title: L4

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

description: methylation profiling using bisulfite converted

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing:
Data was analysed using R version 3.4.1 (2017-06-30). Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘Champ’ R package (v. 2.12.0), with quality control options set as default. The quality control step retained 759772 probes, which were used for further analysis. Probes overlapped with SNP (79662) and with a detection pvalue < 0.01 (3447), beadcount <3 in at least 5% of samples in one or more samples (2582) were eliminated. X or Y chromosomes probes (17432), non-cg probes (2915), and probes aligning to multiple locations (46) and unannotated probes were also removed from analysis. No background correction was carried out. SWAN normalisation was applied, with the ‘method’ option set to “minfi”. The SWAN normalized samples were assigned with respective genome coordinates based on probe name and manifest file (Illumina Inc., USA).
The file 'matrix_signal_intensities.txt' includes: Unmethylated signal (B) and methylated signal (A) intensities

source_name: genomic DNA from L4 Blood (father of proband)

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

value: blood

value: M

value: Normal


title: P135

status: Public on Oct 01 2019

type: SRA

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Total RNA was extracted from whole blood drawn from kidney transplant recipients prior to transplantation (baseline), and mRNA sequencing was performed on an Illumina HiSeq4000 sequencer.

library_source: transcriptomic

data_processing:
The reads with good quality were firstly aligned to human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering for reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription level across samples, followed by quantile normalization and batch correction
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: whole blood

extract_protocol:
total RNA wasextracted from pretransplant whole blood of kideny transplant recipeints
The library was generated standard TrueSeq mRNA library generation kit (Illumina Inc)
standard mRNA library

tag: set

tag: acr before or at 6m

tag: death censored graft loss

tag: follow up days


title: P134


title: SAMPLE 6: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_6

type: genomic

city: Tsu

first: Akihiro

last: Ikuno

state: Mie

address: 1577 Kurimamachiyacho

department: Bioresources

country: Japan

institute: Mie University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip array. The primer hybridized to the DNA was extended and labeled using labeled nucleotides.

scan_protocol: After fluorescent staining of labeled primer,  the arrays were scanned using Illumina iScan® System. All these processes were performed according to the standard Illumina protocol.

data_processing:
Raw IDAT files were processed using Methylation module (Version 1.90) in GenomeStudio software (V2011.1, Illumina) or the ChAMP package in R 3.4.3.
In processing with GenomeStudio, normalization was performed using negative control probes to generate average β values of early or advanced stage degeneration group. And then, the methylation data were filtered for probes with a detection P > 0.01 or sex chromosomes.
In processing with the ChAMP package,  Raw methylation data were imported with the minfi method, and normalized with the SWAN method. By default setting, raw data were filtered for probes with a detection P > 0.01, non-CpG site, SNP-related probe list(PMID: 27924034), the multi-hit probe list(PMID: 24063430) or sex chromosomes.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Early stage degeneration 6

extract_protocol: Frozen NP tissue samples (200-250 mg wet weight) were pulverized in the presence of liquid nitrogen using a cryopress (Microtech Nichion, Chiba, Japan). DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega, City, WI, USA) according to the manufacturer's instruction.

tag: gender

value: Female

tag: age

tag: grades of degeneration

value: Pfirrmann grades II

tag: disease

value: Spinal trauma

tag: tissue

value: intervertebral disc (IVD)


title: P136


title: SAMPLE 4: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_4

source_name: Early stage degeneration 4

label_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC BeadChip array. The primer hybridized to the DNA was extended and labeled using labeled nucleotides.

value: Male

value: Pfirrmann grades I


title: P133

tag: acr after 6m

value: Borderline


title: CML290

city: Beijing

first: Junling

last: Pang

address: No.12 Zhongguancun South St.,Haidian District

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Sequenced reads were cleaned after removing low quality sequences and adapter. Then cleaned reads were mapped to maize B73 AGPv3 reference genome using tophat2 software with the following key parameters: “-i 5 -I 60000 --library-type fr-unstranded -r 250 --mate-std-dev 60 --no-novel-juncs --microexon-search”. The insertion size (-r) and standard deviation (--mate-std-dev) of paired reads were estimated using “CollectInsertSizeMetrics.jar” plugin in picard tools (http://picard.sourceforge.net). Only reads that are uniquely mapped to the genome were retained for further analysis
Reads count of annotated genes (AGPv3.27) were calculated using R packages “GenomicFeatures” and “GenomicAlignments”. DESeq2 package were used to normalize the reads count among samples and to calculate the FPKM value of genes.
Genome_build: maize B73 (AGPv3 )
Supplementary_files_format_and_content: tab-delimited text files include reads counts or FPKM values for each Sample

molecule: polyA RNA

organism: Zea mays

source_name: 5-DAP kernel

growth_protocol: A maize association mapping population consists of 318 inbred lines, including tropical, subtropical and temperate germplams was planted in one-row plots and incompletely randomized block design with three replicates in Hainan province of China in 2014. Eight ears in each block were self-pollinated, and 10-20 seeds from three to four ears in each block were collected at 5 DAP.

extract_protocol:
The collected seeds in three replications were mixed for total RNA preparation. Total RNA was extracted using RNAprep pure Kit For Plant (TIANGEN, Beijing, China) according to its protocol. Total mRNAs were accumulated using oligo(dT).
Library construction was following the standard protocol (Illumina, Inc.), and pair-end sequencing with 125 bp was carried out for each sample.

tag: inbred lines

value: kernel

tag: developmental stage

value: 5 day after pollination


title: SAMPLE 3: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_3

source_name: Early stage degeneration 3


title: CML298


title: CML20


title: N_079

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

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 Hisat2
mRNA and lncRNA annotated in GencodeV25 were quantified using featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: Blood extracellular vesicle

extract_protocol:
Plasma EV RNAs were extracted by exoRNeasy Serum/Plasma kit.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian

value: Plasma

tag: disease state

value: healthy


title: N_077


title: N_078


title: CML192


title: SAMPLE 2: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_2

source_name: Early stage degeneration 2


title: P131


title: N_076


title: CML324


title: N_080


title: P130


title: CML191


title: N_075


title: N_074


title: CML189


title: P129


title: SAMPLE 5: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_5

source_name: Early stage degeneration 5


title: L2

country: Italy

source_name: genomic DNA from L2 Blood (mother of proband)

value: F


title: P132


title: N_073


title: CML172


title: N_072


title: SAMPLE 1: Human_IVD tissues_Early stage degeneration (Pfirrmann grades I-III)_1

source_name: Early stage degeneration 1

value: Pfirrmann grades III

value: Degenerative disc disease


title: CML171


title: P128


title: P127


title: N_071


title: N_070


title: CML170


title: P125


title: N_069


title: CML165


title: CML163


title: P124


title: N_068


title: P123


title: N_067


title: CML139


title: P122


title: N_066


title: P126


title: P121


title: N_065


title: CML122


title: CML162


title: P120


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C7 gp38

type: RNA

city: Amsterdam

first: Barbara

middle: Florien

last: Westendorp

state: Noord-Holland

address: Meibergdreef 69-71

department: Tytgat Institute for Liver and Intestinal Research

country: Netherlands

institute: Academic Medical Center

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for scanning of the chips.

scan_protocol: The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips, and provide the data stored in DTT format and Cell Intensity File (*.cel) for each GeneChip processed.

data_processing: Robust Multichip Average (RMA) normalization.

