title: Sso-RNAseq rep3

city: Gießen

first: Gabriele

last: Klug

address: Heinrich-Buff-Ring 26-32

department: Molecular- and Microbiology

country: Germany

institute: Justus-Liebig University Gießen

data_processing:
alignment: bowtie2 (v2.3.4) –sensitive
counts: featureCounts
Genome_build: ensembl Sulfolobus_solfataricus_p2.ASM700v1:
Supplementary_files_format_and_content: counts

organism: Saccharolobus solfataricus

source_name: S. solfataricus P2

growth_protocol: S. solfataricus P2 was grown as previously described in a 10 l bioreactor (Evguenieva-Hackenberg et al., 2002) (PMID: 12359717).  Cells were cultivated until an OD600 of 0.8 and harvested by centrifugation at 6,000 g and 4 °C for 10 min.

extract_protocol:
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 sec at 4°C). Each  sample was used for three independent cDNA synthesis. First, an oligonucleotide adapter was ligated  to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse  transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina  TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was  PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit  (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 sec at 4°C). Each  sample was used for three independent cDNA synthesis. First, an oligonucleotide adapter was ligated  to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse  transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina  TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was  PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit  (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.

treatment_protocol: Individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP) analyses were performed as described in König et al. (2010) (PMID: 20601959), with the following alteration that were necessary for the application in S. solfataricus. Cell pellets were washed with PBS, and 0.8 g were resuspended in 40 ml PBS at 4°C, and spread on a large petri dish swimming on an ice-water bath. The cell suspension was crosslinked four times at 254 nm, 300 mJ/cm², cells were mixed in between. Crosslinked cells were harvested as before and stored at -80°C.

tag: density


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G12_AD006

status: Public on Nov 24 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:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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 P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: PTLp

tag: target

value: SSp

tag: gender

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G12_AD001

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G12_AD002


title: Sso-RNAseq rep2

library_source: transcriptomic

molecule: total RNA


title: Brunello_Huh75_37C_SARS-CoV2-B_S18_L001

city: New York

first: John

last: Poirier

address: 550 1st Ave

institute: NYU Langone Health

data_processing:
Trimming performed with cutadapt 2.10
Counts table generated by MaGECK 0.5.9.4
Genome_build: Brunello
Supplementary_files_format_and_content: raw counts table

organism: Homo sapiens

source_name: Huh-7.5 cells

extract_protocol:
Ammonium acetate salt precipitation
Nextera
CRISPR

tag: cell line

value: Huh-7.5 cells

tag: treatment

tag: temperature

tag: replicate

value: B

tag: lane


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD010

value: ACA


title: D. mauritiana, late stage 5, replicate 1

city: Davis

first: Susan

middle: E.

last: Lott

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

description:
mau_st5_1
mRNA
processed data file: sim_mau_crosses_allele_specific_counts.txt
processed data file: mau_sec_crosses_allele_specific_counts.txt

data_processing:
Adapter sequences trimmed using Cutadapt (v. 1.7.1).
Reads aligned to genomes using Tophat2 (v. 2.0.13).
Variants to identify allele-specific reads called using GATK haplotype caller.
Allele-specific reads counted using custom Python and R scripts (available with publication).
Counts normalized to upper quantile for total number of counts mapped per individual to a genome.
Genome_build: D. simulans (version r2.02); D. sechellia (version r1.3); D. mauritiana M17 assembly (Nolte et al., 2013; see Methods in publication).
Supplementary_files_format_and_content: *.txt: Allele-specific counts, mapping each hybrid individual to both parental genomes.

organism: Drosophila mauritiana

source_name: late stage 5 embryo

growth_protocol: Cornmeal media, 25 degrees, population-controlled, eggs collected from mothers 4-14 days old.

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Standard Illumina mRNA-Seq library prep protocols, using Illumina TruSeq kits.

treatment_protocol: Crosses between species as specified, to produce hybrid maternal transcriptomes for stage 2 embryos and hybrid zygotic transcriptomes for late stage 5 embryos.

value: embryo

tag: generation

value: Parental

tag: embryonic stage

value: late stage 5

tag: embryo sex

value: unknown

tag: replicate number


title: Brunello_Huh75_33C_SARS-CoV_C_S16_L004

value: C


title: Brunello_Huh75_37C_SARS-CoV2-B_S18_L004


title: Sso-RNAseq rep1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD008


title: Brunello_Huh75_37C_SARS-CoV2-B_S18_L002


title: D. sechellia x D. mauritiana cross, late stage 5 embryo, replicate 6, XX genotype

description:
secxmau_st5_F_6
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

organism: Drosophila sechellia x Drosophila mauritiana

value: F1 hybrid embryo

value: XX genotype


title: Brunello_Huh75_33C_SARS-CoV_C_S16_L003


title: D. sechellia x D. mauritiana cross, late stage 5 embryo, replicate 5, XX genotype

description:
secxmau_st5_F_5
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G12_AD004


title: Brunello_Huh75_33C_SARS-CoV_C_S16_L002


title: Brunello_Huh75_33C_SARS-CoV_C_S16_L001


title: D. sechellia x D. mauritiana cross, late stage 5 embryo, replicate 3, XY genotype

description:
secxmau_st5_M_3
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: XY genotype


title: Brunello_Huh75_33C_SARS-CoV_B_S15_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD002


title: Brunello_Huh75_33C_SARS-CoV_B_S15_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD002


title: D. sechellia x D. mauritiana cross, late stage 5 embryo, replicate 1, XY genotype

description:
secxmau_st5_M_1
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: D. sechellia x D. mauritiana cross, late stage 5 embryo, replicate 4, XX genotype

description:
secxmau_st5_F_4
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F9_AD006


title: D. sechellia x D. mauritiana F1 backcross, stage 2 embryo, replicate 3

description:
secxmau_st2_3
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

source_name: stage 2 embryo

value: F2 hybrid embryo

value: stage 2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F9_AD002

value: brain

value: PTLp


title: D. sechellia x D. mauritiana cross, late stage 5 embryo, replicate 2, XY genotype

description:
secxmau_st5_M_2
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G11_AD012

value: female


title: D. sechellia x D. mauritiana F1 backcross, stage 2 embryo, replicate 2

description:
secxmau_st2_2
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: Brunello_Huh75_33C_SARS-CoV2_A_S14_L004

value: A


title: Brunello_Huh75_33C_SARS-CoV_B_S15_L001

value: Huh-7.5 cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_G10_AD001

value: SSp

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F9_AD012

value: ACA


title: Brunello_Huh75_33C_SARS-CoV2_A_S14_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD008


title: ATAC-Seq Cdk6_Knockout_p185_transformed

city: Vienna

first: Markus

last: Zojer

address: Josef-Baumanngasse

department: Institute for Pharmakology and Toxokology

country: Austria

institute: University of Veterinary Medicine

data_processing:
Alignment to genome version GRCm38 using BWA  (ATAC-Seq) or STAR (RNA-Seq)
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigWig,raw count file (tab delimited)

source_name: BCR-ABL+ cell lines

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
QIAGEN RNeasy extraction kit
Phenol-Chloroform extraction
RNA-seq: SENSE mRNA-Seq Library Prep kit, 50 bp single-end; ATAC-seq: Libraries were amplified using custom Nextera primers.

value: Pre/Pro-B-cells

tag: genotype


title: Brunello_Huh75_33C_SARS-CoV_B_S15_L002

value: B


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F9_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD006


title: ATAC-Seq Cdk6_Wildtype_p185_transformed


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD004


title: Brunello_Huh75_33C_SARS-CoV2_A_S14_L001


title: Brunello_Huh75_33C_OC43_C_S10_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F9_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F7_AD004


title: diabetic

city: Chicago

first: Timothy

middle: Jon

last: Koh

state: IL

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

data_processing:
Raw data were demultiplexed into single cells using Cell Ranger (10X Genomics).
Genome_build: mm10
Supplementary_files_format_and_content: Gzipped MatrixMarket sparse matrix
Supplementary_files_format_and_content: Tab delimited text: feature (gene) names for sparse matrices
Supplementary_files_format_and_content: Tab delimited text: barcode (cell) names for sparse matrices

molecule: polyA RNA

source_name: Monocytes/macrophages isolated from wounds of diabetic mice on day 6 post-injury

extract_protocol:
Monocytes isolated from skin wounds on non-diabetic and diabetic mice on day 6 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per strain. Fresh cells with viability over 85% processed using the 10x Chromium platform . Libraries sequenced on HiSeq with paired-end reads. Fastq files were generated and iesdemultiplexed into single cells using Cell Ranger software
10X Chromium single-cell 3' polyA RNA-seq

tag: cell type

value: Wound monocytes/macrophages

tag: disease state

value: Diabetic


title: Brunello_Huh75_33C_OC43_C_S10_L002

value: C


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F7_AD006

tag: strain

tag: age


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD010

tag: tissue

tag: source


title: D. sechellia x D. mauritiana F1 backcross, stage 2 embryo, replicate 1

description:
secxmau_st2_1
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: embryo

value: unknown


title: CCL4 wk5  Liver 4

city: Boston

first: Thomas

last: Gan

state: MA

address: 33 Ave Lous Pasteur

department: Genetics and Pharmacogenomics

institute: Merck

description:
RS-720794
CCL4_FPKM.txt

data_processing:
Alignment and differential gene expression analysis was performed in Omicsoft Array Studio version 9.0.8.92.
Cleaned reads were aligned to the mouse and human B38 genome references, for the UUO kidney and primary cells respectively, and the rat B6.0 genome reference for the BDL model, using the Omicsoft Aligner with a maximum of 2 allowed mismatches.
Gene level counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R82 gene models.
Genome_build: Human.B38, Mouse.B38, Rat.B6.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode).

