title: 7970376048_R06C02


title: 7970376001_R02C02

status: Public on Jun 11 2019

type: genomic

city: Newcastle upon Tyne

first: Ed

last: Schwalbe

address: Ellison Place

department: Applied Sciences

country: United Kingdom

institute: Northumbria University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and Infinium MethylationEPIC Beadchips using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Arrays were imported and quality control performed using minfi.
Beta values - A correction for the type of material (FFPE/frozen) was performed by using the removeBatchEffect function of the limma package v.3.24.15. The log2-transformed intensities of the methylated and unmethylated signal were corrected individually. Beta-values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina) and used for all downstream analyses.
GSE130051_beta_values.csv: Beta values; Rows are Samples, columns are ID_REFs.
GSE130051_transposed_beta_values.csv: Beta values; Rows are ID_REFs, columns are Samples.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: medulloblastoma

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from medulloblastoma samples using standard extraction protocols.

tag: cohort

tag: tissue

value: Medulloblastoma

tag: subgroup

tag: subtype


title: 7970376048_R02C02


title: 7970376001_R03C02


title: 7970376001_R04C01


title: 7970376048_R03C02


title: 7970376048_R02C01


title: 7970376048_R01C02


title: 7970376048_R05C01


title: 7970368163_R02C02


title: 7970376002_R01C02


title: 7970368163_R03C01


title: 7970376048_R03C01


title: 7970376001_R01C01


title: 7970368139_R03C02


title: 7970368163_R02C01


title: 7970368139_R04C02


title: 7970368163_R01C02


title: 7970368139_R02C02

value: MBNOS


title: 7970368139_R01C02


title: 7970368139_R02C01


title: 7970368130_R06C01


title: 7970368139_R03C01


title: 7970376002_R04C02


title: 7970368130_R03C02


title: 7970368130_R01C02


title: 7970368130_R02C01


title: 7970368130_R03C01


title: 7970368124_R05C01


title: 7970368130_R05C02


title: 7970368124_R01C02


title: 7970368106_R01C02


title: 7970368124_R01C01


title: 7970368106_R03C01


title: 7970368069_R01C01


title: 7970368069_R04C02


title: 7970368069_R03C02


title: 7970368069_R02C02


title: 7970368069_R06C02


title: 7970368068_R05C01


title: 7970368068_R06C02


title: 7970368069_R05C02


title: 7970368069_R02C01


title: 7970368068_R04C02


title: 7970368068_R05C02


title: 7970368068_R04C01


title: 7970368045_R06C01


title: 7970368068_R02C01


title: 7970368068_R02C02


title: 7970368045_R05C01


title: 7970368045_R03C01


title: 7970368045_R03C02


title: 7970368124_R02C02


title: 7970368007_R05C01


title: 7970368045_R01C01


title: 7970368069_R05C01


title: 7970368007_R04C02


title: 7970368003_R04C01


title: 7970368003_R06C02


title: 7970368003_R04C02


title: 7970368003_R03C01


title: 7810920097_R04C02


title: 7970368003_R02C01


title: 7810920097_R02C02


title: 7810920079_R03C01


title: 7810920079_R04C02


title: 7810920097_R03C02


title: 7810920097_R02C01


title: 7970368003_R02C02


title: 7810920079_R03C02


title: 7810920079_R06C01


title: 7810920079_R06C02


title: 7810920078_R05C01


title: 7810920079_R01C02


title: 7810920097_R06C01


title: 7810920078_R04C02


title: 7810920078_R02C02


title: 7810920078_R04C01


title: 7810920078_R03C02


title: 7810920078_R03C01


title: 7810920078_R02C01


title: 7810920077_R05C02


title: 7970368003_R03C02


title: 7810920078_R01C02


title: 7810920077_R04C02


title: 7810920080_R06C02


title: 7810920080_R06C01


title: 7810920077_R02C01


title: 7810920077_R01C02


title: 7810920071_R05C01


title: 7810920069_R05C01


title: 7810920069_R05C02


title: 7810920071_R02C02


title: 7810920068_R04C02


title: 7810920069_R03C01


title: 7796806110_R02C01


title: 7810920069_R01C01


title: 7810920068_R03C02


title: 9761749106_R03C02


title: 9761749106_R06C02


title: 9761749106_R04C01


title: 9761749106_R01C02


title: 9761749106_R03C01


title: 7810920071_R01C02


title: 9761749073_R03C01


title: 7796806110_R04C02


title: 9761749106_R05C01


title: 9761749106_R02C01


title: 9761749106_R01C01


title: 9761749073_R04C01


title: 7810920077_R03C02


title: 7810920071_R06C01


title: 9647455169_R03C02


title: 9647455180_R04C01


title: 9647455150_R05C02


title: 9647455180_R03C01


title: 7810920071_R04C02


title: 7810920068_R04C01


title: 9647455149_R03C02


title: 9647455144_R05C01


title: 9647455143_R03C02


title: 9761749106_R02C02


title: 9647455143_R02C01


title: 9647455137_R06C02


title: 9647455143_R06C02


title: 9647455137_R05C02


title: 9647455137_R06C01


title: 200925700136_R04C01

value: Previously unpublished - sample from St. Jude collection


title: 200882160027_R04C01


title: 9647455137_R03C01


title: 200793300001_R03C01


title: 200876170073_R07C01


title: 200790260060_R01C01


title: 9647455136_R06C01


title: 9647455137_R05C01


title: 9647455136_R03C01


title: 9647455136_R05C02


title: 200876170031_R06C01


title: 9647455136_R05C01


title: 200788260028_R02C01


title: 200788260028_R05C01


title: 9647455136_R01C02


title: 200784530098_R01C01


title: 9647455136_R02C02


title: 9647455149_R02C02


title: 9647455134_R06C02


title: 9647455143_R06C01


title: 9647455143_R01C01


title: 200784530092_R05C01


title: 9647455134_R05C02


title: 200784530092_R02C01


title: 9647455134_R03C01


title: 9647455136_R06C02


title: 200772270059_R01C01


title: 200772270024_R07C01


title: 200683690020_R03C01


title: 200683690036_R04C01


title: 9422493121_R04C02


title: 9422493121_R03C02


title: 200683690020_R02C01


title: 200683690020_R01C01


title: 9422493121_R05C01


title: 200683690019_R08C01


title: 200683690019_R07C01


title: 9422493121_R02C01


title: 9422493121_R01C02


title: 9422493121_R01C01


title: 200683690019_R06C01


title: 9422493120_R06C01


title: 200683690017_R02C01


title: 9422493120_R06C02


title: 200784530092_R07C01


title: 9422493120_R05C02


title: 200681380036_R08C01


title: 9422493120_R05C01


title: 9647450105_R06C01


title: 200681380036_R07C01


title: 9647450105_R05C01


title: 9422493120_R04C01


title: 9422493120_R03C01


title: 200681380036_R06C01


title: 200681380036_R05C01


title: 9422493120_R02C02


title: 9422493120_R02C01


title: 200681380036_R01C01


title: 200681380014_R06C01


title: 200681380014_R04C01


title: 9422493120_R01C02


title: 9422491044_R06C01


title: 9422491044_R05C02


title: 200681380014_R03C01


title: 9422491044_R04C02


title: 9422491044_R05C01


title: 200683690004_R03C01


title: 200681380014_R02C01


title: 9422491044_R03C02


title: 200681380014_R01C01


title: 200681380014_R07C01


title: 9422491044_R02C02


title: 200661940004_R08C01


title: 9422491044_R03C01


title: 200661940004_R07C01


title: 200661940004_R06C01


title: 200673610045_R06C01


title: 9422491044_R01C02


title: 9422491044_R02C01


title: 9422491044_R01C01


title: 9422491032_R06C02


title: 200661940004_R03C01


title: 200661940004_R02C01


title: 200661940004_R01C01


title: 9422491032_R06C01


title: 9422491032_R05C02


title: 9422491032_R05C01


title: 200661820053_R07C01


title: 200661820053_R06C01


title: 200661820053_R04C01


title: 9422491032_R03C02


title: 200661820053_R05C01


title: 9422491032_R02C02


title: 200661820053_R02C01


title: 200661820033_R08C01


title: 9422491011_R06C01


title: 200661820033_R03C01


title: 9422491011_R05C02


title: 9422491011_R04C02


title: 200654520054_R05C01


title: 200654520049_R05C01


title: 200654430024_R08C01


title: 200654430024_R07C01


title: 9422491011_R03C01


title: 9422491011_R01C01


title: 9422491011_R01C02


title: 200654430024_R05C01


title: 9421912049_R06C01


title: 200654430024_R06C01


title: 9421912041_R06C01


title: 9421912041_R05C02


title: 9422491032_R04C02


title: 200654430024_R01C01


title: 9421912041_R05C01


title: 200654430023_R07C01


title: 9421912041_R04C02


title: 9422491011_R06C02


title: 9421912041_R04C01


title: 200654430023_R06C01


title: 9421912041_R03C02


title: 200654430023_R04C01


title: 200654430023_R05C01


title: 200654430023_R03C01


title: 9421912041_R03C01


title: MRC5 si-lsg1-76 (IonXpress_004)

type: SRA

city: Edinburgh

first: Juan

middle: Carlos

last: Acosta

address: Crewe Rd South

department: Cancer Research UK - Edinburgh Centre

institute: The University of Edinburgh

library_source: transcriptomic

data_processing:
Ampliseq processing: the torrent suite software version for BAM File generation was Torrent Suite v 5.2.0 Depth of reads= 10 million/sample
two-step alignment approach for RNA-seq alignment. First, TopHat (v.2.0.3)  was used with the following settings: '-r 70 --mate-std-dec 90' for paired-end reads from Illumina RNA-seq; and â€˜-r 200â€™ for single-end reads from Proton RNA-seq. Second, unmapped reads from step one were realigned with Bowtie2 [30] using the â€œâ€“very-sensitive-localâ€ method.
HTseq(v0.6) was used for calculating raw read counts of Proton RNA-seq
raw read counts for AmpliSeq was produced by the ampliSeqRNA plugin v5.2.0.3 available for Ion TorrentTM sequencing platforms
Genome_build: UCSC hg19
Supplementary_files_format_and_content: raw counts

molecule: total RNA

source_name: MRC5 human diploid fibroblast cells

growth_protocol: Cells were maintained in DMEM + 10% FBS, 1% anti-anti, 1% geneticin

extract_protocol:
RNA was extracted using the Qiagen Rneasy plus kit following manufacturer's protocol
Libraries were prepared using the  Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (#A26325) ,Ion Xpress™ Barcode Adapters 1-96 Kit (#4474517) and Ion Library TaqMan™ Quantitation Kit (#4468802)

treatment_protocol: Cells were induced to senescence by LSG1 KD or by overexpression of oncogenic KRAS

tag: cell line

tag: cell type

value: diploid fibroblast cells

tag: genotype

value: LSG1 knockdown

tag: phenotype

value: Ribosome maturation induced senescence


title: MRC5 si-lsg1-76 (IonXpress_006)


title: MRC5 KRAS(G12V) (IonXpress_016)

value: KRas(V12D) overexpression

value: Oncogene-induced senescence


title: MRC5 si-con18 (IonXpress_005)

value: control

value: Control


title: MRC5 KRAS(G12V) (IonXpress_008)


title: MRC5 si-lsg1-76 (IonXpress_002)


title: 200654430024_R04C01


title: 200654430023_R02C01


title: MRC5 si-con18 (IonXpress_003)


title: MRC5 si-con18 (IonXpress_001)


title: 200654430023_R01C01


title: 9421912041_R02C01


title: IMR90 ER:RAS siTLR2 5 days IonXpress_022

source_name: IMR90 human diploid fibroblast cells

extract_protocol:
RNA was extracted using the Qiagen Rneasy plus kit following manufacturer's protocol
Libraries were prepared using the  Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (#A26325) ,Ion Xpress™ Barcode Adapters 1-96 Kit (#4474517) and Ion Library TaqMan™ Quantitation Kit (#4468802)
RNA-seq (ampli-seq)

treatment_protocol: Cells were induced to senescence by addition of 100nM 4OHT and tranfected with siRNA every 2 days.

