title: WM989-A6G3_Fluidigm COL19_ROW15_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW10_sample19

status: Public on May 26 2017

type: SRA

city: Philadelphia

first: Eduardo

middle: A

last: Torre

state: PA

department: Bioengineering

country: USA

institute: University of Pennsylvania

description: fluidigmRPM

library_source: transcriptomic

data_processing:
Drop-seq data processing was performed using Drop-seq_tools-1.0.1 ( http://mccarrolllab.com/dropseq/ ), and following protocol described in seqAlignmentCookbook_v1.1Aug2015.pdf
Data were aligned to reference genome builds hg38 (Human) and mm10 (Mouse) via STAR version 2.4.2a. We used reference transcriptome annotations Gencode21 (Human) and Refseq mm10 (Mouse).
For DropSeq, reads with low-quality base in either cell or molecular barcode were filtered and reads were trimmed for contaminating primer or poly-A sequence. Sequencing errors in barcodes were inferred and corrected, as implemented by Drop-seq_tools-1.0.1. Uniquely mapped reads, with <= 1 insertion or deletion, were used in quantification. To account for differences in molecule recovery, cell measurements were normalized to UMI per million (UPM).
Fluidigm sequence data were demultiplexed using mRNASeqHT_demultiplex.pl ( https://www.fluidigm.com/c1openapp/scripthub/script/2015-08/mrna-seq-ht-1440105180550-2) .
Demultiplexed data were processed in the same manner as Drop-seq data, with a few modifications: 5’ ends of reads were not trimmed, and reads (rather than UMI) were used for quantification. To account for differences in molecule recovery and sequencing depth, cell measurements were normalized to reads per million (RPM).
Genome_build: hg38 (Human) and mm10 (Mouse)
Supplementary_files_format_and_content: .txt files represent either raw count data or count data normalized to UMI per million (in the case of DropSeq) or read per million (in the case of Fluidigm)

molecule: total RNA

organism: Homo sapiens

source_name: Melanoma cells

growth_protocol: WM989-A6G3 cells were routinely passaged on Tu2% media.

extract_protocol:
DropSeq libraries were built according to Macoscko et. al, protocol v3.1 (http://mccarrolllab.com/dropseq/). Fluidigm libraries were constructed according to the manufacturer's instructions.
DropSeq libraries were built according to Macoscko et. al, protocol v3.1 (http://mccarrolllab.com/dropseq/). Fluidigm libraries were constructed according to the manufacturer's instructions.
single cell RNA-seq

tag: cell type

value: melanoma


title: WM989-A6G3_Fluidigm COL19_ROW12_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW09_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW11_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW07_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW06_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW08_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW03_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW05_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW01_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW04_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW02_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW40_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW38_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW37_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL19_ROW17_sample19

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW35_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW33_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW32_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW34_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW31_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW30_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW29_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW28_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW23_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW24_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW25_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW21_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW20_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW19_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW39_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW17_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW15_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW13_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW22_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW18_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW12_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW11_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW10_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW08_sapme18

description: fluidigmRPM


title: Ct_1

city: Jerusalem

first: uriya

last: Bekenstein

address: Safra

department: Dept. of Biological Chemistry

country: Israel

institute: HUJI

description: Frontal cortex RNA of mouse

data_processing:
86-bp long reads. percent of quality (Q30) reads was 94-95%.
Reads were aligned (90% mapping) to the mouse transcriptome (TopHat2), Using the DeSeq software via R platform
Supplementary_files_format_and_content: ENSEMBLE ID PER ANIMAL, AS TEXT FILE

organism: Mus musculus

source_name: Fronral cortex

extract_protocol:
RNA was extracted by miRNeasy kit (QIAGEN), RNA quality determined with 6000-Nano Bioanalyzer (Agilent, Santa Clara, CA.), and samples with RIN values ranged between 8 and 8.9 were used
Sequencing-compatible poly A-terminated single-end libraries were generated using an RNA Library prep kit (NEBNext® Multiplex, E7330S, New England Biolabs) following manufacturer’s instructions, with 12 amplification rounds
poly A-terminated single-end libraries: Libraries were sequenced on a NextSeq Series Sequencing System (The HUJ Center for Genomic Technologies) using two Illumina chips (Illumina 500® NextSeq High Output v2 Kit, FC-404-2005, Illumina).

treatment_protocol: Mice were anesthetized with isoflurane prior to cervical dislocation and their brain regions including frontal cortices were dissected and collected

tag: strain

value: FVB/N

tag: genotype

value: CamK

tag: dox, days

tag: Sex

value: Male


title: WM989-A6G3_Fluidigm COL18_ROW27_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW04_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW36_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW16_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW26_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW06_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW02_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW03_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW01_sapme18

description: fluidigmRPM


title: KO animals 1, 2, 3 pooled (cerebellum)

status: Public on May 27 2017

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

country: Germany

institute: GenXPro GmbH

description: MACE (massive analysis of cDNA ends)

