title: Intact Muscle

city: Créteil

first: Léo

last: Machado

state: Ile-De-France

address: 8 rue du Général Sarrail, Equipe 10 - Inserm U955

description:
10X Genomics single-nuclei atlas
Muscle_Nuclear_Atlas.rds

data_processing:
For bulk RNA-seq: data processing pipeline Sequana version 0.9.19
For 10X genomics: data processing pipeline Cell Ranger version 3.0.2
For Smart-Seq2: data processing pipeline using Star version 2.4.0, cutadapt version 1.11, featureCounts version 1.4.5-p3
Differential expression for bulk RNA-seq using DESeq2 version 1.18.1
Data analysis for Smart-Seq2 using Scater version 1.8.4 and Slingshot version 1.4
Data analysis for 10X genomics using Seurat version 3.0.2
Genome_build: mm10
Supplementary_files_format_and_content: Liver_Nuclear_Atlas.rds: R object, processed Seurat object
Supplementary_files_format_and_content: Muscle_Nuclear_Atlas.rds: R object, processed Seurat object
Supplementary_files_format_and_content: single_cell_muscs_time_course.rds: R object, processed SCE object
Supplementary_files_format_and_content: bulk_muscs_time_course.csv: Table, DESeq2 output

source_name: Skeletal muscle cells

extract_protocol:
For single-nuclei: Single-cell Gel Bead-In-EMulsions (GEMs) were generated using a Chromium Controller  instrument (10x Genomics).           For bulk RNA-seq : Quick RNA FFPE kit (Zymo, R1008) following instructions (without tissue digestion step)  For smart-seq2 single-cell RNA-seq: Pax7-nGFP cells were sorted single-cell by FACS in 96 well plates (4titude, 4ti-0960). Each well contained 2.5 µl PKD buffer (Qiagen, 1034963)  supplemented with 1:16 proteinase K (Qiagen, 19131). Prior to RNA separation, plates were  decrosslinked for 1 h at 56 °C. RNA separation was performed on a Hamilton STAR  according to the G&T-seq protocol (Macaulay et al., 2015) .
For single-nuclei: Sequencing libraries were prepared using Chromium Single Cell  3’ Reagent Kits (10x Genomics, 1000074), according to the manufacturer’s instructions. For bulk RNA-seq: Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input  Mammalian following the manufacturer’s instructions (Clontech, 635005). for smart-seq2 single-cell: cDNA libraries were generated based on the Smart-seq2 protocol (Picelli et al., 2014).
For single-nuclei: Libraries were then sequenced by pair with a  HighOutput flowcel using an Illumina Nextseq 500 with the following mode: 26 base-pairs  (bp) (10X Index + UMI), 8 bp (i7 Index) and 57 bp (Read 2). For bulk RNA-seq2: Sequencing was performed with the Illumina HiSeq 2500  system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven  indexing cycles, to obtain 65 bp single-end reads. Sequencing data were processed with  Illumina Pipeline software (Casava version 1.9). For smart-seq2 single-cell RNA-seq: 384 single-cell libraries were pooled  together and sequenced single-end 50 bp on a single lane of a HiSeq4000 (Illumina).

treatment_protocol: For muscle injury: Bacl2, for liver injury: Ccl4, for fixation: PFA, for dissociation: collagenase/dispase

tag: tissue treatment

value: Intact

tag: preparation method

value: Single-nuclei

tag: fixation status

value: Fresh


title: blood_203273630214_R08C01

status: Public on Jan 31 2021

type: genomic

city: Tuebingen

first: Vanessa

last: Nieratschker

address: Calwerstr. 14

department: Department of Psychiatry and Psychotherapy

country: Germany

institute: University of Tuebingen

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: For background and dye bias correction, the preprocessNoob() function from the minfi package was applied. Additionally, we excluded 59 single nucleotide polymorphism (SNP) probes, 19,632 sex chromosome probes, 53,315 cross-reactive and polymorphic probes, 4,081 poorly performing probes (i.e. probes with a beadcount < 3 in 5% of the samples and probes with a detection p-value > 0.05 in at least 1% of the samples), and 98,983 known invariant probes (inter-quantile range (IQR, 0.1 - 0.9) < 0.02). To adjust for the bias originating from the two different bead types present on the BeadChip array, Beta-Mixture Quantile (BMIQ) normalization was performed . To reduce batch effects of different runs, chips and rows, the ComBat() function was applied. The estimateCellCounts.wmln() function from the wateRmelon package was used to estimate the relative proportions of monocytes, granulocytes, CD4+ and CD8+ T cells, B cells and natural killer cells. Adjustment for cell type composition was done by using the statistical estimates in a regression-based approach.

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the QIAamp Blood Maxi Kit (Qiagen, Hilden, GER) according to manufacturer’s instructions

tag: age

tag: Sex

value: F

tag: sad

value: no

tag: ela


title: blood_203273630223_R03C01

value: M


title: Injured Muscle

type: SRA

country: France

institute: INSERM

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Injured


title: blood_203273630214_R06C01

value: yes


title: blood_203273630214_R07C01


title: SAMPLE 2_GFP(low)

type: RNA

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

institute: University of Cologne

hyb_protocol: Agilent miRNA labeling and hybridization Kit

scan_protocol: Agilent G2505C scanner

data_processing: Genespring 14.9, Normalization: Shift to 75 percentile

source_name: skin

extract_protocol: Trizol for RNA isolation

tag: tissue

value: skin

tag: cell type

value: fibroblast-like cells

tag: molecule subtype

value: miRNA


title: Dissociated Muscle

value: Dissociated


title: blood_203273630235_R08C01


title: blood_203273630223_R05C01


title: SAMPLE 1_GFP(low)

label_protocol: Agilent miRNA labeling and hybridization Kit


title: blood_203273630235_R07C01


title: sample3: testis 15-15-6

city: Davis

first: Trish

last: Berger

address: One Shields Avenue

department: Animal Science

country: USA

institute: University of California

data_processing:
Illumina files (Vincent J. Coates Genomics Sequencing Laboratory) were imported into CLC Genomics Workbench 11 software.
QC report for each index inspected and reads trimmed from each index.
Reads were mapped in CLC Genomics Workbench 11 software to Sus Scrofa 11.1 reference genome.
Data normalization (within software) was reads per kilobase per million mapped reads (RPKM).
Experiments (comparisons between treatments at an age) were set up within the CLC Genomics Workbench software.
Genome_build: Sus scrofa 11.1 (Ensembl)
Supplementary_files_format_and_content: Excel files containing RPKM value and other parameters for each gene for each sample

organism: Sus scrofa

source_name: testis

growth_protocol: Animals were managed consistent with normal pig production practices, transitioned to a starter diet, and weaned at 3 1/2 weeks of age.

extract_protocol:
RNA was extracted with Trizol reagent.
Libraries were constructed using TruSeq RNA kits (Illumina) with initial step being isolation of the polyA mRNA using oligo-dT magnetic beads.

treatment_protocol: Animals were orally dosed with either the letrozole treatment or the canola oil vehicle weekly.

value: testis

tag: treatment

value: vehicle

value: 2 weeks

tag: genetic bkgd

value: PIC


title: blood_203273630266_R08C01


title: blood_203273630223_R04C01


title: SAMPLE 5_GFP(low)


title: blood_203273630214_R05C01


title: Intact Liver

description:
10X Genomics single-nuclei atlas
Liver_Nuclear_Atlas.rds

source_name: Liver cells


title: Queen_VHQ

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

data_processing:
Trinity used to assemble a de novo transcriptome
RSEM used to calculate normalised gene counts per Trinity transcript
Supplementary_files_format_and_content: Trinity fasta transcriptome files (.fnn) and tab-delimited RSEM files for each queen/worker which include TPM/FPKM and expected count for each sample.

organism: Vespula vulgaris

source_name: Whole brain

extract_protocol:
All wasps were collected directly from their nests during the daytime, placed immediately into RNAlater (Ambion, Invitrogen) and stored at -20°C until further use. Total RNA was extracted using the RNeasy Universal Plus Mini kit (Qiagen, #73404)
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

tag: caste

value: Queen

value: whole brain


title: Injured Liver

value: Single-nuclei


title: Queen_RHSQ


title: Dissociated Liver

value: Fresh


title: Queen_MH5Q


title: Queen_MH2Q


title: H3K27me3 late_2_cell Pcgf1/6 matKO spike-in

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by Trim Galore (version 0.6.4) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CUT&RUN, mm10 for general CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -N 1 -L 25 --no-mixed --no-discordant" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.3.1) with the parameters "--scaleFactor Scaling_factor --binSize 50 --normalizeUsing RPKM".
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
For allele-specific analysis of CUT&RUN in the B6 or B6/129 x PWK F1 hybrid embryos, B6/129 and PWK SNPs were masked as "N" in the reference genome.
MACS2 (version 2.1.2) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H2AK119ub1 and H3K27me3 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Preimplantation embryo

extract_protocol:
For CUT&RUN sample collection, MII oocytes, zygotes, and preimplantation embryos were briefly incubated in Acidic Tyrode’s solution supplemented with 0.5% Polyvinylpyrrolidone (PVP) and 50 mM NaCl to gently remove zona pellucida, and then washed in M2 media (Merck Millipore, MR-015-D). Polar bodies (PBs) of zygotes were removed by gentle pipetting with a narrow glass capillary in M2 media containing 5 µg/ml Cytochalasin B (Merck, C6762) and 0.1 µg/ml Colcemid (Merck, 10295892001). PBs of preimplantation embryos were removed by gentle pipetting in Trypsin/EDTA solution (Merck, T4049) supplemented with 0.5% PVP. After PB removal, the oocytes/embryos were washed with M2 media followed by 0.2% BSA/PBS. Pronuclear stage 5 (PN5) zygotes, early 2-cell, late 2-cell, morula, and blastocyst embryos were collected at 11-12, 18-19, 30, 72, and 96 hpi with 500-1,000 blastomeres served for each CUT&RUN experiment.
For CUT&RUN,libraries were prepared as previously described (Inoue,A., et al., 2018, Genes Dev 32, 1525-1536). For spike-in CUT&RUN, 1,600 Drosophila S2 cells (Thermo Fisher, R69007) were first captured to BioMag Plus Concanavalin A beads (Bang Laboratories, Inc). After the beads were thoroughly resuspended, they were split into two 1.5 ml tubes, and then 500 CTR and KO FGOs were added to each of the tubes. The antibodies used were rabbit anti-H2AK119ub1 (1/100, Cell Signaling Technology, #8240) and rabbit anti-H3K27me3 antibody (1/100, Diagenode, #C15410069). For RNA-seq, libraries were prepared as previously described. Briefly, cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA, 634890) according to the manufacturer’s instructions. Two hundred picograms of cDNA were used for the library construction by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to the manufacturer’s instructions.

tag: antibody

tag: strain

value: B6.129 x PWK

tag: developmental stage

tag: genotype

value: Pcgf1/6 double maternal knockout


title: Queen_MH1Q


title: H3K27me3 late_2_cell Pcgf1/6 CTR spike-in

value: wild type


title: blood_203273630214_R04C01

value: M

value: no


title: Worker5_VvulW5

value: Worker


title: H3K27me3 FGO Pcgf6 KO rep2

description: H3K27me3_FGO_Pcgf6_KO_merge_replicates.bigwig

source_name: Fully grown oocyte

value: Full-grown oocyte

value: Pcgf6 knockout


title: H3K27me3 FGO Pcgf6 KO rep1


title: Worker4_VvulW4


title: H3K27me3 FGO Pcgf1 KO rep2

description: H3K27me3_FGO_Pcgf1_KO_merge_replicates.bigwig

value: Fully grown oocyte

value: Pcgf1 knockout


title: Worker3_VvulW3


title: Worker2_VvulW2


title: SAMPLE 6_GFP(high)

source_name: wound

value: wound

value: myofibroblast

value: miRNA


title: OldEx5

city: Hong Kong

first: Ho

last: Ko

address: 30-32 Ngan Shing Street, Shatin

department: Medicine and Therapeutics

country: China

institute: The Chinese University of Hong Kong

data_processing:
The multiple fastq files were aligned to mm10 reference genome by Cellranger software (v3.0.0)
Follow the stadard Seurat (v3.1.5) process pipeline, cells were undergo quality control by following criterias: 1. Lower than 5% or higher than 95% UMI count. 2. The proportion of mitochondrial genes > 20%.
After normalization (by SCTransform function), the dimension reduction and clustering was finished by UMAP and Seurat FindNeighbors and FindClusters function on first 30 components of PCA results.
The primary cell type was identified by well-known marker genes. Any cluster with dual marker genes expression was removed.
Genome_build: mm10
Supplementary_files_format_and_content: Standard 10X cellranger output files: 1. Sparse matrix (mtx), each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column). 2.The meta file contained the batch, age, sample names, clustering results and cell type identified in Seurat.