label: Biotin

organism: Mus musculus

source_name: Sorted colon fibroblasts Epcam-CD45-CD31-gp38+

label_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, and staining of the chips. GeneChip Mouse Transcriptome Array 1.0 (MTA 1.0) (Affymetrix) according to the standard protocols of the Dutch Genomics Service and Support Provider  (MAD, Science Park, University of Amsterdam, Netherlands)

growth_protocol: Villincre-ERT2-ZsGreen-IhhKO-ApcKO mice were used for colon isolation and flow-sorting experiments

extract_protocol: 2 ng RNA was amplified and labeled using 3’ IVT pico kit Affymetrix RNA amplification kit (Nugene) according to manufacturer’s protocol

treatment_protocol: RNA from the colons was extracted with Agencourt RNAdvance Cell v2 kit (Beckman Coulter, Beverly, Massachusetts, USA) according to manufacturers’ protocol including DNA digestion step. RNA integrity and concentration were quantified with BioAnalyzer (Agilent Technologies).

value: Colon

tag: cell type

tag: genotype


title: P119


title: CML118


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C9 gp38

value: Sorted colon fibroblasts Epcam-CD45-CD31-gp38+


title: N_063


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C6 gp38


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C4 gp38


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C5 gp38


title: CML130


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C3 gp38


title: P118


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C2 gp38


title: CML116


title: N_061


title: P117


title: N_062


title: N_064


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, C1 gp38


title: CML115


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhKO-ApcKO, B9 gp38


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B8 gp38


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B7 gp38


title: P116


title: N_060


title: CML114


title: N_059


title: CML121


title: CIMBL98


title: P115


title: N_057


title: P113


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B5 gp38


title: CIMBL96


title: CIMBL95


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B4 gp38


title: P112


title: P111


title: CIMBL94


title: N_055


title: CIMBL93


title: P110


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B3 gp38


title: N_054


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, A9 gp38


title: P114


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B1 gp38


title: N_058


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A8 gp38


title: N_053


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B2 gp38


title: CIMBL91


title: CIMBL92


title: P108


title: P107

value: ACR or Borderline

value: ACR


title: CIMBL90


title: N_052


title: N_051


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A6 gp38


title: CIMBL89


title: P106


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A5 gp38


title: N_056


title: CIMBL88


title: P109


title: N_050


title: N_049


title: P105


title: P103


title: N_047


title: N_048


title: P104


title: CIMBL84


title: CIMBL83


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A4 gp38


title: P102


title: P101


title: CIMBL82


title: N_045


title: CIMBL81


title: N_046


title: P100


title: CIMBL86


title: P99


title: N_044


title: CIMBL7


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A3 gp38


title: N_043


title: Female  SOX9 KO E16.75 mouse UGS epithelium, biological rep5

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

description: Gene expression data from the female SOX9 KO E16.75 mouse UGS epithelium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GC3000 G7.

data_processing: The data was extracted and processed using Affymetrix Command Console version 3.2.4.1515W

label: biotin

source_name: Mouse fetal UGS epitelium_Sox9 KO

label_protocol: All samples were end-terminus labeled following the guidelines of the Affymetrix GeneChip WT terminal labeling an hybridization user manual target (P/N 702808 Rev. 7)

growth_protocol: The UGS (with bladder and urethra intact) was harvested from male and female C57BL/6J conditional Sox9 knockout (ShhCre/+; Sox9fl/fl) and littermate control (Shh+/+; Sox9+/fl) fetuses embryos at E16.75.

extract_protocol: Rneasy lipid tissue mini kit extraction of total RNA and was performed according to the manufacturer's instructions.

treatment_protocol: 1% trypsin and collagenase was added to the tissue. The mesenchyme was seperated from the epithelium with a microscope, and the bladder and urethra epithelium was removed, leaving only the UGS epithelium

value: urogenital sinus (UGS) epithelium

tag: background strain

value: ShhCre/+; Sox9fl/fl


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A2 gp38


title: Female  SOX9 KO E16.75 mouse UGS epithelium, biological rep3


title: Female  SOX9 KO E16.75 mouse UGS epithelium, biological rep4


title: Female  SOX9 KO E16.75 mouse UGS epithelium, biological rep2


title: P98


title: N_042


title: CIMBL79


title: Female SOX9 KO E16.75 mouse UGS epithelium, biological rep1


title: P97


title: N_041


title: CIMBL77


title: Female littermate control E16.75 mouse UGS epithelium, biological rep4

description: Gene expression data from the female littermate control E16.75 mouse UGS epithelium

source_name: Mouse fetal UGS epitelium_littermate control

value: Shh+/+; Sox9+/fl


title: CIMBL75


title: CIMBL74


title: Female littermate control E16.75 mouse UGS epithelium, biological rep5


title: N_040


title: P95


title: P94


title: P93


title: N_039


title: N_038


title: CIMBL71


title: CIMBL70


title: CIMBL6


title: Female littermate control E16.75 mouse UGS epithelium, biological rep1


title: N_037


title: Female littermate control E16.75 mouse UGS epithelium, biological rep2


title: Female littermate control E16.75 mouse UGS epithelium, biological rep3


title: Male SOX9 KO E16.75 mouse UGS epithelium, biological rep6

description: Gene expression data from the male SOX9 KO E16.75 mouse UGS epithelium


title: N_036


title: P96


title: P92


title: CIMBL69


title: P91


title: P89


title: Male SOX9 KO E16.75 mouse UGS epithelium, biological rep5


title: P90


title: N_035


title: N_034


title: N_033


title: Male SOX9 KO E16.75 mouse UGS epithelium, biological rep4


title: CIMBL63


title: N_032


title: P88


title: P87


title: N_031


title: CIMBL60


title: Male SOX9 KO E16.75 mouse UGS epithelium, biological rep2


title: Male SOX9 KO E16.75 mouse UGS epithelium, biological rep3


title: Male SOX9 KO E16.75 mouse UGS epithelium, biological rep1


title: Male littermate control E16.75 mouse UGS epithelium, biological rep6

description: Gene expression data from the male littermate control E16.75 mouse UGS epithelium


title: CIMBL68


title: Male littermate control E16.75 mouse UGS epithelium, biological rep5


title: N_030


title: CIMBL5


title: P85


title: CIMBL59


title: CIMBL62


title: CIMBL66


title: P83


title: P84


title: N_029


title: N_027


title: N_028


title: P82


title: P86


title: CIMBL55


title: small RNA 12 mo dif

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: small RNA

data_processing:
MethylC-seq: was performed as described in (Schmtiz et al. 2013)
RNA-seq: was performed using TopHat v2.0.13 and Cufflinks v2.2.1
Small RNA-seq: was performed using bowtie v1.1.1
Genome_build: Glycine max assembly v2 reference genome
Supplementary_files_format_and_content: tab delimited text file, see "Methylome_header_descriptions.txt", "RNA_column_header_descriptions.txt" and "Small_RNA_header_descriptions.txt" for column headers

organism: Glycine max

source_name: old differentiated embryo, non-embryogenic, non-regeneratable, non-transformable

extract_protocol: MethylC–seq following Urich M, et al Nature Biotech. 2016, RNA-seq for the Illumina TruSeq strand-specific kit and small RNA-seq following the Illumina TruSeq smRNA seq kit

tag: tissue/developmental stage

value: globular embryo

value: 12 months

tag: cultivar

value: Jack

tag: treatment

value: 20 mg/l of 2,4 D medium, Embryo Maintenance


title: Male littermate control E16.75 mouse UGS epithelium, biological rep4


title: Male littermate control E16.75 mouse UGS epithelium, biological rep3


title: Male littermate control E16.75 mouse UGS epithelium, biological rep2


title: Male littermate control E16.75 mouse UGS epithelium, biological rep1


title: P81

tag: set

value: Discovery

tag: acr before or at 6m

tag: death censored graft loss


title: small RNA 12 mo globular

description: small RNA

source_name: old globular embryo, embryogenic, non-regeneratble, non-transformable

