title: D25 pericyte-like cells from H9 hPSC line (independent differentiation B)

city: La Jolla

middle: D

last: Gastfriend

state: CA

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Reads were mapped to the human transcriptome (hg38) using HISAT2 v2.1.0
Transcript abundances (FPKM) were quantified using Cufflinks v2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: FPKM values for each sample were combined into a single Excel

source_name: Human pluripotent stem cell line

extract_protocol:
Total RNA was extracted from frozen cell pellets using the Rneasy Mini Kit (Qiagen) with Qiashredder homogenization and Dnase I treatment according to manufacturer protocols.
Total RNA was subjected to poly-A selection for mRNA and libraries prepared using the TruSeq Stranded mRNA Prep Kit (Ilumina) according to manufacturer protocols.

tag: cell line


title: Primary brain pericytes 1

status: Public on Mar 13 2019

type: SRA

first: Benjamin

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: Isolated from human brain

value: Not applicable


title: Primary brain pericytes 2


title: before the loading

type: RNA

city: TOKYO

first: Taku

last: Saito

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

department: Orthopaedic Surgery, Faculty of Medicine

country: Japan

institute: The University of Tokyo

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: Primary chondrocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Mouse primary chondrocytes were seeded in silicon stretch chambers coated with fibronectin at a concentration of 1×10e5 cells/chamber. After 48 hours, cyclic tensile strain (0.5 Hz, 10% elongation) was applied for 30 minutes using STB-140 mechanical stretch system.

tag: cell type

value: Primary chondrocytes

tag: age

tag: strain


title: SUM159T-P63-V5_no dox_d5_2

city: Washington

first: Gray

middle: Waite

last: Pearson

state: DC

address: 3970 Reservoir Rd NW

department: Department of Oncology

institute: Georgetown University

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: Human cancer cell lines

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: SUM159 trailblazers

tag: expression vector

tag: treatment condition

tag: treatment time

value: 5 days


title: HMC-1.2_US_4

city: marseille

first: Amira

last: Ben Amara

address: 27  Boulevard Leï Roue

country: France

institute: IHU-CRCM

description: Purified cells

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner  G2505C. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software10.7.3.1 (Agilent Technologies).

data_processing: Microarray data analysis was performed using the GeneSpring software. Raw data were filtered and normalized, unsupervised and supervised analyses were done using hierarchical clustering, principal composant analysis (PCA) and the signicantly modulated genes using GeneSpring Software (Agilent Technologies). Genes were considered to be differentially expressed when fold change (FC) was  FC ≥ 2 with p-value (p) was p < 0.001 in at least one of the 3 pair combinations. Gene Ontology (GO) annotations attributed to biological processes and corrected p ≤ 0.001 (Bonferroni correction) allow us to identify the biological functions that were modulated,

source_name: cell line MHC-1.2

label_protocol: In brief, 300 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: The human mast cell line HMC-1.2 was cultured in Iscove's Modified Dulbecco's Medium (IMDM, Life Technologies) supplemented with 10% fetal bovine serum (FBS), 100 IU/ml penicillin and 50 µg/ml streptomycin (Life Technologies) at 37°C.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -80°C.

treatment_protocol: Cells were cultured at 37°C for 8 hours with or without NM1or NM2 before processing RNAs extraction.

tag: condition

value: untreated


title: D25 pericyte-like cells from H9 hPSC line (independent differentiation C)


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_41

city: Nijmegen

first: Leonie

middle: M

last: Kamminga

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_41_NDCII_sample_0041

data_processing:
RNA-seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with --quantMode geneCounts
Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1
ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters
Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2
ChIP-seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e-02 relative to respective ChIP input track.
RNAseq reads from dissected hearts were demultiplexed and processed following the CEL-Seq pipeline (https://github.com/yanailab/CEL-Seq-pipeline)
Normalized counts were obtained with Monocle version 2.4.0
Genome_build: GRCz10
Supplementary_files_format_and_content: Gene counts (.txt); peak files in BED format

molecule: polyA RNA

organism: Danio rerio

source_name: heart

growth_protocol: Zebrafish (Danio rerio), were housed at 27.5°C in a 14/10h light/dark cycle. The evening before spawning, one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. (Kimmel et al., 1995).

extract_protocol:
RNA-seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit
RNA-seq: extraction was followed by fragmentation, cDNA synthesis, and KAPA-HYPERprep library preparation

value: TU/TLF mixed background

value: heart

tag: genotype


title: HMC-1.2_NM1_1

description: Purified cells

value: C. burnetii phase 1  pathogenic phase


title: SUM159T-P63-V5_+dox_d5_1

description: replicate 1

value: 1ug/ml doxycycline


title: HMC-1.2_US_1

description: Purified cells


title: HMC-1.2_NM2_3

description: Purified cells

value: C. burnetii phase 2  non-pathogenic phase


title: SUM159T-P63-V5_no dox_d5_1

description: replicate 1


title: SUM159T-P63-V5_+dox_d5_2

description: replicate 2


title: SUM159T-WT_+dox_d5_2

description: replicate 2

value: empty pLIX vector


title: SUM159T-WT_no dox_d5_2

description: replicate 2


title: D25 pericyte-like cells from CS03n2 hPSC line


title: D45 pericyte-like cells from H9 hPSC line


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_39

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_39_NDCII_sample_0039


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_42

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_42_NDCII_sample_0042


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_38

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_38_NDCII_sample_0038


title: D25 pericyte-like cells from H9 hPSC line (independent differentiation A)


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_37

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_37_NDCII_sample_0037


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_36

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_36_NDCII_sample_0036


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_35

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_35_NDCII_sample_0035


title: D22 pericyte-like cells from H9 hPSC line


title: D55 neural crest stem cells from H9 hPSC line


title: D25 pericyte-like cells from IMR90C4 hPSC line


title: Danio_rerio_RNAseq_singleHeart_3dpf_mut_40

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_40_NDCII_sample_0040


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_34

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_34_NDCII_sample_0034


title: D15 neural crest stem cells from H9 hPSC line


title: HMC-1.2_NM2_1

description: Purified cells


title: D19 pericyte-like cells from H9 hPSC line


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_33

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_33_NDCII_sample_0033


title: SUM159T-WT_no dox_d5_1

description: replicate 1


title: aged MSC (60y)

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

country: Germany

institute: Universitätsklinikum Düsseldorf

description:
60y
Sample name: SAMPLE 15

scan_protocol: Standard Illumina scanning protocol for HumanHT-12 v3.0 Gene Expression Bead Chips

data_processing: The data were normalised using quantile normalisation from R/Bioconductor

source_name: mesenchymal stromal cells

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand  reverse transcription step, followed by a single in vitro transcription  (IVT) amplification that incorporates biotin-labeled nucleotides.  Subsequent steps include array hybridization, washing, blocking, and  streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively  detected for downstream analysis.

growth_protocol: The culture of MSCs and iMSCs was carried out in MEM α, nucleosides, GlutaMAX™ with addition of 10% fetal bovine serum (Biochrom AG), penicillin/streptomycin and nonessential amino acids (all from Life Technologies). MSCs and iMSCs were expanded with a seeding density of 1000 cells per cm2. iMSCs were cultured in the same conditions from passage four.  Pluripotent stem cells (iPS-cells and human embryonic stem cells H1 and H9 (#WA01 and #WA09, respectively)) were cultured in unconditioned medium. The medium contained KO-DMEM, supplementation of 20% serum replacement, sodium pyruvate, nonessential amino acids, L-glutamine, penicillin/streptomycin and 0.1mM β-mercaptoethanol (all from Life Technologies). Supplementation with basic fibroblast growth factor (bFGF) (Preprotec) to a final concentration of 8ng/ml was carried out before media change every day. Passaging of pluripotent stem cells was carried out with a splitting ratio of 1:3. Passaging was conducted manually using a syringe needle and a pipette under a binocular microscope. Mitomycin-C inactivated mouse embryonic fibroblasts (MEFs) were used as feeder cells seeded on cell culture dishes coated with Matrigel (BD) to culture iPS-cells a hESCs. MSC culture was carried out at 37°C and 5% CO2 in a humidified atmosphere. Pluripotent stem cell culture was carried out under the same condition with additional hypoxic conditions in 5% O2.

extract_protocol: The DNA + RNA + Protein Extraction Kit (Roboklon) was used to extract total RNA from MSCs iPS-cells and iMSCs. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: Retroviral-based reprogramming with pMX vector-based over-expression of OCT4, SOX2, KLF4, and c-MYC was carried out as previously described (Hossini, A. et al., 2015). Episomal plasmid based reprogramming was performed using the Human MSC (Mesenchymal Stem Cell) Nucleofector® Kit (Lonza, VPE-1001) in combination with the Amaxa Nucleofector II® (Lonza) according to the descriptions of the manufacturer. The plasmid combination 7F-2 was delivered to the MSCs as previously described (Yu, J. et al., 2011). Episomal plasmid-based reprogramming of aged MSC (62y) was carried out using N2B27 medium supplemented with 8ng/ml bFGF and 50µg/ml L-ascorbic acid (Sigma-Aldrich) (Gao, Y., et al., 2013). The culture conditions were changed to mTeSR™1 (Stem Cell Technologies) after 14 days (Yu, J., et al., 2011).    Gao, Y., Yang, L., Chen, L., Wang, X., Wu, H., Ai, Z., Du, J., Liu, Y., Shi, X., Wu, Y., et al. (2013). Vitamin C facilitates pluripotent stem cell maintenance by promoting pluripotency gene transcription. Biochimie 95, 2107-2113.    Hossini, A.M., Megges, M., Prigione, A., Lichtner, B., Toliat, M.R., Wruck, W., Schröter, F., Nuernberg, P., Kroll, H., Makrantonaki, E., et al. (2015). Induced pluripotent stem cell-derived neuronal cells from a sporadic Alzheimer's disease donor as a model for investigating AD-associated gene regulatory networks. BMC Genomics 16.    Yu, J., Chau, K.F., Vodyanik, M.A., Jiang, J., and Jiang, Y. (2011). Efficient feeder-free episomal reprogramming with small molecules. PLoS ONE 6.  .

