title: Control ECFCs replicate 4

city: Boston

first: Joyce

last: Bischoff

state: MA

address: One Blackfan Circle

institute: Boston Children's Hospital

library_source: transcriptomic

data_processing:
The raw reads were mapped onto the human genome (version hg19) using STAR (version 2.7.3a).
Next, differentially expressed genes were detected by Cuffdiff (version 2.2.1).
Gene expression levels were normalized using FPKM (fragments per kilobase of transcript per million fragments mapped) by Cuffdiff with the parameter --library-norm-method classic-fpkm.
Assembly: hg19
Supplementary files format and content: Excel file containing FPKM values, log2 fold change and P-values of all the genes.

molecule: total RNA

organism: Homo sapiens

source_name: umbilical cord blood

growth_protocol: Human umbilical cord blood-derived ECFC were isolated as described and expanded in culture by plating on fibronectin (0.1 μg/cm2)-coated tissue culture dishes at a density of 15,000 - 20,000 cells/cm2 in Endothelial Cell Growth Medium-2 (Lonza) which consists of Endothelial Cell Growth Basal Medium-2 (EBM-2), SingleQuot supplements (all except hydrocortisone and GA-1000), 20% heat-inactivated fetal bovine serum (FBS, Hyclone) and 1X glutamine-penicillin-streptomycin solution (GPS, ThermoFisher).

extract_protocol:
Total cellular RNA was extracted from ECFC-control and ECFC-CD45 with a RNeasy Micro extraction kit (Qiagen, Valencia, CA).
RNA libraries were prepared using a NEBNExt Ultra II directional RNA library prep kit.

treatment_protocol: The endogenous CD45 promoter in ECFCs was activated using a CRISPR/inactive Cas9 synergistic activation mediator (SAM) transcriptional activation system, available from Santa Cruz Biotechnology (CD45 Lentiviral Activation Particles (h2) Cat# sc-400245-LAC-2) and Control Lentiviral Activation Particles Cat# sc-437282).

value: umbilical cord blood

tag: cell type

value: ECFC

tag: genotype

value: WT

tag: treatment

value: control


title: Control ECFCs replicate 5

status: Public on May 03 2023

type: SRA

country: USA

tag: tissue


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H6_ad008

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted 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
Assembly: 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
Library strategy: snmC-seq2 & 3

molecule: genomic DNA

organism: Mus musculus

source_name: brain

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

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

value: brain

tag: source

value: VTA

tag: target

value: STR

tag: Sex

value: male


title: Control ECFCs replicate 3


title: Control ECFCs replicate 2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H4_ad001

value: HY

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H2_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H2_ad002


title: Control ECFCs replicate 1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H3_ad008


title: CD45-positive ECFCs replicate 5

value: activaton of the endogenous CD45 promoter


title: CD45-positive ECFCs replicate 4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H3_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H1_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H1_ad012

value: female


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H1_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H1_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H1_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H3_ad006


title: CD45-positive ECFCs replicate 3


title: CD45-positive ECFCs replicate 1


title: CD45-positive ECFCs replicate 2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H1_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H2_ad010


title: MPO, 2hrs, Rep2

city: Mainz

first: Yulia

last: Kargapolova

state: Rheinland-Pfalz

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
fastp --in1 $col1 --in2 $col2 --detect_adapter_for_pe --html $col4/log/$col7"_fastp.html" --json $col4/log/$col7"_fastp.json" --out1 $col5/$col7"_R1_trim.fastq.gz" --out2 $col5/$col7"_R2_trim.fastq.gz" -R $col4/log/$col7"_fastp2.log" -Q --correction --trim_poly_g --length_required 10 --thread 8 &> $col4/log/$col7"_fastp.log"
bwa mem -t 6 -M -k 15 -r 1 $col3 $col5/$col7"_R1_trim.fastq.gz" $col5/$col7"_R2_trim.fastq.gz" |  samtools sort -@6 -o $col5/$col7"_sorted_all.bam" - 2> $col4/log/$col7"_bwa_sort.log"
picard-tools MarkDuplicates I=$col5/$col7"_sorted_all.bam"  O=$col4/$col7"_sorted_all_NoDup.bam"  ASSUME_SORTED=true METRICS_FILE=$col4/log/$col7"_picardMarkDup_all.txt" 2> $col4/log/$col7"_picard.log"
samtools view -@ 8 -h -q 1 -F 1024 -F 1804 -F 524 -f 2 $col4/$col7"_sorted_all_NoDup.bam" | awk '{if($3 != "chrM" && $3 !/KI27 && $3 !/GL00/){print $0}}' | samtools sort -@ 8 -O bam -o $col5/$col7_sorted_all_rmChrM.bam -
samtools sort -n -@ 16 $col4/$col7"_FINAL_sorted.bam" -o $col4/$col7"_FINAL_namesorted.bam" 2> $col4/log/$col7"_nameSort.log"
genomeCoverageBed -ibam $col4/$col7"_FINAL_sorted.bam" -pc -bg  -trackopts 'name=$col7 visibility=2 color=255,30,30' > $col4/$col7"_FINAL_sorted.bedgraph" &> $col4/log/$col7_"genomeCoverageBed.log"
bamCoverage --numberOfProcessors 16 --binSize 10 --smoothLength 25 --normalizeUsing RPGC --effectiveGenomeSize $col9 --bam $col4/$col7"_FINAL_sorted.bam" -o $col4/$col7"_FINAL_sorted.bw"
macs2 callpeak --verbose 3 -t $col4/$col7"_FINAL_sorted.bam" -n $col4/$col7"_FINAL_MACS2BAMPE" --min-length 100 --max-gap 50 -g $col8 -q 0.05 --keep-dup all --format BAMPE --call-summits 2> $col4/log/$col7"_macs2.log"
Genrich -t $col4/$col7_FINAL_sorted.bam -o $col4/$col7_FINAL_Genrich.narrow -r -e chrM -E $col6 -j -y -q 0.05 -f $col4/$col7_reUSE_Genrich.log -v 2> $col4/log/$col7_Genrich.log" >> $col4/log/$col7"_commands.log
intersectBed -v -a $col4/$col7"_FINAL_MACS2BAMPE_peaks.narrowPeak" -b $col6 > $col4/$col7"_FINAL_MACS2BAMPE_Cleanpeaks.narrowPeak"
ataqv --peak-file $col4/$col7"_FINAL_MACS2BAMPE_Cleanpeaks.narrowPeak"  --metrics-file $col4/ataqv/$col7"MACS2BAMPE.json.gz" --name $col7"Macs2" --excluded-region-file $col6 --tss-file $col10  --tss-extension 1000 --ignore-read-groups $col11 $col4/$col7"_sorted_all_NoDup.bam" > $col4/log/$col7".ataqvMac.out"
Assembly: hg38
Supplementary files format and content: narrowpeak format: A narrowPeak (.narrowPeak) file is used by the ENCODE project to provide called peaks of signal enrichement based on pooled, normalized (interpreted) data. It is a BED 6+4 format.