tag: age


title: CIMBL52

value: kernel

value: 5 day after pollination


title: CIMBL51


title: N_022

value: Plasma

value: healthy


title: N_024


title: P79

tag: follow up days


title: CIMBL58


title: CIMBL50


title: CIMBL54


title: small RNA 8 yr globular

description: small RNA

source_name: old globular embryo, embryogenic, non-regeneratable, non-transformable

value: 8 year


title: P80


title: P77


title: N_023


title: small RNA 6 mo globular rep1

description: small RNA

source_name: globular embryo,embryogenic, regeneratable, transformable

value: 6 months


title: Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcWT, A1 gp38

value: Colon

value: Sorted colon fibroblasts Epcam-CD45-CD31-gp38+


title: small RNA 6 mo globular rep2

description: small RNA


title: N_021


title: N_026


title: small RNA 4-day subculture rep3

description: small RNA

value: 10 weeks + 4 days


title: small RNA 6 mo globular rep3

description: small RNA


title: P78

source_name: whole blood


title: CIMBL4


title: N_025


title: P76


title: CIMBL53


title: N_020


title: CIMBL49


title: P75


title: N_019


title: small RNA 4-day subculture rep1

description: small RNA


title: CIMBL48


title: P74


title: CIMBL47


title: P73


title: CIMBL43


title: small RNA 6 wk diff rep1

description: small RNA

source_name: Differentiated embryo, non-embryogenic

value: differentiated embryo

value: 6 weeks


title: small RNA 6 wk diff rep3

description: small RNA


title: CIMBL42


title: CIMBL40


title: N_017


title: small RNA 6 wk diff rep2

description: small RNA


title: P72


title: P71


title: small RNA 6 wk globular rep2

description: small RNA

source_name: young globular embryo tissue, embryogenic, regeneratable, non-transformable

value: 40 mg/l of 2,4 D medium, Embryo Initiation


title: small RNA 4-day subculture rep2

description: small RNA

value: globular embryo


title: CIMBL3

source_name: 5-DAP kernel


title: P70


title: N_014


title: P69


title: N_016


title: N_013


title: N_015


title: CIMBL38


title: P68


title: small RNA 24h+2,4-D rep3

description: small RNA

source_name: 3-5 mm cotyledon, for embryo initiation

value: cotyledon

value: 24 hours


title: CIMBL32


title: N_012

source_name: Blood extracellular vesicle


title: small RNA 6 wk globular rep1

description: small RNA

value: Jack


title: P67

value: Discovery


title: small RNA 6 wk globular rep3

description: small RNA

source_name: young globular embryo tissue, embryogenic, can regenerate, non-transformable

value: 20 mg/l of 2,4 D medium, Embryo Maintenance


title: N_018


title: small RNA 24h+2,4-D rep2

description: small RNA


title: N_011


title: CIMBL2

value: kernel

value: 5 day after pollination


title: P66


title: small RNA 24h+2,4-D rep1

description: small RNA


title: P65


title: CIMBL29


title: small RNA 24h-2,4-D

description: small RNA


title: CIMBL28


title: N_010

value: Plasma

value: healthy


title: mRNA 8 yr globular

description: mRNA

value: 8 year


title: P63


title: CIMBL27


title: P64


title: N_008


title: N_007


title: N_009


title: CIMBL25


title: P62


title: mRNA 12 mo globular

description: mRNA

value: 12 months


title: N_006


title: mRNA 12 mo dif

description: mRNA


title: CIMBL23


title: P61


title: mRNA 6 mo globular rep3

description: mRNA

value: 6 months


title: mRNA 6 mo globular rep2

description: mRNA


title: P60


title: N_004


title: CIMBL22


title: mRNA 6 mo globular rep1

description: mRNA


title: P58


title: CIMBL21


title: N_003


title: mRNA 4-day subculture rep3

description: mRNA

value: 10 weeks + 4 days


title: CIMBL1


title: CIMBL19


title: mRNA 4-day subculture rep2

description: mRNA


title: P56


title: N_001


title: PDAC_150

value: PDAC


title: mRNA 4-day subculture rep1

description: mRNA


title: N_002


title: CIMBL18


title: CIMBL17


title: P55


title: PDAC_149


title: mRNA 6 wk diff rep2

description: mRNA

value: differentiated embryo

value: 6 weeks


title: mRNA 6 wk diff rep3

description: mRNA


title: N_005


title: P54


title: P59


title: P53


title: CIMBL15


title: mRNA 6 wk diff rep1

description: mRNA


title: PDAC_147


title: CIMBL157


title: P52


title: P57


title: mRNA 6 wk globular rep3

description: mRNA

value: globular embryo


title: CIMBL156


title: PDAC_146


title: PDAC_145


title: mRNA 6 wk globular rep2

description: mRNA


title: PDAC_144


title: mRNA 6 wk globular rep1

description: mRNA


title: CIMBL153


title: mRNA 24h+2,4-D rep3

description: mRNA

source_name: 3-5 mm cotyledon, for embyro initiation

value: cotyledon

value: 40 mg/l of 2,4 D medium, Embryo Initiation


title: P49


title: CIMBL16


title: CIMBL152


title: PDAC_148


title: CIMBL150


title: PDAC_142


title: CIMBL147


title: P47


title: P48


title: mRNA 24h+2,4-D rep1

description: mRNA

value: 24 hours

value: Jack


title: CIMBL145


title: mRNA 24h-2,4-D rep3

description: mRNA


title: P46

value: Discovery


title: PDAC_140


title: PDAC_141


title: P51


title: CIMBL144

value: kernel


title: P50


title: mRNA 24h-2,4-D rep2

description: mRNA


title: P45


title: P44


title: PDAC_139


title: CIMBL142

value: 5 day after pollination


title: PDAC_143

value: Plasma


title: PDAC_138


title: CIMBL141


title: P43


title: CIMBL140


title: Methylome 12 mo dif

description: genomic DNA

library_source: genomic

data_processing:
Library strategy: MethylC–seq
MethylC-seq: was performed as described in (Schmtiz et al. 2013)
RNA-seq: was performed using TopHat v2.0.13 and Cufflinks v2.2.1
Small RNA-seq: was performed using bowtie v1.1.1
Genome_build: Glycine max assembly v2 reference genome
Supplementary_files_format_and_content: tab delimited text file, see "Methylome_header_descriptions.txt", "RNA_column_header_descriptions.txt" and "Small_RNA_header_descriptions.txt" for column headers