value: mesenchymal stromal cells

tag: cell source

value: from bone marrow of 60y old person


title: H1_b

description:
replicate b
Sample name: SAMPLE 13

source_name: embryonic stem cells

value: embryonic stem cells

value: embryonic stem cell line H1


title: fetal MSC 2

description:
H1537
Sample name: SAMPLE 18

value: from fetal bone marrow 55 days post conception (fetus H1537)


title: H9_a

description:
replicate a
Sample name: SAMPLE 14

value: embryonic stem cell line H9


title: fetal MSC 1

description:
H1536
Sample name: SAMPLE 17

value: from fetal bone marrow 55 days post conception (fetus H1536)


title: iMSC (hESC H1)

description:
H1
Sample name: SAMPLE 11

source_name: mesenchymal stromal cells derived from embryonic stem cells

value: derived from embryonic stem cell line H1


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_32

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_32_NDCII_sample_0032


title: iMSC (fetal, line 1, viral)

description:
H1536
Sample name: SAMPLE 10

source_name: iPSCs-derived mesenchymal stromal cells

value: iPSCs-derived mesenchymal stromal cells

value: derived from iPSC (MSC, fetal, line 1, viral)


title: H1_a

description:
replicate a
Sample name: SAMPLE 12


title: HMC-1.2_US_2

description: Purified cells

value: untreated


title: SUM159T-WT_+dox_d5_1

description: replicate 1

value: SUM159 trailblazers

value: 5 days


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_31

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_31_NDCII_sample_0031

value: TU/TLF mixed background

value: heart


title: iPSC (MSC, fetal, line 1, episomal 2)

description:
H1536
Sample name: SAMPLE 9

source_name: induced pluripotent stem cells (iPSCs)

value: induced pluripotent stem cells (iPSCs)

value: from fetal MSC 1 using episomal plasmids


title: LL_siNEG_2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
base calling: HiSeq Control Software 2.2.58 / NextSeq Control Software 2.1.2
alignment:tophat2 (2.0.14)
transcript assembly: cufflinks (2.2.1)
FPKM generation: cufflinks (2.2.1)
coverage generation: bedtools genomecov (2.19.0)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph format

source_name: mouse LL leukemia cell line

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, 50U/ml penicillin, 50μg/ml streptomycin, 2mM L-glutamine. FMH9 cultures were supplemented with 50ng/ml stem cell factor, 5ng/ml granulocyte-macrophage colony-stimulating factor, 5ng/ml interleukin-3, and 5ng interleukin-6, while KL cells (GV and JF, unpublished) and LL cells required 2ng/ml interleukin-3. All cytokines were purchased from Peprotech EC (London, UK).

extract_protocol:
RNA was extracted using RNeasy mini kit (QIAGEN)
Libraries were prepared via the Illumina TruSeq® Stranded mRNA library preparation protocol according to manufacturer's instructions

treatment_protocol: In total, 5 x106 FMH9, KL, or LL cells were electroporated with 300mM of Myb siRNA (s70212, Ambion, Life Technologies) or a scrambled negative control siRNA (4390843 Silencer Select Negative Control #1 – Life Technologies). Using an Amaxa 4D-nucleofector with solution SF Cell Line (V4XC-2024, Lonza) and program EO-100 for FMH9 cells or solution P3 Primary Cells (V4XP-3024, Lonza) and program DS-120 for KL and LL cells.

tag: cebpa mutational status

value: biallelic LP30


title: iPSC (MSC, 62y, episomal)

description:
62y
Sample name: SAMPLE 5

value: derived  from MSCs from 62y old person using retroviruses


title: LL_siNEG_1


title: aged MSC (70y)

description:
70y
Sample name: SAMPLE 16

value: mesenchymal stromal cells

value: from bone marrow of 70y old person


title: iPSC (MSC, fetal, line 1, viral)

description:
H1536
Sample name: SAMPLE 7

value: from fetal MSC 1 using retroviruses


title: H9 human pluripotent stem cells


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_29

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_29_NDCII_sample_0029


title: LL_siMYB_2


title: FMH9_siNEG_1

source_name: mouse FMH9 myelomonocytic leukaemia cell line

value: WT


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_28

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_28_NDCII_sample_0028


title: fetal MSC 3

description:
H1555
Sample name: SAMPLE 6

value: from fetal bone marrow 55 days post conception (fetus H1555)


title: Danio_rerio_ChIPseq_spikein_3dpf_H3K27me3_r4

description: ChIPseq of H3K27me3 in 3 days post fertilization Danio rerio rnf2 KO embryos with Drosophila chromatin

library_source: genomic

molecule: genomic DNA

source_name: whole embryo

extract_protocol:
ChIP-seq: Embryos of 3 dpf were fixed, deyolked, and homogenized using pestles and sonication to isolate the chromatin
ChiP-Seq: For spike-in experiments zebrafish chromatin was mixed with Drosophila spike-in chromatin and incubated overnight with H2Aγ and RING1B antibodies (H2Aγ Active Motif 104597; RING1B cell signaling D22F2) or with H2Aγ and H3K27me3 antibodies (H2Aγ Active Motif 104597; Millipore 07-449). In the regular non-spike in experiment zebrafish chromatin was  incubated with the H3K27me3 antibody overnight (Millipore 07-449). After o/n antibody incubation the chromatin was extensive washed. The resulting ChIP-DNA was used as input for KAPA-HYPERprep library preparation

value: whole embryo

value: 3 dpf

tag: chip antibody

value: H3K27me3 (Millipore 07-449); H2Aγ (Active Motif 104597)


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_23

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_23_NDCII_sample_0023


title: Danio_rerio_ChIPseq_spikein_3dpf_H3K27me3_r3


title: Danio_rerio_ChIPseq_spikein_3dpf_H3K27me3_r2


title: Vitamin D LPS mouse 8

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

hyb_protocol: All processing was performed by Edinburgh Genomics

data_processing: Scan data were processed in the R environment using oligo (and rma) package (v1.42.0), with data summarised at transcript level with pd.mogene.2.1.st (v3.14.1).

source_name: CD11c+ BMDC

growth_protocol: BMDC were generated in the presence of recombinant GM-CSF (Peprotech, London, UK) for 9 days as previously described (13). Briefly, bone marrow was collected from femurs and tibias of B10.PLxC57BL/6 mice, and clusters within the bone marrow suspension were dispersed by vigorous pipetting. Red blood cells were lysed with RBC lysis buffer (Sigma-Aldrich, Dorset, UK) for 1 minute and washed once in cell culture medium. Cells were seeded into 6 well plates at 2x105/ml in 2 ml of cell culture medium with the addition of 20ng/ml GM-CSF. At day 3, a further 2mls of cell culture medium containing 20ng/ml GM-CSF was added to each well. On day 6, 2ml of culture supernatant was removed and replaced with 2 ml fresh culture medium containing 20ng/ml GM-CSF. Vehicle (100% ethanol) or 1,25(OH)2D3 was added to the BMDC culture media at the concentration indicated in the text initially and at all subsequent media changes. At day 9, the BMDC cells were harvested and CD11c+ cells were isolated by FACS. The CD11c+ BMDC were re-plated at 2x106 BMDC/ml in cell culture medium, 5ng/ml of GM-CSF with 0.1µg/ml Ac1-9(4Tyr) MBP for an additional 18 hours. 0.1µg/ml lipopolysaccharide (LPS) was added to some overnight CD11c+ BMDC cultures (Sigma-Aldrich, Dorset UK). No 1,25(OH)2D3 was added to the culture media during the overnight stimulation with LPS and MBP.

extract_protocol: RNA was extracted from CD11c+BMDC using commercially available kits (RNeasy Mini Kit). RNA purity was analysed by spectrophotometer (Thermo Scientific NanoDrop 1000, 260/280 ratio =2). RNA integrity number (RIN >8) was assessed by electropheogram. Sense strand cDNA preparation from RNA samples was generated and labelled using Ambion WT expression kit (Life Technologies, Paisley, UK) and Affymetrix GeneChip-WT terminal labelling kit according to manufacturer’s instructions.

treatment_protocol: There were 4 treatment groups : a)vehicle no LPS b) vitamin D no LPS c) Vehicle LPS d) Vitamin D LPS

tag: gender

value: female


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_24

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_24_NDCII_sample_0024


title: Danio_rerio_ChIPseq_spikein_3dpf_H3K27me3_wt2

description: ChIPseq of H3K27me3 in 3 days post fertilization Danio rerio wild type embryos with Drosophila chromatin


title: aged MSC (62y)

description:
62y
Sample name: SAMPLE 4

value: from bone marrow of 62y old person


title: iPSC (MSC, 74y, viral)

description:
74y
Sample name: SAMPLE 2

value: derived  from MSCs from 74y old person using retroviruses


title: iMSC (74y, viral)

description:
74y
Sample name: SAMPLE 3

value: iPSCs-derived mesenchymal stromal cells

value: derived from iPSC (MSC, 74y, viral)


title: Danio_rerio_ChIPseq_spikein_3dpf_rnf2_r4

description: ChIPseq of rnf2 protein in 3 days post fertilization rnf2 KO Danio rerio embryos

value: TU/TLF mixed background

value: RING1B (Cell Signaling D22F2); H2Aγ (Active Motif 104597)


title: Vitamin D LPS mouse 7

scan_protocol: All processing was performed by Edinburgh Genomics


title: Danio_rerio_ChIPseq_spikein_3dpf_rnf2_r3


title: LL_siMYB_1

value: biallelic LP30


title: Vitamin D LPS mouse 6

label_protocol: All processing was performed by Edinburgh Genomics


title: aged MSC (74y)

description:
74y
Sample name: SAMPLE 1

value: from bone marrow of 74y old person


title: FMH9_siNEG_2


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_27

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_27_NDCII_sample_0027

value: heart


title: FMH9_siMYB_1


title: Danio_rerio_RNAseq_singleHeart_2dpf_mut_26

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_26_NDCII_sample_0026


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_21

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_21_NDCII_sample_0021


title: Danio_rerio_ChIPseq_spikein_3dpf_rnf2_r2


title: FMH9_siMYB_2


title: Danio_rerio_ChIPseq_spikein_3dpf_rnf2_wt1

description: ChIPseq of rnf2 protein in 3 days post fertilization wild type Danio rerio embryos


title: Danio_rerio_ChIPseq_spikein_3dpf_H3K27me3_wt1


title: Vitamin D LPS mouse 5


title: Vitamin D LPS mouse 3


title: Vitamin D LPS mouse 4


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_20

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_20_NDCII_sample_0020


title: Vitamin D LPS mouse 1


title: Vehicle LPS mouse 6


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_19

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_19_NDCII_sample_0019


title: Vitamin D LPS mouse 2


title: Danio_rerio_RNAseq_3dpf_mut8

description: Total RNA (rRNA depleted) of 3 days post fertilization Danio rerio rnf2 KO embryos


title: Vehicle LPS mouse 5


title: Danio_rerio_ChIPseq_spikein_3dpf_input_r2

description: ChIPseq input in 3 days post fertilization Danio rerio rnf2 KO embryos with Drosophila chromatin

value: None (Input)


title: Danio_rerio_ChIPseq_spikein_3dpf_input_wt2

description: ChIPseq input in 3 days post fertilization Danio rerio wild type embryos with Drosophila chromatin


