title: CEMBA180426_8B_3_CEMBA180426_8B_4_E10_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_E11_ad004

status: Public on Sep 04 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: SSp

tag: Sex

value: male

tag: age

tag: strain


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title: CEMBA180426_8B_3_CEMBA180426_8B_4_B5_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B3_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B3_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B2_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B6_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B3_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B12_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B12_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B12_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B12_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B4_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B12_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B3_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B11_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B3_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B10_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B12_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_B1_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad010


title: YueLab-Muscle-WGBS

city: CHICAGO

first: Yu

last: Luan

state: Illinois

address: 303 E. Superior Simpson Querrey 7-518

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
RNA-seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac, H3K4me3 ChIP-seq were called using MACS2 with the following  setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5.For the ATAC-seq, the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain, we called the peak using Homer with the parameter “-region -size 1000”, and peaks within 5 kb were merged together.
HiC matrix was generated using HiC-Pro
WGBS data were mapped to in silico bisulfite-converted zebrafish genome reference by using Bismark
For the scATAC-seq, the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC-seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode.
Genome_build: zv10(GRCz10)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged

organism: Danio rerio

source_name: YueLab-Muscle-WGBS

growth_protocol:
RNA-seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions
ChIP-seq, ATAC-seq, Hi-C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions

extract_protocol:
RNA-seq: For each RNA-seq experiment, the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk, ten 1-dpf fish were dechorionated with pronase and trunk were cut off for RNA-seq. For embryonic neuron, green cells from Tg(Huc:Kaede) cells were sorted by FACS and approxinately 20,000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol (Invitrogen).
RNA-seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit (Agilent) according to the manufacturer’s protocol. Briefly, polyA RNA was purified from 1000 ng of total RNA using oligo (dT) beads (Invitrogen). Extracted RNA was first fragmented, then followed by reverse transcription, end repair, adenylation, adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 50 bp high-throughput sequencing using HiSeq 2500 (Illumina).
ChIP-seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP-seq lysis buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 50 mM EDTA, 1X proteinase inhibitor cocktail). Next, 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W, duty factor 5, 200 per burst. Sonication time is variable, depending on tissue types. To check the chromatin fragmentation size, 20 µL of input chromatin was reverse crosslinked in elution buffer (20 mM Tris-HCl, pH 8.0, 1% SDS, 1 mM EDTA) at 65 °C overnight, treated with Rnase A and proteinase K and purified by phenol-chloroform extraction. Input DNA was then loaded on a Lonza flash gel to make sure that the majority of DNA size distributes between 100-300 bp. To prepare antibody-beads complex, 3 µg of histone H3K27ac antibody (Active Motif, 39133) or H3K4me3 antibody (EMD Millipore, 07-473) was mix with 12 µL M-280 sheep anti-rabbit IgG Dynabeads (ThermoFisher, 11203D) in 150 µL of 5 mg/mL BSA/1X PBS buffer, with rotation at 4 °C for 3 h. After incubation, antibody-beads complex was washed once with BSA/1X PBS buffer. About 200 µg chromatin was used per IP. Equal volume of master mix (1X TE, 2% Triton X-100, 0.2% sodium deoxycholate, 2X proteinase inhibitor cocktail) was mixed with 200 µg chromatin and then incubated with antibody-beads complex overnight with rotation. The next morning, the beads were washed 5 times with cold RIPA wash buffer (20 mM Tris-HCl, pH 8.0, 1% NP-40, 0.7% sodium deoxycholate, 500 mM LiCl, 1 mM EDTA, 1X proteinase inhibitor cocktail). Then the chromatin bound on the beads was eluted by 150 µL of elution buffer at 65 °C for 30 min.
ChIP-seq: To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow  fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.
ATAC-seq: Tuebingen adult tissues were ground in liquid nitrogen,resuspended in 1 mL of lysis buffer (1X PBS, 0.2% NP-40, 5% BSA, 1 mM DTT, protease inhibitors), followed by incubation at  4 °C for 10 min on an overhead shaker. After that, lysate was filtered through 40 m cell strainer and nuclei were collected at 1000X g for 5 min.
ATAC-seq: Tagmentation was performed immediately according to ATAC-seq protocol reported previously(Buenrostro et al., 2013)
Hi-C: For brain tissue, two adult Tuebingen brains were slightly ground into small granules in liquid nitrogen and resuspended in 1 mL of cold hypotonic buffer (20 mM Tris-HCl, pH 8.0, 10 mM NaCl, 20 mM EDTA). Granular brains were then dounce homogenized with loose pestle for 20 times. The top of the homogenate was carefully transferred into a new tube and fixed with 2% formaldehyde at room temperature for 10 min. 0.2 M of glycine was added to stop fixation. For muscle tissue, 60 mg of Tuebingen muscle was first chopped into small pieces and digested by 0.25% trypsin at room temperature for 30 min. After neutralization with FBS, muscle cells were resuspended in cold 1X PBS and fixed with 2% of formaldehyde at room temperature for 10 min. 0.2 M glycine was then added to stop fixation.
Hi-C: Hi-C experiments on adult zebrafish brain and muscle tissues were performed according to previously published protocol(Rao et al., 2014). The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems) and then followed by pair-end 2X 100 bp high-throughput sequencing using HiSeq 2500  or HiSeq 4000(Illumina).
WGBS: Tübingen adult tissues were dissected, and the genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, 69504). Then 1 µg of genomic DNA of each adult tissue was subjected to bisulfite conversion using EZ DNA Methylation-Gold Kits
WGBS: The final libraries were prepared using the Accel-NGS® Methyl-Seq DNA Library Kit.
scATAC-seq: Single-cell ATAC-seq (scATAC-seq) was performed in one female brain and one male brain, respectively, on the 10X Genomics platform. To isolate nuclei, freshly dissected single brain was transferred to 1 mL NbActiv1 medium (BrainBits, NbActiv1 500) with a wide-bore pipette tip to break the tissue into small pieces. Then the tissue was broken up completely using regular-bore pipette tips followed by filtering through a 30 µm cell strainer. The isolated cells were spun down at 500 g for 5 min at 4 °C and then lysed in 100 µL chilled 0.1X Lysis Buffer (10 mM Tris HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA,0.01% Tween-20, 0.01% NP40 and 0.001% digitonin) on ice for 5 min. Then 1 mL chilled Wash Buffer (10 mM Tris HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20) was added to the lysed cells and cells were spun down at 500 g for 5 min at 4 °C. At last, 300 µL chilled Diluted Nuclei Buffer (10x Genomics, PN 2000153/2000207) was added to resuspend the nuclei. The nuclei were filtered again using a 30 µm cell strainer before cell counting
scATAC-seq: Around 12,000 nuclei were used for one Tn5 tagmentation reaction, and the scATAC-seq library was prepared and sequenced exactly according to the company’s user guide.

value: Tuebingen

tag: tissue

value: Muscle


title: YueLab-Skin-WGBS

source_name: YueLab-Skin-WGBS

value: Skin


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A9_ad012


title: YueLab-Testis-WGBS

source_name: YueLab-Testis-WGBS

value: Testis


title: YueLab-brain-HiC-rep1

description: Hi-C(DpnII)

source_name: YueLab-brain-HiC

value: Brain


title: YueLab-Spleen-WGBS

source_name: YueLab-Spleen-WGBS

value: Spleen


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A7_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A8_ad008


title: HNECs (passage 4, donar 1) in 12-well plate treated with medium

type: RNA

city: Paris

first: Daniela

last: Tudor

address: 22, rue Mechain

department: Infection, Immunity  and Inflammation

country: France

institute: INSERM U1016

hyb_protocol: Labeled RNA is hybridized to GeneChip miRNA 4.0 microarrays (Affymetrix) at 48°C for 20h and then washed and stained with a Streptavidin-PE solution.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data (cel files) and metrics for Quality Controls. Data were normalized using R with miRNA40_Hs_MIRBASEF CDF version 22 of brain array.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Primary human nasal epithelial cells

label_protocol: 500 ng of total RNA was labeled using the FlashTag Biotin RNA Labeling Kit (Thermofisher)

growth_protocol: Primary human nasal epithelial cells (HNECs, from two donars, purchased from PromoCell, Heidelberg, Germany) were grown in MEMα (Minimum Essential Medium α, Thermo Fisher) supplemented with 10 % fetal calf serum (FCS, Eurobio, Courtaboeuf, France) and 1% penicillin/streptomycin.