source_name: HUVECs

extract_protocol:
50,000 to 100,000 cells were precipitated, washed with PBS and resuspended in die-cold ATAC Lysis Buffer. Cell pellet was transfered to a PCR tube on ice, span down and, supernatant removed. Cell pellet was further resuspended in a Tagmentation buffer. After tagmentation reaction, performed for 1 hour at 37 degrees celsius, the tagmented DNA was isolated and quantified by Qubit.
ATAC-Sequencing was performed with help of Active Motif ATAC-Seq kit as per manufacturer instructions.

treatment_protocol: HUVEC cells were pre-treated with MPO for 2 or 8 hours; for control experiments media was changed accordingly.

tag: cell line

value: HUVECs

value: Human Endothelial Cells

value: wild type

value: MPO treated, 2 hours


title: MPO, 8hrs, Rep2

value: MPO treated, 8 hours


title: MPO, 8hrs, Rep1


title: MPO, 2hrs, Rep1


title: Ctr, Rep3

value: no treatment


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H12_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H12_ad008


title: Ctr, Rep1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H12_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H12_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H11_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H12_ad010


title: Ctr, Rep2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H11_ad010


title: MPO22

description: polyA-enriched total RNA-Seq

data_processing:
Sequenced reads were mapped with STAR v2.2.2a with parameters --outFilterMatchNminOverLread 0.4 --outFilterScoreMinOverLread 0.4  --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were mapped to exons were counted by htseq-count using the following parameters: minimum alignment 30
Assembly: hg19
Supplementary files format and content: raw read counts (output of htseq-count), bigWig files (strant-specific), raw fastq files.

growth_protocol: Human Umbilical Vein Endothelial Cells, pooled from several donors, were purchased from Lonza and cultured in FBS reduced Endopan 3 media. HUVEC cells of passages 5-10 were used for experiments. MPO treatment was performed with protein purified from human blood (Planta) and at 1 μg/ml final concentration.

extract_protocol:
HUVEC cells were grown until pass. 10 max in serum-reduced endothelial cell culture medium (Endopan 3). Cells were treated with Myeloperoxidase protein (MPO)  in Trizol (Life Technologies) and total RNA was isolated and DNase-treated using the Direct-zol RNA miniprep kit as per manufacturer’s instructions (Zymo Research).
polyA-enriched RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human Umbilical Vein Endothelial Cells

tag: passage

value: wt


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H11_ad008


title: MPO21

description: polyA-enriched total RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H11_ad007


title: MPO81

description: polyA-enriched total RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H11_ad002


title: MPO82

description: polyA-enriched total RNA-Seq


title: Q9It 2

description: polyA-enriched total RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H10_ad008


title: non-treated 2

description: polyA-enriched total RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H10_ad007


title: Q9It 1

description: polyA-enriched total RNA-Seq


title: non-treated 1

description: polyA-enriched total RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H10_ad001


title: MPO2h2_siRNAILF3 [S60]

description: 3'-end RNA-Seq

data_processing:
Reads were mapped to exons were counted by htseq-count using the following parameters: minimum alignment 30
Assembly: hg19
Supplementary files format and content: raw read counts (output of htseq-count), bigWig files (strand-specific), raw fastq files.

extract_protocol:
Total RNA was isolated using  Direct-Zol RNA purification kit (Zymo Research) as recommended by manufacturer.
3’-end RNA-seq was used as a lower-cost alternative to mRNA-seq. Libraries were prepared from total RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen), and paired-end sequenced on a HiSeq4000 platform (Illumina) generating ~15 × 106 100 nt-long reads per sample.

treatment_protocol: Universal negative control siRNA (Sigma) and ILF3 siRNA1 and ILF3 siRNA2 (Sigma) were used in ILF3 knockdown experiments (ILF3_1 PDSIRNA2D, Sigma, SASI_Hs01_00242960, SASI_Hs01_00242961, Mission siRNA Universal Negative Control #1, SIC001). RNAiMAX (ThermoFisher) and Opti-MEM (ThermoFisher) were used for transfection. To ensure an ideal knockdown rate, HUVECs were cultured in complete Endopan3 medium on 6-well plates (overnight), and shifted to no-antibiotic Endopan3 medium for siRNA transfection. Transfection was done according to the protocol provided by ThermoFisher. Knockdown efficiency was assessed by qPCR 24 hours and by western blot 72 hours after transfection. MPO treatment was performed 70 hours post-KD, cells were collected 74 hours post-KD for RNA isolation.