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_18

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_18_NDCII_sample_0018


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_22

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_22_NDCII_sample_0022


title: Danio_rerio_ChIPseq_spikein_3dpf_rnf2_wt2


title: Danio_rerio_RNAseq_3dpf_mut7


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_16

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_16_NDCII_sample_0016


title: Danio_rerio_RNAseq_3dpf_mut6


title: Danio_rerio_RNAseq_3dpf_mut1


title: Danio_rerio_RNAseq_3dpf_mut5


title: Danio_rerio_RNAseq_3dpf_wt13

description: Total RNA (rRNA depleted) of 3 days post fertilization Danio rerio wild type embryos

value: TLF

value: wild type


title: Vehicle LPS mouse 3


title: Vehicle LPS mouse 4


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_17

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_17_NDCII_sample_0017


title: Danio_rerio_RNAseq_3dpf_wt12


title: Danio_rerio_RNAseq_singleHeart_3dpf_wt_15

description:
RNAseq of dissected hearts from 3 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_3dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_15_NDCII_sample_0015


title: Danio_rerio_RNAseq_3dpf_mut3


title: Vehicle LPS mouse 2


title: Vehicle LPS mouse 1


title: Danio_rerio_RNAseq_3dpf_wt1


title: Danio_rerio_RNAseq_3dpf_wt11


title: Danio_rerio_RNAseq_3dpf_mut2


title: Danio_rerio_RNAseq_3dpf_wt4


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_14

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_14_NDCII_sample_0014


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_11

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_11_NDCII_sample_0011


title: Danio_rerio_RNAseq_3dpf_wt5


title: Vitamin D no LPS mouse 3


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_13

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_13_NDCII_sample_0013


title: Danio_rerio_RNAseq_3dpf_wt3


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_9

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_9_NDCII_sample_0009


title: Danio_rerio_RNAseq_3dpf_wt2


title: trt-1_dcr-1_1

city: Chapel Hill

first: Shawn

last: Ahmed

state: North Carolina

address: 216 Fordham Hall, 133 Medical Drive

institute: UNC Genetics Department

description:
SMALL_RNA_TD1_GATCAG_S12
trt-1 dcr-1 1

data_processing:
3’ Adapter sequence removed using bbduk.sh from the bbmap package
5’ and 3’ four nucleotide barcodes removed using bbduk.sh from the bbmap package
Reads converted to fasta format and mapped to the C. elegans genome (WS251) using bowtie with the following options: -M 1 -v 0 -best -strata
Reads mapping to subtelomeres (2kb of sequence adjacent to telomeres) counted. Read counts normalized by dividing by the total number of mapped reads in each library and multiplied by 1000000
Genome_build: WS251
Supplementary_files_format_and_content: normalized 22G read counts at subtelomeres for each sample expressed as reads per million mapped reads

organism: Caenorhabditis elegans

source_name: trt-1_dcr-1_mixed stage_whole worm

growth_protocol: Animals were grown at 20°C on 100 mm NGM plates seeded with OP50 bacteria

extract_protocol:
RNA was extracted using Trizol (Ambion)  followed by isopropanol precipitation. RNA samples were treated with 20U RNA 5’ polyphosphatase (Lucigen, RP8092H) for 30 minutes at 37°C to remove 5’ triphosphate groups.
Library preparation and sequencing was performed at the UNC School of Medicine High-Throughput Sequencing Facility (HTSF). RNA-seq libraries were prepared using the NEXTflex Small RNA Library Prep Kit for Illumina (Bioo Scientific). Four nucleotide barcodes were added to the 5’ and 3’ ends of inserts during library preparation. Libraries were sequenced on an Illumina HiSeq 2500 to produce approximately twenty million 50 bp single-end reads per library.

tag: genotype/variation

value: trt-1 dcr-1

tag: Stage

value: Mixed stage

tag: tissue

value: whole worm

tag: molecule subtype

value: small RNA


title: trt-1_dcr-1_2

description:
SMALL_RNA_TD2_TAGCTT_S11
trt-1 dcr-1 2


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_12

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_12_NDCII_sample_0012


title: RNA sequencing dkppx strain Rep 1

city: Faridabad

first: Ramandeep

last: Singh

state: Haryana

address: NCR-BSC

department: Vaccine and Infectious Disease Research Centre

country: India

institute: Translational Health Science and Technology Institute

data_processing:
The preproceed reads were aligned to the Mycobacterium tuberculosis H37Rv genome downloaded from ENSEMBL genome browser.
Alignment of the reads was performed using TOPHAT Program (Version 2.1.1)
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Functional annotation by DAVID
The diiferential gene expression analysis with 2.0 fold change and p<0.05 is shown in the file named Differentially expressed genes

organism: Mycobacterium tuberculosis H37Rv

source_name: Microbe

growth_protocol: Mycobacterium tuberculosis cells wild type or dkppx mutant strain were grown in Middlebrook 7H9 medium at 37 degree C with contant shaking.

extract_protocol:
The bacterial pellets were resuspended in Trizol and RNA was isolated and purified using RNAeasy columns.
The purified RNA was shipped to Aggrigenome Labs Pvt Ltd (India). RNA integrity was checked using Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). Ribosomal RNA was removed from total RNA sample using Ribo-ZeroTM Magantic kit (Bacteria) as per manufacturer’s recommendations (Epicentre). RNA cleanup was performed using Agencourt RNACleanTM XP Beads (Beckman Coulter). RNA was fragmented followed by random priming for first strand cDNA synthesis and second strand synthesis.
Adapters were ligated and the library was cleaned up twice using Agencourt RNACleanTM XP Beads followed by 14 PCR amplification cycles. Amplified library was further cleaned up using AMPure XP Beads (Beckman Coulter Inc). The quality of library was checked using Standard Sensitivity NGS Fragment Analysis Kit on an Advanced Analytical Fragment Analyzer. Library was quantified using qPCR as per Illumina Sequencing Library qPCR quantification guide and sequencing was performed at Illumina HiSeq2000.

treatment_protocol: Above mentioned strains were sub-cultured in fresh 7H9 medium and allowed for further growth at 37 degree celcius. When optical density (OD 600nm)reached mid-log phase, the cultures were harvested by centrifugation at 8000 rpm.

value: double mutant strain

tag: growth phase

value: mid-log phase cultures


title: Vitamin D no LPS mouse 1

value: female


title: U266

city: Atlanta

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description: tagmentation accessible DNA

data_processing:
ATAC-seq FASTQ files were aligned to the human genome (GRCh37) using bowtie2 (v2.2.6).
Mapped SAM files were converted to BAM files and putative PCR duplicates were marked using SAMtools (v1.7)
Regions with accessible chromatin were determined with MACS2 (v2.1.0.20151222) with the following parameters "-g hs -q 0.01".
The union of all regions with chromatin accessibility were determined in R/Bioconductor (v3.4.4) using the GenomicRanges package (v1.30.3).
Data were normalized for reads per peak per million (RPPM) = reads x 106 / (total # of autosomal reads x fraction of reads in peaks)
Genome_build: GRCh37

source_name: Myeloma cell line

growth_protocol: Cells were cultured at a density of 0.2-1.0 x 106 cells per mL in RPMI 1640 (Corning: 14-030-CV) with 10% FBS, 1% Pen-strep (Corning: 30-002-CI), 1% L-glutamine (Corning: 25005CI), and 1% HEPES (Corning: 25-060-CI).  Cell lines were validated using sequencing and phenotypic characterization.

extract_protocol:
Cells were pelleted at 500g for 10 min and lysed in nuclei lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2 ,0.1% IGEPAL)
Nuclei were pelleted at 500g for 30 min and tagmented with 2 mLTn5 (Illumina) for 60 min at 37°C prior to protein digestion with 2 mL 10 mg/mL Proteinase K at 40°C for 60 minutes.  Libraries were size selected with SPRI beads (AMPure, Kapa Biosystems) prior to 12 rounds of PCR amplification.

treatment_protocol: Cells as indicated were treated with 10 uM lenalidomide and analyzed on day 3.

tag: cell line

tag: treatment


title: RNA sequencing dkppx strain Rep 2

tag: strain


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_8

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_8_NDCII_sample_0008

tag: cell type

tag: age


title: XG-6

description: tagmentation accessible DNA


title: trt-1_2

description:
SMALL_RNA_T2_ACAGTG_S2
trt-1 2

source_name: trt-1_mixed stage_whole worm


title: Vehicle no LPS mouse 1


title: Vitamin D no LPS mouse 2


title: PE1

description: tagmentation accessible DNA


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_10

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_10_NDCII_sample_0010


title: Vehicle no LPS mouse 3


title: Vehicle no LPS mouse 2


title: RNA sequencing parental cells Rep 1

value: Parental strain


title: RPMI8226-Len

description: tagmentation accessible DNA

value: 10 uM lenalidomide


title: RNA sequencing parental cells Rep 2


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_7

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_7_NDCII_sample_0007

value: TU/TLF mixed background


title: wild-type_1

description:
SMALL_RNA_W1_CGGAAT_S10
wild-type 1

source_name: wild-type_mixed stage_whole worm


title: EGFRvIII driven glioma; biological rep 3

city: Genoa

first: Paolo

last: Malatesta

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

data_processing:
The sequence reads passed quality filters and were analyzed at gene level with the following methods:
STAR for the alignment;
Rsem for generating read counts;
edgeR for normalization.
genome build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million values for each sample, generated by edgeR

source_name: Cell explanted from EGFRvIII driven glioma and sorted by FACS for DsRed Expression

growth_protocol: Embryonic neural precursors were obtained from Balb/c or Ink/Arf -/- Balb/c mouse embryos at day 14. Cells were plated at a density of 3.6e5 cells per cm^2 onto Matrigel-coated 24-well plates in DMEM-F12 added with B27 supplement, human bFGF and EGF (10 ng/ml). Immediately after plating, Balb/c cells were transduced with retroviral vectors encoding PDGF-B and DsRed; Ink/Arf -/- Balb/c cells were transduced with retroviral vectors encoding EGFRvIII and DsRed. After 10 days, 2e4 transduced cells were intracranially inoculated in adult BALB/c mice.