value: 20 mg/l of 2,4 D medium, Embryo Maintenance


title: P42


title: Methylome 8 yr globular

description: genomic DNA

value: 8 year


title: mRNA 24h+2,4-D rep2

description: mRNA


title: PDAC_137


title: CIMBL13


title: Methylome 12 mo globular

description: genomic DNA

value: 12 months


title: PDAC_135


title: PDAC_136


title: P41


title: Methylome 6 mo globular rep3

description: genomic DNA

value: 6 months


title: CIMBL133


title: P40


title: mRNA 24h-2,4-D rep1

description: mRNA


title: CIMBL139


title: PDAC_134


title: PDAC_133


title: CIMBL129


title: Methylome 6 mo globular rep2

description: genomic DNA


title: P38


title: Methylome 6 mo globular rep1

description: genomic DNA


title: Methylome 4-day subculture rep3

description: genomic DNA

value: 10 weeks + 4 days


title: CIMBL127


title: P37


title: P36


title: PDAC_131

value: PDAC


title: Methylome 4-day subculture rep2

description: genomic DNA


title: PDAC_132


title: CIMBL125


title: CIMBL124


title: PDAC_130


title: Methylome 4-day subculture rep1

description: genomic DNA


title: Methylome 6 wk diff rep3

description: genomic DNA

value: differentiated embryo


title: CIMBL123


title: PDAC_128


title: P33


title: CIMBL122


title: P32

value: ACR or Borderline


title: CIMBL121


title: Methylome 6 wk diff rep1

description: genomic DNA

value: 6 weeks


title: PDAC_126


title: P31


title: P39


title: Methylome 6 wk globular rep3

description: genomic DNA

value: globular embryo


title: PDAC_125


title: CIMBL120


title: PDAC_129


title: CIMBL11


title: P30


title: P35


title: CIMBL119


title: P29


title: PDAC_124


title: Methylome 24h+2,4-D rep3

description: genomic DNA

value: cotyledon

value: 40 mg/l of 2,4 D medium, Embryo Initiation


title: Methylome 6 wk globular rep2

description: genomic DNA

value: Jack


title: PDAC_122


title: P28

value: Discovery


title: Methylome 6 wk globular rep1

description: genomic DNA


title: P27


title: P34


title: Methylome 6 wk diff rep2

description: genomic DNA


title: Methylome 24h+2,4-D rep2

description: genomic DNA

value: 24 hours


title: CIMBL115

value: kernel

value: 5 day after pollination


title: CIMBL116


title: PDAC_121

value: Plasma


title: PDAC_127


title: P26


title: Methylome 24h+2,4-D rep1

description: genomic DNA


title: CIMBL114


title: CIMBL113


title: PDAC_120


title: PDAC_119


title: Methylome 24h-2,4-D

description: genomic DNA


title: PDAC_123


title: P25


title: CIMBL111


title: PDAC_118


title: CIMBL10


title: P23


title: P24


title: CD-HR6

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: This sample is associated with two SRR at SRA. One contains the mapped reads and the other contains the unmapped reads.

data_processing:
RNA-sequencing reads were aligned to the rat reference genome RNO5.0 using STAR version2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups (v1.98). The BAM files are sorted with Sambamba v0.4.5 and transcript abundances are quantified with HTSeq-count version 0.6.1p1 using the union mode
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: Raw read counts per gene

organism: Rattus norvegicus

source_name: heart apex

extract_protocol:
RNA in the heart apex was isolated using Trizol and measured (NanoDrop spectrophotometer ND-1000, ThermoFischer Scientific Inc.). Polyadenylated mRNA fraction was isolated using Poly(A) Beads (NEXTflex).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)

treatment_protocol: To develop advanced CKD, rats underwent 2/3 bilateral ablation of renal mass by coagulating branches of both renal arteries under isoflurane anaesthesia (5% induction, 1.5–2% maintenance). All rats received an intramuscular injection of analgesia straight after and one day after surgery (Buprenorphine, 0.05 mg/kg). Subsequently, development of CKD was accelerated with L-NNA, a NO-synthase inhibitor (200 mg/L) in drinking water and animals were fed standard powdered chow (CRM-FG; Special Diet Services Ltd., Witham, Essex, UK) supplemented with 6% NaCl, until proteinuria reached 200 mg/24h at which point L-NNA and 6% NaCl were discontinued. CKD animals were included into the transplantation protocol when proteinuria reached 100 mg/24h (without L-NNA and without 6% NaCl) and, where applicable, were matched with healthy control rats with intact kidneys. We used orthotopic left kidney transplantation, with subsequent removal of the right native kidney 10-14 days after transplantation. Cold ischemia- and warm ischemia- times were 30 minutes each and all isografts were perfused and placed in organ preserving solution Viaspan (Bristol Meyers Squibb, Hoofddorp, Netherlands) prior to transplantation. Kidney transplantation was performed under isoflurane anaesthesia (5% induction, 1.5–2% maintenance) and analgesia was provided straight after and one day after surgery (Buprenorphine, 0.05 mg/kg i.m.). Six weeks after transplantation ts were sacrificed, perfused with 0.9% NaCl via the aorta, and tissues were collected and weighed. Transverse mid LV samples were fixed in 4% paraformaldehyde and the heart apexes were snap frozen and stored at -80°C.

tag: strain

value: Lewis

tag: recipient disease status

value: Healthy recipient

tag: donor disease status

value: CKD donor

value: heart apex


title: CD-HR5

tag: tissue


title: CIMBL108

tag: inbred lines

tag: developmental stage


title: CIMBL109


title: PDAC_116

tag: disease state

value: PDAC


title: P21


title: PDAC_115


title: P22


title: CIMBL106


title: CD-CR5

value: CKD recipient


title: HD-CR5

value: Healthy donor


title: HD-HR6


title: CIMBL105


title: PDAC_114


title: P20

value: ACR or Borderline


title: P19


title: PDAC_113


title: CIMBL102


title: P18


title: P17


title: CD-HR3


title: PDAC_112


title: CD-HR2


title: CIMBL100


title: PDAC_111


title: PDAC_117


title: CHUAN48-2


title: PDAC_110


title: CD-HR1


title: P16


title: CHENG698


title: P15


title: HD-HR5


title: HD-HR4


title: PDAC_109


title: PDAC_108


title: CHANG7-2


title: P14


title: P13


title: CF773-2


title: HD-HR3


title: P12


title: CHANG3


title: PDAC_107


title: CA47


title: CD-HR4


title: P11


title: PDAC_106


title: HD-HR1


title: PDAC_105


title: CD-CR4


title: BZN

value: BZN


title: BY855


title: HD-HR2


title: PDAC_104


title: P10


title: PDAC_103


title: HD-CR4


title: BY815


title: P9


title: P8


title: P7


title: PDAC_102


title: CD-CR3


title: BY809


title: P5


title: PDAC_100


title: BY807


title: PDAC_099


title: CD-CR1


title: CD-CR2


title: HD-CR2


title: BY4960


title: P3


title: PDAC_098


title: BY4944


title: PDAC_097


title: BY4839


title: HD-CR3


title: PDAC_096


title: BY813


title: CD-CR6


title: B77


title: PDAC_101


title: PDAC_095


title: B151


title: RNA-Seq queen head (experiment 2)

city: Tel Aviv

first: Assaf

last: Zemach

address: Haim Levanon

department: School of Plant Sciences and Food Security

country: Israel

institute: Tel Aviv University

description:
differential_gene_expression.txt
rs_exp2_qhe

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold (Amel_4.5), allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
Identifying differential methylation between various samples was performed by Fisher Exact Test using the number of Cs (methylated cytosines) and Ts (unmethylated cytosines) of any pair of samples. A site was determined to be differentially methylated if its p-value was lower than 0.001 in both biological replicates.
Percent methylation change: This number was calculated by dividing the difference in methylation level between two samples by the level of methylation in the sample with the higher methylation level. For example, percent-methylation-change between embryo and W. larva was calculated as follows:  Embryo mCG-W.larva mCGEmbryo mCG ifEmbryo mCG>W.larva mCG  -W.larva mCG-Embryo mCGW.larva mCGifEmbryo mCG<W.larva mCG
Gene expression: Raw Illumina RNA-Seq 100 base reads were first mapped to the most recent honey bee genome assembly (Amel_4.5; (Elsik et al., 2014)) using Tophat (Trapnell et al., 2012), with the following changes to the default Tophat v2.0.1 parameters –I 100000 (maximum intron length) and --no-novel-juncs (limiting the alignment to v3.2 honey gene annotation). Gene expression abundance and changes were calculated using the Cufflinks and Cuffdiff softwares (Trapnell et al., 2012) based on the honeybee 4.5 genome, as well as the v3.2 gene annotation file and default parameters with the addition of --min-reps-for-js-test. Differential expression was considered as statistically significant when the q-value (FDR correction) was lower than 0.05 and the FPKM fold change between two samples was higher than two.
Genome_build: Amel_4.5
Genome_annotation: OGS 3.2 scaffolds
Supplementary_files_format_and_content: GFF - Annotation of methylated CG sites
Supplementary_files_format_and_content: TXT (tab-delimited table) - Table of FPKM and differential expression of genes (rows) for each or between pairs of samples (cols).

