title: CEMBA181204_4G_3_CEMBA181204_4G_4_A4_ad002


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A4_ad007

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: LSX

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad002


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A3_ad008


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad007


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad004


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad012


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad010


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad006


title: High_R. salmoninarum-infected_fish5

type: RNA

city: St. John's

first: Khalil

last: Eslamloo

state: Newfoundland and Labrador

address: 0 Marine Lab Rd.

department: Ocean Sciences

country: Canada

institute: Memorial University of Newfoundland

hyb_protocol: The labeled aRNA (i.e. 825 ng) of each experimental sample was mixed with an equal amount of labeled aRNA of the common reference, and the resulting pool was fragmented based on the manufacturer's instructions (Agilent, Mississauga, ON). Each labelled aRNA pool (i.e. an individual sample and common reference) was co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray (GEO accession # GPL11299). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following the manufacturer's instructions.

scan_protocol: The microarray slides were scanned at 5 µm resolution using SureScan Microarray Scanner System (Agilent Technologies, Santa Clara, CA) and Microarray Scan Control Software following the Agilent HD 2-color gene expression microarrays scan protocol.

data_processing: Agilent Feature Extraction Software v12.0 (Agilent Technologies) was used to extract and Loess-normalize the signal intensity data. Thereafter, using GeneSpring Software v14.9 (Agilent Technologies), the data were quality-checked so that probes with low and marginal quality as well as absent values in more than 25% of all 15 arrays were removed from the dataset.

molecule: total RNA

organism: Salmo salar

source_name: Live R. salmoninarum-injected fish at 13 days post-infection, with high pathogen load (H-BKD).

label_protocol: Five individuals per group (5 control, 5 L-BKD and 5 H-BKD; 15 samples in total) were used for microarray experiment. The microarray experiment was conducted using a common reference design. The mRNA of each sample was amplified and then labelled using 1 µg of DNase-treated and column-purified RNA and Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion®, Carlsbad, CA, USA), according to the kit’s procedure. A common reference was prepared using a pool of all 15 samples (15 µg aRNA from each sample) involved in the microarray experiment. The experimental samples (Control, L-BKD and H-BKD) were labelled with Cy5 (GE Healthcare, Buckinghamshire, UK), whereas the common reference samples were labelled with Cy3 (GE Healthcare), based on the manufacturer’s protocol.

extract_protocol:
Infection, sampling and sample selection: Atlantic salmon in the BKD group were injected with 200 µl of R. salmoninarum to obtain final concentration of 2 × 10^8 colony-forming units (CFU) per fish. Fish in the control group were injected with 200 µl of sterile KDM-2 medium. After 13 days of infection, fish were euthanized using overdose of Benzocaine, and the head kidney of the each individual was sampled for transcriptome analyses. The collected samples were stored in RNAlater at 4°C for 24 h. Then, RNAlater was removed, and samples were kept at -80 °C until RNA extraction. Using a TaqMan qPCR assay, fish (n=5) with no infection from Control group as well as fish showing high (H-BKD) or low (L-BKD) infection level (i.e. expression level of R. salmoninarum 16S ribosomal RNA) from the BKD group were selected for microarray analyses.
Total RNA was extracted from TRIzol-lysed samples, following the manufacturer’s instructions. Total RNA samples were on-column DNase-treated and column-purified using PureLinkTM RNA Mini Kit (Thermo Fisher Scientific) and PureLinkTM DNAse set (Thermo Fisher Scientific), according to the manufacturer’s protocol. The high-purity RNA samples (e.g. A260/230 and A260/280 ratios > 1.8) with tight 18S and 28S ribosomal RNA bands were used for the microarray analysis.

tag: tissue

value: head kidney

tag: life stage

value: parr

source_name: pool of RNAs from all samples involved in the microarray experiment


title: High_R. salmoninarum-infected_fish3


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A10_ad007


title: High_R. salmoninarum-infected_fish2


title: Low_R. salmoninarum-infected_fish2

source_name: Live R. salmoninarum-injected fish at 13 days post-infection, with low pathogen load (L-BKD).


title: High_R. salmoninarum-infected_fish1


title: Low_R. salmoninarum-infected_fish5


title: Low_R. salmoninarum-infected_fish4


title: Low_R. salmoninarum-infected_fish1


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A12_ad008


title: Low_R. salmoninarum-infected_fish3


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A10_ad012


title: Control_fish5

source_name: Sterile KDM-2-injected fish at 13 days post-injection (Control).


title: High_R. salmoninarum-infected_fish4


title: Control_fish4


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A10_ad010


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A10_ad002


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A10_ad008


title: Control_fish1


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad012


title: Control_fish2


title: Control_fish3


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad010


title: MCF7_parental_rep3

city: Ann Arbor

first: Andrea

middle: M

last: Pesch

state: MI

address: 1301 Catherine

department: Radiation Oncology

institute: University of Michigan

description: Gene expression data from MCF-7 cells treated with vehicle (DMSO) for 16 hours

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Human Gene 2.1 ST plate, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592).

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.6.1

label: biotin

organism: Homo sapiens

source_name: MCF-7, parental, 16 hour vehicle

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: MCF-7 and T47D parental cells were grown and plated in 6 well plates in DMEM media with FBS. MCF-7 and T47D CDK4/6 inhibitor-resistant cells were grown in 1uM drug until the day prior to the assay when cells were plated in drug-free media.

extract_protocol: After washing with 1x PBS, cells were lysed in 700uL Qiazol and phenol-chloroform extraction was performed using the Qiagen RNeasy kit with an on-column DNAse digestion.

treatment_protocol: Cells were treated with either vehicle, palbociclib (75nM for MCF-7, 40nM for T47D), ribociclib (200nM for MCF-7, 100nM for T47D), or abemaciclib  (40nM for MCF-7, 20nM for T47D) for 16 hours.

tag: cell line

tag: treatment

value: 16 hour vehicle


title: MCF7_parental_rep2


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad008


title: MCF7_parental_rep1


title: MCF7_palbo_16hour_rep3

description: Gene expression data from MCF-7 cells treated with palbociclib for 16 hours

source_name: MCF-7, palbociclib, 16 hours

value: palbociclib, 16 hours


title: MCF7_palbo_16hour_rep2


title: MCF7_palbo_16hour_rep1


title: T47D_abemaAR_16hour_rep3

description: Gene expression data from T47D abemaciclib-resistant cells treated with abemaciclib for 16 hours

source_name: T47D, abemaAR, abemaciclib 16 hours

value: T47D abemaciclib-resistant cells

value: abemaciclib, 16 hours


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H9_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H8_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H8_ad004


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad004


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H8_ad002


title: CEMBA181204_4G_3_CEMBA181204_4G_4_A1_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H7_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H7_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H6_ad006


title: T47D_abema_16hour_rep3

description: Gene expression data from T47D cells treated with abemaciclib for 16 hours

source_name: T47D, abemaciclib, 16 hours


title: T47D_abemaAR_16hour_rep1


title: T47D_abema_16hour_rep1


title: T47D_riboAR_16hour_rep3

description: Gene expression data from T47D ribociclib-resistant cells treated with ribociclib for 16 hours

source_name: T47D, riboAR, ribociclib16 hours

value: T47D ribociclib-resistant cells

value: ribociclib, 16 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H9_ad002


title: T47D_ribo_16hour_rep3

description: Gene expression data from T47D cells treated with ribociclib for 16 hours

source_name: T47D, ribociclib, 16 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H6_ad004


title: T47D_abemaAR_16hour_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H6_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H5_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H5_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H7_ad004


title: T47D_riboAR_16hour_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H5_ad006


title: T47D_riboAR_16hour_rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H4_ad004


title: T47D_ribo_16hour_rep2


title: T47D_palboAR_16hour_rep2

description: Gene expression data from T47D palbociclib-resistant cells treated with palbociclib for 16 hours

source_name: T47D, palboAR, palbo 16 hours

value: T47D palbociclib-resistant cells


title: T47D_ribo_16hour_rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H4_ad006


title: T47D_palboAR_16hour_rep3


title: T47D_palbo_16hour_rep1

description: Gene expression data from T47D cells treated with palbociclib for 16 hours

source_name: T47D, palbociclib, 16 hours


title: T47D_palboAR_16hour_rep1


title: T47D_palbo_16hour_rep2


title: T47D_vehicle_rep3

description: Gene expression data from T47D cells treated with vehicle (DMSO) for 16 hours

source_name: T47D, parental, 16 hour vehicle


title: T47D_palbo_16hour_rep3


title: T47D_vehicle_rep2


title: T47D_abema_16hour_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H3_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H2_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H3_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H2_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H2_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H11_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H11_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H4_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H11_ad002


title: DNase-seq from UC Davis FAANG chicken spleen rep B

first: Colin

last: Kern

address: 9500 Gilman Dr

institute: UC San Diego

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the default arguments
Reads were aligned with BWA mem 0.7.17 to the galGal6 genome
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: galGal6
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.05 --broad

organism: Gallus gallus

source_name: Spleen

extract_protocol:
DNase-seq datasets were generated by the Stam Lab at University of Washington using a previously published protocol. Briefly, cryopreserved nuclei were slowly defrosted on ice, pelleted at 500g, and resuspended in 37°C DNase I digestion buffer (13.5 mM Tris-HCL pH 8.0, 87 mM NaCl, 54 mM KCl, 6 mM CaCl2, 0.9 mM EDTA, 0.45 mM EGTA, 0.45 mM spermidine). After a 3 minute incubation, the reaction was stopped with 2x stop buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 0.1% SDS, 100 mM EDTA pH 8.0, 1 mM spermidine, 0.3 mM spermine). Samples were treated with RNase for 1 hour at 37°C, then an additional hour at 55°C with proteinase K.
DNA fragments were isolated, libraries prepared, and sequenced on Illumina’s Hiseq 2500 with 50bp paired-end sequencing.