tag: days of 4oht treatment for ras induction


title: 9421912024_R06C01


title: IMR90 ER:RAS siTLR10 5 days IonXpress_023


title: IMR90 ER:RAS siNon-Target 8 days IonXpress_021


title: 200627670064_R08C01


title: MRC5 KRAS(G12V) (IonXpress_024)


title: 9421912024_R05C01


title: 200627670054_R07C01


title: IMR90 ER:RAS siTLR10 5 days IonXpress_020


title: IMR90 ER:RAS siTLR2 5 days IonXpress_019


title: IMR90 ER:RAS siNon-Target 5 days IonXpress_018


title: 9421912024_R04C02


title: IMR90 ER:STOP siNon-Target 5 days IonXpress_017


title: 200627670054_R06C01


title: IMR90 ER:RAS siTLR10 5 days IonXpress_015


title: 9421912024_R04C01


title: 200627670054_R05C01


title: IMR90 ER:RAS siNon-Target 8 days IonXpress_013


title: IMR90 ER:RAS siTLR2 5 days IonXpress_014


title: IMR90 ER:RAS siTLR10 5 days IonXpress_012


title: 9421912041_R02C02


title: 200627670054_R02C01


title: 200627670054_R01C01


title: IMR90 ER:RAS siTLR2 5 days IonXpress_011


title: IMR90 ER:RAS siNon-Target 5 days IonXpress_010


title: IMR90 ER:STOP siNon-Target 5 days IonXpress_009


title: 9421912024_R03C01


title: 9421912024_R03C02


title: 9421912024_R02C02


title: 200627670053_R08C01


title: IMR90 ER:RAS siTLR10 5 days IonXpress_007


title: IMR90 ER:RAS siNon-Target 8 days IonXpress_005


title: IMR90 ER:RAS siTLR10 5 days IonXpress_004


title: IMR90 ER:RAS siTLR2 5 days IonXpress_003


title: IMR90 ER:RAS siNon-Target 5 days IonXpress_002


title: 9421912022_R05C01


title: 200627670053_R02C01


title: 9421912022_R04C02


title: 200627670018_R06C01


title: 9421912022_R04C01


title: 200627670053_R01C01


title: 9421912022_R02C01


title: 200627670018_R02C01


title: 9421912024_R02C01


title: 9421912016_R05C02


title: 200603290063_R08C01


title: IMR90 ER:RAS siTLR2 5 days IonXpress_006


title: 9421912016_R04C02


title: 9421912022_R06C01


title: 200627670053_R07C01


title: 42c_ale6

city: San Diego

first: Anand

last: Sastry

state: CA

address: 9500 Gilman Dr

department: Bioengineering

country: USA

institute: University of California, San Diego

data_processing:
Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v0.12.8 with parameters -X 1000 -n 2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.1.1 with the option --library-type fr-firststrand
Genome_build: ASM584v2
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Total RNA isolated from E. coli

growth_protocol: Cells were grown to mid-log phase aerobically at 42°C on M9 Supplemented with 4g/L D-Glucose

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell culture was treated with the RNAprotect reagent (Qiagen).

value: Evolved

value: Total RNA isolated from E. coli


title: 42c_ale9


title: 42c_ale1

value: WT


title: 42c_ale2


title: 42c_ale10


title: 42c_ale4


title: 200603290063_R05C01


title: wt_42c


title: 42c_ale5


title: 42c_ale3


title: 42c_ale8


title: 9421912016_R04C01


title: 200603290063_R03C01


title: IMR90 ER:STOP siNon-Target 5 days IonXpress_001


title: 9421912016_R03C02


title: 200603290063_R02C01


title: 200627670018_R07C01


title: 9421912016_R02C01


title: 200603290063_R01C01


title: 9421912016_R01C02


title: 200603290061_R08C01


title: NK IL-2 donor 3_RNA-seq

city: London

first: May

last: Sabry

address: Rowland Hill Street

department: Cancer Institute

institute: University College London

data_processing:
data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software v2.19
Fastq files were then aligned to the human genome UCSC hg38 using RNA-STAR 2.5.2b then UMI deduplicated using Je-suite (1.2.1)
Reads per transcript were counted using FeatureCounts and differential expression was estimated using the BioConductor package SARTools, a DESeq2 wrapper
All annotation and sequences were obtained from Illumina iGenomes (http://emea.support.illumina.com/sequencing/sequencing_software/igenome.html).
Functional annotation analysis using gene ontology (GO) terms was performed on gene data sets that met the cutoff values ( >1 Log2fold change, P-value <0.05) using the Panther Classification System gene list analysis tool (http://pantherdb.org)
Genome_build: hg38
Supplementary_files_format_and_content: Differential expression statistics from Deseq

molecule: polyA RNA

source_name: natural killer cells

growth_protocol: NK cells were isolated from healthy donor PBMCs by negative selection (NK cell enrichment kit; StemCell Technologies) according to the manufacturer’s instructions. Freshly isolated NK cells were maintained in complete medium (CM) (RPMI 1640 supplemented with 10% v/v fetal bovine serum and 2mM L-glutamine; all from Life Technologies). The leukemic cell lines K562 and CTV-1 were maintained in CM.

extract_protocol:
positive selection for CD56. RNA was extracted from the samples using the RNAqueousTM Micro Kit (Thermo Fisher Scientific) and stored at −80°C pending analysis
For Library preparation, 100ng of total RNA was processed using the KAPA mRNA HyperPrep Kit (p/n KK8580) according to the manufacturer’s instructions. Briefly, mRNA was isolated from total RNA using Oligo dT beads to pull down poly-adenylated transcripts. The purified mRNA was fragmented using chemical hydrolysis (heat and divalent metal cation) and primed with random hexamers. Strand-specific, first strand cDNA was generated using Reverse Transcriptase in the presence of Actinomycin D. This allows for RNA-dependent synthesis while preventing spurious DNA-dependent synthesis. The second cDNA strand was synthesized using dUTP in place of dTTP in order to mark the second strand. The resultant cDNA is then “A-tailed” at the 3’ end to prevent self-ligation and adapter dimerization. Full-length xGen adaptors (IDT) containing two unique 8bp sample-specific indexes, a unique molecular identifier (N8) and a T overhang are ligated to the A-Tailed cDNA. Successfully ligated cDNA molecules were then enriched with limited cycle PCR (14 cycles – the actual number is dependent on the amount of input RNA). The high fidelity polymerase employed in the PCR is unable to extend through uracil. This means only the first strand cDNA is amplified for sequencing, making the library strand specific (first-strand). For Sequencing, libraries to be multiplexed in the same run are pooled in equimolar quantities, calculated from Qubit and Bioanalyser fragment analysis. Samples were sequenced on the NextSeq 500 instrument (Illumina) using a 75bp single read run with a corresponding 8bp UMI read

treatment_protocol: NK cell stimulation was achieved by co-incubating  NK cells (1x10^6) with K562 or CTV-1 cells (2x10^6), or the exogenous cytokine IL-2 (200IU/ml) for 16 hours at 37ºC, 5% v/v CO2 in CM.

value: peripheral blood

value: natural killer cells

tag: stimulation

value: 16 hours


title: NK IL-2 donor 2_RNA-seq


title: NK IL-2 donor 1_RNA-seq


title: 9403904132_R05C01


title: NK CTV-1 donor 3_RNA-seq

value: 6 hours


title: NK CTV-1 donor 2_RNA-seq


title: 200603290061_R07C01

value: Medulloblastoma


title: 200603290061_R02C01


title: 9403904132_R04C01


title: 9403904132_R04C02


title: NK K562 donor 3_RNA-seq


title: 200603290061_R06C01


title: NK CTV-1 donor 1_RNA-seq


title: 200603290061_R05C01


title: NK K562 donor 2_RNA-seq


title: 200603290037_R07C01


title: 9403904132_R02C01


title: 9403904132_R03C01


title: 9403904132_R02C02


title: NK alone donor 1_RNA-seq


title: NK alone donor 3_RNA-seq


title: NK alone donor 2_RNA-seq


title: 9403904120_R06C01


title: 200603290037_R05C01


title: 9403904120_R05C02


title: 200603290037_R04C01

value: MBNOS


title: 9403904120_R04C02


title: NK K562 donor 1_RNA-seq


title: 200603290061_R01C01

value: Previously unpublished - sample from St. Jude collection


title: 200603290037_R03C01


title: 200603290037_R01C01


title: 9403904120_R03C02


title: 9403904120_R03C01


title: 200603290037_R02C01


title: 200603290001_R07C01


title: 9403904120_R04C01


title: 9403904120_R02C02


title: GAa24-1-GAa24_WT8_Adapter2_8M

city: Charlestown

first: Ana

last: Griciuc

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital

description: Samples_WT_FAD_FADTRKO_8M_complete_RPKM_table.xlsx

data_processing:
The program STAR was used to map sequencing reads (fastqs) to the mouse (mm10) reference genome.
Gene expression counts were calculated using the program HTSeq based on the latest Ensembl annotation for mm10/GRCm38.
The R package edgeR was used to make differential gene expression calls from these counts at a two-fold cut-off and false discovery rate (FDR)<0.05 threshold.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

organism: Mus musculus

source_name: Brain

extract_protocol:
Brains were removed, microglia were isolated using CD11b/CD45 FACS sorting and RNA was extracted. Illumina TruSeq Stranded mRNA LT Prep Kit (Cat# RS-122-2101) was used with 100 ng of RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: age

value: 8 months


title: GAa23-4-GAa23_FAD_TRKO7_Adapter15_8M


title: GAa23-3-GAa23_FAD_TRKO6_Adapter18_8M


title: GAa24-3-GAa24_FAD_TRKO9_Adapter7_8M


title: GAa23-2-GAa23_FAD10_Adapter14-ready_8M


title: GAa24-2-GAa24_FAD6_Adapter4_8M


title: GAa23-1-GAa23_FAD9_Adapter6-ready_8M


title: GAa24-4-GAa24_FAD8_Adapter16_8M


title: 9403904120_R02C01


title: GAa25-1-GAa25_WT9_Adapter6_8M


title: dermal mac_cx3cr1low_rep2

type: RNA

city: Freiburg

first: Philipp

last: Henneke

address: Breisacher Str. 115

department: CCI

country: Germany

institute: Universitätsklinikum Freiburg

hyb_protocol: 4,5 µg of SPIA cDNA was fragmented, terminally biotin-labeled and hybridized to Affymetrix Mouse Gene 2.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: Fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by the Affymetrix GeneChip Command Console v4.1.3 software.

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: Biotin

source_name: mouse dermis, CX3CR1low

label_protocol: Sample preparation for microarray hybridization was carried out as described in the NuGEN Ovation PicoSL WTA System V2 and NUGEN Encore Biotin Module manuals (NuGEN Technologies, Inc, San Carlos, CA, USA).

growth_protocol: SPF animal facility, no earclipping

extract_protocol: Total RNA was extracted from sorted cells with the Rneasy Micro Kit (Qiagen) as per manufacturer's instructions.