molecule: polyA RNA

source_name: Brain

growth_protocol: C57BL/6J mal mice were provided by the Laboratory Animal Service Center of CUHK and maintained at controlled temperature (22 – 23°C) with an alternating 12-hour light/dark cycle with free access to standard mouse diet and water

extract_protocol:
We adapted a previously described dissociation protocols optimized for single brain vascular cells isolation from both young and old mouse brains. Briefly, mice were deeply anesthetized and perfused transcardially with 20 ml of ice-cold phosphate buffered saline (PBS). Mice were then rapidly decapitated, and whole brains were immersed in ice-cold Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific). The brain tissues were cut into small pieces and dissociated into single cells using a modified version of the Neural Tissue Dissociation kit (P) (130-092-628, Miltenyi Biotec). Myelin debris was removed using the Myelin Removal kit II (130-096-733, Miltenyi Biotec) according to the manufacturer’s manual. Cell clumps were removed by serial filtration through pre-wetted 70 μm (#352350, Falcon) and 40 μm (#352340, Falcon) nylon cell strainers. Centrifugation was performed at 300 xg for 5 minutes at 4°C. The final cell pellets were resuspended in 500 – 1000 μl FACS buffer (DMEM without phenol red (Thermo Fisher Scientific), supplemented with 2% fetal bovine serum (Thermo Fisher Scientific)).
Chromium Single Cell 3′ Reagent Kit v3
Drop-seq (10X Gemonic)

treatment_protocol: Exenatide (5 nmol/kg/day, Byetta, AstraZeneca LP) was intraperitoneally (I.P.) administered starting at 17 – 18 months old for 4 – 5 weeks respectively prior to single-cell RNA sequencing experiments.

value: Brain

value: 18 - 20 months

tag: mice number


title: blood_203273630223_R01C01

value: F

value: yes


title: blood_203273630178_R08C01


title: Worker_W7

organism: Vespa crabro

value: whole brain


title: H3K27me3 FGO Pcgf1 KO rep1


title: blood_203273630178_R05C01


title: Worker_W6


title: Worker1_VvulW1


title: Young5

value: 2 - 3 months


title: Worker_W5


title: blood_203273630214_R02C01


title: RNA-seq ExE Pcgf1/6 matKO rep3

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by Trim Galore (version 0.6.4) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CUT&RUN, mm10 for general CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -N 1 -L 25 --no-mixed --no-discordant" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.3.1) with the parameters "--scaleFactor Scaling_factor --binSize 50 --normalizeUsing RPKM".
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
For allele-specific analysis of CUT&RUN in the B6 or B6/129 x PWK F1 hybrid embryos, B6/129 and PWK SNPs were masked as "N" in the reference genome.
MACS2 (version 2.1.2) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H2AK119ub1 and H3K27me3 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: Extraembryonic ectoderm (ExE)

value: B6.129 x PWK

value: Extraembryonic ectoderm (ExE)

value: Pcgf1/6 double maternal knockout


title: Worker_W3

value: Worker


title: blood_203273630178_R06C01


title: Old5


title: RNA-seq ExE Pcgf1/6 matKO rep2


title: Worker_W1


title: RNA-seq ExE Pcgf1/6 matKO rep4


title: blood_203273630178_R01C01

value: no


title: blood_203273630214_R01C01

value: M


title: blood_203273630162_R08C01


title: RNA-seq ExE Pcgf1/6 matKO rep1


title: blood_203273630178_R04C01


title: blood_203273630178_R03C01


title: blood_203273630235_R05C01


title: blood_203273630214_R03C01


title: Queen_VCQ2

value: Queen


title: blood_203273630178_R02C01


title: RNA-seq ExE Pcgf1/6 CTR rep2

value: wild type


title: Queen_VCG5

value: Gyne


title: RNA-seq ExE Pcgf1/6 CTR rep1


title: blood_203273630178_R07C01


title: blood_203273630159_R08C01


title: blood_203273630162_R07C01


title: Queen_VCG4


title: Queen_VCG3


title: blood_203273630162_R03C01


title: RNA-seq morula B6xPWK rep2

value: B6 x PWK

value: morula


title: Queen_VCG2


title: RNA-seq morula B6xPWK rep1


title: blood_203273630162_R04C01


title: Worker_VC1


title: RNA-seq morula PWKxB6 rep1

value: PWK x B6


title: blood_203273630162_R05C01


title: blood_203273630162_R06C01


title: blood_203273630159_R07C01


title: RNA-seq morula Pcgf1/6 matKO rep2


title: RNA-seq morula Pcgf1/6 CTR rep2


title: RNA-seq morula Pcgf1/6 CTR rep1


title: RNA-seq morula Pcgf1/6 matKO rep1


title: C9: White LUSC 9

city: Durham

first: Jennifer

last: Freedman

address: 905 South Lasalle Street

institute: Duke Cancer Institute

hyb_protocol: Targets were hybridized to the Affymetrix Human Clariom D Array

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
RNA expression value derived from Transciptome Analysis Console software
Raw data were processed and analyzed with TAC-4.0.025 using sst-rma-combined-dabg algorithm. Pos/Neg AUC threshold was set at 0.6 and other perameters were set as default. Data were reanalyzed using CEL files by excluding outliers.

label: biotin

source_name: Resected LUSC tissue

label_protocol: Affymetrix WT PLUS reagent kit was used to generate amplified and biotinylated sense-strand DNA targets from total RNA that provided a complete and unbiased coverage of the transcriptome

growth_protocol: Tissue cores were harvested from archival formalin-fixed, paraffin-embedded tissue blocks from resected LUSC using 4mm punches

extract_protocol: Genomic DNA and total RNA were simultaneously isolated from tissue cores using AllPrep DNA/RNA FFPE Kit (Qiagen)

tag: race

value: White

value: Lung


title: C7: White LUSC 7


title: C8: White LUSC 8


title: C6: White LUSC 6


title: blood_203273630159_R05C01

value: F


title: blood_203273630162_R01C01

value: yes


title: RNA-seq FGO Pcgf1/6 KO rep2

value: Full-grown oocyte

value: Pcgf1/6 double knockout


title: RNA-seq FGO Pcgf1/6 KO rep1


title: Queen_VCG1

value: whole brain


title: RNA-seq FGO Pcgf1/6 CTR rep2


title: C3: White LUSC 3


title: RNA-seq FGO Pcgf1/6 CTR rep1


title: blood_203273630159_R04C01


title: C20: White LUSC 20


title: blood_203273630159_R03C01


title: C5: White LUSC 5


title: blood_203273630159_R06C01


title: C2: White LUSC 2


title: C4: White LUSC 4


title: C19: White LUSC 19


title: H3K27me3 morula Pcgf1/6 matKO rep1

data_processing:
Library strategy: CUT&RUN
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by Trim Galore (version 0.6.4) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CUT&RUN, mm10 for general CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -N 1 -L 25 --no-mixed --no-discordant" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.3.1) with the parameters "--scaleFactor Scaling_factor --binSize 50 --normalizeUsing RPKM".
For RNA-seq, all reads after trimming by Trim Galore (version 0.6.4) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.3) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
For allele-specific analysis of CUT&RUN in the B6 or B6/129 x PWK F1 hybrid embryos, B6/129 and PWK SNPs were masked as "N" in the reference genome.
MACS2 (version 2.1.2) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H2AK119ub1 and H3K27me3 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

value: B6.129 x PWK

value: Pcgf1/6 double maternal knockout


title: H3K27me3 morula Pcgf1/6 matKO rep2


title: C18: White LUSC 18


title: RNA-seq morula PWKxB6 rep2


title: H3K27me3 morula Pcgf1/6 matKO rep3


title: blood_203273630145_R08C01


title: C16: White LUSC 16


title: H3K27me3 morula Pcgf1/6 CTR rep3


title: blood_203273630162_R02C01

value: no


title: C17: White LUSC 17


title: H3K27me3 morula Pcgf1/6 CTR rep1


title: H3K27me3 FGO Pcgf1/6 KO rep2


title: blood_203273630145_R07C01


title: H3K27me3 morula Pcgf1/6 CTR rep2


title: C14: White LUSC 14


title: H3K27me3 FGO Pcgf1/6 KO rep1


title: C15: White LUSC 15


title: C13: White LUSC 13


title: blood_203273630159_R02C01


title: H3K27me3 FGO Pcgf1/6 CTR rep2


title: C12: White LUSC 12


title: blood_203273630145_R03C01

value: M


title: blood_203273630159_R01C01


title: H3K27me3 FGO Pcgf1/6 CTR rep1


title: C10: White LUSC 10


title: H2AK119ub1 FGO Pcgf1/6 KO spike-in rep2


title: H2AK119ub1 FGO Pcgf1/6 KO rep1


title: blood_203273630145_R05C01


title: C1: White LUSC 1


title: blood_203273630145_R02C01


title: blood_203273630145_R04C01


title: blood_203273630100_R04C01


title: A8: African American LUSC 8

value: African American


title: blood_203273630145_R01C01


title: blood_203273630100_R07C01


title: A7: African American LUSC 7


title: C11: White LUSC 11


title: blood_203273630077_R08C01


title: blood_203273630100_R03C01


title: A6: African American LUSC 6


title: H2AK119ub1 mESC 5K_cells

source_name: Embryonic stem cell

value: embryonic stem cell

value: wild type


title: H2AK119ub1 FGO Pcgf1/6 CTR spike-in rep2


title: H2AK119ub1 mESC 500_cells


title: H2AK119ub1 mESC 1K_cells


title: blood_203273630100_R08C01


title: blood_203273630100_R06C01


title: blood_203273630100_R02C01


title: blood_203273630145_R06C01


title: A9: African American LUSC 9


title: blood_203273630100_R01C01


title: H2AK119ub1 mESC 250_cells


title: A4: African American LUSC 4


title: A5: African American LUSC 5


title: Non-Mycorrhized Orchid Rep 3

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

country: Italy

institute: Università di Udine

data_processing:
Adapter removal and trimming of bases with phred quality score lower than 10 were performed using bbduk version 38.32.
Transcriptome assembly was performed using the reads from all replicates and all conditions using Trinity version 2.5.1.
Reads from each sample were then aligned against the assembled transcriptome using Hisat2 2.0.4.
The assembler Stringtie (1.3.5) was used to refine the individual transcriptome based on realignment of the reads on the transcriptome, and to merge and harmonize the transcriptome of each sample into a unique consensus transcriptome.
Taxonomic classification of the reads and of the reconstructed transcripts was performed using kraken2 (Wood and Salzberg 2014) against the nt database.
Htseq-count was used to count reads mapping on the genes classified as belonging to plants or fungi.
Differential expression analysis was performed separately in plant and fungal transcripts using DEseq2 version 1.26.0.
Genome_build: There is no genome assembly for Limodorum abortivum; however, the transcriptome assembly can be retrieved at the following: DOI: 10.17605/OSF.IO/35XUP (https://osf.io/35xup/)
Supplementary_files_format_and_content: *.txt: Htseq-count output for each replicate.