value: spleen


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H10_ad002


title: T47D_vehicle_rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H10_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H10_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H1_ad006


title: DNase-seq from UC Davis FAANG chicken spleen rep A


title: DNase-seq from UC Davis FAANG chicken skeletal muscle rep B

source_name: Muscle

value: skeletal muscle


title: MCF7_riboAR_16 hour_rep1

description: Gene expression data from MCF-7 ribociclib-resistant cells treated with ribociclib for 16 hours

source_name: MCF-7 riboAR, ribociclib, 16 hours

value: MCF-7 ribociclib-resistant cells


title: DNase-seq from UC Davis FAANG chicken skeletal muscle rep A


title: MCF7_AbemaAR_16 hour_rep1

description: Gene expression data from MCF-7 abemaciclib-resistant cells treated with abemaciclib for 16 hours

source_name: MCF-7 abemaAR, abemaciclib, 16 hours

value: MCF-7 abemaciclib-resistant cells


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G9_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: MCF7_ribo_16hour_rep1

description: Gene expression data from MCF-7 cells treated with ribociclib for 16 hours

source_name: MCF-7, ribociclib, 16 hours


title: MCF7_riboAR_16 hour_rep3


title: MCF7_AbemaAR_16 hour_rep3


title: DNase-seq from UC Davis FAANG chicken lung rep A

source_name: Lung

value: lung


title: MCF7_ribo_16hour_rep2


title: MCF7_ribo_16hour_rep3


title: MCF7_abema_16hour_rep3

description: Gene expression data from MCF-7 cells treated with abemaciclib for 16 hours

source_name: MCF-7, abemaciclib, 16 hours


title: MCF7_riboAR_16 hour_rep2


title: MCF7_abema_16hour_rep2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G9_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G9_ad006


title: DNase-seq from UC Davis FAANG chicken lung rep B


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G8_ad006


title: DNase-seq from UC Davis FAANG chicken liver rep B

source_name: Liver

value: liver


title: MCF7_AbemaAR_16 hour_rep2


title: MCF7_abema_16hour_rep1


title: DNase-seq from UC Davis FAANG chicken liver rep A


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H1_ad004

value: LSX


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G8_ad002

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G7_ad002


title: DNase-seq from UC Davis FAANG chicken hypothalamus rep B

source_name: Hypothalamus

value: hypothalamus


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G7_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G7_ad004


title: DNase-seq from UC Davis FAANG chicken cerebral cortex rep A

source_name: Cortex

value: cerebral cortex


title: DNase-seq from UC Davis FAANG chicken cerebellum rep B

source_name: Cerebellum

value: cerebellum


title: DNase-seq from UC Davis FAANG chicken cerebellum rep A


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G6_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G6_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G6_ad002


title: DNase-seq from UC Davis FAANG chicken cerebral cortex rep B


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G4_ad006


title: DNase-seq from UC Davis FAANG chicken adipose rep A

source_name: Adipose

value: adipose


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G4_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G5_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G4_ad002


title: Giardia_R1, oocyte

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

library_source: transcriptomic

data_processing:
Libraries were pooled and sequenced on an Illumina HiSeq 2500 by The Centre for Applied Genomics at The Hospital for Sick Children. 50 base-pair single-end reads were demultiplexed and converted to FASTQ format using bcl2fastq2 v2.17 (Illumina)
Reads were mapped by STAR 2.5.2a (Dobin et al., 2013) to the G. lamblia genome release 43 (2019-04-19) obtained from GiardiaDB.org
Genes were quantified using Cufflinks 2.2.1
Downstream analyses were then performed with R version 3.5.2, using in-house scripts.
Genome_build: G. lamblia release-43 https://giardiadb.org/giardiadb/app/downloads/release-43/GintestinalisAssemblageAWB/
Supplementary_files_format_and_content: Tab separated values files contain FPKMs for each gene in both samples

molecule: polyA RNA

organism: Giardia duodenalis

source_name: Trophozoite

growth_protocol: G. lamblia trophozoites were grown in filtered modified TYI-S-33 medium in 10ml polystyrene tubes at 37°C

extract_protocol:
RNA was extracted from trophozoites with hot acid phenol as described in Collart & Oliviero, Current protocols in molecular biology (1993)
Poly(A) selected RNA was used to generate libraries with Illumina’s TruSeq stranded mRNA library preparation kit according to the manufacturer’s protocol and sequenced at The Center for Applied Genetics (SickKids).

treatment_protocol: Cells were untreated

tag: developmental stage

value: Trophozoite

value: untreated


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G3_ad002


title: GL_R1_08, oocyte

treatment_protocol: Cells were incubated with 1mM 4SU for 10 hours. Human and D. melanogaster RNA was added to sample for library preparation

value: incubated with 1mM 4SU for 10 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G3_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G3_ad006


title: 5 mixed samples (day0_unstim, day5_unstim, day5_LAIV, day9_unstim, day9_LAIV)

city: Irvine

first: Lisa

last: Wagar

address: 843 Health Sciences Rd

institute: University of California Irvine

description: targeted mRNA

data_processing:
all steps were performed using the automated BD Rhapsody pipeline with default selections
Supplementary_files_format_and_content: csv files for VDJ metrics, number of VDJ calls per cell, number of mRNA molecules per cell, barcoding tags, and mRNA metrics
_1_final_seq1mergedLW_VDJ_metrics.csv (VDJ metrics)
_1_final_seq1mergedLW_VDJ_perCell.csv (VDJ counts)
_4_Combined_final_seq1mergedLW_DBEC_MolsPerCell.csv (mRNA molecules per cell)
_4_final_seq1mergedLW_Sample_Tag_Calls.csv (sample tags)
_4_final_seq1mergedLW_Sample_Tag_Metrics.csv (sample tag metrics)
final_seq1mergedLW_Metrics_Summary.csv (mRNA metrics)

source_name: tonsil, tonsil organoid

extract_protocol: sorted cells were run through the Rhapsody pipeline following manufactuerer's instructions

tag: cell type

value: T and B cells

tag: time

value: 0 days, 5 days, 9 days post-stimulation

tag: stimulation

value: none, live-attenuated influenza vaccine

tag: barcode

value: barcode 1 - barcode 5


title: Si-AC010789.1 HCT116 cell [Si1]

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

country: China

institute: The Second Hospital of Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.6 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -g 10
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: GRCh38.91
Supplementary_files_format_and_content: raw fragment counts for each Sample

growth_protocol: Cells were cultured with DMEM supplemented with 10% fetal bovine serum and penicillin-streptomycin at 37℃ in 5% CO2 and 95% air

extract_protocol:
Total RNA was extracted from HCT116 cells with AC010789.1 knockdown using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell s were transfected with the short interfering RNA (siRNA) specific for AC010789.1 or negative control according to the manufacturer's instructions.

tag: genotype/variation

value: siRNA specific for AC010789.1


title: control HCT116 cell [N2]

source_name: control HCT116 cell

value: control


title: Si-AC010789.1 HCT116 cell [Si3]


title: control HCT116 cell [N3]


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G12_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G2_ad004


title: control HCT116 cell [N1]


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G11_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G11_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G11_ad002


title: DNase-seq from UC Davis FAANG chicken adipose rep B


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G10_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G10_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G5_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G5_ad004


title: Si-AC010789.1 HCT116 cell [Si2]


title: CEMBA181204_4G_1_CEMBA181204_4G_2_G10_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F9_ad008


title: ipf1880fep

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

data_processing:
MORE DETAIL REQUESTED
align with cellranger 2 or 3 depends on the timing of sample processed
Genome_build: hg38/GRCh38

source_name: IPF lung explant

extract_protocol:
10x genomics chromium 3' single cell RNAseq kit v2 or v3 dependes on the timing of sample processed
10x 3' single cell RNAseq following 10x genomics instruction

tag: group

value: IPF

value: IPF lung explant

tag: tissue/cell type

value: fibrotic region of IPF lungs


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F9_ad004

value: LSX

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F9_ad007


title: ipf1883fep


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F9_ad006


title: ipf12fep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F8_ad008


title: ipf07fep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F8_ad006


title: ipf05_19


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F8_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F8_ad002


title: ipf07fep17


title: ipf03fep19


title: ipf04fep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F7_ad008


title: ipf02fep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F8_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F7_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F7_ad004


title: ipf04_19


title: ipf01bep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F7_ad002


title: dd49tep17

source_name: donor trachea

value: Donor

value: donor trachea

value: isolated epithelial cells (DAPI-,CD45-,CD31-,CD326+)


title: dd49pep17

source_name: donor proximal airway

value: donor proximal airway


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F6_ad006


title: dd49dep17

source_name: donor distal

value: donor distal


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F6_ad008


title: dd39pep17


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F5_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F6_ad002


title: dd39tep17


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F5_ad007


title: dd10dep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F5_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F5_ad006


title: dd09dep18


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F7_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F3_ad007


title: dd09pep18

source_name: donor trachea+proximal airway

value: donor trachea+proximal airway


title: dd10pep18


title: cc04tep17


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F2_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: ca16nep


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F12_ad006


title: ca12nep


title: ca07


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F2_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F12_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F2_ad002


title: cc04dep17


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F11_ad007


title: ca02


title: dd39dep17


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F11_ad004


title: PDX T-ALL 2 Decitabine Rep3 EPICarray

type: genomic

city: South San Francisco

first: Juliette

last: Roels

address: 1 DNA Way

institute: Genentech

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium HumanMethylationEPIC BeadChip (Illumina) using standard Illumina protocol

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

data_processing:
RnBeads.hg19 in R (versions >3.4). β values were obtained after filtering and normalization using the default preprocessing pipeline.
Normalized (RnBeads, SWAN normalization) Average Beta

label: Cy5 and Cy3

source_name: T-ALL blasts from PDX spleen

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purifiedusing Qiagen DNeasy Kit according to standard instructions

treatment_protocol: mice were randomized in 2 groups of 3 and treated for 5 days with vehicle-only or Decitabine (0.5 mg/kg bodyweight). At day 7, animals were sacrificed, and tumor cells collected from the spleen.

value: T-ALL blasts from PDX spleen

tag: pdx

value: PDX T-ALL 2

value: Decitabine


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F11_ad008

tag: brain region


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F10_ad006

tag: Sex


title: PDX T-ALL 2 Decitabine Rep2 EPICarray


title: PDX T-ALL 2 Decitabine Rep1 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F10_ad007

tag: age


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F10_ad004

tag: strain


title: cc04pep17

tag: tissue


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F10_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F1_ad006


title: PDX T-ALL 1 Decitabine Rep2 EPICarray

value: PDX T-ALL 1


title: PDX T-ALL 1 Decitabine Rep3 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F1_ad007


title: PDX T-ALL 1 Decitabine Rep1 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F1_ad008


title: PDX T-ALL 1 Control Rep3 EPICarray

value: Control


title: PDX T-ALL 1 Control Rep2 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F1_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad006


title: PDX T-ALL 1 Control Rep1 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F1_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad012


title: DNA methylation from Normal thymocytes NL_7B EPICarray

source_name: Normal thymocytes ɣδ CD3+ CD1-

extract_protocol: genomic DNA was extracted by a SDS-containing lysis buffer containing proteinase K and purified by isopropanol precipitation. 250ng of DNA was used for bisulfite conversion by the EZ DNA methylation Kit (Zymo Research).