source_name: Liver

extract_protocol:
Total RNA was extracted from tissue or cultured cells following the instruction of RNeasy Mini QIAcube Kit (Qiagen, #74116).
Sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Illumina, #RS-122-2201) according to the manufacturer’s instructions.  The resulting cDNA libraries were sequenced on an Illumina HiSeqTM 4000 using a 50 base paired-end run.

tag: replicate group

value: Liver


title: Brunello_Huh75_Mock_C_S3_L002

tag: cell line

value: mock


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F6_AD010

value: brain

tag: target

tag: gender


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F8_AD007

value: PTLp


title: Brunello_Huh75_33C_SARS-CoV2_A_S14_L002

tag: treatment

tag: temperature

tag: replicate


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F9_AD008


title: Brunello_Huh75_33C_OC43_B_S9_L004

tag: lane


title: CCL4 wk5  Liver 2

description:
RS-720792
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F6_AD006

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F7_AD012


title: Brunello_Huh75_33C_OC43_C_S10_L003


title: non-diabetic

source_name: Monocytes/macrophages isolated from wounds of non-diabetic mice on day 6 post-injury

value: Non-diabetic


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F6_AD001


title: CCL4 wk5  Liver 1

description:
RS-720791
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F5_AD008


title: CCL4 wk5  Liver 3

description:
RS-720793
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F5_AD006


title: Brunello_Huh75_33C_OC43_C_S10_L001

value: Huh-7.5 cells


title: Brunello_Huh75_33C_OC43_B_S9_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F6_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F5_AD004

value: SSp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F5_AD010


title: CCL4 wk5  Liver 5

description:
RS-720795
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F7_AD007

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F6_AD002


title: CCL4 wk5 ctrl Liver 5

description:
RS-720790
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F5_AD001


title: Brunello_Huh75_33C_OC43_A_S7_L003

value: A


title: CCL4 wk5 ctrl Liver 3

description:
RS-720788
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD012

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD010


title: Brunello_Huh75_33C_OC43_A_S7_L002


title: CCL4 wk5 ctrl Liver 4

description:
RS-720789
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F5_AD002


title: Brunello_Huh75_33C_OC43_B_S9_L002

value: B


title: Brunello_Huh75_33C_OC43_A_S7_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD006


title: Day 4-UUO_5

description:
RS-720967
UUO_FPKM.txt

source_name: kidney

value: kidney


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD004


title: Brunello_Huh75_33C_NL63_C_S6_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F3_AD012


title: Brunello_Huh75_33C_OC43_A_S7_L004


title: CCL4 wk5 ctrl Liver 1

description:
RS-720786
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F3_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F4_AD002


title: CCL4 wk5 ctrl Liver 2

description:
RS-720787
CCL4_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F3_AD001


title: Brunello_Huh75_33C_NL63_C_S6_L001


title: Day 4-UUO_4

description:
RS-720966
UUO_FPKM.txt


title: Brunello_Huh75_33C_NL63_C_S6_L003


title: Brunello_Huh75_33C_NL63_C_S6_L002


title: Day 4-UUO_1

description:
RS-720963
UUO_FPKM.txt


title: Brunello_Huh75_33C_NL63_B_S5_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F3_AD007


title: Day 4-UUO_2

description:
RS-720964
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD012


title: Day 10-UUO_5

description:
RS-720991
UUO_FPKM.txt


title: Brunello_Huh75_33C_NL63_B_S5_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD007


title: Day 10-UUO_3

description:
RS-720989
UUO_FPKM.txt


title: Brunello_Huh75_33C_NL63_B_S5_L002


title: Day 10-UUO_4

description:
RS-720990
UUO_FPKM.txt


title: Brunello_Huh75_33C_NL63_B_S5_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F2_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD010


title: Day 4-UUO_3

description:
RS-720965
UUO_FPKM.txt


title: Day 10-UUO_1

description:
RS-720987
UUO_FPKM.txt


title: Brunello_Huh75_33C_NL63_A_S4_L004


title: Brunello_Huh75_33C_NL63_A_S4_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD007


title: Day 4-Sham_5

description:
RS-720961
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD006


title: Brunello_Huh75_33C_NL63_A_S4_L002


title: Brunello_Huh75_33C_NL63_A_S4_L001


title: Day 4-Sham_4

description:
RS-720960
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F12_AD006


title: Day 4-Sham_3

description:
RS-720959
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F1_AD001


title: Brunello_Huh75_229E_C_S13_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F12_AD004


title: Day 4-Sham_2

description:
RS-720958
UUO_FPKM.txt

source_name: Kidney

value: Kidney


title: Day 10-UUO_2

description:
RS-720988
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD010


title: Brunello_Huh75_229E_C_S13_L002

value: C


title: Day 4-Sham_1

description:
RS-720957
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD007


title: Brunello_Huh75_229E_C_S13_L001


title: Day 10-Sham_5

description:
RS-720985
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD012


title: Brunello_Huh75_229E_B_S12_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD008


title: Day 10-Sham_4

description:
RS-720984
UUO_FPKM.txt


title: Day 10-Sham_3

description:
RS-720983
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD004


title: Brunello_Huh75_229E_B_S12_L002


title: Brunello_Huh75_229E_B_S12_L003


title: Day 10-Sham_2

description:
RS-720982
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD001


title: Day 10-Sham_1

description:
RS-720981
UUO_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F10_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F10_AD001


title: Brunello_Huh75_229E_C_S13_L004


title: Brunello_Huh75_229E_B_S12_L001


title: Brunello_Huh75_33C_OC43_B_S9_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD008


title: Brunello_Huh75_229E_A_S11_L004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_F11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD004


title: N8: normal mouse Nestin low BMSC (V)

city: Cambridge

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Raw reads were trimmed using trimGalore (version 0.4.1) and default options.
Trimmed reads were then aligned to the mm10 genome using Tophat2 (v2.1.0) and options "--no-coverage-search --read-mismatch 1 --max-multihits 1".
Genes were quantified with featurecounts (Liao et al., 2014) and options "-s 2 --primary -T 12 -Q 20 -t exon -g gene_id", using ensembl release 86 annotations.
Normalization and differential expression were performed using Deseq2 version 1.14.1.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrix with genes as rows and samples as columns

source_name: BM

growth_protocol: Fresh mouse primary cells; leukemia was induced with doxycicline and mice were sacrificed once leukemia was evident due to high WBC in peripheric blood.

extract_protocol:
mRNA was obtained using RNeasy kit (Qiagen).
As described in Picelli et al. Nat Protocols 2014; 171-181.

treatment_protocol: Bones were crushed in PBS with collagenase to get a cell suspension. After RBC lysis, cells were sortered as GFP+ CD45- CD31- DAPI-. Pellets were frozen at -80C to following obtain mRNA.

value: bone marrow stromal cells

tag: cell population

value: Nestin low

value: normal


title: N9: normal mouse Nestin low BMSC (VI)


title: Brunello_Huh75_229E_A_S11_L003


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E9_AD001


title: Brunello_Huh75_229E_A_S11_L002


title: N7: normal mouse Nestin low BMSC (IV)


title: N6: normal mouse Nestin low BMSC (III)


title: Brunello_Huh75_229E_A_S11_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD004


title: N5: normal mouse Nestin low BMSC (II)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD001


title: N3: normal mouse Nestin high BMSC (II)

value: Nestin high


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD007

value: brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD006

value: PTLp


title: N4: normal mouse Nestin low BMSC (I)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD008


title: N2: normal mouse Nestin high BMSC (I)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD012

value: female


title: L7: leukemic iMLL-AF9 Nestin low BMSC (IV)

value: leukaemic


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E8_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E7_AD002


title: L6: leukemic iMLL-AF9 Nestin low BMSC (III)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD008


title: L3: leukemic iMLL-AF9 Nestin high BMSC (II)


title: L4: leukemic iMLL-AF9 Nestin low BMSC (I)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD007


title: L2: leukemic iMLL-AF9 Nestin high BMSC (I)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD006


title: L5: leukemic iMLL-AF9 Nestin low BMSC (II)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD010


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD008


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD007


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD001


title: SS_3

city: Chengdu

first: Longhui

last: Zhao

address: No. 9 Section 4, Renmin South Road

country: China

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence;The total clean reads from all libraries were assembled using Trinity as a reference transcriptome.
The expression level of each unigene was expressed as fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: de novo
Supplementary_files_format_and_content: tab-delimited xls file include RPKM values for all Samples

organism: Amolops torrentis

source_name: Brain

extract_protocol:
Samples were preserved in RNA Later (Sigma-Aldrich) and stored at -20 °C, and RNA was harvested using Trizol reagent. The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole brain

tag: stimuli

value: audiovisual


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E5_AD002

value: SSp

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E6_AD012

value: ACA


title: SS_1


title: SY_3

value: acoustic


title: SS_2


title: D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 6, XX genotype

description:
mauxsec_st5_F_3
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

organism: Drosophila mauritiana x Drosophila sechellia

value: embryo

tag: generation

value: F1 hybrid embryo

tag: embryonic stage

value: late stage 5

tag: embryo sex

value: XX genotype

tag: replicate number


title: D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 5, XX genotype

description:
mauxsec_st5_F_2
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: shCRY1 Rep 4

city: Philadelphia

first: Ayesha

last: Shafi

state: PA

address: 233 South 10th Street, 1032 BLSB

institute: Thomas Jefferson University

data_processing:
alignment to hg19 with STAR
Count table generation using Featurecounts
Differential Expression using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix

growth_protocol: C4-2 cells (either shCON or shCRY1) were cultured in hormone proficient media unless otherwise indicated.