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G9_ad012


title: MPO2h1_siRNAILF3 [S59]

description: 3'-end RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G9_ad010


title: ctr3_siRNAILF3 [S58]

description: 3'-end RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H11_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G9_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G9_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G9_ad008


title: ctr2_siRNAILF3 [S57]

description: 3'-end RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_H10_ad010


title: ctr3_siRNActr [S54]

description: 3'-end RNA-Seq


title: MPO2h1_siRNActr [S55]

description: 3'-end RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G8_ad010


title: MPO2h2_siRNActr [S56]

description: 3'-end RNA-Seq


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G8_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G8_ad008


title: ctr2_siRNActr [S53]

description: 3'-end RNA-Seq


title: ctr1_siRNActr [S52]

description: 3'-end RNA-Seq


title: DD

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
Quality-controlled reads were aligned to the reference genome GRCh37.EBVB95-8wt.ERCC using the HISAT aligner
Alignments were counted for each gene using featureCounts package
Filtered trimmed mean of M values (TMM) normalised counts per million (cpm) (EdgeR, filtering out genes less than two gene counts in at least half of the samples) were used for downstream analyses
Supplementary_files_format_and_content: gene_expression_matrix_cpm.csv

source_name: PBMC

growth_protocol: PBMCs (7.5x105 cells per well, in duplicates) were incubated for 24 hours with media (control) or culprit drug before RNA harvesting for transcriptomic analysis.

extract_protocol:
PBMCs were harvested, washed and suspended in RTL lysing buffer (Qiagen, UK) and stored at − 20 °C. Each sample was thawed directly before RNA isolation and whole transcriptome RNA-sequencing. RNA extraction and purification was performed according to manufacturer’s protocol (RNeasy Plus Mini Kit, Qiagen, UK). gDNA Eliminator spin column was used to eliminate DNA contamination in the collected RNA.
Total RNA samples were subjected to indexed cDNA library construction, using the Illumina TruSeq poly(A) + RNA-Seq library construction, according to the manufacturer’s instructions.

tag: group

value: drug

tag: donor

tag: agent

value: dapsone


title: DM

value: control


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G8_ad002

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad012

value: VTA

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad008

value: male


title: VV

value: vancomycin


title: VM


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad007


title: TT

value: teicoplanin


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad004

value: HY

value: MY

value: female


title: C2M


title: TM


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad002


title: C1M


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G7_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G6_ad002


title: whole zebrafish, kif7co63/co63 scoliotic, 6wpf, 3

city: Aurora

first: Nancy

last: Hadley Miller

state: Colorado

department: Orthopedics

description:
Sample column in processed data file:
K7_6w_C3

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Novel Gene Prediction: The Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare can compare Strintie assemblies to reference annotation files and help sort out new genes from known ones.
Quantification: Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential Expression Analysis: Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCz11
Supplementary files format and content: Microsoft Excel Binary File format files with FPKM values for each sample comparing two different conditions
Supplementary files format and content: Tab-delimited .txt readcounts file and FPKMs file.

organism: Danio rerio

source_name: whole zebrafish

growth_protocol: Zebrafish (Danio rerio) were housed at the University of Colorado Anschutz Medical Campus aquatic facility. Husbandry and experimental protocols were approved under the Institutional Animal Care and Use Committee Protocol #00370. Animals were maintained in a 14 hour light/10 hour dark cycle at 28.5 °C.

extract_protocol:
At 4 days past fertilization (dpf), 20 embryos per tube were euthanized and pooled in 1 ml of RNA lysis buffer (Zymo). Embryos were lysed using a VWR Bead Mill Homogenizer with Lysing Matrix A beads (MP Biomedicals). Samples were iced for 5 minutes, lysed for 45 seconds, then iced again for 5 minutes. This process was completed three times to ensure maximal lysis. The same protocol was used to extract RNA for 6 wpf zebrafish, but 1 fish was used per tube. RNA was extracted using the QuickRNA Miniprep (Zymo) using the on-column DNase digestion protocol.
Library construction was done by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using
random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: whole zebrafish

tag: phenotype

value: scoliotic

tag: time

value: 6 weeks post fertilization


title: whole zebrafish, kif7co63/co63 non-scoliotic, 6wpf, 3

institute: University of Colorado Anschutz Medical Campus

description:
Sample column in processed data file:
K7_6w_S3

value: non-scoliotic


title: C1C

value: cefoxitin


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G5_ad012


title: whole zebrafish, kif7co63/co63 scoliotic, 6wpf, 2

description:
Sample column in processed data file:
K7_6w_C2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G6_ad008


title: whole zebrafish, kif7co63/co63 scoliotic, 6wpf, 1

description:
Sample column in processed data file:
K7_6w_C1


title: whole zebrafish, kif7co63/+ , 6wpf, 2

description:
Sample column in processed data file:
H_6w_2


title: whole zebrafish, kif7co63/+ , 6wpf, 3

description:
Sample column in processed data file:
H_6w_3


title: whole zebrafish, kif7co63/co63 non-scoliotic, 6wpf, 1

description:
Sample column in processed data file:
K7_6w_S1


title: whole zebrafish, kif7co63/co63 non-scoliotic, 6wpf, 2

description:
Sample column in processed data file:
K7_6w_S2


title: whole zebrafish, kif7co63/+ , 6wpf, 1

description:
Sample column in processed data file:
H_6w_1


title: whole zebrafish, wild-type, 6wpf, 3

description:
Sample column in processed data file:
AB_6w_3

value: wild-type


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G5_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G5_ad008