organism: Limodorum abortivum

source_name: Root sample

extract_protocol:
Frozen root segments from different individuals were ground in liquid nitrogen using sterile mortar and pestles. Total RNA was extracted from samples following the protocol described by Chang et al. (1993). Genomic DNA was removed using the Turbo DNA-free TM reagent (Ambion, Austin, TX, USA), according to the manufacturer’s instructions.
cDNA libraries were constructed using 2 µg of total RNA and following the TruSeq RNA Sample preparation v.2 kit instructions (Low throughput protocol, Illumina, Inc., CA, USA). Briefly, total RNA samples were polyA-enriched, reverse-transcribed and double-stranded cDNA synthesized. TruSeq adapters were attached to double-stranded cDNA. Enrichment in fragments containing TruSeq adapters on both ends were performed using PCR. The quantity and quality of the enriched libraries were validated using Nanodrop 1000 and Bioanalyzer 2100 respectively. The libraries were normalized to 10 nM of amplicons in 10 mM Tris-HCl, pH 8.5 containing 0.1% Tween 20.

value: Root

tag: mycorrhizal

value: No


title: blood_203273630077_R03C01

tag: age


title: A3: African American LUSC 3


title: Non-Mycorrhized Orchid Rep 2


title: H2AK119ub1 blastocyst rep2

value: C57BL/6 (B6) x PWK

value: blastocyst


title: blood_203273630077_R04C01

tag: Sex


title: A21: African American LUSC 21

value: Lung


title: blood_203273630077_R01C01

tag: sad


title: blood_203273630077_R02C01

value: F

tag: ela


title: H2AK119ub1 blastocyst rep1


title: Non-Mycorrhized Orchid Rep 1

tag: tissue


title: H2AK119ub1 FGO Pcgf1/6 CTR rep1


title: blood_203273630077_R05C01

value: yes


title: blood_203273630077_R06C01


title: H2AK119ub1 morula rep2

value: morula


title: Mycorrhized Orchid Rep 3

value: Yes


title: A20: African American LUSC 20


title: A2: African American LUSC 2


title: Mycorrhized Orchid Rep 2


title: A19: African American LUSC 19


title: A18: African American LUSC 18


title: H2AK119ub1 morula rep1


title: blood_203273630077_R07C01


title: Mycorrhized Orchid Rep 1


title: Angiopolybia Worker

organism: Angiopolybia pallens

value: Worker

value: whole brain


title: H2AK119ub1 late_2_cell rep1


title: blood_203273630044_R07C01


title: A16: African American LUSC 16


title: H2AK119ub1 late_2_cell rep2

value: late-c-cell


title: H2AK119ub1 early_2_cell rep2


title: A15: African American LUSC 15


title: H2AK119ub1 early_2_cell rep1


title: Angiopolybia Queen

value: Queen


title: A13: African American LUSC 13


title: H2AK119ub1 1_cell rep2


title: A14: African American LUSC 14


title: H2AK119ub1 1_cell rep1


title: H2AK119ub1 MII oocyte rep2

source_name: MII oocyte

value: MII oocyte


title: A11: African American LUSC 11

value: African American


title: blood_203273630044_R02C01

value: M


title: T-ALL cell_CXCL12_biological rep2

city: Madrid

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

country: Spain

institute: CIB-CSIC

description: Gene expression data from T-ALL cells treated 15min with CXCL12

hyb_protocol: RNA was hybridized to Clariom™ S Human Array following manufacturer’s instructions in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC)

label: Biotin

source_name: Jurkat cells treated 15min with CXCL12

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

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

treatment_protocol: Jurkat cells were cultured in starving conditions (without serum) for 90 min and then stimulated or not with CXCL12 (100 ng/ml) for 15 min.

tag: cell line

value: Jurkat


title: H2AK119ub1 MII oocyte rep1

value: wild type


title: T-ALL cell_CXCL12_biological rep3


title: A12: African American LUSC 12


title: H2AK119ub1 FGO oocyte rep2

value: Full-grown oocyte


title: T-ALL cell_CXCL12_biological rep1


title: A10: African American LUSC 10


title: T-ALL cell_control_biological rep3

description: Gene expression data from T-ALL cells untreated

source_name: Jurkat cells untreated


title: T-ALL cell_control_biological rep2


title: blood_203273630044_R06C01


title: blood_203273630044_R05C01

value: no


title: A1: African American LUSC 1


title: blood_203273630044_R04C01


title: H2AK119ub1 7d oocyte rep2

source_name: Growing oocyte

value: 7d growing oocyte


title: blood_203273630044_R01C01

source_name: blood


title: H2AK119ub1 FGO oocyte rep1


title: blood_203273630044_R03C01


title: 18_12P3_susp

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

institute: university Paris Sud11

description: Colorectal cancer derived sample.

hyb_protocol: WT plus Affymetrix chemistry.

scan_protocol: Scan of Clariom S human slide on Affymetrix microarray station.

data_processing: RMA normalization TAC 4.0 software.

source_name: cell line 12P

label_protocol: WT plus Affymetrix chemistry.

growth_protocol: TSIPs coming from CRC PDX’s were formed during three days in suspension.

extract_protocol: Total RNA was extracted from the cell culture and a quantity of 100 ng was investigated to start microarray probe synthesis.

treatment_protocol: None or 3 days inside a 3D collagen-I network.

value: suspension


title: KD_seedling_Rep2

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
The processed reads were aligned to the rice genome, Oryza sativa Indica
Gene expressions were calculated using CuffLinks (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Supplementary_files_format_and_content: FPKM values of the genes obtained using Cuffdiff are provided as tsv format

organism: Oryza sativa

source_name: Five weeks old seedlings

extract_protocol:
Total RNA from 5 week old seedlings of both wild-type and transgenic knock-down lines were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subspecies, cultivar

value: Genotype:Rice, Indica, Pusa Basmati 1 (PB1)

tag: transgenic line

value: KD


title: KD_seedling_Rep1


title: Vertical_Lobe_Whole_2

city: St Augustine

first: Leonid

middle: L

last: Moroz

state: FL

address: 9505 Ocean Shore Blvd

institute: University of Florida

description:
ObVerticalLobeTissue-3226-T25
O_bimaculoides_TPM_NextSeqRuns

data_processing:
Base calling and initial adapter trimming performed by Illumina Real Time Analysis v2
Additional adapter trimming and alignment to annotated genome performed using Trimmomatic (v0.32) and STAR (v2.3).
Quantification to produce transcripts per million mapped reads (TPMs) was produced by Rsubread (v1.22.3) and edgeR (v3.14.0)
Genome_build: Reference Genome: PRJNA270931, Reference assembly: GCA_001194135.1
Supplementary_files_format_and_content: TPMs for all samples were generated by Rsubread (v1.22.3) and edgeR (v3.14.0) using reference assembly gene models.  We used the default parameters of featureCounts to summarize the reads, except as follows: isPairedEnd = TRUE; maxFragLength = 800; allowMultiOverlap = TRUE; countMultiMappingReads = FALSE

organism: Octopus bimaculoides

source_name: RNA extracted from whole tissue

extract_protocol:
For tissue transcriptomes, RNA was extracted from whole tissues and subsequently converted to cDNA. Single neurons were processed without RNA extraction to cDNA.
cDNA was constructed with reverse transcriptase, sequencing library was made using NEBNEXT Ultra I or II Library Construction for Illumina.


title: 17_12P2_susp

description: Colorectal cancer derived sample.

tag: treatment


title: OE_seedling_Rep2

value: OE


title: Optic_Lobe_Periphery-Plexiform_One_Neuron

description:
Ob_1OptDeepRetinaCell5_3-3-J25
O_bimaculoides_TPM_NextSeqRuns

source_name: Single Neurons Isolated from dissociated nervous tissue


title: H2AK119ub1 7d oocyte rep1


title: blood_203271750007_R07C01

value: F

value: yes


title: OE_seedling_Rep1


title: blood_203271750007_R06C01


title: Brachial_Ganglion

description:
4_Ob_ArmCord-J13
O_bimaculoides_TPM_NextSeqRuns


title: WT_seedling_Rep2

value: WT


title: 16_12P1_susp

description: Colorectal cancer derived sample.


title: blood_203271750007_R04C01


title: Optic_Lobe_Deep-Medulla_One_Neuron

description:
Ob_1OptMedullaCell5_3-3-I25
O_bimaculoides_TPM_NextSeqRuns


title: blood_203271750007_R05C01


title: blood_203271750003_R07C01


title: Medial_Superior_Frontal_Lobe

description:
2_Ob_MSF-H13
O_bimaculoides_TPM_NextSeqRuns


title: T-ALL cell_control_biological rep1


title: blood_203271750007_R01C01


title: blood_203271750007_R02C01


title: 13_14P1_susp

description: Colorectal cancer derived sample.

source_name: cell line 14P


title: blood_203271750007_R03C01


title: 14_14P2_susp

description: Colorectal cancer derived sample.


title: blood_203271750003_R08C01


title: 12_9C3_susp

description: Colorectal cancer derived sample.

source_name: cell line 9C


title: 11_9C2_susp

description: Colorectal cancer derived sample.


title: Vertical_Lobe_One_Large_Efferent_Neuron

description:
Ob_1LgEff_Neuron3_3-3-G25
O_bimaculoides_TPM_NextSeqRuns


title: Vertical_Lobe_Whole_1

description:
1_Ob_VL-G13
O_bimaculoides_TPM_NextSeqRuns


title: 10_9C1_susp

description: Colorectal cancer derived sample.


title: blood_203271750003_R05C01


title: Stellate_Ganglion

description:
1_Ob_Steallate_ganglion-G14
O_bimaculoides_TPM_NextSeqRuns


title: WT_seedling_Rep1


title: 09_12P3_coll

description: Colorectal cancer derived sample.

value: collagen


title: blood_203271750003_R06C01


title: blood_203273630044_R08C01


title: 15_14P3_susp

description: Colorectal cancer derived sample.


title: Stellate_Ganglion_One_Neuron

description:
Ob_1Stell_g_cell_6_3-3-D25
O_bimaculoides_TPM_NextSeqRuns


title: Vertical_Lobe_One_Amacrine_Neuron

description:
Ob_1VL-AmNeuron6_3-3-E25
O_bimaculoides_TPM_NextSeqRuns


title: 08_12P2_coll

description: Colorectal cancer derived sample.


title: blood_203271750003_R04C01


title: 07_12P1_coll

description: Colorectal cancer derived sample.


title: Superior_Frontal_Lobe_3

description:
9E_ObRNA_101SupFr_C
O_bimaculoides_TPM_96WellPlate


title: blood_203271750003_R02C01


title: Vertical_Lobe-Medial_3

description:
9F_ObRNA_86VL-M_C
O_bimaculoides_TPM_96WellPlate


title: 05_14P2_coll

description: Colorectal cancer derived sample.


title: Retina_3

description:
9C_3926_52_R_Ret_B 6980x4
O_bimaculoides_TPM_96WellPlate

value: Retina


title: blood_203271750003_R03C01


title: blood_203271750002_R08C01


title: blood_203271750002_R06C01


title: blood_203271750003_R01C01


title: Branchial_Heart_Auricle_3

description:
9D_3921_O.bimacTissue R_Brach heart aur
O_bimaculoides_TPM_96WellPlate


title: 04_14P1_coll

description: Colorectal cancer derived sample.


title: Superior_Buccal_Lobe-Anterior_3

description:
9B_3877_6_SupBuccG_A_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: 06_14P3_coll

description: Colorectal cancer derived sample.


title: 02_9C2_coll

description: Colorectal cancer derived sample.