data_processing:
Sequencing on Illumina HiSeq 2000, basecalling pipeline: HiSeq Control Software 1.5.15.1, RTA 1.13.48.0, CASAVA-1.8.2, Flow cell version: HiSeq Flow Cell v3, Kit version: TruSeq SBS Kit v3
Sequences were cleaned from duplicates ("TrueQuant"), Bases with low sequencing quality were trimmed.
The trimmed reads were mapped to NCBI RefSeq mouse sequences and UCSC genome version mm9.2 using "SOAP2.2" with the following parameters “-p 16 -r 2 -v 5 -w 10 -g 1“
Expression analysis was performed by in-house scripts and DEGSeq (R-package)
Genome_build: NCBI RefSeq mouse sequences, mm9.2
Supplementary_files_format_and_content: Tab-delimited text files contain read counts, normalized read counts, p-values, fold changes

source_name: cerebellum

extract_protocol:
After cervical dislocation, cerebellum, midbrain and liver were dissected from homozygous wild-type (Atxn2+/+) and knock-out (Atxn2-/-) mice at 6, 12 and 24 weeks of age. Total RNA was extracted from these tissues by homogenization in 1 ml of Trizol® Reagent per 50 – 100 mg of tissue using a Pellet Pestle® Motor tissue homogenizer (Kontes, The Glass Company). One µg total RNA was digested with a DNase I Amplification Grade Kit (Invitrogen, Karlsruhe) in a reaction volume of 10 µl per tube in order to eliminate DNA during RNA purification prior to reverse transcription (RT-PCR) amplification.
For preparation of MACE libraries, poly-adenylated mRNA was isolated from 1 μg of the large fraction of total RNA using Dynabeads® mRNA Purification Kit (Life Technologies GmbH) and cDNA was produced by first and second strand synthesis using the SuperScript® III First-Strand Synthesis System (Life Technologies GmbH). , but with modified, barcoded poly-T adapters that are suitable to bind on the Illumina Hiseq2000 flow cell and that are biotinylated at the very 5′ end. After cDNA production, the biotinylated cDNA was random-fragmented to reach an average size of 250 bps, the 3′ends were captured by streptavidin beads and GenXPro’s TrueQuant adapters were ligated. Ten barcoded samples were sequenced simultaneously in one lane of an Illumina Hiseq2000 with 1 × 100 bps.

tag: tissue

value: cerebellum

tag: age

value: 6 months


title: WM989-A6G3_Fluidigm COL17_ROW39_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW38_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW40_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW14_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW36_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW37_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW35_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW33_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW30_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW32_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW31_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW29_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW09_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW34_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW27_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW28_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW26_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW05_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL18_ROW07_sapme18

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW24_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW25_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW23_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW22_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW21_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW19_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW20_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW16_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW15_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW12_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW13_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW10_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW09_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW11_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW08_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW06_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW04_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW01_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW03_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW40_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW05_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW02_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW38_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW39_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW37_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW35_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW18_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW34_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW33_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW36_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW17_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW14_sample17

description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW30_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW32_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW25_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW31_sampl16

description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW22_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW21_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW18_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW20_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW16_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL17_ROW07_sample17

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW13_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW12_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW15_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW14_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW11_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW10_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW09_sampl16

description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW03_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW37_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW40_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW36_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW35_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW34_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW38_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW33_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW32_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW39_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW17_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW31_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW30_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW28_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW29_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW19_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW24_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW23_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW22_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW20_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW21_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW27_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW26_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL16_ROW07_sampl16

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW18_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW19_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW17_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW15_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW16_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW10_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW13_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW14_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW08_sample15

description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW07_sample15

description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW05_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW01_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW04_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW02_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW03_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL15_ROW25_sample15

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW40_sample14

description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW25_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW24_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW14_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW12_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW19_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW17_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW21_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW18_sample14

description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW11_sample14

description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW35_sample14

description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW38_sample14

description: fluidigmRPM


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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW22_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW16_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW06_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW09_sample14

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL14_ROW05_sample14

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title: WM989-A6G3_Fluidigm COL14_ROW08_sample14

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description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW23_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW22_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW20_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW19_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW18_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW15_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW32_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW16_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW38_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW17_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW12_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW14_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW13_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW09_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW08_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW10_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW07_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW05_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW06_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW02_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW01_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW04_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW40_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW39_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW03_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW37_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW38_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW36_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW35_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW11_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW33_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW32_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW24_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW31_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW28_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW26_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW25_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW29_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW27_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW21_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW18_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW14_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW15_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW16_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW12_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW17_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW19_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW34_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW11_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW10_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW20_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW13_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL07_ROW21_sample7

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW30_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW09_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW23_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW06_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW22_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW07_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW08_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW39_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW05_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW03_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW02_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW04_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL06_ROW01_sample6