value: ear skin

value: macrophage


title: dermal mac_cx3cr1bright_rep1

source_name: mouse dermis, CX3CR1high


title: dermal mac_cx3cr1int_rep2

source_name: mouse dermis, CX3CR1int


title: dermal mac_cx3cr1int_rep1


title: dermal mac_cx3cr1bright_rep2


title: dermal mac_cx3cr1low_rep1


title: GAa22-4-GAa22_FAD_TRKO8_Adapter19_8M


title: 200603290001_R05C01


title: 9403904120_R01C02


title: GAa22-2-GAa22_FAD5_Adapter12_8M


title: GAa22-3-GAa22_FAD7_Adapter13_8M


title: 200603290001_R08C01


title: GAa22-1-GAa22_WT7_Adapter5_8M


title: 9403904120_R01C01


title: 200603290001_R02C01


title: GAa21-3-GAa21_FAD1_Adapter18_8M


title: 200603290001_R01C01


title: GAa21-1-GAa21_WT2_3_Adapter6_8M


title: GAa20-3-GAa20_FAD_TRKO1_2_Adapter13_8M


title: GAa20-2-GAa20_FAD4_Adapter12_8M


title: GAa20-4-GAa20_FAD_TRKO3_Adapter19_8M


title: 200603290001_R06C01


title: 200598360048_R07C01


title: 9403904116_R03C02


title: GAa19-4-GAa19_FAD_TRKO5_Adapter5_8M


title: 200598360048_R06C01


title: 9403904116_R03C01


title: GAa19-3-GAa19_FAD2_Adapter16_8M


title: 200598360048_R03C01


title: 9403904116_R04C01


title: GAa20-1-GAa20_FAD3_Adapter5_8M


title: 200598360048_R02C01


title: 9403904096_R06C02


title: 200598360048_R01C01


title: 9403904116_R02C01


title: GAa18-1-GAa18_FAD11_Adapter14_8M

description: Samples_FAD_FADCDKO_8M_complete_RPKM_table.xlsx


title: GAa19-1-GAa19_WT1_Adapter2_8M


title: GAa18-2-GAa18_FAD_CDKO11_Adapter15_8M


title: 9403904096_R05C02


title: GAa18-3-GAa18_FAD_CDKO12_Adapter18_8M


title: GAa21-4-GAa21_FAD_TRKO4_5_Adapter15_8M


title: GAa17-4-GAa17_FAD_CDKO7_Adapter18_8M


title: 9403904116_R05C01


title: GAa17-3-GAa17_FAD_CDKO5_Adapter15_8M


title: 9403904096_R05C01


title: GAa17-2-GAa17_FAD7_Adapter5_8M


title: 200598360029_R05C01


title: 9403904096_R04C01


title: GAa19-2-GAa19_WT6_Adapter4_8M


title: GAa16-3-GAa16_FAD_CDKO9_Adapter7_8M


title: GAa16-4-GAa16_FAD_CDKO10_Adapter16_8M


title: 200598360029_R02C01


title: 9403904096_R03C01


title: GAa16-2-GAa16_FAD3_Adapter4_8M


title: GAa15-4-GAa15_FAD_CDKO4_Adapter19_8M


title: 9403904096_R02C01


title: GAa16-1-GAa16_FAD10_Adapter2_8M


title: 9403904096_R01C02


title: GAa15-3-GAa15_FAD_CDKO8_Adapter12_8M


title: 200498360002_R02C01


title: GAa15-1-GAa15_FAD1_Adapter5_8M


title: 9403904096_R01C01


title: 200598360029_R06C01


title: GAa4-4-GAa4_FAD_CDKO1_Adapter19_8M


title: 9403904011_R06C02


title: GAa3-4-GAa3_FAD5_Adapter19_8M


title: GAa15-2-GAa15_FAD9_Adapter6_8M


title: GAa17-1-GAa17_FAD6_Adapter6_8M


title: GAa3-2-GAa3_FAD_CDKO3_Adapter6_8M


title: 9403904011_R06C01


title: 200598360029_R03C01


title: GAa2-4-GAa2_FAD8_Adapter7_8M


title: 9403904011_R05C02


title: 9403904011_R05C01


title: GAa2-3-GAa2_FAD_CDKO6_Adapter16_8M


title: 200598360029_R01C01


title: GAa1-4-GAa1_FAD_CDKO2_Adapter16_8M


title: GAa14-1-GAa14_FAD4_Adapter7_4M

description: Samples_All_groups_at_4M_complete_RPKM_table.xlsx

value: 4 months


title: 9403904011_R04C02


title: GAa11-4-GAa11_FAD_CDKO4_Adapter19_4M


title: GAa12-3-GAa12_WT12_Adapter18_4M


title: GAa4-1-GAa4_FAD4_Adapter2_8M


title: 9403904011_R02C02


title: GAa11-2-GAa11_FAD9_Adapter12_4M


title: GAa11-3-GAa11_FAD_CDKO3_Adapter13_4M


title: 9403904011_R01C01


title: GAa10-4-GAa10_FAD_TRKO9_Adapter15_4M


title: 9297949152_R01C01


title: GAa1-3-GAa1_FAD2_Adapter7_8M


title: GAa10-1-GAa10_WT13_Adapter6_4M


title: fibroblast cell line from AM patient

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

description: Gene expression in fibroblasts of patient-7

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression v2 8x60K Microarray.  072363) for 17 hours at 65 ℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: fibroblast cell line from AM patient

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling 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.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

value: Fibroblast

tag: gender

value: Female


title: 9297949124_R02C02


title: GAa9-4-GAa9_FAD_CDKO_TRKO1_Adapter_19_4M


title: Normal oral tissue patient No.8

description: Gene expression in normal tissue of patient-8

source_name: Normal oral tissue patient No.8

value: Normal oral tissue

value: Male


title: Normal oral tissue patient No.4

description: Gene expression in normal tissue of patient-4

source_name: Normal oral tissue patient No.4


title: Normal oral tissue patient No.6

description: Gene expression in normal tissue of patient-6

source_name: Normal oral tissue patient No.6


title: GAa13-1-GAa13_FAD_CDKO_TRKO2_Adapter7_4M


title: human ameloblastoma cell line

description: Gene expression in ameloblasotma cells of patient-7

source_name: human ameloblastoma cell line

value: Ameloblastoma


title: Normal oral tissue patient No.5

description: Gene expression in normal tissue of patient-5

source_name: Normal oral tissue patient No.5


title: Normal oral tissue patient No.7

description: Gene expression in normal tissue of patient-7

source_name: Normal oral tissue patient No.7


title: 9297949124_R04C02


title: 8359018159_R06C02


title: GAa8-4-GAa8_FAD_CDKO1_Adapter19_4M


title: GAa11-1-GAa11_FAD13_Adapter6_4M


title: GAa8-3-GAa8_FAD7_Adapter13_4M


title: GAa10-3-GAa10_FAD_CDKO2_Adapter18_4M


title: 8359018159_R05C02


title: GAa10-2-GAa10_FAD10_Adapter14_4M


title: Normal oral tissue patient No.1

description: Gene expression in normal tissue of patient-1

source_name: Normal oral tissue patient No.1


title: Normal oral tissue patient No.3

description: Gene expression in normal tissue of patient-3

source_name: Normal oral tissue patient No.3


title: GAa7-4-GAa7_FAD_TRKO7_Adapter15_4M


title: GAa8-1-GAa8_WT9_Adapter5_4M

value: WT


title: Normal oral tissue patient No.2

description: Gene expression in normal tissue of patient-2

source_name: Normal oral tissue patient No.2


title: 7973201167_R06C01

source_name: medulloblastoma


title: GAa9-3-GAa9_FAD6_Adapter13_4M-


title: AM tumor patient No.8

description: Gene expression in AM8 tumor

source_name: AM tumor patient No.8


title: GAa7-3-GAa7_FAD8_Adapter18_4M


title: GAa7-1-GAa7_WT8_Adapter6_4M


title: GAa6-3-GAa6_FAD1_Adapter13_4M


title: GAa6-1-GAa6_WT1_Adapter5_4M


title: 7973201167_R05C01


title: GAa9-1-GAa9_WT10_Adapter5_4M


title: AM tumor patient No.6

description: Gene expression in AM6 tumor

source_name: AM tumor patient No.6


title: 7973201167_R03C01


title: 7973201167_R03C02


title: GAa5-4-GAa5_FAD_TRKO3_Adapter16_4M

source_name: Brain


title: GAa6-4-GAa6_FAD_TRKO1_Adapter19_4M


title: GAa5-3-GAa5_FAD11_Adapter14_4M


title: 7973201167_R02C01


title: Mouse 10T1/2, Mutant + Tamoxifen + inhibitor 3 [ChIP-seq]

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
ChIP-seq reads were trimmed and filtered for quality with trim_galore v0.4.5, backed by version 1.15 of cutadapt, with a quality setting of 15.
Reads were aligned to the mm9 genome assembly, using default settings in bowtie2, version 2.3.4.1.
Duplicate reads were removed with MarkDuplicates in Picard, version 2.16.0.
For read density visualization, bigWig files were created with the bamToBed, slopBed, and genomeCoverageBed programs in version 2.27.1 of bedtools, and wigToBigWig in v359 of the UCSC utilities.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads.

growth_protocol: 10T1/2 cells were obtained from ATCC and cultured at 37C in 5% CO2 in high glucose DMEM supplemented with 10% FBS.

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

tag: genotype/variation

tag: treatment

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: Mouse 10T1/2, Mutant + Tamoxifen + inhibitor 2 [ChIP-seq]

value: H3K9me2 (Abcam, ab1220)


title: 7973201131_R05C02


title: AM tumor patient No.7

description: Gene expression in AM7 tumor

source_name: AM tumor patient No.7


title: AM tumor patient No.3

description: Gene expression in AM3 tumor

source_name: AM tumor patient No.3


title: Mouse 10T1/2, Mutant + Tamoxifen + inhibitor 1 [ChIP-seq]


title: Mouse 10T1/2, Mutant + Tamoxifen 2 [ChIP-seq]

value: Tamoxifen


title: Mouse 10T1/2, Mutant + Tamoxifen 3 [ChIP-seq]


title: AM tumor patient No.5

description: Gene expression in AM5 tumor

source_name: AM tumor patient No.5


title: D869/18: ASD patient

city: Olomouc

first: Zuzana

last: Čapková

state: Czech Republic

address: I.P. Pavlova 6

department: Department of Medical Genetics

country: Czech Republic

institute: University Hospital Olomouc

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: The array image was acquired using Affymetrix GeneChip® Command Console (version 4.0.0.1567G). Copy number values were extracted and converted from CEL files into CYCHP files using Chromosome Analysis Suite software (v.3.3.0.139) in default manner using CYTO2 algorythm v.s. 2.2.0. Reference file was CytoScan HD Array.na33.r2, ChAS Browser was NefAffx Build hg19 (20170803).

source_name: Peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell  of peripheral blood using saline method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: diagnosis

value: autism spectrum disorders (ASD)

value: M

tag: facial dysmorphia

value: no


title: GAa5-1-GAa5_WT2_Adapter2_4M


title: Mouse 10T1/2, Mutant + Tamoxifen 1 [ChIP-seq]


title: 7973201131_R06C01

tag: cohort

tag: tissue

value: Medulloblastoma


title: AM tumor patient No.1

description: Gene expression in AM1 tumor

source_name: AM tumor patient No.1


title: AM tumor patient No.2

description: Gene expression in AM2 tumor

source_name: AM tumor patient No.2


title: AM tumor patient No.4

description: Gene expression in AM4 tumor

source_name: AM tumor patient No.4


title: D188/18: ASD patient

value: F


title: 7973201126_R05C02

tag: subgroup

tag: subtype


title: 7973201131_R02C02


title: Mouse 10T1/2, Mutant 2 [ChIP-seq]

tag: cell line


title: D1886/17: ASD patient


title: Mouse 10T1/2, Mutant 1 [ChIP-seq]


title: Mouse 10T1/2, Wildtype + Tamoxifen + inhibitor 3 [ChIP-seq]


title: Mouse 10T1/2, Wildtype + Tamoxifen + inhibitor 2 [ChIP-seq]


title: Mouse 10T1/2, Mutant 3 [ChIP-seq]


title: D1096/18: ASD patient


title: D308/17: ASD patient


title: 7973201126_R05C01


title: 7973201126_R02C01


title: Mouse 10T1/2, Wildtype + Tamoxifen 3 [ChIP-seq]


title: D129/16: ASD patient


title: Mouse 10T1/2, Wildtype + Tamoxifen + inhibitor 1 [ChIP-seq]


title: Mouse 10T1/2, Wildtype + Tamoxifen 2 [ChIP-seq]


title: 7973201123_R04C02


title: D1614/15: ASD patient


title: Mouse 10T1/2, Wildtype 3 [ChIP-seq]


title: D1410/15: ASD patient


title: 7973201123_R04C01


title: Mouse 10T1/2, Wildtype + Tamoxifen 1 [ChIP-seq]


title: D1274/15: ASD patient


title: Mouse 10T1/2, Wildtype 1 [ChIP-seq]


title: Mouse 10T1/2, Wildtype 2 [ChIP-seq]


title: 7973201123_R03C01


title: 7973201123_R01C01


title: Hippocampus CA1, Pvalb-cre positive cells, H11 (PatchSeq)