extract_protocol:
RNA Seq was prepared as previously described (Dylgjeri et al 2019)
RNA-Seq libraries were constructed using Illumina TruSeq Stranded Total RNA Library Prep  kits according to manufacturer instructions

treatment_protocol: Cells were treated with 10 ng/ml Doxycycline for 72 hours prior to harvest

tag: cell type

value: prostate cancer cells

tag: genotype/varition


title: D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 4, XX genotype

description:
mauxsec_st5_F_1
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

tag: tissue


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E4_AD006

tag: strain

tag: age

tag: source


title: shCRY1 Rep 3

tag: cell line


title: SY_1


title: D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 3, XY genotype

description:
mauxsec_st5_M_3
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: XY genotype


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD002

tag: target

tag: gender


title: shCRY1 Rep 1


title: D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 2, XY genotype

description:
mauxsec_st5_M_2
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: shCON Rep 4

value: shCON


title: shCRY1 Rep 2


title: SJ_3

value: visual


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD001

value: brain

value: PTLp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD012

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD006


title: SJ_2

value: whole brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD008


title: D. mauritana x D. sechellia cross, late stage 5 embryo, replicate 1, XY genotype

description:
mauxsec_st5_M_1
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: D. mauritana x D. sechellia F1 backcross, stage 2 embryo, replicate 2

description:
mauxsec_st2_2
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: F2 hybrid embryo

value: stage 2

value: unknown


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E3_AD004

value: SSp


title: D. mauritana x D. sechellia F1 backcross, stage 2 embryo, replicate 3

description:
mauxsec_st2_3
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt


title: shCON Rep 2


title: SY_2

value: acoustic


title: W_3

value: blank contrast


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD010

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD007

value: male


title: shCON Rep 1


title: D. mauritana x D. sechellia F1 backcross, stage 2 embryo, replicate 1

description:
mauxsec_st2_1
mRNA
processed data file: mau_sec_crosses_allele_specific_counts.txt

value: embryo


title: W_2


title: Day7-Spleen-hACE2-9

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced with 50bp single end reads on an Illumina HiSeq3000.
The reads were mapped with STAR 2.5.3a to the human genome (hg38) for the cultured human cell libraries or mouse genome (mm10) for the mouse cell libraries.
The counts for each gene were obtained using --quantMode GeneCounts in STAR commands, and the other parameters during alignment were set to default.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for each sample

source_name: mouse spleen cells

growth_protocol: All animal studies were approved by the Animal Research Committee, University of California, Los Angeles. Male C57Bl/6 mice (000664, Jackson Labs) (14-17 weeks) were housed in groups and fed standard chow diets. AAV9-CMV-hACE2 (AAV- 200183, Vector Biolabs) or control AAV9-CMV-eGFP viruses were purchased from Vector Biolabs. Animals were injected intravenously with 100-μl injection containing 2x1012 genomic copies of AAV-CMV-hACE2 or control (AAV-CMV-eGFP). Animals were housed in BSL-3 facility for the duration of the experiment (n=5/cage). Cage food weight and individual mouse body weight were recorded daily after SARS-CoV- 2 virus infection.

extract_protocol:
All samples were stored in RNA later stabilization solution and subsequently total RNA was extracted using RNA mini Kit (7326830, BioRad). cDNA was synthesized by using iScript cDNA Synthesis Kit (1708890, BioRad) and qPCR performed.
For RNA-sequencing, libraries were prepared by the Technology Center for Genomics & Bioinformatics at UCLA using Illumina TruSeq Stranded Total RNA Sample Prep kit and sequenced with 50bp single end reads on an Illumina HiSeq3000.

treatment_protocol: SARS-CoV-2, isolate USA-WA1/2020, was got from the Biodefense and Emerging Infections (BEI) Resources of the National Institute of Allergy and Infectious Diseases (NIAID). SARS-CoV-2 was passaged once in Vero-E6 cells (ATCC) and viral stocks were aliquoted and stored at -80 C. Virus titer was determined by plaque assay using Vero E6 Cells. 200μL of SARS-CoV2 (0.5 x 106 PFU/mL) was injected intraperitoneally.

value: mouse spleen cells

tag: treatment


title: W_1


title: CRY1 - Veh - Input

data_processing:
alignment to hg19 genome using Bowtie2
peak calling using macs2
Genome_build: hg19
Supplementary_files_format_and_content: BED file

source_name: CRY1 Veh Input

growth_protocol: C4-2 cells were cultured in hormone proficient media

extract_protocol:
ChIP was performed as previously described (McNair et al 2018)
Swift BioSciences  ACCEL-NGS 2S Plus DNA Library

treatment_protocol: Cells were treated with maintained in hormone profiecient media 24 hrs prior to harvest

value: prostate cancer cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD004


title: Day7-Spleen-hACE2-8


title: SJ_1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD006


title: CRY1 - Veh 2 - IP

source_name: CRY1 Veh ChIP-Seq

tag: chip antibody

value: CRY1 (Hoffmann et al, 2014)


title: Day7-Spleen-hACE2-6


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD002


title: shCON Rep 3

value: shCON


title: HD_2

value: dark contrast


title: CRY1 - Veh 1 - IP


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E2_AD001

value: brain

value: PTLp


title: HD_1

value: whole brain


title: Day7-Spleen-hACE2-10


title: sox17_intestine_DsRedx_3

city: HK

first: Zilong

last: WEN

address: Academic Bld., HKUST, Clearwater Bay, Kowloon

department: Division of Life Science

country: Hong Kong

institute: Hong Kong University of Science and Technology

description: 2x150 paired-end sequence reads

data_processing:
Raw reads were first aligned to zebrafish reference genome danRer11 using STAR aligner with default parameters.
Read count per gene was then calculated using the FeatureCount program with default parameters.
TPM(transcripts per million) was calculated according to standard formula.
Genome_build: danRer11
Supplementary_files_format_and_content: comma-separated values file including read counts and TPM values for each sample

organism: Danio rerio

source_name: specific cells types in zebrafish intestine

extract_protocol:
30-50 cells for each sample were sorted into lysis buffer (0.2% Triton X-100 solution) by fluorescence-activated cell sorting (FACS) for direct reverse transcription and cDNA amplification
cDNA library was generated based on SMART-seq2 protocol. Three duplicated samples for each cell type were sent to Novogene for Illumina Hiseq X Ten 150 bp pair-end sequencing.

value: intestine

value: adult

tag: genotype


title: sox17_intestine_DsRedx_2

description: 2x150 paired-end sequence reads


title: Day7-Spleen-eGFP-5

value: AAV-CMV-eGFP


title: HCT116_DNMT1_KO_untreated_day_40

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

institute: University of Edinburgh

data_processing:
Raw Illumina sequencing output from the NextSeq were converted to paired FASTQ files without demultiplexing using ‘bcl2fastq’ and default settings (v2.17.1.14). These FASTQ files were then demultiplexed using custom python scripts considering indexes with perfect matches to the sample indexes. The different lanes for each sample were then combined.
Sequencing quality was assessed with FASTQC (v0.11.4). Low quality reads and remaining adaptors were removed using TrimGalore (v0.4.1, Settings: --adapter AGATCGGAAGAGC --adapter2 AAATCAAAAAAAC). NuGen adaptors contain extra diversity bases to facilitate sequencing. These were removed using the ‘trimRRBSdiversityAdaptCustomers.py’ Python script provided by NuGen (v1.11). The paired end reads were then aligned to the mm10 genome using Bismark (v 0.16.3 with Bowtie2 v2.2.6 with settings: -N 0 -L 20) before PCR duplicates were identified and removed using the 6bp UMIs present in the index reads and the ‘nudup.py’ Python script supplied by NuGen (v2.3). Aligned BAM files were processed to report coverage and number of methylated reads for each CpG observed. Forward and reverse strands were combined using Bismark’s methylation extractor and bismark2bedgraph modules with custom Python and AWK scripts.
Processed RRBS files were assessed for conversion efficiency based on the proportion of methylated reads mapping to the λ genome spike-in (>99.5% in all cases).
BigWigs were generated from RRBS data using CpGs with coverage ≥5
Genome_build: hg38
Supplementary_files_format_and_content: Processed coverage values for each CpG observed in sample. CpG position and total coverage (T) and methylated coverage (M) combining both strands. Columns = chr, start, end, T, M. Positions are 0-based, ie BED format.
Supplementary_files_format_and_content: bigWig files for each sample also supplied. Only contain CpGs with coverage >= 5 in that sample.

source_name: Human cell line

growth_protocol: HCT116, DNMT1 KO, DNMT3B KO, and DKO cells were gifts from B. Vogelstein (Rhee et al 2002 PMID: 11932749). Cells were cultured in McCoy’s 5A medium (Gibco) supplemented with 10% fetal calf serum (Life technologies) and penicillin-streptomycin antibiotics at 140 and 400 µg/ml respectively.