title: Olfactory_Lobe

description:
9A_O.bimac 117 OlfLobe_C
O_bimaculoides_TPM_96WellPlate


title: Chromatophores_2

description:
8H_3914_O.bimacTissue Blue ring chrom lavey left
O_bimaculoides_TPM_96WellPlate

value: Chromatophores


title: blood_203271750002_R07C01


title: NA20822 cell line replicate 2

city: New York

first: Jeremiah

last: Li

state: NY

address: 430 E 29th St 14th Floor, 14th Floor

institute: Gencove

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

hyb_protocol: samples were incubated at 48C overnight before undergoing enzymatic base extension and fluorescent staining

scan_protocol: the beadchips were scanned using the iScan system (Illumina)

data_processing: genomic DNA was genotyped using the Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)

label: 2D barcodes

source_name: purified gDNA

label_protocol: sample vials containing gDNA extract were stored and individually labeled with unique 2D-barcodes

extract_protocol: an automated magnetic bead purification protocol (Hamilton Microlab STAR w/ Promega ReliaPrep Isolation system) was used to extract genomic DNA that was eluted in TE buffer (pH 8.0, 1mM EDTA)


title: 03_9C3_coll

description: Colorectal cancer derived sample.


title: Stellate_Ganglion_3

description:
8G_3911_108 O.bimacTissue R_SG_C 131000x4
O_bimaculoides_TPM_96WellPlate


title: blood_203271750002_R03C01


title: blood_203271750002_R04C01


title: NA20822 cell line replicate 3


title: NA20822 cell line replicate 1


title: FL05 monoculture

city: Barcelona

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

institute: IDIBAPS

description: FL05 monoculture

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing: Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).

source_name: Follicular lymphoma cells from lymph node biopsy

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: FL were set at  2x106 cells/ml  w/wo M2 macrophages (ratio 4:1)

extract_protocol: Total RNA was extracted using the Trizol  reagent

treatment_protocol: Follicular lymphoma (FL) patient samples from lymph node biopsies were in co-culture or not with M2 macrophages (generated from healthy donors) for 48h

tag: disease

value: Follicular lymphoma

tag: protocol

value: monoculture


title: FL05+ M2 co-culture

description: FL05+ M2 co-culture

value: M2 co-cultured 48h


title: Buccal_Muscle

description:
8F_3899_BuccMusc_06.30.17_Obimac_63800x4
O_bimaculoides_TPM_96WellPlate


title: NA20821 cell line replicate 3


title: Superior_Buccal_Lobe-Anterior_2

description:
8D_3946__SupBuccG_B
O_bimaculoides_TPM_96WellPlate


title: NA20821 cell line replicate 2


title: blood_203271750002_R05C01

value: M


title: FL04 monoculture

description: FL04 monoculture


title: FL03+ M2 co-culture

description: FL03+ M2 co-culture


title: blood_203271750001_R08C01


title: Stellate_Ganglion_2

description:
8C_3928_30_L_SG_A 54100x4
O_bimaculoides_TPM_96WellPlate


title: Chromatophores_1

description:
8B_3891_81_Chr.ByRingNoBlu_B_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: blood_203271750001_R07C01


title: NA20821 cell line replicate 1


title: NA20805 cell line replicate 3


title: FL03 monoculture

description: FL03 monoculture


title: Arm_Cord-Proximal_to_Brachial_Crown_3

description:
8A_3903_57_ProxAC_B_06.30.17_Obimac_5970x4
O_bimaculoides_TPM_96WellPlate


title: Inferior_Frontal_Lobe_3

description:
7H_ObRNA_23InfFr_A
O_bimaculoides_TPM_96WellPlate


title: FL02 monoculture

description: FL02 monoculture


title: blood_203271750001_R03C01


title: 01_9C1_coll

description: Colorectal cancer derived sample.


title: NA20805 cell line replicate 2


title: NA20805 cell line replicate 1


title: blood_203271750001_R04C01


title: FL02+ M2 co-culture

description: FL02+ M2 co-culture


title: FL01 monoculture

description: FL01 monoculture


title: NA20804 cell line replicate 3


title: blood_203271750001_R01C01


title: 3dpRSta2Gut2

first: John

last: Rawls

state: NC

address: 323 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University

data_processing:
Basecalls were performed using CASAVA v1.8 (Illumina).
Fastq files were trimmed for adapter sequences using Trim galore in Galaxy (www.usegalaxy.org) (version 0.4.3.1).
Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy (version 1.1.6) to yield sorted BAM files.  Aligned reads in BAM files were counted using htseq-count in Galaxy (version 0.9.1) to generate counts files.
Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy (version 2.5.0.0) for visualization in the UCSC Genome Browser.
Counts files generated via htseq-count were used to estimate log2 fold changes in gene expression via Deseq2 (Version 3.10) in R (Version 3.6).
Genome_build: zv10

organism: Danio rerio

source_name: Intestine

growth_protocol: All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated, all fish were maintained on a 14-hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water (6g sea salt, 1.5g calcium sulfate, 0.75g sodium bicarbonate, 10-12 drops methylene blue, 10L water) at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1-day post-fertilization (dpf), embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system (system water). Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank, with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation, feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 (Skretting). Over the 21 days of starvation and 21 days of refeeding, we observed no mortality.

extract_protocol:
Frozen intestinal samples stored in Trizol at -80oC were homogenized using Zirconium oxide beads (Biospec, 11079107) and a Vortex Genie2 (Scientific Industries, 1311-V) fitted with a Vortex Adapter (Scientific Industries, 13000-V1-24) in three 45-second intervals. Samples were put on ice in-between homogenization to prevent overheating.  Following homogenization, a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube, to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation, samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set (Thermo Fisher, 12185010) and the PureLink RNA Mini kit (Thermo Fisher, 12183025) according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at -80oC until submission to the Duke Sequencing and Genomic Technologies Core.
RNA-seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 (50bp single-end read) according to the manufacturer's instructions. Prior to library preparation, RNA was extracted using the Ribozero Gold Kit (Cat #20020598) according to the manufacturer's instructions.

value: Intestine

value: Starved-Refed at 21 days

tag: tank

value: Starved tank 2

tag: age (dpf = days post-fertilization)

value: 81 dpf


title: FL01+ M2 co-culture

description: FL01+ M2 co-culture


title: FL04+ M2 co-culture

description: FL04+ M2 co-culture


title: Arm_Cord-Proximal_to_Brachial_Crown_2

description:
7F_3925_15_ProxAC_A 1460x4
O_bimaculoides_TPM_96WellPlate


title: 3dpRSta2Gut1


title: Vertical_Lobe-Medial_2

description:
7E_ObRNA_44VL-M_B
O_bimaculoides_TPM_96WellPlate


title: blood_203271750002_R02C01

data_processing: For background and dye bias correction, the preprocessNoob() function from the minfi package was applied. Additionally, we excluded 59 single nucleotide polymorphism (SNP) probes, 19,632 sex chromosome probes, 53,315 cross-reactive and polymorphic probes, 4,081 poorly performing probes (i.e. probes with a beadcount < 3 in 5% of the samples and probes with a detection p-value > 0.05 in at least 1% of the samples), and 98,983 known invariant probes (inter-quantile range (IQR, 0.1 - 0.9) < 0.02). To adjust for the bias originating from the two different bead types present on the BeadChip array, Beta-Mixture Quantile (BMIQ) normalization was performed . To reduce batch effects of different runs, chips and rows, the ComBat() function was applied. The estimateCellCounts.wmln() function from the wateRmelon package was used to estimate the relative proportions of monocytes, granulocytes, CD4+ and CD8+ T cells, B cells and natural killer cells. Adjustment for cell type composition was done by using the statistical estimates in a regression-based approach.

value: no


title: NA20804 cell line replicate 1


title: 3dpRSta1Gut3

value: Starved tank 1


title: NA20803 cell line replicate 3


title: 3dpRSta1Gut1


title: Sub-Esophageal-Middle

description:
7C_3944__SubEsoMid_A
O_bimaculoides_TPM_96WellPlate

value: Sub-Esophageal-Middle


title: 3dpRFed2Gut3

value: Continuously fed

value: Fed tank 2


title: Supra-Esophageal_Lobes-Remaining_Basal_and_Subfrontal_3

description:
7D_3929_71_SupEsoRest_B 14200x4
O_bimaculoides_TPM_96WellPlate


title: NA20803 cell line replicate 2


title: NA20803 cell line replicate 1


title: Hectocotylus

description:
7B_S109 ObTiss Hect_C
O_bimaculoides_TPM_96WellPlate

value: Hectocotylus


title: 3dpRFed2Gut2


title: blood_203271750002_R01C01

value: F

value: yes


title: blood_203271750001_R02C01


title: blood_203271750007_R08C01


title: Dorsal_Basal_Lobe_3

description:
7A_3882_28_Dorsal Basal_A_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: 3dpRFed1Gut3

value: Fed tank 1


title: NA20802 cell line replicate 3


title: NCCIT_DAC_NUGEN_OxBS_1

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files for each sample were processed using the Bioconductor package “SeSAMe” (Version 1.2.0) for extraction of probe signal intensity values, normalization of probe signal intensity values, and calculation of β-values from the normalized probe signal intensity values. CpG probes with a detection p-value > 0.05 in any one sample were excluded from the analysis.

label: Cy5 and Cy3

source_name: NCCIT pluripotent embryonal carcinoma

label_protocol: Standard Illumina protocol

growth_protocol: NCCIT cells were grown in RPMI media supplemented with 10% FBS and antibiotics (P/S). Cell culturing utilized standard laboratory practices and cells were grown and incubated at 37°C containing 5% CO2. Cells were treated with 1X PBS, 1 mM 5'aza-2'deoxycytidine (DAC), or 1 mM DAC plus 57 mM Vitamin C (VitC). DAC treated cells were pulsed with DAC for 24 hours and then with 1X PBS for the remaining 48 hours. VitC treated cells were treated every 24 hours. Cells were harvested at 72 hours post initial treatments.

extract_protocol: Cells were lysed overnight at 37°C in 2 mls of TE-SDS buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 0.5% SDS), supplemented with 100 μl of 20 mg/ml proteinase K. DNA was purified by phenol:chloroform extraction in three phases: (1) 100% phenol, (2) phenol:chloroform:isoamyl alcohol (25:24:1), and (3) chloroform:isoamyl alcohol (24:1). For each phase, the aqueous layer was combined with the organic layer in a 1:1 ratio. Samples were quickly shaken, allowed to sit on ice for approximately 5 minutes, and then separated by centrifugation at 1,693 RCF for 5 minutes at 4°C. The top aqueous layer was then transferred to a new tube for the next organic phase. Following extraction, DNA was precipitated with 1/10 volume 3 M sodium acetate pH 4.8 and 2.5 volumes 100% ethanol and stored overnight at -20°C. Precipitated DNA was pelleted by centrifugation at 17,090 RCF for 30 minutes at 4°C. The pelleted DNA was washed twice with 70% ethanol, allowed to dry for 15 minutes, and resuspended in TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Samples were then treated with 1 mg/ml RNAse A at 37°C for 30 minutes and then re-purified by ethanol precipitation as described above.

treatment_protocol: Extracted gDNA was converted with upstream modifications to bisulfite conversion to aid in distinguishing 5mC from 5hmC. Tet-assisted bisulfite (TAB) conversion was done to observe 5hmC, oxidative bisulfite (OxBS) conversion was done to observe 5mC,  and bisulfite conversion (BS) was done to observe both 5mC and 5hmC. ZYMO indicates bisulfite conversion was done with the ZYMO EZ DNA methylation kit (Catalog #:D5001) and NUGEN indicates bisulfite conversion was done with NuGEN TrueMethyl oxBS Module, Tecan Genomics, Inc. (Catalog #: 0414-32).