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Table of total number of detected mRNA molecules from each gene in each cell

source_name: hippocampus CA1

extract_protocol:
After recording from the soma, weak negative pressure was applied in order to aspirate the recorded cell into the glass capillary patch electrode. Using positive pressure the pipette content was quickly ejected into a 1 mL drop of RNase-free lysis buffer (1 mM C1-P1-T31, 10uM dNTP, 10% Triton X, 100mM DTT, 2U/ul Takara Rnase inhibitor) placed on the side of a 0.2 mL RNase free tight-lock tube (TubeOne). The sample was rapidly spun down (5-10 s) and stored at 80 before reverse transcription (RT).
Reverse transcription, PCR amplification and sequencing were manually performed in the same way as for Dataset A described in Fuzik et al. Nat Biotechnol. 2016 Feb;34(2):175-183.

treatment_protocol: Whole-cell patch-clamp recordings were performed as previously described (Muñoz-Manchado et al., Cereb. Cortex 26 (2016), pp. 96-105) on 5HT3aEGFP, Pvalbcre::RCE and Pvalbcre::tdTomato animals. Prior to brain dissection, animals were transcardially perfused using ice-cold oxygenated cutting solution (in mM): 87 NaCl, 2.5 KCl, 1.25 NaH2PO4, 26 NaHCO3, 75 sucrose, 12.5 glucose. Electrophysiological parameters were acquired using depolarizing and hyperpolarizing current steps.

value: 32 days

tag: ID

value: hippocampus CA1

tag: electrophysiological properties

value: FS

tag: interneuron cell class

value: Pvalb

tag: pvalb-cre positive interneurons

value: Yes


title: Hippocampus CA1, Pvalb-cre positive cells, H09 (PatchSeq)

value: 23 days


title: D1273/15: ASD patient


title: Hippocampus CA1, Pvalb-cre positive cells, G09 (PatchSeq)

value: 33 days


title: Hippocampus CA1, Pvalb-cre positive cells, G10 (PatchSeq)

value: 28 days


title: 7973201076_R04C01


title: Hippocampus CA1, Pvalb-cre positive cells, F10 (PatchSeq)


title: D593/15: ASD patient


title: 7973201076_R03C01


title: 7973201076_R02C01


title: D579/15: ASD patient


title: Hippocampus CA1, Pvalb-cre positive cells, F09 (PatchSeq)


title: D577/15: ASD patient


title: 7973201076_R01C02


title: Hippocampus CA1, Pvalb-cre positive cells, E11 (PatchSeq)


title: Hippocampus CA1, Pvalb-cre positive cells, E10 (PatchSeq)


title: Hippocampus CA1, Pvalb-cre positive cells, E09 (PatchSeq)


title: D982/14: ASD patient


title: Hippocampus CA1, Pvalb-cre positive cells, D11 (PatchSeq)


title: Hippocampus CA1, Pvalb-cre positive cells, D10 (PatchSeq)


title: 7973201051_R05C02


title: Hippocampus CA1, Pvalb-cre positive cells, G11 (PatchSeq)


title: Hippocampus CA1, Pvalb-cre positive cells, C09 (PatchSeq)


title: Hippocampus CA1, Pvalb-cre positive cells, D09 (PatchSeq)


title: 7973201051_R05C01


title: 7973201051_R06C02


title: D970/14: ASD patient


title: D981/14: ASD patient


title: 7973201051_R03C02


title: D56/16: ASD patient

value: yes


title: 7973201051_R04C01


title: Hippocampus CA1, Pvalb-cre positive cells, A10 (PatchSeq)


title: Hippocampus CA1, Pvalb-cre positive cells, B09 (PatchSeq)


title: Liver-RE ZT20 Replicate 3

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

data_processing:
Basecalling performed using RTA version 1.18.64
Demultiplexing performed using CASAVA version 1.8.2
Alignment to reference assembly mm10 and known splice junctions extracted from the RefSeq database performed using ELAND v2e (Illumina)
Mapping results filtering performed using in-house tools
Read counting for each gene and normalization to RPKM values performed using in-house tools
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression results (RPKM values) of the standard RNAseq analysis are reported in the Excel file RNAseq_expression_results.xlsx for all 72 replicates. Exonic and intronic expression results (RPKM values) resulting from the EISA analysis described in Gaidatzis et al., Nat. Biotech., 2015, are reported in the Excel files EISA_exonic_expression_results.xlsx and EISA_intronic_expression_results.xlsx respectively for all 72 replicates.

source_name: Liver harvested at ZT20 with BMAL1 knockout and reconstituted in liver

extract_protocol:
Total RNA was extracted from liver with TRIzol (Invitrogen), followed by precipitation with isopropanol and ethanol.
Library construction was performed according to the Illumina TruSeq Total RNA stranded protocol.  The input quantity for total RNA was 1ug and rRNA was depleted  using ribo-zero rRNA gold removal kit (human/mouse/rat). The rRNA depleted RNA was chemically fragmented for three minutes.  First strand synthesis used random primers and reverse transcriptase to make cDNA.  After second strand synthesis the ds cDNA was cleaned using AMPure XP beads and the cDNA was end repaired and then the 3’ ends were adenylated.  Illumina barcoded adapters were ligated on the ends and the adapter ligated fragments were enriched by nine cycles of PCR. The resulting libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip.  The concentrations for the libraries were normalized and then multiplexed together.  The concentration for denaturation was 2nM and the final concentration for clustering was 200pM.  The multiplexed libraries were sequenced by the Genomics High-Throughput Facility at the University of California – Irvine on six lanes using single end 100 cycles chemistry for the HiSeq 4000.   The version of HiSeq control software was HCS 3.4.0.38 with real time analysis software, RTA 2.7.7.

tag: strain background

value: Liver-RE BMAL1-stop-FL

value: 8-12 weeks

tag: time of harvest

value: liver


title: Hippocampus CA1, Pvalb-cre positive cells, A12 (PatchSeq)

tag: age


title: D1374/17: ASD patient

value: autism spectrum disorders (ASD)

tag: gender


title: Liver-RE ZT20 Replicate 2

tag: genotype/variation


title: D1739/17: ASD patient


title: Hippocampus CA1, Pvalb-cre positive cells, B10 (PatchSeq)


title: 7973201051_R03C01


title: D1583/17: ASD patient

value: M


title: Liver-RE ZT20 Replicate 1


title: D854/14: ASD patient

value: no


title: Hippocampus CA1, Pvalb-cre positive cells, C11 (PatchSeq)


title: 7973201043_R05C02

value: Medulloblastoma


title: Liver-RE ZT16 Replicate 3

source_name: Liver harvested at ZT16 with BMAL1 knockout and reconstituted in liver


title: Liver-RE ZT16 Replicate 2


title: Liver-RE ZT16 Replicate 1


title: Liver-RE ZT12 Replicate 3

source_name: Liver harvested at ZT12 with BMAL1 knockout and reconstituted in liver


title: 7973201043_R04C02


title: Liver-RE ZT12 Replicate 2


title: D938/18: ASD patient

value: F


title: Liver-RE ZT12 Replicate 1


title: 7973201043_R04C01


title: D831/18: ASD patient


title: D241/18: ASD patient


title: D1869/17: ASD patient


title: 7973201043_R02C01


title: Liver-RE ZT08 Replicate 2

source_name: Liver harvested at ZT8 with BMAL1 knockout and reconstituted in liver


title: Liver-RE ZT08 Replicate 1


title: D840/15: ASD patient


title: paf1∆trf4∆_3 Tiling Array

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description:
Trf4Paf1.Plus.Strand.bedgraph
Trf4Paf1.Minus.Strand.bedgraph
trf4paf1.m.window.20.bedgraph
trf4paf1.p.window.20.bedgraph
paf1trf4.vs.trf4.plus.window.20.bedgraph
paf1trf4.vs.trf4.minus.window.20.bedgraph
all_rna_before_limma.csv
paftrfVStrf.all.fix.csv
downregulated_regions_paf1trf4_vs_trf4_window_20_1.5-fold_annotations.bed
upregulated_in_paf1trf4_vs_trf4_window_20_1.5-fold_annotations.bed
total RNA reverse transcribed into cDNA in the presence of Actinomycin D using both oligodT and random heximers and biotinylated

hyb_protocol: not provided

scan_protocol: Affymetrix 7G scanner

data_processing:
Data was analyzed using R, Python and Shell commands described in detail in the linked manuscript
Bedgraph files for each strand are provided with and without sliding window (20bp) smoothing. Bedgraph files of the difference between the strains compared in this study are also provided with a 20bp sliding window normalization applied. Calculated averages of probe intensities over gene annotations prior to Limma analysis as well as the Limma analysis results are provided. Finally annotations for differentially regulated transcripts are provided in BED6 format.
*Strand.bedgraph = averaged bedgraph (no smoothing)
*20.bedgraph = bedgraph smoothed with a 20 probe (~160bp) sliding window. There are smoothed average genome-wide bedgraphs and smoothed differential results bedgraphs.
all_rna_before_limma.csv = results file transcripts genes before limma analysis
*all.fix.csv = results file for transcripts after limma analysis
*annotations.bed = results file de novo identified differentially expressed transcripts

label: biotin

organism: Saccharomyces cerevisiae

source_name: KY2276 S. cerevisiae grown to log phase in YPD

label_protocol: RNA samples (100 µg total) were DNase treated (Fermentas #EN0521, Waltham, Ma) and purified using an RNeasy kit (Qiagen #74104, Hilden Germany). RNA was reverse transcribed into cDNA in the presence of 6 ng/µL actinomycin D to prevent antisense artifacts (*Perocchi/Steinmetz), fragmented, and labeled with a 3’ biotin tag.

growth_protocol: Cells were grown in YPD supplemented with 400 µM tryptophan to a cell density of 1.8-2.5 x 107 cells/mL and harvested by centrifugation at 3000 rpm for 3 minutes.

extract_protocol: For RNA extraction pelleted cells were resuspended in 12 mL AE buffer (50 mM NaOAc pH 5.2, 10mM EDTA) and combined with an equal volume of acid phenol SDS to a concentration of 0.8%. After incubation at 65 ˚C for 10 minutes and centrifugation the aqueous phase was re-extracted first with PCI (25 phenol: 24 chloroform: 1 isoamyl-alcohol) and then chloroform. Extracted RNA was precipitated by addition of an equal volume of isopropanol and a tenth volume of 3M NaOAc pH 5.2 and incubation on ice for 10 minutes. RNA was pelleted by centrifugation, washed with 70% EtOH, dried and resuspended in TE buffer (pH 7.0). All RNA samples used in tiling array analysis were checked by agarose gel electrophoresis.

tag: strain

value: MATa leu2[delta]0 ura3[delta]0 trf4[delta]::CLONAT paf1[delta]::KANMX

tag: genotype


title: 7973201008_R06C02

source_name: medulloblastoma


title: Liver-RE ZT04 Replicate 2

source_name: Liver harvested at ZT4 with BMAL1 knockout and reconstituted in liver


title: D1814/16: ASD patient

tag: diagnosis

tag: facial dysmorphia


title: D377/17: ASD patient


title: 7973201008_R05C02

tag: cohort

tag: tissue


title: paf1∆trf4∆_2 Tiling Array


title: paf1∆trf4∆_1 Tiling Array


title: 7973201008_R05C01

tag: subgroup

tag: subtype


title: adult mac_cx3cr1bright_rep2

hyb_protocol: Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the dUTP residues followed by a terminal labeling with biotin. 3,8 µg of fragmented and labeled ss cDNA were hybridized to Affymetrix Mouse Gene 2.1 ST Array Plates. For hybridization, washing, staining and scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

scan_protocol: For scanning an Affymetrix GeneTitan system, controlled by the Affymetrix GeneChip Command Console software v4.2, was used.

source_name: mouse dermis, CX3CR1bright

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT Pico Reagent Kit User Guide (Affymetrix, Inc., Santa Clara, CA, USA).