extract_protocol:
Genomic DNA was extracted from cells using DNeasy Blood & Tissue Kit according to the manufacturer’s protocol with some modifications. RNase A/T1 Cocktail (Ambion AM2286) was added to proteinase K and samples were incubated at 37°C for 1hr to remove RNA. At the final step, DNA was eluted with ddH2O instead of AE buffer. DNA was quantified by Nanodrop and Qubit.
200ng of purified DNA samples were processed using the Ovation RRBS Methyl-Seq system kit (NuGen Technologies) according to instructions with modifications. Briefly, 0.5ng unmethylated phage λ DNA (NEB) was spiked into each sample to allow assessment of bisulfite conversion efficiency. The methylation-insensitive restriction enzyme MspI was then used to digest the genomic DNA, and digested fragments were ligated to adapters. Adapter-ligated fragments were then repaired before bisulfite conversion with the Qiagen Epitect Fast Bisulfite Conversion kit. Bisulfite-treated adapter-ligated fragments were amplified by 9 cycles of PCR and purified using Agencourt RNAClean XP beads. Libraries were quantified using the Qubit dsDNA HS assay and assessed for size and quality using the Agilent Bioanalyzer DNA HS kit. Library preparation and sequencing was performed by the Edinburgh Clinical Research Facility.

treatment_protocol: Cells were plated at ~20% confluency. Next day cells were treated with freshly prepared 1µM 5-aza-dC (Sigma Aldrich) for 24 hrs. Cell pellets were collected at different time points following treatment and genomic DNA was extracted using DNeasy Blood & Tissue Kit (QIAGEN) following the manufacturer’s instructions.

tag: timepoint (days)

value: HCT116 cells lacking DNMT1


title: HCT116_DNMT1_KO_aza_treated_day_40


title: HCT116_DNMT1_KO_aza_treated_day_22


title: Day7-Spleen-eGFP-4


title: HD_3

tag: stimuli


title: sox17_intestine_DsRedx_1

description: 2x150 paired-end sequence reads


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E1_AD008

source_name: C57BL/6J P56 Mouse Brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E1_AD006

value: SSp

value: female


title: Day7-Spleen-eGFP-2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E1_AD002


title: sox17_intestine_GFP_3

description: 2x150 paired-end sequence reads


title: HCT116_DNMT1_KO_aza_treated_day_16


title: Day7-Spleen-eGFP-1


title: sox17_intestine_GFP_2

description: 2x150 paired-end sequence reads


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E1_AD001


title: HCT116_DNMT1_KO_aza_treated_day_6


title: Day7-Lung-hACE2-6

source_name: mouse lung cells

value: mouse lung cells


title: HCT116_DNMT1_KO_aza_treated_day_13


title: sox17_intestine_GFP_1

description: 2x150 paired-end sequence reads


title: HCT116_DNMT1_KO_aza_treated_day_3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E12_AD010

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E12_AD006


title: Day7-Lung-eGFP-4


title: Day7-Lung-eGFP-5


title: HCT116_DNMT3B_KO_untreated_day_40

value: HCT116 cells lacking DNMT3B


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E1_AD004


title: sox17_gill_DsRedx_2

description: 2x150 paired-end sequence reads

source_name: specific cells types in zebrafish gill

value: gill


title: HCT116_DNMT3B_KO_aza_treated_day_28


title: sox17_gill_DsRedx_1

description: 2x150 paired-end sequence reads


title: HCT116_DNMT1_KO


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E12_AD004


title: Day7-Lung-hACE2-10


title: sox17_gill_DsRedx_3

description: 2x150 paired-end sequence reads


title: Day7-Kidney-hACE2-9

source_name: mouse kidney cells

value: mouse kidney cells


title: HCT116_DNMT3B_KO_aza_treated_day_40


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E12_AD002

value: male


title: sox17_gill_GFP_2

description: 2x150 paired-end sequence reads


title: Day7-Kidney-hACE2-8


title: Day7-Kidney-hACE2-10


title: HCT116_DNMT3B_KO_aza_treated_day_22


title: sox17_gill_GFP_1

description: 2x150 paired-end sequence reads


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E12_AD012


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E12_AD001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD008


title: HCT116_DNMT3B_KO_aza_treated_day_16


title: HCT116_DNMT3B_KO_aza_treated_day_13


title: Day7-Lung-hACE2-8


title: Day7-Lung-eGFP-2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD007


title: sox17_gill_GFP_3

description: 2x150 paired-end sequence reads


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD004


title: Day7-Kidney-eGFP-3


title: HCT116_DNMT3B_KO_aza_treated_day_3


title: HCT116_DNMT3B_KO


title: HCT116_DNMT3B_KO_aza_treated_day_6


title: HCT116_untreated_day_40

value: HCT116 cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD002


title: Day7-Kidney-eGFP-5


title: Day7-Kidney-eGFP-1


title: Day7-Heart-hACE2-9

source_name: mouse heat cells

value: mouse heat cells


title: Day7-Heart-hACE2-8


title: HCT116_aza_treated_day_28


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD008

value: brain


title: HCT116_aza_treated_day_40


title: Day7-Heart-hACE2-6


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E11_AD001

value: PTLp


title: HCT116_aza_treated_day_22


title: Day7-Heart-eGFP-5


title: Bull4 (#10085), 16 months

city: Québec

first: Marc-André

last: Sirard

state: Québec

address: 2325 Rue de l'Université

department: Département des sciences animales

country: Canada

institute: Université Laval

description:
DE-10m vs 16m.txt
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
SVD-16m

data_processing:
Illumina adapters were removed and reads were quality-trimmed using Trimmomatic v0.36 (ILLUMINACLIP:adapters.fa:2:30:15 MINLEN:10)
Trimmed reads were aligned to a synthetic reference of all bovine miRNAs (miRBase v21), tRNAs (GtRNADB, http://lowelab.ucsc.edu/GtRNAdb/Btaur6/Btaur6-stats.html), and ncRNAs (ENSEMBL release 98) using bowtie v1.2.2  (options --best --strata -k 1 -m 1).
Differential expression was assessed using the DESeq package (Source code available at https://bitbucket.org/ericfournier2/mas_mirna).
Genome_build: N/A
Supplementary_files_format_and_content: space-separated values containing the raw counts, normalized counts and differential analyses for the various contrasts.

organism: Bos taurus

source_name: Spermatozoa

extract_protocol:
For each treatment, five straws of semen were thawed in 37°C water for 1 min and the content was combined. After washing twice with PBS, the pellets were resuspended in 60 μL PBS and each sperm suspension was added to 33.3 μL sperm lysis buffer (4M Guanidine Thiocyanate, 5% Tween 20, 5% Triton X-100, 120 mM EDTA, and 120 mM Tris-HCl pH 8.0), 3.3 μL Proteinase K (20 mg/mL), and 3.3 μL 0.1M DTT, then incubated for 15 min at 60°C with gentle shaking (20 rpm). Small RNAs were extracted with the miRNeasy Mini Kit (QIAGEN, Toronto, ON, Canada, Cat. # 217004) following the manufacturer’s instructions. Briefly, 700 μL QIAzol lysis reagent were added to the previous mixture and then moved to a QIAshredder homogenizer column (QIAGEN, Toronto, ON, Canada, Cat. # 79654). After centrifugation at 13,300 rpm for 2 min at RT, the flow through was transferred to a new tube and kept at RT for 5 min to further dissociate nucleoprotein complexes. Chloroform (140 μL) was added and the samples were shaken vigorously for 15 s. The samples were left at RT for 2-3 min and then centrifuged at 12,000 g for 15 min at 4°C. The upper aqueous phase of each sample was transferred to a new collection tube, 1.5 volume of absolute ethanol was added, and the solution was moved to an RNeasy Mini spin column to absorb the RNAs. The flow through was discarded after centrifugation and 40 μL DNase buffer (27 Kunitz units) were added directly to the middle of the membrane in the column and then incubated at RT for 15 min. The column was further washed with the provided buffer RWT once and buffer RPE twice. The column was placed into a new 2 mL collection tube and the RNAs were dissolved in 30 μL elution buffer. The integrity and concentration of sperm RNA were evaluated with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
The libraries of sperm small RNAs were constructed according to the manual of TruSeq Small RNA Library Prep Kit (Illumina, U.S.A., v02) with minor modifications. In brief, RNA 3’ and 5’ adapters were ligated to an average of 87 ng of sperm RNA in 5 µl nuclease-free water. The adapter-ligated RNA was then reverse transcribed in the presence of RNA RT Primer, first strand buffer, dNTP Mix, DTT, RNase inhibitor, and SupserScript II Reverse Transcriptase according to the protocol and incubated at 50°C for 1 hour. For each sample, two primers: the same RNA PCR Primer 1 and a specific RNA PCR Primer index were used for 11 cycles of amplification. The amplified RNA libraries were resolved on a 6% Novex TBE gel for 35 min at 145 V, and DNA fragments ranging from 145 to 400 bp, which represented original RNA sizes of 20 to275 bp, were cut and purified by ethanol precipitation. The pellets were dissolved in 10 μL elution buffer (10 mM Tris-HCl, pH 8.5) and the purity and concentration of the libraries were checked by NanoDrop. Sequencing was done on an Illumina Hiseq 2500 at McGill University (Montreal, QC, Canada) following the recommended protocol.