title: whole zebrafish, wild-type, 6wpf, 2

description:
Sample column in processed data file:
AB_6w_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G4_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G4_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G4_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G5_ad007


title: whole zebrafish, wild-type, 6wpf, 1

description:
Sample column in processed data file:
AB_6w_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G6_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G4_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad008


title: whole zebrafish pooled, kif7co63/co63 , 4dpf, 2

description:
Sample column in processed data file:
K7_4d_3

source_name: whole zebrafish pooled

value: whole zebrafish pooled

value: 4 days post fertilization


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G8_ad007

value: brain


title: C2C

value: drug


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad010

value: VTA

value: STR


title: whole zebrafish pooled, kif7co63/+ , 4dpf, 2

description:
Sample column in processed data file:
H_4d_4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad004


title: whole zebrafish pooled, kif7co63/+ , 4dpf, 1

description:
Sample column in processed data file:
H_4d_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad006


title: whole zebrafish pooled, kif7co63/co63 , 4dpf, 1

description:
Sample column in processed data file:
K7_4d_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad002

value: male


title: Lar1HC 2

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

country: China

institute: Zhejiang University

description: Replicate 2 of library Lar1HC

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Data for the wild type (WT) were extracted from GSE218933. Screening differentially expressed genes was conducted between the paired library (Lar1MC/WTMC; Lar1HC/WTHC). FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Assembly: Beauveria bassiana
Supplementary files format and content: Excel files, including Gene ID, annotation, FPKM values, log2(fold change), P-value, and FDR-value for the paired sample.

organism: Beauveria bassiana

growth_protocol: On the bassi of Czapek-Dox broth, the carbon and nitrogen sources are replaced with trehalose and peptone, respectively, and resultant medium is named as TPB medium. Conidia suspension (100 ul,5X10^6 conidia ml-1) of the indicated strain were inoculated in TPB included with  linoleic acids. Linoleic concentrations are set at 0.05 (MC) and 0.1% (HC). The inoculated medium was incubated at 25 °C for 3 day.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia were harvested from culture media

tag: strain

tag: time point

value: 3 days

tag: concentration

value: Linoleic concentrations are set at 0.1% (HC)

value: mycelia


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad012

value: female


title: whole zebrafish pooled, wild-type, 4dpf, 2

description:
Sample column in processed data file:
AB_4d_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad010


title: whole zebrafish pooled, wild-type, 4dpf, 1

description:
Sample column in processed data file:
AB_4d_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad008


title: Lar1HC 1

description: Replicate 1 of library Lar1HC


title: Lar1MC 2

description: Replicate 2 of library Lar1MC

value: Linoleic concentrations are set at 0.05


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad006

value: HY

value: MY


title: WTHC rep 2

description:
Replicate 2 of library WTHC
WTCK-WTHC.xls

data_processing:
Illumina Hiseq X Ten used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana with the precision of no more than two nucleotide mismatch.
All mapped genes were quantified in terms of the expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) with Cufflinks software.
Screening differentially expressed genes in paired library (WTCK/WTLC; WTCK/WTMC; WTCK/WTHC). FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Assembly: Beauveria bassiana
Supplementary files format and content: Excel files, including Gene ID, annotation, FPKM values, log2(fold change), P-value, and FDR-value for the paired sample.

source_name: Wild type

growth_protocol: On the bassi of Czapek-Dox broth, the carbon and nitrogen sources are replaced with trehalose and peptone, respectively, and resultant medium is named TPB medium. Conidia suspension (100 ul,5X10^6 conidia ml-1) of B. bassiana were inoculated in TPB included with  linoleic acids. Linoleic concentrations are set at 0 (CK), 0.005 (LC), 0.05 (MC), and 0.1% (HC). The inoculated medium was incubated at 25 °C for 3 day.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates and leaves.

tag: linoleic acid conc


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G2_ad002


title: WTHC rep 1

description:
Replicate 1 of library WTHC
WTCK-WTHC.xls


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad012


title: Lar1MC 1

description: Replicate 1 of library Lar1MC


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G3_ad007


title: WTMC rep 2

description:
Replicate 2 of library WTMC
WTCK-WTMC.xls


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad008


title: WTMC rep 1

description:
Replicate 1 of library WTMC
WTCK-WTMC.xls


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad007


title: WTCK rep 2

description:
Replicate 2 of library WTCK
WTCK-WTLC.xls; WTCK-WTMC.xls;WTCK-WTHC.xls


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad004


title: WTLC rep 1

description:
Replicate 1 of library WTLC
WTCK-WTLC.xls


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad002


title: WTLC rep 2

description:
Replicate 2 of library WTLC
WTCK-WTLC.xls


title: WTCK rep 1

description:
Replicate 1 of library WTCK
WTCK-WTLC.xls; WTCK-WTMC.xls;WTCK-WTHC.xls


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad006


title: Subcutaneous fat GFP_REP4

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

data_processing:
Alignment was performed using HISAT2 against genome build GRCm38
Quantification and differential expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: feature counts were generated using DESeq2

source_name: subcutaneous fat

extract_protocol:
Upon sacrifice, tissues were instantly frozen in liquid nitrogen. Frozen tissues were homogenized in QIAzol, and following chloroform phase separation RNA was prepared from the pink phase using Qiagen miRNeasy kits as per original protocol. Total RNA quality was validated with BioAnalyzer (all samples had eRIN >8.2).
RNA libraries were prepared using KAPA Stranded mRNA-Seq Kit.