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW40_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW38_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW37_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW35_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW31_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW36_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW34_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW32_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW29_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW30_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW27_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW23_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW24_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW25_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW22_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW28_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW33_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW26_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW21_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW17_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW19_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW20_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW18_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW16_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW15_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW11_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW13_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW14_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW12_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW08_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW09_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW07_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW06_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW05_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW03_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW02_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW40_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW38_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW36_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW37_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW35_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW32_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW39_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW30_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW31_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW34_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW29_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW10_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW28_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW27_sample4

description: fluidigmRPM


title: Lu130_Suz12_ChIPSeq

city: Meguro-ku

first: Atsushi

last: Kaneda

state: Tokyo

address: 4-6-1 Komaba

department: RCAST

country: Japan

institute: The University of Tokyo

library_source: genomic

data_processing:
Basecalls performed using Illumina pipeline softwqre
ChIPseq reads were aligned to the NCBI Build #36 (UCSC hg18) reference human genome, using ELAND (Illumina mapping program)
Genome_build: hg18

molecule: genomic DNA

growth_protocol: Lu130 and H209 were cultured in RPMI1640 containing penicillin and streptomycin, supplemented with 10% fetal bovine serum at 37 °C in 5% CO2. DMS53 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing penicillin and streptomycin, supplemented with 10% fetal bovine serum at 37 °C in 5% CO2. SAEC was cultured according to supplier’s instruction using SAGM BulletKit and Reagent Pack (Lonza).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature and were prepared for ChIP. Briefly, cells were crosslinked with 1% formalin for 10 min, and crosslinked cell lysates underwent fragmentation by sonication and incubated with antibodies bound to protein A-sepharose beads (50% slurry) overnight at 4 ºC. The beads were washed several times and eluted with elution buffer (1% SDS, 0.1 M NaHCO3). The eluates were treated with 1.5 μg of pronase 2 hr at 42 ºC then incubated at 65 ºC over night to reverse the crosslinks. The ChIP’ed DNA was purified by phenol/chroloform treatment and precipitated with LiCl and 70% ethanol.
Sample preparation for ChIP-seq was performed according to the manufacturer's instructions (Illumina). Briefly, size fractionated DNA was extracted and a single adenosine was added using Klenow exo– (3' and 5' exo minus; Illumina). Illumina adaptors were then added and DNA was subjected to 20 cycles of PCR according to manufacturer's instructions.

tag: cell line

value: Small cell lung cancer cell line

tag: chip antibody

value: Suz12 (D39F6, Cell Signaling, rabbit monoclonal)


title: WM989-A6G3_Fluidigm COL04_ROW26_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL05_ROW04_sample5

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW22_sample4

description: fluidigmRPM


title: Lu130_H3K27me3_ChIPSeq

value: H3K27me3 (07-142, Upstate, abbit polyclonal)


title: DMS53_H3K27me3_ChIPSeq


title: WM989-A6G3_Fluidigm COL04_ROW21_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW33_sample4

description: fluidigmRPM


title: SAEC_H3K27me3_ChIPSeq

value: SAEC

value: Normal small airway epithelial cell


title: WM989-A6G3_Fluidigm COL04_ROW19_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW20_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW18_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW17_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW16_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW15_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW13_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW12_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW10_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW08_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW14_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL08_ROW31_sample8

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW06_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW09_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL08_ROW24_sample8

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW07_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW23_sample4

description: fluidigmRPM


title: H209_H3K27me3_ChIPSeq


title: WM989-A6G3_Fluidigm COL04_ROW05_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW04_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW03_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW01_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW02_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW40_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW39_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW38_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW35_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW11_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW34_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW36_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW37_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW33_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW31_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW32_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW30_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW29_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW28_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW27_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW24_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW23_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW26_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW22_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW21_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW16_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW19_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW20_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW18_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW15_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW14_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW13_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW12_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW11_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW09_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW10_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW07_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW06_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW08_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW05_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW25_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW03_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW40_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW02_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW37_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW38_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW35_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW17_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW39_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW33_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW31_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW32_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW34_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW36_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW28_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW30_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW29_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW27_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW24_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW25_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW23_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW26_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW04_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW20_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL03_ROW01_sample3

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW19_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW18_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW16_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW15_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW14_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW17_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW13_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW12_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW11_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW09_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW08_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW07_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW05_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW10_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW03_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW04_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW21_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW22_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW02_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW01_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW40_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW39_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW36_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW37_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW35_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW25_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL04_ROW24_sample4

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW34_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW30_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW32_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW29_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW28_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW27_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW26_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL02_ROW06_sample2

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW24_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW25_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW22_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW23_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW21_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW20_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW17_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW38_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW16_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW14_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW18_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW12_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW15_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW11_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW31_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW07_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW10_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW09_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW08_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW33_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW05_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW06_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW04_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW02_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW01_sample1

description: fluidigmRPM


title: WM989-A6G3_Fluidigm COL01_ROW19_sample1

description: fluidigmRPM


title: WM989-A6G3_DropSeq

description: dropseqUPM


title: WM989-A6G3_Fluidigm COL01_ROW03_sample1

description: fluidigmRPM


title: Microfilaria Ivermectin 7 day exposure replicate 2

city: Athens

first: Adrian

middle: J.

last: Wolstenholme

state: GA

address: 501 DW Brooks Dr.

