title: liver E28-rep16

description:
test
M19E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD007_indexed

status: Public on Sep 09 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: PAL

tag: Sex

value: male

tag: age

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD006_indexed


title: liver E28-rep6

type: RNA

city: Mont de Marsan

first: Marianne

last: Houssier

address: 371 rue du ruisseau

department: GB

country: France

institute: INRA NUMEA/IUT UPPA

description:
test
M8E28

data_processing:
Results were analyzed using the Fluidigm real-time PCR analysis software v.4.1.3. The first part of the analysis is to clean up the data with the Fluidigm real-time PCR analysis software v.4.1.3.
Data were pre-processed for expression analysis as follows: the cycle threshold (Ct) values registered from amplifications that generated melting curves with aberrant Tm (melting temperature) or with products giving rise to a double peak in melting curves (corresponding to a mixture of expected and aberrant PCR products) were removed.
The selectHKgenes function with the Vandesompele method of the SLqPCR package was used with RStudio (Version 1.2.1335) to choose the five most stable housekeeping genes. The five housekeeping genes for the relative quantification of mRNA levels of target genes were SDHA, GLUT8, PDHA1, POL2 and Luciferase. In all cases, PCR efficiency values ranged between 1.90 and 2.
The analyses were done with RStudio with : Relative gene expression= (((E-target)^(ΔCt-target))/(geomean((E-ref)^(ΔCt-ref))). E = efficiency, Ct= threshold cycle, 〖ΔCt〗_target=〖Ct 〗_(control )-〖Ct 〗_sample, 〖ΔCt〗_ref=〖Ct 〗_(control )-〖Ct 〗_sample, 〖Ct 〗_(control ) = average Ct of all samples.
normalized expression = 2^-ΔCt, where ΔCt = Ct target- Ct HKG
fold change= relative expression = (((E-target)^(ΔCt-target))/(geomean((E-ref)^(ΔCt-ref))) with ΔCt_target (or ref)=〖Ct_control-Ct_sample and Ct_control = average Ct of all samples (for each gene)

label: EvaGreen

molecule: total RNA

organism: Anas platyrhynchos x Cairina moschata

source_name: liver at embryonic day 28

label_protocol: 6.5 ng of each cDNA were initially preamplified (10 min 95°C activation and 14 PCR cycles (15 sec 95°C and 4 min 60°C) with PreAmp Master Mix (100-5581, Fluidigm) and a pool containing all the primers targeting all the genes (200nM), excluding the 16S rRNA primer sets. Preamplified sample were diluted at 1/5 after an exonuclease treatment (M02935, NEB). In order to prepare samples for loading into the integrated fluidic circuits (IFC), a mix was prepared consisting of 440 μL 2X TaqMan Master Mix (Applied Biosystem, 4369016), 44 μL 20× DNA Binding Dye Sample Loading Reagent (100-7609, Fluidigm), 44µl 20X Evagreen (31000, Biotium) plus 132 μL TE, and 6 μL of this mix was dispensed to each well of a 96-well assay plate. 2µL of preamplified and diluted cDNA sample was added to each well and the plate was briefly vortexed and centrifuged. For the assays, 5 μL of each Assay (5 μM each primer in primer-mix (2X assay loading reagent (100-7611, Fluidigm) and Tris EDTA) were dispensed to each Detector Inlet of the 96.96 IFC. Following priming of the IFC in the IFC Controller HX, 5 μL of the cDNA sample + reagent mix and 5 µl of Assay were dispensed to each Sample Inlet of the 96.96 IFC. After loading the assays and samples into the IFC in the IFC Controller HX, the IFC was transferred to the BioMark and PCR was performed using the following thermal protocol : Thermal Mix of 50 °C, 2 min; 70 °C, 30min; 25°C, 10min, Hot Start at 50 °C, 2 min; 95°C, 10 min, PCR Cycle of 35 cycles of (95 °C, 15 s; 60 °C, 60 s), and Melting analysis (60°C, 30s; 95°C,1°C/3s)

extract_protocol: Samples were frozen in liquid nitrogen. Total RNA was isolated from frozen tissue according to the Ribozol method (VWR Life Science). Total RNA concentration was measured by spectrophotometry (optical density at 260 nm) using a Biotek EPOCH 2 microplate reader with Take3 Plate, and all the samples were normalized at 500 ng/ μl. The integrity of total RNA was analyzed by electrophoresis. An amount of 3µg RNA was reverse-transcribed to cDNA with Iscript Reverse Transcription Supermix for RTqPCR (Bio-Rad, USA) with duplicates of samples. DNA contamination was prevented by DNase treatment. Reverse transcription reaction was done in CFX384 (Bio-Rad, USA) according to this program: 25 °C/5 min, 46 °C/20 min, 95 °C/1 min.

tag: tissue

value: liver

tag: developmental stage


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD008_indexed


title: liver E28-rep7

description:
test
M9E28


title: liver E28-rep4

description:
test
M6E28


title: liver E28-rep14

description:
test
M16E28


title: liver E28-rep15

description:
test
M18E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B5_AD012_indexed


title: liver E28-rep19

description:
test
M22E28


title: liver E28-rep1

description:
test
M2E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B5_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B5_AD010_indexed


title: liver E28-rep5

description:
test
M7E28


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B5_AD008_indexed


title: ChIPseq Hoxc10:c13.2 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc10:c13.2(402))] replicate 2

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

data_processing:
Basecall conversion to fastq files was performed using Picard (v 2.8.2)
Alignment: ChIP-seq reads were aligned to the mm10 genome using Bowtie (v1.0.1) (Langmead, Trapnell, Pop, & Salzberg, 2009), using options “-q --best --strata -m 1 --chunkmbs 1024”.
Binding Event Detection: Genome-wide TF binding events.txt were called in each condition using MultiGPS (v0.74) (Mahony et al., 2014). EdgeR (v3.22.5) was used within the MultiGPS framework to test whether genomic sites were differentially bound by TFs (Robinson, McCarthy, & Smyth, 2010). A genomic site was defined as shared by TFs if significant binding events.txt were called in both TF ChIP-seq experiments (q-value < 0.001), and the TFs did not display differential read enrichment at that site as estimated by EdgeR (q-value > 0.01). A binding event was defined as “TF1>TF2” if a MultiGPS peak was called in TF1 ChIP-seq (q-value < 0.001), TF1 exhibited a greater log fold-change with respect to the input ChIP-seq than TF2, and TF1 and TF2 were significantly differentially bound as defined by EdgeR (q-value < 0.01). A similar strategy was applied to perform multi-way ChIP-seq comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: MultiGPS: MultiGPS output files
Supplementary_files_format_and_content: BED: Conversion of MultiGPS output files to BED format, centered on the MultiGPS binding event location

source_name: ES-derived embryoid bodies+3D RA+SAG with induced transcription factors

growth_protocol: mESC lines were cultured in 2-inhibitors based medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), supplemented with 2.5% ESC-grade fetal bovine serum (vol/vol, Corning), N2 (Gibco), B27 (Gibco), 2mM L-glutamine (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (Millipore), 3μM CHIR (BioVision) and 1 μM PD0325901 (Sigma)) on 0.1% gelatin (Millipore) coated plates at 37 °C, 8% CO2.

