title: F1392repl

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: MOLM13_sgLKB1e2

status: Public on Mar 12 2018

type: SRA

city: Cold Spring Harbor

first: Yusuke

last: Tarumoto

state: NY

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

library_source: transcriptomic

data_processing:
Sequencing reads were mapped into reference human genome hg19 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
Genome_build: hg19
Supplementary_files_format_and_content: txt, normalized RPKM

molecule: polyA RNA

organism: Homo sapiens

source_name: actue myeloid luekemia

growth_protocol: Cells were cultured in RPMI with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq library was prepared using Illumina TruSeq sample prep kit v2 according to the manufacture's protocol. Briefly, polyA RNA was selected and fragmented enzymatically. First strand of cDNA was synthesized using Super Script II reverse transcriptase, and then second strand was synthesized. Double-stranded cDNA was end-repaired, 3'-adenylated, ligated with indexed adaptor, and then PCR-amplified.

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout, or treated with DMSO or 100 nM HG-9-91-01 for 2 hrs

tag: cell line

value: MOLM-13 cell

tag: treatment

value: day 5 after sgLKB1e2 guideRNA infection


title: F1197repl

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description:
ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high
processed data file:
gene_expression_3273_samples_and_136_replicates_transformed.csv
transcript_expression_3273_samples_and_136_replicates.csv

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC RepeatMasker track (downloaded March 14, 2011).
Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38.
Remaining reads were aligned using TopHat2 2.0.12 or 2.0.13 (default parameters except for --mate-inner-dist X (estimated in previous step), --mate-std-dev Y (estimated in previous step), --library-type fr-firststrand, --no-coverage-search, --max-insertion-length 20, --max-deletion-length 20, --read-gap-length 20, --read-edit-dist 22) to the human genome reference GRCh38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014).
Gene expression data in FPKM were generated using cufflinks 2.2.1 (default parameters except –GTF, --frag-bias-correct GRCh38.fa, --multi-read-correct, --library-type fr-firststrand, --total-hits-norm, --max-bundle-frags 10000000). The resulting data was was post-processed by collapsing on 30,865 unique gene symbols (sum of FPKM values of each matching transcript), adding to each expression measurement 0.1 FPKM, and performing a log2 transformation.
PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect to available clinical characteristics. Before subtyping tumors in this study, gene expression of the PAM50 genes for each tumor was centered to the reference set separately using custom R scripts.
Single-gene classifiers (SGCs) and multi-gene classifiers (MGCs) were trained for ER, PgR, HER2, Ki67 (SGC and MGC) and NHG (MGC only) on the expression of the single underlying gene (ESR1, PGR, ERBB2 or MKI67) or multiple genes (5000 most varying genes across all samples) of a 405 sample cohort using consensus pathology scores as labels. Classifier training was performed by selecting expression thresholds that maximize prediction concordance to the consensus scores (SGCs) and nearest shrunken centroids using the pamr R package (MGCs). The classifiers were used to predict the biomarker status in a validation cohort of 3273 samples from patients enrolled in the SCAN-B study.
Genome_build: Human genome reference GRCh38/hg38.
Supplementary_files_format_and_content: Gene expression in FPKM in CSV format.

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 or NextSeq 500 instrument.

value: NextSeq 500

tag: age at diagnosis

tag: tumor size

value: NodeNegative

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1101repl

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype

value: LumB


title: F1167repl

tag: age at diagnosis

tag: tumor size

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

value: LumA


title: F1143repl

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F437repl

tag: age at diagnosis

tag: tumor size

value: NodePositive

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F685repl

tag: scan-b external id

tag: instrument model

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F405repl

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F327repl

tag: scan-b external id

tag: instrument model

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F274repl

tag: age at diagnosis

tag: tumor size

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F282repl

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F185repl

tag: age at diagnosis

tag: tumor size

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F229repl

tag: scan-b external id

tag: instrument model

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F1581repl

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F54repl

tag: scan-b external id

tag: instrument model

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F1515repl

tag: age at diagnosis

tag: tumor size

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F2407

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F49repl

tag: age at diagnosis

tag: tumor size

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F30repl

tag: scan-b external id

tag: instrument model

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F1928

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1748

tag: scan-b external id

tag: instrument model

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F1918

tag: age at diagnosis

tag: tumor size

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F1925

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F785repl

tag: age at diagnosis

tag: tumor size

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype

value: Basal


title: F1141

tag: scan-b external id

tag: instrument model

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F1079

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1648

tag: scan-b external id

tag: instrument model

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F1207

tag: age at diagnosis

tag: tumor size

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F724

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1140

tag: age at diagnosis

tag: tumor size

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F371

tag: scan-b external id

tag: instrument model

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F1368

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F1713

tag: scan-b external id

tag: instrument model

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: F505

tag: age at diagnosis

tag: tumor size

tag: er status

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc


title: F8

tag: scan-b external id

tag: instrument model

tag: lymph node group

tag: lymph node status

tag: ki67 prediction sgc

value: Normal

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F498

tag: age at diagnosis

tag: tumor size

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: pam50 subtype


title: RNA-seq-Panc-1-3P2

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description:
Panc-1 xenograft (primary tumor: pancreas) mouse 2
Panc-1_3P2

data_processing:
RNA-seq reads were trimmed down to 100 bases and processed by Tophat2 and Bowtie2 using hg19 version of index files.
FPKM calculation was performed by using Cuffdiff.
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the 7 samples (SUIT-2) and 5 samples (Panc-1) were summarized into genes_SUIT-2.fpkm_tracking and genes_Panc-1.fpkm_tracking, respectively.

growth_protocol: All sublines were maintained in vitro and harvested for RNA-seq analysis.

extract_protocol:
Total RNA was isolated with RNeasy (Qiagen).
cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-Seq Kit v.2 (Life Technologies).

treatment_protocol: SUIT-2 and Panc-1 cells were cultured in 6 well plate for over night.

tag: cell lines

tag: histology

value: pancreatic adenocarcinoma


title: RNA-seq-Panc-1-3Liv2

description:
Panc-1 xenograft (liver metastasis) mouse 2
Panc-1_3Liv2


title: RNA-seq-Panc-1-3Liv1

description:
Panc-1 xenograft (liver metastasis) mouse 1
Panc-1_3Liv1


title: RNA-seq-SUIT-2-3sc2

description:
SUIT-2 xenograft (primary tumor: subcutaneous) mouse 2
SUIT-2_3sc2


title: RNA-seq-SUIT-2-3sc1

description:
SUIT-2 xenograft (primary tumor: subcutaneous) mouse 1
SUIT-2_3sc1


title: RNA-seq-Panc-1-3P1

description:
Panc-1 xenograft (primary tumor: pancreas) mouse 1
Panc-1_3P1


title: RNA-seq-SUIT-2-3L1

description:
SUIT-2 xenograft (lung metastasis) mouse 1
SUIT-2_3L1


title: RNA-seq-parental-Panc-1

description:
parental Panc-1
Panc-1_P

source_name: parental Panc-1


title: RNA-seq-SUIT-2-3P2

description:
SUIT-2 xenograft (primary tumor: pancreas) mouse 2
SUIT-2_3P2


title: RNA-seq-SUIT-2-3P1

description:
SUIT-2 xenograft (primary tumor: pancreas) mouse 1
SUIT-2_3P1


title: RNA-seq-parental-SUIT-2

description:
parental SUIT-2
SUIT-2_P

source_name: parental SUIT-2


title: RNA-seq-SUIT-2-3L2

description:
SUIT-2 xenograft (lung metastasis) mouse 2
SUIT-2_3L2


title: WT1

city: Buffalo

first: Zhen

last: Yan

address: 124 Sherman Hall

department: Physiology and Biophysics

institute: University at Buffalo

data_processing:
Basecalling was performed with bcl2fastq version 2.17.1.14
Mapping to genome with TopHat (v2.1.1) with default parameters
Expression level was quantified as Read Count using htseq-count (HTSeq/0.6.1) and genes.gtf (mm10)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include Read Count value for each sample

organism: Mus musculus

source_name: wild type

extract_protocol:
Total RNA Extraction with TRIZOL Reagent and Purification with QIAGEN. RNeasy Mini Kit(cat # 74104).
cDNA libraries were prepared using the TrueSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Young mice (5-6 weeks old) were treated with saline or romidepsin (0.25 mg/kg, i.p., once daily for 3 days). Animals were sacrificed 1 day later after the last treatment for tissue collection.

tag: age

value: Young; 5-6 weeks old

tag: genotype/variation

value: wild type

tag: tissue

value: prefrontal cortical slices

tag: cell type

value: neurons


title: ROM2

tag: treated with

value: romidepsin (0.25 mg/kg, i.p., once daily for 3 days)


title: WT3


title: SAL3

value: saline


title: SAL1


title: SAL2


title: ROM1


title: WT2


title: SIC_InfectedMO_liveCA_t120_S18

city: cambridge

first: Toni

middle: Marie

last: Delorey

state: ma

address: 415 main street

institute: Broad Institute

description:
Sorted, single macrophages infected with live C. albicans
CA_singlecells_gene_exp_matrix
MO_singlecells_gene_exp_matrix

data_processing:
QC and file trimming and sample demultiplexing was done with Picard version 1.107 and Trimmomatic.
BWA alignment version 0.7.10-r789.) to mouse transcriptome GRCm38/mm10 , the C. albcains transcriptome SC5314 version A21-s02-m09-r1 or a combined transcriptome containing both of these referenes ;  Multi-reads (reads that aligned to both host and pathogen transcripts) were discarded.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Each host or pathogen sample file were aligned to its corresponding reference using Bowtie2 and RSEM (v.1.2.21).
For subpopulation samples, transcript abundance was estimated using transcripts per million (TPM). For subpopulation samples, TPM was calculated using edgeR in the Trinity package version 2.1. Genes were considered differentially expressed only if they had a 4-fold change difference (> 4 FC) in TPM values and a false discovery rate below or equal to 0.001 (FDR < 0.001), unless specified otherwise. For single macrophages infected with C. albicans, samples were aligned to the combined transcriptome as described above and RSEM was used to calculate TPM.
Genome_build: mouse transcriptome GRCm38/mm10; C. albcains transcriptome SC5314 version A21-s02-m09-r1 ; or a combined transcriptome made from mergeing these files
Supplementary_files_format_and_content: TPM matrix

molecule: total RNA

organism:
Candida albicans
Mus musculus

source_name: macrophage and C. albicans

growth_protocol: Prior to collection, samples were grown at 37 degrees in 5% CO2 for either 0, 1, 2 or 4 hours in RPMI 1640 media

extract_protocol:
Subpopulation samples were harvested, collected via FACs, flash frozen on dry ice, and RNA was extracted after bead mill lysis in tubes containg RLT and BME and the Qiagen Rneasy mini kit. Single, C. albicans infected libraries were sorted into wells of a 96 well plate containining RLT and BME, and frozen at -80 utnil cDNA synthesis. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Smart-seq2 was used to create cDNA, Nextera XT kits were used to make libraries;subpopulation and single infect cells were sequenced on Illumina's Nextseq. Candida only samples were sequenced on Illumina's Miseq

treatment_protocol: Prior to collection, macrophages were grown alone in RPMI, C. albicans was grown alone in RPMI or C. albicans and macrophages were miexed together and collected over time.