extract_protocol: Total RNA was extracted using Trizol. RNA quality was assessed with Agilent 2100 bioanalyzer according to manufacturer instructions (Agilent Technologies).

treatment_protocol: Confluent HNECs in 12-well plate were stimulated with medium or P1 (clade B, 125μM) for 6 hours, at 37°C.

tag: treatment

value: medium


title: HNECs (passage 5, donar 2) in 12-well plate treated with medium


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A7_ad004


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A7_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A7_ad006


title: HNECs (passage 6, donar 1) in 12-well plate treated with medium


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad012


title: HNECs (passage 6, donar 1) in 12-well plate treated with P1 (clade B, 125μM)


title: YueLab-Kidney-WGBS

source_name: YueLab-Kidney-WGBS

value: Kidney


title: YueLab-Liver-WGBS

source_name: YueLab-Liver-WGBS

value: Liver


title: YueLab-Colon-WGBS

source_name: YueLab-Colon-WGBS

value: Colon


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad007


title: YueLab-H3K9me3-H3K9me2-Input-Testis-rep2

description:
processed data file:
YueLab-ChIP-seq-testis_H3K9me2.peak.gz
YueLab-ChIP-seq-testis_H3K9me3.peak.gz


title: HNECs (passage 4, donar 1) in 12-well plate treated with P1 (clade B, 125μM)


title: YueLab-Brain-WGBS

source_name: YueLab-Brain-WGBS


title: YueLab-H3K9me3-H3K9me2-Input-Testis-rep1


title: YueLab-H3K9me3-H3K9me2-Input-Spleen-rep2

description:
processed data file:
YueLab-ChIP-seq-spleen_H3K9me2.peak.gz
YueLab-ChIP-seq-spleen_H3K9me3.peak.gz


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A5_ad012


title: YueLab-Blood-WGBS

source_name: YueLab-Blood-WGBS

value: Blood


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad008


title: YueLab-H3K9me3-H3K9me2-Input-Spleen-rep1


title: YueLab-H3K9me3-H3K9me2-Input-Skin-rep2

description:
processed data file:
YueLab-ChIP-seq-skin_H3K9me2.peak.gz
YueLab-ChIP-seq-skin_H3K9me3.peak.gz


title: YueLab-Heart-WGBS

source_name: YueLab-Heart-WGBS

value: Heart


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad006


title: HNECs (passage 5, donar 2) in 12-well plate treated with P1 (clade B, 125μM)


title: YueLab-H3K9me3-H3K9me2-Input-Skin-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A6_ad004


title: YueLab-Intestine-WGBS

source_name: YueLab-Intestine-WGBS

value: Intestine


title: YueLab-H3K9me3-H3K9me2-Input-Muscle-rep2

description:
processed data file:
YueLab-ChIP-seq-muscle_H3K9me2.peak.gz
YueLab-ChIP-seq-muscle_H3K9me3.peak.gz


title: YueLab-H3K9me3-H3K9me2-Input-Liver-rep2

description:
processed data file:
YueLab-ChIP-seq-liver_H3K9me2.peak.gz
YueLab-ChIP-seq-liver_H3K9me3.peak.gz


title: YueLab-H3K9me3-H3K9me2-Input-Muscle-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A5_ad001


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A5_ad010


title: YueLab-H3K9me3-H3K9me2-Input-Liver-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A5_ad006


title: YueLab-H3K9me3-H3K9me2-Input-Kidney-rep1

description:
processed data file:
YueLab-ChIP-seq-kidney_H3K9me2.peak.gz
YueLab-ChIP-seq-kidney_H3K9me3.peak.gz


title: YueLab-H3K9me3-H3K9me2-Input-Kidney-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad012


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A5_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad001


title: YueLab-H3K9me3-H3K9me2-Input-Intestine-rep1

description:
processed data file:
YueLab-ChIP-seq-intestine_H3K9me2.peak.gz
YueLab-ChIP-seq-intestine_H3K9me3.peak.gz


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad007


title: YueLab-H3K9me3-H3K9me2-Input-Heart-rep1

description:
processed data file:
YueLab-ChIP-seq-heart_H3K9me2.peak.gz
YueLab-ChIP-seq-heart_H3K9me3.peak.gz


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad006


title: YueLab-H3K9me3-Testis-rep2

tag: chip-seq antibody

value: Abcam, ab8898


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad004


title: YueLab-H3K9me3-H3K9me2-Input-Colon-rep2

description:
processed data file:
YueLab-ChIP-seq-colon_H3K9me2.peak.gz
YueLab-ChIP-seq-colon_H3K9me3.peak.gz


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A5_ad007


title: YueLab-H3K9me3-H3K9me2-Input-Brain-rep1

description:
processed data file:
YueLab-ChIP-seq-brain_H3K9me2.peak.gz
YueLab-ChIP-seq-brain_H3K9me3.peak.gz


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A4_ad010


title: YueLab-H3K9me3-H3K9me2-Input-Colon-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A3_ad010


title: YueLab-H3K9me3-H3K9me2-Input-Heart-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A3_ad012


title: YueLab-H3K9me3-Testis-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A3_ad006


title: YueLab-H3K9me3-H3K9me2-Input-Brain-rep2


title: YueLab-H3K9me3-Spleen-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A3_ad004


title: YueLab-H3K9me3-Spleen-rep1


title: YueLab-H3K9me3-H3K9me2-Input-Intestine-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A3_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A3_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad012


title: YueLab-H3K9me3-Muscle-rep2


title: YueLab-H3K9me3-Skin-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad001


title: YueLab-H3K9me3-Muscle-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad007


title: YueLab-H3K9me3-Skin-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad010


title: YueLab-H3K9me3-Liver-rep1


title: YueLab-H3K9me3-Kidney-rep2


title: YueLab-H3K9me3-Kidney-rep1


title: YueLab-H3K9me3-Intestine-rep1


title: YueLab-H3K9me3-Intestine-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A12_ad012


title: YueLab-H3K9me3-Heart-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A12_ad010


title: YueLab-H3K9me3-Heart-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A12_ad007


title: YueLab-H3K9me3-Liver-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A12_ad008


title: YueLab-H3K9me3-Colon-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A12_ad004


title: YueLab-H3K9me3-Colon-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad012


title: YueLab-H3K9me3-Brain-rep2


title: YueLab-H3K9me3-Brain-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad010


title: YueLab-H3K9me2-Testis-rep2

value: Cell Signaling, 4658


title: YueLab-H3K9me2-Testis-rep1


title: YueLab-H3K9me2-Spleen-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A2_ad004

value: SSp


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad007

value: male


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad006


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad004


title: YueLab-H3K9me2-Spleen-rep1

value: Tuebingen


title: YueLab-H3K9me2-Skin-rep2


title: YueLab-H3K9me2-Skin-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A11_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad010


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad012


title: YueLab-H3K9me2-Muscle-rep2

value: Muscle


title: YueLab-H3K9me2-Muscle-rep1


title: YueLab-H3K9me2-Liver-rep2


title: YueLab-H3K9me2-Liver-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad004


title: YueLab-H3K9me2-Kidney-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad001


title: YueLab-H3K9me2-Intestine-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad012


title: YueLab-H3K9me2-Intestine-rep1


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad001


title: YueLab-H3K9me2-Heart-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad007