tag: breed

value: Holstein Friesian

value: 16 months

value: Spermatozoa


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD010


title: HCT116_aza_treated_day_13


title: Bull4 (#10085), 12 months

description:
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
SVD-12m

value: 12 months


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD004


title: HCT116_aza_treated_day_16


title: Bull4 (#10085), 10 months

description:
DE-10m vs 16m.txt
normalized_counts.txt
raw_counts.txt
SVD-10m

value: 10 months


title: Day7-Kidney-eGFP-2

value: AAV-CMV-eGFP


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD002

value: SSp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD007


title: Bull3 (#10051), 12 months

description:
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
MM-12m


title: Bull3 (#10051), 16 months

description:
DE-10m vs 16m.txt
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
MM-16m


title: Day7-Heart-hACE2-10


title: Day7-Heart-eGFP-1


title: HCT116_aza_treated_day_6


title: DKO_gfp_experiment_2

value: DKO_gfp (HCT116)

value: HCT116 lacking DNMT1 and DNMT3B. Expressing GFP


title: Day7-Heart-eGFP-2


title: Day7-Heart-eGFP-4


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_E10_AD001


title: HCT116_aza_treated_day_3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D9_AD004

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D9_AD002


title: Bull2 (#06622), 16 months

description:
DE-10m vs 16m.txt
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
VL-16m


title: Day3-Lung-hACE2-3

value: mouse lung cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D8_AD012

value: ACA


title: Day3-Lung-hACE2-1


title: Day3-Lung-hACE2-2


title: DKO_dnmt3b_catDead_experiment_2

value: DKO_dnmt3b_catDead (HCT116)

value: HCT116 lacking DNMT1 and DNMT3B. Expressing catalytically dead DNMT3B


title: Bull2 (#06622), 10 months

description:
DE-10m vs 16m.txt
normalized_counts.txt
raw_counts.txt
VL-10m


title: Bull2 (#06622), 12 months

description:
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
VL-12m


title: DKO_experiment_2

value: DKO (HCT116)

value: HCT116 lacking DNMT1 and DNMT3B


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D8_AD010

value: brain

value: PTLp


title: HCT116_experiment_2

value: HCT116 cells


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D8_AD008

value: male


title: Day3-Lung-eGFP-2


title: DKO_dnmt3b_catDead_experiment_1


title: Bull1 (#03981), 16 months

description:
DE-10m vs 16m.txt
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
SC-16m

value: Holstein Friesian

value: 16 months

value: Spermatozoa


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D8_AD002

value: SSp


title: DKO_dnmt3b_experiment_1

value: DKO_dnmt3b (HCT116)

value: HCT116 lacking DNMT1 and DNMT3B. Expressing DNMT3B


title: Bull3 (#10051), 10 months

description:
DE-10m vs 16m.txt
normalized_counts.txt
raw_counts.txt
MM-10m

value: 10 months


title: Bull1 (#03981), 12 months

description:
DE-12m vs 16m.txt
normalized_counts.txt
raw_counts.txt
SC-12m

value: 12 months


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D8_AD001


title: Day3-Lung-eGFP-1

value: mouse lung cells

value: AAV-CMV-eGFP


title: HCT116_experiment_1


title: Day3-Liver-hACE2-3

source_name: mouse liver cells

value: mouse liver cells


title: DKO_dnmt3b_experiment_2


title: Krogan_Plasmid_DNA_library_S48_L004

data_processing:
Trimming performed with cutadapt 2.10
Counts table generated by MaGECK 0.5.9.4
Genome_build: Krogan
Supplementary_files_format_and_content: raw counts table

molecule: other

organism: synthetic construct

source_name: Krogan plasmid DNA library

tag: sample type

value: Krogan plasmid DNA library

tag: temperature

tag: replicate

value: A

tag: lane


title: Krogan_Plasmid_DNA_library_S48_L003


title: Day3-Liver-hACE2-1

tag: tissue


title: Day3-Lung-eGFP-3


title: Day3-Liver-eGFP-3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD008

tag: strain

value: brain

value: ACA


title: DKO_experiment_1

value: DKO (HCT116)

value: HCT116 lacking DNMT1 and DNMT3B


title: Day3-Liver-eGFP-2


title: Krogan_Plasmid_DNA_library_S48_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD007

tag: age

value: PTLp

value: male


title: Krogan_Plasmid_DNA_library_S48_L002


title: Bull1 (#03981), 10 months

description:
DE-10m vs 16m.txt
normalized_counts.txt
raw_counts.txt
SC-10m

value: Holstein Friesian

tag: cell type

value: Spermatozoa


title: Brunello_Plasmid_DNA_library_S20_L004

source_name: Brunello plasmid DNA library

value: Brunello plasmid DNA library


title: Day3-Liver-eGFP-1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D8_AD004

tag: source

value: SSp

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD006

tag: target


title: Brunello_Plasmid_DNA_library_S20_L003


title: Day3-Liver-hACE2-2


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD010

tag: gender


title: Day3-Kidney-hACE2-3

value: mouse kidney cells

tag: treatment


title: Day3-Kidney-hACE2-2


title: Brunello_Plasmid_DNA_library_S20_L002


title: Brunello_Plasmid_DNA_library_S20_L001


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD001


title: Peritoneum_PBS_Tg

type: RNA

city: Kyoto

first: Takuya

last: Ishimura

state: Kyoto

address: Sakyo-ku Syogoinkawaharatyo 54

department: Nephrology

country: Japan

institute: Kyoto University

hyb_protocol: Each sample was hybridized to an Affymetrix mouse genome 430 2.0 array at TAKARA Bio (Shiga, Japan).Hybridization control was GeneChip Eukaryotic Hybridization Control Kit and hybridization was perfomed for2 hours at 45C in 60rpm by GeneChip Hybridization Oven 640

scan_protocol: The genechips were scanned by a GeneChip Scanner 3000.

data_processing: Data normalization, log transformation, statistical analysis, and pattern study were performed with the GeneChip Operating Software Ver.1.4

label: biotin

label_protocol: Complementary RNA probes were generated using the GeneChip Expression 3′-Amplification Reagents for IVT Labeling Kit (Applied Biosystems, Foster city, CA)

extract_protocol: Total RNA from the parietal peritoneum was extracted by RNeasy Mini Kit (Qiagen) in these mice.

tag: strain background

tag: genotype/variation

value: SAP-BNP-Tg

value: peritoneum

value: ethanol/PBS


title: Day3-Kidney-hACE2-1


title: Day3-Kidney-eGFP-3

value: AAV-CMV-eGFP


title: Peritoneum_PBS_WT

value: WT


title: Peritoneum_CG_Tg

value: chlorhexidine gluconate


title: Australian AD S77

first: Eric

last: Vornholt

state: NY

address: 800 E. Leigh St. Box 980126

institute: Icahn School of Medicine

description: miRNA

hyb_protocol: Each labeled sample was hybridized onto a GeneChip miRNA 3.0 Array.

scan_protocol: Each array was scanned on the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) and raw probe intensities stored in .CEL files by the GeneChip Operating Software (GCOS v1.4).

data_processing: Array quality was assessed by monitoring the ratios of GAPDH and by the percentage of Present genes (%P) and array exhibiting GAPDH 3‚ 3.0 and %P > 40% were considered of good quality. Expression values were calculated following the pre-processing procedure: 1) GCRMA background correction, 2) log2 transformation, 3) quantile normalization and 4) median-polish probeset summarization using Partek Genomics Suite (PGS) v6.23 (PGS; Partek Inc., St. Louis, MO). The batch effect removal option in PGS was used to control for batch effect. mRNA and miRNA microarray quality was further assessed using a principal components analysis (PCA) which was conducted on the expression values for both array types in which samples were plotted along the first three principle components (PCs) to identify potential microarray outliers.

source_name: prefrontal cortex

label_protocol: Total RNA (500ng) from each specimen was labeled using the FlashTag‚ Biotin HSR RNA labeling kit (Affymetrix). Each RNA sample was spiked with 5 different oligonucleotides as positive endogenous controls to assess the efficiency of the labeling reaction. The RNA samples were subjected to a brief Poly(A) tailing reaction followed by ligation of a biotinylated signal molecule.

extract_protocol: Total RNA containing the small RNA fraction was isolated from 100mg fresh frozen tissue from the prefrontal cortex (PFC) using the mirVana-PARIS kit (Life Technologies, Carlsbad, CA) following manufacturer's protocols. RNA concentration was measured using the Quant-iT Broad Range RNA Assay kit (Life Technologies) and the RNA Integrity Number (RIN) was measured on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

value: prefrontal cortex

tag: diagnosis

value: Control

tag: Sex

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: Australian AD S76

description: miRNA

tag: tissue

value: Alcohol

tag: age


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D7_AD004

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT 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 INTACT
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

tag: strain

value: brain

tag: source

value: PTLp

tag: target

tag: gender


title: Australian AD S80

description: miRNA

tag: diagnosis


title: Day3-Kidney-eGFP-2

tag: treatment


title: Australian AD S82

description: miRNA

tag: Sex

tag: rin


title: Day3-Kidney-eGFP-1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D6_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D6_AD010

value: ACA


title: 2011-376 RNA115 [control]