tag: strain

value: C57BL/6 and SC5314-GFP-mCherry

tag: single infected macrophage plate number

tag: genotype

value: C57BL/6 primary, bone derived macrophages and SC5314-Neut5L-GFP-mCherry C. albicans


title: SIC_InfectedMO_liveCA_t120_S16


title: SIC_InfectedMO_liveCA_t120_S17


title: SIC_InfectedMO_liveCA_t120_S13


title: SIC_InfectedMO_liveCA_t120_S11


title: SIC_InfectedMO_liveCA_t120_S19


title: SIC_InfectedMO_liveCA_t120_S14


title: SIC_InfectedMO_liveCA_t120_S10


title: SIC_InfectedMO_liveCA_t120_S194


title: InfectedMO_liveCA_t120_REPC1

description:
Sorted subpopulation samples
CA_subpops_gene_exp_matrix
MO_subpops_gene_exp_matrix


title: InfectedMO_liveCA_t240_1_REPA1


title: InfectedMO_liveCA_t60_REPB1


title: InfectedMO_liveCA_t240_1_REPC1


title: InfectedMO_liveCA_t240_1_REPB1


title: InfectedMO_liveCA_t120_REPA1


title: InfectedMO_liveCA_t0_REPB1


title: InfectedMO_liveCA_t0_REPC1


title: InfectedMO_deadCA_t240_1_REPC3


title: InfectedMO_liveCA_t0_REPA1

value: C57BL/6 C57BL/6 primary, bone derived macrophages and tagged SC5314-Neut5L-GFP-mCherry C. albicans


title: InfectedMO_liveCA_CA_t60_REPA1


title: InfectedMO_deadCA_t240_1_REPB3


title: InfectedMO_liveCA_t60_REPC1


title: InfectedMO_deadCA_t240_1_REPA3


title: Exposed_CA_t60_REPB4

description:
Sorted subpopulation samples
CA_subpops_gene_exp_matrix

organism: Candida albicans

source_name: C. albicans

value: SC5314-Neut5L-GFP-mCherry C. albicans


title: Exposed_CA_t240_1_REPA4


title: InfectedMO_deadCA_t120_REPA3


title: Exposed_CA_t60_REPC4


title: Exposed_CA_t240_1_REPC4


title: InfectedMO_deadCA_t120_REPB3


title: InfectedMO_deadCA_t120_REPC3


title: Exposed_CA_t60_REPA4


title: Ct_Unexposed_CA_REPB

description:
C. albicans not exposed to macrophages and not sorted  subpopulation samples
CA_subpops_gene_exp_matrix


title: Exposed_CA_t0_REPB4


title: Exposed_CA_t120_REPB4


title: Exposed_CA_t0_REPC4


title: Exposed_CA_t120_REPA4


title: Exposed_CA_t240_1_REPB4


title: Exposed_CA_t0_REPA4


title: SIC_InfectedMO_liveCA_t240_S287


title: SIC_InfectedMO_liveCA_t240_S284


title: SIC_InfectedMO_liveCA_t240_S283


title: SIC_InfectedMO_liveCA_t240_S286


title: SIC_InfectedMO_liveCA_t240_S285


title: SIC_InfectedMO_liveCA_t240_S282


title: SIC_InfectedMO_liveCA_t240_S277


title: SIC_InfectedMO_liveCA_t240_S278


title: SIC_InfectedMO_liveCA_t240_S279


title: SIC_InfectedMO_liveCA_t240_S276


title: Exposed_CA_t120_REPC4


title: SIC_InfectedMO_liveCA_t240_S288


title: Ct_Unexposed_CA_REPA

description:
C. albicans not exposed to macrophages and not sorted
CA_subpops_gene_exp_matrix


title: SIC_InfectedMO_liveCA_t240_S274


title: SIC_InfectedMO_liveCA_t240_S275


title: SIC_InfectedMO_liveCA_t240_S272


title: SIC_InfectedMO_liveCA_t240_S281


title: SIC_InfectedMO_liveCA_t240_S264


title: SIC_InfectedMO_liveCA_t240_S269


title: SIC_InfectedMO_liveCA_t240_S267


title: SIC_InfectedMO_liveCA_t240_S266


title: SIC_InfectedMO_liveCA_t240_S268


title: SIC_InfectedMO_liveCA_t240_S270


title: SIC_InfectedMO_liveCA_t240_S261


title: SIC_InfectedMO_liveCA_t240_S260


title: SIC_InfectedMO_liveCA_t240_S258


title: SIC_InfectedMO_liveCA_t240_S255


title: SIC_InfectedMO_liveCA_t240_S253


title: SIC_InfectedMO_liveCA_t240_S254


title: SIC_InfectedMO_liveCA_t240_S252


title: SIC_InfectedMO_liveCA_t240_S251


title: SIC_InfectedMO_liveCA_t240_S259


title: SIC_InfectedMO_liveCA_t240_S250


title: SIC_InfectedMO_liveCA_t240_S273


title: SIC_InfectedMO_liveCA_t240_S249


title: SIC_InfectedMO_liveCA_t240_S271


title: SIC_InfectedMO_liveCA_t240_S265


title: SIC_InfectedMO_liveCA_t240_S246


title: SIC_InfectedMO_liveCA_t240_S263


title: SIC_InfectedMO_liveCA_t240_S247


title: SIC_InfectedMO_liveCA_t240_S248


title: SIC_InfectedMO_liveCA_t240_S262


title: SIC_InfectedMO_liveCA_t240_S244


title: SIC_InfectedMO_liveCA_t240_S245


title: SIC_InfectedMO_liveCA_t240_S241


title: SIC_InfectedMO_liveCA_t240_S240


title: SIC_InfectedMO_liveCA_t240_S239


title: SIC_InfectedMO_liveCA_t240_S237


title: SIC_InfectedMO_liveCA_t240_S238


title: SIC_InfectedMO_liveCA_t240_S243


title: SIC_InfectedMO_liveCA_t240_S256


title: SIC_InfectedMO_liveCA_t240_S257


title: SIC_InfectedMO_liveCA_t240_S230


title: SIC_InfectedMO_liveCA_t240_S233


title: SIC_InfectedMO_liveCA_t240_S229


title: SIC_InfectedMO_liveCA_t240_S227


title: SIC_InfectedMO_liveCA_t240_S225


title: SIC_InfectedMO_liveCA_t240_S228


title: SIC_InfectedMO_liveCA_t240_S232


title: SIC_InfectedMO_liveCA_t240_S231


title: SIC_InfectedMO_liveCA_t240_S222


title: SIC_InfectedMO_liveCA_t240_S226


title: SIC_InfectedMO_liveCA_t240_S224


title: SIC_InfectedMO_liveCA_t240_S221


title: SIC_InfectedMO_liveCA_t240_S220


title: SIC_InfectedMO_liveCA_t240_S223


title: SIC_InfectedMO_liveCA_t240_S219


title: SIC_InfectedMO_liveCA_t240_S236


title: SIC_InfectedMO_liveCA_t240_S218


title: SIC_InfectedMO_liveCA_t240_S242


title: SIC_InfectedMO_liveCA_t240_S215


title: SIC_InfectedMO_liveCA_t240_S214


title: SIC_InfectedMO_liveCA_t240_S211


title: SIC_InfectedMO_liveCA_t240_S216


title: SIC_InfectedMO_liveCA_t240_S209


title: SIC_InfectedMO_liveCA_t240_S212


title: SIC_InfectedMO_liveCA_t240_S235


title: SIC_InfectedMO_liveCA_t240_S234


title: SIC_InfectedMO_liveCA_t240_S207


title: SIC_InfectedMO_liveCA_t240_S206


title: SIC_InfectedMO_liveCA_t240_S210


title: SIC_InfectedMO_liveCA_t240_S205


title: SIC_InfectedMO_liveCA_t240_S208


title: SIC_InfectedMO_liveCA_t240_S204


title: SIC_InfectedMO_liveCA_t240_S199


title: SIC_InfectedMO_liveCA_t240_S203


title: SIC_InfectedMO_liveCA_t240_S200


title: SIC_InfectedMO_liveCA_t240_S202


title: SIC_InfectedMO_liveCA_t240_S201


title: SIC_InfectedMO_liveCA_t240_S197


title: SIC_InfectedMO_liveCA_t240_S195


title: SIC_InfectedMO_liveCA_t240_S194


title: SIC_InfectedMO_liveCA_t240_S213


title: SIC_InfectedMO_liveCA_t240_S193


title: SIC_InfectedMO_liveCA_t240_S217


title: SIC_InfectedMO_liveCA_t240_S198


title: SIC_InfectedMO_liveCA_t240_S196


title: SIC_InfectedMO_liveCA_t120_S96


title: SIC_InfectedMO_liveCA_t120_S90


title: SIC_InfectedMO_liveCA_t120_S93


title: SIC_InfectedMO_liveCA_t120_S91


title: SIC_InfectedMO_liveCA_t120_S89


title: SIC_InfectedMO_liveCA_t120_S94


title: SIC_InfectedMO_liveCA_t120_S83


title: SIC_InfectedMO_liveCA_t120_S82


title: SIC_InfectedMO_liveCA_t120_S88


title: SIC_InfectedMO_liveCA_t120_S81


title: SIC_InfectedMO_liveCA_t120_S8


title: SIC_InfectedMO_liveCA_t120_S79


title: SIC_InfectedMO_liveCA_t120_S80


title: SIC_InfectedMO_liveCA_t120_S77


title: SIC_InfectedMO_liveCA_t120_S74


title: SIC_InfectedMO_liveCA_t120_S73


title: SIC_InfectedMO_liveCA_t120_S69


title: SIC_InfectedMO_liveCA_t120_S72


title: SIC_InfectedMO_liveCA_t120_S71


title: SIC_InfectedMO_liveCA_t120_S68


title: SIC_InfectedMO_liveCA_t120_S70


title: SIC_InfectedMO_liveCA_t120_S7


title: SIC_InfectedMO_liveCA_t120_S9


title: SIC_InfectedMO_liveCA_t120_S64


title: SIC_InfectedMO_liveCA_t120_S67


title: SIC_InfectedMO_liveCA_t120_S61


title: SIC_InfectedMO_liveCA_t120_S65


title: SIC_InfectedMO_liveCA_t120_S63


title: SIC_InfectedMO_liveCA_t120_S6


title: SIC_InfectedMO_liveCA_t120_S62


title: SIC_InfectedMO_liveCA_t120_S60


title: SIC_InfectedMO_liveCA_t120_S58


title: SIC_InfectedMO_liveCA_t120_S54


title: SIC_InfectedMO_liveCA_t120_S56


title: SIC_InfectedMO_liveCA_t120_S57


title: SIC_InfectedMO_liveCA_t120_S51


title: SIC_InfectedMO_liveCA_t120_S50


title: SIC_InfectedMO_liveCA_t120_S52


title: SIC_InfectedMO_liveCA_t120_S53


title: SIC_InfectedMO_liveCA_t120_S49


title: SIC_InfectedMO_liveCA_t120_S5


title: SIC_InfectedMO_liveCA_t120_S47


title: SIC_InfectedMO_liveCA_t120_S46


title: SIC_InfectedMO_liveCA_t120_S45


title: SIC_InfectedMO_liveCA_t120_S44


title: SIC_InfectedMO_liveCA_t120_S59


title: SIC_InfectedMO_liveCA_t120_S43


title: SIC_InfectedMO_liveCA_t120_S41


title: SIC_InfectedMO_liveCA_t120_S40


title: SIC_InfectedMO_liveCA_t120_S39


title: SIC_InfectedMO_liveCA_t120_S38


title: SIC_InfectedMO_liveCA_t120_S37


title: SIC_InfectedMO_liveCA_t120_S36


title: SIC_InfectedMO_liveCA_t120_S4


title: SIC_InfectedMO_liveCA_t120_S35


title: RNF6 siRNA3

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: HT29_RNF6 siRNA

growth_protocol: The human HT29 colorectal cancer cell were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of HT29 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The human RNF6 siRNA were introduced into the HT29 colorectal cells, while nonspecific siRNA was used as negative controls.