extract_protocol:
Cells were collected 24h and 48h after Doxycycline (Dox) treatment. Crosslinking was performed at room temperature in 1mM DSG (ProteoChem) for 15min, followed by the addition of 1% FA (vol/vol) for an additional 15min. After quenching with Glycine, cells were divided into ~25-30x106 aliquots, pelleted by centrifugation and frozen at -80°C. After thawing cells on ice, lysis was performed in 5mL of 50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 10% glycerol (vol/vol), 0.5% Igepal (vol/vol), 0.25% Triton X-100 (vol/vol) with 1× protease inhibitors (Roche, 11697498001) for 10 min at 4 °C. Cells were centrifuged for 5min, resuspended in 5mL of 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA pH 8.0, 0.5 mM EGTA pH 8.0 with 1× protease inhibitors, and incubated for 10 min at 4 °C on a rotating platform. Cells were centrifuged for 5min and resuspended in 2mL of Sonication Buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1% Triton X-100 (vol/vol), 0.1% sodium deoxycholate (wt/vol), 0.1% SDS (vol/vol) with 1× protease inhibitors). Sonication was performed by splitting each sample to 2 Bioruptor tubes with sonication beads and using the Bioruptor Pico (Diagenode) for 18 cycles of 30 sec on and 30 sec off into an average size of approximately 200 bp. Immunoprecipitation was performed for 16h at 4 °C on a rotating platform by incubating with Dynabeads protein-G (Thermo Fisher Scientific) conjugated with 5 µg of one of the following antibodies: mouse monoclonal antibody to Flag (Sigma, F1804) or rabbit polyclonal antibody to HA (Abcam, ab9110).
lllumina DNA sequencing libraries were prepared with one third of the ChIP sample or a 1:100 dilution of the input sample in water. Library preparation was performed by end repair, A-tailing and ligating Illumina-compatible Bioo Scientific multiplexed adapters. Unligated adapters were removed using Agencourt AmpureXP beads (Beckman Coulter). Amplification was performed by PCR with Phusion polymerase (New England Biolabs) and TruSeq primers (Sigma). Libraries were gel purified (Qiagen) between 250 and 550bp in size. Final quantification of the library was performed using the KAPA library amplification kit on the Roche Lightcycler 480 before pooling.

treatment_protocol: Embryoid bodies (EBs) were obtained by plating trypsinized (Gibco) mESCs in AK medium (Advanced DMEM/F12:Neurobasal (1:1) medium (Gibco), 7% KnockOut SR (vol/vol) (Gibco), 2 mM L-glutamine, 0.1 mM ß-mercaptoethanol and penicillin–streptomycin (Gibco),) at 37 °C, 5% CO2 (day -2). On day 0, EBs were split 1:2 and AK medium was replenished and supplemented with 1 μM all-trans retinoic acid and 0.5 μM smoothened agonist (SAG) (Millipore, 566660). TF induction was performed by adding 3 μg/mL of Doxycycline (Sigma, D9891) on day 2. For ChIP-seq experiments, 3-3.5x10^6 mESCs were plated in 245mm x 245mm square dishes (Corning).

tag: strain genotype/variation

tag: treatment

value: EB + 3 Days RA + SAG, D2+24hours Dox

tag: cell type

value: Embryoid Bodies

tag: chip target

tag: chip antibody

value: Sigma, F1804


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B5_AD002_indexed


title: liver E24-rep18

description:
test
M22E24

source_name: liver at embryonic day 24


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B5_AD004_indexed


title: ChIPseq Hoxc10:c13.1 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc10:c13.1(401))] replicate 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B4_AD012_indexed


title: liver E24-rep17

description:
test
M21E24


title: liver E24-rep15

description:
test
M19E24


title: liver E24-rep20

description:
test
M24E24


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_3_B6_AD004_indexed


title: liver E24-rep10

description:
test
M14E24


title: liver E24-rep11

description:
test
M15E24


title: ChIPseq Hoxc13:c10.2 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc13:c10.2(400))] replicate 2


title: liver E28-rep2

description:
test
M3E28


title: ChIPseq Hoxc13:c10.1 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc13:c10.1(399))] replicate 2


title: liver E24-rep14

description:
test
M18E24


title: liver E24-rep13

description:
test
M17E24


title: ChIPseq Hoxc10:c13.2 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc10:c13.2(402))] replicate 1


title: liver E24-rep19

description:
test
M23E24


title: ChIPseq Hoxc10:c13.1 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc10:c13.1(401))] replicate 1


title: liver E24-rep9

description:
test
M11E24


title: liver E24-rep7

description:
test
M9E24


title: liver E28-rep3

description:
test
M4E28


title: liver E24-rep8

description:
test
M10E24


title: ChIPseq Hoxc13:c10.1 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc13:c10.1(399))] replicate 1


title: liver E24-rep16

description:
test
M20E24


title: liver E24-rep5

description:
test
M7E24


title: liver E24-rep3

description:
test
M4E24


title: Exp2_SQ_1_GEXL

city: San Francisco

first: Jennifer

middle: Anne

last: Smith

address: 513 Parnassus Ave HS1102

department: Diabetes Center

institute: University of California, San Francisco

description: Experiment 2

library_source: transcriptomic

data_processing:
Fastq files from 10x gene expression library were processed with Cell Ranger, using default parameters.
Genome_build: FASTQ were aligned using the Cell Ranger pipeline (10x Genomics, Inc., version 3.0.2) using mouse genome reference dataset (GRCm38/Ensembl/10x, 3.0.2)
Supplementary_files_format_and_content: For each sample, gene expression (GEX) tar file contains a named count matrix of genes by cells for all cells passing filter

molecule: polyA RNA

source_name: SQ tumor

extract_protocol:
FACS-sorted live CD45+ tumor infiltrating cells from the subcutaneous tumor were washed and resuspended in PBS with 0.04% BSA to a concentration of 1000 cell/μL
Libraries were prepared using 10x Genomics Chromium Single Cell 5’ Reagent (GEX + VDJ) Kit according to manufacturer’s protocol
10x Genomics Chromium Single Cell 5’

tag: sort selection

tag: tumor group

value: SQ only


title: 3T3 cells processed with SNARE-seq2 protocol (ATACseq)

first: Kun

last: Zhang

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

institute: University of California, San Diego

data_processing:
Library strategy: SNARE-seq2
R1/R2 reads and R1/R2/R3 reads.  For R1/R2/R3 reads: R1 = biological, R2 = technical, R3 = biological. R2 contains cellular barcodes sequences.
Deindexer was used to demultiplex reads according to sample barcodes from first round of barcoding for both ATAC and RNA libraries
snaptools 1.4.8 and Minimap2 2.11-r797 to map ATAC libraries
STAR-2.5.1b to map RNA libraries
dropest 0.8.6 to generate RNA count matrices and dropestr to filter cells
ArchR 0.9.4 to generate peak calls and cell by peak matrices
Genome_build: hg38/mm10
Supplementary_files_format_and_content: gz compressed tar archive of features-barcodes matrix

source_name: NIH/3T3 cells

growth_protocol: GM12878 cell line was grown in RPMI-1640 culture medium supplemented with 15% FBS and 2 mM L-glutamine at 37 ºC in a 5% CO2 humidified incubator. A549 cell line was grown in F-12K medium supplemented with 10% FBS at 37 ºC in a 5% CO2 humidified incubator.  NIH/3T3 was grown in Dulbecco’s Modified Eagle’s Medium supplemented with 10% FBS at 37 ºC in a 5% CO2 humidified incubator.

extract_protocol: 1-3 M cells were spun down at 300 g for 5 min at 4C and then washed twice with chilled 1x PBS. Cells were resuspended in 1.2 mL of 1x PBS with RNase Inhibitors (0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors) and filtered through 30 uM CELLTRICS strainers. GM12878 nuclei were extracted from cells with ATAC lysis buffer with 0.1% NP-40 resuspended in 1x PBS with RNase Inhibitors then fixed with 1% formaldehyde. 3T3/A549/GM12878 cells without nuclei extraction were fixed by adding 3 mL of 1.33% formaldehyde and mixed by pipetting followed by incubation on ice for 10 min. GM12878 cells were pelleted at 500 g for 5 min at 4C then resuspended in a resuspension buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM magnesium chloride, 0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors, 0.1% wt/vol BSA) and permeabilized with lysis buffer (10 mM Tris-HCl, 10 mM sodium chloride, 3 mM magnesium chloride, 0.04 U/uL SUPERase In RNase Inhibitor, 0.04 U/uL Enzymatics RNase Inhibitors, 0.1% wt/vol BSA, 0.1% v/v NP-40) for 3 min on ice. 3T3/A549 cells were frozen after fixation in 1x PBS with 10% (v/v) DMSO and 0.1% (wt/vol) BSA for three weeks then washed and permeabilized as described for fresh GM12878 cells. Post permeabilization (or fixation in the case of nuclei), sample were processed using SNARE-seq2 starting from tagmentation step.