tag: aav

value: GFP


title: Subcutaneous fat LCN_REP3


title: Subcutaneous fat LCN_REP1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad004


title: Subcutaneous fat LCN_REP2


title: Subcutaneous fat LCN_REP4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad007


title: Subcutaneous fat GFP_REP3


title: Subcutaneous fat GFP_REP2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G12_ad002


title: 1091-B6C3-M42-P14-M-CB

city: Seattle

first: Christopher

middle: H

last: Seward

state: WA

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute

data_processing:
Raw reads were demultiplexed by Genewiz
STAR v2.7.5a was used to map paired end reads (mm10/GRCm38 genome and Ensembl v102 annotation) and quantify gene expression
Read counts were tabulated with STAR and differential expression was determined using EdgeR v3.12
Genome_build: mm10/GRCm38 genome and Ensembl v102 annotation
Supplementary_files_format_and_content: STAR feature count tables containing the ensemble ID, total read count for each ID, forward read count for each ID, and reverse read count for each ID

source_name: Cerebellum tissue of brain

growth_protocol: Galnt17 knockout (KO) heterozygous (Galnt17-/+) mouse sperm samples were purchased from the Knockout Mouse Project (KOMP) repository ((http://velocigene.com/komp/detail/16112); official allele name Galnt17tm1.1(KOMP)Vlcg), and used to generate Galnt17 KO mice at the University of Illinois Transgenic mouse facility by in vitro fertilization of C57BL/6J females. The resulting Galnt17-/+ animals were then interbred to obtain Galnt17 KO homozygous (Galnt17-/-) pups. Since homozygous pups were not born live on the C57BL/6 background, we bred the mice to C57BL/6J X C3H/He F1 (B6C3) F1 hybrid animals and obtained live, healthy pups and fertile adults.

extract_protocol:
CB tissues were collected from P14 B6C3 WT and Wbscr17-/-, and RNA was purified using Trizol followed by 45 min of RNase-free DNase I treatment (NEB) and RNA Clean & Concentrator Kit (Zymo Research). The quality of RNA was tested by Agilent BioAnalyzer and Qubit
RNA-seq libraries were generated using Illumina TruSeq RNA Library Prep Kits. Samples were sequenced as 150 bp paired end reads (≥ 23 million read pairs per sample) on Illumina Hi-Seq 4000 sequencer through the GENEWIZ sequencing service

tag: age

value: Male

value: Cerebellum tissue of brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G11_ad012

tag: tissue


title: Subcutaneous fat GFP_REP1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G11_ad010

tag: source


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G11_ad007

tag: target


title: 1090-B6C3-M41-P14-M-CB

tag: Sex


title: 1023-Wbscr17KOKO-H40-P14-M-CB


title: 1089-B6C3-M39-P14-M-CB


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G11_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G11_ad004


title: 1022-Wbscr17KOKO-H39-P14-M-CB


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad012


title: ATAC Smad4 KO Day2 rep2

city: Berlin

first: Pavel

last: Tsaytler

address: Ihnestrasse  63-73

institute: MPI Molecular Genetics

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Smad4_KO_Day2_rep1and2.bw

data_processing:
For RNA-Seq, reads were subjected to quality control using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed using cutadapt (version 2.9) (Martin, https://doi.org/10.14806/ej.17.1.200) to remove adapter sequences. Alignment was performed using Hisat2 (version 2.1.0) (Kim, 2019) with the following arguments: --no-mixed --no-discordant. The index files for Hisat2 were built using mm10 reference genome containing chromosomes 1-19, X, Y and M, and splice sites and exon data from refSeq annotations. The resulting sam format files were then converted to bam format, sorted and indexed using samtools (version 1.9) (Li, 2009). FPKM values were calculated using Cuffdiff (version 2.2.1) (Trapnell, 2010) with the following arguments: -u -no-effective-length-correction -b.
For ChIP-Seq, reads were trimmed to 50 bp length. The trimmed reads were aligned to the reference genome using bowtie2 (version 2.2.4) (Langmead, 2012) with the following arguments: -3 5 -I 100 -X 500 --no-discordant --no-mixed. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. For visualization, the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing CPM --extendReads 200 --smoothLength 9 -bs 3 -ignore chrM.
For ATAC-Seq, reads were trimmed to 40 bp length and adapter sequences were removed using cutadapt. The trimmed reads were aligned to the reference genome using bowtie (version 1.1.2) (Langmead, 2009) with the following arguments: -y -v 2 --best --strata -m 3 -k 1 -S -X 2000 --allow-contain. Sam files containing mapped paired-end reads were converted to bam files, sorted and indexed using samtools. Reads mapped to chr M and Y or known ATAC artifact regions (ENCODE) were removed using samtools. Possible PCR duplicates were removed using Picard (version 1.103, https://broadinstitute.github.io/picard). For visualization, the reads from biological replicates were combined, and the data were normalized and converted to bigWig format using bamCoverage tool from deepTools with the following arguments: --normalizeUsing RPCG --effectiveGenomeSize 2652783500 --extendReads 200 --smoothLength 9 -bs 3 -ignore chrY chrM.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files representing density for ATAC-Seq and ChIP-Seq
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each RNA-Seq sample for refseq genes

source_name: in vitro differentiated ES cells

growth_protocol: ES cells were deprived of feeder cells and cultured for 24 hours. Cells were then dissociated, and 40,000 cell/ml cell suspension was plated onto tissue culture plates in 5 µl droplets. Plates were then inverted and incubated for 24 hours. Drops containing mES cell aggregates (corresponding to differentiation day 0, or ES) were then pooled and resuspended in differentiation medium: 48% (v/v) DMEM/F12 (ThermoFisher; 11320033), 48% (v/v) Neurobasal medium (ThermoFisher; 21103049), 1% (v/v) 200 mM L-glutamine (Lonza; BE17-605E), 1% (v/v) penicillin and streptomycin, 1% (v/v) B27 (Gibco; 17504044), 0.5% (v/v) N2 (Gibco; 17502048), 0,5% (v/v) 7.5% BSA fraction V (Gibco; 15260037), 0.1 mM thioglycerol (Sigma-Aldrich; M1753) supplemented with 20 ng/ml mouse recombinant Bmp4 (R&D Systems; 5020-BP-010). To start differentiation, mESC aggregates resuspended in differentiation medium containing Bmp4 were immediately plated on plates pre-coated with fibronectin (Calbiochem; 341631). Differentiation medium supplemented with Bmp4 was refreshed every 24 hours.