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad006


title: YueLab-H3K9me2-Heart-rep1


title: YueLab-H3K9me2-Colon-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad004


title: YueLab-H3K9me2-Colon-rep1


title: YueLab-H3K9me2-Brain-rep2


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A10_ad008


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad008


title: YueLab-H3K9me2-Kidney-rep1


title: YueLab-H3K9me2-Brain-rep1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad012


title: YueLab-ATACseq-Testis-rep1

source_name: YueLab-ATACseq-Testis


title: YueLab-ATACseq-Skin-rep1

source_name: YueLab-ATACseq-Skin

value: Skin


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad001


title: YueLab-ATACseq-Kidney-rep1

source_name: YueLab-ATACseq-Kidney


title: YueLab-ATACseq-Intestine-rep1

source_name: YueLab-ATACseq-Intestine


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad004


title: YueLab-ATACseq-Colons-rep1

source_name: YueLab-ATACseq-Colons

value: Colons


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad002


title: CEMBA180426_8B_3_CEMBA180426_8B_4_A1_ad010


title: YueLab-ATACseq-BRAIN-rep3

source_name: YueLab-ATACseq-BRAIN

value: BRAIN


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H8_ad010


title: YueLab-ATACseq-Heart-rep1

source_name: YueLab-ATACseq-Heart


title: YueLab-ATACseq-Brain-rep1

source_name: YueLab-ATACseq-Brain

value: Brain


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H8_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H8_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H8_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H7_ad002


title: YueLab-ATACseq-Brain-rep2


title: YueLab-ATACseq-Spleen-rep1

source_name: YueLab-ATACseq-Spleen

value: Spleen


title: YueLab-ATACseq-Liver-rep1

source_name: YueLab-ATACseq-Liver


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H7_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H7_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H9_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H7_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H7_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad008


title: gall bladder epithelium, ΔcdtB infected replicate 2, 7 day infection

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

country: Germany

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1200_Jun14 extraction protocol. The extracted single color raw data txt files were further analyzed using R and the associated BioConductor package limma. Agilent FE software processed green and red signals were extracted and background removal and between-array normalization using the quantile method was applied.

label_protocol: RNA was labeled with the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Human gall bladder cells were grown in corresponding media as described in the accompanying publication (materials and methods).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany).

treatment_protocol: Cells were cultured in air-liquid-interface cultures (mucosoids) in the described media. Stable cultures were infected with Salmonella enterica Paratyphi A wild type or a isogenic deletion mutant for cdtB or left uninfected as control. Infected cells were harvested at 2 or 7 days after infection.

value: gall bladder

tag: cell type

value: epithelium

tag: bacteria strain

value: dCdtB

tag: timepoint

tag: culture type

value: air-liquid-interface culture

tag: replicate


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad004


title: gall bladder epithelium, uninfected replicate 1, 7 days

value: NI


title: gall bladder epithelium, uninfected replicate 2, 7 days


title: gall bladder epithelium, ΔcdtB infected replicate 1, 7 day infection


title: gall bladder epithelium, ΔcdtB infected replicate 2, 2 day infection


title: gall bladder epithelium, WT infected replicate 1, 7 day infection

value: WT


title: gall bladder epithelium, WT infected replicate 2, 7 day infection


title: gall bladder epithelium, uninfected replicate 2, 2 days


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H7_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H5_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad001


title: gall bladder epithelium, WT infected replicate 2, 2 day infection


title: gall bladder epithelium, ΔcdtB infected replicate 1, 2 day infection


title: gall bladder epithelium, WT infected replicate 1, 2 day infection


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H5_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H5_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H5_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H6_ad010


title: ES_MERVL::tdTomato Dppa2/4 KO+Dppa2/4 Mut-GFP, biological rep 3

first: Jack-Christophe

last: Cossec

address: 28 rue du Dr. Roux

institute: Institut Pasteur

description: Gene expression data

hyb_protocol: Following fragmentation, 3.5 ug of ss-cDNA were hybridized for 16 hr at 45C on GeneChip Mouse gene 2.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard Genechip Scanner 3000.

data_processing: The data were analyzed using the Transcriptome Analysis Console (TAC) software, Affymetrix.

label: Biotin

source_name: mouse embryonic stem cells

label_protocol: ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (UserGuide GeneChip WT plus reagent kit, Affymetrix).

growth_protocol: Cells were maintained in KSR (knock-out serum replacement medium, GIBCO): DMEM + Glutamax supplemented with 15% KSR, LIF, 0.1 mM, 2-mercaptoethanol, non-essential amino acid and penicillin/streptomycin on gelatin-coated plates.

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

value: mouse embryonic stem cells

tag: genotype/variation


title: ES_MERVL::tdTomato Dppa2/4 KO+Dppa2/4 Mut-GFP, biological rep 2

description: Gene expression data


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H5_ad002


title: ES_MERVL::tdTomato Dppa2/4 KO+Dppa2/4 Mut-GFP, biological rep 1

description: Gene expression data


title: ES_MERVL::tdTomato Dppa2/4 KO+Dppa2/4 WT-GFP, biological rep 1

description: Gene expression data


title: ES_MERVL::tdTomato Dppa2/4 KO+Dppa2/4 WT-GFP, biological rep 3

description: Gene expression data


title: ES_MERVL::tdTomato Dppa2/4 KO+Dppa2/4 WT-GFP, biological rep 2

description: Gene expression data


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad004


title: gall bladder epithelium, uninfected replicate 1, 2 days


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad007


title: CAM+mML56_1

city: Seoul

first: GooTaeg

last: Oh

address: 52, Ewhayeodae-gil

department: Department of Life Sciences

country: South Korea

institute: Ewha Womans University

description: The anti-inflammatory role of Ninj1 was verified by treating macrophages with the peptide Ninj11-56 (ML56), which mimic the soluble form of Ninj1 (sNinj1).

library_source: transcriptomic

data_processing:
The sequence reads were counted by StringTie-1.3.044 and fragments per kilobase of transcript per million mapped reads (FPKM) was used as a normalized expression level.
The downstream analysis such as drawing heatmap was done by using R packages (ver. 3.4.1).
Genome_build: mm10
Supplementary_files_format_and_content: CMA+mML56_CountMatrix_kallisto.gene

source_name: Peripheral blood mononuclear cells

growth_protocol: Peripheral blood samples from 10- to 16-week-old C57BL/6J (B6) mice (n=60, 1 ml per mouse) were collected in EDTA-coated tubes, pooled according to the experimental requirements. The CD11b-selected monocyte suspension was cultured for 6 or 7 days with RPMI/FBS plus 30 ng/ml M-CSF.

extract_protocol:
Total RNA of M(LPS/IFNγ)s was manually extracted using the method as described above and purified by using ethanol precipitation.
The mRNA-seq libraries were prepared using NEXTflex Rapid Directional mRNA-Seq Kit (Bioo Scientific).

treatment_protocol: For activation in vitro, mouse differentiated macrophages were stimulated with lipopolysaccharide (LPS, 500 ng/ml) and IFNγ (20 ng/ml) to M(LPS/IFNγ)s, which were classically activated macrophages (CAMs).

value: blood

value: macrophages


title: CAM+mML56


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad012

value: SSp

value: male


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad001


title: M_M-CSF


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad008


title: CAM


title: ES_MERVL::tdTomato Dppa2/4 KO, biological rep 2

description: Gene expression data


title: Ninj1-Wt_CAM

description: To explore the association between Ninj1 deletion and macrophage activation, we assessed the expression pattern of inflammation-related genes in the setting of a Ninj1 deficiency.

data_processing:
The sequence reads were counted by StringTie-1.3.044 and fragments per kilobase of transcript per million mapped reads (FPKM) was used as a normalized expression level.
The downstream analysis such as drawing heatmap was done by using R packages (ver. 3.4.1).
Genome_build: mm10
Supplementary_files_format_and_content: WT_KO_M1_Counts_normalized.xlsx

source_name: BMDMs

growth_protocol: BM cells were isolated from the femurs and tibias of Ninj1+/+ and Ninj1-/- mice at 6 weeks of age and cultured in DMEMs containing 20% FBS and 20 μM β-mercaptoethanol for 16 hours. The suspended cells were plated and treated with 20 ng/ml recombinant human/mouse macrophage colony-stimulating factor (M-CSF, 30ng/ml) for 7 days to differentiate macrophages.