treatment_protocol: 3T3 cells amd A549 cells were fixed with 1% formaldehyde and cryopreserved in 1x PBS with 10% (vol/vol) DMSO and 0.1% (wt/vol) BSA for three weeks. GM12878 cells were freshly fixed with 1% formaldeyhyde and ran in two separate experiments. GM12878 nuclei were lysed in cell lysis buffer with RNase Inhibitors (10 mM Tris pH 7.4, 10 mM sodium chloride, 3 mM magnesium chloride, 0.1% v/v NP-40, Superase RNase Inhibitors, Enzymatics RNase Inhibitors) then fixed with 1% formaldehyde. Fixed samples were processed with SNARE-seq2 protocol.

tag: cell line

value: NIH/3T3 cells

value: fixed and cryopreserved for 3 weeks


title: 3T3 cells processed with SNARE-seq2 protocol (RNAseq)


title: Exp2_SQ_Li_1_GEXL

description: Experiment 2


title: Exp2_SQ_Li_2_GEXL

description: Experiment 2

value: SQ plus Liver


title: Exp1_SQ_LI_GEXL

description: Experiment 1


title: Exp2_SQ_2_GEXL

description: Experiment 2


title: liver E24-rep4

description:
test
M6E24


title: ChIPseq Hoxc13:c10.2 in EB-Day3[D0+RA+SAG][D2+24hDox(iFlag.Hoxc13:c10.2(400))] replicate 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD012_indexed


title: liver E24-rep2

description:
test
M3E24


title: Exp1_SQ_GEXL

description: Experiment 1


title: liver E24-rep1

description:
test
M2E24


title: liver E24-rep6

description:
test
M8E24


title: liver E20-rep20

description:
test
M27E20

source_name: liver at embryonic day 20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_A12_AD004_indexed


title: liver E20-rep17

description:
test
M1E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_A10_AD006_indexed


title: liver E20-rep16

description:
test
M19E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD010_indexed


title: liver E20-rep15

description:
test
M18E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD008_indexed


title: liver E20-rep14

description:
test
M16E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD007_indexed


title: liver E20-rep13

description:
test
M15E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD001_indexed


title: liver E20-rep11

description:
test
M13E20


title: liver E20-rep12

description:
test
M14E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD006_indexed


title: liver E20-rep18

description:
test
M20E20


title: liver E20-rep10

description:
test
M12E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H8_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H8_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H8_AD004_indexed


title: liver E20-rep8

description:
test
M10E20


title: liver E20-rep7

description:
test
M9E20


title: liver E20-rep9

description:
test
M11E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H8_AD002_indexed


title: liver E20-rep4

description:
test
M6E20


title: liver E20-rep1

description:
test
M2E20


title: liver E20-rep3

description:
test
M5E20


title: liver E20-rep6

description:
test
M8E20


title: liver E20-rep2

description:
test
M3E20


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H7_AD008_indexed


title: liver E16-rep19

description:
test
M22E16

source_name: liver at embryonic day 16


title: liver E16-rep20

description:
test
M23E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H7_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H7_AD004_indexed


title: liver E16-rep17

description:
test
M20E16


title: liver E16-rep18

description:
test
M21E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H6_AD004_indexed


title: liver E20-rep19

description:
test
M21E20


title: liver E16-rep16

description:
test
M1E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H6_AD007_indexed


title: liver E16-rep15

description:
test
M19E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H7_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H5_AD007_indexed


title: liver E16-rep12

description:
test
M15E16


title: liver E16-rep13

description:
test
M16E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H5_AD006_indexed


title: liver E16-rep11

description:
test
M14E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H5_AD004_indexed


title: liver E16-rep10

description:
test
M13E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD012_indexed


title: liver E16-rep8

description:
test
M11E16


title: liver E16-rep9

description:
test
M12E16


title: liver E16-rep5

description:
test
M8E16


title: liver E16-rep14

description:
test
M18E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H8_AD001_indexed


title: liver E16-rep7

description:
test
M10E16


title: liver E16-rep6

description:
test
M9E16


title: liver E16-rep4

description:
test
M7E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD002_indexed


title: liver E16-rep3

description:
test
M6E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD004_indexed


title: liver-E12-rep20

description:
test
M25E12

source_name: liver at embryonic day 12


title: liver E16-rep2

description:
test
M5E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD001_indexed


title: liver E16-rep1

description:
test
M2E16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H4_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H3_AD008_indexed


title: liver-E12-rep16

description:
test
M20E12


title: liver-E12-rep17

description:
test
M21E12


title: liver-E12-rep18

description:
test
M22E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H3_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H3_AD004_indexed


title: liver-E12-rep15

description:
test
M1E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H2_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H2_AD002_indexed


title: liver-E12-rep10

description:
test
M13E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H1_AD004_indexed


title: liver-E12-rep13

description:
test
M18E12


title: liver-E12-rep12

description:
test
M17E12


title: liver-E12-rep11

description:
test
M15E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H2_AD001_indexed


title: liver-E12-rep8

description:
test
M11E12


title: liver-E12-rep7

description:
test
M10E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H1_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H3_AD007_indexed


title: liver-E12-rep6

description:
test
M8E12


title: liver-E12-rep14

description:
test
M19E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H12_AD012_indexed


title: liver-E12-rep9

description:
test
M12E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H12_AD010_indexed


title: liver-E12-rep4

description:
test
M6E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H12_AD002_indexed


title: liver-E12-rep5

description:
test
M7E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H12_AD001_indexed


title: liver-E12-rep3

description:
test
M5E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H12_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD010_indexed


title: Plasma exosomes [WT207]

city: Genova

first: Roberta

last: Resaz

address: via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description:
WT207_G6
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA

data_processing:
Data processing, categorization, normalization, filtering, imputation and differential expression was carried out by PIPE-T galaxy tool. Ct values falling within the range 14-32 were categorized as reliable values as recommended by the manufacturer guidelines. Global mean normalization was used to reduce any technical variability introduced in the data by the RT-qPCR experiments. Only Exo-miR with at most 5% of missing values were retained for the analysis to reduce the bias introduced by imputation. Mestdagh method was employed to assign a numeric expression value to missing values. The rank product method implemented by RankProd R package was used to identify significant differentially expressed microRNA.
Non-normalized matrix file reports raw Ct values. Ct value of 40 indicates a missing value.

label: FAM

source_name: Plasma exosomes

label_protocol: Exo-miR were analyzed by the TaqMan Array Card Technology. Exo-miR were reverse transcribed with the TaqMan microRNA Reverse Transcription Kit, using the MegaplexTM RT primers Rodent Pool A (Thermo Fisher Scientific, Monza, MB, Italy). Pre-amplification of cDNA was performed with TaqMan PreAmp Master Mix and MegaplexTM Pre-Amp primers Rodent Pool A. The pre-amplification product was diluted according to the manufacturer’s instructions and used to perform microRNA profiling on the ViiATM 7 Real-Time PCR System.

extract_protocol: Exosomes isolation and RNA extraction from plasma was performed with the exoRNeasy Serum/Plasma Midi kit (Qiagen Italia, Milano, Italy).