extract_protocol:
The cells were lysed in 50 μl of cold lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuged at 500g, 4°C for 10 min. The pellet was resuspended in the transposition reaction mix (25 μl 2x TD buffer, 2.5 μl Tn5 transposase, 22.5 μl H2O) and incubated at 37°C for 30 minutes. After incubation, the reaction was stopped with the addition of PB buffer (Qiagen) and the tagmented DNA was purified using the MinElute kit (Qiagen).
The DNA was combined with the ATAC index PCR primers and 2x Kapa HiFi Hotstart Ready Mix and pre-amplified (98°C 30 seconds, 5x [98°C 10 seconds, 63°C 30 seconds, 72°C 1 minute] in a 50 μl volume. To determine the remaining cycles to avoid potential over-amplification, 5 μl of the pre-amplification mix was combined with the primers, 1x Evagreen SYBR green (Jena Biosciences) and 2x Kapa HiFi Hotstart Ready Mix in a 15 μl total volume and run for 30 cycles on a StepOne Plus. The remaining 45 μl of pre-amplified samples were amplified for a further 6-7 cycles and the libraries were purified using MinElute column (Qiagen). The libraries were quantified using the Qubit DNA HS assay and the library sizes were validated using DNA HS Bioanalyzer chips.

treatment_protocol: The cells were trypsinized, and the trypsin was inactivated by washing with cold PBS containing 2% BSA. For each sample, 50,000 cells were collected, washed with 1 ml cold PBS and pelleted by centrifugation.

tag: differentiation stage

value: Day 2


title: ATAC Smad4 KO Day2 rep1


title: ATAC Smad4 KO Day1 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Smad4_KO_Day1_rep1and2.bw

value: Day 1


title: ATAC Smad4 KO Day1 rep1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad002

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad004


title: ATAC Smad4 WT Day1 rep1

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Smad4_WT_Day1_rep1and2.bw


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G1_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad001


title: ATAC Smad4 WT Day2 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Smad4_WT_Day2_rep1and2.bw


title: ATAC Smad4 WT Day2 rep1


title: ATAC Eomes T dKO Day3 rep1

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Eomes_T_dKO_Day3_rep1and2.bw

value: Day 3


title: ATAC Eomes T dKO Day3 rep2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F9_ad012

value: VTA


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F9_ad010

value: STR


title: 1021-Wbscr17KOKO-H38-P14-M-CB


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G11_ad001

value: male


title: ATAC Smad4 WT Day1 rep2


title: ATAC Eomes T dKO Day2 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Eomes_T_dKO_Day2_rep1and2.bw


title: ATAC Eomes T dKO Day2 rep1


title: ATAC T KO Day3 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_T_KO_Day3_rep1and2.bw


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F9_ad008


title: ATAC T KO Day3 rep1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_G10_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F9_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F9_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F9_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F8_ad012


title: ATAC Eomes KO Day2 rep2

description:
in vitro differentiated cardiac mesoderm progenitors
ATAC_Eomes_KO_Day2_rep1and2.bw


title: ATAC Eomes KO Day2 rep1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F8_ad008


title: prp2_C

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 453 Biotech

institute: Cornell University

data_processing:
Sequenced reads were trimmed of adapter sequence with fastp (version 0.19.5) with parameters --adapter_sequence CTGTCTCTTATACACATCT --adapter_sequence_r2 CTGTCTCTTATACACATCT
Trimmed reads were aligned with hisat2 (version 2.2.1) with parameters --max-intronlen 2000 --no-unal
Aligned reads were filtered of low quality mappings with samtools view (version 1.6) with parameters -q 5
premature and mature reads were counted using custom scripts (available at github.com/zdwyer)
Sequenced reads were downsampled using custom scripts (available at github.com/zdwyer)
Genome_build: R64-2.1 (SGD)
Supplementary_files_format_and_content: tab-delimitted text files include intron (Gene;IntronNo), Mature counts, Premature Counts for each sample and replicate

organism: Saccharomyces cerevisiae

source_name: Culture

growth_protocol: Single colonies were inoculated into liquid YPD media and grown overnight at 25℃ with shaking at 200rpm. Overnight cultures were then inoculated into fresh liquid YPD, seeding cultures at OD600 =0.05 and grown to mid-log phase (OD600 =.8)

extract_protocol:
Temperature shifted cells were collected via vacuum filtration, flash frozen in liquid nitrogen, and pellets were stored at -80˚C. RNA was extracted using Phenol:Chloroform extraction as presented in Xu et al. Nature Methods 2019
Libraries were prepared using MPE-seq as presented in Xu et al. Nature Methods 2019 using 10ug RNA input

treatment_protocol: Cells were shifted to 37˚C with shaking at 200 rpm for 15 minutes.