treatment_protocol: untreated

value: ear skin

tag: cell type

value: macrophage


title: trf4∆_3 Tiling Array

description:
Trf4.Plus.Strand.bedgraph
Trf4.Minus.Strand.bedgraph
trf4.m.window.20.bedgraph
trf4.p.window.20.bedgraph
paf1trf4.vs.trf4.plus.window.20.bedgraph
paf1trf4.vs.trf4.minus.window.20.bedgraph
all_rna_before_limma.csv
paftrfVStrf.all.fix.csv
downregulated_regions_paf1trf4_vs_trf4_window_20_1.5-fold_annotations.bed
upregulated_in_paf1trf4_vs_trf4_window_20_1.5-fold_annotations.bed
total RNA reverse transcribed into cDNA in the presence of Actinomycin D using both oligodT and random heximers and biotinylated

value: MATa leu2[delta]0 ura3[delta]0 trf4[delta]::CLONAT


title: 7973201008_R03C01


title: Liver-RE ZT04 Replicate 1


title: adult mac_cx3cr1low_rep2

source_name: mouse dermis, CX3CR1low


title: adult_mac_cx3cr1low_rep1


title: Liver-RE ZT08 Replicate 3


title: D1873/16: ASD patient


title: 7973201043_R01C02


title: Liver-RE ZT00 Replicate 2

source_name: Liver harvested at ZT0 with BMAL1 knockout and reconstituted in liver


title: 7973201008_R02C02


title: Liver-RE ZT04 Replicate 3


title: trf4∆_2 Tiling Array


title: 7973201008_R06C01


title: trf4∆_1 Tiling Array


title: D1277/08: ASD patient


title: D140/17: ASD patient


title: Liver-RE ZT00 Replicate 1


title: KO ZT20 Replicate 3

source_name: Liver harvested at ZT20 with BMAL1 knockout

value: BMAL1 knockout


title: paf1∆_3 Tiling Array

description:
Paf1.Plus.Strand.bedgraph
Paf1.Minus.Strand.bedgraph
paf1.p.window.20.bedgraph
paf1.m.window.20.bedgraph
paf1.vs.wt.plus.window.20.bedgraph
paf1.vs.wt.minus.window.20.bedgraph
all_rna_before_limma.csv
pafVSwt.all.fix.csv
downregulated_in_paf1_vs_wt_window_20_1.5-fold_annotations.bed
upregulated_in_paf1_vs_wt_window_20_1.5-fold_annotations.bed
total RNA reverse transcribed into cDNA in the presence of Actinomycin D using both oligodT and random heximers and biotinylated

value: MATa leu2[delta]0 ura3[delta]0 paf1[delta]::KANMX


title: 7973201008_R02C01


title: adult mac_cx3cr1bright_rep1


title: 7973201008_R01C02


title: D538/16: ASD patient


title: Liver-RE ZT00 Replicate 3


title: paf1∆_2 Tiling Array


title: D407/16: ASD patient


title: KO ZT20 Replicate 2


title: KO ZT20 Replicate 1


title: paf1∆_1 Tiling Array


title: 7970376040_R05C01


title: WT_3 Tiling Array

description:
Wild.Plus.Strand.bedgraph
Wild.Minus.Strand.bedgraph
wt.p.window.20.bedgraph
wt.m.window.20.bedgraph
paf1.vs.wt.plus.window.20.bedgraph
paf1.vs.wt.minus.window.20.bedgraph
all_rna_before_limma.csv
pafVSwt.all.fix.csv
downregulated_in_paf1_vs_wt_window_20_1.5-fold_annotations.bed
upregulated_in_paf1_vs_wt_window_20_1.5-fold_annotations.bed
total RNA reverse transcribed into cDNA in the presence of Actinomycin D using both oligodT and random heximers and biotinylated

value: MATa leu2[delta]0 ura3[delta]0

value: WT


title: 7970376040_R04C02


title: D349/16: ASD patient


title: D1320/14: ASD patient


title: KO ZT16 Replicate 2

source_name: Liver harvested at ZT16 with BMAL1 knockout


title: WT_2 Tiling Array


title: 7970376040_R02C02


title: KO ZT16 Replicate 1


title: D10/16: ASD patient

source_name: Peripheral blood


title: WT_1 Tiling Array


title: 7970376040_R01C02


title: D121/16: ASD patient

value: yes


title: 7970376040_R06C01


title: KO ZT12 Replicate 3

source_name: Liver harvested at ZT12 with BMAL1 knockout


title: KO ZT12 Replicate 2


title: D101/16: ASD patient


title: H2AE57A_MNase-seq_Rep2

description: Raw files include chr VIII, processed data files do not. See referenced article for details.

data_processing:
Alignment was performed with HISAT2 (MNase-seq) or bowtie2 (ChIP-seq).
Filtering was performed with the SAMtools suite.
Data processing and visualization were performed with deepTools2 and IGV2.4.13.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files were produced by deepTools2 and contain either MNase-seq or H3 ChIP-seq content information genome-wide. sgr files contain base coordinate scores for H3 ChIP-seq data.

growth_protocol: S. cerevisiae was grown to mid-log phase in SC medium.

extract_protocol:
NEBNext Ultra II (NEB, E7645)
Total chromatin was isolated by bead beating in 1XFA + 0.5% SDS buffer with PMSF.

treatment_protocol: Cells were formaldehyde crosslinked at a final concentration of 1% formaldehyde.

tag: plasmid

value: pCEC02 = HIS3/CEN/ARS/hta1E57A-HTB1


title: H2AE57A_MNase-seq_Rep1


title: D1/16: ASD patient


title: KO ZT16 Replicate 3

value: 8-12 weeks


title: 7970376008_R03C02


title: 7970376008_R05C01


title: D370/16: ASD patient


title: WT_MNase-seq_Rep2

source_name: WT

value: pAY01 = HIS3/CEN/ARS/HTA1-HTB1


title: 7970376008_R02C02


title: 7970376008_R01C02


title: KO ZT12 Replicate 1

value: liver


title: WT_MNase-seq_Rep1


title: D1468/15: ASD patient

value: autism spectrum disorders (ASD)


title: KO ZT08 Replicate 3

source_name: Liver harvested at ZT8 with BMAL1 knockout


title: 7970368138_R06C01


title: D1377/15: ASD patient

value: M

value: no


title: KO ZT08 Replicate 2


title: D1300/15: ASD patient


title: KJ012

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used to convert BCL to fastq format, coupled with adaptor trimming
STAR (version 2.4.0.1) was used to map reads to the reference genome
The GenomicAlignments R package (Release 3.6) was used to count reads per gene using gene annotations from the TxDb.Hsapiens.UCSC.hg19.knownGene R package (Release 3.6)
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: tab-delimited text files include raw read count and TPM values for each sample, respectively

extract_protocol:
Qiagen RNAeasy Mini Kit
Illumina TruSeq RNA prep kit

tag: time

tag: treatment

value: DMSO

value: TruSeq


title: 7970368138_R04C02

value: Medulloblastoma


title: D1295/15: ASD patient


title: KO ZT08 Replicate 1

tag: strain background


title: KJ011


title: KO ZT04 Replicate 3

source_name: Liver harvested at ZT4 with BMAL1 knockout

tag: time of harvest


title: 7970368138_R04C01


title: KJ010


title: D1293/15: ASD patient


title: KO ZT04 Replicate 2

tag: age


title: KJ009


title: D1222/15: ASD patient

tag: gender


title: 7970368138_R01C02


title: KO ZT00 Replicate 3

source_name: Liver harvested at ZT0 with BMAL1 knockout

tag: genotype/variation


title: 7970368138_R01C01


title: D1194/15: ASD patient

value: F


title: KJ008


title: 7970368088_R06C02


title: D1069/15: ASD patient


title: KJ007


title: D1059/15: ASD patient


title: KO ZT00 Replicate 2


title: 7970368088_R06C01


title: KO ZT00 Replicate 1


title: KJ006


title: 7970368088_R04C01


title: D1650/14: ASD patient


title: KJ005


title: WT ZT20 Replicate 3

source_name: Liver harvested at ZT20


title: D940/15: ASD patient


title: KJ004


title: WT ZT20 Replicate 2


title: D952/15: ASD patient


title: 7970368088_R03C01


title: KO ZT04 Replicate 1


title: KJ003


title: 7970368052_R05C02

value: MBNOS


title: D924/15: ASD patient


title: 7970368052_R05C01


title: WT ZT16 Replicate 3

source_name: Liver harvested at ZT16


title: KJ002


title: KJ001


title: WT ZT16 Replicate 2


title: D836/15: ASD patient


title: 7970368052_R04C02


title: D801/15: ASD patient


title: WT ZT16 Replicate 1


title: 7970368052_R04C01


title: D835/15: ASD patient


title: 7970368052_R03C02


title: WT ZT12 Replicate 2

source_name: Liver harvested at ZT12


title: Epi-CE

city: Cambridge

first: Alfonso

last: Martinez Arias

address: Downing

department: Genetics

institute: University of Cambridge

description: E14Tg2A were grown on a 0.5% Plasma Fibronectin in PBS (with Calcium and Magnesium) coated culture flask with N2B27 supplemented with 12ng/ml FGF2 and 25ng/ml Activin A (Epi-media) for at least 4 passages. These cells considered as EpiSCs. EpiSCs were plated at a 5x104 cells/cm2 density in a 0.5% Fibronectin pre-coated flask with Epi-media for the first day. Day 2 is followed by increasing the concentration of FGF2 to 20ng/ml in the base medium of N2B27 and removing Activin A. On day 3, N2B27 is supplemented with 3μM Chiron which is added to the 20ng/ml FGF2.

data_processing:
Illumina sequencing (HiSeq 4000)
Cell Ranger version 1.3.1 (10x Genomics) was used to process raw sequencing data
Seurat R package version 2.0 was used to read the data from Cell Ranger to R and build the expression matrix
Gene expression was quantified by UMI counts
Genome_build: mm10
Supplementary_files_format_and_content: ProcessedRaw_counts.txt contains the UMI counts matrix where the rows are the genes and the columns are cells. cellsData.txt contains information about the cells: unique cell ID and the sample names (ES-NMP, Epi-CE, Epi-CE-T, Epi-NMP)

source_name: In vitro caudal epiblast like cells derived from mouse EpiSCs

extract_protocol:
10x Genomics single cell transcriptomic service was used to sequence our 4 different samples. 8,700 cells from each sample were loaded into the 10x Chromium system.
The preparation of the libraries and the Illumina sequencing (HiSeq 4000) was done by the Cambridge 10X genomics services.

value: EpiSCs derived caudal epiblast cells

tag: passages

tag: strain


title: Epi-CE-T

description: Epi-CE-T were cultured from Bra:GFP cell line at the same way as Epi-CE with the modification that after 72 hours the cells were sorted for positive GFP cells only.

source_name: T/Brachury positive expressing cells from the Epi-CE population


title: Epi-NMP

description: Epi-CE cells were detached from the culture flask using Accutase and seeded on a flask coated with 0.5% Fibronectin at a dense of 5x104 cells/cm2. The cells were grown for 2 days in N2B27 supplemented with 20ng/ml FGF2 and 3μM Chiron.

source_name: In vitro NMPs derived from Epi-CE

value: EpiSCs derived neural mesodermal progenitor cells


title: WT ZT12 Replicate 3


title: 7970368052_R02C01

source_name: medulloblastoma


title: 7970368088_R01C02


title: WT ZT20 Replicate 1


title: ES-NMP

description: E14Tg2A cells were plated at a density of 4.44x103 cells/cm2 in a 0.1% gelatine coated flask with a base medium of N2B27 for 2 days. After 48hr N2B27 is supplemented with 3μM of CHIR99021 for additional 24hr, which are in total 72hr.

source_name: In vitro NMPs derived from mouse ESCs

value: ESCs derived neural mesodermal progenitor cells


title: 7970368052_R01C01


title: WT ZT08 Replicate 3

source_name: Liver harvested at ZT8

value: WT


title: WT ZT12 Replicate 1


title: D405/15: ASD patient

tag: diagnosis


title: D768/14: ASD patient

tag: facial dysmorphia


title: 7970368048_R06C02

tag: cohort


title: 7970368048_R05C02

tag: tissue


title: WT ZT08 Replicate 1


title: D82/12: ASD patient


title: CrectLJ

city: Aurora

first: Hong

last: Li

state: CO

department: Craniofacial Biology

institute: University of Colorado Denver Anschutz Medical Campus

description: 10XGenomics 3' v2 chemistry

data_processing:
Sequencing was performed on Illumina Hiseq 4000 with v4 chemistry
Cellranger toolkit version 2.0 from 10XGenomics was used for de-multiplexing, alignmentment, and unique molecular identifier (UMI) counting with the default setting.
Genome_build: mm10
Supplementary_files_format_and_content: .tsv files contain the cell bacodes and the gene infomation. .mtx filles contain the gene by cell barcodes matrices.