organism: Apis mellifera

source_name: Queen head

growth_protocol: European honey bees were grown in Langstroth hives at the Harry H. Laidlaw Jr. Honey Bee Research Facility at University of California Davis.

extract_protocol:
Total RNA samples were isolated using the RNeasy mini kit (QIAGEN #74106) including on-column DNase treatment. mRNA was purified from 10–50 μg of total RNA by two cycles of poly-A enrichment using the Oligotex kit (QIAGEN #72022) followed by an rRNA removal step using the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 ml of RNase free water and fragmented with 1 ml of fragmentation buffer (Ambion, #AM8740) at 70 C. Reactions were stopped after 5 min by adding 1 ml stop buffer, and RNA was purified by ethanol precipitation. cDNA was synthesized from 100–300 ng of mRNA using SuperScript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized according to the instructions using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). DNA was cleaned with a QIAquick PCR spin column (QIAGEN, #28106), sequencing adapters were ligated according to the Illumina protocol, and the library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530).
Bands around 300 bp were gel purified and libraries were sequenced on the Illumina HiSeq 2000 platform at the Vincent J. Coates Genomic Sequencing Laboratory at UC Berkeley to generate single-end 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
RNA-Seq: Total RNA samples were isolated using the RNeasy mini kit (QIAGEN #74106) including on-column DNase treatment. mRNA was purified from 10–50 mg of total RNA by two cycles of poly-A enrichment using the Oligotex kit (QIAGEN #72022) followed by an rRNA removal step using the RiboMinus Eukaryote Kit for RNA-Seq (Invitrogen #A1083702). Precipitated mRNA samples were eluted with 9 ml of RNase free water and fragmented with 1 ml of fragmentation buffer (Ambion, #AM8740) at 70 C. Reactions were stopped after 5 min by adding 1 ml stop buffer, and RNA was purified by ethanol precipitation. cDNA was synthesized from 100–300 ng of mRNA using SuperScript III reverse transcriptase (Invitrogen #18080-051). Double-stranded DNA was synthesized according to the instructions using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). DNA was cleaned with a QIAquick PCR spin column (QIAGEN, #28106), sequencing adapters were ligated according to the Illumina protocol, and the library was amplified by 18 cycles of PCR using Phusion DNA polymerase (NEB, #F-530). Bands around 300 bp were gel purified and libraries were sequenced on the Illumina HiSeq 2000 platform at the Vincent J. Coates Genomic Sequencing Laboratory at UC Berkeley to generate single-end 100 base reads.

value: head

value: mature

tag: caste

value: queen


title: P6

value: Discovery


title: BS-seq drone sperm (experiment 2)

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold (Amel_4.5), allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
Identifying differential methylation between various samples was performed by Fisher Exact Test using the number of Cs (methylated cytosines) and Ts (unmethylated cytosines) of any pair of samples. A site was determined to be differentially methylated if its p-value was lower than 0.001 in both biological replicates.
Percent methylation change: This number was calculated by dividing the difference in methylation level between two samples by the level of methylation in the sample with the higher methylation level. For example, percent-methylation-change between embryo and W. larva was calculated as follows:  Embryo mCG-W.larva mCGEmbryo mCG ifEmbryo mCG>W.larva mCG  -W.larva mCG-Embryo mCGW.larva mCGifEmbryo mCG<W.larva mCG
Gene expression: Raw Illumina RNA-Seq 100 base reads were first mapped to the most recent honey bee genome assembly (Amel_4.5; (Elsik et al., 2014)) using Tophat (Trapnell et al., 2012), with the following changes to the default Tophat v2.0.1 parameters –I 100000 (maximum intron length) and --no-novel-juncs (limiting the alignment to v3.2 honey gene annotation). Gene expression abundance and changes were calculated using the Cufflinks and Cuffdiff softwares (Trapnell et al., 2012) based on the honeybee 4.5 genome, as well as the v3.2 gene annotation file and default parameters with the addition of --min-reps-for-js-test. Differential expression was considered as statistically significant when the q-value (FDR correction) was lower than 0.05 and the FPKM fold change between two samples was higher than two.
Genome_build: Amel_4.5
OGS 3.2 scaffolds
Supplementary_files_format_and_content: genome_annotation: GFF Annotation of methylated CG sites

source_name: Drone sperm

extract_protocol:
Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: sperm

value: drone


title: PDAC_094


title: B11

value: kernel

value: 5 day after pollination


title: P4


title: CpWT +Dox rep. #2

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C_parapsilosis/CDC317 or C_tropicalis/MYA3404 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: C. tropicalis MYA3404 or C. parapsilosis/CDC317 genome from Candida Genome Database
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

organism: Candida parapsilosis

source_name: fungal cells

growth_protocol: C. parapsilosis wild-type (ELY70) and tetO-CpUME6 (ELY194) strains as well as C. tropicalis wild-type (ELY5) and tetO-CtUME6 (ELY184) strains have been previously described (Lackey, et al., Eukaryot. Cell 12(10):1356-1368 (2013)). Standard growth conditions for all strains were in yeast extract-peptone-dextrose (YEPD) at 30°C.

extract_protocol:
Total RNA was extracted using the hot acid phenol protocol (Ausubel, et al., Current Protocols in Molecular Biology, 1992)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For RNA preparation and cell fixing, strains were initially grown overnight at 30°C in 5 mL of YEPD in the presence (tetO-CpUME6 and tetO-CtUME6 strains) or absence (CpWT and CtWT strains) of 20 ug/mL Dox. Saturated overnight cultures were washed twice in ddH2O and resuspended in 5 mL ddH2O. Next, 10 uL of this cell suspension was diluted in 10 mL of ddH2O. For C. parapsilosis strains, either 1 mL or 2 mL of this diluted culture was used to inoculate 50 mL of synthetic complete (SC) medium in the presence and absence of 100 ng/mL Dox and cells were grown at 30°C for 36 hours prior to harvesting 1 mL for fixing and 5 mL for RNA preparation. For C. tropicalis strains, either 1 mL or 2 mL of the diluted culture was used to inoculate 50 mL of YEPD + 50% fetal bovine serum (FBS) (Atlanta Biologicals) in the presence and absence of 100 ng/mL Dox and cells were grown at 30°C for 24 hours prior to harvesting 1 mL for fixing and 5 mL for RNA preparation.