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling Illumina CASAVA v1.8.2
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The sequencing reads were processed by MAP-RSeq v.1.2 workflow [1], the Mayo Bioinformatics Core pipeline. The alignment in MAPRseq was performed with TopHat 2.0.6 and the gene counts was obtained using HTSeq-count v0.5.3p9
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file includes raw gene counts

source_name: corneal endothelium

extract_protocol:
RNA libraries were prepared using TruSeq RNA  Sample Prep Kit v2 (Illumina, San Diego, CA).
Briefly, poly(A)  mRNA was purified from total RNA using oligo(dT) magnetic  beads, fragmented at 95 °C for 8 min, eluted from the beads, and  primed for first-strand cDNA synthesis using SuperScript III  reverse transcriptase and random primers (Invitrogen). Second-  strand cDNA synthesis was performed using DNA polymerase  I and RNase H, and double-stranded cDNA was purified  using a single AMPure XP bead cleanup step (Agencourt,  Danvers, MA). The cDNA ends were repaired and phosphorylated  using Klenow fragment, T4 polymerase, and T4 polynucleotide  kinase, followed by a single AMPure XP bead cleanup  step. The blunt-ended cDNAs were modified to include a single  3 -adenylate residue using Klenow exo  (3  to 5  exo ), and  paired-end DNA adaptors (Illumina) with a single T base overhang  at the 3 -end were ligated to the A-tailed cDNA population.  Unique indexes, included in the standard TruSeq kits (12-  Set A and 12-Set B), were incorporated at the adaptor ligation  step for multiplex sample loading on the flow cells. The resulting  constructs were purified by two consecutive AMPure XP  bead cleanup steps and enriched by 12 cycles of PCR using  primers included in TruSeq RNA Sample Prep Kit v2. Libraries  were loaded onto paired-end flow cells at concentrations of  8–10 pM to generate cluster densities of 700,000/mm2 using  cBot and cBot Paired-end Cluster Kit v3 (Illumina) following  the manufacturer’s standard protocol. The flow cells were  sequenced as 51   2 paired-end reads on an Illumina HiSeq  4000 system using TruSeq SBS Sequencing Kit v3 and SCS  v1.4.8 data collection software.

tag: group

value: corneal endothelium

tag: batch


title: Australian AD S74

description: miRNA

tag: brain weight

tag: ph

tag: pmi

tag: hemisphere


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D6_AD004

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: SSp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D6_AD012

value: female


title: 2011-325 RNA84 [control]


title: Day3-Heart-hACE2-2

source_name: mouse heart cells

value: mouse heart cells


title: 2011-305 RNA89 [control]


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D6_AD002

value: male


title: Australian AD S69

description: miRNA

tag: neuropathology

tag: hepatology

tag: toxicology

tag: smoking


title: Day3-Heart-hACE2-3

tag: tissue


title: Day3-Heart-hACE2-1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D6_AD001

tag: strain

tag: age

tag: source

tag: target


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD012

tag: gender


title: Australian AD S73

description: miRNA

tag: diagnosis

tag: Sex

tag: rin


title: Australian AD S70

description: miRNA

tag: brain weight


title: TREM2_KO_rep2

city: Oxford

first: Devika

last: Agarwal

address: JR hospital, Headley way

department: The MRC Weatherall Institute of molecular medicine

institute: University of Oxford

data_processing:
2 lanes of Paired-end files (75bp) were generated for each sample.
Quantified transcript abundance counts were obtained  for each sample with the tool Salmon (v0.12.0) using mapping-based mode with default parameters, automatic library type-inference, and the additional command line arguments “validatemappings”, “seqBias”, “posBias” and “gcBias”.
Count data was imported into R using tximport and protein-coding genes with less than 10 reads across the 9 samples used in the comparison were filtered out
Differential gene expression was performed in DESeq2 using the Wald test with an FDR threshold of 0.05
Genome_build: GRCh38 (Ensembl release 95)
Supplementary_files_format_and_content: Salmon quantification files (quant.sf) for each sample with transcript length , effective length , estimated abundances and TPM values

growth_protocol: iPSC-macrophages were differentiated as described in van Wilgenburg et al (2013) PLoS One. 8:8. Free-floating macrophage precursors were harvested from Differentiation Factories at 7, 8, and 9 weeks from the start of differentiation, and seeded in 6 well-plates at 1.5 million cells/well in macrophage media (X-VIVO15 media with 100 ng/mL M-CSF, 2 mM Glutamax, 100 U/mL penicillin and 100 μg/mL streptomycin), and incubated for 7 days at 37 °C/5% CO2.

extract_protocol:
Lysates were passed through QIAshredder columns (QIAGEN) and the total RNA extracted using a QIAGEN RNeasy Mini kit, according to the manufacturer’s protocol using on-column DNase treatment (QIAGEN). RNA samples were eluted in 30 µL of RNase-free water. The quantity and quality of RNA was measured by Nanodrop and RNA Tapestation (Agilent), with measured RNA integrity (RIN) values ≥8.4.The mRNA fraction was selected from the total RNA for each sample before conversion to cDNA.
 Poly-A library preparation and sequencing accroding to standard illumina protocols.

tag: differentiation age

value: 8 weeks

tag: genotype

value: KO

tag: cell type

value: human microglia-like iPSC-macrophages (pMac) from isogenic induced pluripotent stem cell (iPSC) line


title: Day3-Heart-eGFP-3

tag: treatment

value: AAV-CMV-eGFP


title: TREM2_KO_rep3

value: 9 weeks


title: TREM2_KO_rep1

value: 7 weeks


title: Australian AD S68

description: miRNA

value: prefrontal cortex

value: Control

tag: ph

tag: pmi

tag: hemisphere

tag: neuropathology

tag: hepatology


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD008

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: strain

tag: age

tag: tissue


title: TREM2_R47H_rep2

value: Male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD010

value: brain

tag: source

tag: target

tag: gender


title: TREM2_R47H_rep3

tag: Sex

tag: rin


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD006

value: PTLp


title: TREM2_R47H_rep1

tag: differentiation age


title: Day3-Fat-hACE2-3

source_name: mouse fat cells

value: mouse fat cells


title: Day3-Heart-eGFP-1


title: Australian AD S65

description: miRNA

tag: diagnosis

tag: brain weight

tag: toxicology

tag: smoking


title: Australian AD S66

description: miRNA

tag: ph

tag: pmi


title: WT_rep3

tag: genotype

value: Wild-Type

tag: cell type


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD004

tag: strain

value: SSp


title: WT_rep2


title: Australian AD S64

description: miRNA

value: Alcohol

tag: age

tag: hemisphere

tag: neuropathology

tag: hepatology


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD002

tag: tissue

tag: source

tag: target

tag: gender


title: Day3-Fat-hACE2-1

tag: treatment


title: Australian AD S61

description: miRNA

tag: diagnosis

tag: Sex

tag: rin

tag: brain weight


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D5_AD001


title: Australian AD S62

description: miRNA

tag: ph

tag: pmi

tag: toxicology

tag: smoking


title: Day3-Heart-eGFP-2

value: mouse heart cells


title: Day3-Fat-eGFP-1


title: Day3-Fat-eGFP-3


title: WT_rep1

tag: differentiation age

tag: genotype

tag: cell type


title: Day3-Fat-eGFP-2


title: Lung 6h TGFb1 3

description:
US-1508645
Fibroblasts_FPKM.txt

source_name: Fibroblast

tag: replicate group

value: Lung 6h TGFb1

value: Lung

value: Fibroblast


title: Australian AD S57

description: miRNA

tag: tissue

tag: age

tag: hemisphere

tag: neuropathology

tag: hepatology


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD012

tag: strain

tag: source

tag: target

value: ACA

tag: gender

value: female


title: Australian AD S60

description: miRNA

tag: diagnosis

tag: Sex

tag: rin

tag: brain weight

tag: ph


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD008

value: male


title: Lung 6h TGFb1 2

description:
US-1508620
Fibroblasts_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD006


title: Australian AD S56

description: miRNA

tag: pmi

tag: toxicology

tag: smoking


title: Lung 6h TGFb1 1

description:
US-1508697
Fibroblasts_FPKM.txt

tag: replicate group

tag: tissue

tag: cell type


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD007

tag: age


title: Australian AD S54

description: miRNA

tag: hemisphere

tag: neuropathology

tag: hepatology


title: Australian AD S48

description: miRNA


title: Day3-Fat-hACE2-2

tag: treatment


title: lung 6h CTRL 3

description:
US-1508637
Fibroblasts_FPKM.txt

value: lung 6h CTRL


title: PSCN (rep3)

city: Houston

first: Pawel

middle: K

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson

data_processing:
Raw paired-end reads were processed to remove artifacts and low-quality sequences using Trimmomatic and aligned to the murine GRCm38 genome using Hisat2 software. Gene counts for uniquely mapped reads were generated using Stringtie and differential expression determined by DESeq2 software. Statistical P-values significance were corrected for multiple hypothesis testing using the Benjamini-Hochberg false discovery rate (FDR) method. We identify differentially expressed genes (DEGs) at FDR<5%
Genome_build: GRCm38
Supplementary_files_format_and_content: DESeq2 Output
Supplementary_files_format_and_content: Stringtie output with Gene Counts

source_name: Lung Squamous Cell Carcinoma Biopsy from PSCN Mouse

extract_protocol:
Total RNA was extracted from tumor biopsies using Trizol reagent. The purified RNA was quantified and quality controlled (Bioanalyzer, Agilent) and sequencing libraries were generated using TruSeq Stranded Total RNA kit. The RNA-seq libraries were sequenced using Illumina HiSeq 3000 platform (pair end 76 nt analysis). Sample preparation and sequencing performed at MD Anderson Advanced Technology Genomics Core.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype


title: PSCN (rep1)


title: Australian AD S51

description: miRNA

value: prefrontal cortex

tag: diagnosis


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD002

city: La Jolla

tag: strain

tag: source

tag: target

tag: gender


title: PSC (rep3)

source_name: Lung Squamous Cell Carcinoma Biopsy from PSC Mouse

value: NSD3 WT


title: PSCN (rep2)


title: Lung 48h TGFb1 3

description:
US-1508642
Fibroblasts_FPKM.txt

value: Lung 48h TGFb1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD001

value: brain


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D4_AD004

value: PTLp


title: PSC (rep2)


title: lung 6h CTRL 2

description:
US-1508616
Fibroblasts_FPKM.txt


title: Lung 48h TGFb1 2

description:
US-1508685
Fibroblasts_FPKM.txt


title: lung 6h CTRL 1

description:
US-1508683
Fibroblasts_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D3_AD008


title: PSC (rep1)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D3_AD006


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D3_AD007


title: Lung 48h CTRL 2

description:
US-1508633
Fibroblasts_FPKM.txt

value: Lung 48h CTRL


title: AM332

city: Kuopio

first: Mikael

last: Marttinen

address: Yliopistonranta 1E

department: Biomedicine

country: Finland

institute: University of Eastern Finland

data_processing:
FastQC version 0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to examine the quality of the RNA sequencing reads. Illumina sequencing adapter sequences were removed, and reads were quality trimmed using the Trimmomatic version 0.38 (Bolger et al., 2014). The obtained trimmed reads were then mapped against the ribosomal and mitochondrial reference sequences (build mm10) using the Bowtie 2 version 2.2.3 (Langmead et al., 2012). Successfully mapped reads were abandoned. The rest of the reads were subjected to pseudo alignment to mouse reference transcriptome (build mm10) and transcript abundance analysis using kallisto version 0.44.0 (Bray et al, 2016).
Transcript abundance estimates were collapsed to gene-level counts using R package tximport version 1.10.1 (Soneson, 2016). Gene-level counts were pre-filtered (mean of gene count > 10) and variance stabilized using R package DESeq2 version 1.22.2 (Love et al., 2014). Observed batch effect was corrected using removeBatchEffect function from limma version 3.38.3 (Ritchie et al., 2015).
Genome_build: Mm10
Supplementary_files_format_and_content: .csv file containing variance stabilised data filtered for low count genes and batch corrected. Rows are features (genes), columns are cases (mice).

source_name: TWD A-tg Tau-tg

growth_protocol: The mice were kept in a controlled environment (constant temperature, 22 ± 1 °C, humidity 50 – 60 %, lights on 07:00-19:00), with food and water available ad libitum.

extract_protocol:
The hippocampus tissue samples of all female mice were collected into microcentrifuge tubes and weighed. Samples were homogenized in 250 µl of phosphate-buffered saline (DPBS, Lonza, Walkersville, MD, USA) using a stirrer. Fractions of homogenates were taken to RNA isolation (50 µl of homogenate and 500 µl Tri Reagent (Sigma-Aldrich, St. Louis, MO, USA)
Library preparation and sequencing was conducted in Finnish Functional Genomics Centre (FFGC), Turku Centre for Biotechnology, University of Turku and Åbo Akademi University. The quality of the total RNA samples as well as prepared libraries was ensured with Advanced Analytical Fragment Analyzer. Sample and library concentration was measured with Qubit® Fluorometric Quantitation, Life Technologies. Library preparation was done according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047). The 45 libraries with good quality were pooled in one pool and run in 2 lanes. The samples sequenced using Illumina HiSeq 3000 instrument. Single-read sequencing with 1 x 50 bp read length was used, followed by 8 + 8 bp dual index run.

treatment_protocol: The dietary intervention started at the age of 7 months, so that half of the mice / group received a chow mimicking typical western diet (TWD; Adjusted Calories diet, TD 88137, Harlan Tecklad, Madison, WI, USA, with 21% w/w fat, 0.15 % cholesterol and 35% sucrose) while the other half continued with standard rodent chow (STD) (5% w/w fat and 0% cholesterol) until sacrificed at the age of 13 months.

value: Hippocampus

value: transgenic for both APP/PS1 and tau P301L (A+T+)

tag: diet

value: typical western diet

tag: batch


title: Lung 48h CTRL 3

description:
US-1508687
Fibroblasts_FPKM.txt

data_processing:
Alignment and differential gene expression analysis was performed in Omicsoft Array Studio version 9.0.8.92.
Cleaned reads were aligned to the mouse and human B38 genome references, for the UUO kidney and primary cells respectively, and the rat B6.0 genome reference for the BDL model, using the Omicsoft Aligner with a maximum of 2 allowed mismatches.
Gene level counts, and FPKM, were determined by the OSA algorithm as implemented in Omicsoft Array Studio and using Ensembl.R82 gene models.
Genome_build: Human.B38, Mouse.B38, Rat.B6.0
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample. Each column corresponds to one sample (barcode).


title: Australian AD S46

city: New York

description: miRNA

value: Alcohol

tag: Sex

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: toxicology

tag: smoking


title: Australian AD S45

description: miRNA

tag: tissue

tag: age

tag: hemisphere

tag: neuropathology

tag: hepatology


title: Australian AD S43

description: miRNA

tag: diagnosis


title: AM325

source_name: TWD A-wt Tau-tg

tag: strain

tag: genotype

value: tau P301L transgenic (AwT+)


title: Australian AD S42

description: miRNA


title: Lung 48h CTRL 1

description:
US-1508652
Fibroblasts_FPKM.txt

tag: replicate group

value: Lung

tag: cell type

value: Fibroblast


title: Australian AD S40

description: miRNA

tag: Sex


title: AM316

source_name: TWD A-wt Tau-wt

tag: gender

value: female

value: wild type

tag: diet

tag: batch


title: Australian AD S30

description: miRNA

value: Control

tag: rin

tag: brain weight

tag: ph

tag: pmi


title: Australian AD S27

description: miRNA

tag: tissue

value: prefrontal cortex

tag: age

tag: toxicology

tag: smoking


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D3_AD001

source_name: C57BL/6J P56 Mouse Brain

tag: source

tag: target

value: SSp

value: male


title: Lung 24h TGFb1 3

description:
US-1508681
Fibroblasts_FPKM.txt

value: Lung 24h TGFb1


title: Australian AD S33

description: miRNA

tag: diagnosis

tag: hemisphere

tag: neuropathology

tag: hepatology


title: Australian AD S35

description: miRNA

tag: Sex


title: AM324

tag: strain

tag: gender

tag: genotype

tag: diet


title: AM317

tag: batch


title: PM323

source_name: STD A-tg Tau-wt

value: APP/PS1 transgenic (A+Tw)

value: standard diet


title: AM315

source_name: STD A-wt Tau-tg

value: Hippocampus


title: Lung 24h TGFb1 2

description:
US-1508605
Fibroblasts_FPKM.txt

tag: replicate group

tag: cell type


title: Lung 48h TGFb1 1

description:
US-1508655
Fibroblasts_FPKM.txt

value: Lung 48h TGFb1

tag: tissue


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD012

tag: age

value: brain

value: PTLp

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D3_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD007


title: Lung 24h CTRL 3

description:
US-1508629
Fibroblasts_FPKM.txt

value: Lung 24h CTRL


title: AM314

value: tau P301L transgenic (AwT+)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D3_AD004


title: Australian AD S26

description: miRNA

value: Alcohol

value: Male

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: toxicology

tag: smoking


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD006

tag: source

tag: target

value: female


title: Lung 24h TGFb1 1

description:
US-1508684
Fibroblasts_FPKM.txt

value: Lung

value: Fibroblast


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD010

tag: strain


title: Australian AD S24

description: miRNA

value: prefrontal cortex

tag: diagnosis

tag: Sex

tag: hemisphere

tag: neuropathology

tag: hepatology


title: Lung 24h CTRL 2

description:
US-1508650
Fibroblasts_FPKM.txt

tag: replicate group

tag: cell type


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD004

tag: age

tag: tissue

value: SSp

tag: gender


title: Australian AD S25

description: miRNA

value: Control

tag: rin

tag: brain weight

tag: ph


title: Australian AD S20

description: miRNA

tag: pmi

tag: toxicology

tag: smoking


title: AM313

tag: strain

tag: genotype

tag: diet

tag: batch


title: Lung 24h CTRL 1

description:
US-1508634
Fibroblasts_FPKM.txt


title: human primary hepatic stellate cells replicate9

description:
US-1564058
Stellate_FPKM.txt

source_name: stellate cell

value: Liver 24h CTRL

value: Liver

value: stellate cell


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD002

tag: source

tag: target

value: male


title: AM308

source_name: STD A-wt Tau-wt

value: Hippocampus

value: wild type

value: standard diet


title: AM309

value: APP/PS1 transgenic (A+Tw)


