnesium to roughly 300 bp using the KAPA HyperPrep RNA-seq kit (Roche). The KAPA Hyper RNA-seq kit and Illumina-compatible adapters (IDT) were used for the remaining library construction. Adapter ligated molecules were cleaned using Kapa pure beads (Kapa Biosciences), amplified with Kapa HIFI enzyme. Each library was then analyzed for fragment size on an Agilent’s Tapestation and quantified by qPCR (KAPA Library Quantification Kit) on Quantstudio 5 (Thermo Fisher Scientific). Libraries were then multiplexed and sequenced on 2x150 flow cell on the NovaSeq platform (Illumina) at University of Colorado Anschutz Medical Campus Genomics and Microarray Core.

treatment_protocol: On Mission Elapsed Day 11, a subset of the HT-29 cultures were infected with ~1x10^7 CFU wild type S. Typhimurium (estimated multiplicity of infection/m.o.i. of ~1-10). The remaining cultures served as time-matched uninfected controls. Six hours post-infection, all cultures were fixed in RNAlater II.


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A3_ad002

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad007


title: Ground Infected-1

description:
Groud control-cultured HT-29 cells infected for 6 hr with WT S. Typhimurium; Space Shuttle mission STS-131
CN143_S21_L003_R1_001


title: Dog 3, Sample 0, Basal insulin

description:
processed data header: 4537-JG-8
Raw_Normalzed_Gene_Counts_Matrix.txt

value: 9-10 months

value: wild type


title: Oil + Hypoxia 2 (48 h exposure, 48 h depuration)

data_processing:
Bases Called using Illumina HiSeq Control Software
Initial processing of data was performed using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany).  Adaptor sequences and low quality reads were trimmed, paired ends matched, and reads aligned to the C. variegatus genome
Reads were aligned to C. variegatus genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: C. variegatus genome (NCBI genome ID 13078)
Supplementary_files_format_and_content: CSV text files including TPM expression values

extract_protocol:
Qiagen RNEasy, according to manufacturer's protocol
NuGen mRNA Library Construction, sequenced on Illumina NovaSEQ to generate 2 x 150 bp reads

treatment_protocol: Larvae were exposed to one of four conditions: control, hypoxia, oil, or oil plus hypoxia.  Larvae (n =20) were placed in mesh cups, with three replicate cups per treatment.  All larvae were exposed for 48 h and depurated in clean, normoxic water for an additional 48 h.  Exposures were conducted in flow through systems delivering test solutions at a rate of 2L/h.  Hypoxic conditions were achieved via bubbling of nitrogen gas through test solutions until dissolved oxygen reached  £ 2 mg/L O2.  Environmental conditions were held at 15 ppt and 30°C across treatments and tanks were monitored daily for temperature and salinity.  Dissolved oxygen was monitored every six hours to ensure maintenance of oxic regimes.  Following 48h of depuration, larvae were sampled and stored in RNA later at -80°C until further analysis.

tag: oil concentration (tpah50, µg/l)

value: less than or equal to 2 mg/ml


title: Oil + Hypoxia 1 (48 h exposure, 48 h depuration)


title: Oil + Hypoxia 3 48 h

value: 6 days post-hatch


title: Dog 4, Sample 1, Insulin stimulated

description:
processed data header: 4537-JG-12
Raw_Normalzed_Gene_Counts_Matrix.txt

value: insulin


title: PFNF54-Pfs16-GFP-LUC early stage (stageII-III) gametocytes 24 h after experiment initiation- untreated

source_name: PFNF54-Pfs16-GFP-LUC EG UT 24 RNA

value: Early stage (stageII-III) gametocytes 24 h after experiment initiation- untreated


title: Oil + Hypoxia 2 48 h


title: IP-Rbbp4 FF

value: Rbbp4 FF

tag: cell type

value: Embryonic stem cells

value: Protein A/G Plus-Agarose(Santa Cruz,sc-2003)


title: Input-Rbbp4 FF


title: Dog 2, Sample 0, Basal insulin

description:
processed data header: 4537-JG-4
Raw_Normalzed_Gene_Counts_Matrix.txt