value: Human postnatal thymus

tag: disease state

value: Normal thymocytes ɣδ CD3+ CD1-


title: DNA methylation from Normal thymocytes NL_6B EPICarray

source_name: Normal thymocytes ɣδ CD3+ CD1+

value: Normal thymocytes ɣδ CD3+ CD1+


title: PDX T-ALL 2 Control Rep3 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad008


title: PDX T-ALL 2 Control Rep1 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad010


title: PDX T-ALL 2 Control Rep2 EPICarray


title: DNA methylation from Normal thymocytes NL_7 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad004


title: DNA methylation from Normal thymocytes NL_11B EPICarray

source_name: Normal thymocytes SP8+ (Single Positive) CD3+


title: DNA methylation from Normal thymocytes NL_6 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E9_ad002


title: ED456849-4

city: Los Angeles

first: Antoni

last: Ribas

address: 9-954 Factor Bldg

department: Medicine, HemOnc Division

institute: University of California, Los Angeles

description: polyA RNA

data_processing:
RNAseq reads were aligned using HISAT2 to the human reference genome GRCh38.
FPKM values were generated using Stringtie.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: Melanoma

extract_protocol:
Qiagen
Takara Bio SMART-Seq: SMART-Seq v4 Ultra Low Input RNA Kit
RNA sequening was performed on Illumina HiSeq 2500 with 2x75 bp reads.

tag: sample type

value: Tumor Biopsy

tag: individual

tag: cohort

value: Cohort C Expansion

tag: visit

value: DAY 15

tag: site description

value: METASTATIC SITE

tag: site

value: LYMPH NODE

tag: braf mutation


title: ED456749-4

description: polyA RNA

value: Cohort B Expansion

value: SKIN

tag: treatment


title: ED349212-4

description: polyA RNA

value: SCREENING


title: ED349213-4

description: polyA RNA


title: ED349210-4

description: polyA RNA


title: ED456746-4

description: polyA RNA


title: ED349211-4

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_F2_ad006

value: LSX

value: male


title: ED456705-4

description: polyA RNA


title: ED349209-4

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad012


title: ED308743-4

description: polyA RNA

value: Cohort A Expansion


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad010


title: DNA methylation from Normal thymocytes NL_1B EPICarray

source_name: Normal thymocytes DP CD4+CD8+ (Double Positive) CD3+


title: ED308715-4

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_H1_ad002


title: ED150226-4

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad008


title: ED150223-4

description: polyA RNA


title: ED150222-4

description: polyA RNA

value: PRIMARY SITE


title: DNA methylation from Normal thymocytes NL_1 EPICarray

value: Normal thymocytes DP CD4+CD8+ (Double Positive) CD3+


title: ED102646-4

description: polyA RNA


title: DNA methylation from Normal thymocytes NL_2B EPICarray

source_name: Normal thymocytes DP CD4+CD8+ (Double Positive) CD3-


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad007


title: DNA methylation from Normal thymocytes NL_11 EPICarray

value: Normal thymocytes SP8+ (Single Positive) CD3+


title: DNA methylation from Normal thymocytes NL_10B EPICarray

source_name: Normal thymocytes SP4+ (Single Positive) CD3+

value: Human postnatal thymus


title: ED102644-4

description: polyA RNA

value: SCREEN FAIL


title: DNA methylation from Normal thymocytes NL_10 EPICarray

value: Normal thymocytes SP4+ (Single Positive) CD3+


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad004


title: DNA methylation from Normal thymocytes NL_9B EPICarray

source_name: Normal thymocytes ISP CD4+ (Immature Single Positive) CD3,8,34- CD28+


title: ED092632-4

description: polyA RNA

value: Tumor Biopsy

value: LIVER


title: ED092631-4

description: polyA RNA


title: DNA methylation from Normal thymocytes NL_9 EPICarray

value: Normal thymocytes ISP CD4+ (Immature Single Positive) CD3,8,34- CD28+


title: ED092629-4

description: polyA RNA

value: METASTATIC SITE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E7_ad012


title: ED092630-4

description: polyA RNA

value: LYMPH NODE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E8_ad002


title: ED092633-4

description: polyA RNA


title: ED092628-4

description: polyA RNA


title: DNA methylation from Normal thymocytes NL_2 EPICarray

value: Normal thymocytes DP CD4+CD8+ (Double Positive) CD3-


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E7_ad006


title: DNA methylation from Normal thymocytes NL_5B EPICarray

source_name: Normal thymocytes CD34+4+

value: Normal thymocytes CD34+4+


title: ED092626-4

description: polyA RNA

value: SCREENING


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E7_ad010

value: LSX


title: DNA methylation from Normal thymocytes NL_5 EPICarray


title: ED092627-4

description: polyA RNA

value: Cohort B Expansion

value: SKIN


title: EB635808-4

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E7_ad007

value: male


title: DNA methylation from Normal thymocytes NL_4B EPICarray

source_name: Normal thymocytes CD34+4-1+

value: Normal thymocytes CD34+4-1+


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E7_ad002


title: F16_4_S12

city: Singapore

first: Ankur

last: Sharma

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute Of Singapore

description: ROI.csv file (Shows the relationship between RCC files and sample ID/ROI ID; Each RCC file can have multiple ROIs)

hyb_protocol: GeoMx Digital Spatial Profiling by NanoString technologies

data_processing:
Normalised to signal to noise ratio data is obtained from NanoString Technologies
Highly variable genes are handpicked from principal component analysis
Normalised to signal to noise ratio data stored in comma delimited file.

source_name: Human fetal liver

value: Fetal liver

tag: tissue type

value: Fetal


title: DNA methylation from Normal thymocytes NL_4 EPICarray

value: Human postnatal thymus


title: EB635672-4

description: polyA RNA

value: DAY 15


title: ED102642-4

description: polyA RNA

value: Tumor Biopsy

value: Cohort C1


title: EB343275-4

description: polyA RNA

value: Cohort A Expansion

value: PRIMARY SITE


title: F16_4_S10

scan_protocol: GeoMx Digital Spatial Profiling by NanoString technologies


title: DNA methylation from Normal thymocytes NL_3B EPICarray

source_name: Normal thymocytes CD34+ 4- 1-

value: Normal thymocytes CD34+ 4- 1-


title: EB343257-4

description: polyA RNA

value: METASTATIC SITE

value: LYMPH NODE


title: DNA methylation from T-ALL ALL_2036 EPICarray

source_name: Blast from the bone marrow

value: Blast from the bone marrow

value: T-ALL


title: F16_4_S8

label_protocol: GeoMx Digital Spatial Profiling by NanoString technologies


title: DNA methylation from Normal thymocytes NL_3 EPICarray


title: F16_4_S9

extract_protocol: GeoMx Digital Spatial Profiling by NanoString technologies


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad012

value: LSX


title: AH432131-4

description: polyA RNA

value: Cohort C Expansion

value: DAY 43

value: THYROID NODULE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad008

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad010


title: AH293877-4

description: polyA RNA

value: Thyroid


title: F16_4_S7

value: Fetal liver

value: Fetal


title: F16_4_S6


title: AG663510-4

description: polyA RNA

value: Tumor Biopsy

value: SCREEN FAIL

value: SCREENING


title: F16_4_S5


title: F16_4_S11


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad004


title: AG432754-4

description: polyA RNA

value: Cohort A Expansion

value: PRIMARY SITE

value: SKIN


title: F16_4_S4


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad002


title: F16_4_S3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E5_ad006


title: F16_4_S2


title: AG406173-4

description: polyA RNA

value: Cohort B Expansion

value: DAY 15

value: METASTATIC SITE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E5_ad012

value: LSX


title: EB342815-4

description: polyA RNA

value: Cohort C1


title: F16_4_S1


title: F14_5_S12


title: F14_5_S11


title: AG373553-4

description: polyA RNA

value: LIVER


title: AG390710-4

description: polyA RNA

value: DAY 43

value: CHEST WALL


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E5_ad008

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E6_ad007


title: AG207712-4

description: polyA RNA

value: Cohort B1


title: F14_5_S10

value: Fetal liver

value: Fetal


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E5_ad007


title: F14_5_S9


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E4_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E4_ad012


title: F14_5_S8


title: AG431115-4

description: polyA RNA

value: Tumor Biopsy

value: STOMACH


title: AG089494-4

description: polyA RNA

value: Cohort A1

value: DAY 90 FOLLOW UP


title: DNA methylation from T-ALL ALL_1617 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E4_ad010


title: F14_5_S7


title: F14_5_S6


title: AG058023-4

description: polyA RNA

value: Cohort A Expansion

value: DAY 15

value: LYMPH NODE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E4_ad007

value: LSX


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E5_ad010


title: AG058022-4

description: polyA RNA

value: SCREENING

value: METASTATIC SITE

value: PELVIC WALL MASS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E4_ad004