extract_protocol:
At the apparence of first neurogical symptoms, brain tumors were removed, microdissected and sorted by FACS by using teh fluorescent reported DsRed. RNA was harvested using Trizol reagent. Samples were sent to BGI (Hong Kong) for sequencing on BGISEQ-500 platform.
Library were prepared by BGI (Hong Kong) Oligo (dT) magnetic beads are used to selectmRNA with polyA tail, or hybridize the rRNA with DNA probe and digest the DNA/RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the targetRNA after purification. 2) Fragmentthe targetRNA and reverse transcription to double-strand cDNA (dscDNA) by N6 randomprimer. 3) End repair the dscDNA with phosphate at5' end and stickiness 'A' at3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR productby heatand the single strand DNA is cyclized by splintoligo and DNA ligase

value: Balb/c

value: Ink/Arf -/-


title: PCM6

description: tagmentation accessible DNA


title: trt-1_1

description:
SMALL_RNA_T1_CTCAGA_S1
trt-1 1


title: Neural progenitor cells transduced with PDGF-b

source_name: Neural progenitors dissociated from E14 mouse embryos, transduced with PDGF-b and sorted by FACS for DsRed


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_6

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_6_NDCII_sample_0006

source_name: heart


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_3

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_3_NDCII_sample_0003


title: PDGF-B driven glioma; biological rep 3

source_name: Cell explanted from PDGF-B driven glioma and sorted by FACS for DsRed Expression


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_2

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_2_NDCII_sample_0002


title: RPMI8226-Ctrl

description: tagmentation accessible DNA


title: MM1S-Ctrl

description: tagmentation accessible DNA


title: OPM2-Len

description: tagmentation accessible DNA


title: PDGF-B driven glioma; biological rep 2


title: LP1

description: tagmentation accessible DNA


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_9

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_9_NDCII_sample_0023

value: 1 dpf


title: OPM2-Ctrl

description: tagmentation accessible DNA


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_5

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_5_NDCII_sample_0005

value: heart


title: Danio_rerio_RNAseq_singleHeart_2dpf_wt_4

description:
RNAseq of dissected hearts from 2 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_2dpf_2sd_expressedGenes_normCounts.txt
NDCII_1_4_NDCII_sample_0004


title: OCIMY5

description: tagmentation accessible DNA


title: L363-Len

description: tagmentation accessible DNA


title: EGFRvIII driven glioma; biological rep 2


title: AFM9 Bisulfite-Seq

city: Los Angeles

first: Carrie

last: Breton

address: 2001 N Soto St

department: Preventive Medicine

institute: University of Southern California

data_processing:
Real-Time Analysis Software (Version 2.7.6 for HiSeq4000)
Sequences were aligned to GRCh37, using the Wildcard Alignment Tool (WALT). Mappd read files (.mr) were then used to generate methylome files (.meth) using the Methpipe pipeline.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: BED files were generated using the MethPipe pipeline. Scores represent the estimated methylation level (column 5) and the number of reads overlapping that site (column 6)

source_name: Cord blood CD4+ cells

extract_protocol:
DNA was isolated from sorted CD4+ cells using the Qiagen All Prep DNA/RNA/miRNA kit (Qiagen, 80224)
Libraries were prepared by BGI at Shenzhen (Shenzhen, China), using 500 ng of DNA. Adapter-ligated libraries were bisulfite treated using the EZ DNA Methylation-Gold Kit (Zymo Research).

value: Cord blood CD4+ cells

tag: race/ethnicity

value: Hispanic white

tag: group

value: Smoke-exposed


title: EGFRvIII driven glioma; biological rep 1

tag: genotype


title: AFMX Bisulfite-Seq

value: Unexposed


title: MM1S-Len

description: tagmentation accessible DNA


title: iPSC (MSC, fetal, line 1, episomal 1)

description:
H1536
Sample name: SAMPLE 8

value: induced pluripotent stem cells (iPSCs)

tag: cell source

value: from fetal MSC 1 using episomal plasmids


title: AFMS Bisulfite-Seq


title: AFMW Bisulfite-Seq


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_4

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_4_NDCII_sample_0017


title: AFMP Bisulfite-Seq


title: AFL1 Bisulfite-Seq


title: wild-type_2

description:
SMALL_RNA_W2_CTAGCT_S9
wild-type 2

value: wild type

value: Mixed stage

value: whole worm

value: small RNA


title: Bacillus subtilis KM283 grown in Mannose [Mannose.1.B]

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

description: Bacillus subtilis KM283 replicate 2, grown in Mannose

hyb_protocol: The protocol was performed as described in Hendriksen et al., 2008 (PMID: 18024519)

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots ) were filtered out of all data sets.Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data.

organism: Bacillus subtilis

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences

growth_protocol: Cells were grown to OD600 of 0.25 in GM17 media

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Hendriksen et al., 2007; Hendriksen et al., 2008a). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: growth media

value: Mannose


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_7

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_7_NDCII_sample_0020


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_1

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_1_NDCII_sample_0014


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_6

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_6_NDCII_sample_0019


title: L363-Ctrl

description: tagmentation accessible DNA


title: Bacillus subtilis KMO grown in Mannitol [Mannitol.2.B]

description: Bacillus subtilis KMO   replicate 4, grown in Mannitol

source_name: Bacillus subtilis KMO grown in Mannitol

value: KMO

value: Mannitol


title: AFLU Bisulfite-Seq


title: Bacillus subtilis KMO grown in Mannos [Mannose.2.B]

description: Bacillus subtilis KMO   replicate 4, grown in Mannose

source_name: Bacillus subtilis KMO grown in Mannos

value: Mannos


title: AFHX Bisulfite-Seq


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_5

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_5_NDCII_sample_0018

value: TU/TLF mixed background


title: KMS21BM

description: tagmentation accessible DNA


title: Bacillus subtilis KM283 grown in Mannose [Mannose.2.A]

description: Bacillus subtilis KM283 replicate 3, grown in Mannose


title: KMS28

description: tagmentation accessible DNA


title: PDGF-B driven glioma; biological rep 1

value: Balb/c


title: Bacillus subtilis KMO grown in Mannitol [Mannitol.1.A]

description: Bacillus subtilis KMO   replicate 1, grown in Mannitol


title: Bacillus subtilis KM283 grown in Mannitol [Mannitol.1.B]

description: Bacillus subtilis KM283 replicate 2, grown in Mannitol


title: KMS34

description: tagmentation accessible DNA


title: AFLK Bisulfite-Seq


title: AFHK Bisulfite-Seq


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_3

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_3_NDCII_sample_0016

value: heart

value: 1 dpf


title: KMS27-Len

description: tagmentation accessible DNA

value: 10 uM lenalidomide


title: AFL0 Bisulfite-Seq

value: Cord blood CD4+ cells

value: Hispanic white


title: AFGX Bisulfite-Seq

value: Smoke-exposed


title: Bacillus subtilis KMO grown in Mannose [Mannose.1.A]

description: Bacillus subtilis KMO   replicate 1, grown in Mannose

source_name: Bacillus subtilis KMO grown in Mannose


title: Bacillus subtilis KMO grown in Maltose [Maltose.2.B]

description: Bacillus subtilis KMO   replicate 4, grown in Maltose

source_name: Bacillus subtilis KMO grown in Maltose

value: Maltose


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_6

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_6_NDCII_sample_0007


title: KMS12PE

description: tagmentation accessible DNA


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_5

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_5_NDCII_sample_0006


title: KMS27-Ctrl

description: tagmentation accessible DNA


title: AFKU Bisulfite-Seq

value: Unexposed


title: Bacillus subtilis KM283 grown in Maltose [Maltose.2.A]

description: Bacillus subtilis KM283 replicate 3, grown in Maltose


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_4

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_4_NDCII_sample_0005


title: KMS26

description: tagmentation accessible DNA


title: AFKI Bisulfite-Seq


title: AFGH Bisulfite-Seq


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_3

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_3_NDCII_sample_0004


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_9

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_9_NDCII_sample_0010


title: AFFT Bisulfite-Seq


title: Danio_rerio_RNAseq_singleHeart_1dpf_mut_2

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio rnf2 KO embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
mut_1_2_NDCII_sample_0015


title: Bacillus subtilis KMO grown in Glucose [Glucose.2.B]

description: Bacillus subtilis KMO   replicate 4, grown in Glucose

source_name: Bacillus subtilis KMO grown in Glucose

value: Glucose


title: KMS20

description: tagmentation accessible DNA


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_7

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_7_NDCII_sample_0008


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_11

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_11_NDCII_sample_0013


title: Bacillus subtilis KM283 grown in Mannitol [Mannitol.2.A]

description: Bacillus subtilis KM283 replicate 3, grown in Mannitol


title: AFFQ Bisulfite-Seq


title: KMS18

description: tagmentation accessible DNA


title: AFGS Bisulfite-Seq


title: Input-FBP1 S169A

status: Public on Mar 12 2019

city: Guangzhou

first: Bo

last: Li

address: 74 Zhongshan 2nd Rd.

country: China

institute: Sun Yat-sen University

data_processing:
Mapped the Human genome sequence (NCBIH37) by using bowtie2 (version 2.2.9)
Uniquely mapped reads using bamflag
Peaks were called using MACS2 (version 2.1.1.20160309) -g hs -q 0.05 -m 5 50
mm10
macs2

source_name: HCC

growth_protocol: Cell lines were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 2 mM Glutamine, 100 units/ml penicillin and 100 mg/ml streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody (EZH2 and H3K27me3) or streptavidin beads (FBP1-avi).
Illumina sequencing libraries were prepared from ChIP and input DNAs by performing standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation (NEBNext® Ultra™ II DNA Library Prep, NEB, E7103).

treatment_protocol: Cell lines with vector control,  FBP1 wild-type (WT), FBP1 S169A or FBP1-avi re-expression.