extract_protocol:
Total RNA of Ninj1+/+ or Ninj1-/- M(LPS/IFNγ)s was manually extracted using the method as described above and purified by using ethanol precipitation.
The mRNA-seq libraries were prepared using NEXTflex Rapid Directional mRNA-Seq Kit (Bioo Scientific).

treatment_protocol: For activation in vitro, differentiated BMDMs were stimulated with lipopolysaccharide (LPS, 500 ng/ml) and IFNγ (20 ng/ml) to M(LPS/IFNγ)s, which were classically activated macrophages (CAMs).

value: bone-marrow


title: ES_MERVL::tdTomato, biological rep 3

description: Gene expression data


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad010


title: ES_MERVL::tdTomato Dppa2/4 KO, biological rep 3

description: Gene expression data


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H4_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad006


title: scRNA-seq of mouse atherosclerotic aorta_biological rep 2-1

description: We performed single cell RNA sequencing of live aortic CD45+ cells extracted from atherosclerotic (western diet for 13weeks) aortic single cells of Apolipoprotein e-deticient (Apoe-/-) mice.

data_processing:
For each cell, we applied two quality measures to the filtered gene-cell-barcode matrix: mitochondrial genes (<10%), and gene count (range from 200 to 5,000) from the R package Seurat v3.1.1 (https://satijalab.org/seurat/)
The remaining data was log-normalized and then used in downstream analysis after z-transformation. Top-ranked 2,000 variably expressed genes were selected using ‘vst’ algorithms in Seurat FindVariableFeatures function and then used to compute the principal components (PCs).
To characterize myeloid cells, we first extracted cell clusters with expression of canonical macrophage (Adgre1, Csf1r, Fcgr1, and Lyz2) or dendritic cell (Zbtb46, Itgax, and Flt3) markers and confidently defined 3,002 myeloid cells.
Genome_build: mm10
Supplementary_files_format_and_content: cell metadata; Index orig.ident nCount_RNA nFeature_RNA percent.mt seurat_clusters
Supplementary_files_format_and_content: gene-cell UMI count matrix
Supplementary_files_format_and_content: gene-cell log-normalized value matrix

source_name: atherosclerotic aorta

extract_protocol:
Each cell suspension was subjected to 3’ single-cell RNA sequencing using the GemCode system (10x Genomics), following the manufacturer’s instructions.
Libraries were sequenced on an Illumina HiSeq and mapped to the mouse mm10 reference genome using the Cell Ranger toolkit (version 3.0.2).

value: aorta

value: CD45+ leukocyte

value: Apoe-/-


title: Ninj1-Ko_CAM


title: scRNA-seq of mouse atherosclerotic aorta_biological rep 2-2


title: scRNA-seq of mouse atherosclerotic aorta_biological rep 1-2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H3_ad004


title: ES_MERVL::tdTomato, biological rep 2

description: Gene expression data


title: scRNA-seq of mouse atherosclerotic aorta_biological rep 1-1


title: ES_MERVL::tdTomato Dppa2/4 KO, biological rep 1

description: Gene expression data


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad012


title: LSK cells from K36M mice-replicate 2

city: Boston

first: Justin

last: Brumbaugh

state: MA

address: 185 Cambridge St.  CPZN4200

institute: Massachusetts General Hospital

data_processing:
Basecalls performed using CASAVA version 1.7
Subsequent to demultiplexing and adapter trimming, fastqs were mapped to mm10 with splice-aware aligner STAR vers-2.3.0 using mm10 Ensembl gtf
To calculate RPKM expression values, sequencing reads were counted over an assembly of all putative exons for each gene and normalized by the length of the exon assembly and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression values in RPKM for each sample are given in a  tab-delimited table.

molecule: polyA RNA

source_name: LSK cells from K36M mice

growth_protocol: Mice were maintained according to protocol in a pathgen free facility.

extract_protocol:
Bone marrow was harvested from mice and subjected to red blood cell lysis in ACK buffer.  The sample was then filtered and stained for lineage markers (Mac1, Gr1, B220, CD3e, Ter119), Sca1, and cKit.  Cells were sorted via FACS for lineage marker negative, Sca1 positive, cKit positive cells.  Resulting cells were processed using a Qiagen RNeasy Plus Micro kit.
cDNA was generated using Truseq total RNA kit (Illumina Inc.) according to the manufacturer's protocol. End repair, A-tailing, adapter ligation  and PCR amplification was carried out according to manufacturer's instructions with modifications described elsewhere (Bowman et al., BMC Genomics 2013).

treatment_protocol: Mice were treated with 2 mg/ml doxycycline in drinking water, supplemented with 10 mg/ml sucrose.

value: rtTA in Rosa26, H3K36M in Col1a1, B6/129 background

value: bone marrow

value: lineage negative, Sca1 positive, and cKit positive hematopoietic stem/progenitor cells

value: 6-8 weeks


title: LSK cells from K36M mice-replicate 3


title: LSK cells from K36M mice-replicate 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad007


title: LSK cells from K9M mice-replicate 2

source_name: LSK cells from K9M mice

value: rtTA in Rosa26, H3K9M in Col1a1, B6/129 background


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad010


title: LSK cells from rtTA control mice-replicate 3

source_name: LSK cells from rtTA control mice

value: rtTA in Rosa26, B6/129 background


title: LSK cells from K9M mice-replicate 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H12_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad008


title: LSK cells from K9M mice-replicate 3


title: LSK cells from rtTA control mice-replicate 1


title: LSK cells from rtTA control mice-replicate 2


title: ES_MERVL::tdTomato, biological rep 1

description: Gene expression data


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H12_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H12_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H12_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H2_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H11_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad004


title: 253_kidney_3_control

city: Bilthoven

first: Paul

last: Wackers

address: Antonie van Leeuwenhoeklaan

country: Netherlands

institute: RIVM

data_processing:
Torrent Suite version 5.0.4 was used for basecalling
The FASTQ files were subjected to a quality control procedure, and checked for any biases and outliers in terms of library size, read length distribution, mean read quality distribution, mean quality for each position in the read, and base frequency for each position in the read. Reads smaller than 25 bases were removed, and the reads were mapped to the ERCC spike sequences using Bowtie (1) and to the transcriptome (based on GRCh38, downloaded from Ensembl, release 84) using Tmap (2,3). The number of mapped reads were counted for each gene. The numbers were compiled into an expression matrix, which was subjected to further analysis.
Filtering: transcripts had to be sequenced at least three times per sample and two times per experimental group within gender
Normalization and statistical analysis was done using DESeq2
Genome_build: Ensembl Homo_sapiens.GRCh38
Supplementary_files_format_and_content: CountTable_transc.txt; a counttable, first column contains ensembl id, following columns contain raw counts of each transcript per sample

source_name: Kidney

extract_protocol:
Total RNA was extracted using QIAzol lysis Reagent and miRNAeasy Mini Kits (QIAGEN, Hilden, Germany), following Qiagen protocol. Addition of wash buffers RPE and RWT (QIAGEN) was done mechanically by using the QIAcube (QIAGEN, Hilden, Germany) via the miRNAeasy program. Isolated RNA was and stored at −80 °C
ERCC RNA Spike-In Control mix 1 (Thermo Fisher Scientific) was added to the total RNA and Poly(A) RNA was prepared using the Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific). Bar-coded RNA libraries were generated according to the manufacturers’ protocols using the Ion Total RNA-Seq Kit v2 and the Ion Xpress RNA-Seq bar coding kit (Thermo Fisher Scientific). The size distribution and yield of the barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes (Agilent Technologies). Sequencing templates were prepared on the Ion Chef System using the Ion PI IC 200 Kit (Thermo Fisher Scientific). Sequencing was performed on an Ion Proton System using Ion PI v2 chips (Thermo Fisher Scientific) according to the instructions of the manufacturer.