tag: cell line

value: human colorectal cancer cells

tag: passage

value: RNF6 knockdown


title: Control siRNA3

source_name: HT29_Control siRNA

value: wild type; control


title: SIC_InfectedMO_liveCA_t120_S33


title: RNF6 siRNA2


title: SIC_InfectedMO_liveCA_t120_S31


title: SIC_InfectedMO_liveCA_t120_S30


title: Control siRNA1


title: SIC_InfectedMO_liveCA_t120_S48


title: SIC_InfectedMO_liveCA_t120_S34


title: Control siRNA2


title: SIC_InfectedMO_liveCA_t120_S32


title: RNF6 siRNA1


title: SIC_InfectedMO_liveCA_t120_S29


title: SIC_InfectedMO_liveCA_t120_S288


title: SIC_InfectedMO_liveCA_t120_S287


title: SIC_InfectedMO_liveCA_t120_S283


title: SIC_InfectedMO_liveCA_t120_S280


title: SIC_InfectedMO_liveCA_t120_S286


title: SIC_InfectedMO_liveCA_t120_S278


title: SIC_InfectedMO_liveCA_t120_S276


title: SIC_InfectedMO_liveCA_t120_S274


title: SIC_InfectedMO_liveCA_t120_S273


title: SIC_InfectedMO_liveCA_t120_S28


title: SIC_InfectedMO_liveCA_t120_S277


title: SIC_InfectedMO_liveCA_t120_S271


title: SIC_InfectedMO_liveCA_t120_S270


title: SIC_InfectedMO_liveCA_t120_S268


title: SIC_InfectedMO_liveCA_t120_S27


title: SIC_InfectedMO_liveCA_t120_S267


title: SIC_InfectedMO_liveCA_t120_S275


title: SIC_InfectedMO_liveCA_t120_S261


title: SIC_InfectedMO_liveCA_t120_S263


title: SIC_InfectedMO_liveCA_t120_S262


title: SIC_InfectedMO_liveCA_t120_S265


title: SIC_InfectedMO_liveCA_t120_S260


title: SIC_InfectedMO_liveCA_t120_S257


title: SIC_InfectedMO_liveCA_t120_S253


title: SIC_InfectedMO_liveCA_t120_S256


title: SIC_InfectedMO_liveCA_t120_S251


title: SIC_InfectedMO_liveCA_t120_S254


title: SIC_InfectedMO_liveCA_t120_S26


title: SIC_InfectedMO_liveCA_t120_S255


title: SIC_InfectedMO_liveCA_t120_S258


title: SIC_InfectedMO_liveCA_t120_S249


title: SIC_InfectedMO_liveCA_t120_S247


title: SIC_InfectedMO_liveCA_t120_S250


title: SIC_InfectedMO_liveCA_t120_S246


title: SIC_InfectedMO_liveCA_t120_S244


title: SIC_InfectedMO_liveCA_t120_S25


title: SIC_InfectedMO_liveCA_t120_S243


title: SIC_InfectedMO_liveCA_t120_S245


title: SIC_InfectedMO_liveCA_t120_S242


title: SIC_InfectedMO_liveCA_t120_S240


title: SIC_InfectedMO_liveCA_t120_S24


title: SIC_InfectedMO_liveCA_t120_S241


title: SIC_InfectedMO_liveCA_t120_S237


title: SIC_InfectedMO_liveCA_t120_S236


title: SIC_InfectedMO_liveCA_t120_S266


title: SIC_InfectedMO_liveCA_t120_S234


title: SIC_InfectedMO_liveCA_t120_S248


title: SIC_InfectedMO_liveCA_t120_S230


title: SIC_InfectedMO_liveCA_t120_S232


title: SIC_InfectedMO_liveCA_t120_S231


title: SIC_InfectedMO_liveCA_t120_S23


title: SIC_InfectedMO_liveCA_t120_S223


title: SIC_InfectedMO_liveCA_t120_S229


title: SIC_InfectedMO_liveCA_t120_S227


title: SIC_InfectedMO_liveCA_t120_S224


title: mESC_dCas9-Cat3a_noGuide_dox_48h_WGBS

city: Cambridge

first: Jocelyn

last: Charlton

state: MA

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

library_source: genomic

data_processing:
WGBS : 10 bp were clipped from the WGBS raw sequencing reads at either end. The reads were then aligned to the mm9 build of the mouse genome using BSmap.  DNA methylation calling for individual CpG sites was performed using mcall from the MOABS package.
RRBS: Sequenced reads were aligned to the mm9 of hg19 reference genome using BSmap for WGBS. Custom scripts were used to determine whether cytosines were methylated or unmethylated by observing bisulfite conversion of unmethylated cytosines in comparison to the reference sequence.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: Bed files. WGBS: chrom, start, end, ratio, totalC, methC, strand, next, Plus, totalC, methC, Minus, totalC, methC, localSeq   RRBS: chr, start, end, methC/totalC, ratio (out of 1000)

molecule: genomic DNA

source_name: mESCs

growth_protocol: ES cells were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and 105 U LIF

extract_protocol:
genomic DNA was purified using Phenol/Chloroform extraction
WGBS: 100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research), eluting in 15 µl low TE buffer. To minimize loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences). The libraries were sequenced for 100-bp paired-end reads on an Illumina HiSeq 2500 sequencer. RRBS: Genomic DNA was quantified using a Qubit® 2.0 Fluorometer, and quality-assessed on an Agilient 2200 TapeStation D1000 ScreenTape.  RRBS was performed on 20ng of each sample using the NuGen Ovation® RRBS Methyl-Seq System.  Barcoded samples were pooled in groups of 8 immediately prior to Bisulfite Conversion with the Qiagen EpiTect® Fast Bisulfite Conversion kit.  Library pools were purified with a 1X Agencourt RNA XP bead clean-up and sequenced on an Illumina HiSeq® 2500 Sequencing System. All protocols were carried out according to manufacturer's recommendations except where specified.

treatment_protocol: Doxycycline was used induce expression of dCas9 or Dnmt3a/b

value: mESCs

tag: molecule subtype

value: bisulfite converted DNA


title: mESC_dCas9-Cat3a_noGuide_Nodox_d0_WGBS


title: mESC_dCas9-Cat3a_Dazlguide_dox_7d_WGBS


title: SIC_InfectedMO_liveCA_t120_S222


title: SIC_InfectedMO_liveCA_t120_S221


title: mESC_dCas9-Cat3a_Dazlguide_dox_48h_WGBS


title: SIC_InfectedMO_liveCA_t120_S235


title: SIC_InfectedMO_liveCA_t120_S233


title: SIC_InfectedMO_liveCA_t120_S220


title: Uninfected_MO_t60_REPC2

description:
Sorted subpopulation samples
MO_subpops_gene_exp_matrix

value: C57BL/6 primary, bone derived macrophages


title: SIC_InfectedMO_liveCA_t120_S22


title: SIC_InfectedMO_liveCA_t120_S226


title: SIC_InfectedMO_liveCA_t120_S225


title: Uninfected_MO_t60_REPB2


title: SIC_InfectedMO_liveCA_t120_S218


title: Uninfected_MO_t240_1_REPC2


title: SIC_InfectedMO_liveCA_t120_S217


title: SIC_InfectedMO_liveCA_t120_S215


title: Uninfected_MO_t120_REPC2


title: SIC_InfectedMO_liveCA_t120_S214


title: Uninfected_MO_t120_REPB2


title: SIC_InfectedMO_liveCA_t120_S213


title: Uninfected_MO_t120_REPA2


title: SIC_InfectedMO_liveCA_t120_S212


title: SIC_InfectedMO_liveCA_t120_S211


title: Uninfected_MO_t0_REPB2


title: Uninfected_MO_t0_REPA2


title: Uninfected_MO_t240_1_REPA2


title: SIC_InfectedMO_liveCA_t120_S210


title: YplP-L-CS

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: Cold Shock

data_processing:
mapping of reads was done using: bowtie2 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus subtilis 168
Supplementary_files_format_and_content: Tab delimited text file

organism: Bacillus subtilis

source_name: Cell culture

growth_protocol: Cells were grown as shaken cultures (220 rpm) in SMM+glucose at 37C to an OD of 0.5

extract_protocol: Cell were lysed using glassbeads and totRNA was isolated using phenol/chloroform and the NorGen Total RNA purification kit (Cat #17200, Biotek Corp, Canada)

treatment_protocol: At and OD of 0.5, cultures were transferred to 15C or remained at 37C and grown for 0.5 h or 2 h

value: Mutant

tag: time point

value: Exponential Growth


title: YplP-S-CS 1

description: Cold Shock

value: Stationary Growth


title: YplP-L-37


title: YplP-S-CS 2

description: Cold Shock


title: Uninfected_MO_MO_t60_REPA2


title: M17

type: RNA

city: Beijing

first: Yong

last: Zhao

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Biomembrane and Membrane Biotechnology

institute: Institute of Zoology, Chinese Academy of Sciences

description: M17 macrophages

hyb_protocol: Each Slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188‐5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: M17 macrophages

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Primary mouse peritoneal macrophages were obtained from the peritoneal exudates of 6-to-8-week-old B6 mice as described previously 31. The peritoneal exudates cells were washed twice with PBS solution and adjusted to 1×106 cells/ml in DMEM cultured for 3-4 h at 37oC and 5% CO2. The non-adherent cells were removed by washing with warm PBS. The purity of macrophages was analyzed by FCM (Beckman, CA), using a mouse macrophage marker F4/80. The adherent cells constituted more than 90% of F4/80+ macrophages.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: M0: control medium; M1:IFNr (20h) + LPS (6h);M2:IL-4,48h;M17:IL-23,72h

value: M17 macrophages


title: YplP-S-37


title: DrosophilaFemale_CSCy3xorbdecCy5_rep5

city: Montpellier

first: Isabelle

last: Busseau

address: 141 rue de la Cardonille

department: Institut de Génétique Humaine

country: France

institute: CNRS

description: Spots with high local background or contaminating fluorescence were flagged manually. The local background, calculated for each spot as the median of the fluorescence intensities of four squares surrounding the spot, was subtracted from the foreground fluorescence intensity.

hyb_protocol: Prior to hybridization, excess oligonucleotides were removed from the arrays by shaking the arrays twice for 1 min in 0.2% SDS. Arrays were then washed two times in distilled water. Labeled cDNA was added to microarray hybridization buffer version 2 (Amersham Biosciences) with a final concentration of 50% formamide, denatured at 95°C for 3 min, and applied to the microarrays in individual chambers of an automated slide processor (Amersham Biosciences). Hybridization was carried out at 37°C for 16 h. Hybridized slides were washed at 37°C successively with 1x SSC (0.15 M NaCl plus 0.015 M sodium citrate)-0.2% SDS for 10 min, twice with 0.1x SSC-0.2% SDS for 10 min, with 0.1x SSC, for 1 min and with isopropanol before air drying.

scan_protocol: Microarrays were scanned at 10-µm resolution in both Cy3 and Cy5 channels with a GenePix 4200AL scanner with a variable photo multiplier tube voltage to obtain maximal signal intensities with <0.1% probe saturation. ArrayVision software was used for feature extraction.