value: 1 mM 5'aza-2'deoxycytidine OxBS


title: Vertical_Lobe-Mediolateral-Left_3

description:
6H_ObRNA_46VL-LfML_B
O_bimaculoides_TPM_96WellPlate


title: NA20802 cell line replicate 2


title: Gill

description:
6G_O.bimac 126 Gill_C
O_bimaculoides_TPM_96WellPlate

value: Gill


title: 21dpSSta2Gut3

value: Starved


title: blood_203271750001_R06C01

institute: University of Tuebingen


title: NCCIT_NoTx_NUGEN_OxBS_1

value: NoTx OxBS


title: Branchial_Heart_Ventricle_3

description:
7G_3932__Brachial heart Ventricle 16.7x4
O_bimaculoides_TPM_96WellPlate


title: 3dpRFed1Gut2

value: Intestine


title: NA20802 cell line replicate 1

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: Optic_Lobe_Deep-Medulla_2

description:
6F_3886_51_L_OLDeep_B_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: NA20798 cell line replicate 3


title: blood_203271750001_R05C01


title: 21dpSSta2Gut2


title: Vertical_Lobe-Lateral-Right_3

description:
6E_ObRNA_85VL-RtLL_C
O_bimaculoides_TPM_96WellPlate


title: NA20798 cell line replicate 2


title: 21dpsSta2Gut1


title: Vertical_Lobe-Lateral-Left_3

description:
6D_5_ObA_VL.Lft.Mediolateral (Actually Lat Lat)
O_bimaculoides_TPM_96WellPlate


title: 21dpSSta1Gut2


title: Vertical_Lobe-Mediolateral-Right_3

description:
6C_3_ObA_VL.Rt.Mediolateral
O_bimaculoides_TPM_96WellPlate


title: 21dpSFed2Gut3


title: NA20514 cell line replicate 3


title: NCCIT_DAC_ZYMO_TAB_2

value: 1 mM 5'aza-2'deoxycytidine TAB


title: NA20804 cell line replicate 2


title: Vertical_Lobe-Mediolateral-Left_2

description:
6B_4_ObA_VL.Lft.Mediolateral
O_bimaculoides_TPM_96WellPlate


title: NCCIT_DAC_NUGEN_BS_1

value: 1 mM 5'aza-2'deoxycytidine NUGEN


title: NCCIT_NoTx_NUGEN_BS_1

value: NoTx NUGEN


title: NA20798 cell line replicate 1


title: 21dpsFed2Gut1

value: 81 dpf


title: NCCIT_DACVitC_ZYMO_TAB_1

value: 1 mM 5'aza-2'deoxycytidine 57 mM Vitamin C TAB


title: NA20514 cell line replicate 2


title: NCCIT_DACVitC_ZYMO_TAB_2


title: Arm_Cord-Near_tip

description:
6A_3904_60_DistAC_B_06.30.17_Obimac_8650x4
O_bimaculoides_TPM_96WellPlate


title: 21dpSFed1Gut3


title: NA20514 cell line replicate 1


title: NCCIT_DACVitC_NUGEN_OxBS_1

value: 1 mM 5'aza-2'deoxycytidine 57 mM Vitamin C OxBS


title: NCCIT_DAC_ZYMO_TAB_1


title: Arm_Cord-Proximal_to_Brachial_Crown_1

description:
5G_S99 ObTiss ProxAC_C
O_bimaculoides_TPM_96WellPlate


title: NCCIT_NoTx_ZYMO_TAB_2

value: NoTx TAB


title: NA20513 cell line replicate 1


title: 3dpSSta1Gut2

value: Starved tank 1


title: 21dpSFed1Gut1

value: Continuously fed


title: Superior_Buccal_Lobe-Anterior_1

description:
5F_3947__SupBuccG_C
O_bimaculoides_TPM_96WellPlate


title: Vertical_Lobe-Lateral-Left_2

description:
5E_ObRNA_89VL-lFLL_C
O_bimaculoides_TPM_96WellPlate


title: 3dpSSta2Gut2

value: Starved tank 2


title: Supra-Esophageal_Lobes-Remaining_Basal_and_Subfrontal_2

description:
5D_3901_29_SupEsoRest_A_06.30.17_Obimac_26600x4
O_bimaculoides_TPM_96WellPlate


title: Salivary_Gland-Posterior_2

description:
5H_O.bimac 118 PostSalGl_C
O_bimaculoides_TPM_96WellPlate


title: NA20513 cell line replicate 2


title: NCCIT_NoTx_ZYMO_TAB_1


title: NA20507 cell line replicate 2


title: Supra-Esophageal_Lobes-Remaining_Basal_and_Subfrontal_1

description:
5C_O.bimac 113 SupEsoRest_C
O_bimaculoides_TPM_96WellPlate


title: NCCIT_DACVitC_ZYMO_BS_2

value: 1 mM 5'aza-2'deoxycytidine 57 mM Vitamin C ZYMO


title: NCCIT_DAC_ZYMO_BS_2

value: 1 mM 5'aza-2'deoxycytidine ZYMO


title: NCCIT_DACVitC_ZYMO_BS_1


title: 3dpSFed2Gut3

value: Fed tank 2


title: NA20507 cell line replicate 1


title: NA20513 cell line replicate 3


title: 3dpSSta2Gut3


title: White_Body

description:
5B_3950_ White Body 1
O_bimaculoides_TPM_96WellPlate


title: 3dpSSta1Gut1


title: 3dpSFed2Gut2


title: NCCIT_NoTx_ZYMO_BS_1

value: NoTx ZYMO


title: Inferior_Frontal_Lobe_2

description:
5A_ObRNA_65InfFr_B
O_bimaculoides_TPM_96WellPlate


title: 3dpSFed1Gut1

value: Fed tank 1


title: Gonad-Female_(Ova)

description:
4H_3957_ Female Gonad (Ova)2
O_bimaculoides_TPM_96WellPlate


title: NCCIT_DAC_ZYMO_BS_1


title: NA20503 cell line replicate 2


title: NA20503 cell line replicate 1


title: Dorsal_Basal_Lobe_2

description:
4G_S112 ObTiss DorsBas_C
O_bimaculoides_TPM_96WellPlate


title: NA20507 cell line replicate 3

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: Sub-Vertical_Lobe_3

description:
4D_22_ObA_SubVL
O_bimaculoides_TPM_96WellPlate


title: NA20503 cell line replicate 3


title: NCCIT_DACVitC_NUGEN_BS_1

value: 1 mM 5'aza-2'deoxycytidine 57 mM Vitamin C NUGEN


title: NA20502 cell line replicate 1


title: Superior_Frontal_Lobe_2

description:
4E_ObRNA_59SupFr_B
O_bimaculoides_TPM_96WellPlate


title: NA20502 cell line replicate 3


title: NCCIT_NoTx_ZYMO_BS_2


title: NA20502 cell line replicate 2


title: Vertical_Lobe-Mediolateral-Left_1

description:
4C_ObRNA_88VL-LfML_C
O_bimaculoides_TPM_96WellPlate


title: NA20412 cell line replicate 3


title: Sub-Esophageal_Lobe-Posterior

description:
4B_3902_56_SubEsoPost_B_06.30.17_Obimac_7190x4
O_bimaculoides_TPM_96WellPlate


title: NA20412 cell line replicate 2


title: Vertical_Lobe-Lateral-Right_2

description:
4A_ObRNA_43VL-RtLL_B
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from placenta sample GDM-049

city: Toronto

first: Zain

last: Awamleh

address: 686 Bay street

country: Canada

institute: Sickkids

description: gestational diabetes mellitus (diabetes in pregnancy)

hyb_protocol: bisulphite converted DNA was converted using EpiTect PLUS Bisulfite Kit, QIAGEN and hybridised to Illumina Infinium 450K Beadchip using standard Illumina protocol

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

data_processing: minfi Bioconductor package

source_name: human placenta

extract_protocol: Genomic DNA was extracted using standard phenol-chloroform methods

tag: disease status

value: GDM


title: NA20412 cell line replicate 1


title: Genomic DNA from placenta sample GDM-047


title: Genomic DNA from placenta sample GDM-048


title: Peruvian, NTL Patient, 188

city: Toulouse

first: Juan Pablo

last: Cerapio

address: Av 2 Hubert Curien

institute: CRCT

hyb_protocol: Oxidative-bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol.

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

data_processing: Noob (normal-exponential out-of-band) normalization.

label: Cy3, Cy5

source_name: Peruvian NTL tissue from Patient 188

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted twice with phenol and once with chloroform, precipitated in ethanol, and resuspended in TE buffer (10 mM Tris; 0.1 mM EDTA; pH 8.0).

treatment_protocol: Sampling protocol: about 50 mg of HCC, as well as NTL from tumor-free margins of the resected surgical pieces, were harvested, flash-frozen in liquid nitrogen, and kept at -150°C for long-term storage.

value: non-tumor liver

tag: disease state

value: hepatocellular carcinoma (HCC)

tag: subject id

value: Patient 188

tag: gender

value: Female

tag: hbv

value: Negative

tag: mtdna haplotypes

value: B


title: NA20362 cell line replicate 3


title: Peruvian, NTL Patient, 190

source_name: Peruvian NTL tissue from Patient 190

value: Patient 190

tag: age

value: Positive

value: A


title: Peruvian, NTL Patient, 200

source_name: Peruvian NTL tissue from Patient 200

value: Patient 200

value: Male

value: D


title: Systemic_Heart-Output

description:
3E_3920_O.bimacTissue Systemic heart output
O_bimaculoides_TPM_96WellPlate


title: Peruvian, NTL Patient, 180

source_name: Peruvian NTL tissue from Patient 180

value: Patient 180


title: NA20362 cell line replicate 2


title: Systemic_Heart-Intake

description:
3G_3916_O.bimacTissue Systemic heart intake
O_bimaculoides_TPM_96WellPlate


title: Peruvian, NTL Patient, 120

source_name: Peruvian NTL tissue from Patient 120

value: Patient 120


title: Genomic DNA from placenta sample GDM-044


title: Peruvian, NTL Patient, 179

source_name: Peruvian NTL tissue from Patient 179

value: Patient 179

value: C


title: Genomic DNA from placenta sample GDM-045

value: GDM


title: Peruvian, NTL Patient, 201

source_name: Peruvian NTL tissue from Patient 201

value: non-tumor liver

value: Patient 201


title: NA20362 cell line replicate 1


title: Optic_Lobe_Deep-Medulla_1

description:
3C_3884_49_R_OLDeep_B_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from placenta sample GDM-042


title: Peruvian, NTL Patient, 117

source_name: Peruvian NTL tissue from Patient 117

value: hepatocellular carcinoma (HCC)

value: Patient 117


title: Peruvian, NTL Patient, 121

source_name: Peruvian NTL tissue from Patient 121

value: Patient 121

value: Female

value: Negative


title: Optic_Gland

description:
3A_S111 ObTiss OpticGl_C
O_bimaculoides_TPM_96WellPlate

source_name: RNA extracted from whole tissue


title: NA20359 cell line replicate 2


title: Skin

description:
2G_3934__Skin 2050x4
O_bimaculoides_TPM_96WellPlate

value: Skin


title: NA20359 cell line replicate 1


title: Peruvian, NTL Patient, 116

source_name: Peruvian NTL tissue from Patient 116

value: Patient 116

value: B


title: Vertical_Lobe-Lateral-Left_1

description:
3D_ObRNA_47VL-lFLL_B
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from placenta sample GDM-041


title: Genomic DNA from placenta sample GDM-043


title: Genomic DNA from placenta sample GDM-040

description: normal glucose tolerance pregnancy

value: NGT


title: NA20357 cell line replicate 3


title: Aorta

description:
2E_3897_Aorta_06.30.17_Obimac_6130x4
O_bimaculoides_TPM_96WellPlate

value: Aorta


title: Genomic DNA from placenta sample GDM-037


title: Peruvian, NTL Patient, 104

source_name: Peruvian NTL tissue from Patient 104

value: Patient 104

value: Male

value: Positive

value: A


title: Peruvian, NTL Patient, 106

source_name: Peruvian NTL tissue from Patient 106

value: Patient 106

value: D


title: Peruvian, NTL Patient, 100

source_name: Peruvian NTL tissue from Patient 100

value: non-tumor liver

value: Patient 100


title: NA20357 cell line replicate 2

source_name: purified gDNA


title: Peruvian, NTL Patient, 109

source_name: Peruvian NTL tissue from Patient 109

value: hepatocellular carcinoma (HCC)