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad006

value: ACA,PL,ILA


title: Dog 3, Sample 2, Insulin stimulated

description:
processed data header: 4537-JG-10
Raw_Normalzed_Gene_Counts_Matrix.txt


title: Hypoxia 3 (48 h exposure, 48 h depuration)


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad012

value: male


title: Oil + Hypoxia 3 (48 h exposure, 48 h depuration)


title: Dog 3, Sample 1, Insulin stimulated

description:
processed data header: 4537-JG-9
Raw_Normalzed_Gene_Counts_Matrix.txt


title: Dog 2, Sample 1, Insulin stimulated

description:
processed data header: 4537-JG-5
Raw_Normalzed_Gene_Counts_Matrix.txt


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad010


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad010


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad006


title: Flight Infected 1-2

description:
Flight-cultured HT-29 cells infected for 6 hr with WT S. Typhimurium; Space Shuttle mission STS-131
CN53_2_S18_L003_R1_001


title: Dog 2, Sample 3, Insulin stimulated

description:
processed data header: 4537-JG-7
Raw_Normalzed_Gene_Counts_Matrix.txt


title: PAC high DP 2 + LPS

city: Frederiksberg C

first: Andrew

last: Williams

state: --- Select One ---

address: Dyrlægevej 100

institute: University of Copenhagen

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Affymetrix

label: biotin

source_name: RAW 264.7 cells

label_protocol: Affymetrix

growth_protocol: Cells were grown under standard culture conditons (no more than 20 passages)

extract_protocol: Total RNA extracted with Qiagen RNAeasy kits.

treatment_protocol: Cells were pre-treated with PAC (15µg/mL) for 30 minutes, following either stimulation with LPS (500 ng/mL) or mock treatment for 6 hours

value: RAW 264.7 macrophages

tag: treatment

value: LPS treated + high PAC


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad008

city: La Jolla

tag: strain


title: Dog 2, Sample 2, Insulin stimulated

description:
processed data header: 4537-JG-6
Raw_Normalzed_Gene_Counts_Matrix.txt


title: MDCK infection rep3 - uninfected total RNA

description:
PR8_infection_FPKM.xlsx
PR8 _t3_UI

source_name: MDCK cells

extract_protocol:
MDCK total RNA were extracted using RNeasy Mini Kit (QIAGEN). A549 total RNA were extracted using TRIzol.
MDCK cDNA libraries were prepared using the Clontech Pico SMARTer Stranded Total RNA-Seq kit v2. For the third MDCK infection, the RNA was also prepped by Illumina TruSeq Stranded mRNA Rrep kit to isolate mRNA only. A549 cDNA libraries were prepared using the Stranded Total RNA v2 PicoMammalian kit (Takara).

value: immortalized kidney epithelial cells

tag: cell line

value: MDCK

value: uninfected


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad002

tag: brain region


title: Oil + Hypoxia 1 48 h

tag: age


title: PAC medium DP 2 + LPS

value: LPS treated + medium PAC


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A2_ad004

tag: Sex


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad002


title: Dog 1, Sample 3, Insulin stimulated

description:
processed data header: 4537-JG-3
Raw_Normalzed_Gene_Counts_Matrix.txt

value: 9-10 months


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad001


title: Normoxic Control 3 96 h

value: 8 days post-hatch

value: greater than or equal to  5 mg/ml


title: Hypoxia 2 (48 h exposure, 48 h depuration)

value: less than or equal to 2 mg/ml


title: Dog 1, Sample 2, Insulin stimulated

description:
processed data header: 4537-JG-2
Raw_Normalzed_Gene_Counts_Matrix.txt

value: wild type

value: insulin


title: Hypoxia 1 (48 h exposure, 48 h depuration)


title: Dog 1, Sample 1, Insulin stimulated

description:
processed data header: 4537-JG-1
Raw_Normalzed_Gene_Counts_Matrix.txt


title: Flight Infected 1-1

description:
Flight-cultured HT-29 cells infected for 6 hr with WT S. Typhimurium; Space Shuttle mission STS-131
CN53_1_S17_L003_R1_001