data_processing: Fluorescence intensity ratios from each microarray were normalized using the R package SMA (statistical microarray analysis) by the local weight regression (lowess) algorithm called print-tip (Yang, Y. H., Dudoit, S., Luu, P., Lin, D. M., Peng, V., Ngai, J., and Speed, T. P. (2002) Nucleic Acids Res. 30, e15)

organism: Drosophila melanogaster

source_name: Female CS

label_protocol: Cyscribe post-labelling Kit (Amersham)

growth_protocol: Standard fly culture

extract_protocol: TRIZOL Invitrogen

tag: Whole females aged 3 days from the wild-type Canton S (CS) stock

source_name: female orbdec

tag: Whole females aged 3 days from the mutant orbdec stock homogeneized to CS


title: Uninfected_MO_MO_t0_REPC2


title: DrosophilaFemale_CSCy5xorbdecCy3_rep1

source_name: Female orbdec


title: M2

description: M2 macrophages

source_name: M2 macrophages

value: M2 macrophages


title: IP_Orb_6H4Cy3 x ovarian_pACy5

type: mixed

molecule: other

extract_protocol:
Ovaries of well-fed 2- to 3-day old wild-type females (30) were
dissected in 1x PBS and frozen immediately on dry ice. Ovary extract
was prepared by adding 100 ml of ice-cold IP buffer (20 mM Hepes,
pH 7.5, 150 mM NaCl, 2.5 mM MgCl2, 250 mM sucrose, 0.05%
NP40, 0.5% Triton X-100, 1 mM PMSF, 1 mg/ml pepstatin A, 10
mg/ml aprotinin, 1 mg/ml leupeptin) and homogenizing with a plastic
pestle in a 1.5 ml microfuge tube with 3-4 freeze/thaw cycles. The
homogenate was centrifuged at 3000 rpm for 5 minutes. The supernatant
was removed and mixed with 40 units of RNasin, 30 ml of antibody coupled
protein-A beads (Bio-Rad) for 2 hours to overnight at 4°C on
a rotator. The IP mix was centrifuged at low speed in the cold room
to remove the supernatant. The protein-A beads were then washed 4-
5 times with 20 volumes of IP buffer without MgCl2, phenol/chloroform
extracted and precipitated with glycogen to isolate mRNAs.

tag: Immunoprecipitation of ovarian extract with 6H4 anti-Orb monoclonal antibody

source_name: Ovarian pA

extract_protocol: Total RNA was extracted from ovaries or from whole females using TRIZOL (Invitrogen) and poly(A+) RNA was selected using the RNeasy kit (Qiagen)

tag: Poly(A+) RNA extracted from ovaries of 3 days old wild-type (w1118) females


title: M0

description: M0 macrophages

source_name: M0 macrophages

value: M0 macrophages


title: WT-S-CS

description: Cold Shock

value: Wild Type


title: DrosophilaFemale_CSCy3xorbdecCy5_rep4

tag: Whole females aged 3 days from the mutant orbdec stock homogenized to CS


title: DrosophilaFemale_CSCy5xorbdecCy3_rep2


title: M1

description: M1 macrophages

source_name: M1 macrophages

value: M1 macrophages


title: SIC_InfectedMO_liveCA_t120_S209

value: C57BL/6 and SC5314-GFP-mCherry

value: C57BL/6 primary, bone derived macrophages and SC5314-Neut5L-GFP-mCherry C. albicans


title: DrosophilaFemale_CSCy3xorbdecCy5_rep2

source_name: Females CS


title: IP_Orb_6H4Cy3xIP_12CA5Cy3

type: other

source_name: IP-6H4 Orb

tag: Immunoprecipitation of ovarian extract with 12CA5 anti-HA-Tag monoclonal antibody


title: DrosophilaFemale_CSCy3xorbdecCy5_rep1


title: IP_Orb_6H4Cy5 x ovarian_pACy3


title: DrosophilaFemale_CSCy3xorbdecCy5_rep3


title: Ct_Unexposed_MO_REPA

description:
macrophages not exposed to C. albicans and not sorted  subpopulation samples
MO_subpops_gene_exp_matrix

source_name: macrophage


title: WT-L-37


title: SIC_InfectedMO_liveCA_t120_S208

source_name: macrophage and C. albicans


title: WT-S-37


title: WT-L-CS

description: Cold Shock


title: SIC_InfectedMO_liveCA_t120_S207


title: SIC_InfectedMO_liveCA_t120_S206


title: CandidaOnly_t4_repa

source_name: C. albicans

value: SC5314-Neut5L-GFP-mCherry C. albicans


title: SIC_InfectedMO_liveCA_t120_S21


title: SIC_InfectedMO_liveCA_t120_S205


title: CandidaOnly_t4_repb


title: CandidaOnly_t2_repc


title: Ct_Unexposed_MO_REPB


title: CandidaOnly_t2_repa


title: SIC_InfectedMO_liveCA_t120_S203


title: SIC_InfectedMO_liveCA_t120_S201


title: SIC_InfectedMO_liveCA_t120_S204


title: CandidaOnly_t2_repb


title: CandidaOnly_t1_repa


title: CRISPRa_Control_rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: CRISPR activation, empty sgRNA vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were cultured under standard conditions (37°C, 95% humidity, and 5% CO2) in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS (Thermo Fisher Scientific), 1% of an antibiotic–antimycotic solution (10 mg/ml streptomycin and 10 000 units of penicillin/ml in 0.9% NaCl; Sigma-Aldrich, Munich, Germany), and 10 µg/ml blasticidin (selection antibiotic).

extract_protocol: RNA from cultured cells was extracted with the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany) as recommended by the supplier. The quality of RNA samples was confirmed by capillary electrophoresis using the Agilent 2100 bioanalyzer (all samples showed RIN=10).

treatment_protocol: The cells were not treated. The different cell clones derived from H2009 cells by applying CRISPR activation technology, as previously described, were compared.

value: lung adenocarcinoma cells

tag: genotype/variation

value: CRISPR activation to overexpress 14q32 miRNAs, empty sgRNA vector

tag: sgrna vector

value: Empty


title: SIC_InfectedMO_liveCA_t120_S199


title: CandidaOnly_t1_repc


title: CRISPRa_Control_rep1

tag: cell type


title: CandidaOnly_t1_repb


title: SIC_InfectedMO_liveCA_t120_S197


title: SIC_InfectedMO_liveCA_t120_S196


title: CandidaOnly_t0_repc


title: CandidaOnly_t0_repb


title: SIC_InfectedMO_liveCA_t120_S195


title: CandidaOnly_t0_repa


title: SIC_InfectedMO_liveCA_t120_S200


title: CRISPRa_Control_rep3


title: CRISPRa_sgRNA-B_rep1

source_name: CRISPR activation, sgRNA B

value: CRISPR activation to overexpress 14q32 miRNAs, single guide RNA B

value: sgRNA-B


title: CRISPRa_sgRNA-A_rep2

source_name: CRISPR activation, sgRNA A

value: CRISPR activation to overexpress 14q32 miRNAs, single guide RNA A

value: sgRNA-A


title: CRISPRa_sgRNA-A_rep3


title: CRISPRa_sgRNA-B_rep3


title: CRISPRa_sgRNA-B_rep2


title: Pooled Hypothalamic RNA from mice with developmental NMDAR antagonism_rep2

status: Public on Mar 11 2018

city: Riyadh

first: Katharine

middle: Sara

last: Collison

state: Riyadh

address: Takhasussi Street

department: Department of Cell Biology

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

hyb_protocol: The labeled and fragmented DNA was hybridized to Mouse Gene 1.0 ST Array for 17 hours at 45°C and 60rpm. Arrays were washed and stained on the Affymetrix fluidics station 450.

scan_protocol: Genechip were scanned using Genechip 7G scanner.

data_processing: The data were analyzed with Partek Genomics Suite using RMA (Robust Multi-Array Average) settings and quantile normalization method was applied. Intensities less than log value of 6 were filtered. Fold change cut-off was ±1.4Significant DEGs were based on criteria of p-value <0.05 and False Discovery Rate<0.05.

label: Biotin

source_name: Hypothalamus

label_protocol: 5.5ug of fragmented cDNA was end labeled according to standard Affymerix protocol using Affymetrix Genechip WT terminal labeling kit.

growth_protocol: C57Bl/6J mice were housed 3/cage in a controlled environment (pathogen-free conditions of 12 h light/dark cycle, 22 ± 2°C) with standard chow and water available ad libitum. The breeding and care of the animals were in accordance with the protocols approved by the Animal Care and Use Committee of the King Faisal Specialist Hospital & Research Centre

extract_protocol: Total RNA was extracted from snap frozen Hypothalamus using RNeasy Lipid mini kit (Qiagen UK)

treatment_protocol: Aspartame and the orally-active water-soluble drug CGP 39551 were administered in the drinking water  at 46mg/Kg bw and 5mg/Kg body weight respectively. At 21 weeks mice were euthanized and the hypothalamus was snap-frozen for RNA extraction.

tag: Sex

value: Male

tag: tissue

value: Hypothalamus

tag: age

value: 21 weeks


title: Pooled Hypothalamic RNA from aspartame-exposed mice with developmental NMDAR antagonism_rep2.

tag: strain


title: CRISPRa_sgRNA-A_rep1

tag: cell line


title: Pooled Adrenal RNA from aspartame-exposed mice with developmental NMDAR antagonism_rep2.

source_name: Adrenal tissue

extract_protocol: Total RNA was extracted from snap frozen Adrenals using RNeasy Lipid mini kit (Qiagen UK)

treatment_protocol: Aspartame and the orally-active water-soluble drug CGP 39551 were administered in the drinking water  at 46mg/Kg bw and 5mg/Kg body weight respectively. At 21 weeks mice were euthanized and the adrenal glands were snap-frozen for RNA extraction.

value: adrenal gland


title: Pooled Hypothalamic RNA from aspartame-exposed mice_rep1


title: Pooled Hypothalamic RNA from aspartame-exposed mice_rep2


title: Pooled Hypothalamic RNA from Control mice_rep2


title: Pooled Hypothalamic RNA from aspartame-exposed mice with developmental NMDAR antagonism_rep1.


title: Pooled Hypothalamic RNA from Control mice_rep3


title: Pooled Hypothalamic RNA from mice with developmental NMDAR antagonism_rep1


title: Hepatocellular carcinoma SMMC-7721 cells_si-Negative control-PRMT5

first: Shengli

last: Li

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
HTseq-count was used to calculate read counts for each gene and lncRNA and then counts were normalized into FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hepatocyte

growth_protocol: Cells were cultured at 37°C in a humidified incubator with 5% CO2 in Dulbecco’s modified Eagle’s medium supplemented with 10% foetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin, and 8mg/L antibiotic Tylosin tartrate against mycoplasma.

extract_protocol:
Total RNA of cells was harvested using Trizol reagent. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA-seq libraries were prepared using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat#E7420L) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using RNAseq protocols

treatment_protocol: Treated the cells with small interference RNA (siRNA) oligonucleotides which include si-Negative control-LINC01138, si-LINC01138-1, si-LINC01138-2, si-Negative control-PRMT5, si-PRMT5-1, si-PRMT5-2. Transfections of siRNA (75 nM) were performed with Lipofectamine 2000.

value: liver

value: human liver cancer


title: Pooled Hypothalamic RNA from aspartame-exposed mice with developmental NMDAR antagonism_rep3.


title: Hepatocellular carcinoma SMMC-7721 cells_si-PRMT5-1


title: Pooled Hypothalamic RNA from aspartame-exposed mice_rep3


title: Pooled Adrenal RNA from mice with developmental NMDAR antagonism_rep3


title: Pooled Hypothalamic RNA from Control mice_rep1


title: Hepatocellular carcinoma SMMC-7721 cells_si-LINC01138-2


title: Pooled Adrenal RNA from aspartame-exposed mice with developmental NMDAR antagonism_rep1.


title: Pooled Adrenal RNA from aspartame-exposed mice with developmental NMDAR antagonism_rep3.