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E5_ad002


title: AG139465-4

description: polyA RNA

value: Cohort B1

value: PRIMARY SITE

value: SKIN


title: F14_5_S3

value: Fetal liver

value: Fetal


title: AG058021-4

description: polyA RNA

value: Tumor Biopsy

value: Cohort C Expansion

value: Right Upper Back Subcutaneous Nodule


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E3_ad006


title: AF933562-4

description: polyA RNA

value: Cohort A2


title: F14_5_S5


title: AF877144-4

description: polyA RNA

value: LUNG


title: AG139466-4

description: polyA RNA

value: Cohort B Expansion


title: F14_5_S2


title: AG355355-4

description: polyA RNA

value: DAY 15

value: LYMPH NODE


title: AF872963-4

description: polyA RNA

value: AMENTIM


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E3_ad012

value: LSX


title: F14_5_S1


title: AF872962-4

description: polyA RNA

value: METASTATIC SITE


title: F14_S12


title: AF851707-4

description: polyA RNA

value: SCREENING


title: F14_S11


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E3_ad004

value: male


title: DNA methylation from T-ALL ALL_1393 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: AF851703-4

description: polyA RNA

value: LIVER


title: F14_S10

value: Fetal liver

value: Fetal


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E3_ad002


title: AF851702-4

description: polyA RNA

value: Tumor Biopsy

value: SCREEN FAIL


title: F14_5_S4


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E4_ad002


title: AF807556-4

description: polyA RNA

value: Cohort A Expansion


title: F14_S8


title: F14_S9


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E2_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E2_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E2_ad010


title: AF807555-4

description: polyA RNA

value: LUNG


title: F14_S7


title: AF807554-4

description: polyA RNA

value: Cohort A2


title: F14_S6


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E3_ad010


title: AF807553-7

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E2_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E3_ad007


title: AF807552-4

description: polyA RNA

value: Cohort B1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E2_ad007


title: F14_S5


title: AF791939-4

description: polyA RNA

value: Cohort C1

value: DAY 15

value: RIGHT LEG MASS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E12_ad007

value: LSX


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E2_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E12_ad002


title: F14_S4


title: AF791938-4

description: polyA RNA

value: SCREENING

value: METASTATIC SITE

value: RIGHT SUBPATELLAR SOFTMASS


title: F14_S3


title: F14_S2


title: F14_S1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E12_ad012

value: male


title: AF791937-4

description: polyA RNA

value: LIVER


title: AF791102-11

description: polyA RNA

value: LYMPH NODE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E12_ad008


title: P15_T_S12

source_name: hepatocellular carcinoma (HCC)

value: Liver

value: Tumor


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E11_ad008


title: AF791100-4

description: polyA RNA

value: Tumor Biopsy


title: P15_T_S10


title: P15_T_S11


title: AF782298-4

description: polyA RNA

value: SCREEN FAIL

value: CHEST WALL


title: DNA methylation from T-ALL ALL_1056 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: P15_T_S9


title: AF782296-4

description: polyA RNA

value: Cohort B Expansion


title: AF782297-4

description: polyA RNA

value: Cohort A Expansion

value: PRIMARY SITE

value: LEFT NECK MASS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E11_ad004

value: LSX


title: P15_T_S8


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E11_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E11_ad006


title: AF760349-4

description: polyA RNA

value: Cohort C1

value: DAY 15

value: METASTATIC SITE

value: SKIN


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E11_ad010

value: male


title: P15_T_S6

value: Liver


title: P15_T_S5

value: Tumor


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E11_ad002


title: AF748797-4

description: polyA RNA

value: Tumor Biopsy

value: DAY 43

value: LYMPH NODE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad004


title: P15_T_S4


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad008


title: P15_T_S3


title: AF659329-4

description: polyA RNA

value: LIVER


title: AF659343-4

description: polyA RNA

value: Cohort B1

value: DAY 90 FOLLOW UP


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad012


title: AF659328-4

description: polyA RNA

value: Cohort A2

value: SUBCLAVICULAR


title: P15_T_S2


title: P15_T_S1


title: AF659313-4

description: polyA RNA

value: SCREENING

value: LEFT NECK


title: P15_T_S7


title: P15_N_S12

value: Adjacent Normal


title: AF498700-4

description: polyA RNA

value: SCREEN FAIL


title: DNA methylation from T-ALL ALL_0644 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: AF498633-4

description: polyA RNA

value: Cohort B Expansion

value: METASTATIC SITE

value: RIGHT POSTERIOR ABDOMINAL MASS


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad006

value: LSX

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad002


title: P15_N_S10

value: Liver


title: P15_N_S9


title: P15_N_S8


title: AF498632-4

description: polyA RNA

value: Tumor Biopsy

value: PRIMARY SITE

value: LUNG


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad012


title: AF760365-4

description: polyA RNA

value: Cohort C1

value: DAY 43

value: SKIN


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad008


title: P15_N_S7


title: AF453318-6

description: polyA RNA

value: Cohort A1

value: DAY 15

value: SUBCUTANEOUS FLANK


title: AF453314-6

description: polyA RNA

value: SCREENING

value: ANTERIOR NECK


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E10_ad010


title: P15_N_S6

value: Adjacent Normal


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad007


title: P15_N_S5


title: AF442082-6

description: polyA RNA

value: Cohort B1

value: METASTATIC SITE


title: P15_N_S11


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad004

value: LSX


title: AF502607-4

description: polyA RNA


title: CEMBA181204_4G_1_CEMBA181204_4G_2_E1_ad002

value: male


title: P15_N_S4

value: Liver


title: AF442081-6

description: polyA RNA

value: Tumor Biopsy

value: SCREEN FAIL

value: BONE


title: AF748769-4

description: polyA RNA

value: Cohort C1

value: LYMPH NODE


title: AF423324-6

description: polyA RNA

value: R. LEG MASS


title: P15_N_S3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad006


title: P15_N_S2


title: DNA methylation from T-ALL ALL_0360 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: AF409138-6

description: polyA RNA

value: Cohort A2

value: SUBCUTANEOUS NODULE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad012


title: AF409156-6

description: polyA RNA

value: DAY 15


title: P15_N_S1

value: Adjacent Normal


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad010


title: AF408864-6

description: polyA RNA

value: LUNG


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad008


title: P14_T_S11

value: Tumor


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad007

value: LSX


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad004

value: male


title: P14_T_S10

value: Liver


title: P14_T_S9


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D9_ad002


title: AF395376-6

description: polyA RNA

value: Tumor Biopsy

value: Cohort B1

value: SCREENING

value: METASTATIC SITE


title: AF365765-20

description: polyA RNA

value: Cohort B Expansion

value: LT GROIN MASS


title: AF395361-6

description: polyA RNA

value: SCREEN FAIL

value: SPINE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D8_ad012


title: DNA methylation from T-ALL ALL_0245 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: P14_T_S8


title: P14_T_S7


title: AF365762-6

description: polyA RNA

value: DAY 15

value: LYMPH NODE


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D8_ad010


title: AF365760-6

description: polyA RNA


title: P14_T_S6


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D8_ad008


title: AF308488-6

description: polyA RNA

value: Cohort A1

value: SUBCUTANEOUS FLANK NODULE


title: P14_T_S5

value: Tumor


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D8_ad007

value: LSX

value: male


title: P14_T_S12

value: Liver


title: AF241881-6

description: polyA RNA

value: Tumor Biopsy

value: CHEST WALL


title: P14_T_S4


title: DNA methylation from T-ALL ALL_0173 EPICarray


title: P14_T_S3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D8_ad002


title: AF408846-6

description: polyA RNA

value: Cohort A2

value: SCREENING

value: METASTATIC SITE

value: LUNG


title: AF241866-3

description: polyA RNA

value: LIVER


title: P14_T_S2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad006


title: P14_T_S1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad012


title: P14_N_S12

value: Adjacent Normal


title: P14_N_S10


title: P14_N_S9


title: P14_N_S7


title: P14_N_S6


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad006


title: P14_N_S11


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad012


title: P14_N_S2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D5_ad012


title: P14_N_S8


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D7_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad008


title: P14_N_S4


title: P14_N_S5


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D8_ad004


title: P8_T_S12


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D4_ad012


title: P14_N_S1


title: P8_T_S11


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D4_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad002


title: P8_T_S10


title: P8_T_S9


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D4_ad010


title: P14_N_S3


title: P8_T_S8


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D6_ad004


title: P8_T_S7


title: P8_T_S5


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D3_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D3_ad010


title: P8_T_S2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D3_ad007


title: P8_T_S1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D3_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D2_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D3_ad002


title: P8_N_S10


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D2_ad010


title: P8_N_S12


title: P8_T_S4


title: P8_N_S9


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D12_ad008


title: P8_N_S8


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D2_ad006


title: P8_N_S11


title: P8_N_S7


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D12_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D4_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D4_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D12_ad012


title: P8_N_S6


title: P8_T_S6


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D3_ad012


title: P8_N_S5


title: P8_T_S3


title: P8_N_S4


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D12_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D12_ad010


title: P8_N_S3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D11_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D11_ad010


title: P8_N_S2


title: P8_N_S1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D11_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D11_ad007


title: E:H:p

city: tianjin

first: Peng

last: Zhang

state: Tianjin

address: No.38 Tongyan Road, Jinnan

institute: Nankai University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole E. coli MG1655 genome using Bowtie v2.2.3
The reads numbers mapped to each gene was counted using HTSeq v0.6.1 [42], differential expression analysis was performed using the DEGSeq R package (1.20.0) [43]. The P values were adjusted using the Benjamini & Hochberg method [44], and corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: GCF_000801205.1

organism: Escherichia coli

source_name: E. coli

growth_protocol: all the RP4-carrying strains were cultured in LB broth at 37℃, shaking at 200 RPM

extract_protocol:
RP4-carrying strains were collected, flash frozen by liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext Ultra II RNA Library Prep Kit for Illumina was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: all the RP4-carrying strains were cultured in non-selective LB

tag: genotype

value: evolved RP4-carrying strains


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D12_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D10_ad007


title: A:H:p

value: ancestral RP4-carrying strains


title: DNA methylation from T-ALL ALL_2328 EPICarray

value: Blast from the bone marrow

value: T-ALL


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D10_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D10_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D10_ad004


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D10_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D1_ad010


title: DNA methylation from T-ALL ALL_2177 EPICarray


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D1_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D1_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D1_ad002


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D1_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C9_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C9_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C8_ad012


title: RagBcl6plusCD3-DP-KO2

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

description:
DP-KO2
UCLGNS1256-12-RagplusCD3-ISP-KO2_S12_L001

data_processing:
Base Calling was done using the RTA package from Illumina
Alignment was done on the transcriptome using the Burrows-Wheeler Aligner (BWA) package
Expression levels in Reads Per Million Kilobases (RPKM).
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated file including RPKM values for each Sample.

source_name: Murine Embryonic DP thymocytes

extract_protocol:
RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher, Cat. KIT0202) performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RagKOControl and RagKOBcl6coKO E17.5 thymocytes were treated with 1ug/ml anti-CD3 for 2 day on milipore filters. Thymi were mashed and stained for CD25, CD4 and CD8. thymocytes were sorted into ISP (CD4-CD8+) and DP (CD4+CD8+). Unstimulated thymocytes were sorted for CD25+ cells. RNA was extracted from all these cell subsets.