source_name: lambdoid junction

extract_protocol:
Following microdissection, lambdoidal junction tissues from 4 to 5 embryos were pooled together and treated with 750µl of 0.25% trypsin-EDTA at 37°C for 10 mins with gentle agitation. The reaction was stopped by adding 750µl of DMEM with 10% FBS.  The mixture was then pipetted up and down 20 times with wide orifice tips to assist in cell dispersion, and the cells were collected by centrifugation at 300 g for 3 mins. Cells were washed in PBS with 0.4% BSA twice, and then filtered through Flowmi 40µM cell strainer before proceeded for single cell RNA-seq.
Libraries were prepared with the 10XGenomics single cell 3’ v2 kit according to the manufacturer’s instructions.

value: microdissted regions of the upper face where the nasal and maxillary prominences are juxtaposed

tag: genotype

value: Crect; ROSA26-lacZ


title: WT ZT04 Replicate 3

source_name: Liver harvested at ZT4

value: 8-12 weeks


title: C57LJ

description: 10XGenomics 3' v2 chemistry

value: wild-type


title: D731/15: ASD patient

source_name: Peripheral blood


title: D443/12: ASD patient


title: WT ZT04 Replicate 2

value: liver


title: 7970368048_R02C02

extract_protocol: Genomic DNA was extracted and purified from medulloblastoma samples using standard extraction protocols.

tag: subgroup

tag: subtype


title: D953/10: ASD patient

value: autism spectrum disorders (ASD)


title: WT ZT04 Replicate 1


title: 7970368048_R01C02


title: 7970368048_R03C02


title: WT ZT00 Replicate 3

source_name: Liver harvested at ZT0


title: D684/13: ASD patient

value: M


title: 7970368048_R01C01


title: D538G_Input (ChIP-seq)

city: Salt Lake CIty

first: Jason

last: Gertz

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Sequencing reads were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
MACS2 was used to call peaks with a p-value cutoff of 1*10-10 and a mfold parameter between 15 and 100. MACS2 also generated normalized bedgraphs.
Differential binding sites were identified by using DESeq2 to compare counts per million.
Genome_build: hg19

source_name: Endometrioid adenocarcinoma

growth_protocol: Ishikawa ESR1 LBD mutant and wildtype cells were cultured in full media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. At least 5 days prior to inductions, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific), since phenol-red is estrogenic, with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
Fixation was performed by treating cells with 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via cell scraping in Farnham lysis buffer supplemented with protease inhibitors.
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with an Anti-FLAG (Sigma-Aldrich M2) antibody that recognizes a FLAG tag on ESR1.

treatment_protocol: Media was changed 1 day prior to inductions and Ishikawa ESR1 mutant and wildtype clonal cell lines were induced with DMSO or 10 nM E2 for one hour.

tag: cell line

value: Ishikawa D538G ESR1

value: D538G ESR1

tag: chip antibody


title: D467/11: ASD patient

value: no


title: WT_Input  (ChIP-seq)

value: Ishikawa WT ESR1

value: WT ESR1


title: WT ZT08 Replicate 2


title: D406/15: ASD patient

value: F


title: D546/14: ASD patient


title: D1743/12: ASD patient


title: WT ZT00 Replicate 2


title: 7970368039_R04C01

data_processing:
Arrays were imported and quality control performed using minfi.
Beta values - A correction for the type of material (FFPE/frozen) was performed by using the removeBatchEffect function of the limma package v.3.24.15. The log2-transformed intensities of the methylated and unmethylated signal were corrected individually. Beta-values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina) and used for all downstream analyses.
GSE130051_beta_values.csv: Beta values; Rows are Samples, columns are ID_REFs.
GSE130051_transposed_beta_values.csv: Beta values; Rows are ID_REFs, columns are Samples.

value: Medulloblastoma


title: 7970368048_R04C02


title: D1018/14: ASD patient


title: D1196/14: ASD patient


title: MacP3_3

first: Patrice

last: Zeis

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: library of 96 Cx3cr1gfp/+ Dermis Macrophages

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. In addition we annotated the EGFP sequence from the pEGFP-N1 vector (https://www.ncbi.nlm.nih.gov/nuccore/U55762) used to generate the CX3CR1-GFP reporter mice. This procedure resulted in 34,112 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9 + gfp sequence from pEGFP-N1 vector (https://www.ncbi.nlm.nih.gov/nuccore/U55762)
Supplementary_files_format_and_content: TSV files, columns represent CXR3CR1 high/mid/low macrophages, rows represent the geneid and the values in the file are the quantified number of transcripts.

source_name: Dermis

extract_protocol:
Mouse ears were digested with Dispase (0.25 U/ml), Collagenase II (1 mg/ml), and DNase I in HBSS with 10% FCS for 2 h at 1400 rpm and 37°C. Cells were filtered, stained and sorted as CD45+, CD11b+, CD64+, Lin- in a 384-well plate.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

value: ear skin

value: 7 weeks

tag: cell type

value: Cx3cr1gfp/+ Dermis Macrophages


title: MacP3_4


title: 7970368039_R03C01

first: Ed

last: Schwalbe

institute: Northumbria University


title: 7970368039_R02C02


title: D538GClone3_DMSO (RNA-seq)

data_processing:
Reads were aligned to the human genome using HISAT2.
Sam files were converted to bam files and sorted with Samtools.
To quantify reads that mapped to UCSC Known Genes, we used featureCounts from the Subread package.
Reads were normalized and analyzed for differential enrichment using the DESeq2 package in R.
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts (raw and normalized) in a text file

extract_protocol:
Following treatments cells were washed with PBS and harvested with buffer RLT plus (Qiagen) containing 1% beta-mercaptoethanol (Sigma-Aldrich). Cells were passed through a 21-gauge needle and syringe (Sigma-Aldrich) to lyse genomic DNA before RNA was extracted and purified using a Quick RNA Mini Prep kit (Zymo Research).
Using the KAPA Stranded mRNA-Seq kit (KAPA Biosystems), poly(A) selected libraries were created with 500 ng of input RNA per sample.

treatment_protocol: Media was changed 1 day prior to inductions and cells were treated with either DMSO (vehicle) or 10 nM (estradiol) E2 for 8 hours. For prolonged estrogen samples, wildtype cell lines were cultured in phenol-red free RPMI with 10% charcoal-dextran stripped fetal bovine serum and 1% pen-strep for up to 25 days. Cells were treated with 10 nM E2 every 2 days with media changes, and cell lysates were collected at the following time points: day 10, day 15, day 20, day 25.

value: Ishikawa D538G ESR1 clone 3

tag: treatment

value: 0.1% DMSO

tag: time

value: 8 hrs


title: D538GClone2_DMSO (RNA-seq)

value: Ishikawa D538G ESR1 clone 2


title: MacP3_2

tag: age


title: D538GClone1_E2 (RNA-seq)

value: Ishikawa D538G ESR1 clone 1

value: 10nM E2


title: 7970368039_R05C01

value: MBNOS


title: D1471/14: ASD patient

value: autism spectrum disorders (ASD)

tag: gender

value: M


title: D538GClone3_E2 (RNA-seq)

value: D538G ESR1


title: D538GClone1_DMSO (RNA-seq)


title: MacP3_1


title: WT ZT00 Replicate 1

tag: strain background

tag: genotype/variation

value: WT

value: 8-12 weeks

tag: time of harvest

value: liver


title: 7970368035_R05C01

value: Medulloblastoma


title: 7970368035_R06C02


title: MacP2_3

tag: strain

value: ear skin


title: 7970368035_R03C02


title: D1611/14: ASD patient

tag: diagnosis

tag: facial dysmorphia

value: yes


title: D1522/14: ASD patient

value: no


title: WTClone2_E2_25D (RNA-seq)

value: Ishikawa WT ESR1 clone 2

value: WT ESR1

value: 25 days


title: D538GClone2_E2 (RNA-seq)

value: Ishikawa D538G ESR1 clone 2

value: 8 hrs


title: MacP2_2

tag: tissue

value: 7 weeks

value: Cx3cr1gfp/+ Dermis Macrophages


title: D767/14: ASD patient

value: autism spectrum disorders (ASD)


title: D1647/14: ASD patient

value: M


title: MacP2_1


title: 7970368035_R03C01

tag: cohort


title: WTClone2_E2_15D (RNA-seq)

tag: genotype

value: 10nM E2

value: 15 days


title: WTClone2_E2_20D (RNA-seq)

value: 20 days


title: D1721/14: ASD patient


title: D1319/14: ASD patient


title: 7970368034_R05C01

tag: subgroup

tag: subtype


title: ChIP-seq_CBP_Resting

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using Bowtie2 (version 2.2.5, Langmead et al., 2012 Nat Methods) with default parameters.
HOMER (version 4.9.1, Heinz et al., 2010) was used to generate bigWig files.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

source_name: Primary human monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit.

treatment_protocol: Cells were treated with or without IFN-γ (100 U/ml) for 48 hours and then stimulated with LPS (10 ng/ml) for 3 hours

value: peripheral blood

value: monocytes

tag: antibody

value: anti-CBP (Santa Cruz sc-369)


title: MacP2_4

value: ear skin

tag: cell type


title: WTClone2_E2_10D (RNA-seq)

tag: cell line

tag: treatment

value: 10 days


title: 7970368039_R01C01

city: Newcastle upon Tyne

value: Medulloblastoma


title: 7970368034_R05C02


title: D1808/14: ASD patient

value: no


title: 7970368034_R03C01


title: D120/14: ASD patient

value: F


title: WTClone1_E2_15D (RNA-seq)

value: Ishikawa WT ESR1 clone 1

value: WT ESR1

tag: time


title: WTClone1_E2_20D (RNA-seq)


title: 7970368034_R02C01

value: MBNOS


title: D1845/14: ASD patient

tag: gender


title: ChIP-seq_CBP_IFNg


title: WTClone1_E2_25D (RNA-seq)

value: 25 days


title: WTClone1_E2_10D (RNA-seq)


title: ChIP-seq_CBP_IFNg-LPS


title: D1993/14: ASD patient

value: autism spectrum disorders (ASD)


title: ChIP-seq_CBP_LPS


title: RNA-seq_LPS_rep2

data_processing:
FastQC was used to evaluate quality of sequenced reads (http://www.bioinformatics.babraham.ac.uk/project/fastqc). Contaminated adaptor portions of sequenced reads were trimmed using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/project/trim_galore).
Sequenced reads were mapped to reference human genome (hg19 assembly) using STAR aligner (2.5.2b, Dobin et al., 2013 Bioinformatics) with default parameters.
Cufflinks version 2.2.1 (Trapnell et al., 2012 Nat Protoc) was used to estimate the abundance (FPKM) of transcripts.
Genome_build: hg19
Supplementary_files_format_and_content: Text file (normalized expression level)

extract_protocol:
RNA extraction kit from QIAGEN, according to company's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: none, LPS


title: 7970368032_R05C01


title: WTClone2_E2_8hrs (RNA-seq)

value: Ishikawa WT ESR1 clone 2

value: 10nM E2

value: 8 hrs


title: D1938/14: ASD patient

value: M


title: 7970368032_R06C02


title: RNA-seq_LPS_rep1

value: peripheral blood

value: monocytes


title: D781/16: ID patient

value: intellectual disabilities (ID)


title: D1474/15: ID patient


title: 7970368032_R03C01


title: RNA-seq_IFNg-LPS_rep1

value: IFN-g, LPS


title: 7970368032_R02C01

value: Medulloblastoma


title: WTClone1_DMSO_8hrs (RNA-seq)

value: 0.1% DMSO


title: WTClone1_E2_8hrs (RNA-seq)


title: D1137/18: ID patient

value: no


title: RNA-seq_IFNg-LPS_rep2


title: 7970368032_R01C02


title: ChIP-seq_STAT3_Resting_rep2

description: antibody: anti-STAT3 (Santa Cruz sc-482)

value: Resting


title: D538GClone3_Rep2_DMSO (ChIP-seq)