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad010


title: Normoxic Control 1 96 h


title: CD21 subset of Goat  at day 5

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

country: India

institute: ICAR-NBAGR

description: Gene expression in CD21

data_processing: Initially, the quality-filtered reads from control and infected samples (0 days and 5 days post vaccination) were mapped to Goat/Sheep genome using Bowtie2. The mapped reads were then assembled using RNA-Seq by expectation maximization (RSEM).

organism: Capra hircus

source_name: PBMCs of Goat at 5dpv

extract_protocol:
Total RNA from each subset-CD4+, CD8+, CD14+, CD21+ and CD335+ of PBMCs of control (Goat & Sheep) and vaccinated (Goat & Sheep) were isolated using the RNeasy Mini kit (Qiagen GmbH, Germany). The integrity and quantity of isolated RNA were assessed  based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples were found greater than 8.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies). Libraries were sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Goat and Sheep were subjected to Sungri/96 PPRV vaccination and PBMCs were isolated from them at 0 day (control i.e. just before vaccination) and before the development of antibody response (5 days post vaccination i.e. 5dpv). The RNA was  isolated from each subsets of PBMCs of both species.

tag: infection status

value: 5 day


title: CD335 subset of Goat  at day 0

description: Gene expression in CD335

source_name: PBMCs of Goat at day 0

value: 0 day


title: PAC high DP 3 + LPS


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad008


title: PAC low DP 3 + LPS

value: LPS treated + low PAC


title: Normoxic Control 3 48 h

value: 6 days post-hatch

tag: salinity (ppt)


title: CD21 subset of Goat  at day 0

description: Gene expression in CD21


title: PAC high DP 1 + LPS


title: PAC low DP 2 + LPS


title: PAC medium DP 3 + LPS


title: LPS 2

value: LPS treated only


title: Normoxic Control 2 48 h

tag: oxygen concentration


title: Hypoxia 3 48 h


title: CD14 subset of Goat  at day 0

description: Gene expression in CD14


title: MDCK infection rep3 - uninfected mRNA

description:
PR8_infection_FPKM.xlsx
PR8 _m3_UI

data_processing:
All the raw RNA-Seq reads were first trimmed off adapters and removed low-quality bases by Trimmomatic and checked for quality using FASTQC
All the trimmed reads with a minimum read length of 38bp and average quality per base higher than 30 were mapped into the combined genome of host+IAV by STAR v2.5.3a
The expression level of all the genes, including host and viral genes, were quantified by Cufflinks
Genome_build: CanFam3.1 for MDCK cells, GRCh38.p13 for A549 cells, and NCBI Taxon ID 211044 for IAV PR/8/34
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A12_ad004

value: ACA,PL,ILA

value: male


title: Oil 3 (48 h exposure, 48 h depuration)


title: Hypoxia 1 48 h


title: Hypoxia 2 48 h


title: PAC medium DP 1 + LPS

value: RAW 264.7 macrophages


title: CD8 subset of Goat  at day 0

description: Gene expression in CD8


title: MDCK infection rep2 - uninfected total RNA

description:
PR8_infection_FPKM.xlsx
PR8 _t2_UI

value: immortalized kidney epithelial cells

value: MDCK


title: CD335 subset of Goat  at day 5

description: Gene expression in CD335


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad012


title: Normoxic Control 1 48 h


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad004


title: CD4 subset of Goat  at day 5

description: Gene expression in CD4


title: PAC medium DP 3

value: Medium PAC treated


title: Normoxic Control 2 96 h


title: PAC high DP 1

value: High PAC treated


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad007


title: Oil 2 48 h exposure


title: CD14 subset of Goat  at day 5

description: Gene expression in CD14


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad006


title: RNA-Seq (+)Harringtonine bio_rep2 tech_rep2

city: Worcester

first: Carrie

last: Kovalak

state: MA

address: 365 Plantation Street

department: RNA Therapeutics Institute

institute: University of Massachusetts Medical School

data_processing:
Prior to alignment, adaptor sequences and long stretches (≥ 20 nt) of adenosines were trimmed from read 3′ ends.
All libraries were filtered for reads aligning to repeat regions, as defined by RepeatMasker, using STAR v2.5.3a.
Remaining reads were aligned with STAR on two-pass mode allowing a maximum of 3 mismatches per pair and highly penalized deletions and insertions.
Mapped reads were then filtered for low mapping quality (MAPQ < 5) and/or duplicated reads, identified with the MarkDuplicates tool (Picard v2.17.8).
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files containing mapped and filtered reads

source_name: HEK293 (+) Harringtonine

growth_protocol: HEK293 cells were grown at 37C in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/ streptomycin.