tag: genotype/variation

value: WT

tag: hepatocellular adenoma diagnosis

value: No tumor

tag: amyloidosis diagnosis

value: No amyloidosis

value: Plasma exosomes

tag: time

value: 1 day


title: liver-E12-rep2

description:
test
M3E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD008_indexed

tag: brain region

tag: Sex


title: liver-E12-rep1

description:
test
M2E12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H12_AD007_indexed

tag: age

tag: strain


title: liver E20-rep5

description:
test
M7E20

tag: tissue

tag: developmental stage


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD004_indexed


title: Plasma exosomes [WT206]

description:
WT206_G6
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD001_indexed


title: Plasma exosomes [WT104]

description:
WT104_G6
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H10_AD010_indexed


title: Plasma exosomes [WT215]

description:
WT215_G3
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT224]

description:
WT224_G4
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT203]

description:
WT203_G5
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT222]

description:
WT222_G5
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT223]

description:
WT223_G4
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT221]

description:
WT221_G5
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H10_AD008_indexed


title: Plasma exosomes [WT213]

description:
WT213_G3
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H10_AD004_indexed


title: Plasma exosomes [WT220]

description:
WT220_G2
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT204]

description:
WT204_G3
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G9_AD007_indexed


title: Plasma exosomes [WT218]

description:
WT218_G2
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G9_AD008_indexed


title: Plasma exosomes [WT225]

description:
WT225_G1
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT226]

description:
WT226_G1
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G9_AD006_indexed


title: Plasma exosomes [WT219]

description:
WT219_G2
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [WT217]

description:
WT217_G1
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO986]

description:
KO986_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA

value: Amyloidosis


title: Plasma exosomes [KO976]

description:
KO976_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G8_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G9_AD002_indexed


title: Plasma exosomes [KO846]

description:
KO846_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: Plasma exosomes [KO856]

description:
KO856_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA

value: Tumor


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G8_AD006_indexed

value: PAL


title: Plasma exosomes [KO1274]

description:
KO1274_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G8_AD002_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G8_AD001_indexed


title: Plasma exosomes [KO1265]

description:
KO1265_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: Plasma exosomes [KO1270]

description:
KO1270_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H7_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G8_AD012_indexed


title: Plasma exosomes [KO1239]

description:
KO1239_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G7_AD008_indexed


title: Plasma exosomes [KO1215]

description:
KO1215_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1183]

description:
KO1183_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G7_AD010_indexed


title: Plasma exosomes [KO1176]

description:
KO1176_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G7_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G7_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD008_indexed


title: Plasma exosomes [KO1141]

description:
KO1141_G6_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD007_indexed


title: Plasma exosomes [KO978]

description:
KO978_G5_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: Plasma exosomes [KO953]

description:
KO953_G5_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD006_indexed


title: Plasma exosomes [KO947]

description:
KO947_G5_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD012_indexed


title: Plasma exosomes [KO1558]

description:
KO1558_G5_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD012_indexed


title: Plasma exosomes [KO1412]

description:
KO1412_G5_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1087]

description:
KO1087_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1038]

description:
KO1038_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: Plasma exosomes [KO1413]

description:
KO1413_G5_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1198]

description:
KO1198_G5_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD008_indexed


title: Plasma exosomes [KO1011]

description:
KO1011_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: Plasma exosomes [KO1124]

description:
KO1124_G5_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1385]

description:
KO1385_G5_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_H11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD004_indexed


title: Plasma exosomes [KO1749]

description:
KO1749_G4_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD002_indexed


title: Plasma exosomes [KO1379]

description:
KO1379_G5_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is present.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G4_AD010_indexed


title: Plasma exosomes [KO1542]

description:
KO1542_G4_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1541]

description:
KO1541_G4_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1313]

description:
KO1313_G6_Tumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G4_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G4_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G4_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G3_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G3_AD002_indexed


title: Plasma exosomes [KO1731]

description:
KO1731_G2_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1160]

description:
KO1160_G3_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G3_AD004_indexed


title: Plasma exosomes [KO1096]

description:
KO1096_G3_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1652]

description:
KO1652_G2_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G3_AD001_indexed


title: Plasma exosomes [KO1536]

description:
KO1536_G2_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1061]

description:
KO1061_G4_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1730]

description:
KO1730_G2_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G2_AD010_indexed


title: Plasma exosomes [KO1767]

description:
KO1767_G1_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G2_AD008_indexed


title: Plasma exosomes [KO1508]

description:
KO1508_G2_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G2_AD004_indexed


title: Plasma exosomes [KO1496]

description:
KO1496_G3_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1492]

description:
KO1492_G3_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G2_AD002_indexed


title: Tumor budding-3, biological rep3

city: Tianjin

first: Yanrong

last: Liu

address: No.220, Tongyan Road

country: China

institute: Tianjin international biomedical joint research institute

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 mm8 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: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Homo sapiens

source_name: Tumor budding cells

extract_protocol:
The samples were lysed with TRIzol to isolate the total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectal cancer

value: Tumor budding cells


title: Tumor budding-2, biological rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G1_AD006_indexed


title: Tumor center-3, biological rep3

source_name: Tumor center cells

value: Tumor center cells


title: Tumor budding-1, biological rep1


title: Tumor center-1, biological rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G1_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G1_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G1_AD004_indexed


title: Tumor center-2, biological rep2


title: Plasma exosomes [KO1510]

description:
KO1510_G3_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G1_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD012_indexed


title: Plasma exosomes [KO1746]

description:
KO1746_G2_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Plasma exosomes [KO1768]

description:
KO1768_G1_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA


title: Murine ESC 46C in N2B27 for 2 days, seeded at 5172 cells/cm^2 (high-density), biological replicate no. 3

city: Delft

first: Hirad

last: Daneshpour

address: Van der Maasweg 9

country: Netherlands

institute: TU Delft

data_processing:
We analyzed the resulting RNA-Seq data (.fastq files) as previously described (Trapnell et al., Nat Protoc 2012).
We removed the adapter contamination, polyA read through, and low quality tails for each sample by using BBDuk (JGI, version 36.85) with following settings: k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20.
We performed read aligment using TopHat (version 2.1.1) with Bowtie (version 2.2.9.0).
We performed read assembly and analysis of differential gene expression data using Cufflinks (version 2.2.1).
We optionally used R package called CummeRbund (version 2.7.2) from Bioconductor (version 3.11) to analyze and visualize RNA-seq data.
We then compared and analyzed normalized abundance measurements (FPKM) for genes of interest and for each sample.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Output from Cuffdiff analysis with raw counts of sequencing reads
Supplementary_files_format_and_content: Normalized abundance measurements

source_name: Murine embryonic stem cells (ESC)

growth_protocol: We routinely passaged (i.e., every 2 days at 80% confluency with 1/10 dilution) 46C cells in 10-cm diameter plates coated with 0.1% gelatin with 10-mL of FBS-based (serum) pluripotency medium supplemented with 1000 U/mL leukemia inhibitory factor (LIF).

extract_protocol:
We extracted total RNA from cell-lysates by following protocol of PureLink RNA Mini Kit (Ambion, Life Technologies).
We prepared cDNA library from polyA-RNA by following protocol of 3' mRNASeq Library Preparation Kit (Quant-Seq, Lexogen).

treatment_protocol: We triggered a 2-day differentiation of 46C cells by seeding the cells onto new 10-cm diameter plates with fresh N2B27 medium as a function of three initial cell-population densities (862,1931 and 5172 cells/cm^2).

tag: sample type

value: This cell line was generated by gene targeting in WT murine ES cells (E14TG2a). The open reading frame of the Sox1 gene is replaced with the coding sequence for enhanced green fluorescent protein (GFP) and an internal ribosome entry site (IRES)-linked puromycin resistance gene. Described in Ying et al., Meth Enzym 2003 & Ying et al., Nat Biotech 2003

tag: origin

value: Derived from E14TG2a (WT), 129/Ola mice


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD008_indexed


title: Plasma exosomes [KO1732]

description:
KO1732_G1_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA

tag: cell type


title: Murine ESC 46C in N2B27 for 2 days, seeded at 5172 cells/cm^2 (high-density), biological replicate no. 2


title: Spermatogenic stem cell-shLSD1

city: yangzhou

first: Qisheng

last: Zuo

state: Jiangshu

address: wenhui road 48#

institute: Yangzhou University

description: total RNA

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 mm8 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: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample，Matrix table with raw gene counts for every gene and every sample

organism: Gallus gallus

source_name: Spermatogenic stem cell

growth_protocol: Fertilized eggs hatched to 18.5 days were harvested to obtain testes for the isolation of SSC. The testis tissue was digested with collagenase for 30 minutes, and then with trypsin. Cells were cultured in DMEM containing 10% FBS at 37°C and 5% CO2 saturated humidity.