tag: strain background

tag: developmental stage

value: Murine Embryonic E16.5 anti-CD3 stimulated ISP thymocytes in vitro

tag: culture condition

value: E16.5 thymi Stimulated with anti-CD3 for 2days


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C8_ad010

tag: brain region

value: LSX

tag: Sex

tag: age


title: RagBcl6plusCD3-DP-KO1

description:
DP-KO1
UCLGNS1256-11-RagplusCD3-DP-KO2_S11_L001


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C8_ad008

value: male

tag: strain


title: CEMBA181204_4G_1_CEMBA181204_4G_2_D1_ad007


title: RagBcl6plusCD3-DP-Control1

description:
DP-Control1
UCLGNS1256-9-RagplusCD3-DP-KO1_S9_L001


title: RagBcl6plusCD3-DP-Control2

description:
DP-Control2
UCLGNS1256-10-RagplusCD3-ISP-KO1_S10_L001


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C8_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C7_ad012


title: RagBcl6plusCD3-ISP-KO2

description:
ISP-KO2
UCLGNS1256-8-RagplusCD3-ISP-WT2_S8_L001

source_name: Murine Embryonic ISP thymocytes

value: Murine Embryonic E16.5 anti-CD3 stimulated DP thymocytes in vitro


title: RagBcl6plusCD3-ISP-KO1

description:
ISP-KO1
UCLGNS1256-7-RagplusCD3-DP-WT2_S7_L001


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C7_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C7_ad007


title: RagBcl6plusCD3-ISP-Control2

description:
ISP-Control2
UCLGNS1256-6-RagplusCD3-ISP-WT1_S6_L001


title: RagBcl6plusCD3-ISP-Control1

description:
ISP-Control1
UCLGNS1256-5-RagplusCD3-DP-WT1_S5_L001


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C7_ad010


title: RagBcl6-CD25-KO2

description:
CD25-KO2
UCLGNS1256-4-RagBcl6-CD25-KO2_S4_L001

source_name: Murine Embryonic CD25 thymocytes

value: Murine Embryonic E16.5 Unstimulated CD25 thymocytes

value: E16.5 Unstimulated CD25 thymocytes


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C5_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C5_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C7_ad006


title: RagBcl6-CD25-Control2

description:
CD25-Control2
UCLGNS1256-2-RagBcl6-CD25-WT2_S2_L001


title: RagBcl6-CD25-KO1

description:
CD25-KO1
UCLGNS1256-3-RagBcl6-CD25-KO1_S3_L001


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C5_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C4_ad006


title: RagBcl6-CD25-Control1

description:
CD25-Control1
UCLGNS1256-1-RagBcl6-CD25-WT1_S1_L001


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C5_ad012


title: IFNGR1_NS_0_rep1: IFNGR1_primary-fibroblasts_non-stimulated_rep1

city: Paris

first: Jeremy

last: Manry

address: 24 boulevard du Montparnasse

country: France

institute: INSERM, Institut Imagine

description: replicate 1

data_processing:
The RNA-seq fastq files were first inspected with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure that the raw data were of high quality.
For each subject, the four fastq files generated were then mapped to the human reference genome (Ensembl GRCh37 release 75) with STAR v.2.7.3a in the two-pass mode
The mapping quality of each bam file was then evaluated with RSeQC
Reads were quantified to generate gene-level feature counts from the read mapping, with HTSeq-count v.0.11.2
Genome_build: Ensembl GRCh37 release 75
Supplementary_files_format_and_content: Raw counts were obtained using HTSeq-count v.0.11.2

source_name: primary fibroblasts

extract_protocol:
Total RNA was extracted from primary fibroblasts from patients or healthy controls with the the miRNeasy Mini Kit (Zimo), and treated with DNAse (Zymo) to remove residual genomic DNA. Quality controls were performed and all RNA samples were of good quality (RIN>8).
RNA-Seq libraries were prepared with the Illumina RiboZero TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on the Illumina NextSeq platform in the 150-nt, paired-end configuration. Each library was sequenced twice.

tag: cell type

value: primary fibroblasts

value: no treatment

tag: treatment dose

tag: treatment duration


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C4_ad012


title: IFNGR1_ifng_8_rep2: IFNGR1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep2

description: replicate 2

value: IFN-γ

value: 8 hours


title: IFNGR1_NS_0_rep2: IFNGR1_primary-fibroblasts_non-stimulated_rep2

description: replicate 2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C4_ad008


title: IFNGR1_ifng_8_rep1: IFNGR1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep1

description: replicate 1


title: IFNGR1_ifng_2_rep2: IFNGR1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep2

description: replicate 2

value: 2 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C4_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C4_ad007


title: IFNGR1_ifng_2_rep1: IFNGR1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep1

description: replicate 1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C3_ad006


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C3_ad012


title: IFNGR1_ifna_8_rep2: IFNGR1_primary-fibroblasts_stimulated-IFN-α-8hours_rep2

description: replicate 2

value: IFN-α


title: IFNGR1_ifna_8_rep1: IFNGR1_primary-fibroblasts_stimulated-IFN-α-8hours_rep1

description: replicate 1


title: FN108.0: Genomic DNA from sperm of nut-fed individual FN108 (baseline)

city: Salt Lake City

first: Albert

last: Salas-Huetos

state: UT

address: 675S Arapeen Dr

department: Andrology

institute: University of Utah

description: Purified sperm sample

hyb_protocol: A total of 500ng of extracted DNA was bisulfite converted with EZ-96 DNA Methylation-Gold kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s recommendations specifically for use with Illumina array platforms. The converted DNA was then hybridized to Infinium® MethylationEPIC BeadChip microarrays (Illumina) array and analyzed according to Illumina protocols at the University of Utah Genomics Core Facility.

data_processing: Data from microarrays were processed by using the minfi Bioconductor package (minfi; package at http://www.bioconductor.org) and Useq bioinformatics software package (https://sourceforge.net/projects/useq/).

source_name: Semen sample 81

label_protocol: Standard Illumina protocols.

extract_protocol: Genomic DNA was extracted from purified sperm samples using QIAamp DNA Mini kit according to manufacturer protocol.

treatment_protocol: Prior to DNA isolation, a somatic cell lysis methodology was performed by incubation sperm samples with somatic cell lysis buffer, which contained both 0.1% SDS and 0.5% Triton X-100 (in Milli-Q® water), on ice.

tag: gender

value: Male

tag: sample type

value: Sperm

tag: baseline or final intervention

value: Baseline


title: FN115.0: Genomic DNA from sperm of nut-fed individual FN115 (baseline)

description: Purified sperm sample

source_name: Semen sample 91


title: FN118.0: Genomic DNA from sperm of nut-fed individual FN118 (baseline)

description: Purified sperm sample

source_name: Semen sample 95


title: FN114.0: Genomic DNA from sperm of control individual FN114 (baseline)

description: Purified sperm sample

source_name: Semen sample 89


title: GFP_TREM2_KO_DeadNeurons3

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

institute: University of California, Irvine

data_processing:
Dataset quality was assessed using FASTQC.
Low quality reads and Illumina adapters were trimmed using BBDuk.
Reads aligning with rRNA or PhiX were filtered out using BBDuk.
Filtered dataset quality was confirmed with FASTQC.
Reads were pseudoaligned to the GRCh38 genome using the quant command in Kallisto v0.46.0.
Kallisto abundance files were analyzed using DESeq2 v1.26.0 and TXimport v1.14.2.
Genome_build: GRCh38 release 97
Supplementary_files_format_and_content: Text files containing the raw counts (RawCounts*.tsv), Variance Stabilizing Transformation counts (VSTCounts*.tsv), TXimport Transcript to Gene mapping (tx2gene_GRCh38_97.tsv), and Kallisto read abundance files (*_abundance.h5) for each single-cell sample.

source_name: iPSC-derived microglia

growth_protocol: Growth protocols explicitly defined in Transcriptomic and functional deficits in human TREM2-/- microglia impair response to Alzheimer's pathology in vivo (Nature Communications).

extract_protocol:
Samples were lysed in RLT and isolated using RNeasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated for 24 hrs.

tag: cell line

tag: cell genotype

value: TREM2 KO

value: iPSC-derived microglia

value: Dead Neurons


title: FN111.0: Genomic DNA from sperm of control individual FN111 (baseline)

description: Purified sperm sample

source_name: Semen sample 85


title: FN109.0: Genomic DNA from sperm of control individual FN109 (baseline)

description: Purified sperm sample

source_name: Semen sample 83


title: FN115.3: Genomic DNA from sperm of nut-fed individual FN115 (final)

description: Purified sperm sample

source_name: Semen sample 92

value: Final


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C3_ad010

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

value: LSX

value: male


title: FN111.3: Genomic DNA from sperm of control individual FN111 (final)

description: Purified sperm sample

source_name: Semen sample 86


title: GFP_TREM2_KO_DeadNeurons2

tag: treatment


title: FN118.3: Genomic DNA from sperm of nut-fed individual FN118 (final)

description: Purified sperm sample

source_name: Semen sample 96


title: FN109.3: Genomic DNA from sperm of control individual FN109 (final)

description: Purified sperm sample

source_name: Semen sample 84


title: FN117.0: Genomic DNA from sperm of nut-fed individual FN117 (baseline)

description: Purified sperm sample

source_name: Semen sample 93


title: FN106.3: Genomic DNA from sperm of control individual FN106 (final)

description: Purified sperm sample

source_name: Semen sample 80


title: IFNGR1_ifna_2_rep2: IFNGR1_primary-fibroblasts_stimulated-IFN-α-2hours_rep2

description: replicate 2


title: FN114.3: Genomic DNA from sperm of control individual FN114 (final)

description: Purified sperm sample

source_name: Semen sample 90


title: FN108.3: Genomic DNA from sperm of nut-fed individual FN108 (final)

description: Purified sperm sample

source_name: Semen sample 82


title: FN106.0: Genomic DNA from sperm of control individual FN106 (baseline)

description: Purified sperm sample

source_name: Semen sample 79


title: FN117.3: Genomic DNA from sperm of nut-fed individual FN117 (final)

description: Purified sperm sample

source_name: Semen sample 94


title: FN097.3: Genomic DNA from sperm of control individual FN097 (final)

description: Purified sperm sample

source_name: Semen sample 74


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C3_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: GFP_TREM2_KO_DeadNeurons1


title: FN104.3: Genomic DNA from sperm of nut-fed individual FN104 (final)

description: Purified sperm sample

source_name: Semen sample 78


title: FN101.3: Genomic DNA from sperm of nut-fed individual FN101 (final)

description: Purified sperm sample

source_name: Semen sample 76


title: FN113.0: Genomic DNA from sperm of control individual FN113 (baseline)

description: Purified sperm sample

source_name: Semen sample 87


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C2_ad006


title: IFNGR1_ifna_2_rep1: IFNGR1_primary-fibroblasts_stimulated-IFN-α-2hours_rep1

description: replicate 1

source_name: primary fibroblasts


title: IFNAR1_NS_0_rep2: IFNAR1_primary-fibroblasts_non-stimulated_rep2

description: replicate 2


title: FN101.0: Genomic DNA from sperm of nut-fed individual FN101 (baseline)