value: Doxycycline, 100 ng/mL


title: B113


title: CpWT -Dox rep. #1

value: absence of Dox


title: PDAC_093

value: Plasma


title: P2


title: CpWT -Dox rep. #2


title: HD-CR1

value: Lewis

value: heart apex


title: B111


title: PDAC_092

value: PDAC


title: PDAC_091


title: B110


title: RNA-Seq worker head (experiment 2)

description:
differential_gene_expression.txt
rs_exp2_whe

source_name: Worker head

value: worker


title: P1

value: ACR or Borderline


title: RNA-Seq worker pupa (experiment 2)

description:
differential_gene_expression.txt
rs_exp2_wpu

source_name: Worker pupa

value: pupa


title: RNA-Seq worker larva (experiment 2)

description:
differential_gene_expression.txt
rs_exp2_wla

source_name: Worker larva

value: larva


title: tetO-CpUME6 -Dox rep. #2


title: PDAC_090


title: 975-12


title: PDAC_089


title: 9642


title: RNA-Seq worker embyro (experiment 2)

description:
differential_gene_expression.txt
rs_exp2_emb

source_name: Worker embryo

value: embryo


title: PDAC_088


title: RNA-Seq drone larva (experiment 2)

description:
differential_gene_expression.txt
rs_exp2_dla

source_name: Drone Larva


title: tetO-CpUME6 +Dox rep. #2


title: RNA-Seq queen head (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_qhe

value: head

value: mature

value: queen


title: tetO-CpUME6 +Dox rep. #1


title: 835B


title: RNA-Seq drone head (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_dhe

source_name: Drone head

value: drone


title: CpWT +Dox rep. #1


title: 835A

value: kernel


title: RNA-Seq drone larva (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_dla


title: US-10024581.1.CBMRUANXX_4

city: Stanford

first: Erik

last: Ingelsson

state: California

address: 300 Pasteur Drive

institute: Stanford University

description:
barcode:
US-10024581
MaleHFDVATWT

data_processing:
Alignment and quantification performed using STAR 2.5.3a
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene expression counts

source_name: MaleHFDVATWT

extract_protocol:
RNA extraction protocol not provided.
RNA libraries were prepared for sequencing using standard protocols

value: visceral adipose

tag: Sex

value: Male

tag: diet

value: HFD

tag: fam13a genotype

value: WT


title: PDAC_086

value: Plasma


title: 7884-4HT

value: 5 day after pollination


title: 7327


title: US-10024580.1.CBMRUANXX_4

description:
barcode:
US-10024580
MaleHFDVATWT


title: PDAC_085

value: PDAC


title: PDAC_084


title: RNA-Seq worker head (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_whe

value: worker


title: PDAC_083


title: US-10024579.1.CBMRUANXX_4

description:
barcode:
US-10024579
MaleHFDVATWT


title: US-10024578.1.HYKKCBCXY_1

description:
barcode:
US-10024578
MaleHFDVATWT


title: RNA-Seq worker pupa (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_wpu


title: tetO-CpUME6 -Dox rep. #1

tag: treatment

value: absence of Dox


title: RNA-Seq worker larva (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_wla


title: 647


title: 526018


title: US-10024584.1.CBMRUANXX_4

description:
barcode:
US-10024584
MaleHFDVATKO

source_name: MaleHFDVATKO

value: KO


title: PDAC_081


title: US-10024585.1.CBMRUANXX_4

description:
barcode:
US-10024585
MaleHFDVATKO


title: 5213

source_name: 5-DAP kernel


title: RNA-Seq worker embyro (experiment 1)

description:
differential_gene_expression.txt
rs_exp1_embyro


title: US-10024583.1.CBMRUANXX_4

description:
barcode:
US-10024583
MaleHFDVATKO


title: PDAC_082


title: BS-seq queen head (experiment 2)

extract_protocol:
All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.


title: PDAC_087


title: 4F1


title: PDAC_080


title: 478-BC6


title: US-10024582.1.CBMRUANXX_4

description:
barcode:
US-10024582
MaleHFDVATKO


title: PDAC_079


title: US-10024557.1.CBMRUANXX_1

description:
barcode:
US-10024557
MaleChowVATWT

source_name: MaleChowVATWT

value: Chow


title: 4019


title: BS-seq drone head (experiment 2)

extract_protocol:
Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.


title: US-10024556.1.CBMRUANXX_1

description:
barcode:
US-10024556
MaleChowVATWT


title: BS-seq drone larva (experiment 2)

extract_protocol:
Drone larvae were obtained at about 3rd and 4th instar developmental stages. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: larva


title: 335M


title: BS-seq worker head (experiment 2)

extract_protocol:
Worker heads were collected from bees newly emerged from their own growing cells. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: head


title: 335F


title: BS-seq worker pupa (experiment 2)

extract_protocol:
Worker pupae were collected at about pink eyes developmental stage. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: pupa


title: 268


title: US-10024555.1.CBMRUANXX_1

description:
barcode:
US-10024555
MaleChowVATWT


title: US-10024554.1.CBMRUANXX_1

description:
barcode:
US-10024554
MaleChowVATWT


title: 177


title: PDAC_076

source_name: Blood extracellular vesicle


title: PDAC_077


title: BS-seq queen head (experiment 1)

value: mature

value: queen


title: PDAC_078


title: 150

value: kernel


title: US-10024561.1.CBMRUANXX_1

description:
barcode:
US-10024561
MaleChowVATKO

source_name: MaleChowVATKO

value: visceral adipose


title: PDAC_075


title: US-10024560.1.CBMRUANXX_1

description:
barcode:
US-10024560
MaleChowVATKO

value: Male


title: BS-seq worker embyro (experiment 2)

extract_protocol:
Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.

value: embryo


title: BS-seq drone head (experiment 1)

value: drone


title: BS-seq worker larva (experiment 2)

extract_protocol:
Worker larvae were obtained at about 3rd and 4th instar developmental stages. All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen. About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).
Sequencing on the Illumina GAII and HiSeq 2000 platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 50, 76 and 100 base reads.
Honey bee samples were collected in two rounds (for two biological replicates). Worker embryos (eggs) were transferred from honeycomb cells into microcentrifuge tubes (50 per/tube). Drone and worker larvae were obtained at about 3rd and 4th instar developmental stages. Worker pupae were collected at about pink eyes developmental stage. Worker heads were collected from bees newly emerged from their own growing cells. Drone heads were collected from the same colony as drone larvae and worker embryos, larvae, pupae, and adult heads were collected from. Semen was collected from mature drones essentially as described in (Robinson et al., 2000). All samples were flash frozen in liquid nitrogen immediately upon collection. Except for queen heads, for which we used a single head per experiment, the rest of the biological sampling consisted of a mix of individuals, three larvae/pupae/heads, 50 embryos, and 20ul of semen.
BS-Seq: About 500 ng of genomic DNA was isolated from various honey bee developmental stages, fragmented by sonication, end repaired, and ligated to custom synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (QIAGEN), as outlined in the manufacturer’s instructions. The bisulfite-converted libraries were then amplified by PCR using ExTaq DNA polymerase (Takara Bio) for 12–14 cycles. The enriched libraries were purified using the solid-phase reversible immobilization method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent). Sequencing on the Illumina GAII and HiSeq platform was performed at the Vincent J. Coates Genomic Sequencing Laboratory at the University of California, Berkeley, USA (UC Berkeley) to generate single-end 76 and 100 base reads.


title: PDAC_074

value: Plasma


title: 1462

extract_protocol:
The collected seeds in three replications were mixed for total RNA preparation. Total RNA was extracted using RNAprep pure Kit For Plant (TIANGEN, Beijing, China) according to its protocol. Total mRNAs were accumulated using oligo(dT).
Library construction was following the standard protocol (Illumina, Inc.), and pair-end sequencing with 125 bp was carried out for each sample.