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

treatment_protocol: LSD1 interfered expression vector was constructed and transfected into SSCs

value: testis

value: isolated in vivo

tag: treatment

value: with the treatment of Interference LSD1


title: Spermatogenic stem cell-Blank

description: total RNA

value: with on treatment


title: Murine ESC 46C in N2B27 for 2 days, seeded at 5172 cells/cm^2 (high-density), biological replicate no. 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD007_indexed


title: Murine ESC 46C in N2B27 for 1 day, seeded at 5172 cells/cm^2 (high-density), biological replicate no. 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD006_indexed


title: Plasma exosomes [KO1650]

description:
KO1650_G1_NoTumor
Plasma exosomes of a murine model of GSD-1a (LS-G6pc-/- mice).
Knock-out. Amyloidosis is absent.
microRNA

value: No tumor


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD002_indexed


title: Murine ESC 46C in N2B27 for 1 day, seeded at 5172 cells/cm^2 (high-density), biological replicate no. 2


title: Murine ESC 46C in N2B27 for 1 day, seeded at 5172 cells/cm^2 (high-density), biological replicate no. 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G12_AD001_indexed


title: Murine ESC 46C in N2B27 for 2 days, seeded at 1931 cells/cm^2 (middle-density), biological replicate no. 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD010_indexed


title: Murine ESC 46C in N2B27 for 2 days, seeded at 1931 cells/cm^2 (middle-density), biological replicate no. 1


title: Plasma exosomes [WT115]

description:
WT115_G4
Plasma exosomes of wild type mice
Wild type. Amyloidosis is absent.
microRNA

value: WT

value: No amyloidosis


title: Murine ESC 46C in N2B27 for 1 day, seeded at 1931 cells/cm^2 (middle-density), biological replicate no. 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD002_indexed


title: Murine ESC 46C in N2B27 for 2 days, seeded at 862 cells/cm^2 (low-density), biological replicate no. 2


title: Murine ESC 46C in N2B27 for 2 days, seeded at 862 cells/cm^2 (low-density), biological replicate no. 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD010_indexed


title: Murine ESC 46C in N2B27 for 2 days, seeded at 862 cells/cm^2 (low-density), biological replicate no. 1


title: Murine ESC 46C in N2B27 for 1 day, seeded at 862 cells/cm^2, biological replicate no. 3


title: Murine ESC 46C in N2B27 for 1 day, seeded at 862 cells/cm^2, biological replicate no. 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD007_indexed


title: Murine ESC 46C in N2B27 for 1 day, seeded at 862 cells/cm^2, biological replicate no. 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD006_indexed


title: Murine ESC 46C in serum+LIF (passaged every 2 days at 80% confluency with 1/10 dilution), biological replicate no. 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD004_indexed


title: Murine ESC 46C in serum+LIF (passaged every 2 days at 80% confluency with 1/10 dilution), biological replicate no. 2


title: Murine ESC 46C in N2B27 for 2 days, seeded at 1931 cells/cm^2 (middle-density), biological replicate no. 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G11_AD012_indexed


title: Murine ESC 46C in N2B27 for 1 day, seeded at 1931 cells/cm^2 (middle-density), biological replicate no. 2


title: Murine ESC 46C in N2B27 for 1 day, seeded at 1931 cells/cm^2 (middle-density), biological replicate no. 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F9_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_G10_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F9_AD010_indexed


title: Murine ESC 46C in serum+LIF (passaged every 2 days at 80% confluency with 1/10 dilution), biological replicate no. 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F9_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F9_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD004_indexed


title: SAM24370907 Bone Marrow WT_untreated

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
!
Supplementary_files_format_and_content: RPKM

source_name: SAM24370907 Bone Marrow WT_untreated

extract_protocol:
Bone marrow cells from femurs and tibia of wild-type C57BL/6N mice were cultured in Roswell Park Memorial Institute (RPMI) medium
supplemented with 10% heat-inactivated fetal bovine serum, 2 mM glutamine, 50 Î¼M 2-mercaptoethanol (Gibco), 100 U/ml penicillin, and 100 Î¼g/ml streptomycin (Gibco) and 50 ng/ml
of recombinant M-CSF (R&D Systems) on non-tissue culture treated 15 cm plates. On day 5 of culture, cells were harvested and 5 million cells were re-plated onto non-tissue culture
treated 10 cm plates in fresh media (same as that described above). After 2 additional days of culture, BMDMs from 3 individual mice (each corresponding to an independent biological replicate)
were harvested by scraping. Total RNA was isolated from cells and purified using RNeasy mini kits and on-column DNAse digestion per manufacturer (Qiagen) protocol.
0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

tag: samid

value: Bone Marrow

tag: genotype


title: SAM24370909 Bone Marrow WT_untreated

source_name: SAM24370909 Bone Marrow WT_untreated


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD007_indexed


title: OdP8

city: Great Chesterford

first: Nicolas

last: Gambardella

state: Essex

address: Lewis House, Great Chesterford Court

country: United Kingdom

institute: aSciStance Ltd

description:
sex:
MFM
Ribosome-attached mRNA
BAC-Trap RNA-seq

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim Galore version: 0.4.2_dev (a wrapper for Cutadapt 1.9.1 with parameters  -f fastq -e 0.1 -q 20 -O 1 and FastQC)
Reads were mapped to GRCm38 whole genome using HiSAT2 v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
After RNA-Seq Quality Control, reads were quantified using the RNA-Seq pipeline of SeqMonk v0.34. All reads overlapping an exon were counted, all reads from all exons of all isoforms added, counting each one once.
Counts Per Million reads (CPM) were calculated dividing reads from all exons of all isoforms by the size of the library in reads, multiplied by 1 million.
Genome_build: GRCm38

source_name: dorsal striatum

growth_protocol: Mouse lines were maintained as heterozygotes on a C57Bl/6J background. Mice were maintained on a 12 h light/dark cycle (light off 7:00 pm) and had, before the beginning the experiment, free access to water and food.

extract_protocol:
Each tissue piece was homogenized in 1 mL of lysis buffer (20 mM HEPES KOH, pH 7.4, 5 mM MgCl2, 150 mM KCl, 0.5 mM dithiothreitol, 100 µg mL-1 CHX (Sigma # C7698-1g), protease (Roche #11836170001) and RNAse inhibitors (Ambion # AM2694, Fisher # PR-N2515) with successively loose and tight glass-glass 2 ml Dounce homogenizers. Each homogenate was centrifuged at 2,000 x g, at 4°C, for 10 min.  The supernatant was separated from cell debris, and supplemented with NP-40 (EDM Biosciences) to a final concentration of 10 µL mL-1 and DHPC (Avanti Polar lipids) to a final concentration of 30 mM. After mixing and a 5-minute incubation on ice, the lysate was cleared for 10 minutes at 20,000 x g. A mixture of streptavidin-coated magnetic beads was incubated 35 minutes at room temperature with biotinylated protein L and then 1 h with GFP antibody and added to the supernatant and incubated overnight at 4°C with gentle end-over rotation.  After incubation, beads were collected with a magnetic rack and washed 5 times with high-salt washing buffer (20 mM HEPES-KOH, pH 7.4, 5 mM MgCl2, 150 µl 1M, 350 mM KCl, 10 µL mL-1 NP-40) and immediately placed in “RTL plus” buffer (Qiagen). The mRNA was purified using the RNase micro KIT (Qiagen).
Five ng of RNA were used for reverse-transcription, performed with the Ovation RNA-Seq System V2 (Nugen). cDNA was quantified by fluorimetry, using the Quant-iT Picogreen reagent and ultra-sonicated using a Covaris S2 sonicator with the following parameters: duty cycle 10 %, intensity 5, 100 cycles/burst, 5 minutes. Two hundreds ng of sonicated cDNA were then used for library construction using the Illumina TruSeq RNA sample prep kit, starting at the End-Repair step, and following the manufacturer’s instructions. The libraries were quantified with the Bio-Analyzer high-sensitivity DNA kit, multiplexed and sequenced on an Illumina HiSeq 2500 instrument. At least 20 million 50-bp paired-end reads were collected for each sample.