description: Purified sperm sample

source_name: Semen sample 75


title: GFP_TREM2_WT_DeadNeurons3

source_name: iPSC-derived microglia

value: TREM2 WT


title: FN093.3: Genomic DNA from sperm of control individual FN093 (final)

description: Purified sperm sample

source_name: Semen sample 70


title: IFNAR1_NS_0_rep1: IFNAR1_primary-fibroblasts_non-stimulated_rep1

description: replicate 1


title: GFP_TREM2_WT_DeadNeurons2


title: IFNAR1_ifng_8_rep2: IFNAR1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep2

description: replicate 2


title: FN096.0: Genomic DNA from sperm of nut-fed individual FN096 (baseline)

description: Purified sperm sample

source_name: Semen sample 71


title: FN113.3: Genomic DNA from sperm of control individual FN113 (final)

description: Purified sperm sample

source_name: Semen sample 88


title: GFP_TREM2_WT_DeadNeurons1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C2_ad010


title: IFNAR1_ifng_8_rep1: IFNAR1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep1

description: replicate 1


title: GFP_TREM2_KO_Untreated3

value: Untreated


title: GFP_TREM2_KO_Untreated2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C2_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C2_ad008


title: IFNAR1_ifng_2_rep1: IFNAR1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep1

description: replicate 1

value: primary fibroblasts


title: IFNAR1_ifng_2_rep2: IFNAR1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep2

description: replicate 2


title: GFP_TREM2_KO_Untreated1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C2_ad002


title: GFP_TREM2_WT_Untreated3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C12_ad008


title: FN096.3: Genomic DNA from sperm of nut-fed individual FN096 (final)

description: Purified sperm sample

source_name: Semen sample 72


title: GFP_TREM2_WT_Untreated2


title: IFNAR1_ifna_8_rep1: IFNAR1_primary-fibroblasts_stimulated-IFN-α-8hours_rep1

description: replicate 1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C12_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C2_ad004


title: FN097.0: Genomic DNA from sperm of control individual FN097 (baseline)

description: Purified sperm sample

source_name: Semen sample 73


title: IFNAR1_ifna_2_rep2: IFNAR1_primary-fibroblasts_stimulated-IFN-α-2hours_rep2

description: replicate 2


title: FN093.0: Genomic DNA from sperm of control individual FN093 (baseline)

description: Purified sperm sample

source_name: Semen sample 69


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C12_ad010


title: IFNAR1_ifna_2_rep1: IFNAR1_primary-fibroblasts_stimulated-IFN-α-2hours_rep1

description: replicate 1


title: IFNAR1_ifna_8_rep2: IFNAR1_primary-fibroblasts_stimulated-IFN-α-8hours_rep2

description: replicate 2


title: FN104.0: Genomic DNA from sperm of nut-fed individual FN104 (baseline)

description: Purified sperm sample

source_name: Semen sample 77


title: ADRC5_TREM2_KO_Untreated3


title: HSE.IFNAR1_NS_0_rep2: HSE.IFNAR1_primary-fibroblasts_non-stimulated_rep2

description: replicate 2

value: no treatment


title: ADRC5_TREM2_KO_Untreated2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C3_ad004


title: HSE.IFNAR1_NS_0_rep1: HSE.IFNAR1_primary-fibroblasts_non-stimulated_rep1

description: replicate 1


title: ADRC5_TREM2_KO_Untreated1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad004


title: HSE.IFNAR1_ifng_8_rep2: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep2

description: replicate 2

value: IFN-γ


title: ADRC5_TREM2_WT_Untreated3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad012


title: HSE.IFNAR1_ifng_8_rep1: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep1

description: replicate 1

value: 8 hours


title: GFP_TREM2_WT_Untreated1


title: ADRC5_TREM2_WT_Untreated2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad010


title: HSE.IFNAR1_ifng_2_rep2: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep2

description: replicate 2

value: 2 hours


title: ADRC5_TREM2_WT_Untreated1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad007


title: HSE.IFNAR1_ifng_2_rep1: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep1

description: replicate 1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad006


title: HSE.IFNAR1_ifna_8_rep2: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-α-8hours_rep2

description: replicate 2

value: IFN-α


title: FN091.3: Genomic DNA from sperm of nut-fed individual FN091 (final)

description: Purified sperm sample

source_name: Semen sample 68

value: Male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C11_ad002


title: HSE.IFNAR1_ifna_8_rep1: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-α-8hours_rep1

description: replicate 1


title: WT mouse cornea/limbus rim

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

data_processing:
Sequencing data was demultiplexed using Cell Ranger mkfastq version 2.1.1
FASTQ files were aligned and counted to mm10 (10X Genomics transcript version 1.2.0) using Cell Ranger count version 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited matrix and cloupe output files from Cell Ranger count

source_name: cornea/limbus

extract_protocol:
Whole eyes were harvested from a single healthy beclin1 het (beclin1 +/-) female and a healthy C57/BL6 wild type littermate control (28 day old) female mouse. The lens, retina, iris, and trabecular network were removed leaving the entire ocular anterior segment, from which most of the conjunctiva was carefully dissected and discarded. The corneal rims were subsequently digested at 37°C for 2 hours with 2 ml of 1 mg/mL collagenase A (Sigma-Aldrich) in DMEM containing 10% FBS, 50 μg/mL gentamicin, and 1.25 μg/mL amphotericin B.  After 2hr incubation, the corneal rims were rinsed once with PBS without Ca2+-Mg2+. Clusters were further digested with 0.25% trypsin and 1 mM EDTA at 37°C for 20 minutes with intermediate gentle pipetting to yield single cells. After trypsin digestion, cells were rinsed once with DMEM+10% FCS media to deactivate and remove trypsin. The cells were rinsed twice with sterile PBS containing 0.04% BSA. After final centrifugation, cells were resuspended in 60ul of PBS containing 0.04% BSA to achieve 700-1200 cells/ul, and filtered into an Eppendorf tube by using Flowmi Cell Strainer (Fisher Scientific). Cell viability was checked and accepted with at least an 80% viability score. Such cells were processed for scRNA-seq using 10XGenomics pipeline in the Northwestern University NUseq Core.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

tag: genotype/variation

value: WT

value: female

value: 28 days

tag: tissue

value: cornea/limbus rim


title: Beclin1 +/- mouse cornea/limbus rim

tag: strain background

value: Beclin1 +/-


title: INPUT_non-CINs_P2_Rep2

city: San Francisco

first: Kenneth

last: Lim

department: Psychiatry

institute: UCSF

data_processing:
Basecalls performed using standard Illumina pipeline
ChIP-seq reads were aligned to the mm10 genome assembly using BWA version 0.7.15
Data were filtered using samtools view version 1.10 using a MAPQ cutoff of 30.
peaks were called using MACS2 version 2.2.7 with the following setting: broad peak calling (active), broad-peak pvalue cutoff (0.01), qvalue cutoff (0.01), fragment extension (200), no-model (active), no-lambda (active).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools bamCoverage version 3.4.3 with the following setting: output type (bigwig), bin-size (10), fragment extension (200), normalize (RPKM), ignore duplicates (active). Scores represent: RPKM.
Supplementary_files_format_and_content: peak text files

source_name: microdissected cerebral cortical tissue from P2 Gad67-GFP mice

growth_protocol: Cerebral cortex tissue was dissected from Gad67-GFP heterozygote pups at P2. Samples represent pooled tissue from 2-3 litters.

extract_protocol:
Nuclear extracts were prepared from sorted cells and digested with MNase to obtain mono- and di-nucleotide fragments. Digested chromatin was dialysed overnight. Input control chromatin was set aside, and immunoprecipitation reactions were performed with antibodies against H3K27ac (Millipore Cat# 05-1334, RRID:AB_1977244) or H3K27me3 (Millipore Cat# 07-449, RRID:AB_310624). Precipitated fractions were purified using Dynabeads (Invitrogen) and RNase-treated prior to library construction.
Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 180-300 bp on a BluePippin (Sage Science), quality control tested on a Bioanalyzer (Agilent) and sequenced on a HiSeq 4000 (Illumina).

treatment_protocol: The tissue was dissociated using the Papain Dissociation System (Worthington) according to the manufacturer’s instructions. Dissociated cells were separated by fluorescence activated cell sorting on a FACSAria II machine (BD Biosciences). Sorted GFP-positive CINs and GFP-negative non-CINs were collected separately into DMEM with 20% FBS.

value: cerebral cortex

tag: developmental stage

value: postnatal day 2

value: GFP-negative cells

tag: chip antibody


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C12_ad007

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

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

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: LSX

tag: Sex

value: male


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad008

tag: age

tag: strain


title: INPUT_non-CINs_P2_Rep1

tag: cell type


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad004


title: HSE.IFNAR1_ifna_2_rep1: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-α-2hours_rep1

description: replicate 1

value: primary fibroblasts

tag: treatment dose

tag: treatment duration


title: INPUT_CINs_P2_Rep2

value: GFP-positive cells


title: HSE.IFNAR1_ifna_2_rep2: HSE.IFNAR1_primary-fibroblasts_stimulated-IFN-α-2hours_rep2

description: replicate 2


title: C3_NS_0_rep1: CTRL3_primary-fibroblasts_non-stimulated_rep1

description: replicate 1

value: no treatment


title: INPUT_CINs_P2_Rep1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad010


title: H3K27me3_non-CINs_P2_Rep2

value: H3K27me3 (Millipore Cat# 07-449, RRID:AB_310624)


title: C3_NS_0_rep2: CTRL3_primary-fibroblasts_non-stimulated_rep2

description: replicate 2


title: C3_ifng_8_rep2: CTRL3_primary-fibroblasts_stimulated-IFN-γ-8hours_rep2

description: replicate 2

value: IFN-γ

value: 8 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad007


title: FN089.3: Genomic DNA from sperm of nut-fed individual FN089 (final)

description: Purified sperm sample

source_name: Semen sample 64

tag: gender

value: Male

tag: sample type

value: Sperm

value: Final


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad006


title: FN090.0: Genomic DNA from sperm of control individual FN090 (baseline)

description: Purified sperm sample

source_name: Semen sample 65

tag: baseline or final intervention

value: Baseline


title: FN090.3: Genomic DNA from sperm of control individual FN090 (final)

description: Purified sperm sample

source_name: Semen sample 66


title: FN088.0: Genomic DNA from sperm of control individual FN088 (baseline)