extract_protocol:
RNA was isolated in TRIzol using the Direct-zol RNA Kit (Zymo Research, R2062).
Deep sequencing libraries were prepared from three biological replicates per condition using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche, 08098131702) with a modified protocol as follows.  Isolated RNA (7 ug; Quantified using Qubit RNA Broad Range Assay Kit (Thermo Fischer Scientific, Q10210) was first treated with Turbo DNase using the standard protocol (Thermo Fischer Scientific, AM2239).  Treated RNA (1 ug) was then used as input at the rRNA depletion step in the KAPA kit protocol.  To generate 200-550 nt fragments, fragmentation was carried out for 5 minutes at 94°C and samples immediately chilled on ice.  Following seven amplification cycles using the dual index adapters (5 uL of a 1.5 uM per uL dilution; final concentration of 10 nM) from the KAPA Dual-Indexed Adapter Kit (KK8722) (Roche, 08278555702), PCR products containing 200 to 550 nt inserts were size selected using SPRIselect beads (Beckman Coulter Life Sciences, B23318) and quantified using the Qubit dsDNA Broad Range Assay Kit (Thermo Fischer Scientific, Q32850).  As each library contained a unique barcode, all libraries (3 biological replicates + or - harringtonine treatment) were mixed and sequenced on an Illumina NextSeq 550 instrument using the High Output Kit v2.5 (Illumina, Inc., 20024908). All libraries were loaded at 1.8 pm with 5% PhiX and all data was written to BaseSpace (Illumina, Inc.).

treatment_protocol: Cells were subjected (+) or not (–) to a one hour treatment with harringtonine (2 ng/mL) prior to harvesting.

tag: cell line background

value: Harringtonine (2 ng/mL), one hour

tag: cellular fraction

value: Whole cell

tag: biological replicate

tag: technical replicate


title: CD8 subset of Goat  at day 5

description: Gene expression in CD8


title: Oil 2 (48 h exposure, 48 h depuration)

value: 8 days post-hatch

value: greater than or equal to  5 mg/ml


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A10_ad006

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56


title: PAC low DP 1 + LPS


title: PAC medium DP 1


title: PAC low DP 3

value: Low PAC treated


title: PAC medium DP 2


title: PAC high DP 3


title: Control 2 96 h


title: LPS 3


title: PAC high DP 2


title: PAC low DP 1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad001


title: Oil 1 (48 h exposure, 48 h depuration)


title: Oil 3 48 h exposure


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A10_ad012


title: RNA-Seq (+)Harringtonine bio_rep2 tech_rep1


title: LPS 1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A11_ad002


title: CD4 subset of Goat  at day 0

description: Gene expression in CD4


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A10_ad008


title: Oil 1 48 h exposure


title: Control 3

value: Mock treated cells


title: RNA-Seq (+)Harringtonine bio_rep3 tech_rep1


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A10_ad007


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A10_ad004


title: PAC low DP 2


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A10_ad010


title: Control 1 96 h


title: RNA-Seq (+)Harringtonine bio_rep3 tech_rep2


title: A549 infection Delta-HA rep3 - uninfected total RNA

description:
Delta_HAPB1_FPKM.xlsx
3-naive-0

source_name: A549 cells

value: adenocarcinomic alveolar basal epithelial cells

value: uninfected


title: CEMBA190108_6A_1_CEMBA190108_6A_2_A1_ad012


title: Control 3 96 h


title: RNA-Seq (-)Harringtonine bio_rep3 tech_rep2

source_name: HEK293 (-) Harringtonine

value: Untreated