title: Pooled Adrenal RNA from aspartame-exposed mice_rep1


title: Pooled Adrenal RNA from mice with developmental NMDAR antagonism_rep2


title: Pooled Hypothalamic RNA from mice with developmental NMDAR antagonism_rep3


title: Pooled Adrenal RNA from aspartame-exposed mice_rep3


title: Hepatocellular carcinoma SMMC-7721 cells_si-LINC01138-1


title: Pooled Adrenal RNA from aspartame-exposed mice_rep2


title: Hepatocellular carcinoma SMMC-7721 cells_si-Negative control-LINC01138


title: genomic DNA from 9721367028_R05C02

status: Public on Mar 10 2018

type: genomic

city: Los Angeles

first: Ritz

last: Beate

state: California

address: 650 Charles E Young Dr. South

department: Epidemiology

institute: UCLA Fielding School of Public Health

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: R software v3.4.2

label: Cy3, Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from whold blood samples using the Qiagen Gentra Puregene Blood Kit according to standard instructions

tag: disease state

value: Parkinson's disease (PD)

tag: gender

value: Female

tag: ethnicity

value: Caucasian

value: whole blood


title: genomic DNA from 9721367028_R06C01


title: genomic DNA from 9721367028_R04C01


title: genomic DNA from 9721367028_R03C02

value: PD-free control


title: genomic DNA from 9721367028_R04C02

value: Hispanic


title: genomic DNA from 9721367028_R01C02


title: genomic DNA from 9721367028_R02C02


title: genomic DNA from 9721367028_R02C01


title: genomic DNA from 9721367028_R03C01


title: Pooled Adrenal RNA from Control mice_rep3


title: genomic DNA from 9721366162_R06C01


title: genomic DNA from 9721366162_R03C02


title: genomic DNA from 9721367028_R01C01


title: Pooled Adrenal RNA from mice with developmental NMDAR antagonism_rep1


title: genomic DNA from 9721366162_R06C02


title: genomic DNA from 9721366162_R05C02


title: genomic DNA from 9721366162_R04C02


title: genomic DNA from 9721366162_R05C01


title: genomic DNA from 9721366162_R02C02


title: genomic DNA from 9721367028_R06C02


title: Caco-2_shOCC-1-1

city: Chengdu

first: Yang

last: Lan

address: No. 29 Wangjiang Road

department: Center for Functional Genomics and Bioinformatics

institute: Sichuan University

description: Gene expression data from Caco-2 cells expressing shOCC-1-1

hyb_protocol: Fragmented cRNAs were hybridized on the PrimeView (Affymetrix) chip, and then the chip was washed and stained following the manufacturer's standard protocol.

scan_protocol: Fluorescent signal was scanned by GeneChip Scanner 3000 (Affymetrix) and converted into digital data (.CEL) using Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Gene expression data were preprocessed using Robust Multi-array Average (RMA) algorithm.

source_name: Caco-2 cells expressing shOCC-1-1

label_protocol: Total RNA was converted into cRNA and labeled with biotin using MessageAmp Premier RNA Amplification Kit (#1792, Ambion) according to the manufacturer's instructions.

growth_protocol: Caco-2 cells were cultured in MEM media supplemented with 20% fetal bovine serum.

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

treatment_protocol: Caco-2 cells were transduced with shRNA lentiviruses, selected by 1 μg/ml puromycin for 5 days and grown in media without puromycin for 24 h before microarray analysis.