description: Purified sperm sample

source_name: Semen sample 61


title: H3K27me3_non-CINs_P2_Rep1


title: C3_ifng_8_rep1: CTRL3_primary-fibroblasts_stimulated-IFN-γ-8hours_rep1

description: replicate 1

source_name: primary fibroblasts


title: H3K27me3_CINs_P2_Rep2


title: FN089.0: Genomic DNA from sperm of nut-fed individual FN089 (baseline)

description: Purified sperm sample

source_name: Semen sample 63


title: FN087.0: Genomic DNA from sperm of control individual FN087 (baseline)

description: Purified sperm sample

source_name: Semen sample 59


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C10_ad002


title: H3K27me3_CINs_P2_Rep1


title: FN088.3: Genomic DNA from sperm of control individual FN088 (final)

description: Purified sperm sample

source_name: Semen sample 62


title: C3_ifng_2_rep1: CTRL3_primary-fibroblasts_stimulated-IFN-γ-2hours_rep1

description: replicate 1

value: 2 hours


title: H3K27ac_non-CINs_P2_Rep2


title: C3_ifna_8_rep2: CTRL3_primary-fibroblasts_stimulated-IFN-α-8hours_rep2

description: replicate 2

value: IFN-α


title: FN086.3: Genomic DNA from sperm of nut-fed individual FN086 (final)

description: Purified sperm sample

source_name: Semen sample 58


title: H3K27ac_non-CINs_P2_Rep1

value: cerebral cortex


title: FN083.3: Genomic DNA from sperm of nut-fed individual FN083 (final)

description: Purified sperm sample

source_name: Semen sample 56


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C1_ad010


title: FN083.0: Genomic DNA from sperm of nut-fed individual FN083 (baseline)

description: Purified sperm sample

source_name: Semen sample 55


title: C3_ifna_8_rep1: CTRL3_primary-fibroblasts_stimulated-IFN-α-8hours_rep1

description: replicate 1


title: FN082.3: Genomic DNA from sperm of control individual FN082 (final)

description: Purified sperm sample

source_name: Semen sample 54


title: FN086.0: Genomic DNA from sperm of nut-fed individual FN086 (baseline)

description: Purified sperm sample

source_name: Semen sample 57


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C1_ad008


title: C3_ifna_2_rep2: CTRL3_primary-fibroblasts_stimulated-IFN-α-2hours_rep2

description: replicate 2


title: C3_ifng_2_rep2: CTRL3_primary-fibroblasts_stimulated-IFN-γ-2hours_rep2

description: replicate 2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C1_ad006


title: C3_ifna_2_rep1: CTRL3_primary-fibroblasts_stimulated-IFN-α-2hours_rep1

description: replicate 1


title: H3K27ac_CINs_P2_Rep2

value: postnatal day 2


title: FN087.3: Genomic DNA from sperm of control individual FN087 (final)

description: Purified sperm sample

source_name: Semen sample 60


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C1_ad012


title: FN072.0: Genomic DNA from sperm of control individual FN072 (baseline)

description: Purified sperm sample

source_name: Semen sample 49


title: VCP TG 5w 3

city: Atlanta

first: Hongyu

last: Qiu

state: GA

address: 100 Piedmont Ave

department: Center of Molecular and Translational Medicine

institute: Georgia State University

data_processing:
Illumina Casava1.8 software used for basecalling.
Hard trimming and adaptor trimming were performed by Trimmomatic v0.35. The trimmed reads were aligned and quantified to the mouse reference genome NCBI GRCm38 with kallisto v0.43.1 with default parameter settings. The quantified gene expression profiles were used for differential expression gene (DEG) analysis.
The trimmed fastq files were aligned by 2-pass mode of STAR v2.5.4b with default parameter setting to generate bam files for isoform analysis.
The gene expression profiles (Transcript per million or TPM) were used as the input for DEG analysis by using DESeq2. Differential expressed genes were based on FDR < 0.05.
The bam files were used as the input for isoform analysis by using LeafCutter. A splicing event was labeled significantly if the FDR < 0.05.
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM gene expression matrix

source_name: Heart

extract_protocol:
Total RNA was extracted from LV tissues using Qiagen miRNeasy kit.
Illumina TruSeq Stranded mRNA Sample Prep kit was used to construct RNA-seq libraries.

treatment_protocol: Mice were submitted to transverse aortic constriction (TAC) for 5 weeks to induce pressure overload. A sham operation was used as control. Heart tissues were collected after terminal physiological measurements.

value: FVB

value: left ventricular

value: 3-5 months

value: VCP TG 5 weeks TAC


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C1_ad002

city: La Jolla

source_name: C57BL/6J Male P56 Mouse Brain

value: LSX

value: male


title: C2_NS_0_rep2: CTRL2_primary-fibroblasts_non-stimulated_rep2

description: replicate 2

value: primary fibroblasts

value: no treatment


title: FN074.0: Genomic DNA from sperm of control individual FN074 (baseline)

description: Purified sperm sample

source_name: Semen sample 51


title: VCP TG 5w 2


title: FN068.0: Genomic DNA from sperm of nut-fed individual FN068 (baseline)

description: Purified sperm sample

source_name: Semen sample 47


title: C2_NS_0_rep1: CTRL2_primary-fibroblasts_non-stimulated_rep1

description: replicate 1


title: FN082.0: Genomic DNA from sperm of control individual FN082 (baseline)

description: Purified sperm sample

source_name: Semen sample 53


title: FN068.3: Genomic DNA from sperm of nut-fed individual FN068 (final)

description: Purified sperm sample

source_name: Semen sample 48


title: VCP TG 5w 1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B9_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B9_ad012


title: C2_ifng_8_rep2: CTRL2_primary-fibroblasts_stimulated-IFN-γ-8hours_rep2

description: replicate 2

source_name: primary fibroblasts

value: IFN-γ

value: 8 hours


title: WT 5w 4

value: WT 5 weeks TAC


title: C2_ifng_8_rep1: CTRL2_primary-fibroblasts_stimulated-IFN-γ-8hours_rep1

description: replicate 1


title: WT 5w 3


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B9_ad007


title: C2_ifng_2_rep2: CTRL2_primary-fibroblasts_stimulated-IFN-γ-2hours_rep2

description: replicate 2


title: H3K27ac_CINs_P2_Rep1

source_name: microdissected cerebral cortical tissue from P2 Gad67-GFP mice

value: GFP-positive cells


title: WT 5w 2


title: FN064.3: Genomic DNA from sperm of control individual FN064 (final)

description: Purified sperm sample

source_name: Semen sample 46

value: Male

value: Sperm

value: Final


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B8_ad012


title: C2_ifng_2_rep1: CTRL2_primary-fibroblasts_stimulated-IFN-γ-2hours_rep1

description: replicate 1

value: 2 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B9_ad008


title: FN063.3: Genomic DNA from sperm of control individual FN063 (final)

description: Purified sperm sample

source_name: Semen sample 44


title: FN072.3: Genomic DNA from sperm of control individual FN072 (final)

description: Purified sperm sample

source_name: Semen sample 50


title: CEMBA181204_4G_1_CEMBA181204_4G_2_C1_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B8_ad010


title: C2_ifna_8_rep2: CTRL2_primary-fibroblasts_stimulated-IFN-α-8hours_rep2

description: replicate 2

value: IFN-α


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B8_ad008


title: C2_ifna_8_rep1: CTRL2_primary-fibroblasts_stimulated-IFN-α-8hours_rep1

description: replicate 1


title: FN074.3: Genomic DNA from sperm of control individual FN074 (final)

description: Purified sperm sample

source_name: Semen sample 52


title: VCP TG 2w 3

data_processing:
Illumina Casava1.8 software used for basecalling.
Hard trimming and adaptor trimming were performed by Trimmomatic v0.35. The trimmed reads were aligned and quantified to the mouse reference genome NCBI GRCm38 with kallisto v0.43.1 with default parameter settings. The quantified gene expression profiles were used for differential expression gene (DEG) analysis.
The trimmed fastq files were aligned by 2-pass mode of STAR v2.5.4b with default parameter setting to generate bam files for isoform analysis.
The gene expression profiles (Transcript per million or TPM) were used as the input for DEG analysis by using DESeq2. Differential expressed genes were based on FDR < 0.05.
The bam files were used as the input for isoform analysis by using LeafCutter. A splicing event was labeled significantly if the FDR < 0.05.
Genome_build: GRCm38

treatment_protocol: Mice were submitted to transverse aortic constriction (TAC) for 2 weeks or 5 weeks to induce pressure overload. A sham operation was used as control. Heart tissues were collected after terminal physiological measurements.

value: FVB

value: 2 weeks TAC

value: VCP TG


title: VCP TG 2w 2

value: left ventricular

value: 3-5 months


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B8_ad007

value: LSX

value: male


title: FN062.3: Genomic DNA from sperm of nut-fed individual FN062 (final)

description: Purified sperm sample

source_name: Semen sample 42


title: VCP TG 2w 1


title: C2_ifna_2_rep2: CTRL2_primary-fibroblasts_stimulated-IFN-α-2hours_rep2

description: replicate 2

value: primary fibroblasts


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B7_ad008


title: WT 5w 1


title: WT 2w 4

value: Wild type


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B7_ad010


title: C2_ifna_2_rep1: CTRL2_primary-fibroblasts_stimulated-IFN-α-2hours_rep1

description: replicate 1


title: WT 2w 3


title: FN091.0: Genomic DNA from sperm of nut-fed individual FN091 (baseline)

description: Purified sperm sample

source_name: Semen sample 67

value: Baseline


title: C1_NS_0_rep2: CTRL1_primary-fibroblasts_non-stimulated_rep2

description: replicate 2

value: no treatment


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B7_ad012


title: FN061.3: Genomic DNA from sperm of control individual FN061 (final)

description: Purified sperm sample

source_name: Semen sample 40


title: FN064.0: Genomic DNA from sperm of control individual FN064 (baseline)

description: Purified sperm sample

source_name: Semen sample 45


title: WT 2w 2


title: C1_NS_0_rep1: CTRL1_primary-fibroblasts_non-stimulated_rep1

description: replicate 1


title: C1_ifng_8_rep2: CTRL1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep2

description: replicate 2

value: IFN-γ

value: 8 hours


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B7_ad007


title: WT 2w 1


title: FN062.0: Genomic DNA from sperm of nut-fed individual FN062 (baseline)