tag: genotype


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F8_ad007


title: prp2_B


title: prp2_A


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F7_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F7_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F6_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F7_ad012


title: WT_B

value: WT


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F6_ad010


title: WT_A


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F6_ad008


title: CAFs siPostn4

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

description: Treatment Postn #4

data_processing: Bulk RNAseq analysis: On average we received 30 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.

source_name: Primary human breast cancer-associated fibroblasts (CAFs)

growth_protocol: Primary human breast CAFs were cultured on 0.5% gelatin-coated plates and maintained in HG-DMEM supplemented with 20% fetal bovine serum (FBS), 10 ng/mL bFGF, Plasmocin, and antibiotics/antimycotics in humidified atmosphere with 5% CO2 and 20% O2 at 37C.

extract_protocol:
Fibroblasts were extracted for bulk RNA sequencing.
Library was constructed at UVA Genome Analysis and Technology Core.

treatment_protocol: Primary human breast CAFs were treated with 75 nm human periostin-targeting stealth siRNA (si-POSTN) (ThermoFisher siRNA ID: HSS116400) or 75 nm non-targeting scramble control siRNA (si-Control) (DHARMACON D-001810-02-05) for 5 hours, then media was replaced. This siRNA transfection was repeated the next day, and fibroblasts were harvested 24-hours following the second siRNA transfection.

tag: cell type

tag: treatment

value: si-POSTN


title: CAFs siPostn2

description: Treatment Postn #2

value: Primary human breast cancer-associated fibroblasts (CAFs)


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F5_ad012

value: female


title: CAFs siPostn1

description: Treatment Postn #1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F6_ad007


title: CAFs siCon4

description: Control #4

value: si-Control


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F5_ad010


title: CAFs siCon2

description: Control #2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F5_ad004

value: HY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F5_ad007


title: CAFs siCon1

description: Control #1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F8_ad002

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad010


title: HCT116 cells, tunicamycin, 24h, biol rep 3 [TN3]

city: Daejeon

first: Doyeong

last: Ku

address: Daehak-ro, 291

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
gene_count_matrix_TN.csv
results_TN.csv
TN3

data_processing:
Read counts were normalized by DESeq2 analysis.
Read counts of 3 replicates were compared against 3 replicates with the control group.
DEG gene list was ordered by the lowest adjusted p-values.
Supplementary files format and content: cvs
Supplementary files format and content: gene count, Differentially expressed gene analysis

growth_protocol: HCT116 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
TRIzol (Ambion) was added directly to the cell pellet obtained after centrifugation at 10,000 g for 30 sec. After precipitation of the extracted nucleic acids, DNase I (TaKaRa) was treated to remove DNA, and purified RNA was reverse transcribed using RevertAid reverse transcriptase
RNA libraries for RNA-seq were prepared using STruSeq Stranded Total RNA LT Sample Prep Kit (Gold) following TruSeq Stranded Total RNA Sample Prep Guide, Part #  15031048 Rev. E

treatment_protocol: In HCT116 cells, 5 µg/ml of OA or TN was treated for 24h in RPMI1640 media supplemented with 10% FBS. DMSO was used as control treatment.

tag: cell line

value: human colon cancer cell

value: tunicamycin


title: WT_C


title: HCT116 cells, tunicamycin, 24h, biol rep 2 [TN2]

description:
gene_count_matrix_TN.csv
results_TN.csv
TN2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad004


title: CAFs siPostn3

description: Treatment Postn #3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad002


title: HCT116 cells, DMSO, 24h, biol rep 2 [TNctrl2]

description:
gene_count_matrix_TN.csv
results_TN.csv
TNctrl2

value: DMSO


title: HCT116 cells, DMSO, 24h, biol rep 1 [TNctrl1]

description:
gene_count_matrix_TN.csv
results_TN.csv
TNctrl1


title: HCT116 cells, oligomycin A, 24h, biol rep 3 [OA3]

description:
gene_count_matrix_OA.csv
results_OA.csv
OA3

value: oligomycin A


title: HCT116 cells, oligomycin A, 24h, biol rep 1 [OA1]

description:
gene_count_matrix_OA.csv
results_OA.csv
OA1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F3_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F3_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F3_ad012


title: HCT116 cells, DMSO, 24h, biol rep 3 [OActrl3]

description:
gene_count_matrix_OA.csv
results_OA.csv
OActrl3


title: HCT116 cells, oligomycin A, 24h, biol rep 2 [OA2]

description:
gene_count_matrix_OA.csv
results_OA.csv
OA2


title: CAFs siCon3

description: Control #3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F3_ad004


title: HCT116 cells, DMSO, 24h, biol rep 2 [OActrl2]

description:
gene_count_matrix_OA.csv
results_OA.csv
OActrl2


title: HCT116 cells, DMSO, 24h, biol rep 1 [OActrl1]

description:
gene_count_matrix_OA.csv
results_OA.csv
OActrl1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F4_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F2_ad012


title: HCT116 cells, tunicamycin, 24h, biol rep 1 [TN1]

description:
gene_count_matrix_TN.csv
results_TN.csv
TN1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F2_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F2_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F3_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F3_ad007


title: HCT116 cells, DMSO, 24h, biol rep 3 [TNctrl3]

description:
gene_count_matrix_TN.csv
results_TN.csv
TNctrl3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F2_ad010


title: LuCaP_93_WGBS

first: Brian

last: Hanratty

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

data_processing:
Reads were trimmed with Trim Galore 0.6.6
Trimmed reads were aligned to UCSC hg19 and methylation at each base called with Bismark 0.23.0
Methylation call files were subsetted to bedGraph format and then converted to bigWig with UCSC bedGraphToBigWig
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Prostate cancer patient derived xenograft

growth_protocol: subcutaneous patient derived xenograft as detailed in PMID: 28156002

extract_protocol:
As detailed in PMID: 34312180
TruSeq
Paired-end

value: LuCaP 93


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F2_ad001

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F2_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F1_ad012


title: LuCaP_77_WGBS

value: Prostate cancer patient derived xenograft

value: LuCaP 77


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F1_ad008

value: VTA

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F1_ad001

value: male


title: 8HQ/FAC-3

city: Beijing

first: Anjian

last: Xu

address: No. 95 Yong'an road, Xicheng District, Beijing

institute: Capital medical university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
genome build mm9
tab-delimited text files include FPKM values for each Sample

source_name: 8HQ/FAC treated HepG2 cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2 cells were treated with 10uM DMSO, 8HQ, FAC or 8HQ/FAC for 6 hours.