department: Infectious Diseases

institute: University of Georgia

data_processing:
Read mapping: was performed using TopHat v2.0.14
Raw count extraction: was performed using HTSEQ v0.6.1p1
Genome_build: Brugia malayi wormbase assembly WS253
Supplementary_files_format_and_content: Tab-delimited txt file, raw count matrix

organism: Brugia malayi

source_name: total RNA

growth_protocol: Mongolian gerbils (Meriones unguiculatus) were infected with L3 larvae of Brugia malayi ip. Infected animals were maintained for four months until infections were patent.

extract_protocol: RNA-Seq for the Illumina' TruSeq strand-specific kit

treatment_protocol: Infected gerbils were treated with either 6mg/kg DEC, 0.2 mg/kg Ivermectin or 1mg/kg albendazole, or left untreated. The adult worms and microfilariae were isolated 1 day or 7 days after treatment.

tag: sex/stage

value: Microfilaria

tag: isolation time, post treatment

value: Day 7

tag: replicate

tag: drug treatment

value: Ivermectin


title: Microfilaria Ivermectin 7 day exposure replicate 1


title: Microfilaria Ivermectin 1 day exposure replicate 1

value: Day 1


title: WM989-A6G3_Fluidigm COL01_ROW13_sample1

description: fluidigmRPM


title: Microfilaria Ivermectin 1 day exposure replicate 3


title: Male Ivermectin 7 day exposure replicate 2

value: Male worm


title: Male Ivermectin 1 day exposure replicate 2


title: Male Ivermectin 1 day exposure replicate 3


title: Male Ivermectin 1 day exposure replicate 1


title: Male Ivermectin 7 day exposure replicate 1


title: Female Ivermectin 7 day exposure replicate 3

value: Female worm


title: Female Ivermectin 7 day exposure replicate 2


title: Asthmatics_d7_GKH12

city: Cincinnati

first: Gurjit

last: Khurana Hershey

state: Ohio

address: 3333 Burnet Avenue

department: Division of Asthma Research

institute: Cincinnat Children's Hospital Medical Center

description:
GKH12
Processed data file: RawCount.txt
Processed data file: countsTable.txt

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8.
Sequenced reads were mapped to hg19 whole genome using TopHat v2.0.3 with default parameters.
Number of reads was calculated for each Entrez gene.
Differential expression analysis was performed using edgeR.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RawCount.txt: Tab-delimited text file includes the raw counts. Genes in rows and samples in columns.
Supplementary_files_format_and_content: countsTable.txt: Tab-delimited text file includes the Reads Per Kilobase of transcript per Million mapped reads (RPKM) normalized values of the raw counts. Genes in rows and samples in columns.

source_name: Nasal epithelial cells, asthmatic, 1 week post infection

extract_protocol:
RNA was extracted from the nasal epithelial samples using Qiagen AllPrep DNA/RNA Mini Kit®, Hilden, Germany.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Asthmatics and non-asthmatic controls were inoculated with HRV-A16, and nasal epithelial samples were obtained 7 days before, 36 hours after, and 7 days after viral inoculation.

tag: disease status

value: Asthmatic

value: Adult

value: Nasal epithelial

tag: treatment

value: HRV-A16 infection

tag: time point

value: One week post infection


title: Asthmatics_d7_GKH18

description:
GKH18
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Asthmatics_d7_GKH21

description:
GKH21
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Female Ivermectin 1 day exposure replicate 2


title: Asthmatics_d2_GKH20

description:
GKH20
Sample not analyzed due to insufficient quality.
Processed data file: RawCount.txt
Processed data file: countsTable.txt

source_name: Nasal epithelial cells, asthmatic, 2 days post infection

value: Two days post infection


title: Female Ivermectin 1 day exposure replicate 3


title: Asthmatics_d7_GKH6

description:
GKH6
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Asthmatics_d7_GKH3

description:
GKH3
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Female Ivermectin 1 day exposure replicate 1


title: Microfilaria Diethylcarbamizine 7 day exposure replicate 2

value: Diethylcarbamazine


title: Asthmatics_d2_GKH17

description:
GKH17
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Male Ivermectin 7 day exposure replicate 3


title: Microfilaria Ivermectin 1 day exposure replicate 2


title: Asthmatics_d2_GKH5

description:
GKH5
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Asthmatics_d2_GKH11

description:
GKH11
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Female Ivermectin 7 day exposure replicate 1


title: Microfilaria Diethylcarbamizine 7 day exposure replicate 1


title: Asthmatics_d2_GKH2

description:
GKH2
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Microfilaria Diethylcarbamizine 1 day exposure replicate 3


title: Asthmatics_d-7_GKH16

description:
GKH16
Processed data file: RawCount.txt
Processed data file: countsTable.txt

source_name: Nasal epithelial cells, asthmatic, baseline

value: One week before infection


title: Microfilaria Diethylcarbamizine 1 day exposure replicate 2


title: Asthmatics_d-7_GKH10

description:
GKH10
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Asthmatics_d-7_GKH4

description:
GKH4
Sample not analyzed due to insufficient quality.
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Asthmatics_d-7_GKH1

description:
GKH1
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Microfilaria Diethylcarbamizine 1 day exposure replicate 1