value: FBP1 S169A

value: Liver cancer cell

tag: passages


title: KMS12BM

description: tagmentation accessible DNA


title: Input-PCDH

value: vector control


title: ChIP-FBP1 S169A-H3K27me3 (1.289X)


title: AFG8 Bisulfite-Seq


title: ChIP-PCDH-H3K27me3


title: ChIP-FBP1 S169A-EZH2


title: KMS11

description: tagmentation accessible DNA


title: Bacillus subtilis KMO grown in Maltose [Maltose.1.A]

description: Bacillus subtilis KMO   replicate 1, grown in Maltose

value: KMO


title: Bacillus subtilis KMO grown in Glucose [Glucose.1.A]

description: Bacillus subtilis KMO   replicate 1, grown in Glucose


title: Karpas620-Len

description: tagmentation accessible DNA


title: Input-FBP1 WT

value: FBP1 WT


title: Bacillus subtilis KM283 grown in Glucose [Glucose.2.A]

description: Bacillus subtilis KM283 replicate 3, grown in Glucose


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_2

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_2_NDCII_sample_0003


title: Karpas620-Ctrl

description: tagmentation accessible DNA


title: Danio_rerio_RNAseq_singleHeart_1dpf_wt_1

description:
RNAseq of dissected hearts from 1 days post fertilization Danio rerio wild type embryos
singleHearts_monocle_1dpf_2sd_expressedGenes_normCounts.txt
W_1_1_NDCII_sample_0002


title: Bacillus subtilis KM283 grown in Maltose [Maltose.1.B]

description: Bacillus subtilis KM283 replicate 2, grown in Maltose


title: Liver_AAFM405

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
Fastq files were quality controlled using FastQC (Babraham Bioinformatics) and any adapter sequences, as well as twelve bases from the five prime end, were removed and mapped to the hg19 version of the human genome using STAR (v. 2.4.0a)
The SAM files produced from STAR were de-duplicated using Samtools (v. 0.1.19) and converted to bed files.
Quantification of gene expression was then performed using the python script rpkforgenes.py  and the UCSC hg19 refGene.txt annotation file archive-2012-03-09- 03-24-41
The obtained gene counts were then analyzed using the DESeq2 bioconductor package
Prior to differential expression analysis, genes with low reads maximum read count across samples (<20) were removed. The function DESeq was used for differential expression analysis with default settings.
Differentially expressed genes with an adjusted pvalue of <0.00001 and an absolute log2 fold change of > 4 were carried forward for CLICK analysis
Genome_build: UCSC hg19 refGene.txt annotation file archive-2012-03-09- 03-24-41
Supplementary_files_format_and_content: hESC_hepat_diff_count_matrix.txt is a count matrix with gene names in the first column and sample names in the first row. The matrix is an unfiltered raw count of reads mapping to UCSC hg19 refGene.txt  annotation file archive-2012-03-09- 03-24-41.

source_name: adult Liver

growth_protocol: Liver samples for RNAseq were collected under an approved IRB in collaboration with Planned Parenthood of the Pacific Southwest. Human fetal hepatocytes used in this study were isolated from Fetal Liver (gestation age = 17 weeks) obtained from Advanced Bioscience Resources (ABR) following a previously publish method [2]. Isolated fetal hepatocytes were then maintained in the stage 5 condition described above for the duration of the experiment. Freshly isolated adult hepatocytes (HAHs) were obtained from Samsara Sciences and cultured in DMEM (Life Technologies) supplemented with 1% ITS (Corning), 1% Antibiotic-Antimycotic solution (Life Technologies).

extract_protocol:
Total RNA was isolated using the mirVana miRNA Isolation Kit (Life Technologies, Inc.)
The RNA was quantified (Qubit RNA Assay Kit, Life Technologies, Inc.), and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent). 500 ng of total RNA was used as input for the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc.) and sequencing libraries were generated according to the manufacturer’s protocol. Briefly, the ribosomal RNA was depleted using RiboZero Gold (Illumina, Inc.), followed by a fragmentation step. The fragmented RNA was then copied into first strand cDNA using random primers and reverse transcriptase. Next, second strand cDNA synthesis was achieved using DNA Polymerase I and RNase H. The cDNA was then ligated to Illumina supplied adapters and enriched with PCR to create the final cDNA libraries.

treatment_protocol: Differentiation conditions were as follows: Stage 1. Definitive Endoderm induction was performed as described [1] in Chemically Defined Medium (CDM) for 3 days. Briefly, hPSCs were differentiated into mesendoderm in presence of Ly294002 (10uM, Calbiochem), Activin A (100ng/ml, Stemgent), BMP4 (10ng/ml, R&D), FGF2 (25ng/ml, Biopioneer) and CHIR 99021(3uM, Tocris) for 24 hours. For the next 48 hours cells were exposed to Ly294002 (10uM), Activin A (100ng/ml), BMP4 (10ng/ml) and FGF2 (25ng/ml). Stage 2. DE cells were then committed to Posterior Foregut (PFG) Cells. We tested several combinations of factors in RPMI (Invitrogen) supplemented with B27 supplement (Invitrogen), including a range of doses of Activin A (Stemgent), Noggin (R&D) and IWR-1 (Seleckchem), as described in Fig. 2. The final condition that was identified to result in the highest yield of PFG cells, and which was used in subsequent experiments, was 1uM of IWR-1 in RPMI/B27. Stage 3. For establishment of improved hepatic commitment conditions, PFG cells were exposed for 4 days to different combinations of: TGFβ inhibitor SB431452 (10uM, Tocris), BMP4 (10ng/ml), Retinoic Acid (RA, 2uM, Sigma), and IWR-1(1uM) in RPMI medium supplemented with B27. The final condition that was identified to result in the highest yield of hepatic gut cells, and which was used in subsequent experiments, was BMP4, SB and IWR-1. Stage 4. Stage 4 conditions were established by maintaining cells during 4 days in a medium permissive for hepatic progenitors consisting of RPMI (Invitrogen) with 1% ITS (Invitrogen), 0.1% bovin serum albumin (BSA, Invitrogen), 4.5 mM nicotinamide (Sigma), 0.1 nM Zinc 3 Sulfate heptahydrate and 10-8 M hydrocortisone (Sigma), supplemented with HGF (20ng/ml, Peprotech), with the addition of combinations of: VEGF (20ng/ml, Peprotech), CHIR99001 (3uM) and TGFβ (10ng/ml, Peprotech). The final condition that was identified to result in the highest yield of proliferative hepatoblasts, and which was used in subsequent experiments, was HGF, CHIR, VEGF and TGFβ. Stage 5. Stage 5 conditions were established by maintaining hepatic progenitors 4 days in a medium permissive for hepatocytes culture (consisting of stage 4 medium complemented with 1nM triiodothyroxine 3 (T3)) in presence of HGF (20ng/ml) and different combinations of: Notch inhibitor Compound E (CE) (0.5uM, VWR), TGFβ inhibitor SB431452 (5uM) and oncostatin M (OSM) (20ng/ml, Peprotech). The final condition that was identified to result in the highest functionality of hepatocytes was HGF, CE and S

tag: developmental stage

value: adult Liver

tag: rnaseq protocol

value: PolyA Selection

value: liver


title: St4_b

source_name: Differentiated human embryonic stem cells

value: Stage 4


title: St3_b

value: Stage 3

value: Differentiated human embryonic stem cells


title: Liver_ABFE481


title: St2_a

value: Stage 2


title: Bacillus subtilis KM283 grown in Glucose [Glucose.1.B]

description: Bacillus subtilis KM283 replicate 2, grown in Glucose

tag: genotype/variation


title: Input-FLBIO-FBP1

source_name: hepatocyte

value: Liver normal cell


title: ChIP-FLBIO-FBP1


title: AFFR Bisulfite-Seq

value: Cord blood CD4+ cells

value: Hispanic white

value: Smoke-exposed


title: ChIP-FBP1 WT-H3K27me3 (1.854X)


title: HTR8/SVneo: shControl

city: shanghai

first: ql

last: zheng

address: xiangyin

institute: immunity

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files containing include RPKM values for each Sample

growth_protocol: Cells were grown in RIPM-1640 media supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from HTR8 cell lines infected with shControl or shALKBH5 using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HTR8/Svneo cells infected with lentiviral shControl or shALKBH5

value: trophoblast


title: H1112

description: tagmentation accessible DNA

source_name: Myeloma cell line


title: ChIP-FBP1 WT-EZH2


title: ChIP-PCDH-EZH2


title: Undiff_b

source_name: human embryonic stem cells

value: Undifferentiated

value: human embryonic stem cells


title: St4_a


title: XPC1

city: Leganes

first: carlos

last: leon

state: Madrid

address: Avenida Universidad 30

department: Bioengineering

country: Spain

data_processing:
Quality control analysis on the resulting fastq sequencing files was performed using FastQC. Reads were adapter trimmed using cutadapt version 1.3 with the parameters -q 30 -m 50 -a AGATCGGAAGAGC. Trimmed reads were aligned to Ensembl version 38.81 of the Homo sapiens genome with tophat2 version 2.0.13 using default parameters (except "-r -70 --mate-std-dev 75" to specify insert sizes).
The bam files were sorted by name using picard-tools (version 1.115) SortSam. Read counts were generated using htseq-count version 0.6.0 in unstranded mode, and Python version 2.7.3, with parameters -m union -i gene_id -t exon.
RNA-Seq data were normalized using the Trimmed Mean of M values (TMM). An adjustment for possible batch effects due to the need to use different chips for the sequencing was performed using the R package ComBat
Genome_build: Ensembl version 38.81 of the Homo sapiens genome
Supplementary_files_format_and_content: normalized counts of 18 samples

source_name: Skin

growth_protocol: Fibroblasts were isolated by mechanical and enzymatic digestion and cultured in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum  and 1% Antibiotic-Antimycotic

extract_protocol:
Total RNA was isolated from confluent primary fibroblasts using RNeasy kit
cDNA libraries for each sample were generated using the TruSeq RNA Sample Preparation Kit
Samples were prepared in two batches for a total of 18 libraries. Ligation and library integrity was verified using a DNA chip on the Agilent 2100 Bioanalyzer. Sample libraries ligated with unique adapter sequences were multiplexed six to a lane and were sequenced using Illumina HiSeq HO v4 125 paired end sequencing

treatment_protocol: Culture medium was changed 24h before harvesting the cells.