value: kidney

tag: patient

tag: biopt number

tag: diet

value: Control

value: F


title: 229_kidney_3_control


title: 225_kidney_3_control


title: 218_kidney_3_control

value: M


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H12_ad002


title: 216_kidney_3_control


title: 238_kidney_3_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H12_ad007


title: 212_kidney_3_control


title: 210_kidney_3_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H10_ad010


title: 204_kidney_3_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad012


title: 234_kidney_3_ccpr

value: CCPR


title: 224_kidney_3_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G9_ad007

value: SSp


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G9_ad001

value: male


title: 219_kidney_3_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G9_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G9_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G9_ad008


title: 248_kidney_3_ccpr


title: 205_kidney_3_ccpr


title: 202_kidney_3_ccpr


title: 201_kidney_3_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad007


title: 253_kidney_1_control


title: 206_kidney_3_ccpr


title: 213_kidney_3_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad010


title: 208_kidney_3_control


title: 229_kidney_1_control


title: 203_kidney_3_control


title: 238_kidney_1_control


title: 225_kidney_1_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_H1_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G8_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad012


title: 218_kidney_1_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad010


title: 210_kidney_1_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad006


title: 208_kidney_1_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad004


title: 204_kidney_1_control


title: 248_kidney_1_ccpr


title: 224_kidney_1_ccpr


title: 206_kidney_1_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad012


title: 234_kidney_1_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad007


title: 213_kidney_1_ccpr


title: 219_kidney_1_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad010


title: 205_kidney_1_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad006


title: 216_kidney_1_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad004


title: 212_kidney_1_control


title: 202_kidney_1_ccpr


title: 201_kidney_1_ccpr


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad008


title: 203_kidney_1_control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G7_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad001


title: replicate 2, 8 minutes rif treatment

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

data_processing:
First the 3' adapter sequecne was removed from the reads using a custom python script.  Any remaining rRNA reads in the sample were removed, and the remaining non rRNA reads were aligned to the NA1000 genome using bowtie 0.12.8.   The 5' end of each read was recorded after alignment, and the RPKM values were calculated for all features with >24 read counts in a given timepoint. The time course of RPKM values for a given were used for mRNA half-life determination.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: RPKM for each gene in the time-course.

organism: Caulobacter vibrioides

growth_protocol: 25mL Caulobacter crescentus NA1000 cultures were grown to mid-log in M2G minimal medium.

extract_protocol:
After all cell samples were collected, the total RNA was extracted as in Al-Husini et al. Mol Cell 2020.
Total RNA was first depleted of rRNA using the ribozero gram negative kit, and verified using the agilent bioanalyzer.  Library prepration was the same as for total RNA from Ingolia et al. Science 2009.
Partial base hydrolysis was followed by 3' adenylated adapter ligation to each RNA sample.  After 3' ligation, RT-PCR was used to make a cDNA, which was then circularized and then amplified by PCR with primers to include an indexing barcode on each sample.  Samples from each biological replicate set were then pooled and seqeunced on a lane of a Hiseq 2500 (U. Texas-Austin).

treatment_protocol: A 1mL aliquot of cells were extracted and placed into 2mL of RNA protect reagent prior to rifampicin treatment, gently vortexed, and stored at room temp.  Rifampicin was then added into the culture (100ug/mL rifampicin final concentration) and the culture was incubated at 28C at 200rpm until the indicated timepoint.  At each timepoint, 1mL of cell suspenion was added to 2mL of RNA protect reagent, gently vortexed, and stored at room temp.


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G6_ad001


title: replicate 2, 4 minutes rif treatment


title: replicate 2, 15 minutes rif treatment


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad006


title: replicate 2, 2 minutes rif treatment


title: replicate 2, 1 minute rif treatment


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad010


title: replicate 1, 4 minutes rif treatment


title: replicate 1, 2 minutes rif treatment


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad002


title: replicate 1, 15 minutes rif treatment


title: replicate 2, pre-treatment


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad008


title: replicate 1, 8 minutes rif treatment


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad004


title: replicate 1, pre-treatment


title: replicate 1, 1 minute rif treatment


title: hy5 BA Replicate 2

city: Chapel Hill

first: Charles

last: Hodgens

state: North Carolina (NC)

address: 250 Bell Tower Drive

department: GMB

institute: UNC Chapel Hill

data_processing:
alignment - star
quantification - salmon
Genome_build: TAIR10
Supplementary_files_format_and_content: count files quantified by Salmon

organism: Arabidopsis thaliana

source_name: Root mRNA

growth_protocol: plants were germinated and grown vertically for one week on 0.5x MS solid plant growth media

extract_protocol:
Frozen tissue was pulverized and CTAB-extracted, then cleaned with two chloroform washes before final resuspension in water
mRNA was oligo-dT purified, heat-fragmented, and primed with random primers for cDNA synthesis before end-repair, A-tailing, and ligation to Kapa TruSeq adapters

treatment_protocol: Root and shoot tissue were separate by scalpel blade and root tissue was submerged in either vehicle control media (1/2x MS liquid media) or treatment media (1/2x MS liquid media with 0.1 uM benzyl adenine)

tag: genotype

value: cytokinin


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad001

tag: brain region


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G5_ad010

tag: Sex


title: hy5 BA Replicate 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G4_ad012

tag: age


title: hy5 Control Replicate 2

value: control


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G3_ad004

tag: strain


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G3_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G3_ad010


title: hy5 Control Replicate 1


title: WT BA Replicate 2

value: wild type


title: WT BA Replicate 1


title: WT Control Replicate 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G3_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G3_ad012


title: WT Control Replicate 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G2_ad008


title: HEK 293 cells, DDX3-wt PAR-CLIP, Replicate 2

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
RNA fragments crosslinked to DDX3-wt
PAR-CLIP

data_processing:
Ribo-seq fastq files were stripped of the adapter sequences using cutadapt. UMI sequences were removed and reads were collapsed to fasta format. Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs and miRNA (retrieved using the UCSC table browser) using bowtie2 in the 'local' alignment mode.
Reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 32 .gtf file. A maximum of 3 mismatches and mapping to a maximum of 50 positions was allowed. De-novo splice junction discovery was disabled for all datasets. Only the best alignment per each read was retained.
For RNA-seq and Ribo-seq, only reads mapping for more than 25nt were used for to construct count tables.
Peak calling for PAR-CLIP reads was performed with PARalyzer v1.5 in the "EXTEND_BY_READ" mode using the following parameters:
BANDWIDTH=3
CONVERSION=T>C
MINIMUM_READ_COUNT_PER_GROUP=5
MINIMUM_READ_COUNT_PER_CLUSTER=5
MINIMUM_READ_COUNT_FOR_KDE=5
MINIMUM_CLUSTER_SIZE=8
MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER=1
MINIMUM_CONVERSION_COUNT_FOR_CLUSTER=3
MINIMUM_READ_COUNT_FOR_CLUSTER_INCLUSION=5
MINIMUM_READ_LENGTH=18
MAXIMUM_NUMBER_OF_NON_CONVERSION_MISMATCHES=0
Peaks with more than 10 reads were retained for subsequent analysis.
Differential analysis was performed with uniquely mapping reads using DESeq2. Concordant changes were defined using an FDR cutoff of 0.01 for RNA-seq and Ribo-seq individually, and ensuring the same directionality in the calculated fold changes.
Changes in translation efficiency were calculated using DESeq2 by using RNA-seq or Ribo-seq as an additional covariate.
Translationally regulated genes were defined using an FDR cutoff of 0.05 from the likelihood ratio test included in DESeq2, against a reduced model with no difference between RNA-seq and Ribo-seq counts.
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text or BigWig tracks

source_name: HEK 293 FlpIn Trex flagHA-DDX3-wt

growth_protocol: HEK 293 FlpIn TRex cells (Invitrogen R78007) were cultured in DMEM supplemented with 10% Fetal Bovine Serum (FBS). Stable cell lines expressing inducible flag-HA-DDX3 were generated as described (Spitzer et al., PMID: 24011039)

extract_protocol:
smallRNA sequencing library
For  RNA-sequencing, Cells were resuspended in Trizol (Invitrogen) and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the RNeasy kit (Qiagen). Ribosome profiling (Calviello et al., PMID: 26657557) and PAR-CLIP (Maatz et al., PMID: 28369676) were performed as described.
See column "library construction protocol" in the SAMPLES section.