description: Purified sperm sample

source_name: Semen sample 41

value: Male

value: Sperm


title: C1_ifng_8_rep1: CTRL1_primary-fibroblasts_stimulated-IFN-γ-8hours_rep1

description: replicate 1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B7_ad006


title: C1_ifng_2_rep2: CTRL1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep2

description: replicate 2

value: 2 hours


title: C1_ifng_2_rep1: CTRL1_primary-fibroblasts_stimulated-IFN-γ-2hours_rep1

description: replicate 1


title: VCPTG sham 3

source_name: Heart

value: sham


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B6_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B6_ad010


title: VCP TG sham 4

value: FVB


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B6_ad007


title: VCP TG sham 2


title: C1_ifna_8_rep2: CTRL1_primary-fibroblasts_stimulated-IFN-α-8hours_rep2

description: replicate 2

value: IFN-α


title: VCPTG sham 1

value: VCP TG


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B6_ad004


title: C1_ifna_8_rep1: CTRL1_primary-fibroblasts_stimulated-IFN-α-8hours_rep1

description: replicate 1


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B6_ad002


title: C1_ifna_2_rep2: CTRL1_primary-fibroblasts_stimulated-IFN-α-2hours_rep2

description: replicate 2


title: WT sham 4

value: left ventricular


title: FN061.0: Genomic DNA from sperm of control individual FN061 (baseline)

description: Purified sperm sample

source_name: Semen sample 39


title: FN063.0: Genomic DNA from sperm of control individual FN063 (baseline)

description: Purified sperm sample

source_name: Semen sample 43


title: WT sham 3

value: 3-5 months


title: C1_ifna_2_rep1: CTRL1_primary-fibroblasts_stimulated-IFN-α-2hours_rep1

description: replicate 1


title: FN055.0: Genomic DNA from sperm of nut-fed individual FN055 (baseline)

description: Purified sperm sample

source_name: Semen sample 37


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B5_ad006

value: LSX


title: FN054.0: Genomic DNA from sperm of control individual FN054 (baseline)

description: Purified sperm sample

source_name: Semen sample 35


title: FN054.3: Genomic DNA from sperm of control individual FN054 (final)

description: Purified sperm sample

source_name: Semen sample 36

value: Final


title: WT sham 2


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B5_ad010

value: male


title: FN053.3: Genomic DNA from sperm of nut-fed individual FN053 (final)

description: Purified sperm sample

source_name: Semen sample 34


title: WT sham 1

value: Wild type


title: ATAC-seq from UC Davis FAANG pig spleen rep P350

first: Colin

last: Kern

institute: UC San Diego

data_processing:
Reads were trimmed with Trim Galore! 0.4.5 with the -atac argument
Reads were aligned with BWA mem 0.7.17 to the Sscrofa11.2 and ARS-UCD1.2 genomes
Alignments were filtered with Samtools 1.10 using arguments -F 1804 -q 30
Duplicates were removed with Picard toolkit 2.18.17
Genome_build: susScr11,bosTau9
Supplementary_files_format_and_content: bam file, aligned reads generated by data processing steps
Supplementary_files_format_and_content: bed file, peak calls using Macs 2.1.1 -q 0.05 --broad

organism: Sus scrofa

source_name: Spleen

extract_protocol:
Cryopreserved nuclei prepared from fresh tissue were slowly thawed on ice, centrifuged for 5 minutes at 500 rcf, and resuspended in cold PBS. Nuclei were then washed once with cold ATAC-seq cell lysis buffer and resuspended with cold PBS for counting on a hemocytometer. Approximately 200K cryopreserved nuclei were centrifuged, supernatant aspirated, then treated with 50μl transposition mix (25μl TD buffer,2.5 μl TDE1, 22.5 μl ddH2O) for 1 hour at 37°C and 300 rpm. DNA was purified using the MinElute PCR purification kit (Qiagen, #28004, Germantown, MD) and diluted with 10μl EB buffer. DNA was amplified with primers whose detailed descriptions are found in Buenrostro et al. (2013).
Libraries were purified using the MinElute PCR purification kit and run on Agilent Bioanalyzer (Agilent, Santa Clara, CA) for quality traces. Size-selection on libraries for 150-250bp fragments was performed on PippinHT system (Sage Science, Beverly, MA). Libraries were sequenced on Illumina’s NextSeq with PE 40bp reads.

value: spleen


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B5_ad007


title: PER117 DMSO Rep1 RNA-seq

data_processing:
RNA sequencing reads were aligned to GRCh38 using STAR (version 2.4.2a)42 and quantified on Gencode v24.
Normalization of counts was done using DESeq2.
Genome_build: hg38

source_name: T-ALL cell line PER-117

growth_protocol: Cell lines were cultured in RPMI-1640 medium supplemented with 10 or 20% fetal calf serum, 100 U/ml penicillin, 100 µg/ml streptomycin, and 2 mM L-glutamine at 37°C with 5% CO2.

extract_protocol:
RNA extraction was performed using the miRNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep FWD kit (Lexogen)

treatment_protocol: Cell lines were treated with 1μM Decitabine or DMSO control for 48h

tag: cell line

value: DMSO

value: T-ALL cell line


title: ATAC-seq from UC Davis FAANG pig spleen rep P348


title: FN049.3: Genomic DNA from sperm of control individual FN049 (final)

description: Purified sperm sample

source_name: Semen sample 32


title: PER117 DMSO Rep3 RNA-seq

tag: treatment


title: PER117 Decitabine Rep3 RNA-seq

value: Decitabine


title: FN045.3: Genomic DNA from sperm of nut-fed individual FN045 (final)

description: Purified sperm sample

source_name: Semen sample 30

value: Male


title: ATAC-seq from UC Davis FAANG pig skeletal muscle rep P350

source_name: Muscle

value: skeletal muscle


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B5_ad002


title: PER117 Decitabine Rep2 RNA-seq


title: FN043.0: Genomic DNA from sperm of nut-fed individual FN043 (baseline)

description: Purified sperm sample

source_name: Semen sample 27

value: Sperm

value: Baseline


title: FN049.0: Genomic DNA from sperm of control individual FN049 (baseline)

description: Purified sperm sample

source_name: Semen sample 31


title: PER117_DMSO_2 RNA-seq


title: ATAC-seq from UC Davis FAANG pig skeletal muscle rep P348


title: FN055.3: Genomic DNA from sperm of nut-fed individual FN055 (final)

description: Purified sperm sample

source_name: Semen sample 38


title: PER117 Decitabine Rep1 RNA-seq


title: FN041.0: Genomic DNA from sperm of nut-fed individual FN041 (baseline)

description: Purified sperm sample

source_name: Semen sample 25


title: ATAC-seq from UC Davis FAANG pig lung rep P350

source_name: Lung

value: lung


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B4_ad008

source_name: C57BL/6J Male P56 Mouse Brain


title: Loucy DMSO Rep3 RNA-seq

source_name: T-ALL cell line Loucy

value: Loucy


title: FN041.3: Genomic DNA from sperm of nut-fed individual FN041 (final)

description: Purified sperm sample

source_name: Semen sample 26


title: ATAC-seq from UC Davis FAANG pig lung rep P348


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B4_ad007


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B4_ad010


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B5_ad012


title: FN043.3: Genomic DNA from sperm of nut-fed individual FN043 (final)

description: Purified sperm sample

source_name: Semen sample 28


title: ATAC-seq from UC Davis FAANG pig liver rep P350

source_name: Liver

value: liver


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B4_ad004


title: FN035.3: Genomic DNA from sperm of control individual FN035 (final)

description: Purified sperm sample

source_name: Semen sample 24


title: Loucy DMSO Rep1 RNA-seq


title: FN034.3: Genomic DNA from sperm of nut-fed individual FN034 (final)

description: Purified sperm sample

source_name: Semen sample 22


title: ATAC-seq from UC Davis FAANG pig liver rep P348


title: FN045.0: Genomic DNA from sperm of nut-fed individual FN045 (baseline)

description: Purified sperm sample

source_name: Semen sample 29


title: ATAC-seq from UC Davis FAANG pig hypothalamus rep P350

source_name: Hypothalamus

value: hypothalamus


title: Loucy DAC Rep2 RNA-seq


title: Loucy DAC Rep3 RNA-seq


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B5_ad004


title: ATAC-seq from UC Davis FAANG pig hypothalamus rep P348


title: FN053.0: Genomic DNA from sperm of nut-fed individual FN053 (baseline)

description: Purified sperm sample

source_name: Semen sample 33


title: FN035.0: Genomic DNA from sperm of control individual FN035 (baseline)

description: Purified sperm sample

source_name: Semen sample 23


title: FN034.0: Genomic DNA from sperm of nut-fed individual FN034 (baseline)

description: Purified sperm sample

source_name: Semen sample 21


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad012


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad010


title: FN031.3: Genomic DNA from sperm of control individual FN031 (final)

description: Purified sperm sample

source_name: Semen sample 20


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad008


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad006


title: ATAC-seq from UC Davis FAANG pig cerebral cortex rep P350

source_name: Cortex

value: cerebral cortex


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad007

value: LSX


title: ATAC-seq from UC Davis FAANG pig cerebellum rep P350

source_name: Cerebellum

value: cerebellum


title: Loucy DMSO Rep2 RNA-seq


title: ATAC-seq from UC Davis FAANG pig cerebral cortex rep P348


title: Molt16 DMSO Rep2 RNA-seq

source_name: T-ALL cell line MOLT-16


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad004

value: male


title: Molt16 DMSO Rep1 RNA-seq


title: FN028.0: Genomic DNA from sperm of control individual FN028 (baseline)

description: Purified sperm sample

source_name: Semen sample 15


title: ATAC-seq from UC Davis FAANG pig cerebellum rep P348


title: CEMBA181204_4G_1_CEMBA181204_4G_2_B3_ad002

source_name: C57BL/6J Male P56 Mouse Brain


title: FN030.3: Genomic DNA from sperm of nut-fed individual FN030 (final)

description: Purified sperm sample

source_name: Semen sample 18

value: Final


title: Molt16 DAC Rep3 RNA-seq


title: FN031.0: Genomic DNA from sperm of control individual FN031 (baseline)

description: Purified sperm sample

source_name: Semen sample 19


title: ATAC-seq from UC Davis FAANG pig adipose rep P350

source_name: Adipose

value: adipose


title: Molt16 DAC Rep2 RNA-seq


title: ATAC-seq from UC Davis FAANG pig adipose rep P348


title: FN028.3: Genomic DNA from sperm of control individual FN028 (final)

description: Purified sperm sample

source_name: Semen sample 16