title: Male Diethylcarbamizine 7 day exposure replicate 3


title: Controls_d7_GKH33

description:
GKH33
Processed data file: RawCount.txt
Processed data file: countsTable.txt

source_name: Nasal epithelial cells, control, 1 week post infection

value: Non-asthmatic


title: Controls_d7_GKH30

description:
GKH30
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: WM989-A6G3_Fluidigm COL05_ROW01_sample5

description: fluidigmRPM

value: melanoma


title: Controls_d7_GKH27

description:
GKH27
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Male Diethylcarbamizine 7 day exposure replicate 2


title: Controls_d7_GKH9

description:
GKH9
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Male Diethylcarbamizine 1 day exposure replicate 3


title: Controls_d7_GKH24

description:
GKH24
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d7_GKH15

description:
GKH15
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d2_GKH23

description:
GKH23
Processed data file: RawCount.txt
Processed data file: countsTable.txt

source_name: Nasal epithelial cells, control, 2 days post infection


title: Controls_d2_GKH29

description:
GKH29
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d2_GKH14

description:
GKH14
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Male Diethylcarbamizine 1 day exposure replicate 1


title: Controls_d2_GKH32

description:
GKH32
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Male Diethylcarbamizine 1 day exposure replicate 2


title: Asthmatics_d-7_GKH19

description:
GKH19
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d2_GKH8

description:
GKH8
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d2_GKH26

description:
GKH26
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d-7_GKH31

description:
GKH31
Sample not analyzed due to insufficient quality.
Processed data file: RawCount.txt
Processed data file: countsTable.txt

source_name: Nasal epithelial cells, control, baseline


title: Female Diethylcarbamizine 7 day exposure replicate 2


title: Female Diethylcarbamizine 7 day exposure replicate 3


title: Controls_d-7_GKH28

description:
GKH28
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d-7_GKH25

description:
GKH25
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Controls_d-7_GKH22

description:
GKH22
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Female Diethylcarbamizine 7 day exposure replicate 1


title: Controls_d-7_GKH7

description:
GKH7
Processed data file: RawCount.txt
Processed data file: countsTable.txt


title: Male Diethylcarbamizine 7 day exposure replicate 1


title: Female Diethylcarbamizine 1 day exposure replicate 2


title: Female Diethylcarbamizine 1 day exposure replicate 1


title: Microfilaria Control 7 day exposure replicate 2

value: Control (DMSO)


title: Mouse_Pu1_ExVivo_Rep1

city: La Jolla

first: Dylan

middle: Derik

last: Skola

state: CA

address: 9500 Gilman Dr.

department: Cellular and Molecular Medicine

institute: UCSD

description: mouse_pu1_exvivo_vsInput_yes_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed

data_processing:
Tag directories for the ChIP-seq experiments were combined into an ex vivo and in vitro pool for each target in both mouse and human. The tag directories for the input DNA were likewise combined. Peaks were then called on the pooled tags with the pooled input DNA as background using HOMER’s findPeaks command with the following parameters for the PU.1 ChIP-seq: “-style factor -size 200 -minDist 200” and the following parameters for the H3K27ac and H3K4me2 ChIP-seq: “-style histone -size 500 -minDist 1000 -region.” The “-tbp” parameter was set to the number of replicates in the pool.   For identifying regions that are deacetylated in vitro, peaks for H3K27ac replicates were called individually, then merged using bedtools. A matrix containing the number of reads in each merged peak in each replicate was generated using HOMER’s annotatePeaks command with the following parameters: “-size given -noadj -tbp 1”. The read count matrix was then loaded into R and the limma package with voom normalization was used to identify peaks where the reads were reduced more than two-fold in vitro at an FDR of 0.05.
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