tag: tissue

value: Dermal fibroblasts

value: 3 to 7

tag: diagnosis

value: Xeroderma pigmentosum C


title: ChIP-PCDH-IgG (10X)

value: vector control

value: Liver cancer cell


title: XPC2


title: St2_b

city: La Jolla

value: PolyA Selection


title: Undiff_a


title: St5_3_a

value: Stage 5_3


title: KS1

value: Kindler syndrome


title: St3_a

value: Stage 3

value: Differentiated human embryonic stem cells


title: RDEB7

value: Recessive dystrophic epidermolysis bullosa


title: RDEB9


title: KS2


title: Liver_364_ribozero

source_name: fetal Liver

value: fetal Liver

value: Ribo Depletion

value: liver


title: Liver_370


title: DE_b

value: Definitive Endoderm


title: DE_a


title: HTR8/SVneo: shALKBH5

value: trophoblast


title: Liver_369


title: XPC3


title: KS3


title: RDEB6


title: RDEB8


title: RDEB5


title: RDEB3


title: RDEB4


title: RDEB2


title: Control 3

value: Healthy


title: MCF10AsiSIER_4OHT2h_XRCC4_chip

city: Milano

first: Pier Giuseppe

last: Pelicci

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
ChIP-seq: reads were aligned to the hg18 genome assembly using bwa version 0.6.2 with the default parameters
ChIP-seq: low-quality and multiple-mapping reads were removed using Samtools with option ‘‘-q 1’
ChIP-seq: duplicates (reads with the same start and end position mapping) that are potential PCR artifacts are removed with samtools rmdup -s
ChIP-seq: peaks were called using MACS 1.4.1 with default setting
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq: bigwig files were obtained with a combination of bedtools (v2.16.1) sub-commands: aligned reads (bam) were converted in bed with bamToBed and extended to approximately 200 bp with slopbed; then genomeCoverageBed were used to generate the wig file, which in turn is transformed to bigwig with the UCSC Genome Browser utility wigToBigWig.

growth_protocol: ChIP-seq: MCF10A-AsiSIER cells were routinely grown by re-plating adherent cultures (typically 8 × 10^5 cells into a tissue-culture dish 100mm) in a medium composed of DMEM (Lonza) and HAM's F12 (GibcoLife Technologies) 1:1, supplemented with horse serum 1%, hydrocortisone 0,5mg/ml, hEGF10ug/ml, insulin 5mg/ml, glutamine 0,5% and 100 ng/ml of cholera toxin.

extract_protocol:
ChIP-seq: Cells were cross-linked by adding formaldehyde to the culture medium to a final concentration of 1% (8 min at RT). Cross-linking was stopped by addition of glycine to a final concentration of 125 mM. Cells were washed twice with PBS and lysed in SDS buffer: 100 mM NaCl, 50 mM Tris HCl (pH 8.1), 5 mM EDTA (pH 8), 0.5% SDS, and protease inhibitors. Chromatin lysate was then pelleted and resuspended in IP buffer (100 mM NaCl, 100 mM Tris HCl at pH 8.1, 5 mM EDTA at pH 8, 0.3% SDS, 1.7% Triton X-100), where it was directly sonicated prior to overnight incubation with antibodies .
ChIP-seq: Libraries were prepared according to HT-ChIP-Seq Library Preparation Protocol. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3´→ 5´ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of indexed oligo adaptors which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with amplification primers for 14 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: ChIP-seq: MCF10A-AsiSIER cells were treated for 2 hours with 4-Hydroxytamoxifen 300nM (final conc), adding the drug directly into the medium.

value: normal mammary gland

value: 4-Hydroxytamoxifen (4OHT) 300 nM for 2h

tag: chip antibody

value: XRCC4 (Sigma, HPA006801)


title: RDEB1

value: Dermal fibroblasts

value: 3 to 7


title: MCF10AsiSIER_DRB_XRCC4_chip

value: 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) 20 mM, 30 min


title: Control 2


title: MCF10AsiSIER_washout_after DRB_XRCC4_chip

value: 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) 20 mM, 30 min+washout 1 hour


title: MCF10AsiSIER_NT_PARP1_chip

value: not treated

value: PARP1 (Active Motif, #39559)


title: MCF10AsiSIER_DRB_POL2_S5_chip

value: POLR2A-phosphoS5 (Abcam, ab5131)


title: MCF10AsiSIER_NT_XRCC4_chip


title: MCF10AsiSIER_NT_POL2_S2_chip

value: POLR2A-phosphoS2 (Bethyl Laboratories, A300-654A)


title: Control 1


title: MCF10AsiSIER_NT_TOP1_chip

value: Camptothecin (8 mM, 15 min)

value: TOP1 (Abcam, ab3825)


title: Control, biological rep3

city: London

first: Paul

middle: T.

last: Sharpe

state: Please select one below:

address: Guy's hospitial

department: Centre for Craniofacial and Regenerative Biology

institute: King's College London

description: Gene expression data from Ring1b deletion samples than control samples.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse dental pulp cell

label_protocol: After cDNA synthesis, an in vitro transcription (IVT) amplification was done to obtain sufficient amounts of labelled cRNA target for analysis with arrays. The unlabelled cRNA is then reverse transcribed in the first-stand cDNA synthesis step of the second cycle using random promers. Subsequenctly, the T7-Oligo (dT) promoter Primer was used in the second-strand cDNA synthesis to generate double-stranded cDNA template contining T7 promoter sequences, and double-stranded cDNA was then amplified and labeled using a biotinylated nucleotide analog/ribonucleotide mix in the second IVTreaction. The labeled cRNA was then cleaned up and fragmented before hybridisation.

extract_protocol: Total RNA were extracted by RNeasy Micro Kit (Qigen) and purified with Ambion® DNA-free™ DNase Treatment. The Ovation® Pico WTA System V2 used to amplify cDNA from total RNA.

treatment_protocol: Mice were injected with 4-hydroxy tamoxinfen (OHT) (40mg/kg body weight) for Ring1 deletion or corn oil for control mice at postnatal 9 days and 13 days and sacrified at postnatal 17 days.

value: mouse dental pulp

value: Ring1a-/-;Ring1b flox/flox ;CreERT2


title: Control, biological rep2


title: Ring1 deletion, biological rep3

value: Ring1a-/-;Ring1b cko/cko ;CreERT2


title: Ring1 deletion, biological rep2


title: Control, biological rep1


title: Ring1 deletion, biological rep1


title: PBYSM1

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 1
raw data file: PBYSM12_252828211743_4.txt

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

organism: Rattus norvegicus

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: On G15, pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females. The rats prenatally exposed (G15) to betamethasone had repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered infantile spasms and autistic behavior. Pups were treated with saline on days 13, 14 and 15 prior to NMDA administration .

tag: Sex

value: male

value: Sprague-Dawley

value: hypothalamic paraventricular nucleus

tag: prenatal exposure

value: betamethasone

tag: condition

value: infantile spasms and autistic behavior

tag: postnatal treatment

value: saline


title: 937S_MSCB-008

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

institute: Centro Nacional de Análisis Genómico

data_processing:
Primary data analysis was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Sequenced reads were filtered for low-complexity or low-quality sequence.
MARS-Seq libraries were mapped as single-end reads with the GEMTools 1.7.0 RNA pipeline on the mouse  genome reference.
For MARS-seq samples, gene quantification was performed using UMI corrected transcript information to correct for amplification biases.
Genome_build: Assembly GRCm38. Gencode release M8.
Supplementary_files_format_and_content: Tab-separated values (.tsv) files containing gene expression values (rows) as UMI counts for each cell (columns).

source_name: bone marrow

growth_protocol: We used 'reprogrammable mice' containing a doxycycline-inducible OSKM cassette and thetetracycline transactivator. pre-B cells were isolated from 8- to 16-week-old female mice. Mice were housed in standard cages under 12-h light–dark cycles and fed ad libitum with a standard chow diet.    After isolation, pre-B cells were grown in RPMI medium supplemented with 10% FBS and 10ng/ml IL-7 (Peprotech), L-glutamine, nonessential amino acids, β-mercaptoethanol (Life Technologies) as well as penicillin/streptomycin. All cell lines were routinely tested for mycoplasma contamination.

extract_protocol:
CD19+ pre-B cells were isolated from the bone marrow of these mice using monoclonal antibody to CD19 (clone 1D3, BD Pharmingen #553784) and MACS sorting (Miltenyi Biotech). Cell purity was confirmed to be >98% CD19+ by FACS using an LSRII machine (BD).
To construct single cell libraries from polyA-tailed RNA, we applied massively parallel single-cell RNA sequencing (MARS-Seq; Jaitin et al., Science 2014).  This methodology generates paired-end reads where read 1 contains the transcript sequence and read 2 the cell and UMI barcodes. Briefly, single cells were FACS-sorted into 384-well plates, containing lysis buffer and reverse-transcription (RT) primers. The RT primers contained the single cell barcodes and unique molecular identifiers (UMIs) for subsequent de-multiplexing and correction for amplification biases, respectively.

treatment_protocol: For transdifferentiation pre-B cells were infected with C/EBPα-ER-hCD4 retrovirus produced by the PlatE retroviral packaging cell line (Cell Biolabs, # RV-101). The cells were expanded for 48hrs on Mitomycin C-inactivated S17 feeders grown in RPMI medium supplemented with 10 ng/mL each of IL-7 (Peprotech) and hCD4+ were sorted (FACSaria, BD). For transdifferentiation C/EBPα was induced by treating the cells with 100 nM β-Estradiol (E2) in medium supplemented with 10 ng/mL each of IL-7 (Peprotech), IL-3 (Peprotech) and human colony-stimulating factor 1 (hCSF-1). For reprogramming hCD4+ cells were plated at 500 cells/cm2 in gelatinized plates (12 wells) on irradiated MEF feeders in RPMI medium and pre-treated for 18h with E2 to induce C/EBPα. After E2 washout the cultures were switched to serum-free N2B27 medium supplemented with 10 ng/ml IL-4, IL-7 and IL-15 at 2 ng/ml and treated with 2 μg/ml of doxycycline to activate OSKM. From day 2 onwards the N2B27 medium was supplemented with 20% KSR (Life Technologies), 3 μM CHIR99021 and 1uM PD0325901(2i medium).