value: Patient 109


title: Genomic DNA from placenta sample GDM-035

description: normal glucose tolerance pregnancy

source_name: human placenta


title: Peruvian, NTL Patient, 095

source_name: Peruvian NTL tissue from Patient 095

value: Patient 095


title: Systemic_Heart-Clear_Vessel

description:
2D_3919_O.bimacTissue Systemic heart clear vessel
O_bimaculoides_TPM_96WellPlate


title: NA20351 cell line replicate 3


title: NA20357 cell line replicate 1


title: Peruvian, NTL Patient, 092

source_name: Peruvian NTL tissue from Patient 092

value: Patient 092

value: Negative


title: NA20359 cell line replicate 3


title: Genomic DNA from placenta sample GDM-034

description: normal glucose tolerance pregnancy


title: Superior_Frontal_Lobe_1

description:
2B_ObRNA_17SupFr_A
O_bimaculoides_TPM_96WellPlate


title: NA20351 cell line replicate 2


title: Genomic DNA from placenta sample GDM-046

value: GDM


title: Genomic DNA from placenta sample GDM-033


title: Inferior_Buccal_Ganglion

description:
2A_S90 ObTiss InfBuccG_C
O_bimaculoides_TPM_96WellPlate


title: Peruvian, NTL Patient, 088

source_name: Peruvian NTL tissue from Patient 088

value: Patient 088

value: B


title: Peruvian, NTL Patient, 091

source_name: Peruvian NTL tissue from Patient 091

value: Patient 091


title: Optic_Lobe_Periphery-Plexiform_3

description:
2F_O.bimac 121 R_OLPeriph_C
O_bimaculoides_TPM_96WellPlate


title: Sucker-Large

description:
2C_3898_LgSucker_06.30.17_Obimac_48800x4
O_bimaculoides_TPM_96WellPlate

value: Sucker-Large


title: NA20320 cell line replicate 3

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: Dorsal_Basal_Lobe_1

description:
1H_3888_70_DorsBas_B_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: Mantle

description:
1G_S104 ObTiss Mantle_C
O_bimaculoides_TPM_96WellPlate

value: Mantle


title: Genomic DNA from placenta sample GDM-038

description: normal glucose tolerance pregnancy

value: NGT


title: NA20320 cell line replicate 2


title: Genomic DNA from placenta sample GDM-030

description: normal glucose tolerance pregnancy


title: Peruvian, NTL Patient, 083

source_name: Peruvian NTL tissue from Patient 083

value: Patient 083

value: Male


title: Peruvian, NTL Patient, 101

source_name: Peruvian NTL tissue from Patient 101

value: Patient 101

value: Positive

value: C


title: Gonad-Male

description:
1F_O.bimac 120 MALE Gonad_C
O_bimaculoides_TPM_96WellPlate

value: Gonad-Male


title: NA20320 cell line replicate 1


title: Genomic DNA from placenta sample GDM-031

description: normal glucose tolerance pregnancy


title: Optic_Lobe_Periphery-Plexiform_2

description:
1E_3885_50_L_OLPeriph_B_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: Peruvian, NTL Patient, 093

source_name: Peruvian NTL tissue from Patient 093

value: non-tumor liver

value: hepatocellular carcinoma (HCC)

value: Patient 093


title: Peruvian, NTL Patient, 099

source_name: Peruvian NTL tissue from Patient 099

value: Patient 099

value: Female

value: D


title: NA20351 cell line replicate 1


title: NA20298 cell line replicate 3


title: Sub-Vertical_Lobe_2

description:
1D_3887_64_SUBVL_B_06.29.17_Obimac_35900x4
O_bimaculoides_TPM_96WellPlate


title: NA20298 cell line replicate 2


title: Stellate_Ganglion_1

description:
1C_3930_72_L_SG_B 868x4
O_bimaculoides_TPM_96WellPlate


title: NA20298 cell line replicate 1


title: Branchial_Heart_Ventricle_2

description:
1A_3912_O.bimacBrHeartVent
O_bimaculoides_TPM_96WellPlate


title: NA19984 cell line replicate 3


title: Genomic DNA from placenta sample GDM-029

description: normal glucose tolerance pregnancy


title: Genomic DNA from placenta sample GDM-028

description: gestational diabetes mellitus (diabetes in pregnancy)

value: GDM


title: Esophagus

description:
12H_3896_Esoph_06.30.17_Obimac_65100x4
O_bimaculoides_TPM_96WellPlate

value: Esophagus


title: Genomic DNA from placenta sample GDM-026


title: NA19984 cell line replicate 2


title: Optic_Lobe_Deep-Medulla_3

description:
12G_S91 ObTiss R_OLDeep_C
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from placenta sample GD-023

description: normal glucose tolerance pregnancy


title: Peruvian, NTL Patient, 054

source_name: Peruvian NTL tissue from Patient 054

value: Patient 054


title: NA19984 cell line replicate 1


title: Genomic DNA from placenta sample GDM-025


title: Systemic_Heart

description:
12F_O.bimac 124 SystHeart_C
O_bimaculoides_TPM_96WellPlate

source_name: RNA extracted from whole tissue


title: Genomic DNA from placenta sample GDM-024


title: Peruvian, NTL Patient, 047

source_name: Peruvian NTL tissue from Patient 047

value: Patient 047


title: Peruvian, NTL Patient, 034

source_name: Peruvian NTL tissue from Patient 034

value: Patient 034

value: A


title: Peruvian, NTL Patient, 070

source_name: Peruvian NTL tissue from Patient 070

value: Patient 070

value: Male

value: B


title: Genomic DNA from placenta sample GDM-020

description: normal glucose tolerance pregnancy

value: NGT


title: Genomic DNA from placenta sample GDM-022


title: NA19923 cell line replicate 3


title: Genomic DNA from placenta sample GDM-021


title: NA19923 cell line replicate 2


title: Sub-Esophageal_Lobe-Anterior

description:
12D_3893_12_SubEsoAnt_A_06.30.17_Obimac_67800x10
O_bimaculoides_TPM_96WellPlate


title: Retina_1

description:
12C_S95 ObTiss L_Ret_C
O_bimaculoides_TPM_96WellPlate

value: Retina


title: Peruvian, NTL Patient, 025

source_name: Peruvian NTL tissue from Patient 025

value: non-tumor liver

value: Patient 025

value: Positive


title: NA19923 cell line replicate 1

source_name: purified gDNA


title: Salivary_Gland-Posterior_1

description:
12B_3907_34 O.bimacTissue PostSalGl_A
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from placenta sample GDM-018


title: NA19922 cell line replicate 3


title: Branchial_Heart_Auricle_2

description:
12A_3918_O.bimacTissue L_Brach heart aur
O_bimaculoides_TPM_96WellPlate


title: NA19922 cell line replicate 2


title: Genomic DNA from placenta sample GDM-017


title: Vertical_Lobe-Mediolateral-Right_2

description:
11G_ObRNA_45VL-RtML_B
O_bimaculoides_TPM_96WellPlate


title: Peruvian, NTL Patient, 015

source_name: Peruvian NTL tissue from Patient 015

value: hepatocellular carcinoma (HCC)

value: Patient 015


title: Peruvian, NTL Patient, 026

source_name: Peruvian NTL tissue from Patient 026

value: Patient 026


title: Genomic DNA from placenta sample GDM-013

description: normal glucose tolerance pregnancy

source_name: human placenta


title: Genomic DNA from placenta sample GDM-011

description: normal glucose tolerance pregnancy


title: Peruvian, NTL Patient, 068

source_name: Peruvian NTL tissue from Patient 068

value: Patient 068

value: C


title: NA19914 cell line replicate 3

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: Genomic DNA from placenta sample GDM-016

value: GDM


title: NA19914 cell line replicate 2


title: Vertical_Lobe-Lateral-Right_1

description:
11E_1_ObA_VL.Rt.LateralLateral
O_bimaculoides_TPM_96WellPlate


title: Salivary_Gland-Anterior_2

description:
11D_O.bimac 38 AntSalGl_A    305000x2
O_bimaculoides_TPM_96WellPlate


title: Peruvian, HCC Patient, 190

source_name: Peruvian HCC tissue from Patient 190

value: hepatocellular carcinoma

value: Patient 190

value: Female


title: Peruvian, HCC Patient, 201

source_name: Peruvian HCC tissue from Patient 201

value: Patient 201

value: Negative

value: D


title: Vertical_Lobe-Mediolateral-Right_1

description:
11F_3892_87_VL-RtML_C_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from placenta sample GDM-009

description: normal glucose tolerance pregnancy

value: NGT


title: Genomic DNA from placenta sample GDM-004

description: normal glucose tolerance pregnancy


title: Peruvian, HCC Patient, 179

source_name: Peruvian HCC tissue from Patient 179

value: Patient 179

value: Male


title: Sucker-Small

description:
11C_3900_SmSucker_06.30.17_Obimac_1770x4
O_bimaculoides_TPM_96WellPlate

value: Sucker-Small


title: Genomic DNA from placenta sample GDM-012

description: normal glucose tolerance pregnancy


title: Peruvian, HCC Patient, 120

source_name: Peruvian HCC tissue from Patient 120

value: Patient 120

value: Positive

value: B


title: NA19914 cell line replicate 1


title: NA19922 cell line replicate 1


title: NA19625 cell line replicate 3


title: NA19625 cell line replicate 2


title: Peruvian, HCC Patient, 200

source_name: Peruvian HCC tissue from Patient 200

value: hepatocellular carcinoma (HCC)

value: Patient 200


title: Peruvian, NTL Patient, 004

source_name: Peruvian NTL tissue from Patient 004

value: non-tumor liver

value: Patient 004


title: Genomic DNA from cord blood sample GDM.063

source_name: cord blood sample GDM.063

value: GDM


title: Sub-Vertical_Lobe_1

description:
11A_ObRNA_106SUBVL_C
O_bimaculoides_TPM_96WellPlate

source_name: RNA extracted from whole tissue


title: Peruvian, HCC Patient, 121

source_name: Peruvian HCC tissue from Patient 121

value: hepatocellular carcinoma

value: Patient 121


title: NA19625 cell line replicate 1


title: Peruvian, HCC Patient, 109

source_name: Peruvian HCC tissue from Patient 109

value: Patient 109


title: Peruvian, HCC Patient, 116

source_name: Peruvian HCC tissue from Patient 116

value: Patient 116

value: Negative


title: Blood

description:
10H_3952_Blood- Blood Vessel
O_bimaculoides_TPM_96WellPlate

value: Blood


title: NA19471 cell line replicate 3


title: Genomic DNA from placenta sample GDM-003

description: normal glucose tolerance pregnancy

value: NGT


title: Genomic DNA from placenta sample GDM-002

description: normal glucose tolerance pregnancy


title: NA19471 cell line replicate 2


title: Arm_Tip

description:
10F_O.bimac 119 TentTip_C   25900x2
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from cord blood sample GDM.060

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.060


title: Inferior_Frontal_Lobe_1

description:
10E_ObRNA_107InfFr_C
O_bimaculoides_TPM_96WellPlate


title: Peruvian, HCC Patient, 180

source_name: Peruvian HCC tissue from Patient 180

value: Patient 180

value: Male


title: Genomic DNA from cord blood sample GDM.057

description: gestational diabetes mellitus (diabetes in pregnancy)

source_name: cord blood sample GDM.057


title: NA19351 cell line replicate 3

source_name: purified gDNA


title: Genomic DNA from cord blood sample GDM.058

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.058


title: Retina_2

description:
10G_S94 ObTiss R_Ret_C
O_bimaculoides_TPM_96WellPlate

value: Retina


title: Branchial_Heart_Ventricle_1

description:
10D_3913_O.bimacTissue R_Brach Heart vent (Actually Left) 76900x4
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from cord blood sample GDM.056