value: Colorectal cancer

value: OCC-1 knockdown


title: genomic DNA from 9721366162_R03C01


title: Pooled Adrenal RNA from Control mice_rep1


title: Caco-2_shCTRL

description: Gene expression data from Caco-2 cells expressing shCTRL

source_name: Caco-2 cells expressing shCTRL

value: control


title: genomic DNA from 9721367028_R05C01


title: Pooled Adrenal RNA from Control mice_rep2


title: Caco-2_shOCC-1-2

description: Gene expression data from Caco-2 cells expressing shOCC-1-2

source_name: Caco-2 cells expressing shOCC-1-2


title: genomic DNA from 9721366162_R04C01


title: genomic DNA from 9721366162_R01C02


title: genomic DNA from 3999997159_R04C01


title: genomic DNA from 3999997159_R04C02


title: genomic DNA from 9721366162_R01C01


title: genomic DNA from 3999997159_R03C02


title: genomic DNA from 3999997159_R02C02


title: genomic DNA from 3999997159_R01C02


title: genomic DNA from 3999997159_R03C01


title: genomic DNA from 3999997159_R02C01


title: genomic DNA from 3999997159_R01C01


title: genomic DNA from 3999997147_R06C01


title: genomic DNA from 9721366162_R02C01


title: genomic DNA from 3999997147_R05C01


title: genomic DNA from 3999997147_R05C02


title: genomic DNA from 3999997147_R02C02


title: genomic DNA from 3999997132_R05C02


title: genomic DNA from 3999997147_R04C01


title: genomic DNA from 3999997132_R04C01


title: genomic DNA from 3999997132_R06C02


title: genomic DNA from 3999997132_R01C02


title: genomic DNA from 3999997132_R06C01


title: genomic DNA from 3999997147_R01C02


title: genomic DNA from 3999997132_R03C01


title: genomic DNA from 3999997132_R02C02


title: genomic DNA from 3999997147_R03C01


title: genomic DNA from 3999997105_R06C02


title: genomic DNA from 3999997105_R04C01


title: genomic DNA from 3999997105_R06C01


title: genomic DNA from 3999997105_R05C02


title: genomic DNA from 3999997105_R03C01


title: genomic DNA from 3999997105_R01C02


title: genomic DNA from 3999997099_R06C02


title: genomic DNA from 3999997105_R05C01


title: genomic DNA from 3999997105_R02C02


title: genomic DNA from 3999997132_R05C01


title: genomic DNA from 3999997099_R06C01


title: genomic DNA from 3999997147_R06C02


title: genomic DNA from 3999997099_R05C02


title: genomic DNA from 3999997099_R03C02


title: genomic DNA from 3999997099_R04C01


title: genomic DNA from 3999997099_R02C02


title: genomic DNA from 3999997098_R06C02


title: genomic DNA from 3999997098_R05C02


title: genomic DNA from 3999997099_R02C01


title: genomic DNA from 3999997099_R01C02


title: genomic DNA from 3999997099_R01C01


title: genomic DNA from 3999997098_R04C02


title: genomic DNA from 3999997098_R05C01


title: genomic DNA from 3999997098_R03C01


title: genomic DNA from 3999997098_R03C02


title: genomic DNA from 3999997098_R04C01


title: genomic DNA from 3999997097_R04C01


title: genomic DNA from 3999997097_R06C02


title: genomic DNA from 3999997097_R05C01


title: genomic DNA from 3999997098_R01C01


title: genomic DNA from 3999997097_R05C02


title: genomic DNA from 3999997097_R06C01


title: genomic DNA from 3999997099_R04C02


title: genomic DNA from 3999997097_R02C02


title: genomic DNA from 3999997094_R06C02


title: genomic DNA from 3999997094_R06C01


title: genomic DNA from 3999997097_R01C02


title: genomic DNA from 3999997099_R05C01


title: genomic DNA from 3999997094_R05C01


title: genomic DNA from 3999997098_R06C01


title: genomic DNA from 3999997099_R03C01


title: genomic DNA from 3999997094_R02C02


title: genomic DNA from 3999997094_R01C01


title: genomic DNA from 3999997087_R06C01


title: genomic DNA from 3999997087_R06C02


title: genomic DNA from 3999997094_R05C02


title: genomic DNA from 3999997094_R02C01


title: genomic DNA from 3999997094_R01C02


title: genomic DNA from 3999997087_R05C01


title: genomic DNA from 3999997087_R04C02


title: genomic DNA from 3999997087_R02C02


title: genomic DNA from 3999997097_R03C01


title: genomic DNA from 3999997087_R01C02


title: genomic DNA from 3999997098_R02C01


title: genomic DNA from 3999997086_R06C02


title: genomic DNA from 3999997086_R05C02


title: genomic DNA from 3999997086_R06C01


title: genomic DNA from 3999997086_R04C01


title: genomic DNA from 3999997086_R02C02


title: genomic DNA from 3999997086_R03C01


title: genomic DNA from 3999997087_R01C01


title: genomic DNA from 3999997086_R05C01


title: genomic DNA from 3999997085_R05C02


title: genomic DNA from 3999997085_R06C01


title: genomic DNA from 3999997085_R06C02


title: genomic DNA from 3999997086_R01C02


title: genomic DNA from 3999997085_R03C02


title: genomic DNA from 3999997085_R04C02


title: genomic DNA from 3999997085_R05C01


title: genomic DNA from 3999997085_R03C01


title: genomic DNA from 3999997085_R02C02


title: genomic DNA from 3999997087_R02C01


title: genomic DNA from 3999997084_R02C02


title: genomic DNA from 3999997085_R01C02


title: genomic DNA from 3999997084_R04C02


title: genomic DNA from 3999997085_R01C01


title: genomic DNA from 3999997084_R03C02


title: genomic DNA from 3999997084_R05C01


title: genomic DNA from 3999997084_R06C01


title: genomic DNA from 3999997084_R02C01


title: genomic DNA from 3999997084_R01C02


title: genomic DNA from 3999997084_R01C01


title: genomic DNA from 3999997075_R04C02


title: genomic DNA from 3999997075_R03C02


title: genomic DNA from 3999997075_R04C01


title: genomic DNA from 3999997075_R02C01


title: genomic DNA from 3999997075_R03C01


title: genomic DNA from 3999997075_R01C01


title: genomic DNA from 3999997075_R01C02


title: genomic DNA from 3999997075_R02C02


title: genomic DNA from 3999997071_R05C01


title: genomic DNA from 3999997071_R06C01


title: genomic DNA from 3999997071_R06C02


title: genomic DNA from 3999997071_R05C02


title: genomic DNA from 3999997085_R02C01


title: genomic DNA from 3999997071_R04C01


title: genomic DNA from 3999997071_R02C01


title: genomic DNA from 3999997071_R03C02


title: genomic DNA from 3999997071_R01C01


title: genomic DNA from 3999997071_R03C01


title: genomic DNA from 3999997070_R06C01


title: genomic DNA from 3999997071_R04C02


title: genomic DNA from 3999997068_R03C01


title: genomic DNA from 3999997070_R01C02


title: genomic DNA from 3999997070_R05C01


title: genomic DNA from 3999997070_R03C02


title: genomic DNA from 3999997068_R04C01


title: genomic DNA from 3999997070_R02C01


title: genomic DNA from 3999997070_R01C01


title: genomic DNA from 3999997068_R02C02


title: genomic DNA from 3999997068_R02C01


title: genomic DNA from 3999997068_R01C02


title: genomic DNA from 3999997068_R01C01


title: genomic DNA from 3999997053_R06C01


title: genomic DNA from 3999997053_R05C01


title: genomic DNA from 3999997053_R06C02


title: genomic DNA from 3999997053_R04C02


title: genomic DNA from 3999997053_R04C01


title: genomic DNA from 3999997053_R03C02


title: genomic DNA from 3999997053_R05C02


title: genomic DNA from 3999997070_R04C02


title: genomic DNA from 3999997053_R03C01


title: genomic DNA from 3999997053_R02C01


title: genomic DNA from 3999997053_R01C02


title: genomic DNA from 3999997070_R02C02


title: genomic DNA from 3999997048_R04C02


title: genomic DNA from 3999997053_R02C02


title: genomic DNA from 3999997048_R03C01


title: genomic DNA from 3999997048_R01C02


title: genomic DNA from 3999997048_R02C01


title: genomic DNA from 3999997048_R01C01


title: genomic DNA from 3999997048_R03C02


title: genomic DNA from 3999997048_R04C01


title: genomic DNA from 3999997060_R02C01


title: genomic DNA from 3999997060_R01C01


title: genomic DNA from 3999997045_R05C01


title: genomic DNA from 3999997045_R06C01


title: genomic DNA from 3999997045_R06C02


title: genomic DNA from 3999997045_R02C02


title: genomic DNA from 3999997045_R04C02


title: genomic DNA from 3999997045_R02C01


title: genomic DNA from 3999997043_R05C01


title: genomic DNA from 3999997043_R06C01


title: genomic DNA from 3999997053_R01C01


title: genomic DNA from 3999997043_R04C01


title: genomic DNA from 3999997045_R01C01


title: genomic DNA from 3999997043_R04C02


title: genomic DNA from 3999997043_R06C02


title: genomic DNA from 3999997043_R05C02


title: genomic DNA from 3999997043_R02C01


title: genomic DNA from 3999997043_R03C02


title: genomic DNA from 3999997048_R02C02


title: genomic DNA from 3999997043_R01C01


title: genomic DNA from 3999997043_R03C01


title: genomic DNA from 3999984167_R04C01


title: genomic DNA from 3999984167_R03C02


title: genomic DNA from 3999984167_R03C01


title: genomic DNA from 3999997045_R01C02


title: genomic DNA from 3999984167_R02C01


title: genomic DNA from 3999984167_R01C02


title: genomic DNA from 3999984166_R06C02


title: genomic DNA from 3999984167_R02C02


title: genomic DNA from 3999984166_R06C01


title: genomic DNA from 3999984167_R01C01


title: genomic DNA from 3999984166_R04C02


title: genomic DNA from 3999984166_R05C01


title: genomic DNA from 3999984166_R03C01


title: genomic DNA from 3999984166_R04C01


title: genomic DNA from 3999984166_R02C01


title: genomic DNA from 3999984166_R03C02


title: genomic DNA from 3999984166_R01C01


title: genomic DNA from 3999984163_R04C02


title: genomic DNA from 3999984163_R06C01


title: genomic DNA from 3999984163_R03C02


title: genomic DNA from 3999984163_R05C01


title: genomic DNA from 3999984163_R02C02


title: genomic DNA from 3999984163_R01C01


title: genomic DNA from 3999984159_R04C01


title: genomic DNA from 3999984163_R02C01


title: genomic DNA from 3999984163_R01C02


title: genomic DNA from 3999984159_R02C01


title: genomic DNA from 3999984159_R03C01


title: genomic DNA from 3999984156_R06C02


title: genomic DNA from 3999984166_R05C02


title: genomic DNA from 3999984167_R04C02


title: genomic DNA from 3999984159_R01C01


title: genomic DNA from 3999984156_R06C01


title: genomic DNA from 3999984156_R04C02


title: genomic DNA from 3999984156_R05C02


title: genomic DNA from 3999984156_R05C01


title: genomic DNA from 3999984156_R04C01


title: genomic DNA from 3999984156_R01C01


title: genomic DNA from 3999984155_R06C02


title: genomic DNA from 3999984155_R05C01


title: genomic DNA from 3999984156_R02C01


title: genomic DNA from 3999984155_R06C01


title: genomic DNA from 3999984155_R03C02


title: genomic DNA from 3999984155_R03C01


title: genomic DNA from 3999984155_R05C02


title: genomic DNA from 3999984155_R02C01


title: genomic DNA from 3999984156_R03C01


title: genomic DNA from 3999984154_R06C02


title: genomic DNA from 3999984155_R04C01


title: genomic DNA from 3999984154_R06C01


title: genomic DNA from 3999984154_R04C02


title: genomic DNA from 3999984154_R04C01


title: genomic DNA from 3999984154_R03C02


title: genomic DNA from 3999984154_R03C01


title: genomic DNA from 3999984154_R05C01


title: genomic DNA from 3999984154_R02C01


title: genomic DNA from 3999984154_R01C01


title: genomic DNA from 3999984153_R06C02


title: genomic DNA from 3999984153_R06C01


title: genomic DNA from 3999984156_R03C02


title: genomic DNA from 3999984153_R04C01


title: genomic DNA from 3999984153_R03C01


title: genomic DNA from 3999984153_R05C02


title: genomic DNA from 3999984153_R01C02


title: genomic DNA from 3999984155_R01C01


title: genomic DNA from 3999984152_R06C02


title: genomic DNA from 3999984153_R02C02


title: genomic DNA from 3999984153_R05C01


title: genomic DNA from 3999984152_R05C02


title: genomic DNA from 3999984152_R04C02


title: genomic DNA from 3999984154_R05C02


title: genomic DNA from 3999984152_R03C02


title: genomic DNA from 3999984152_R06C01


title: genomic DNA from 3999984152_R02C01


title: genomic DNA from 3999984152_R03C01


title: genomic DNA from 3999984152_R01C01


title: genomic DNA from 3999984150_R04C01


title: genomic DNA from 3999984152_R05C01


title: genomic DNA from 3999984150_R05C01


title: genomic DNA from 3999984150_R06C02


title: genomic DNA from 3999984150_R06C01


title: genomic DNA from 3999984150_R03C01


title: genomic DNA from 3999984150_R02C02


title: genomic DNA from 3999984150_R01C02


title: genomic DNA from 3999984147_R04C02


title: genomic DNA from 3999984146_R06C01


title: genomic DNA from 3999984147_R06C02


title: genomic DNA from 3999984146_R04C02


title: genomic DNA from 3999984152_R04C01


title: genomic DNA from 3999984146_R02C01


title: genomic DNA from 3999984146_R05C01


title: genomic DNA from 3999984146_R01C02


title: genomic DNA from 3999984146_R02C02


title: genomic DNA from 3999984146_R03C02


title: genomic DNA from 3999984146_R01C01


title: genomic DNA from 3999984145_R06C02


title: genomic DNA from 3999984145_R02C02


title: genomic DNA from 3999984145_R03C01


title: genomic DNA from 3999984145_R05C01


title: genomic DNA from 3999984145_R04C01


title: genomic DNA from 3999984150_R05C02


title: genomic DNA from 3999984145_R05C02


title: genomic DNA from 3999984145_R03C02


title: genomic DNA from 3999984142_R06C02


title: genomic DNA from 3999984142_R05C02


title: genomic DNA from 3999984140_R05C01


title: genomic DNA from 3999984142_R04C01


title: genomic DNA from 3999984142_R03C02


title: genomic DNA from 3999984142_R03C01


title: genomic DNA from 3999984140_R05C02


title: genomic DNA from 3999984140_R04C02


title: genomic DNA from 3999984140_R03C02


title: genomic DNA from 3999984140_R01C01


title: genomic DNA from 3999984139_R06C02


title: genomic DNA from 3999984139_R04C01


title: genomic DNA from 3999984128_R06C02


title: genomic DNA from 3999984139_R02C01


title: genomic DNA from 3999984128_R05C02


title: genomic DNA from 3999984139_R02C02


title: genomic DNA from 3999984128_R05C01


title: genomic DNA from 3999984128_R04C02


title: genomic DNA from 3999984128_R04C01