title: human primary hepatic stellate cells replicate8

description:
US-1564098
Stellate_FPKM.txt

tag: replicate group


title: human primary hepatic stellate cells replicate7

description:
US-1564073
Stellate_FPKM.txt

tag: cell type


title: Australian AD S18

description: miRNA

tag: diagnosis

tag: age

tag: Sex

tag: hemisphere

tag: neuropathology

tag: hepatology


title: AM303

tag: tissue

tag: gender


title: AM302


title: Australian AD S13

description: miRNA

tag: rin

tag: brain weight

tag: ph

tag: pmi

tag: toxicology

tag: smoking


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD012

tag: strain

value: brain

tag: source

value: PTLp

tag: target

value: ACA


title: human primary hepatic stellate cells replicate5

description:
US-1564136
Stellate_FPKM.txt

tag: replicate group

value: Liver 6h TGFB

tag: cell type


title: PM292

source_name: STD A-tg Tau-tg

value: female

tag: genotype

value: transgenic for both APP/PS1 and tau P301L (A+T+)

tag: diet

tag: batch


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD008

tag: age


title: SNI.veh-H1

city: Minneapolis

first: Laura

last: Stone

address: 420 Delaware Street SEMMC 294

institute: University of Minnesota

data_processing:
Data was processed according to the Canadian Centre for Computational Genomic GenPipes Methyl-Seq pipeline http://www.computationalgenomics.ca/about_genpipes/
Read Trimming and Quality filtering - Trimmomatic 0.36. trailing 30, minlen 50
Read alignment - Bismark 0.18.1  -N 0 -L 20 -X 500 -p 2 --multicore 3 / bowtie2 2.3.1 / samtools 1.4
Add Read groups -  Picard 2.9.0
Merge SAM files - Picard 2.9.0
Remove Duplicates - Picard 2.9.0
Methylation call - Bismark 0.18.1 bismark_methylation_extractor --no_overlap --comprehensive --gzip --multicore 5 --no_header --bedGraph --buffer_size 20G --cytosine_report
Genome_build: mm10
Supplementary_files_format_and_content: bedgraphs were generated depicting CpG position and scores represent methylation values. Methylated tiles were 250 bp long and overlapped by 125 bp to provide full coverage of the genome.

source_name: Prefrontal Cortex

extract_protocol:
PFC tissue was homogenized and genomic DNA was extracted using the Qiagen DNEasy Blood and Tissue Kit protocol
DNA was bisulfite converted according to the Roche SeqCap Epi Developer M Enrichment system and standard Illumina protocols; Custom Probe Capture Bisulfite Sequencing

tag: tissue

value: Prefrontal Cortex

tag: injury

value: SNI

tag: treatment

value: saline vehicle


title: AM293

tag: gender


title: SNI.veh-B3


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD006

value: SSp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD007


title: human primary hepatic stellate cells replicate3

description:
US-1564057
Stellate_FPKM.txt

extract_protocol:
Total RNA was extracted from tissue or cultured cells following the instruction of RNeasy Mini QIAcube Kit (Qiagen, #74116).
Sequencing was performed using the Truseq stranded total RNA RiboZero library preparation kit (Illumina, #RS-122-2201) according to the manufacturer’s instructions.  The resulting cDNA libraries were sequenced on an Illumina HiSeqTM 4000 using a 50 base paired-end run.

value: Liver 6h CTRL

value: Liver


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D2_AD001

value: male


title: PM288

value: Hippocampus

value: typical western diet


title: SNI.veh-F2


title: human primary hepatic stellate cells replicate4

description:
US-1564117
Stellate_FPKM.txt

value: stellate cell


title: SNI.veh-B1


title: SNI.SAM-H2

value: s-adenosylmethionine


title: human primary hepatic stellate cells replicate6

description:
US-1564092
Stellate_FPKM.txt


title: AM286


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD004

value: brain


title: human primary hepatic stellate cells replicate18

description:
US-1564046
Stellate_FPKM.txt

value: Liver 48h TGFb


title: AM285

source_name: TWD A-tg Tau-wt

value: APP/PS1 transgenic (A+Tw)


title: SNI.SAM-F1


title: PM284


title: human primary hepatic stellate cells replicate17

description:
US-1564061
Stellate_FPKM.txt


title: human primary hepatic stellate cells replicate2

description:
US-1564067
Stellate_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD002

value: PTLp


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D12_AD010

value: ACA

value: female


title: human primary hepatic stellate cells replicate16

description:
US-1564088
Stellate_FPKM.txt


title: 2011-409 RNA136 [control]

source_name: corneal endothelium

tag: group

value: Control

value: corneal endothelium


title: SNI.SAM-D1

value: Prefrontal Cortex

value: SNI


title: Sham.veh-G3

value: Sham

value: saline vehicle


title: PM287

value: tau P301L transgenic (AwT+)


title: AM283

value: Hippocampus


title: Sham.veh-E4


title: AM279

value: transgenic for both APP/PS1 and tau P301L (A+T+)

value: standard diet


title: SNI.SAM-D4

value: s-adenosylmethionine


title: AM278


title: Sham.SAM-G1


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D1_AD001

value: brain

value: SSp

value: male


title: Peritoneum_CG_WT

tag: strain background

tag: genotype/variation

value: WT

value: peritoneum

value: chlorhexidine gluconate


title: AM277

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D12_AD004

value: PTLp


title: Sham.veh-A2

value: Prefrontal Cortex


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D12_AD002


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D12_AD001


title: human primary hepatic stellate cells replicate14

description:
US-1564091
Stellate_FPKM.txt

value: Liver 48h CTRL

value: Liver

value: stellate cell


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D11_AD008

value: ACA


title: PM274

value: Hippocampus

value: tau P301L transgenic (AwT+)


title: human primary hepatic stellate cells replicate11

description:
US-1564063
Stellate_FPKM.txt

value: Liver 24h TGFb


title: PM275

value: standard diet


title: human primary hepatic stellate cells replicate12

description:
US-1564080
Stellate_FPKM.txt


title: Sham.SAM-A3

value: Sham

value: s-adenosylmethionine


title: human primary hepatic stellate cells replicate13

description:
US-1564053
Stellate_FPKM.txt


title: human primary hepatic stellate cells replicate10

description:
US-1564090
Stellate_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D12_AD006

value: brain

value: SSp


title: PM273

value: wild type


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D11_AD007

value: male


title: human primary hepatic stellate cells replicate15

description:
US-1564127
Stellate_FPKM.txt


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D11_AD006

value: female


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D12_AD008

value: PTLp


title: PM272


title: CMFGDSS4

city: Beijing

first: shimeng

last: Huang

address: No. 2 Yuanmingyuan West Road, Haidian District

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® UltraTM NA Library Prep Kit for Illumina® (NEB, USA) 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: The diet with CMFG (100 mg/kg body weight (BW)/day) were pre-fed to the experimental mice for 3 weeks to investigate its prophylactic effects on alleviating DSS induced colitis (2.5% (w/v) DSS in drinking water ad libitum for 7 days). Mice in the DSS group underwent oral gavage of PBS. Colonic tissues were immediately snap-frozen in liquid nitrogen and homogenized. Total RNA recovered from two separate group include DSS and CMFGDSS.

value: colon

value: CMFG+DSS

value: 8 weeks-old


title: Sham.SAM-E3

value: Prefrontal Cortex


title: human primary hepatic stellate cells replicate1

city: Boston

first: Thomas

last: Gan

address: 33 Ave Lous Pasteur

institute: Merck

description:
US-1564072
Stellate_FPKM.txt

value: Liver 6h CTRL

value: Liver

value: stellate cell


title: CMFGDSS5


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D11_AD004


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D11_AD001


title: human primary epithelial tubular_6h TGFB3

description:
US-1583926
Epithelial_FPKM.txt

source_name: epithelial tubular cells

value: Kidney 6h TGFB

value: Kidney

value: epithelial tubular cells


title: human primary epithelial tubular_6h TGFB2

description:
US-1583899
Epithelial_FPKM.txt


title: DSS5

value: DSS


title: CMFGDSS2


title: AM266

value: Hippocampus

value: transgenic for both APP/PS1 and tau P301L (A+T+)

value: typical western diet


title: human primary epithelial tubular_6h CTRL 3

description:
US-1583928
Epithelial_FPKM.txt

value: Kidney 6h CTRL


title: CMFGDSS3

value: female


title: PM271

value: APP/PS1 transgenic (A+Tw)

value: standard diet


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D11_AD002

value: brain

value: PTLp

value: SSp

value: male


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D10_AD010

value: ACA


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D10_AD007


title: PM263


title: human primary epithelial tubular_6h TGFB1

description:
US-1583897
Epithelial_FPKM.txt


title: DSS4

value: colon

value: 8 weeks-old


title: human primary epithelial tubular_6h CTRL 2

description:
US-1583888
Epithelial_FPKM.txt

value: Kidney


title: PM265

value: wild type


title: AM261

value: tau P301L transgenic (AwT+)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D10_AD006


title: human primary epithelial tubular_6h CTRL 1

description:
US-1583922
Epithelial_FPKM.txt

value: epithelial tubular cells


title: DSS3

value: DSS


title: human primary epithelial tubular_48h TGFb3

description:
US-1583934
Epithelial_FPKM.txt

value: Kidney 48h TGFB


title: human primary epithelial tubular_48h TGFb2

description:
US-1583892
Epithelial_FPKM.txt


title: AM260

value: Hippocampus

value: transgenic for both APP/PS1 and tau P301L (A+T+)

value: typical western diet


title: DSS1

value: female


title: AM259

value: APP/PS1 transgenic (A+Tw)


title: 180726_CEMBA_mm_P56_P63_RS2_180726_P1_180726_P2_D10_AD004

value: brain

value: PTLp