treatment_protocol: Cells were subjected to RNA interference as indicated.

tag: RNAi treatment

value: Untreated

tag: rna isolation

value: PAR-CLIP

tag: adapter sequence

value: TGGAATTCTCGGGTGCCA


title: HEK 293 cells, DDX3-wt PAR-CLIP, Replicate 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G3_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad004


title: hESC 3' mRNAseq 1

city: Jeonju-si

first: Myung-Kwan

last: Han

state: Jeollabuk-do

address: Baeje-daero 567

department: Department of Microbiology

institute: Jeonbuk National University Medical School

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2.
Read count extraction and normalization were performed using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include read count values for each Sample.

source_name: H9 Human embryonic stem cells

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: cell type

value: H9 Human embryonic stem cells

tag: passage

tag: origin

value: Human embryo


title: hESC 3' mRNAseq 2


title: hMSSC p14 3' mRNAseq 2

source_name: Human musculoskeletal stem cells

value: ES derived-human musculoskeletal stem cells

value: H9 embryonic stem cells


title: hMSC 3' mRNAseq 1

source_name: Human mesenchymal stem cells

value: Human mesenchymal stem cells

value: Human bone marrow


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G12_ad002


title: hMSC 3' mRNAseq 2


title: hMSC 3' mRNAseq 3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad012


title: KMS11_CRNDEheterozygote_1

first: David

last: GARRICK

address: 1 Av. Claude Vellefaux

department: INSERM U976

institute: Institut de Recherche Saint Louis

description:
OBAD4
The KMS11 cell line was established from a patient with Multiple Myeloma (Namba et al., (1989) In Vitro Cell Dev. Biol. 25(8):723-9).
RMA expression value derived from Expression Console software; gene-level analysis.

hyb_protocol: Hybridization to Affymetrix Human Transcriptome Array 2.0 (ThermoFisher Scientific) was carried out at 45°C for 16 h in an Affymetrix GeneChip Hybridization Oven 640. Washing and staining were carried out on an Affymetrix Fluidics Station 450 using the Affymetrix GeneChip Hybridization, Wash, and Stain Kit (ThermoFisher Scientific) according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw array intensity data files (.CEL) were analysed using the Transcriptome Analysis Console (TAC) v4.0.2 software (ThermoFisher Scientific). Data were normalised using the Robust Multi-Array protocol.

source_name: KMS11 cell line

label_protocol: One nanogram of total RNA was pre-processed for hybridization using the GeneChip™ WT Pico Kit (ThermoFisher Scientific) according to the manufacturer’s instructions with 9 cycles of PCR pre-amplification and 5.5 µg of single-stranded cDNA was used in the final fragmentation and labelling reaction.

growth_protocol: Cells were grown in complete RPMI containing 20% FCS at 37°C / 5% CO2.

extract_protocol: RNA was extracted using the MicroRNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA was analysed on a Eukaryotic Total RNA Pico Bioanalyser chip (Agilent). All samples had RNA Integrity Number > 8.0.

tag: cell line

tag: crnde genotype

value: heterozygous for deleted allele


title: KMS11_CRNDEhomozygote_2

description:
OBAD6
The KMS11 cell line was established from a patient with Multiple Myeloma (Namba et al., (1989) In Vitro Cell Dev. Biol. 25(8):723-9).
RMA expression value derived from Expression Console software; gene-level analysis.

value: homozygous for deleted allele


title: hMSSC p14 3' mRNAseq 3


title: KMS11_CRNDEheterozygote_2

description:
OBAD7
The KMS11 cell line was established from a patient with Multiple Myeloma (Namba et al., (1989) In Vitro Cell Dev. Biol. 25(8):723-9).
RMA expression value derived from Expression Console software; gene-level analysis.


title: KMS11_CRNDEhomozygote_1

description:
OBAD5
The KMS11 cell line was established from a patient with Multiple Myeloma (Namba et al., (1989) In Vitro Cell Dev. Biol. 25(8):723-9).
RMA expression value derived from Expression Console software; gene-level analysis.


title: KMS11_CRNDEwildtype_2

description:
OBAD3
The KMS11 cell line was established from a patient with Multiple Myeloma (Namba et al., (1989) In Vitro Cell Dev. Biol. 25(8):723-9).
RMA expression value derived from Expression Console software; gene-level analysis.


title: KMS11_CRNDEwildtype_1

description:
OBAD1
The KMS11 cell line was established from a patient with Multiple Myeloma (Namba et al., (1989) In Vitro Cell Dev. Biol. 25(8):723-9).
RMA expression value derived from Expression Console software; gene-level analysis.


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad010


title: hMSSC p7 3' mRNAseq 3


title: hMSSC p14 3' mRNAseq 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad007


title: hESC 3' mRNAseq 3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad001


title: hMSSC p7 3' mRNAseq 1


title: hMSSC p7 3' mRNAseq 2


title: Unaff_7

city: Gainesville

first: Eric

middle: T

last: Wang

state: Florida

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

data_processing:
Reads were mapped using STAR
Alternative splicing events were quantified using MISO, values given are percent spliced in (PSI)
Gene expression values were quantified using Kallisto, values are given as TPM
Genome_build: hg19
Supplementary_files_format_and_content: PSI, TPM

source_name: Frontal Cortex

extract_protocol:
Frozen tissues were lysed in Trizol using a tissue homogenizer. RNA was extracted and cleaned using the Direct-zol RNA Miniprep kits.
Strand specific, ribo-minus libraries were constructed using the NEBNext Ultre II Directional RNA library prep kit for Illumina. Samples were amplified using 9-11 PCR cycles in this kit.

treatment_protocol: Autopsy tissue was frozen at -80C until RNA was extracted

tag: source

value: Autopsy

tag: anonymized center identifier

value: A

tag: disease class

tag: tissue

value: Frontal Cortex


title: Unaff_8


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G10_ad012

value: SSp

value: male


title: Unaff_6


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G11_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G10_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad001


title: Unaff_4


title: DM2_3

value: B

value: Myotonic Dystrophy type 2


title: Unaff_3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G10_ad010


title: Unaff_2


title: DM2_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G10_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G10_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad008


title: Unaff_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad006


title: DM2_4


title: DM2_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad004


title: DM1_21

value: C

value: Myotonic Dystrophy type 1


title: DM1_19


title: DM1_20


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad008


title: DM1_18


title: DM1_16

value: D


title: DM1_17


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G10_ad001


title: DM1_15


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad012


title: DM1_11


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F8_ad002


title: DM1_14


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F8_ad007


title: DM1_9


title: DM1_12


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F8_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F8_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F8_ad001


title: DM1_6


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F8_ad006


title: DM1_7


title: DM1_3


title: DM1_2


title: DM1_4


title: DM1_5


title: CEMBA180426_8B_1_CEMBA180426_8B_2_G1_ad012


title: DM1_8


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F9_ad002


title: DM1_13


title: DM1_10


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad006


title: Unaff_5


title: DM1_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad010


title: HEK293 EHMT1_WT F8 cells [CLLAG]