treatment_protocol: Mice were sacrificed by decapitation. The brain was quickly dissected out, placed in cold buffer and then in an ice-cold brain form to cut thick slices from which the PFC was obtained and the NAc and the DS punched out using ice-cold stainless steel cannulas

tag: background strain

value: dorsal striatum

value: D2 receptor-expressing neuron


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD001_indexed

source_name: C57BL/6J Male P56 Mouse Brain

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F8_AD002_indexed

value: male


title: SAM24370908 Bone Marrow WT_untreated

source_name: SAM24370908 Bone Marrow WT_untreated


title: OdP7

source_name: ventral striatum

value: ventral striatum


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F7_AD012_indexed


title: SNU387 NFE2L1-V5 transfected, rep2

city: Suwon

first: SO MEE

last: KWON

address: Worldcup-ro 164

country: South Korea

institute: Ajou University School of Medicine

description: Gene expression data from heapatocellular carcinoma cell line (SNU387)

hyb_protocol: Following fragmentation, Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC). We exported the result with gene level RMA analysis

label: biotin

source_name: SNU387 NFE2L1-V5 transfected, rep2

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer (GeneChip Whole Transcript PLUS reagent Kit). The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Human hepatoma cells (SNU-387 and SNU-423) were purchased from Korean Cell Line Bank (Seoul, Korea) and cultured in RPMI 1640 medium (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (Invitrogen) and antibiotics (Invitrogen) at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA quality check protocol: RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: transfection protocol: Cells were transfected with the plasmids and target siRNA duplexes using FuGENE® HD (Promega) and OligofectamineTM Reagent (Invitrogen), respectively, according to the manufacturer’s instructions

value: Hepatocellular Carcinoma

tag: cel line

tag: transfected with


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F7_AD010_indexed


title: SNU387 pcDNA3 transfected, rep1

source_name: SNU387 pcDNA3 transfected, rep1


title: SNU387 pcDNA3 transfected, rep2

source_name: SNU387 pcDNA3 transfected, rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F7_AD008_indexed


title: SNU423 siNFE2L1 #2 transfected, rep2

description: Gene expression data from heapatocellular carcinoma cell line (SNU423)

source_name: SNU423 siNFE2L1 #2 transfected, rep2

value: siNFE2L1 #2


title: SNU423 siNFE2L1 #3 transfected, rep1

source_name: SNU423 siNFE2L1 #3 transfected, rep1

value: siNFE2L1 #3


title: SNU423 siNC transfected, rep1

source_name: SNU423 siNC transfected, rep1

value: siNC


title: SNU423 siNFE2L1 #2 transfected, rep1

source_name: SNU423 siNFE2L1 #2 transfected, rep1


title: SNU423 siNC transfected, rep2

source_name: SNU423 siNC transfected, rep2


title: OdP6


title: OdP5


title: SNU423 siNFE2L1 #3 transfected, rep2

source_name: SNU423 siNFE2L1 #3 transfected, rep2


title: SNU387 NFE2L1-V5 transfected, rep1

source_name: SNU387 NFE2L1-V5 transfected, rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F7_AD006_indexed


title: OdP4


title: OdP2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F6_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F6_AD006_indexed


title: OdP13

description:
sex:
MFF
Ribosome-attached mRNA
BAC-Trap RNA-seq


title: OdP16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F6_AD004_indexed


title: OdP14


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F6_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F6_AD001_indexed


title: OdP12


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F7_AD002_indexed


title: OdP11


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F5_AD010_indexed


title: OdP10


title: OdP3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F5_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F6_AD010_indexed


title: JAG13

description:
sex:
MMF
Ribosome-attached mRNA
BAC-Trap RNA-seq

value: D1 receptor-expressing neuron


title: EM62

description:
sex:
F??
Ribosome-attached mRNA
BAC-Trap RNA-seq

source_name: prefrontal cortex

value: prefrontal cortex


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F5_AD006_indexed


title: EM59


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F5_AD002_indexed


title: JAG13bis


title: EM56


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F4_AD008_indexed


title: OdP15


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F4_AD012_indexed


title: JAG14


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F4_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F4_AD007_indexed


title: EM52


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F4_AD002_indexed


title: EM51


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F3_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F5_AD007_indexed


title: EM50


title: EM49


title: Arx CKO 4

city: PHILADELPHIA

first: Ana

middle: Gabriela

last: Cristancho

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania/CHOP

data_processing:
Illumina sequence analysis pipeline for mapping reads for individual sequencing runs.
DESeq2 was used for analysis
Reads from all dupplicate sequencing runs for each sample were collapsed prior to differential sequencing analysis.
Independent filter of zero count genes was used.
Genome_build: mm9
Supplementary_files_format_and_content: differential expression data

source_name: Hippocampus and Cortex

growth_protocol: P35-40 mice were anesthesized and cortex and hippocampus was microdissected from 350 mM trnsverse slices

extract_protocol:
Trizol extraction, 5 control (WT) or 4 Arx CKO
SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, Cat#634936) according to manufacturer’s instructions. Some samples were sequences twice to confirm results.

treatment_protocol: Cortical and hippocampal brain regions were dissociated with Papin dissociation system (Worthington) supplemented withtrehalaose. Solutions were oxygenated fofr 30 minutes prior to use. Cells were sorted with FACS for TdTom + PV cells.

value: FACS PV interneurons

value: Arx floxed/Y:PVCreTdTom


title: EM48


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F3_AD006_indexed


title: Arx CKO 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F2_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F3_AD002_indexed


title: EM47


title: EM46


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F2_AD007_indexed


title: EM53


title: Arx CKO 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F1_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F2_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F2_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F1_AD010_indexed


title: control 5

value: PV-CreTdTom


title: control 4


title: EM44


title: EM43


title: control 3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F3_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F1_AD002_indexed


title: EM42


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F1_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F12_AD012_indexed


title: control 2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F1_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F1_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F12_AD008_indexed


title: control 1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F12_AD006_indexed


title: EM45


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F12_AD007_indexed


title: EM41


title: EM40

description:
sex:
FMM
Ribosome-attached mRNA
BAC-Trap RNA-seq


title: Arx CKO 2

description: Biological sample was run in duplicates for one sequencing runs so all reads collapsed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F12_AD002_indexed


title: EM39


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F12_AD004_indexed


title: EM38


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F11_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F11_AD010_indexed


title: 779-Tim4-negative_L001

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

data_processing:
Quality of the raw reads data for each sample was first evaluated using FastQC (version 0.11.3). The Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics. In brief, reads were aligned to the reference transcriptome using TopHat (version 2.0.13) and a second round of quality control was performed after alignment. Cufflinks/CuffDiff (version 2.2.1) was used for expression quantification, normalization, and differential expression analysis. Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff. Diagnostic plots were generated using the CummeRbund R package
Genome_build: GRCm38 mm10
Supplementary_files_format_and_content: read count

source_name: TAMs

extract_protocol:
TAMs were isolated from ID8 bearing mice peritoneal elute wash, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peritoneal cavity

value: tumor associated peritoneal macrophages


title: 783-Tim4-negative_L002


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F11_AD002_indexed


title: 779-Tim4-negative_L002


title: EM37


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F11_AD001_indexed


title: 783-Tim4-negative_L001


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD006_indexed


title: EM36

source_name: dorsal striatum


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD008_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 784-Tim4-negative_L002


title: EM35


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD007_indexed


title: 784-Tim4-negative_L001


title: EM34


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD002_indexed


title: 793-Tim4-negative_L002


title: EM33


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E9_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E9_AD008_indexed


title: 793-Tim4-negative_L001


title: 779-Tim4-positive_L002


title: EM32


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_F10_AD001_indexed


title: EM31


title: 779-Tim4-positive_L001


title: EM29


title: 783-Tim4-positive_L002


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E9_AD007_indexed


title: 783-Tim4-positive_L001


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E8_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E8_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E8_AD002_indexed