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.056


title: Peruvian, HCC Patient, 106

source_name: Peruvian HCC tissue from Patient 106

value: Patient 106

value: Positive

value: D


title: Vertical_Lobe-Medial_1

description:
11B_2_ObA_VL.Medial
O_bimaculoides_TPM_96WellPlate


title: Genomic DNA from cord blood sample GDM.062

source_name: cord blood sample GDM.062


title: Peruvian, HCC Patient, 099

source_name: Peruvian HCC tissue from Patient 099

value: hepatocellular carcinoma (HCC)

value: Patient 099

value: Female


title: Peruvian, HCC Patient, 117

source_name: Peruvian HCC tissue from Patient 117

value: Patient 117

value: B


title: Optic_Lobe_Periphery-Plexiform_1

description:
10C_3879_8_L_OLPeriph_A_06.29.17_Obimac
O_bimaculoides_TPM_96WellPlate


title: Branchial_Heart_Auricle_1

description:
10B_3933__Brachial heart Auricle
O_bimaculoides_TPM_96WellPlate


title: NA19471 cell line replicate 1


title: Salivary_Gland-Anterior_1

description:
10A_O.bimac 122 AntSalGl_C
O_bimaculoides_TPM_96WellPlate


title: Peruvian, HCC Patient, 100

source_name: Peruvian HCC tissue from Patient 100

value: hepatocellular carcinoma

value: Patient 100


title: Peruvian, HCC Patient, 188

source_name: Peruvian HCC tissue from Patient 188

value: Patient 188


title: NA19351 cell line replicate 1


title: NA19351 cell line replicate 2


title: NA19350 cell line replicate 3


title: NA19350 cell line replicate 2


title: Peruvian, HCC Patient, 093

source_name: Peruvian HCC tissue from Patient 093

value: Patient 093

value: Negative

value: C


title: Peruvian, HCC Patient, 101

source_name: Peruvian HCC tissue from Patient 101

value: Patient 101


title: NA19350 cell line replicate 1


title: NA19310 cell line replicate 3


title: no_treat

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Bulk-RNA Seq

data_processing:
Single-Cell RNA Dataset : Chromium barcodes were used for demultiplexing and FASTQ files were generated using the Cellranger(Zheng et al. 2017) mkfastq pipeline. Alignment, filtering and UMI counting were performed using cellranger count. To improve detection of microglia, due to their low RNA content, cellranger reanalyse was used with the --force-cells option set at the inflection point when number of barcodes is plotted against the number of UMIs. Cells were manually filtered such that barcodes containing at least 10 counts corresponding to Cx3cr1, P2ry12 or Fcrls genes were classified as microglia, resulting in a total of 991 cells from the 4 FACS-sorted microglial populations.
Bulk RNA Dataset : Sequencing reads for the murine microglia dataset were sample demultiplexed with Je demultiplex from the JE suite using sequence barcodes in Supplementary table 11. Short sequence unique molecular identifiers (UMIs) from read pair 1 of the demultiplexed sample sequencing reads were discarded from both sequencing read pairs with Prinseq (minimum length 9). Remaining UMIs were clipped with Je clip and added to the sequencing read header to allow UMI deduplication post read mapping. Demultiplexed UMI tagged sequencing reads were filter-trimmed with Trimmomatic and aligned to the mouse genome (GENCODE's GRCm38 primary assembly annotation version vM15) using STAR(only sequencing reads from pair 2 were used for transcript quantification). Read deduplication based on UMIs was performed with Je MarkDupes and transcript read counts calculated with featureCounts. For the in vitro bulk sequencing dataset, demultiplexing was performed as we recently described (Grubman, A. et al. A CX3CR1 Reporter hESC Line Facilitates Integrative Analysis of In-Vitro-Derived Microglia and Improved Microglia Identity upon Neuron-Glia Co-culture. Stem Cell Reports (2020) doi:10.1016/j.stemcr.2020.04.007.) . In short, we used in-house pipelines including a fork of sabre tools (https://github.com/serine/sabre), and demultiplexed UMI-tagged sequencing reads were aligned to the human genome (Ensembl GRCh38 primary assembly) using RNAsik
Genome_build: GRCm38

source_name: iMGLs no treatment

extract_protocol: Libraries were made by individual first strand synthesis which addsthe index sequences indicated above.10ngof each total RNA sample was used as starting material. Following first strand synthesis cDNA of each set was pooled for subsequent processing.2.Final library pool wasQC’d by Qubit, Bioanalyzer and qPCR.Thelibrary poolswerewith mean size of ~330bp at a concentration of ~7.5nM.3.For sequencing, following denaturation 2.2pM of each library pool was clustered on a high output NextSeq run based upon previous results with this type of sample.  4.Clustering density was slightly abovetheoptimal rangefor bothrunsat ~260k/mm2 (optimal 170-230k/mm2). Thenumberof reads passing filter for each run was excellentat ~490million. Percentage of reads >Q30 was good for bothsets with 90% >Q30 for R1 and 75% >Q30 for R2.5.Library is designed so custom R1 primer reads directly into index followed by 10bp UMI.  6.R2 primer reads into RNA in the sense direction and will be best for transcript identification.7.Data is provided as 2matching Fastq files for R1 and R2. No deconvolution has been performed.  These are named using the convention Name_SampleNumber_ReadNumber.  Fastqc files are also provided.

value: iMGL


title: Rap+hTLR1

description: Bulk-RNA Seq

source_name: iMGLs treated with TLR1 and Rapamycin


title: NA19310 cell line replicate 2


title: Genomic DNA from cord blood sample GDM.042

source_name: cord blood sample GDM.042

value: GDM


title: Peruvian, HCC Patient, 091

source_name: Peruvian HCC tissue from Patient 091

value: Patient 091

value: Male

value: A


title: ChIP-seq_Pla-B1h_CycT1_rep2

city: Göttingen

first: Sara

middle: Patricia

last: Monteiro Martins

address: Fassberg 11

department: Molecular Biology

institute: MPI for biophysical chemistry

data_processing:
TT-seq and RNA-seq: Paired-end 75 and 150 bp reads with additional 6 bp of barcodes were obtained for each group of samples. Two replicates were treated with Pladienolide B (Pla-B) and two replicates treated with a control solvent (DMSO). Reads were aligned to the hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium) using STAR 2.6.0 (Dobin et al., 2013), with the following specifications: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0 and alignIntronMax 500000. Bam files were filtered with Samtools (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Expressed transcripts were defined as possessing more than 50 read counts per kilobase (RPK) in two summarized replicates of TT-seq solvent control (DMSO). Prior to quantification, data was normalized by using added RNA spike-in as described previously (Schwalb et al., 2016)
mNET-seq: Paired-end 42 bp reads with additional 6 bp of barcodes were obtained for each of the samples. Reads were trimmed for adapter content with Cutadapt (1.18, RRID:SCR_011841) (Martin, 2011) with -O 12 -m 25 -a TGGAATTCTCGG -A GATCGTCGGACT. mNET-seq data was normalized using S. cerevisiae RNA spike-ins. To this end, a combined genome was generated using the Ensemble genome assembly for both human hg38 (GRCh38) and S. cerevisiae (R64-1-1), against which the reads were mapped using STAR (2.6.0, RRID:SCR_015899) (Dobin et al., 2013). Around 80% and 20% of reads mapped to the human and S. cerevisiae genomes, respectively. Bam files were filtered with Samtools (1.3.1, RRID:SCR_002105) (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Read counts for different features were calculated with HTSeq (0.6.1.p1, RRID:SCR_005514) (Anders et al., 2015). Further data processing was carried out using the R/Bioconductor environment. Antisense bias ratio was determined using positions in regions without antisense annotation with a coverage of at least 100 according to the defined major isoforms. Data was normalized using added S. cerevisiae RNA spike-ins. mNETs-seq coverage was normalized with a median of ratios method (Love et al., 2014) using the antisense corrected counts for S. cerevisiae transcripts with an RPK of 100 or higher in two summarized replicates of mNET-seq solvent control (DMSO).
ChIP-seq: Paired-end 42 or 75 bp reads with additional 6 bp of barcodes were obtained for each of the samples. Reads were aligned using Bowtie 2 (2.3.5, RRID:SCR_005476) (Langmead and Salzberg, 2012) to both human hg38 (GRCh38) and D. melanogaster (BDGP6.28). Bam files were filtered with Samtools (1.3.1, RRID:SCR_002105) (Li et al., 2009) to remove alignments with MAPQ smaller than 7 (-q 7) and only proper pairs (-f2) were selected. Further data processing was carried out using the R/Bioconductor environment. ChIP-seq coverages were obtained from piled-up counts for every genomic position, using physical coverage, that is, counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads. Data was normalized using added D. melanogaster RNA spike-ins. Normalization factors were obtained by dividing the total D. melanogaster read counts for each sample by the total read counts of the sample with the lowest read counts. ChIP-seq coverages were divided by the respective normalization factors.
Major isoform annotation: Salmon (0.13.1, RRID:SCR_017036) (Patro et al., 2017) was used in order to select the major isoforms present in our dataset. RNA-seq samples for 1 h DMSO or 1 uM Pla-B treatments were mapped against curated RefSeq annotated protein-coding isoforms (UCSC RefSeq GRCh38, downloaded in April 2019). For each gene, the major isoform was determined as the one with maximum mean Transcripts Per Million (TPM) value across all RNA-seq samples. Major isoforms were excluded from further analysis if they represented less than 70 % of the gene isoforms based on the calculated mean TPM value. Additionally, major isoforms associated with overlapping genes as well as isoforms located on chromosomes X, Y and M were discarded from further analysis. The final major isoform annotation includes 6,694 isoforms containing 65,976 exons and 59,282 introns.  A total of 5,535 major transcript isoforms of protein-coding genes with RPK >= 50 of TT-seq solvent control (DMSO) were included in the analysis.
Intronless genes annotation: Intronless genes were defined as RefSeq annotated genes comprising one single isoform with one single exon. To avoid effects from neighboring intron-containing genes, only intronless genes at least 1 kb distant from the neighboring intron-containing annotated transcripts (strand independent) were included in the analysis. Moreover, because a long 3Â´ UTR has been recently reported to be alternatively spliced in an intronless gene (FranÃ§ois et al., 2018), only intronless genes with UTRs <= 100 bp were included. A total of 51 expressed protein-coding intronless genes were included in the analysis.
Genome_build: hg20/hg38 (GRCh38) genome assembly (Human Genome Reference Consortium http://hgdownload.soe.ucsc.edu/downloads.html#human)
Supplementary_files_format_and_content: bigwig coverage files

source_name: K562 erythroleukemia cells

growth_protocol: Human K562 cells were obtained from DSMZ (DSMZ no.: ACC-10) and cultured in antibiotic-free RPMI 1640 medium (Thermo Fisher Scientific, 31870–074) supplemented with 10% heat-inactivated fetal bovine serum (Thermo Fisher Scientific, 10500–064) and 2 mM GlutaMAX (Thermo Fisher Scientific, 35050087) at 37 ̊C and 5% CO2. Cells were verified to be free of mycoplasma contamination using Plasmo Test Mycoplasma Detection Kit (InvivoGen, rep-pt1). K562 cells were authenticated at the DSMZ Identification Service according to standards for STR profiling (ASN-0002). Biological replicates were grown independently.

extract_protocol: NEBNext® Ultra™ II DNA Library Prep Kit

treatment_protocol: Cells at a confluency of 300.000 cell/mL were treated with DMSO (1:20.000 dilution, Sigma, D2438) as solvent control or with 1 μM Pladienolide-B from a DMSO-resuspended 20 mM stock (1:20.000 dilution, Santa Cruz, sc-391691).