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

data_processing:
TagDust2 was used to extract unique molecular identifiers which were appended to read names
Reads were mapped to the human reference genome GRCh38 using Hisat2 (v. 2.1.0), including SNP and transcript annotations
Duplicated reads were removed using umitools depup command (options: --paired --unpaired-reads=discard --chimeric-pairs=discard)
Known genes and transcripts were quantified from the corrected BAM alignment files using StringTie2 (options -eB -G)
The script prepDE.py from StringTie2 was used to construct gene expression tables
Genome_build: GRCh38
Supplementary_files_format_and_content: Both are csv files containing gene counts

source_name: HEK293 EHMT1_WT

growth_protocol: DMEM/10%FCS/ penstrep

extract_protocol:
RNeasy Plus Mini Kit with gDNA eliminator (Qiagen)
TrueSeq stranded mRNA sample preparation on the Illumina NovaSeq 6000, 20 million 100bp single reads

treatment_protocol: grown to log phase

value: Human embryonic kidney cell line

tag: genotype/variation


title: HEK293 EHMT1_WT E9 cells [CLLAG]


title: HEK293 EHMT1_Ter G3 cells [CLLAG]

source_name: HEK293 EHMT1_Ter


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad002

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad004

tag: Sex


title: HEK293 EHMT1_Ter E1 cells [CLLAG]


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad012

tag: age


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F6_ad007

tag: strain


title: Obese BC rep13

city: Jeddah

first: Mohammed

middle: Abdullah

last: Hassan

state: Jeddah

address: King Abdulaziz University

department: Department of Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

description:
sample name:
84_S19

data_processing:
The FASTX-Toolkit version version 0.0.13 used to remove adaptor sequences and to filtered low-quality base call and low-quality reads.
TopHat2 program version 2.1.1 used to mapping short filtered sequencing reads to the hg19 human genome in order to identify exon-exon splice junctions.
The quantified genes expression level was done using Subreads package feature counts version 1.6.0.
Differentially gene expression analysis performed using edgeR bioconductor package version 3.10
Genome_build: hg19
Supplementary_files_format_and_content: read count matrix

source_name: Whole blood

extract_protocol:
Whole blood samples from obese and non-obese breast cancer patients were collected in PAXgene™ blood RNA tubes (PreAnalytiX, Switzerland), then the total RNA was isolated using the PAXgeneTM blood RNA kit (Qiagen, UK).
Approximately 2 µg of total RNA was fragmented and end‐repaired using the Illumina directional protocol. Complementary DNA (cDNA) sequencing libraries were constructed using Illumina ®TruSeqTM stranded total RNA sample preparation kit (Illumina, USA) according to the manufacturer’s instructions. The libraries were sequenced using the Nextseq 500 platform (Illumina, Singapore) in paired-end 150-bp mode, according to the manufacturer's protocol.

value: White Blood cells

tag: patient diagnosis

value: breast cancer

tag: obesity status

value: obese


title: Obese BC rep14

description:
sample name:
82_S7


title: Obese BC rep10

description:
sample name:
36_S31


title: Obese BC rep11

description:
sample name:
103_S27


title: Obese BC rep12

description:
sample name:
76_S17


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad001


title: HEK293 EHMT1_Ter H3 cells [CLLAG]


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F7_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad010


title: Obese BC rep9

description:
sample name:
67_S8


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad006


title: Obese BC rep8

description:
sample name:
75_S20


title: Obese BC rep7

description:
sample name:
35_S18


title: HEK293 EHMT1_WT E8 cells [CLLAG]


title: Obese BC rep6

description:
sample name:
38_S32


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad004


title: Obese BC rep5

description:
sample name:
64_S9


title: Obese BC rep4

description:
sample name:
5_S28


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F5_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad001


title: Obese BC rep2

description:
sample name:
39_S33


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad012


title: Obese BC rep3

description:
sample name:
32_S10


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad007


title: Non-Obese BC rep11

description:
sample name:
50_S34

value: non-obese


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad010


title: Non-Obese BC rep12

description:
sample name:
56_S21


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad006


title: Non-Obese BC rep10

description:
sample name:
29_S29


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad002


title: Obese BC rep1

description:
sample name:
70_S1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F4_ad008


title: Non-Obese BC rep6

description:
sample name:
93_S22


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad010


title: Non-Obese BC rep4

description:
sample name:
91_S30


title: Non-Obese BC rep3

description:
sample name:
99_S23


title: Non-Obese BC rep7

description:
sample name:
9_S14


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad001


title: Non-Obese BC rep8

description:
sample name:
8_S25


title: Non-Obese BC rep2

description:
sample name:
10_S5


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad007


title: Non-Obese BC rep1

description:
sample name:
52_S26


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad002


title: WH-MeDIP-Seq 3

city: hefei

last: Liu

address: No. 40 South Agricultural Road

country: China

institute: Anhui Academy of Agricultural Sciences

data_processing:
Illumina Hiseq2500
Raw reads were preprocessed using the FASTX-Toolkit
MeDIP-seq peaks were counted using MACS
The depth of genomic regions was calculated and plotted using an Integrative Genomics Viewer (IGV) Tools software.
Supplementary_files_format_and_content: xls

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
DNA was isolated from tissue with Qiagen DNeasy tissue kit (Qiagen, velencia, CA). Purified DNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), and Qubit (invitrogen,CA,USA), to determine the quantity. High quality DNA (3 μg) was sonicated at intensity 4 for 200 cycles per burst for 55 s  (Covaris S2), and DNA fragments were end repaired, ATP tailed, and adapter ligated with the Sample Preparation Kit(Illumina). Then DNA was recovered by AMPure XP Beads
Libraries were using the Magnetic Methylated DNA Immunoprecipitation Kit (Diagenode) according to the manufacture’s protocol.

tag: tissue samples

value: longissimus dorsi muscle

tag: breed

value: purebred Wannanhua pig

value: female


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad012

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: WH-MeDIP-Seq 1


title: WH-MeDIP-Seq 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad001


title: YY-MeDIP-Seq 3

value: purebred Yorkshire pig


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad008


title: Non-Obese BC rep9

description:
sample name:
7_S3

tag: cell type


title: YY-MeDIP-Seq 1


title: YY-MeDIP-Seq 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F2_ad008


title: Pten -/- R26-ERG non-targeting CRISPR RNA 1

first: Neel

last: Shah

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Differential gene expression and downstream analysis: Visualization Pipeline for RNA-seq (VIPER) pipeline and DEseq2
Genome_build: mm9

source_name: Murine prostate organoid line

growth_protocol: Standard organoid growth media/conditions in 3D matrigel conditions

extract_protocol:
QIAshredder (Qiagen 79656) and RNeasy Mini Kit (Qiagen 74106)
Illumina TruSeq stranded mRNA sample kit

value: Prostate

tag: genotype

value: Pten -/- R26-ERG non-targeting CRISPR


title: Pten -/- R26-ERG non-targeting CRISPR RNA 2


title: Pten -/- R26-ERG ERG CRISPR clone 2 RNA 2

value: Pten -/- R26-ERG ERG CRISPR


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad007

first: Joseph

value: SSp

value: male


title: Pten -/- R26-ERG ERG CRISPR clone 1 RNA 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad006


title: Pten -/- R26-ERG clone 2 RNA 2

value: Pten -/- R26-ERG


title: Pten -/- R26-ERG ERG CRISPR clone 1 RNA 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F3_ad006


title: Non-Obese BC rep5

description:
sample name:
6_S4


title: Pten -/- R26-ERG clone 1 RNA 1


title: Pten -/- R26-ERG clone 2 RNA 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad002


title: Pten -/- clone 2 RNA 2

value: Pten -/-


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad012


title: Pten -/- clone 2 RNA 1


title: Pten -/- R26-ERG ERG CRISPR clone 2 RNA 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad010


title: Pten -/- clone 1 RNA 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad006


title: Wildtype RNA 1

value: Wildtype


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad004


title: Pten -/- R26-ERG ERG CRISPR clone 2 ATAC 2

data_processing:
Peak calling: MACS2
Data analysis: ChiLin 2.0 pipeline
Differential peaks analysis: Containerized Bioinformatics workflow for Reproducible ChIP/ATAC-seq Analysis (CoBRA) package
Data visualization: DeepTools and SitePro
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

growth_protocol: Standard organoid growth media/conditions on 2D collagen-coated plates