title: EM28


title: 784-Tim4-positive_L002


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD012_indexed


title: EM27


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD010_indexed


title: 784-Tim4-positive_L001


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD004_indexed


title: 793-Tim4-positive_L002


title: EM22

description:
sex:
FFM
Ribosome-attached mRNA
BAC-Trap RNA-seq


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E9_AD002_indexed


title: EM23


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD006_indexed


title: 793-Tim4-positive_L001


title: EM30


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E7_AD001_indexed


title: EM21


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E6_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E8_AD012_indexed


title: EM20


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_15

city: Munich

first: Jonas

last: Mir

address: Trogerstraße 30

department: Institut für medizinische Mikrobiologie, Immunologie und Hygiene

country: Germany

institute: Technische Universität München

description:
Sample15
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv

data_processing:
TopHat (version 2.1.1, with Bowtie version 2.2.9.0) was used to map the reads to the mouse genome and R package Genomic Alignments (version 1.2.2) was used to count the reads
Genes that were not expressed in at least one of the samples were filtered out. The remaining genes were used in the analyses comparing the long-term dominators (Sample1 and Sample2) to the rest of the families.
Genes that were not expressed in any of the Samples1 - Sample4 were filtered out. The remaining genes were used in the analyses comparing long-term dominators (Sample1 and Sample2) to acute dominators (Sample3 and Sample4).
R package DESeq2 (version 1.26.0) was used to perform differential gene expression analysis.
R package goseq (version 1.38.0) was used to perform GO term enrichment analysis on differentially expressed genes.
R package fgsea (version 1.12.0) was used to perform gene set enrichment analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table, in csv format, with raw non-zero gene counts that are used in the analyses comparing the long-term dominators (Sample1 and Sample2) to the rest of the families.
Supplementary_files_format_and_content: Matrix table,  in csv format, with raw non-zero gene counts that are used in the analyses comparing long-term dominators (Sample1 and Sample2) to acute dominators (Sample3 and Sample4).

source_name: OT-1 T cells

extract_protocol:
for each T cell family 100 progeny cells were sorted. SMART Seq V4 Ultra low input RNA Kit (Takara) was used according to the manufacture's protocol for extraction.
Nextera XT DNA Kit (Illumina) was used according to the manufacture's protocol for library contruction.

value: CD8 T cell (OT-1)

value: spleen


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_14

description:
Sample14
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E6_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E6_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E6_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E6_AD010_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_13

description:
Sample13
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: EM18

value: dorsal striatum

value: D2 receptor-expressing neuron


title: EM17

source_name: ventral striatum


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_12

description:
Sample12
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD007_indexed

value: PAL

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD006_indexed


title: EM16


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD002_indexed


title: EM15

value: ventral striatum


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD012_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_11

description:
Sample11
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: EM14


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD008_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_9

description:
Sample9
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD012_indexed


title: EM13


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_16

description:
Sample16
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_8

description:
Sample8
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD004_indexed


title: EM19


title: EM12


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_7

description:
Sample7
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD012_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_6

description:
Sample6
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD010_indexed


title: EM10


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD006_indexed


title: EM9


title: EM11


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD001_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_acute_dominator_3

description:
Sample3
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv
rawCounts_long_term_dominators_vs_acute_dominators.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD012_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_10

description:
Sample10
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E3_AD002_indexed


title: EM8

description:
sex:
MMF
Ribosome-attached mRNA
BAC-Trap RNA-seq


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD010_indexed


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_acute_dominator_4

description:
Sample4
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv
rawCounts_long_term_dominators_vs_acute_dominators.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E4_AD006_indexed


title: EM7


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_5

description:
Sample5
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_long_term_dominator_2

description:
Sample2
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv
rawCounts_long_term_dominators_vs_acute_dominators.csv


title: EM6


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD002_indexed


title: EM5


title: MCMV_ie2_SIINFEKL_TCellFamily_d8pi_long_term_dominator_1

description:
Sample1
bulkRNA-Seq of 100 progeny cells
rawCounts_long_term_dominators_vs_rest.csv
rawCounts_long_term_dominators_vs_acute_dominators.csv


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E2_AD001_indexed


title: EM4


title: EM3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E1_AD002_indexed


title: WT CD8+ splenic T cell, target:H3, Tx: StimCD3CD28day3, Rep.4

city: Bronx

first: Michael

middle: Alton

last: Willcockson

state: New York

address: 1300 Morris Park Ave, Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Library strategy: CUT&Tag
Sequencing and base calling was performed by Genewiz (South Plainfield, NJ). The sequencing libraries were multiplexed and clustered on a flowcell. After clustering, the flowcell were loaded on the Illumina HiSeq 4000  according to manufacturer’s instructions.  The samples were sequenced using a 2x150 Paired End (PE) configuration.  Image analysis and base calling were conducted by the HiSeq Control Software (HCS) on the HiSeq instrument.  Raw sequence data (.bcl files) generated from Illumina HiSeq were converted into fastq files and de-multiplexed using Illumina bcl2fastq v. 2.17 program. One mis-match was allowed for index sequence identification.
Raw fastq files were trimmed using Trim Galore (v0.6.2, length 20, e = .1)
Trimmed Fastq files were then aligned to the mouse genome (mm10) using Bowtie2 (version 2.4.1; local, very-sensitive-local, no-unal, no-mixed, no-discordant, phred33, I=1-, X=700).
Reads were sorted and converted to BAM format and duplicates were marked using Sambamba using default parameters (version 0.6.6)
Filtering, duplication removal and read down sampling to equalize reads across samples was performed using Samtools (version 1.1; F= 3340, f = 0x0002)
HOMER (v4.10)  was then used tag directories (makeTagDirectory; default parameters), bedgraphs (makeUCSCfile; default parameters), and to calculate genomic coverage for chromatin types (annotatePeaks.pl; -noann -noadj).
Stimulated samples were downsampled to have the same number of reads as unstimulated samples using samtools (Samtools v 1.1. H1 samples: samtools view -h -@ 4 -s 123.276, H3 samples: samtools view -h -@ 4 -s 123.380).
Genome_build: mm10 (GENCODE Release M20 (GRCm38.p6))
Supplementary_files_format_and_content: HOMER generated bedGraphs.

source_name: CD8+ splenic T cells

extract_protocol:
For CUT&Tag (Kaya-Okur et al., 2019) 100,000 CD8+ T cells were isolated from the spleens of wildtype age- and sex-matched animals by flow cytometry. Additionally, cells were cultured under stimulating conditions for 3 days, as described above, and 100,000 stimulated CD8+ T cells cells were isolated by flow cytometry. 3XFlag-pATn5 was prepared as described in 3XFlag-pATn5 Protein Purification and MEDS-loading (https://www.protocols.io/view/3xflag-patn5-protein-purification-and-meds-loading-8yrhxv6). CUT&Tag library preparation was carried out as described in Bench top CUT&Tag V.2 (https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6). The following primary antibodies were used: IgG (Cell Signaling 4E-BP2), mouse mAb anti-H1 (Santa Cruz sc-8030 AE-4), and mouse mAb anti-H3 (Santa Cruz sc-517576). The following secondary antibodies were used: guinea pig anti-rabbit (Antibodies online ABIN101961), and rabbit anti-mouse (Antibodies online ABIN101785).
Tn5-based libraries were prepared using PCR amplificatin with indexed primers. See CUT&Tag protocol (Kaya-Okur et al., 2019).

treatment_protocol: For the culture of primary T cells FACS sorted cells were cultured in RPMI 1640 supplemented with 15% FBS, 100 IU/mL penicillin and 100 µg/mL streptomycin, 1% glutamine, 1% sodium pyruvate, 50 µM beta-mercaptoethanol, and were incubated at 37ºC with 5% CO2, with or without stimulation. For stimulation of CD8+ T cells, cells were treated with mIL-2 (0.2 ng/mL) and either CD3/CD28 co-stimulatory beads (20µL/mL, ThermoFisher Cat# 11456D) or plate-bound anti-CD3ε (Clone 145-2C11) and soluble anti-CD28 antibodies (Clone 37.51).