value: 5 day after pollination


title: US-10024559.1.CBMRUANXX_1

description:
barcode:
US-10024559
MaleChowVATKO


title: PDAC_073

extract_protocol:
Plasma EV RNAs were extracted by exoRNeasy Serum/Plasma kit.
RNA libraries were prepared for sequencing using SMARTer® Stranded Total RNA-Seq Kit - Pico Input Mammalian

value: PDAC


title: BS-seq worker larva (experiment 1)

value: worker


title: 07KS4


title: US-10024558.1.CBMRUANXX_1

description:
barcode:
US-10024558
MaleChowVATKO


title: PDAC_072


title: US-10024604.1.CBMRUANXX_7

description:
barcode:
US-10024604
FemaleHFDVATWT

source_name: FemaleHFDVATWT

value: Female

value: HFD

value: WT


title: PDAC_071


title: 05W002


title: Monocyte_8

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were demultiplexed, then aligned with TopHat2 (v2.0.3) against the hg19 reference genome
Gene and transcript information was extracted with Partek Genomics Suite (v6.6). Annotated data was normalized using statistical software R (v3.0.2) including DESeq2 package. Normalized read counts lower than 1 were set to the floor value 1.Genes were defined as expressed with normalized RNA-seq values ≥ 10.
Genome_build: hg19
Supplementary_files_format_and_content: Processed DeSeq2 normalized RNA-seq tag counts annotated to the hg19 reference genome

source_name: monocyte

extract_protocol:
RNeasy kits (Qiagen)
100 ng of total RNA was converted to RNA-seq libraries according to manufacturers' protocol with Illumina TruSeq RNA Sample Preparation Kit.

value: healthy


title: Monocyte_7


title: PDAC_070


title: PDAC_067


title: Monocyte_4


title: US-10024602.1.CBMRUANXX_6

description:
barcode:
US-10024602
FemaleHFDVATWT


title: PDAC_066


title: US-10024608.1.CBMRUANXX_7

description:
barcode:
US-10024608
FemaleHFDVATKO

source_name: FemaleHFDVATKO

value: KO


title: Monocyte_5


title: PDAC_069


title: Monocyte_3


title: US-10024607.1.CBMRUANXX_7

description:
barcode:
US-10024607
FemaleHFDVATKO


title: US-10024606.1.CBMRUANXX_7

description:
barcode:
US-10024606
FemaleHFDVATKO


title: Monocyte_2


title: PDAC_065


title: US-10024605.1.CBMRUANXX_7

description:
barcode:
US-10024605
FemaleHFDVATKO


title: Monocyte_1


title: 05WN230


title: PDAC_064


title: US-10024589.1.CBMRUANXX_5

description:
barcode:
US-10024589
MaleHFDSATWT

source_name: MaleHFDSATWT

value: subcutaneous adipose


title: US-10024603.1.CBMRUANXX_7

description:
barcode:
US-10024603
FemaleHFDVATWT


title: Monocyte_6


title: LatsCKO_RNAseq_MI_3

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

data_processing: RNA-seq was performed on Ion Proton. RNA Seq reads were aligned to mm10 (Mus musculus assembly July 2007). Raw read counts were normalized and analyzed for differential gene expression by DESeq2. Metascape (http://metascape.org/) was used for Gene Ontology (GO) analysis to extract the information on gene set and gene network. We supplied the final gene counts exported from STAR  for each experiment  (bulk RNA table) as a proccessed file.

source_name: Cardiac fibroblasts FACS sorted for GFP, Tcf21 lineage marker

growth_protocol: NIH3T3 cells were grown under standard cell culture conditions in DMEM media supplemented with 10% FBS.

extract_protocol: Cardiac fibroblasts, Tcf21 lineage GFP positive,  were isolated from hearts  by langendorff perfusion 3 days after 6-dose tamoxifen injection protocol. Because of limited GFP cells, sorted cells were directly collected in RLT lysis buffer from RNeasy Plus Micro Kit (Qiagen) and SMART-Seq Ultra Low Input RNA Kit to prepare RNA-seq library (Clonetech Laboratories).

tag: genotype

value: Tcf21-iCre; Lats1flox/flox; Lats2flox/flox ; mTmG

tag: cell type

tag: operation

value: Myocardial Infarction


title: PDAC_063


title: PDAC_068


title: US-10024588.1.CBMRUANXX_5

description:
barcode:
US-10024588
MaleHFDSATWT


title: PDAC_062


title: PDAC_061


title: LatsCKO_RNAseq_MI_1

value: Cardiac fibroblasts FACS sorted for GFP, Tcf21 lineage marker


title: US-10024587.1.CBMRUANXX_5

description:
barcode:
US-10024587
MaleHFDSATWT


title: LatsCKO_RNAseq_MI_2


title: US-10024586.1.CBMRUANXX_4

description:
barcode:
US-10024586
MaleHFDSATWT


title: PDAC_060


title: Ctrl_RNAseq_MI_3

value: Tcf21-iCRE; mTmG


title: Ctrl_RNAseq_MI_2


title: nSyb>E196K-NLS rep 3 [EN-26]

city: Antwerp

first: Ligia

middle: Monica

last: Mateiu

address: Universiteitsplein 1

department: Center for Molecular Neurology

country: Belgium

institute: VIB

data_processing:
The raw reads were trimmed and cleaned of adapters with Trimmomatic v0.32
Sequencing quality was assessed with FASTQC software
Reads were mapped using Tophat v2.0.12
Gene expression levels were measured using the counts generated by HTSeq v0.6.1
The gene expression counts were normalized for all samples together and the biological conditions were compared pairwise using DESeq2 v1.14.1
Weighted gene co-expression network analysis was performed (WGCNA)
Genome_build: Drosophila reference genome (ENSEMBL, BDGP6, release 84)
Supplementary_files_format_and_content: read counts; library sized normalized read counts

organism: Drosophila melanogaster

growth_protocol: Drosophila crosses were performed at 25°C, 12 h light/dark cycle, on standard NutriFly medium (FlyStuff)

extract_protocol:
Total RNA was extracted in quadruplicates using the RNAqueous Micro Kit (Ambion Thermo Fisher Scientific)
Twenty cDNA libraries (4 replicates per condition) were constructed from total RNA using poly(A) enrichment of the mRNA (TruSeq unstranded Illumina). Paired-end sequencing data of 75bp read length, generated on NextSeq 500 (Illumina) in 2 batches of 10 samples each, ranged from 74.3 to 139.4 million reads per sample. The cDNA libraries construction and the RNA sequencing were done at the GENECORE-EMBL Genomic Core Facilities (Germany).

tag: genotype/variation

tag: age

value: 10 days

value: Brain


title: US-10024593.1.CBMRUANXX_5

description:
barcode:
US-10024593
MaleHFDSATKO

source_name: MaleHFDSATKO

value: Male


title: US-10024592.1.CBMRUANXX_5

description:
barcode:
US-10024592
MaleHFDSATKO


title: nSyb>E196K-NLS rep 2 [EN-25]


title: siSALL3_96h_2

city: Tokushima

first: Yosuke

last: Matsushita

address: 3-18-15 Kuramoto

department: Institute for Genome Research

institute: Tokushima University

description: Gene expression in TNBC cell line BT-20.

hyb_protocol: 2 μg of Cy3-labeled cRNA was fragmented, and hybridized onto the Agilent-039494 Whole Human Genome Microarray 8x60K slide.

scan_protocol: A slide was scanned by the Agilent Microarray scanner system.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BT-20, siSALL3, 96h

label_protocol: 100 ng of total RNA from each sample was amplified using T7 RNA polymerase with simultaneous Cy3-labeled CTP incorporation.

extract_protocol: Total RNA was extracted 48h and 96h after transfection by NucleoSpin RNA II (TaKaRa Bio, Shiga, Japan).

treatment_protocol: BT-20 was seeded at a density of 2.5 x 10^5 cells per 3.5 cm dish in MEM with 10% FBS, Penicillin G 100 units/ml, Streptomycin 100 ug/ml and amphotericin B 0.025 ug/ml. Cells were transfected with 50nM siRNA (siEGFP or siSALL3) treatment by Lipofectamine RNAiMAX reagent (Life Technologies, Carlsbad, CA) according to manufacturer's protocol.