title: genomic DNA from 3999984128_R03C01


title: genomic DNA from 3999984128_R03C02


title: genomic DNA from 3999984127_R06C01


title: genomic DNA from 3999984115_R06C02


title: genomic DNA from 3999984127_R05C02


title: genomic DNA from 3999984142_R05C01


title: genomic DNA from 3999984127_R03C01


title: genomic DNA from 3999984127_R01C01


title: genomic DNA from 3999984115_R01C02


title: genomic DNA from 3999984115_R04C01


title: genomic DNA from 3999984115_R03C01


title: genomic DNA from 3999984079_R06C02


title: genomic DNA from 3999984115_R05C01


title: genomic DNA from 3999984115_R03C02


title: genomic DNA from 3999984115_R04C02


title: genomic DNA from 3999984079_R06C01


title: genomic DNA from 3999984079_R05C02


title: genomic DNA from 3999984139_R06C01


title: genomic DNA from 3999984139_R04C02


title: genomic DNA from 3999984079_R05C01


title: genomic DNA from 3999984079_R03C02


title: genomic DNA from 3999984078_R06C02


title: genomic DNA from 3999984079_R01C01


title: genomic DNA from 3999984079_R01C02


title: genomic DNA from 3999984127_R01C02


title: genomic DNA from 3999984079_R02C01


title: genomic DNA from 3999984078_R06C01


title: genomic DNA from 3999984078_R05C01


title: genomic DNA from 3999984078_R03C01


title: genomic DNA from 3999984078_R04C02


title: genomic DNA from 3999984078_R03C02


title: genomic DNA from 3999984078_R04C01


title: genomic DNA from 3999984115_R02C02


title: genomic DNA from 3999984078_R05C02


title: genomic DNA from 3999984078_R01C02


title: genomic DNA from 3999984069_R06C02


title: genomic DNA from 3999984078_R02C02


title: genomic DNA from 3999984069_R04C01


title: genomic DNA from 3999984069_R05C02


title: genomic DNA from 3999984069_R04C02


title: genomic DNA from 3999984069_R03C02


title: genomic DNA from 3999984065_R06C01


title: genomic DNA from 3999984069_R01C02


title: genomic DNA from 3999984065_R05C01


title: genomic DNA from 3999984065_R04C02


title: genomic DNA from 3999984065_R03C02


title: genomic DNA from 3999984079_R02C02


title: genomic DNA from 3999984079_R04C02


title: genomic DNA from 3999984065_R02C01


title: genomic DNA from 3999984065_R02C02


title: genomic DNA from 3999984065_R01C01


title: genomic DNA from 3999984063_R06C01


title: genomic DNA from 3999984065_R01C02


title: genomic DNA from 3999984063_R05C01


title: genomic DNA from 3999984063_R04C02


title: genomic DNA from 3999984063_R03C01


title: genomic DNA from 3999984063_R02C02


title: genomic DNA from 3999984063_R01C02


title: genomic DNA from 3999984063_R02C01


title: genomic DNA from 3999984063_R01C01


title: genomic DNA from 3999984061_R06C02


title: genomic DNA from 3999984061_R04C02


title: genomic DNA from 3999984061_R05C02


title: genomic DNA from 3999984061_R02C02


title: genomic DNA from 3999984061_R01C01


title: genomic DNA from 3999984057_R06C01


title: genomic DNA from 3999984057_R06C02


title: genomic DNA from 3999984061_R02C01


title: genomic DNA from 3999984057_R05C02


title: genomic DNA from 3999984057_R04C01


title: genomic DNA from 3999984057_R03C01


title: genomic DNA from 3999984057_R05C01


title: genomic DNA from 3999984057_R02C02


title: genomic DNA from 3999984057_R01C02


title: genomic DNA from 3999984055_R06C01


title: genomic DNA from 3999984063_R04C01


title: genomic DNA from 3999984055_R05C01


title: genomic DNA from 3999984063_R03C02


title: genomic DNA from 3999984055_R04C01


title: genomic DNA from 3999984055_R03C02


title: genomic DNA from 3999984055_R03C01


title: genomic DNA from 3999984061_R03C02


title: genomic DNA from 3999984055_R01C02


title: genomic DNA from 3999984053_R06C02


title: genomic DNA from 3999984055_R02C02


title: genomic DNA from 3999984053_R06C01


title: genomic DNA from 3999984053_R05C01


title: genomic DNA from 3999984053_R04C02


title: genomic DNA from 3999984053_R05C02


title: genomic DNA from 3999984053_R04C01


title: genomic DNA from 3999984053_R03C01


title: genomic DNA from 3999984053_R03C02


title: genomic DNA from 3999984053_R01C02


title: genomic DNA from 3999984050_R06C02


title: genomic DNA from 3999984050_R05C01


title: genomic DNA from 3999984055_R06C02


title: genomic DNA from 3999984053_R01C01


title: genomic DNA from 3999984055_R04C02


title: genomic DNA from 3999984050_R05C02


title: genomic DNA from 3999984050_R06C01


title: genomic DNA from 3999984050_R04C02


title: genomic DNA from 3999984055_R05C02


title: genomic DNA from 3999984050_R04C01


title: genomic DNA from 3999984050_R03C01


title: genomic DNA from 3999984050_R03C02


title: genomic DNA from 3999984050_R02C02


title: genomic DNA from 3999984053_R02C01


title: genomic DNA from 3999984050_R01C02


title: genomic DNA from 3999984045_R05C02


title: genomic DNA from 3999984045_R06C02


title: genomic DNA from 3999984045_R04C01


title: genomic DNA from 3999984045_R02C02


title: genomic DNA from 3999984045_R05C01


title: genomic DNA from 3999984045_R03C01


title: genomic DNA from 3999984045_R04C02


title: genomic DNA from 3999984044_R06C02


title: genomic DNA from 3999984053_R02C02


title: genomic DNA from 3999984044_R05C02


title: genomic DNA from 3999984044_R04C01


title: genomic DNA from 3999984044_R03C02


title: genomic DNA from 3999984044_R04C02


title: genomic DNA from 3999984044_R05C01


title: genomic DNA from 3999984044_R03C01


title: genomic DNA from 3999984044_R01C02


title: genomic DNA from 3999984044_R02C02


title: genomic DNA from 3999984041_R06C01


title: genomic DNA from 3999984041_R05C02


title: genomic DNA from 3999984041_R05C01


title: genomic DNA from 3999984041_R04C01


title: genomic DNA from 3999984041_R01C02


title: genomic DNA from 3999984041_R02C01


title: genomic DNA from 3999984040_R06C02


title: genomic DNA from 3999984040_R06C01


title: genomic DNA from 3999984040_R05C02


title: genomic DNA from 3999984040_R05C01


title: genomic DNA from 3999984040_R03C02


title: genomic DNA from 3999984040_R04C01


title: genomic DNA from 3999984040_R04C02


title: genomic DNA from 3999984040_R03C01


title: genomic DNA from 3999984044_R06C01


title: genomic DNA from 3999984040_R01C01


title: genomic DNA from 3999984039_R06C02


title: genomic DNA from 3999984039_R05C02


title: genomic DNA from 3999984039_R04C02


title: control replicate 2

city: Hospitalet de Llobregat

first: Julián

last: Cerón

state: Barcelona

address: Gran via 199, Hospital Duran i Reynals, planta 3

department: Cancer and Human Molecular Genetics

country: Spain

institute: IDIBELL

data_processing:
processed and aligned using Tophat to produce BAM files.
These BAM files were analyzed using the SeqSolve software, which use Cufflinks/ Cuffdiff for differential gene/transcript expression analyses (Trapnell et al. 2012)
Genome_build: C. elegans reference genome, version WBcel235.74
Supplementary_files_format_and_content: excel file

organism: Caenorhabditis elegans

source_name: wild type N2

growth_protocol: Mix population grown in OP50 at 20C

extract_protocol:
Total RNA purification was performed using the mirVana miRNA isolation kit (Ambion) and mRNA was purified by poly-A capture
Poly(A) enriched samples were multiplexed in libraries by BGI.
paired-end RNA-Sequencing on Illumina Hiseq 91PE platform.  read lenght of 100 bp.Between 11 and 13 millions of reads per sample

treatment_protocol: Cisplatin-treated animals were exposed to 0 µg/ml of cisplatin for 24 hours

tag: treatment


title: genomic DNA from 3999984039_R02C02


title: control replicate 1


title: cisplatin replicate 2

value: 60 µg/ml of cisplatin for 24 hours at 20ºC


title: cisplatin replicate 1


title: genomic DNA from 3999984039_R02C01


title: genomic DNA from 3999984039_R01C02


title: genomic DNA from 3999984039_R01C01


title: genomic DNA from 3999984030_R06C02


title: genomic DNA from 3999984030_R04C02


title: genomic DNA from 3999984030_R01C01


title: genomic DNA from 3999984028_R06C01


title: genomic DNA from 3999984028_R05C02


title: ES_PCGF5_input

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using Bowtie2 with default parameters: -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
For histone modification chipseq, peaks were called using MACS2 (v2.1.0), a q-value of 10^-2 was used as the cutoff; For PCGF5 chipseq, peaks were called using MACS2 (v2.1.0), a p-value of 10^-4 was used as the cutoff;
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlapping analysis was performed using bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS in bed format (https://github.com/taoliu/MACS#output-files).

source_name: 46C mES

growth_protocol:
sample1-6:Sox1-GFP ESC lines were cultured on mitomycin C-inactivated mouse embryo fibroblasts in DMEM high-glucose media containing 15% FBS (Gibco), 1mM sodium pyruvate (Gibco), 1mM non-essential amino acids (Gibco), 1 x GlutaMAX (Gibco), 0.1 mM 2-mercaptoethanol (Gibco), 1000 U/ml leukemia inhibitory factor (LIF), and the 2i inhibitors (3 μM CHIR99021, and 1 μM PD0325901).
sample7-14:For neural differentiation in suspension as described in (Watanabe, K. et al., 2005) , the dissociated ESCs were suspended in the Petri dish and cultured in GMEM (Gibco) supplemented with 8% knockout serum replacement (Gibco), 1 mM Glutamine, 1 mM pyruvate, 0.1 mM nonessential amino acids and 0.1 mM b-mercaptoethanol (Gibco).

extract_protocol:
cells were crosslinked with 2mM EGS [ethylene glycol bis(succinimidylsuccinate)] and crosslink it again with 1％formaldehyde. The cells were sonicated to achieve a chromatin sized of 200-500 bp in SDS lysis buffer containing 1 × protease inhibitor cocktails and 1 mM PMSF. Then the sonicated chromatin was dialyzed with TE buffer containing 150 mM Nacl and incubated with M2-Magnetic beads overnight at 4°C with rotation. Wash twice with TBS-T (Tween-20 at 0.05%), and wash four times with TBS at 4°C. For H2AK119ub1 and H3K27me3, chromatin was extracted in buffer A (10mM Tris-HCL PH=7.9, 1.5mM Mgcl2, 10mM KCL, 0.1% TritonX-100, protease inhibitors). The resultant chromatin was re-suspended in 200ul Buffer B (50 mM Tris–HCl, pH 7.9, 3.5mM MgCl2, 2 mM CaCl2, protease inhibitors) and digested into nucleosomes fragments at 37℃ by adding 5ul 200U/ml MNase. After that, nucleosomes fragments were crosslinked with 0.5% formaldehyde immediately. Magnetic protein A/G beads were washed and added with the recommended antibody for overnight. Immune complexes were washed and Antibody-bound chromatin was reverse-crosslinked, and the ChIPed DNA samples were purified for either ChIP-Seq. The amounts of immunoprecipitated DNA were normalized to the input.
About 10 ng IP DNA and input DNA measured by Qubit Fluorometer (Invitrogen) were used to construct DNA library by using ChIP-Seq Sample Prep Kit (Illumina).

value: embryonic stem cells (ES)

tag: chip/antibody

value: Wild type


title: genomic DNA from 3999984028_R06C02


title: ES_PCGF5


title: genomic DNA from 3999984028_R03C02

value: Male


title: genomic DNA from 3999984025_R06C02


title: genomic DNA from 3999984025_R06C01


title: genomic DNA from 3999984025_R05C02


title: genomic DNA from 3999984025_R05C01


title: wt Th0 cells

first: Aviv

last: Regev

address: 415 Main Street

data_processing:
reads were aligned with TopHat version 2.0.10
differential expression was called with Cuffdiff version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: text format, contains differential expression calls (q1 = wt and q2 = Fas-deficient)

source_name: secondary lymphoid organs (spleen and lymphnodes)

extract_protocol:
total RNA extracted using RNeasy kit (Quiagen) including DNaseI treatment
Preparation of cDNA libraries for sequencing was performed using an RNA ligation method previously described (Levin et al., 2010 PubMedID 20711195). Briefly, 1 μg of total RNA was polyA-selected twice using oligo-dT beads, then Zinc fragmented, DNase treated, and dephosphorylated. Then 3’ RNA-adapter was ligated to the dephosphorylated RNA using T4 RNA Ligase and first strand cDNA synthesis was performed using rTd primers and Affinity Script reverse transcriptase. RNA was then hydrolysed using NaOH. After clean-up, 5’ adapter was ligated to the cDNA and the cDNA was PCR amplified using adapter-complementary primers. Clean-up steps in between reactions were performed using Silane beads.

tag: background strain

value: Sorted naive (defined as CD62L+CD44-CD25-) CD4+ T cells

tag: genotype

value: wildtype

tag: differentiation condition

value: platebound anti-CD3 and anti-CD28 with no cytokines for 48 hours


title: Fas-deficient Th17 cells

value: Fas-/-

value: platebound anti-CD3 and anti-CD28 with TGF-β1 and IL-6 for 48 hours


title: wt Th17 cells


title: Fas-deficient Th0 cells


title: genomic DNA from 3999984039_R03C02

value: Female


title: genomic DNA from 3999984025_R04C01

value: Parkinson's disease (PD)


title: genomic DNA from 3999984025_R03C02

value: whole blood


title: genomic DNA from 3999984030_R04C01

value: PD-free control

value: Caucasian


title: genomic DNA from 3999984028_R04C02


title: genomic DNA from 3999984025_R03C01

value: Hispanic


title: genomic DNA from 3999984025_R02C02


title: genomic DNA from 3999984024_R06C02


title: genomic DNA from 3999984024_R06C01


title: genomic DNA from 3999984025_R01C02


title: genomic DNA from 3999984024_R05C02


title: w1118 gut sample1

city: Solna

first: Jessica

middle: Margareta

last: Lindvall

address: Tomtebodavägen 23A

department: NBIS

institute: SciLifeLab. Stockholm University

hyb_protocol: From Agilent

scan_protocol: Agilent DNA microarray scanner G2505C

data_processing: Signal intensities was quantified from the scanned image by using Feature Extraction Software version 10.7.3.1.Processed an quantile normalized using Partek Genomic Suite software.