value: WT

value: Female


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E1_AD001_indexed


title: WT CD8+ splenic T cell, target:H3, Tx: StimIL2&CD3CD28day3, Rep.2

value: Male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E12_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E12_AD006_indexed


title: WT CD8+ splenic T cell, target:H3, Tx:StimIL2&CD3CD28day3, Rep.1


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: StimIL2&CD3CD28day3, Rep.3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E12_AD002_indexed


title: BdP54

value: D1 receptor-expressing neuron


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: StimIL2&CD3CD28day3, Rep.4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E12_AD004_indexed


title: EM1

value: prefrontal cortex


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E12_AD001_indexed


title: BdP53


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD008_indexed


title: BdP52


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: StimIL2&CD3CD28day3, Rep.2


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: StimIL2&CD3CD28day3, Rep.1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E1_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E1_AD007_indexed


title: WT CD8+ splenic T cell, target:H3, Tx: StimIL2&CD3CD28day3, Rep.3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD006_indexed


title: WT CD8+ splenic T cell, target:H3, Tx: none, Rep.4


title: EM2


title: BdP51


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD002_indexed


title: WT CD8+ splenic T cell, target:H3, Tx: none, Rep.3


title: BdP50

description:
sex:
MFF
Ribosome-attached mRNA
BAC-Trap RNA-seq


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E12_AD008_indexed


title: BdP46


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E10_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E10_AD001_indexed


title: BdP45


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E10_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD012_indexed


title: WT CD8+ splenic T cell, target:H3, Tx: none, Rep.1


title: WT CD8+ splenic T cell, target:H3, Tx: none, Rep.2


title: BdP44


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: none, Rep.4


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD007_indexed


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: none, Rep.3


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD002_indexed


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: none, Rep.2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E11_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD001_indexed


title: WT CD8+ splenic T cell, target:H1 (clone AE4), Tx: none, Rep.1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D8_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D8_AD008_indexed


title: BdP43


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E10_AD007_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_E10_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D8_AD007_indexed


title: WT CD8+ splenic T cell, target:Igg, Tx: none, Rep.1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D8_AD004_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D9_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D8_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD010_indexed


title: 1 mmol/L SAM-treated SW480, biological rep1

city: Budapest

first: Sara

last: Zsigrai

state: Please Select

address: Szentkirályi street

department: 2nd Dept. of Internal Med.

country: Hungary

institute: Semmelweis University

description: Gene expression data from methyl donor-treated cell

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Data were processed for background substraction, normalization and signal summarization applying the SST-RMA (signal space transformation – robust multi-array average) algorithm. TAC 4.0 (Transcriptome Analysis Console 4.0; Affymetrix, Santa Clara, USA) software were used for gene  expression alteration evaluation.

source_name: 1 mmol/L SAM-treated SW480

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HT-29 and SW480 human colon adenocarcinoma cell lines were cultured at 37°C in a 5% CO2 humidified atmosphere and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 80 mg/ml gentamycin and 2 mM L-  glutamine.

extract_protocol: Total RNA was purified by using Rneasy Mini Kit.

treatment_protocol: Treatment with s-adenosylmethionine was carried out in two different concentrations (0.5 mmol/L and 1 mmol/L) directly added to the medium, in parallel to non-treated control cultures.

value: CRC cell line

tag: cell line


title: 1 mmol/L SAM-treated SW480, biological rep3


title: 0.5 mmol/L SAM-treated SW480, biological rep2

source_name: 0.5 mmol/L SAM-treated SW480


title: 1 mmol/L SAM-treated SW480, biological rep2


title: 0.5 mmol/L SAM-treated SW480, biological rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD002_indexed

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

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.


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD004_indexed


title: SAM24370934 Bone Marrow KO_8hr

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: SAM24370934 Bone Marrow KO_8hr

extract_protocol:
Total RNA was extracted using a RNeasy kit with on-column DNase digestion (Qiagen)
and 0.5ug used for library preparation with a TruSeq RNA Sample Preparation Kit v2 (Illumina).
The libraries were multiplexed and then sequenced on a HiSeq4000 (Illumina) to generate 30 million
single end 50 bp reads.

value: Bone Marrow

value: N4bp1 KO

tag: time

value: 8 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD012_indexed

tag: brain region


title: SAM24370931 Bone Marrow WT_8hr

source_name: SAM24370931 Bone Marrow WT_8hr


title: SAM24370912 Bone Marrow KO_untreated

source_name: SAM24370912 Bone Marrow KO_untreated

value: 0 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD006_indexed

tag: Sex


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD007_indexed

tag: age


title: WT CD8+ splenic T cell, target:Igg, Tx: none, Rep.2

tag: strain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D7_AD001_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D8_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD010_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD008_indexed


title: SAM24370924 Bone Marrow KO_2hr

source_name: SAM24370924 Bone Marrow KO_2hr

value: 2 hours


title: 0.5 mmol/L SAM-treated SW480, biological rep3


title: SAM24370932 Bone Marrow WT_8hr

source_name: SAM24370932 Bone Marrow WT_8hr


title: SAM24370941 Bone Marrow KO_16hr

source_name: SAM24370941 Bone Marrow KO_16hr

value: 16 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD007_indexed


title: non-treated SW480, biological rep3

source_name: non-treated SW480


title: non-treated SW480, biological rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD006_indexed


title: non-treated SW480, biological rep2


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD002_indexed


title: SAM24370928 Bone Marrow KO_4hr

source_name: SAM24370928 Bone Marrow KO_4hr

value: 4 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D6_AD001_indexed


title: SAM24370933 Bone Marrow WT_8hr

source_name: SAM24370933 Bone Marrow WT_8hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D5_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D5_AD010_indexed


title: 1 mmol/L SAM-treated HT-29, biological rep2

source_name: 1 mmol/L SAM-treated HT-29


title: SAM24370939 Bone Marrow WT_16hr

source_name: SAM24370939 Bone Marrow WT_16hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D5_AD006_indexed

source_name: C57BL/6J Male P56 Mouse Brain


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D5_AD002_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D5_AD008_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD012_indexed


title: 1 mmol/L SAM-treated HT-29, biological rep3


title: SAM24370911 Bone Marrow KO_untreated

source_name: SAM24370911 Bone Marrow KO_untreated


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D5_AD001_indexed


title: SAM24370920 Bone Marrow WT_2hr

source_name: SAM24370920 Bone Marrow WT_2hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD008_indexed


title: 1 mmol/L SAM-treated HT-29, biological rep1


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD007_indexed


title: SAM24370926 Bone Marrow WT_4hr

source_name: SAM24370926 Bone Marrow WT_4hr


title: 0.5 mmol/L SAM-treated HT-29, biological rep3

source_name: 0.5 mmol/L SAM-treated HT-29


title: 0.5 mmol/L SAM-treated HT-29, biological rep2


title: SAM24370916 Bone Marrow KO_1hr

source_name: SAM24370916 Bone Marrow KO_1hr

value: 1 hours


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD006_indexed

value: PAL


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD004_indexed

value: male


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D4_AD002_indexed


title: SAM24370935 Bone Marrow KO_8hr

source_name: SAM24370935 Bone Marrow KO_8hr


title: 0.5 mmol/L SAM-treated HT-29, biological rep1


title: SAM24370918 Bone Marrow KO_1hr

source_name: SAM24370918 Bone Marrow KO_1hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D3_AD012_indexed


title: non-treated HT-29, biological rep1

source_name: non-treated HT-29


title: SAM24370925 Bone Marrow WT_4hr

source_name: SAM24370925 Bone Marrow WT_4hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D3_AD008_indexed


title: non-treated HT-29, biological rep3


title: non-treated HT-29, biological rep2


title: SAM24370942 Bone Marrow KO_16hr

source_name: SAM24370942 Bone Marrow KO_16hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D3_AD006_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD012_indexed


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D3_AD001_indexed


title: SAM24370927 Bone Marrow WT_4hr

source_name: SAM24370927 Bone Marrow WT_4hr


title: 180919_CEMBA_mm_P56_P63_4H_CEMBA_4H_Set_B_Q_4_D2_AD008_indexed