extract_protocol:
For ChIP-Seq experiments, a cross-linking step with paraformaldehyde was performed immediately after staining but before microglia sorting. Briefly, a subset of human cells, and mouse cells to be used for ChIP-Seq, were washed once after staining, fixed at RT with 1% paraformaldehyde in PBS (Affymetrix 19943 1 LT) for 10 minutes, incubated for 5 min at RT with glycine to a final concentration of 0.125 M for PFA quenching, and washed twice with cold staining buffer. Microglia were then sorted as described above. After sorting, microglia were pelleted and snap-frozen in liquid nitrogen and stored at -80 C until chromatin immunoprecipitation.   Chromatin immunoprecipitation for histone modification H3K4me2, H3K27ac and transcription factor PU.1 was performed as followed, using 500,000 to 2 million microglia per assay. First microglia were briefly thawed on ice and lysed by incubation in 1 ml of lysis buffer (0.5% IGEPAL CA-630, 10 mM HEPES pH 7.9, 85 mM KCl, 1 mM EDTA pH 8.0, in water) for 10 min on ice. Lysate were centrifuge at 800 x rcf for 5 min at 4°C, and pellets were resuspended in 200 l of sonication/immunoprecipitation buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.5 mM EGTA, 0.1% Deoxcycholate, 0.5% Sarkosyl, in water). Sonication was performed with a Bioruptor Standard Sonicator (Diagenode) and consisted of two rounds of 15 min each, alternating stages of 30 sec “sonication-on” with 60 sec “sonication-off”.  Twenty-two microliters of 10% Triton-X were then added to samples (1% final concentration) on ice, and lysates were cleared by centrifugation for 5 min at 18,000 x rcf at 4°C. Two microliters of supernatant were then set aside for input library sequencing controls. Supernatants were then immunoprecipitated on a rotator for 2 h at 4°C with antibody pre-bound to 20 l Protein A Dynabeads (Life Technologies 10001D). The following antibodies were used: H3k4me2 (Millipore, 07030), 2.0 l from stock per sample; H3K27ac (Active Motif, 39135), 1.5 l from stock per sample; and PU.1 (Santa Cruz, sc-352), 3.0 g per sample.   Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA pH 8.0 in water), wash buffer III (10 mM Tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1mM EDTA in water) and TET (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 0.1% Tween-20, in water) and eluted with 1% SDS/TE at room temperature in a final volume of 100 l.   Reverse-crosslinking was then performed on immunoprecipitates and saved input aliquots. First, 6.38 l of 5 M NaCl (final concentration 300 mM) was added to each samples immersed in 100 l SDS/TE. Crosslinking was then reversed by overnight incubation at 65°C in a hot air oven. Potentially contaminated RNA was then digested for 1 h at 37°C with 0.33 mg/ml RNase A, proteins digested for 1 h at 55°C with 0.5 mg/ml proteinase K, and DNA extracted using Sera-Mag SpeedBeads (Thermo Scientific, 6515205050250).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.
Mice were euthanized with CO2 and quickly perfused intracardially with ice-cold DPBS (Mediatech 21-031CV). Whole brains were removed and gently mechanically homogenized on ice as described above. Cells were fractionated by Percoll gradient centrifugation, washed, FC blocked with CD16/32 antibody (1:50, eBioscience 14-0161, clone 93) on ice for 15 min, stained 1:100 with CD11b-APC (BioLegend 101212, clone M1/70) and CD45-Alexa Fluor 488 (BioLegend 103122, clone 30-F11). Microglia were then purified by cell sorting as specified above, with microglia defined as live-CD11b+CD45Low single cells. Typical yield was roughly 250,000 microglia per mouse brain.

tag: culture protocol

tag: time in culture

value: ex vivo

tag: ligands in culture


title: Mouse_Input_ExVivo_Rep5

tag: strain


title: Microfilaria Control 7 day exposure replicate 1

value: Microfilaria

value: Day 7


title: Microfilaria Control 1 day exposure replicate 3

value: Day 1


title: Mouse_Input_ExVivo_Rep4


title: Microfilaria Control 1 day exposure replicate 2


title: Microfilaria Control 1 day exposure replicate 1


title: Mouse_H3K27ac_ExVivo_Rep1

description: mouse_h3k27ac_exvivo_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed


title: Mouse_H3K4me2_ExVivo_Rep1

description: mouse_h3k4me2_exvivo_vsInput_yes_style_histone_region_yes_nfr_no_size_500_minDist_1000_peaks.bed


title: Male Control 7 day exposure replicate 3

value: Male worm


title: Mouse_Input_ExVivo_Rep1


title: Mouse_RNA_ExVivo_Rep5

description:
mouse_rna_read_counts_sample_ids.csv
mouse_rna_tpm_trimmed_sample_ids.csv

data_processing:
The “analyzeRepeats” function of HOMER was used to generate a table of read counts for each experiment using the parameters “-raw -count exons -strand both -condenseGenes” as well as a table of reads per kilobase per million reads (RPKM) values using “-rpkm -normMatrix 1e7 -count exons -strand both -condenseGenes.” The RPKM values were converted to transcripts per million (TPM) by normalizing the expression values in each experiment to a total count of one million. The base-2 logarithm of the TPM values was taken after adding a pseudocount of 1 TPM to each gene.The raw count data from HOMER analyzerepeat.pl program were imported in R (version 3.3.1) and preprocessed with Bioconductor packages. Expression data was filtered with average logTPM value > 2.0.
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