tag: cell type

value: pre-B cell

tag: treatment

tag: induction

value: C/EBPα

tag: fate

tag: time point


title: 937S_MSCB-006


title: 937S_MSCB-004


title: 937S_MSCB-003


title: 937S_MSCB-007


title: 937S_MSCB-009


title: 937S_MSCB-005


title: PBYPM1

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 1
raw data file: PBYPM12_252828211746_4.txt

treatment_protocol: On G15, pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females. The rats prenatally exposed (G15) to betamethasone had repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered infantile spasms and autistic behavior. Pups were treated with PMX53 (a potent C5ar1 antagonist) on days 13, 14 and 15 prior to NMDA administration to determine what effects the treatment had on transcriptome recovery.

tag: strain


title: PBYSM3

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 3
raw data file: PBYSM34_252828211743_3.txt


title: 936S_MSCB-192


title: 937S_MSCB-001


title: PBYSM2

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 2
raw data file: PBYSM12_252828211743_4.txt


title: PBYSM4

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 4
raw data file: PBYSM34_252828211743_3.txt


title: PBYSF3

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 3
raw data file: PBYSF34_252828211748_3.txt

value: female


title: PBYSF4

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 4
raw data file: PBYSF34_252828211748_3.txt


title: 937S_MSCB-002


title: PBYPF3

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 3
raw data file: PBYPF34_252828211741_3.txt


title: PBYPF4

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 4
raw data file: PBYPF34_252828211741_3.txt


title: PBYPM2

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 2
raw data file: PBYPM12_252828211746_4.txt


title: 936S_MSCB-190


title: PBYPM4

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 4
raw data file: PBYPM34_252828211746_3.txt


title: PBYPF1

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 1
raw data file: PBYPF12_252828211741_4.txt


title: PBYSF2

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 2
raw data file: PBYSF12_252828211748_4.txt


title: PBYPF2

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 2
raw data file: PBYPF12_252828211741_4.txt


title: PBYPM3

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with PMX53 P15_Replicate 3
raw data file: PBYPM34_252828211746_3.txt


title: 936S_MSCB-186


title: 936S_MSCB-189


title: PBYSF1

description:
Gene expression in hypothalamic paraventricular nucleus of prenatally exposed to betamethasone_with infantile spasms_postnatally treated with saline P15_Replicate 1
raw data file: PBYSF12_252828211748_4.txt