tag: method protocol

value: ChIP-seq (Morey et al., 2012; Stock et al, 2007)

tag: chip antibody

value: Cyclin T1 antibody (Thermo Fisher, 10009D)


title: Peruvian, HCC Patient, 104

source_name: Peruvian HCC tissue from Patient 104

tag: tissue

value: hepatocellular carcinoma (HCC)

value: Patient 104

value: Positive


title: Genomic DNA from cord blood sample GDM.045

source_name: cord blood sample GDM.045


title: NA19310 cell line replicate 1

source_name: purified gDNA

tag: cell line


title: Genomic DNA from cord blood sample GDM.040

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.040

value: NGT


title: Genomic DNA from cord blood sample GDM.052

source_name: cord blood sample GDM.052


title: hTLR1

description: Bulk-RNA Seq

source_name: iMGLs treated with TLR1


title: NA19308 cell line replicate 3


title: Peruvian, HCC Patient, 095

source_name: Peruvian HCC tissue from Patient 095

value: hepatocellular carcinoma

value: Patient 095


title: ChIP-seq_Pla-B1h_CycT1_rep1


title: Genomic DNA from cord blood sample GDM.037

source_name: cord blood sample GDM.037


title: Genomic DNA from cord blood sample GDM.038

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.038


title: ChIP-seq_DMSO1h_CycT1_rep2


title: NA19308 cell line replicate 2


title: Genomic DNA from cord blood sample GDM.036

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.036


title: ChIP-seq_DMSO1h_CycT1_rep1


title: NA19308 cell line replicate 1


title: Genomic DNA from cord blood sample GDM.039

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.039


title: Genomic DNA from cord blood sample GDM.053

source_name: cord blood sample GDM.053


title: ChIP-seq_Pla-B1h_inputCycT1_rep2


title: Peruvian, HCC Patient, 092

source_name: Peruvian HCC tissue from Patient 092

value: Patient 092

value: D


title: ChIP-seq_Pla-B1h_inputCycT1_rep1


title: NA19307 cell line replicate 2


title: NA19307 cell line replicate 3


title: Genomic DNA from cord blood sample GDM.033

source_name: cord blood sample GDM.033


title: Peruvian, HCC Patient, 068

source_name: Peruvian HCC tissue from Patient 068

value: Patient 068

value: C


title: Genomic DNA from cord blood sample GDM.034

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.034


title: ChIP-seq_DMSO1h_inputCycT1_rep2

source_name: K562 erythroleukemia cells


title: NA19307 cell line replicate 1


title: Peruvian, HCC Patient, 047

source_name: Peruvian HCC tissue from Patient 047

value: Patient 047

value: Female


title: Peruvian, HCC Patient, 054

source_name: Peruvian HCC tissue from Patient 054

value: Patient 054


title: ChIP-seq_DMSO1h_inputCycT1_rep1


title: NA19239 cell line replicate 3

source_name: purified gDNA


title: Genomic DNA from cord blood sample GDM.030

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.030


title: NA19239 cell line replicate 2


title: ChIP-seq_Pla-B1h_PolII_rep2

value: Total Pol II antibody (Diagenode, C15200004)


title: Peruvian, NTL, Patient, 201

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 201,Age: 76,Gender: Male,HBV: Negative,mtDNA haplotypes: D
NTLPER201

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

data_processing: Data were processed in R, normalized using Noob (normal-exponential out-of-band) normalization.

source_name: Peruvian NTL tissue from Patient 201

treatment_protocol: Sampling protocol: About 50 mg of HCC, as well as NTL from tumor-free margins of the resected surgical pieces, were harvested, flash-frozen in liquid nitrogen, and kept at -150°C for long-term storage.

tag: individual

value: Patient, 201

tag: nationality

value: Peruvian

value: Male

value: Negative

value: NTL


title: Peruvian, NTL, Patient, 200

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 200,Age: 42,Gender: Male,HBV: Positive,mtDNA haplotypes: D
NTLPER200

source_name: Peruvian NTL tissue from Patient 200

value: Patient, 200

value: Positive

value: hepatocellular carcinoma (HCC)


title: Peruvian, HCC Patient, 083

source_name: Peruvian HCC tissue from Patient 083

value: hepatocellular carcinoma

value: Patient 083

value: B


title: Genomic DNA from cord blood sample GDM.031

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.031

value: NGT


title: ChIP-seq_Pla-B1h_PolII_rep1

value: ChIP-seq (Morey et al., 2012; Stock et al, 2007)


title: Genomic DNA from cord blood sample GDM.029

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.029


title: NA19239 cell line replicate 1

description: Genomic DNA extracted from B-lymphocytes by Coriell and genotyped using Infinium Global Screening Array (GSAMD-24v1-0_20011747_A1) beadchip (Illumina)


title: Peruvian, NTL, Patient, 191

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 191,Age: 67,Gender: Male,HBV: Negative,mtDNA haplotypes: A
NTLPER191

source_name: Peruvian NTL tissue from Patient 191

value: Patient, 191

value: A


title: Peruvian, HCC Patient, 034

source_name: Peruvian HCC tissue from Patient 034

value: Patient 034

value: Female


title: Genomic DNA from cord blood sample GDM.035

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.035


title: Peruvian, HCC Patient, 088

source_name: Peruvian HCC tissue from Patient 088

value: Patient 088


title: Peruvian, HCC Patient, 015

source_name: Peruvian HCC tissue from Patient 015

value: Patient 015


title: NA19238 cell line replicate 3


title: ChIP-seq_DMSO1h_PolII_rep2

value: Total Pol II antibody (Diagenode, C15200004)


title: ChIP-seq_DMSO1h_PolII_rep1


title: Genomic DNA from cord blood sample GDM.028

source_name: cord blood sample GDM.028

value: GDM


title: NA19238 cell line replicate 2


title: ChIP-seq_Pla-B1h_inputPolII_rep2


title: Genomic DNA from cord blood sample GDM.026

source_name: cord blood sample GDM.026


title: NA19238 cell line replicate 1


title: Peruvian, HCC Patient, 026

source_name: Peruvian HCC tissue from Patient 026

value: Patient 026

value: Male


title: ChIP-seq_Pla-B1h_inputPolII_rep1

source_name: K562 erythroleukemia cells


title: ChIP-seq_DMSO1h_inputPolII_rep2


title: Peruvian, HCC Patient, 025

source_name: Peruvian HCC tissue from Patient 025

value: Patient 025

value: Positive


title: NA19204 cell line replicate 2

source_name: purified gDNA


title: Genomic DNA from cord blood sample GDM.024

source_name: cord blood sample GDM.024


title: NA19204 cell line replicate 3


title: ChIP-seq_DMSO1h_inputPolII_rep1

extract_protocol: NEBNext® Ultra™ II DNA Library Prep Kit (NEB)


title: Peruvian, NTL, Patient, 188

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 188,Age: 94,Gender: Female,HBV: Negative,mtDNA haplotypes: B
NTLPER188

source_name: Peruvian NTL tissue from Patient 188

value: Patient, 188

value: Peruvian

value: Negative

value: hepatocellular carcinoma (HCC)

value: NTL


title: Peruvian, HCC Patient, 004

value: hepatocellular carcinoma

value: Patient 004

value: B


title: Peruvian, NTL, Patient, 120

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 120,Age: 20,Gender: Female,HBV: Positive,mtDNA haplotypes: B
NTLPER120

source_name: Peruvian NTL tissue from Patient 120

value: Patient, 120

value: Female


title: Genomic DNA from cord blood sample GDM.025

source_name: cord blood sample GDM.025


title: Genomic DNA from cord blood sample GDM.023

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.023

value: NGT


title: GFP at 2 hrs μg donor 1 experiment 1 [CWRU003396_S40]

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as normalized Log2(n+0.25) CPM summarized reads

source_name: GFP at 2 hours μg

growth_protocol: The cells were cultured in DMEM/F12 (Life technologies) without phenol red, supplemented with 5% (w/v) horse serum, cholera toxin (Sigma), epidermal growth factor (Peprotech), hydrocortisone (Sigma), insulin (Sigma) and penicillin streptomycin (Life technologies). The cells were maintained at 37oC in a humidified, 5 % (v/v) CO2 incubating chamber. The inducible cells were trypsinized and seeded in fibronectin coated chamber flasks with 30% confluency and cultured for 24 h. To induce SUN1L-KDEL for LINC disruption and GFP-KDEL for control comparison, the media was supplemented  with 1 µg/ml doxycycline. These cells were cultured in doxycycline for 24 h before placing them on the 3-D clinostat.

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using the Truseq Stranded Total RNA HT Kit.

tag: cell line background

value: MCF 10A

tag: cell type

value: Mammary epithelial cells

tag: treatment

value: GFP

tag: gravity

value: μg

tag: timepoint in hours

tag: donor id

tag: experiment


title: NA19204 cell line replicate 1


title: Peruvian, NTL, Patient, 190

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 190,Age: 46,Gender: Female,HBV: Positive,mtDNA haplotypes: A
NTLPER190

source_name: Peruvian NTL tissue from Patient 190

value: Patient, 190

tag: gender

value: A

tag: disease state


title: NA19152 cell line replicate 3


title: Peruvian, NTL, Patient, 121

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 121,Age: 82,Gender: Female,HBV: Negative,mtDNA haplotypes: B
NTLPER121

source_name: Peruvian NTL tissue from Patient 121

value: Patient, 121

tag: hbv

tag: mtdna haplotypes


title: GFP at 0 hrs 1G donor 1 experiment 2 [CWRU003414_S39]

source_name: GFP at 0 hours 1G


title: Peruvian, NTL, Patient, 180

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 180,Age: 34,Gender: Male,HBV: Positive,mtDNA haplotypes: B
NTLPER180

source_name: Peruvian NTL tissue from Patient 180

value: Patient, 180

value: Peruvian

tag: age

value: Male

value: Positive


title: Genomic DNA from cord blood sample GDM.021

source_name: cord blood sample GDM.021

tag: disease status

value: GDM


title: NA19152 cell line replicate 2


title: Peruvian, NTL, Patient, 179

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 179,Age: 33,Gender: Male,HBV: Positive,mtDNA haplotypes: C
NTLPER179

source_name: Peruvian NTL tissue from Patient 179

value: Patient, 179

value: C

value: hepatocellular carcinoma (HCC)

tag: tissue

value: NTL


title: SUN1L at 20 hrs 1G donor 2 experiment 1 [CWRU003413_S38]

source_name: SUN1L at 20 hours 1G


title: Genomic DNA from cord blood sample GDM.019

description: normal glucose tolerance pregnancy

source_name: cord blood sample GDM.019

value: NGT


title: NA19152 cell line replicate 1

tag: cell line


title: Genomic DNA from cord blood sample GDM.018

description: gestational diabetes mellitus (diabetes in pregnancy)

source_name: cord blood sample GDM.018


title: SUN1L at 2 hrs μg donor 2 experiment 2 [CWRU003427_S37]

source_name: SUN1L at 2 hours μg

value: MCF 10A


title: GFP at 2 hrs 1G donor 1 experiment 2 [CWRU003420_S36]

source_name: GFP at 2 hours 1G

value: Mammary epithelial cells


title: Peruvian, NTL, Patient, 116

description:
subject status: Peruvian patients with hepatocellular carcinoma (HCC), subject id: Patient 116,Age: 77,Gender: Male,HBV: Negative,mtDNA haplotypes: B
NTLPER116

source_name: Peruvian NTL tissue from Patient 116

tag: individual

value: Patient, 116

value: Negative

value: B


title: Peruvian, HCC Patient, 070

source_name: Peruvian HCC tissue from Patient 070

value: hepatocellular carcinoma

tag: subject id

value: Patient 070