extract_protocol: Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was then performed. RNA/DNA samples in 10 l of water were incubated for 2.5 hours at 16 C with 5 l the following mix (3x Blue Buffer (Enzymatics), 1.0 l PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 l Sera-Mag SpeedBeads (Thermo Scientific, 651520505025) resuspended in 30 l 20%PEG 8000/2.5 M NaCl and incubation at RT for 15 min and placed on magnet for two rounds of bead washing with 80% EtOH. Beads were then air-dried for 10-12 min and DNA was eluted off the beads by adding 40 l of water. Supernatant was then collected on magnet and placed on ice or stored at -20 C until DNA blunting, poly(A)-tailing, and adapter ligation (see below).   Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, adapter ligation as previously described (2) using barcoded adapters (NextFlex, Bioo Scientific). Prior final PCR amplification, RNA-Seq libraries were digested by 30 min incubation at 37 C with Uracil DNA Glycosylase (final concentration of 0.134 units per l of library volume; UDG, Enzymatics G5010L) to generate strand-specific libraries. Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-325 bp for ChIP-Seq, 200-350 for RNA-Seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  RNA-Seq and ChIP-seq librairies were single-end sequenced for 51 cycles on an Illumina HiSeq 4000 or NextSeq 2500 (Illumina, San Diego, CA) according to manufacturer’s instruction.      Following sorting, 100,000 to 150,000 microglia were pelleted and put in 150 l lysis/Oligo d(t) beads binding buffer (see above) and stored at -80 C until processing. For sequencing library preparation, samples were first thawed at room temperature (RT) and incubated with 20 l Oligo d(t) magnetic beads (NEB, S1419S) in PCR strips for selection of polyadenylated (poly(A)) mRNA as follows: 2 min at 65 C on a PCR cycler and then 10 min at RT. Samples were then placed on collection magnet at RT, and washed serially with 180 l of washing buffer 1 (RNA-WB1; 10 mM Tris-HCl pH 7.5, 0.15 M LiCl, 1 mM EDTA pH 8.0, 0.1% LiDS, 0.1% Triton X-100, in water) and then washing buffer 3 (RNA-WB3; 10 mM Tris-HCl, 0.15 M NaCl, 1 mM EDTA pH 8.0, in water). RNA was eluted from Oligo (t) beads by resuspending the beads in 50 l of elution buffer (EB; 10 mM tris-HCl pH 7.5, 1 mM EDTA pH 8.0, in water) followed by an incubation at 80 C for 2 min on a PCR cycler. The samples were then placed back on the magnet, and the elution buffer supernatant containing the poly(A) RNA was carefully collected and placed on ice.   A second round of poly(A) RNA selection was then performed. Eluted Oligo d(t) beads were first washed on magnet with 150 l EB and then 150 l 2X Oligo d(t) binding buffer (2x DTBB; 20 mM Tris-HCl pH 7.5, 1 M LiCl, 2 mM EDTA pH 8.0, 1% LiDS, 0.1% Triton X-100) and resuspended in 50 l of 2x DTBB. Resuspended Oligo d(t) beads were then added to isolated RNA and incubated at 65 C and RT as described above. Beads were then placed on magnet and washed once with 150 l of RNA-WB1 and then with 30 ul of 1x First-Strand buffer (made from 5x stock; Life Technologies) and transferred in a new PCR strips. Beads were collected on magnet and resuspended in 10 ul of 2x SuperScript III buffer (Life Technologies, 1x First-Strand buffer, 10 mM DTT in water). Resuspended beads were then incubated at 94 C for 9 min to fragment poly(A) RNA. Beads were then placed back on magnet, and the supernatant containing poly(A) RNA was carefully collected and placed on ice.  RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 l of the following mix: 1.5 g Random Primer (Life Technologies 48190-011), 10 M Oligo d(t) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water .Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 l of the following mix: 0.2 g Actinomycin (Sigma A1410), 13.15 mM DTT (Life technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 l of Agentcourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on magnet and bead were washed twice with 150 l of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 l of water.   Second-strand synthesis was


title: Male Control 7 day exposure replicate 2


title: S1pr1_1

city: new york

first: Susan

last: Schwab

state: NY

address: 540 First Avenue

department: Immunology

institute: new york university

description: polyA RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters.
RNAseq: FPKM were obtained using CuffLinks.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *FPKM.txt: Tab-delimited text file includes FPKM values for each RefSeq gene.

source_name: Naïve CD4 T cells, S1pr1-null

extract_protocol:
Total RNA was extracted from samples using the RNeasy Plus Mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies).
TotalScript RNA-Seq Kit (Epicentre).

tag: cell type

value: Naive CD4 T cells from lymph nodes

tag: strain/background

tag: genotype/variation


title: S1pr1_3

description: polyA RNA


title: Female Diethylcarbamizine 1 day exposure replicate 3

value: Female worm


title: S1pr1

description: polyA RNA


title: Ctrl_3

description: polyA RNA

source_name: Naïve CD4 T cells, control

value: Wildtype


title: Mouse_ATAC_7day_Rep2

description: mouse_atac_invitro_vsInput_no_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed

data_processing:
Tag directories for the ATAC-seq experiments were combined into an ex vivo and in vitro pool for both mouse and human. Peaks were then called on the pooled tags using HOMER’s findPeaks command with the following parameters: “-style factor -size 200 -minDist 200” with the “-tbp” parameter was set to the number of replicates in the pool.
Library strategy: ATAC-Seq
Fastq files from sequencing experiments were mapped to either the UCSC genome build hg38 (for human) or mm10 (for mouse). STAR  with default parameters was used to map RNA-Seq experiments (3). Bowtie2 with default parameters was used to map ATAC-Seq and ChIP-Seq experiments (4). HOMER was used to convert aligned reads into “tag directories” for further analysis (2).
Genome_build: mm10
Supplementary_files_format_and_content: Table of unnormalized read counts for RNA-seq, table of TPM values for RNA-seq, BED files of peaks for ATAC-seq and ChIP-seq