tag: cell line

value: triple negative breast cancer cell line

tag: sirna

tag: time


title: Ctrl_RNAseq_MI_1


title: nSyb>E196K-NLS rep 1 [EN-24]

tag: tissue


title: siSALL3_48h_1

source_name: BT-20, siSALL3, 48h


title: PDAC_058

value: Plasma


title: US-10024591.1.CBMRUANXX_5

description:
barcode:
US-10024591
MaleHFDSATKO


title: siSALL3_96h_1


title: siSALL3_48h_2


title: PDAC_057

value: PDAC


title: nSyb>E196K rep 4 [E-23]


title: siEGFP_48h_2

source_name: BT-20, siEGFP, 48h

value: siEGFP


title: siEGFP_96h_1

source_name: BT-20, siEGFP, 96h


title: nSyb>E196K-NLS rep 4 [EN-27]


title: LatsCKO_RNAseq_Sham_3

value: Sham


title: siEGFP_48h_1


title: US-10024590.1.HYKKCBCXY_2

description:
barcode:
US-10024590
MaleHFDSATKO

value: HFD


title: nSyb>E196K rep 3 [E-22]


title: US-10024565.1.CBMRUANXX_2

description:
barcode:
US-10024565
MaleChowSATWT

source_name: MaleChowSATWT

value: Chow

value: WT


title: LatsCKO_RNAseq_Sham_1


title: PDAC_059


title: PDAC_055


title: PDAC_056


title: Ctrl_RNAseq_Sham_2


title: PDAC_053


title: US-10024563.1.CBMRUANXX_2

description:
barcode:
US-10024563
MaleChowSATWT


title: US-10024564.1.CBMRUANXX_2

description:
barcode:
US-10024564
MaleChowSATWT


title: nSyb>WT-NLS rep 3 [WTN-18]

value: nsyb>WT-NLS


title: PDAC_054


title: nSyb>E196K rep 2 [E-21]


title: Ctrl_RNAseq_Sham_1


title: LatsCKO_RNAseq_Sham_2


title: nSyb>E196K rep 1 [E-20]


title: Ctrl_RNAseq_Sham_3


title: nSyb>WT-NLS rep 2 [WTN-17]


title: US-10024569.1.CBMRUANXX_2

description:
barcode:
US-10024569
MaleChowSATKO

source_name: MaleChowSATKO

value: subcutaneous adipose

value: KO


title: US-10024562.1.CBMRUANXX_2

description:
barcode:
US-10024562
MaleChowSATWT


title: nSyb>WT-NLS rep 1 [WTN-16]


title: US-10024568.1.CBMRUANXX_2

description:
barcode:
US-10024568
MaleChowSATKO


title: fes1D HS rep 3

city: Stockholm

first: Claes

last: Andréasson

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description: count_table_HS.txt, fpkm_table_HS.txt

data_processing:
The quality control and data processing were performed by National Genomics Infrastructure NGI, Science for Life Laboratory, Sweden
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite, The quality scale is Sanger / phred33 / Illumina 1.8+.
The sequencing reads were mapped to the sacCer2 genome with ensemble annotation saccharomyces cerevisiae EF2.62 using Tophat v 2.0.4.
The duplicate reads were removed using picard-tools/1.29
Gene counts and FPKM values were estimated using HTSeq v 0.6.1 and Cufflinks v 2.1.1 respectively.
Genome_build: sacCer2, EF2.62
Supplementary_files_format_and_content: a tab-delimited text file include raw counts for all samples
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

organism: Saccharomyces cerevisiae

source_name: Yeast log phase cells

growth_protocol: Cells were grown in YPD at 25°C with or without a 30 min heat shock (HS) at 37°C before harvest.

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit for Yeast (Ambion). The libraries were prepared using Illumina TruSeq Stranded mRNA (polyA-selection)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heat shock

tag: strain

value: count_table_HS.txt, fpkm_table_HS.txt


title: fes1D HS rep 2

description: count_table_HS.txt, fpkm_table_HS.txt


title: PDAC_052


title: nSyb>WT rep 3 [WT-15]

value: nsyb>WT


title: PDAC_050


title: US-10024566.1.CBMRUANXX_2

description:
barcode:
US-10024566
MaleChowSATKO


title: fes1D HS rep 1

description: count_table_HS.txt, fpkm_table_HS.txt


title: PDAC_049


title: PDAC_048


title: nSyb>WT rep 2 [WT-14]

value: 10 days


title: nSyb>WT rep 1 [WT-13]

value: Brain


title: PDAC_047


title: nSyb>+ rep 3 [w-10]

value: nsyb>+


title: PDAC_046


title: US-10024609.1.CBMRUANXX_7

description:
barcode:
US-10024609
FemaleHFDSATWT

source_name: FemaleHFDSATWT

value: Female


title: wild type HS rep 2

description: count_table_HS.txt, fpkm_table_HS.txt

value: wild type


title: PDAC_045

value: Plasma

value: PDAC


title: nSyb>+ rep 2 [w-09]


title: wild type HS rep 1

description: count_table_HS.txt, fpkm_table_HS.txt


title: PDAC_051


title: US-10024615.1.CBMRUANXX_8

description:
barcode:
US-10024615
FemaleHFDSATKO

source_name: FemaleHFDSATKO


title: PDAC_044

source_name: Blood extracellular vesicle


title: nSyb>+ rep 1 [w-08]


title: US-10024614.1.CBMRUANXX_8

description:
barcode:
US-10024614
FemaleHFDSATKO


title: US-10024567.1.CBMRUANXX_2

description:
barcode:
US-10024567
MaleChowSATKO

value: Male


title: PDAC_043


title: wild type HS rep 3

description: count_table_HS.txt, fpkm_table_HS.txt


title: US-10024611.1.CBMRUANXX_8

description:
barcode:
US-10024611
FemaleHFDSATWT

value: HFD


title: US-10024613.1.CBMRUANXX_8

description:
barcode:
US-10024613
FemaleHFDSATKO


title: US-10024612.1.CBMRUANXX_8

description:
barcode:
US-10024612
FemaleHFDSATKO


title: US-10024610.1.CBMRUANXX_7

description:
barcode:
US-10024610
FemaleHFDSATWT


title: PDAC_042


title: US-10024596.1.CBMRUANXX_6

description:
barcode:
US-10024596
MaleHFDLivWT

source_name: MaleHFDLivWT

value: liver


title: US-10024597.1.CBMRUANXX_6

description:
barcode:
US-10024597
MaleHFDLivWT

value: WT


title: PDAC_039


title: PDAC_040


title: PDAC_038


title: siEGFP_96h_2

value: triple negative breast cancer cell line

value: siEGFP


title: VCaP_si7DNAPK

city: San Francisco

first: vishal

last: kothari

state: California(CA)

address: HD300 1450 Third street, PO Box #3110

department: Radiation Oncology

institute: university of California, San francisco

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized for 20 hr at 48C on Human Gene ST 2.1 strip arrays using the Affymetrix Gene Atlas system.

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the oligo Bioconductor packages implemented in the R-statistical environment version 3.1.0. RMA was used to fit log2 transformed expression values.

source_name: VCaP cells treated with DNAPK siRNA

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol from 400 ng total RNA (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: Cell lines were grown in standard media (RPMI1640 for C42B, PC3 and DMEM for DU145 and VCaP cell line).

extract_protocol: RNA was extracted using TRIZOL reagent using manufecturer's protocol.

treatment_protocol: Cells were transfected with either non-targeting  siRNAs or with siRNAs targeting DNAPK. Cells were harvested 48 hours post transfection.

value: VCaP

tag: condition

value: DNAPK knockdown