extract_protocol:
Nuclei were isolated and resuspended in transposition mix (transposase Tn5)
ATAC-seq libraries were amplified as described previously (Buenrostro et al., 2015).
Omni ATAC-seq

treatment_protocol: ATAC samples crosslinked with 1% PFA


title: Pten -/- R26-ERG non-targeting CRISPR ATAC 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad008


title: Pten -/- R26-ERG non-targeting CRISPR ATAC 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad007


title: Pten -/- R26-ERG clone 2 ATAC 1


title: Pten -/- R26-ERG ERG CRISPR clone 1 ATAC 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad002


title: Wildtype RNA 2


title: Pten -/- R26-ERG ERG CRISPR clone 1 ATAC 2


title: Pten -/- clone 1 RNA 2


title: Pten -/- R26-ERG clone 1 RNA 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad008


title: Pten -/- R26-ERG clone 2 ATAC 2


title: Pten -/- R26-ERG clone 1 ATAC 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F10_ad001


title: Pten -/- R26-ERG clone 1 ATAC 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F11_ad007


title: Pten -/- clone 2 ATAC 2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad007


title: Pten -/- clone 2 ATAC 1


title: Pten -/- R26-ERG ERG CRISPR clone 2 ATAC 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad010


title: Pten -/- clone 1 ATAC 1


title: Pten -/- clone 1 ATAC 2


title: Wildtype ATAC 2


title: Wildtype ATAC 1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad001


title: Pten -/- R26-ERG ERG CRISPR clone 1 PolII ChIP

extract_protocol:
SDS or sarkosyl-based ChIP buffer solution; Qiagen PCR purification kit
ThruPLEX DNA-seq Kit (Rubicon Genomics); 8 bp Illumina primers

treatment_protocol: ChIP samples crosslinked with 1% PFA, sonicated to 300-500bp

tag: chip antibody

value: Pol II 8WG16 antibody (sc-56767)


title: Pten -/- R26-ERG clone 2 PolII ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad007


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad006


title: Wildtype_2 PolII ChIP


title: Pten -/- clone 1 PolII ChIP


title: Wildtype_1 PolII ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad002


title: Pten -/- clone 2 PolII ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad010


title: Pten -/- R26-ERG non-targeting CRISPR ERG ChIP

value: ERG Recombinant EPR3864 (Abcam ab92513)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad012


title: Pten -/- R26-ERG ERG CRISPR clone 2 ERG ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad008


title: Pten -/- R26-ERG ERG CRISPR clone 1 ERG ChIP


title: Pten -/- R26-ERG non-targeting CRISPR PolII ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad002


title: Pten -/- R26-ERG clone 2 ERG ChIP


title: Pten -/- R26-ERG ERG CRISPR clone 2 PolII ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F1_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad007


title: Pten -/- R26-ERG clone 1 ERG ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad006


title: Pten -/- clone 2 ERG ChIP


title: Pten -/- R26-ERG clone 1 PolII ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E9_ad004


title: Pten -/- clone 1 ERG ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad001


title: Pten -/- R26-ERG ERG CRISPR clone 2 AR ChIP

value: Anti-Androgen Receptor PG-21 (Millipore 06-680); Recombinant Anti-Androgen Receptor ER179(2) (Abcam ab108341)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad010


title: Pten -/- R26-ERG clone 1 AR ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad012


title: Pten -/- R26-ERG ERG CRISPR clone 1 AR ChIP


title: Wildtype ERG ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E8_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad007


title: Wildtype 2 AR ChIP


title: Wildtype 1 AR ChIP


title: Pten -/- R26-ERG non-targeting CRISPR AR ChIP


title: Pten -/- R26-ERG clone 2 AR ChIP


title: Pten -/- clone 2 AR ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad004


title: Pten -/- R26-ERG ERG CRISPR clone 2 H3K27ac ChIP

value: Anti-H3K27ac (Abcam ab4729)


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad002


title: Pten -/- clone 1 AR ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad012


title: Pten -/- R26-ERG non-targeting CRISPR H3K27ac ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad007


title: Pten -/- R26-ERG clone 2 H3K27ac ChIP


title: Pten -/- R26-ERG clone 1 H3K27ac ChIP


title: Pten -/- R26-ERG ERG CRISPR clone 1 H3K27ac ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E7_ad006


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad002


title: Pten -/- clone 2 H3K27ac ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E6_ad008


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E5_ad010


title: Wildtype H3K27ac ChIP


title: Seq22 / KPY_CRE_3

first: Aaron

middle: L.

last: Moye

address: 1 Blackfan Circle

department: Stem Cell Program

institute: Boston Children's Hospital

data_processing:
VIPER Pipeline (PMID: 29649993)
Genome_build: mm9
Supplementary_files_format_and_content: Cufflinks output (.csv)

source_name: KRAS-G12D / p53-FL/FL organoid lung epithelial cells

growth_protocol: To grow organoids, cells were resuspended and plated in 50% growth factor reduced Matrigel and 50% 3D media (Dulbecco’s Modified Eagle’s Medium/F12 (Invitrogen) supplemented with 10% FBS, penicillin/streptomycin, 1 mM HEPES, and insulin/transferrin/selenium (Corning)) together with supporting neonatal stromal cells on top of a transwell. 3D media was added to the bottom of the well and replaced every other day.

extract_protocol:
Single cell suspensions were made from organoid cultures and EPCAM+ cells were FACS sorted and immediately lysed, RNA was extracted using the protocol and reagents of the Absolutely RNA Microprep Kit (Agilent).
Complementary DNA (cDNA) was synthesized with Clontech SmartSeq v4 reagents from 2ng of RNA. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2ng of sheared cDNA using Takara Thruplex DNAseq reagents according to manufacturer’s protocol. The finished double strand DNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit.
Bulk RNA-Seq

tag: tissue origin

value: Lung

value: Kras LSL-G12D/WT; p53 FL/FL; Rosa26 LSL-YFP/LSL-YFP

tag: culture type

value: organoids


title: Pten -/- clone 1 H3K27ac ChIP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E5_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E5_ad012


title: Seq21 / KPY_EMP_4


title: Seq20 / KPY_NI_4


title: Seq18 / KY_EMP_4

source_name: KRAS-G12D organoid lung epithelial cells

value: Kras LSL-G12D/WT; Rosa26 LSL-YFP/LSL-YFP


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E5_ad008


title: Seq17 / KY_NI_4


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E5_ad002


title: Seq19 / KY_CRE_3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad001


title: Seq16 / KPY_CRE_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad007


title: Seq13 / KY_CRE_2


title: Seq15 / KPY_EMP_3


title: Seq14 / KPY_NI_3


title: Seq12 / KY_EMP_3


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad002


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E5_ad006


title: Seq11 / KY_NI_3


title: Seq10 / KPY_EMP_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad001


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad008


title: Seq7 / KY_NI_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad007


title: Seq8 / KY_EMP_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E4_ad006


title: Seq9 / KPY_NI_2


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad010


title: Seq5 / KPY_EMP_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad006


title: Seq6 / KPY_CRE_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad004


title: Seq4 / KPY_NI_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad002


title: Seq2 / KY_EMP_1


title: Seq3 / KY_CRE_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E3_ad008


title: Seq1 / KY_NI_1


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad012


title: CEMBA180426_8B_1_CEMBA180426_8B_2_F12_ad004


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad001


title: Murine epithelial organoid cells 7 days after in vitro Ad5CMV-Empty treatment

data_processing:
10X Genomics Cell Ranger 3.0.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz  files for each library.

extract_protocol:
Single cell suspensions were made from organoid cultures and EPCAM+ cells were FACS sorted and encapsulated.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 2

value: lung


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad007


title: Murine epithelial organoid cells 7 days after in vitro Ad5CMV-Cre treatment


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad010


title: CEMBA180426_8B_1_CEMBA180426_8B_2_E2_ad004