extract_protocol:
80,000 isolated microglia were lysed in 50 l lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water) on ice and nuclei were pelleted by centrifugation at 500 x rcf for 10 min. Nuclei were then resuspended in 50 l transposase reaction mix (1x Tagment DNA buffer (Illumina 15027866), 2.5 l Tagment DNA enzyme I (Illumina 15027865), in water) and incubated at 37 C for 30 min on a PCR cycler. DNA was then purified with Zymo ChIP DNA concentrator columns (Zymo Research D5205) and eluted with 10 l of elution buffer. DNA was then amplified with PCR mix (1.25 M Nextera primer 1, 1.25 M Nextera primer 2-bar code, 0.6x SYBR Green I (Life Technologies, S7563), 1x NEBNext High-Fidelity 2x PCR MasterMix, (NEBM0541)) for 8-12 cycles, run on a gel for size selection of fragments (160-290 bp), extracted from gel and single-end sequenced for 51 cycles on a HiSeq 4000 or NextSeq 2500.
Mice were euthanized with CO2 and quickly perfused intracardially with ice-cold DPBS (Mediatech 21-031CV). Whole brains were removed and gently mechanically homogenized on ice as described above. Cells were fractionated by Percoll gradient centrifugation, washed, FC blocked with CD16/32 antibody (1:50, eBioscience 14-0161, clone 93) on ice for 15 min, stained 1:100 with CD11b-APC (BioLegend 101212, clone M1/70) and CD45-Alexa Fluor 488 (BioLegend 103122, clone 30-F11). Microglia were then purified by cell sorting as specified above, with microglia defined as live-CD11b+CD45Low single cells. Typical yield was roughly 250,000 microglia per mouse brain.

value: Isolated microglia were plated in 48-, 24, or 6-well plates at the following numbers, respectively:80,000 to 125,000, 150,000 to 200,000, and 1.5 million. Culture media consisted of DMEM/F12 (Life Technologies, 113300-032) supplemented with 5% FBS (heat inactivated, Omega Scientific, FB-12) and 1x Anti-Anti (Life Technologies, 152240-062). No media changes were performed for the duration of the culture experiments. Interleukin-34 (R&D, human 5265-IL-010; mouse 5195-ML-010) was supplemented daily at a concentration of 20 ng/ml. Recombinant human or mouse TGF-b1 cytokine (R&D, human 240-B-002; mouse 7666-MB-005) was supplements daily as a concentration of 10 ng/ml. At the end of the culture experiments, microglia were washed once with cold PBS and either lysed with 150 ml Oligo d(t) beads lysis/binding buffer (100 mM Tris-HCl ph 7.5, 500 mM LiCl, 10 mM EDTA ph 8.0, 1% LiDS, 5 mM DTT, in water) or 150 ml ATAC-Seq lysis buffer (10 mM Tris-HCl ph 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, CA-630, in water; see below), or cross-linked, scraped off the wells and pelleted in preparation of ChIP-Seq experiments (see below).

value: 8 d


title: Ctrl_1

description: polyA RNA


title: Controls_d-7_GKH13

description:
GKH13
Sample not analyzed due to insufficient quality.
Processed data file: RawCount.txt
Processed data file: countsTable.txt

tag: age

value: Adult

value: Nasal epithelial


title: Male Control 7 day exposure replicate 1


title: Male Control 1 day exposure replicate 3


title: Male Control 1 day exposure replicate 2


title: Ctrl

description: polyA RNA


title: Male ethanol vehicle treatment, hypothalamus, biological replicate 3

city: Pittsburgh

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

description: Sample L

data_processing:
Reads were aligned to the GRCm38 genome using Tophat v 2.0.13 (default parameters) for cerebral cortex samples and Tophat v 2.0.9 (default parameters) for hypothalamus samples
Gene expression values were quantified using HTSeq with the union method
Differential expression was performed for genes with >1 CPM in at least 3 samples
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx file contains results for all genes from differential expression analysis

source_name: Male ethanol vehicle treatment, Hypothalamus

growth_protocol: Hypothalamus or cortex dissected from embryonic day 14.5 fetal mouse brain were dissociated into single cells and then cultured as neurospheres

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
The Ilumina Stranded Total RNA-Seq Kit was used to construct the library according to the manufacturer's instructions

treatment_protocol: Neurospheres at third passage were treated with 100 nM dexamethasone or equivalent volumes of ethanol vehicle for 4 hours

value: embryonic day E14.5

tag: gender

value: Male

value: Vehicle

tag: tissue

value: brain

tag: tissue region

value: Hypothalamus

value: neural progenitor/stem cells


title: Mouse_ATAC_ExVivo_Rep2

description: mouse_atac_exvivo_vsInput_no_style_factor_region_no_nfr_no_size_200_minDist_200_peaks.bed

value: ex vivo


title: Male Control 1 day exposure replicate 1

tag: sex/stage

tag: isolation time, post treatment

value: Control (DMSO)


title: Mouse_H3K4me2_ExVivo_Rep2


title: Mouse_ATAC_ExVivo_Rep1