data_processing:
Sequencing reads were aligned to the hg19 build of the human genome using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
MACS2 was used to call peaks with a p-value cutoff of 1*10-10 and a mfold parameter between 15 and 100. MACS2 also generated normalized bedgraphs.
Differential binding sites were identified by using DESeq2 to compare counts per million.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files
Supplementary_files_format_and_content: narrowPeak files (from MACS2)

value: Ishikawa D538G ESR1 clone 3

value: D538G ESR1

value: 1 hr

tag: chip antibody

value: Anti-FLAG (Sigma-Aldrich M2, lot# SLBX2256) antibody that recognizes FLAG tag on ESR1


title: 7970368013_R06C02

value: MBNOS


title: ChIP-seq_STAT3_Resting_rep1


title: D1775/18: ID patient

value: F

value: yes


title: 7970368013_R05C02


title: D538GClone3_Rep1_DMSO (ChIP-seq)


title: ChIP-seq_STAT3_LPS_rep2

value: LPS


title: D1774/17: ID patient


title: 7970368013_R05C01


title: D1848/17: ID patient


title: ChIP-seq_STAT3_LPS_rep1


title: WTClone2_DMSO_8hrs (RNA-seq)

value: Ishikawa WT ESR1 clone 2

value: WT ESR1

value: 8 hrs


title: D538GClone3_Rep2_E2 (ChIP-seq)

value: 10nM E2


title: 7970368032_R04C02


title: D538GClone3_Rep1_E2 (ChIP-seq)


title: D1656/17: ID patient

value: intellectual disabilities (ID)


title: D1279/17: ID patient

value: M


title: ChIP-seq_STAT3_IL10

value: peripheral blood

value: monocytes


title: 7970368013_R04C02

value: Medulloblastoma


title: ChIP-seq_STAT3_IFNg-LPS_rep2

value: IFNg-LPS


title: D538GClone2_Rep2_E2 (ChIP-seq)

value: Ishikawa D538G ESR1 clone 2

value: D538G ESR1


title: D538GClone2_Rep2_DMSO (ChIP-seq)

value: 0.1% DMSO

value: 1 hr

value: Anti-FLAG (Sigma-Aldrich M2, lot# SLBX2256) antibody that recognizes FLAG tag on ESR1


title: ChIP-seq_STAT3_IFNg-LPS_rep1


title: D1034/17: ID patient

value: F

value: yes


title: D538GClone2_Rep1_DMSO (ChIP-seq)


title: 7970368013_R03C01


title: 7970368013_R04C01

value: MBNOS


title: ChIP-seq_STAT3_IFNg_rep2

value: IFNg


title: D332/17: ID patient

value: no


title: D952/17: ID patient


title: ChIP-seq_STAT3_IFNg_rep1


title: 7970368013_R02C02


title: D538GClone1_Rep2_DMSO (ChIP-seq)

value: Ishikawa D538G ESR1 clone 1


title: 7970368013_R01C02


title: D604/17: ID patient

value: intellectual disabilities (ID)


title: 7970368013_R01C01


title: D538GClone2_Rep1_E2 (ChIP-seq)

value: 10nM E2


title: D2/17: ID patient


title: D1690/90: ID patient


title: D538GClone1_Rep2_E2 (ChIP-seq)


title: 7878191130_R06C02


title: ChIP-seq_PU_1_INFg-LPS_rep2

description: antibody: anti-PU.1 (Santa Cruz sc-352)

value: peripheral blood

value: INFg-LPS


title: D538GClone1_Rep1_DMSO (ChIP-seq)


title: 7878191130_R06C01

value: Medulloblastoma


title: ChIP-seq_SMC1_IFNg-LPS

description: antibody: anti-SMC1 (Bethyl Laboratories A300-055A)

value: monocytes

value: IFNg-LPS


title: D726/15: ID patient

value: M


title: ChIP-seq_PU_1_IFNg-LPS_rep1

description: antibody: anti-PU.1 (Santa Cruz sc-352)


title: D538GClone1_Rep1_E2 (ChIP-seq)

value: D538G ESR1


title: D1349/15: ID patient


title: ChIP-seq_PolII_LPS

description: antibody: anti-RNA Polymerase II (Covance MMS-126R)

value: LPS


title: D254/15: ID patient


title: WTClone2_Rep2_DMSO (ChIP-seq)

value: Ishikawa WT ESR1 clone 2

value: WT ESR1

value: 0.1% DMSO

value: 1 hr

value: Anti-FLAG (Sigma-Aldrich M2, lot# SLBX2256) antibody that recognizes FLAG tag on ESR1


title: 7878191130_R03C02


title: ChIP-seq_PolII_IFNg-LPS


title: WTClone2_Rep1_DMSO (ChIP-seq)


title: ChIP-seq_SMC1_LPS


title: 7878191130_R01C02


title: D269/14: ID patient

value: no


title: WTClone2_Rep1_E2 (ChIP-seq)


title: 7878191130_R05C01


title: WTClone2_Rep2_E2 (ChIP-seq)


title: D1066/14: ID patient

value: yes


title: 7878191130_R01C01


title: ChIP-seq_CEBPB_IFNg-LPS_rep1

description: antibody: anti-CEBPB (Santa Cruz sc-150)


title: WTClone1_Rep2_DMSO (ChIP-seq)

value: Ishikawa WT ESR1 clone 1


title: D1939/14: ID patient

value: intellectual disabilities (ID)


title: ChIP-seq_CDK8_Resting

description: antibody: anti-CDK8 (Santa Cruz sc-1521)

value: peripheral blood

value: Resting


title: 6264509032_R06C01

value: Medulloblastoma


title: WTClone1_Rep2_E2 (ChIP-seq)

value: 10nM E2


title: 6222421011_R06C02


title: ChIP-seq_CEBPB_IFNg-LPS_rep2

value: monocytes

value: IFNg-LPS


title: D1940/14: ID patient

value: M


title: WTClone1_Rep1_DMSO (ChIP-seq)


title: D924/07: ID patient


title: 6222421011_R06C01


title: ChIP-seq_CDK8_LPS

value: LPS


title: 7878191130_R04C01


title: D133/14: ID patient


title: WTClone1_Rep1_E2 (ChIP-seq)


title: ChIP-seq_CDK8_IFNg

value: IFNg


title: 6222421011_R04C02


title: D1859/14: ID patient


title: ATAC-seq_LPS_rep1

extract_protocol:
Nuclei were pelleted by centrifugation for 5 min at 500g, 4°C.
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol developed by (Buenrostro et al., 2013); single end protocol.


title: D1278/14: ID patient

value: F


title: ATAC-seq_LPS_rep2


title: 6222421011_R01C02


title: 6222421011_R02C02


title: D689/14: ID patient


title: ATAC-seq_IFNg_LPS_rep1


title: D538GClone3_E2 (ATAC-seq)

data_processing:
ATAC-seq reads were aligned to hg19 using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2.
Sam files were converted to bam files and sorted with Samtools.
Macs2 was used to call peaks without an input control but with a p-value cutoff of 1*10-10.
We used featureCounts from the Subread package in R to quantify reads that aligned to ATAC-seq peaks called .
Reads were normalized and analyzed for differential enrichment using the DESeq2 package for R.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files

extract_protocol:
After treatments, cells were trypsinized and isolated by centrifugation.
ATAC-seq was performed as originally described in Buenrostro et al. 2013

treatment_protocol: Media was changed 1 day prior to inductions and cells were treated with either DMSO (vehicle) or 10 nM (estradiol) E2 for 1 hour or 8 hours. For prolonged estrogen samples, wildtype cell lines were cultured in phenol-red free RPMI with 10% charcoal-dextran stripped fetal bovine serum and 1% pen-strep for up to 25 days. Cells were treated with 10 nM E2 every 2 days with media changes, and cell lysates were collected at the following time points: day 10, day 15, day 20, day 25.

value: Ishikawa D538G ESR1 clone 3

value: D538G ESR1


title: 6164655140_R03C01


title: 6222421011_R03C02


title: ATAC-seq_IFNg_LPS_rep2


title: D538GClone2_DMSO (ATAC-seq)

value: Ishikawa D538G ESR1 clone 2

value: 0.1% DMSO

value: 1 hr


title: H2AE57A_Input-ChIPseq_Rep2

extract_protocol:
Ovation Ultralow v2 kit (NuGEN, 0344)
Total chromatin was isolated by bead beating in 1XFA + 0.5% SDS buffer with PMSF.

tag: plasmid

value: pCEC02 = HIS3/CEN/ARS/hta1E57A-HTB1


title: D538GClone2_E2 (ATAC-seq)


title: ChIP-seq_CDK8_IFNg-LPS


title: 6164655140_R01C01


title: WT_Input-ChIPseq_Rep2

source_name: WT

value: pAY01 = HIS3/CEN/ARS/HTA1-HTB1


title: D538GClone1_DMSO (ATAC-seq)

value: Ishikawa D538G ESR1 clone 1


title: WTClone2_E2_25D (ATAC-seq)

value: Ishikawa WT ESR1 clone 2

value: WT ESR1

value: 25 days


title: D538GClone1_E2 (ATAC-seq)

value: 10nM E2


title: 6026818136_R01C02

value: Medulloblastoma


title: 6026818126_R04C01


title: D538GClone3_DMSO (ATAC-seq)


title: H2AE57A_Input-ChIPseq_Rep1


title: WTClone2_E2_20D (ATAC-seq)

value: 20 days


title: WT_Input-ChIPseq_Rep1


title: D1583/13: ID patient

extract_protocol: Genomic DNA was extracted from mononuclear cell  of peripheral blood using saline method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

value: intellectual disabilities (ID)

value: M

value: yes


title: H2AE57A_H3-ChIPseq_Rep2


title: WTClone2_E2_15D (ATAC-seq)

value: 15 days


title: 6026818126_R01C01


title: H2AE57A_H3-ChIPseq_Rep1


title: WT_H3-ChIPseq_Rep2


title: WTClone2_E2_10D (ATAC-seq)

value: 10 days


title: WTClone1_E2_25D (ATAC-seq)

value: Ishikawa WT ESR1 clone 1


title: WTClone1_E2_20D (ATAC-seq)


title: WT_H3-ChIPseq_Rep1


title: WTClone1_E2_10D (ATAC-seq)


title: WTClone1_E2_15D (ATAC-seq)


title: Exp2 E19_EtOH2

city: Los Angeles

first: Yong

last: Kim

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

description: exosomal small RNA

data_processing:
Adapters and low-quality nucleotides were removed from raw fastq sequences using Cutadapt (v.1.11).
Adapter-free sequences were mapped to the Rat genome (rn5) using bowtie (v.1.1.2) using the parameters ‘-v 1 –k 100 –best –strata’.
Mapped reads were annotated to mature rat miRNA and piRNA. Rat miRNA annotations (rn5) were downloaded from miRBase. Rat piRNA annotations (rn4) were downloaded from piRNABank. Liftover of piRNA annotations rn4 to rn5 was performed since rn5 annotations were not available
Bowtie alignments were annotated to miRNA and piRNA coordinates by requiring the alignment start site to be between -3nt to +2nt positions near the annotated start site and the alignment end site be between -2nt and +3nt of the annotated end site. Multi-mapped reads are distributed 1/n, where n is the number of mapping locations.
DESeq2 (version 1.14.1) was used to further normalize and determine differential expression of miRNA and piRNA species between control and EtOH-treated groups. Reads were aligned to the spike-in control sequences, allowing no mismatches.
Genome_build: rn5, rn4
Supplementary_files_format_and_content: miRNA_piRNA_normalized_read_counts.xlsx

organism: Rattus norvegicus

source_name: amniotic fluid

extract_protocol:
Amniotic fluids were harvested at E16 and E19 and exosomes were isolated for RNA isolation
NEBNext Small RNA Library Prep set
exosomal RNA (20 ng each) was mixed with 1/15 amount of Spike-in RNA

treatment_protocol: Pregnant dams were treated with 0 or 2.5 g/kg of 20% EtOH by oral gavage on embryonic days 5, 8, 10, 12 and 15

value: Sprague-Dawley

value: EtOH

tag: age

value: Embryonic day 19

tag: sample type

value: amniotic fluid


title: Exp2 E19_EtOH1

description: exosomal small RNA

tag: strain


title: WTClone2_E2_8hrs (ATAC-seq)

value: 8 hrs


title: WtPH: PGC-1a4 + TNFa 3

city: Montreal

first: Jennifer

middle: Lynn

last: Estall

state: Quebec

address: 110 avenue des Pins ouest

country: Canada

institute: IRCM

description: microarray expression data from primary hepatocytes

hyb_protocol: standard Affymetrix procedure.