source_name: w1118 gut

label_protocol: Low Input Quick Amp Labelling Kit (Cy3, Agilent)

growth_protocol: Flies were reared under conventional conditions in mixed sex populations at 25 °C

extract_protocol: Total RNA extractions were carried out using TRIsure (Bioline), followed by DNAse treatment with Turbo-DNase (Ambion) and RNA purification using RNeasy (Qiagen)

treatment_protocol: At 10 days of age, female flies were killed and dissected, to separate guts and the rest (flies without guts and heads)

tag: time

value: 10 days

value: gut

tag: strain/genotype


title: genomic DNA from 3999984025_R04C02


title: genomic DNA from 3999984040_R02C01


title: w1118 gut sample3


title: nubRB gut sample4

source_name: nubRB gut

value: w; c564-Gal4>UAS-nubRB


title: w1118 rest sample1

source_name: w1118 rest

value: rest (flies without guts and heads)


title: w1118 rest sample3


title: w1118 gut sample4


title: Pdm2RB gut sample2

source_name: Pdm2RB gut

value: w; c564-Gal4>UAS-Pdm2RB


title: genomic DNA from 3999984024_R05C01

value: Male


title: nubRB rest sample1

source_name: nubRB rest


title: nubRB rest sample3


title: nubRB gut sample1


title: nubRB rest sample2


title: Pdm2RB rest sample4

source_name: Pdm2RB rest


title: nubRB gut sample3a


title: nubRB rest sample4


title: w1118 rest sample4


title: Pdm2RB gut sample4


title: Pdm2RB gut sample1


title: genomic DNA from 3999984024_R04C02


title: Pdm2RB rest sample2


title: Pdm2RB rest sample1


title: Adipocytes (ATCC) guadecitabine 1

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

description: Subcutaneous, primary

data_processing:
For MC-seq data, reads were mapped against GRCh38.p5 using Bowtie version 2.2.9 (-k 20).
A custom perl script was used to obtain only the mapping results with the best alignment score.
Initial differential methylation analysis was carried out using the MethylAction package (version 2.0) in R (version 3.3.1) and Gencode v24 as the annotation (16).
Window sizes of 50 base-pairs were used in the getCounts function of the package.
The Goldmine package (version 1.0) in R was used to assign biological annotation to the joined window results produced by MethylAction (16).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include genes values for each sample

source_name: Adipocytes (ATCC)

growth_protocol: Normal, human primary subcutaneous pre-adipocytes (ATCC PCS-210-010) were grown in fibroblast basal medium (ATCC PCS-201-030) supplemented with phenol red. Preadipocytes were differentiated following an adipogenic differentiation protocol (Fink T, Zachar V. Adipogenic differentiation of human mesenchymal stem cells. Mesenchymal Stem Cell Assays and Applications: Springer; 2011. p 243-51.). Briefly, preadipocytes were seeded at 18,000 cells/cm2. Initiation of adipogenesis was induced by replacing the fibroblast basal medium with adipogenic induction medium (AIM) for 15 days. Oil Red O staining was performed to confirm adipocyte differentiation.

extract_protocol:
On day 4, DNA was harvested from the adipocytes using the AllPrep kit (Qiagen)
DNA from adipocytes, sonicated (180-200bp), and used as input for methylated DNA capture kit (Diagenode) according to manufacturer’s protocol. This kit uses methyl-binding domain protein (MBD) to pull-down with biotin-streptavidin magnetic beads. DNA is eluted with salt buffer.  Libraries were verified using Qubit and Bioanalyzer, prior to sequencing on Illumina NextSeq.
Mecap-seq libraries were prepared with NEXTflex Methyl-Seq1 kit (Bioo Scientific) according to manufacturer’s protocol.

treatment_protocol: In duplicate, subcutaneous, human, primary adipocytes (ATCC) were treated with DMSO control or guadecitabine (100nM, 3X daily).

tag: passage

value: 2-3 passages

tag: agent

value: guadecitabine

value: Primary Subcutaneous Pre-adipocytes; Normal, Human (ATCC PCS-210-010)


title: matr3-f115c_rep3

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Casava software was used for base calling.
Reads were mapped to the human genome (hg19) using OLego, and only uniquely mapped reads were kept for downstream analysis.
Reads were linked to genomic features and raw gene counts were measured using Quantas.
Gene expression normalization and differential expression was measured using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: .txt file reports RPKM values for all genes measured in this study, for all samples

source_name: H4 neuroglioma cells

extract_protocol:
RNA was extracted using Trizol
Total RNA was used to build barcoded TruSeq Stranded mRNA libraries for paired-end sequencing runs by the NextGen DNA sequencing laboratory of the University of Florida Interdisciplinary Center for Biotechnology Research.

value: neuroglioma cell line H4

value: ALS MATR3 overexpression


title: Adipocytes (ATCC) DMSO Control 2

description: Subcutaneous, primary

value: DMSO


title: Adipocytes (ATCC) DMSO Control 1

description: Subcutaneous, primary


title: Adipocytes (ATCC) guadecitabine 2

description: Subcutaneous, primary


title: matr3-f115c_rep2


title: genomic DNA from 3999984024_R04C01

value: Parkinson's disease (PD)

value: Female


title: genomic DNA from 3999984024_R03C02

value: PD-free control

value: whole blood


title: matr3-yfp_rep3

value: WT MATR3 overexpression


title: matr3-f115c_rep1


title: matr3-yfp_rep2


title: genomic DNA from 3999984024_R03C01

value: Hispanic


title: matr3-yfp_rep1


title: genomic DNA from 3999984024_R02C02

value: Caucasian


title: yfp_rep3

value: YFP overexpression


title: genomic DNA from 3999984024_R01C02


title: yfp_rep2


title: yfp_rep1


title: untransfected_rep2

value: control


title: untransfected_rep3


title: genomic DNA from 3999984023_R06C02


title: untransfected_rep1


title: genomic DNA from 3999984023_R06C01


title: genomic DNA from 3999984023_R05C01


title: genomic DNA from 3999984023_R04C01


title: genomic DNA from 3999984023_R03C01


title: Lung_CD11c_cre+_MyD88 fx_0h_rep3

city: RTP

first: Seddon

state: North Carolina

address: 111 T. W. Alexander Dr.,

institute: NIEHS

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg lung.

hyb_protocol: Hybridization was done according to the manufacturer's instructions.

scan_protocol: Gene expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: Raw data was normalized using the Nanostring nCounter software.

label_protocol: 50 ng of each total RNA sample was labeled according to the manufacturer's instructions.

extract_protocol: Frozen lung lobes were homogenized and RNA isolated from whole lungs using the Qiagen Rneasy Mini Kit.

treatment_protocol: Mice were either untreated or sensitized oropharyngeally with 100 ug ovalbumin (OVA)/ 1250 ng standard flagellin (stFLA) for 2 or 6 hours in vivo.  After this time, lungs were isolated and snap frozen for RNA isolation.

tag: background

value: male

value: Lung

tag: timepoint

value: MyD88 fx/fx; Itgax-cre+/Tg


title: Lung_CD11c_cre+_MyD88 fx_2h_rep2

description: Gene expression from MyD88 fx/fx; Itgax-cre+/Tg lung treated with OVA/ stFLA for 2h.

tag: tissue

value: OVA/ stFLA


title: Lung_CD11c_cre+_MyD88 fx_2h_rep3


title: Lung_CD11c_cre+_MyD88 fx_2h_rep1


title: Lung_CD11c_cre+_MyD88 fx_0h_rep2


title: Lung_CD11c_cre+_MyD88 fx_0h_rep1


title: genomic DNA from 3999984023_R01C02

tag: age


title: Lung_SPC_cre+_MyD88 fx_6h_rep3

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg lung treated with OVA/ stFLA for 6h.

value: MyD88 fx/fx; Sftpc-cre+/Tg


title: genomic DNA from 3999984023_R02C02


title: Lung_SPC_cre+_MyD88 fx_6h_rep2


title: genomic DNA from 3999979036_R06C02

value: Male


title: Lung_SPC_cre+_MyD88 fx_6h_rep1


title: genomic DNA from 3999979036_R06C01


title: genomic DNA from 3999984023_R05C02


title: Mesial Temporal Lobe Epilepsy Tissue 4

city: NEW DELHI

first: APARNA

middle: BANERJEE

last: DIXIT

state: AIIMS

address: Room No 7003, 7th Floor, Convegence Block, AIIMS, ANSARI, NAGAR

department: A collaborative project between NBRC & AIIMS

country: India

institute: NATIONAL BRAIN RESERACH CENTRE

hyb_protocol: Labeled DNAs were hybridized to Human DNA methylation Microarray slides (G4495A, AMADID 023795) containing the annotated human 27,627 expanded CpG islands, 5081 UMR regions, 237,227 biological probes with median probe spacing of 97bp followingthe microarray manufacturer’s instructions.

scan_protocol: The slides were subsequently washed and scanned using Agilent scanner P/N G2565BA

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Mesial Temporal Lobe Epilepsy tissue_MeDIP-WGA

label_protocol: 2μg of DNA from the WGAamplified sample (MeDIP-WGA), along with their corresponding whole genomic DNA (input), were labeled usingthe SureTag DNA labeling kit (5190-3400, Agilent)

growth_protocol: Tissues resected from 2 autopsy , 3 MTLE and 4 FCD type II were used for isolating Genomic DNA

extract_protocol: Genomic DNA was extracted using genomic DNAextraction kit (Qiagen, Hilden, Germany) and Methylated DNA was immunoprecipitated using standard protocols  with some modifications.  Briefly, 4 µg MseI digested genomic DNA was immunoprecipitated with 10 µg of monoclonal mouse anti 5-methylcytidine antibody (New England Biolab, Pickering, Ontario and Abcam Inc.Cambridge, MA 02139) a negative control normal mouse IgG (Abcam, ab81032) in a final volume of 500 μl IP buffer (10 mM sodium phosphate (pH 7.0), 140 mM NaCl, 0.05% Triton X-100). We incubated the mixture with 40 μl of Dynabeads and M-280 sheep antibody to mouse IgG (Dynal Biotech) for 12 hr at 4°C and washed it seven times with 700 μl of IP buffer. We then treated the beads with proteinase K for 4 hr at 50°C and recovered the methylated DNA by phenol-chloroform extraction followed by ethanol precipitation. The immunoprecipitated DNA and a sample of input DNA were amplified using GenomePlex Complete Whole Genome Amplification (WGA) kit (Sigma-Aldrich, Saint Louis, Missouri 63103 USA). At each step DNA integrity was analyzed by agarose gel electrophoresis.

treatment_protocol: autopsy were used as non-epileptic controls and MTLE  and FCD tissues were epileptic tissues

tag: subject status

value: Mesial temporal epilepsy (MTLE) patient

value: MALE

value: brain

source_name: Mesial Temporal Lobe Epilepsy input DNA

tag: sample type

value: whole genomic DNA (input)


title: Mesial Temporal Lobe Epilepsy Tissue 3

tag: gender


title: genomic DNA from 3999979036_R05C02

tag: disease state

value: Parkinson's disease (PD)

value: Female

tag: ethnicity


title: Lung_SPC_cre+_MyD88 fx_2h_rep3

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg lung treated with OVA/ stFLA for 2h.

tag: treatment


title: genomic DNA from 3999979036_R04C02

value: whole blood


title: Lung_SPC_cre+_MyD88 fx_0h_rep2

description: Gene expression from MyD88 fx/fx; Sftpc-cre+/Tg lung.


title: Lung_SPC_cre+_MyD88 fx_0h_rep3


title: genomic DNA from 3999979036_R04C01


title: Lung_SPC_cre+_MyD88 fx_0h_rep1


title: genomic DNA from 3999979036_R03C02


title: genomic DNA from 3999979036_R02C02

value: PD-free control


title: Mesial Temporal Lobe Epilepsy Tissue 2


title: Lung_SPC_cre+_MyD88 fx_2h_rep2


title: genomic DNA from 3999979036_R03C01

value: Caucasian


title: Lung_WT_MyD88 fx_6h_rep2

description: Gene expression from MyD88 fx/fx lung treated with OVA/ stFLA for 6h.

value: MyD88 fx/fx


title: Lung_WT_MyD88 fx_6h_rep3


title: Lung_WT_MyD88 fx_6h_rep4


title: Lung_SPC_cre+_MyD88 fx_2h_rep1


title: Lung_WT_MyD88 fx_2h_rep3

description: Gene expression from MyD88 fx/fx lung treated with OVA/ stFLA for 2h.


title: genomic DNA from 3999979036_R02C01


title: genomic DNA from 3999979036_R01C02


title: genomic DNA from 3999979036_R01C01


title: genomic DNA from 3999979020_R01C02


title: Lung_WT_MyD88 fx_2h_rep1