title: 936S_MSCB-180


title: 936S_MSCB-183


title: 936S_MSCB-182


title: 936S_MSCB-179


title: 936S_MSCB-185


title: 936S_MSCB-175


title: 936S_MSCB-174


title: 936S_MSCB-177


title: 936S_MSCB-191


title: 936S_MSCB-176


title: 936S_MSCB-170


title: 936S_MSCB-167


title: 936S_MSCB-173


title: 936S_MSCB-172


title: 936S_MSCB-166


title: 936S_MSCB-168


title: 936S_MSCB-178


title: 936S_MSCB-164


title: 936S_MSCB-181


title: 936S_MSCB-163


title: 936S_MSCB-184


title: 936S_MSCB-161


title: 936S_MSCB-159


title: 936S_MSCB-160


title: 936S_MSCB-158


title: 936S_MSCB-171


title: 936S_MSCB-157


title: 936S_MSCB-156


title: 936S_MSCB-169


title: 936S_MSCB-154


title: 936S_MSCB-152


title: 936S_MSCB-153


title: 936S_MSCB-147


title: 936S_MSCB-148


title: 936S_MSCB-155


title: 936S_MSCB-151


title: 936S_MSCB-146


title: 936S_MSCB-145


title: 936S_MSCB-141


title: 936S_MSCB-142


title: 936S_MSCB-143


title: 936S_MSCB-150


title: 936S_MSCB-144


title: 936S_MSCB-162


title: 936S_MSCB-140


title: 936S_MSCB-138


title: 936S_MSCB-137


title: 936S_MSCB-135


title: 936S_MSCB-139


title: 936S_MSCB-136


title: 936S_MSCB-134


title: 936S_MSCB-132


title: 936S_MSCB-165


title: 936S_MSCB-149


title: 936S_MSCB-133


title: 936S_MSCB-131


title: 936S_MSCB-129


title: 936S_MSCB-130


title: 936S_MSCB-126


title: 936S_MSCB-125


title: 936S_MSCB-123


title: 936S_MSCB-128


title: 936S_MSCB-122


title: 936S_MSCB-118


title: 936S_MSCB-121


title: 936S_MSCB-188


title: 936S_MSCB-124


title: 936S_MSCB-119


title: 936S_MSCB-120


title: 936S_MSCB-115


title: 936S_MSCB-114


title: 936S_MSCB-113


title: 936S_MSCB-110


title: 936S_MSCB-108


title: 936S_MSCB-109


title: 936S_MSCB-112


title: 936S_MSCB-105


title: 936S_MSCB-111


title: 936S_MSCB-107


title: 936S_MSCB-103


title: 936S_MSCB-127


title: 936S_MSCB-106


title: 936S_MSCB-102


title: 936S_MSCB-117


title: 936S_MSCB-104


title: 936S_MSCB-116


title: 936S_MSCB-097


title: 936S_MSCB-098


title: 936S_MSCB-092


title: 936S_MSCB-094


title: 936S_MSCB-093


title: 936S_MSCB-090


title: 936S_MSCB-099


title: 936S_MSCB-091


title: 936S_MSCB-095


title: 936S_MSCB-096


title: 936S_MSCB-089


title: 936S_MSCB-087


title: 936S_MSCB-088


title: 936S_MSCB-085


title: 936S_MSCB-086


title: 936S_MSCB-084


title: 936S_MSCB-083


title: 936S_MSCB-082


title: 936S_MSCB-079


title: 936S_MSCB-081


title: 936S_MSCB-077


title: 936S_MSCB-078


title: 936S_MSCB-080


title: 936S_MSCB-100


title: 936S_MSCB-075


title: 936S_MSCB-073


title: 936S_MSCB-074


title: 936S_MSCB-101


title: 936S_MSCB-067


title: 936S_MSCB-068


title: 936S_MSCB-069


title: 936S_MSCB-070


title: 936S_MSCB-064


title: 936S_MSCB-071


title: 936S_MSCB-066


title: 936S_MSCB-072


title: 936S_MSCB-062


title: 936S_MSCB-065


title: 936S_MSCB-063


title: 936S_MSCB-061


title: 936S_MSCB-060


title: 936S_MSCB-057


title: 936S_MSCB-058


title: 936S_MSCB-055


title: 936S_MSCB-059


title: 936S_MSCB-056


title: 936S_MSCB-076


title: 936S_MSCB-053


title: 936S_MSCB-052


title: 936S_MSCB-051


title: 936S_MSCB-048


title: 936S_MSCB-049


title: 936S_MSCB-050


title: 936S_MSCB-047


title: 936S_MSCB-046


title: 936S_MSCB-045


title: 936S_MSCB-043


title: 936S_MSCB-042


title: 936S_MSCB-044


title: 936S_MSCB-040


title: 936S_MSCB-039


title: 936S_MSCB-041


title: 936S_MSCB-035


title: 936S_MSCB-038


title: 936S_MSCB-037


title: 936S_MSCB-034


title: 936S_MSCB-033


title: 936S_MSCB-036


title: 936S_MSCB-054


title: 936S_MSCB-028


title: 936S_MSCB-031


title: 936S_MSCB-027


title: 936S_MSCB-032


title: 936S_MSCB-029


title: 936S_MSCB-030


title: 936S_MSCB-025


title: 936S_MSCB-026


title: 936S_MSCB-024


title: 936S_MSCB-020


title: 936S_MSCB-021


title: 936S_MSCB-023


title: 936S_MSCB-019


title: 936S_MSCB-017


title: 936S_MSCB-018


title: 936S_MSCB-022


title: 936S_MSCB-187


title: 936S_MSCB-014


title: 936S_MSCB-013


title: 936S_MSCB-016


title: 936S_MSCB-012


title: 936S_MSCB-011


title: 936S_MSCB-010


title: 936S_MSCB-007


title: 936S_MSCB-009


title: 936S_MSCB-008


title: 936S_MSCB-006


title: 936S_MSCB-005


title: 936S_MSCB-004


title: 936S_MSCB-003


title: 935S_MSCB-191

value: transdifferentiation

value: iMac


title: 936S_MSCB-002


title: 935S_MSCB-190


title: 935S_MSCB-192


title: 935S_MSCB-188


title: 935S_MSCB-187


title: 935S_MSCB-185


title: 935S_MSCB-184


title: 935S_MSCB-183


title: 935S_MSCB-189


title: 936S_MSCB-015


title: 935S_MSCB-180


title: 935S_MSCB-181


title: 935S_MSCB-182


title: 935S_MSCB-174


title: 935S_MSCB-173


title: 935S_MSCB-177


title: 935S_MSCB-176


title: 935S_MSCB-179


title: 935S_MSCB-178


title: 935S_MSCB-170


title: 935S_MSCB-169


title: 936S_MSCB-001


title: 935S_MSCB-171


title: 935S_MSCB-172


title: 935S_MSCB-167


title: 935S_MSCB-186


title: 935S_MSCB-168


title: 935S_MSCB-164


title: 935S_MSCB-165


title: 935S_MSCB-163


title: 935S_MSCB-162


title: 935S_MSCB-160


title: 935S_MSCB-157


title: 935S_MSCB-158


title: 935S_MSCB-161


title: 935S_MSCB-159


title: 935S_MSCB-156


title: 935S_MSCB-155


title: 935S_MSCB-153


title: 935S_MSCB-175


title: 935S_MSCB-152


title: 935S_MSCB-154


title: 935S_MSCB-150


title: 935S_MSCB-145


title: 935S_MSCB-147


title: 935S_MSCB-144


title: 935S_MSCB-143


title: 935S_MSCB-142


title: 935S_MSCB-166


title: 935S_MSCB-140


title: 935S_MSCB-138


title: 935S_MSCB-136


title: 935S_MSCB-139


title: 935S_MSCB-137


title: 935S_MSCB-134


title: 935S_MSCB-133


title: 935S_MSCB-130


title: 935S_MSCB-131


title: 935S_MSCB-129


title: 935S_MSCB-127


title: 935S_MSCB-128


title: 935S_MSCB-132


title: 935S_MSCB-151


title: 935S_MSCB-124


title: 935S_MSCB-149


title: 935S_MSCB-126


title: 935S_MSCB-148


title: 935S_MSCB-123


title: 935S_MSCB-125


title: 935S_MSCB-146


title: 935S_MSCB-122


title: 935S_MSCB-141


title: 935S_MSCB-118


title: 935S_MSCB-119


title: 935S_MSCB-117


title: 935S_MSCB-116


title: 935S_MSCB-135


title: 935S_MSCB-114


title: 935S_MSCB-115


title: 935S_MSCB-110


title: 935S_MSCB-113


title: 935S_MSCB-109


title: 935S_MSCB-108


title: 935S_MSCB-112


title: 935S_MSCB-107


title: 935S_MSCB-104


title: 935S_MSCB-105


title: 935S_MSCB-102


title: 935S_MSCB-103


title: 935S_MSCB-106


title: 935S_MSCB-101


title: 935S_MSCB-100


title: 935S_MSCB-098


title: 935S_MSCB-097


title: 935S_MSCB-120


title: 935S_MSCB-095


title: 935S_MSCB-121


title: 935S_MSCB-096


title: 935S_MSCB-093


title: 935S_MSCB-092


title: 935S_MSCB-091


title: 935S_MSCB-111


title: 935S_MSCB-089


title: 935S_MSCB-088


title: 935S_MSCB-086


title: 935S_MSCB-087


title: 935S_MSCB-085


title: 935S_MSCB-083


title: 935S_MSCB-084


title: 935S_MSCB-081


title: 935S_MSCB-082


title: 935S_MSCB-077


title: 935S_MSCB-076


title: 935S_MSCB-075


title: 935S_MSCB-073


title: 935S_MSCB-069


title: 935S_MSCB-078


title: 935S_MSCB-080


title: 935S_MSCB-070


title: 935S_MSCB-094


title: 935S_MSCB-074


title: 935S_MSCB-067


title: 935S_MSCB-090


title: 935S_MSCB-066


title: 935S_MSCB-065


title: 935S_MSCB-072


title: 935S_MSCB-068


title: 935S_MSCB-071


title: 935S_MSCB-063


title: 935S_MSCB-061


title: 935S_MSCB-062


title: 935S_MSCB-059


title: 935S_MSCB-060


title: 935S_MSCB-057


title: 935S_MSCB-054


title: 935S_MSCB-056


title: 935S_MSCB-055


title: 935S_MSCB-079


title: 935S_MSCB-053


title: 935S_MSCB-064


title: 935S_MSCB-048


title: 935S_MSCB-052


title: 935S_MSCB-051


title: 935S_MSCB-046


title: 935S_MSCB-042


title: 935S_MSCB-043


title: 935S_MSCB-049


title: 935S_MSCB-040


title: 935S_MSCB-045


title: 935S_MSCB-039


title: 935S_MSCB-047


title: 935S_MSCB-099


title: 935S_MSCB-041


title: 935S_MSCB-058


title: 935S_MSCB-037


title: 935S_MSCB-038


title: 935S_MSCB-034


title: 935S_MSCB-036


title: 935S_MSCB-035


title: 935S_MSCB-050


title: 935S_MSCB-032


title: 935S_MSCB-028


title: 935S_MSCB-044


title: 935S_MSCB-025


title: 935S_MSCB-024


title: 935S_MSCB-026


title: 935S_MSCB-023


title: 935S_MSCB-027


title: 935S_MSCB-021


title: 935S_MSCB-018


title: 935S_MSCB-019


title: 935S_MSCB-016


title: 935S_MSCB-014


title: 935S_MSCB-011


title: 935S_MSCB-012


title: 935S_MSCB-020


title: 935S_MSCB-022


title: 935S_MSCB-017


title: 935S_MSCB-031


title: 935S_MSCB-015


title: 935S_MSCB-010


title: 935S_MSCB-033


title: 935S_MSCB-009


title: 935S_MSCB-029


title: 935S_MSCB-005


title: 935S_MSCB-007


title: 935S_MSCB-006


title: 935S_MSCB-003


title: 935S_MSCB-004


title: 935S_MSCB-008


title: 935S_MSCB-001


title: 934S_MSCB-189


title: 935S_MSCB-013


title: 934S_MSCB-187


title: 934S_MSCB-186


title: 934S_MSCB-191


title: 934S_MSCB-188


title: 934S_MSCB-192


title: 934S_MSCB-182


title: 934S_MSCB-181


title: 934S_MSCB-177


title: 934S_MSCB-179


title: 934S_MSCB-178


title: 934S_MSCB-180


title: 934S_MSCB-175


title: 934S_MSCB-173


title: 935S_MSCB-002


title: 934S_MSCB-172


title: 934S_MSCB-174


title: 934S_MSCB-183


title: 934S_MSCB-169


title: 934S_MSCB-168


title: 934S_MSCB-170


title: 934S_MSCB-171


title: 934S_MSCB-185


title: 934S_MSCB-167


title: 934S_MSCB-190


title: 934S_MSCB-166


title: 934S_MSCB-165


title: 934S_MSCB-164


title: 934S_MSCB-184


title: 935S_MSCB-030


title: 934S_MSCB-161


title: 934S_MSCB-176


title: 934S_MSCB-162


title: 934S_MSCB-163


title: 934S_MSCB-159


title: 934S_MSCB-157


title: 934S_MSCB-160


title: 934S_MSCB-158


title: 934S_MSCB-149


title: 934S_MSCB-147


title: 934S_MSCB-155


title: 934S_MSCB-152


title: 934S_MSCB-154


title: 934S_MSCB-145


title: 934S_MSCB-143


title: 934S_MSCB-144


title: 934S_MSCB-151


title: 934S_MSCB-148


title: 934S_MSCB-146


title: 934S_MSCB-156


title: 934S_MSCB-142


title: 934S_MSCB-141


title: 934S_MSCB-150


title: 934S_MSCB-140


title: 934S_MSCB-138


title: 934S_MSCB-139


title: 934S_MSCB-135


title: 934S_MSCB-134


title: 934S_MSCB-136


title: 934S_MSCB-133


title: 934S_MSCB-131


title: 934S_MSCB-153


title: 934S_MSCB-132


title: 934S_MSCB-130


title: 934S_MSCB-129


title: 934S_MSCB-128


title: 934S_MSCB-127


title: 934S_MSCB-126


title: 934S_MSCB-137


title: 934S_MSCB-123


title: 934S_MSCB-120


title: 934S_MSCB-124


title: 934S_MSCB-119


title: 934S_MSCB-118


title: 934S_MSCB-115


title: 934S_MSCB-125


title: 934S_MSCB-114


title: 934S_MSCB-112


title: 934S_MSCB-122


title: 934S_MSCB-113


title: 934S_MSCB-116


title: 934S_MSCB-111


title: 934S_MSCB-117


title: 934S_MSCB-110


title: 934S_MSCB-109


title: 934S_MSCB-107


title: 934S_MSCB-103


title: 934S_MSCB-104


title: 934S_MSCB-108


title: 934S_MSCB-106


title: 934S_MSCB-105


title: 934S_MSCB-121


title: 934S_MSCB-101


title: 934S_MSCB-102


title: 934S_MSCB-100


title: 934S_MSCB-098


title: 934S_MSCB-099


title: 934S_MSCB-097


title: 934S_MSCB-096


title: 934S_MSCB-092


title: 934S_MSCB-090


title: 934S_MSCB-095


title: 934S_MSCB-089


title: 934S_MSCB-087


title: 934S_MSCB-094


title: 934S_MSCB-085


title: 934S_MSCB-086


title: 934S_MSCB-093


title: 934S_MSCB-091


title: 934S_MSCB-084


title: 934S_MSCB-082


title: 934S_MSCB-088


title: 934S_MSCB-081


title: 934S_MSCB-083


title: 934S_MSCB-080


title: 934S_MSCB-078


title: 934S_MSCB-079


title: 934S_MSCB-077


title: 934S_MSCB-075


title: 934S_MSCB-074


title: 934S_MSCB-073


title: 934S_MSCB-071


title: 934S_MSCB-070


title: 934S_MSCB-069


title: 934S_MSCB-068


title: 934S_MSCB-067


title: 934S_MSCB-066


title: 934S_MSCB-064


title: 934S_MSCB-065


title: 934S_MSCB-063


title: 934S_MSCB-060


title: 934S_MSCB-062


title: 934S_MSCB-061


title: 934S_MSCB-059


title: 934S_MSCB-058


title: 934S_MSCB-054


title: 934S_MSCB-056


title: 934S_MSCB-053


title: 934S_MSCB-052


title: 934S_MSCB-051


title: 934S_MSCB-050


title: 934S_MSCB-076


title: 934S_MSCB-048


title: 934S_MSCB-049


title: 934S_MSCB-072


title: 934S_MSCB-046


title: 934S_MSCB-045


title: 934S_MSCB-044


title: 934S_MSCB-042


title: 934S_MSCB-041


title: 934S_MSCB-057


title: 934S_MSCB-055


title: 934S_MSCB-035


title: 934S_MSCB-037


title: 934S_MSCB-039


title: 934S_MSCB-033


title: 934S_MSCB-038


title: 934S_MSCB-032


title: 934S_MSCB-030


title: 934S_MSCB-028


title: 934S_MSCB-034


title: 934S_MSCB-026


title: 934S_MSCB-024


title: 934S_MSCB-025


title: 934S_MSCB-040


title: 934S_MSCB-027


title: 934S_MSCB-023


title: 934S_MSCB-043


title: 934S_MSCB-021


title: 934S_MSCB-020


title: 934S_MSCB-018


title: 934S_MSCB-019


title: 934S_MSCB-017


title: 934S_MSCB-016


title: 934S_MSCB-014


title: 934S_MSCB-031


title: 934S_MSCB-013


title: 934S_MSCB-012


title: 934S_MSCB-009


title: 934S_MSCB-007


title: 934S_MSCB-008


title: 934S_MSCB-006


title: 934S_MSCB-005


title: 934S_MSCB-022


title: 934S_MSCB-004


title: 934S_MSCB-003


title: 934S_MSCB-002


title: 934S_MSCB-001


title: 933S_MSCB-192


title: 933S_MSCB-190


title: 933S_MSCB-191


title: 934S_MSCB-015


title: 933S_MSCB-188


title: 933S_MSCB-186


title: 933S_MSCB-189


title: 933S_MSCB-187


title: 933S_MSCB-184


title: 933S_MSCB-185


title: 934S_MSCB-010


title: 933S_MSCB-183


title: 933S_MSCB-181


title: 933S_MSCB-180


title: 933S_MSCB-182