scan_protocol: standard Affymetrix procedure.

data_processing: The data were analyzed with RMA (log2) normalized data using the just.rma function in the affy package in Biocinductor

source_name: primary hepatocytes

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

growth_protocol: 25 mM glucose DMEM supplemented with 0,2% BSA, 2 mM sodium pyruvate, and pen/strep.

extract_protocol: RNeasy Kit column extraction

treatment_protocol: Adenoviral infection (48 hours) followed by treatment for two hours with 2 ng/mL TNFalpha

value: liver

value: WtPH

tag: genotype/variation

value: protein variant

value: primary mouse hepatocytes

tag: isoform

value: TNFalpha


title: Exp2 E19_Control 2

description: exosomal small RNA

value: control


title: WtPH: PGC-1a1 + TNFa 3

tag: tissue

value: wild-type protein over-expressed


title: WtPH: PGC-1a4 + TNFa 2


title: fat cd10+

city: Nanjing City

first: Lijun

last: Ding

address: 321#，Zhongshan Road

department: Department of Obstetrics and Gynecology

country: China

institute: the Affiliated Drum Tower Hospital of Nanjing University Medical School

description:
Sample_Label: F1
Chip_Barcode: H001-1101012052
Chip_Label: F1_H001
adult fat tissues
primary cells

hyb_protocol: OneArray Plus hyb procedure.

scan_protocol: Agilent 0.1 XDR scan procedure.

data_processing:
Data normalization; Identify differentially expressed genes (unlimited statistical comparisons); Principal components analysis; Hierarchical clustering; Gene Ontology and Pathway enrichment analyses (for each list of differentially expressed genes) were carried out by Phalanx Biotech Group.
The screening condition of differential gene is set to log2| Fold change| ≥1 and P<0.05.

source_name: sorted human fat cd10+ adventitial cells

label_protocol: 5 ug Cy5 were used to label the RNA.

growth_protocol: Sorted CD10+ and CD10- adventitial cells were cultured in vitro for one week.

extract_protocol: Total RNA was isolated using TRIzol® (Invitrogen) and treated with DNase Ⅰ(Promega) to remove any contaminating genomic DNA. RNA quality was evaluated using spectrophotometry and denaturing agarose gel electrophoresis.

treatment_protocol: No treatments.

value: male

tag: developmental stage

value: adult

value: fat

value: cd10+ adventitial cells


title: Input / clone #4

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Sequenced DNA reads were mapped to mouse genome (mm10) using Illumina analysis pipeline CASAVA (version 1.8.2) and only the reads that were mapped to unique position were retained.
To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
The initial peak calling was done by HOMER (version 4.6) using two different parameter settings. The stringent setting is the default setting of HOMER: fold change to input ≥ 4, pvalue to input ≤ 1e-4, fold change to local signal ≥ 4 and pvalue to local signal ≤ 1e-4. And a less stringent setting is fold change to input ≥ 2, pvalue to input ≤ 1e-3, fold change to local signal ≥ 2 and pvalue to local signal ≤ 1e-3. The peak size was set as 150bp. Then the peaks of the two replicates called at the stringent setting were merged (allowing at most 200 bp) and only the merged peaks that overlapped the peaks of both replicates at the less stringent setting were called as the peaks of Zbtb24.
Genome_build: mm10
Supplementary_files_format_and_content: The peak locations in bed format

source_name: Zbtb24 KO mES_input

growth_protocol: Mouse ES cells were cultured in serum-containig ES cell medium on gelatin-coated plates.

extract_protocol:
Lysates were clarified from sonicated nuclei and ZBTB24-DNA complexes were isolated with HA antibody.
A modified KAPA LTP Library Preparation Kit Illumina Platform (Kapa Biosystems, Wilmington, MA, USA).

treatment_protocol: A plasmid vector expressing HA-ZBTB24 was transfected into Zbtb24 KO ES cells, and stable clones were obtained after selection with blasticidin.

tag: strain background

value: Zbtb24 KO

value: embryonic stem cells

tag: protein expressed


title: HA-ZBTB24 ChIP / clone #4

source_name: Zbtb24 KO mES_HA-ZBTB24 ChIP

value: HA

tag: chip antibody vendor

value: Cell Signaling Technology (CST)

tag: chip antibody cat. #

tag: chip antibody clone #


title: WtPH: Vector + TNFa 1

tag: cell line

value: Control (baseline)

tag: cell type

value: Control (vector)

tag: treatment


title: Input / clone #3

tag: chip antibody


title: WtPH: PGC-1a1 + TNFa 1

value: liver


title: Exp2 E19_Control 3

description: exosomal small RNA

value: Sprague-Dawley

value: Embryonic day 19

value: amniotic fluid


title: HA-ZBTB24 ChIP / clone #3


title: Exp2 E19_Control 1

description: exosomal small RNA


title: WtPH: PGC-1a4 + TNFa 1

value: WtPH

value: protein variant

value: primary mouse hepatocytes

value: TNFalpha


title: WtPH: Vector + TNFa 3


title: WtPH: Vector + TNFa 2


title: WtPH: PGC-1a4 3

value: vehicle (PBS)


title: WtPH: PGC-1a1 + TNFa 2

value: wild-type protein over-expressed


title: fat cd10-

description:
Sample_Label: F2
Chip_Barcode: H002-1101012054
Chip_Label: F2_H002
adult fat tissues
primary cells

source_name: sorted human fat cd10- adventitial cells

tag: gender

value: male

value: adult

value: fat

value: cd10- adventitial cells


title: Exp2 E16_EtOH2

description: exosomal small RNA

value: EtOH

tag: age

value: Embryonic day 16


title: WTClone2_DMSO_1hr (ATAC-seq)

value: Ishikawa WT ESR1 clone 2

tag: genotype

value: WT ESR1

value: 0.1% DMSO

tag: time

value: 1 hr


title: Exp2 E16_EtOH3

description: exosomal small RNA

tag: strain

value: Sprague-Dawley

tag: sample type

value: amniotic fluid


title: WTClone2_E2_1hr (ATAC-seq)

value: 10nM E2


title: Exp2 E16_EtOH1

description: exosomal small RNA


title: WtPH: PGC-1a4 2

tag: tissue

value: liver

value: WtPH

tag: genotype/variation

value: protein variant

value: primary mouse hepatocytes

tag: isoform


title: WTClone1_E2_1hr (ATAC-seq)

value: Ishikawa WT ESR1 clone 1


title: Exp2 E16_Control 3

description: exosomal small RNA

value: control


title: WTClone1_DMSO_1hr (ATAC-seq)


title: Exp2 E16_Control 2

description: exosomal small RNA


title: WtPH: PGC-1a4 1

value: vehicle (PBS)


title: WtPH: PGC-1a1 3

value: wild-type protein over-expressed


title: WtPH: PGC-1a1 2


title: Exp1 E19_EtOH3

description: exosomal small RNA

value: EtOH

value: Embryonic day 19


title: WTClone1_E2_8hrs (ATAC-seq)

value: 8 hrs


title: Exp1 E19_EtOH2

description: exosomal small RNA


title: Exp1 E19_EtOH1

description: exosomal small RNA


title: Exp1 E19_Control 3

description: exosomal small RNA


title: NK IL2 donor 3

city: London

first: May

last: Sabry

address: Rowland Hill Street

institute: University College London

description: Lymphokine-activated NK cells

hyb_protocol: Samples were hybridized with probes at 65°C for 18 hours before being placed into the automated nCounter™ Prep Station (NanoString Technologies), where samples were affixed to cartridges.

scan_protocol: Cartridges were immediately placed into the nCounter™ Digital Analyzer (Nanostring Technologies) and read at maximum resolution

data_processing: Using nSolver software, QC  was carried out using default QC parameter settings. Then, raw data files  were examined to ensure that counts of positive and negative controls as well as housekeeping/endogenous genes meet expectations. Thereafter, background noise was adjusted by background thresholding using a user-defined threshold count value of 20 counts. Normalization was accomplished using the geometric mean of the positive control counts, and housekeeping genes in the CodeSet Content. Differential expression was calculated by specifying NK alone samples as the baseline of the experiment using nSolver software.

label: Target-probe complex

source_name: Lymphokine-activated NK cells

label_protocol: Batches of 12 separate samples at one time were prepared as per manufacturer’s instructions.  Platform used was human myeloid innate immunity panel (Catalog number XT-CSO-HMMYLD1-12).

growth_protocol: NK cells were isolated from healthy donor PBMCs by positive selection for CD56 (CD56 MicroBeads; Miltenyi Biotec) according to the manufacturer’s instructions. Freshly isolated NK cells were maintained in complete medium (CM) (RPMI 1640 supplemented with 10% v/v fetal bovine serum and 2mM L-glutamine; all from Life Technologies). The  acute lymphoblastic leukemia cell line CTV-1 was maintained in CM.

extract_protocol: To prepare the samples, resting NK cells (5x10^5) were washed twice and incubated alone or mixed with mitomycin-C-treated CTV-1 cells (1x10^6) for 6 hours, or IL-2 (200 IU/ml) for 16 hours at 37°C in 5% v/v CO2. Thereafter, NK cells were selectively enriched from co-culture by CD56 isolation, and RNA was extracted from the samples using the RNAqueousTM Micro Kit (Thermo Fisher Scientific).

treatment_protocol: NK cell stimulation was achieved by co-incubating CD56+ NK cells (1x10^6) with CTV-1 (2x10^6) for 6 or 16 hours, or the exogenous cytokine IL-2 (200IU/ml) for  16 hours at 37ºC, 5% v/v CO2 in CM.

value: peripheral blood

value: natural killer cells


title: RNAP_15

first: James

middle: A

last: Kraemer

address: 31 Ames St, Building 68-570

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Paired-end reads were mapped to the MG1655 genome using bowtie2 using the arguments: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -p 6 -l 40 -X 300.
Bowtie alignments were converted to csv files by mapping reads to gene extent regions
Genome_build: NC_000913.2
Supplementary_files_format_and_content: csv files were generated using custom python scripts. First column represents gene name and second column represents number of reads

organism: Escherichia coli K-12

source_name: Bacterial liquid culture

growth_protocol: E. coli was grown to OD 0.2 before treatment or harvest in M9GAV + nucleobases (1x M9 salts, 0.4% glucose, 0.25% each of l-serine and l-threonine, 0.0375% each of l-asparagine and l-glutamine, 0.015% each of all 16 other natural amino acids, 1× Kao & Michayluk Vitamins, and 0.2 mM of each nucleobase).

extract_protocol:
RNA was extracted by hot trizol lysis and Direct-zol RNA MiniPrep (Zymo). rRNAs were removed using the Ribo-Zero Kit for Gram-negative bacteria (Illumina) and mRNAs were then fragmented with RNA fragmentation reagents (Ambion). First-strand cDNA synthesis was performed with random primers (Invitrogen) and Superscript III. After purifying cDNAs by phenol:chloroform:isoamyl alcohol extraction and precipitation, second-strand synthesis occurred with dUTP (Promega) instead of dTTP and RNase H (NEB), E.coli DNA ligase (NEB), and DNA Pol I (NEB). Sequencing libraries were built as with other libraries, except that the second strand was digested with USER (NEB) after the addition of Y-adaptors.
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with either Phusion (NEB) or Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 250-600 bp.

treatment_protocol: 1 μL of a 1:10 dilution of ERCC RNA Spike-IN Mix 1 was added to frozen cell pellet immediately before extraction.

value: Escherichia coli K12 liquid culture

tag: growth stage

value: exponential phase

value: rpoZ<delta>2-5-kanR rpoC R362A R417A K615A N680A K681A-tetAR, Ptac-relA'

tag: media

value: M9GAV + 0.2 mM nucleobases

tag: growth treatment

value: 150 µM IPTG added for 15 min to induce RelA'


title: NK IL2 donor 1

description: Lymphokine-activated NK cells


title: RNAP_0


title: WtPH: PGC-1a1 1

value: liver

value: WtPH