tag: agent

value: liver


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F1_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F1_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad012


title: 8HQ-2

source_name: 8HQ treated HepG2 cells


title: LuCaP_78_WGBS

value: LuCaP 78


title: 8HQ-3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad008


title: C-2

source_name: DMSO treated HepG2 cells


title: 8HQ/FAC-1


title: 8HQ/FAC-2


title: 8HQ-1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad010

value: female


title: FAC-1

source_name: FAC treated HepG2 cells

value: FAC


title: FAC-2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F1_ad002

value: HY


title: C-3


title: FAC-3


title: C-1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad006

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F12_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad010


title: ZAP1_d2_600_1

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
Library strategy: ChEC-seq
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
paired end alignment to S288C_R64 with bowtie2 (-p8 --local --very-sensitive --trim-to 30 --dovetail)
genome coverage with bedtools (-5 -fs 1 -d)
Assembly: GCA_000146045.2 (R64)
Supplementary files format and content: *.out.gz file contains zipped genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria)

source_name: budding yeast culture at OD=4

growth_protocol: Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD4 in SC medium with glucose

extract_protocol:
Phenol chlorofrom extraction
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. 2015

tag: genetic information

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ZAP1 Δ2 600 SV40 NLS MNase

tag: tagged tf

tag: variant-type

value: DBD


title: ZAP1_d2_500_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ZAP1 Δ2 500 SV40 NLS MNase

value: Truncation


title: ZAP1_d2_500_2


title: ZAP1_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ZAP1 Δ2 200 SV40 NLS MNase


title: ZAP1_d2_500_1


title: ZAP1_d2_500_4


title: ZAP1_d2_600_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E9_ad010

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted 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
Assembly: 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
Library strategy: snmC-seq2 & 3

source_name: brain

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad006


title: ZAP1_d2_200_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad001


title: ZAP1_d2_300_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ZAP1 Δ2 300 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E9_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E9_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F10_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F11_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F10_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F10_ad001


title: TYE7_d2_150_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TYE7 Δ2 150 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F10_ad007

value: VTA


title: ZAP1_d2_400_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ZAP1 Δ2 400 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_F10_ad012

value: STR


title: ZAP1_d2_400_1


title: ZAP1_d2_300_2


title: ZAP1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 ZAP1 MNase

value: TF


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E9_ad012

value: female


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E9_ad001

value: male


title: TYE7_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TYE7 MNase


title: ZAP1_1


title: TEC1_nonDBD_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TEC1 Δ128 195 MNase

value: nonDBD


title: TYE7_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E7_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E6_ad012


title: TOD6_d151_525_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TOD6 Δ151 525 SV40 NLS MNase

value: DBD


title: TEC1_nonDBD_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E8_ad001

value: HY

value: MY


title: TEC1_nonDBD_2


title: TEC1_nonDBD_1


title: TEC1_d351_486_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TEC1 Δ351 486 SV40 NLS MNase

value: Truncation


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E8_ad008

value: brain


title: TEC1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TEC1 Δ2 100 SV40 NLS MNase


title: TYE7_d2_150_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TYE7 Δ2 150 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E8_ad010

value: VTA

value: STR


title: TEC1_d351_486_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E8_ad012


title: TOD6_d151_525_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E7_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E7_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E7_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E6_ad010


title: TEC1_d2_100_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E6_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E6_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E6_ad006


title: TEC1_d251_486_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TEC1 Δ251 486 SV40 NLS MNase


title: TEC1_d251_486_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E7_ad008


title: TEC1_d251_486_2


title: TEC1_d251_486_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E6_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E5_ad012

value: female


title: TEC1_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 TEC1 MNase

value: TF


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E4_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E5_ad008

value: male


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E3_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E4_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E4_ad006


title: SWI5_nonDBD_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI5 Δ546 663 MNase::kanMX

value: nonDBD


title: SWI5_nonDBD_6


title: SWI5_nonDBD_5


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E5_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E5_ad010


title: SWI5_nonDBD_2


title: SWI5_d664_709_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI5 Δ664 709 SV40 NLS MNase::kanMX


title: SWI5_d664_709_1


title: SWI5_d2_500_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI5 Δ2 500 SV40 NLS MNase::kanMX

value: DBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E3_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E4_ad007


title: SWI5_d2_500_7


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E3_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E3_ad001

value: HY

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E3_ad008

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E3_ad002


title: SWI5_d2_500_3


title: SWI5_d2_500_4


title: TEC1_2


title: SWI5_d2_500_1


title: SWI5_nonDBD_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad010


title: SWI5_d2_450_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI5 Δ2 450 SV40 NLS MNase::kanMX

value: Truncation


title: SWI5_d2_450_5


title: SWI5_d2_450_4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad008

value: VTA


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E2_ad006


title: SWI5_d2_200_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI5 Δ2 200 SV40 NLS MNase::kanMX


title: SWI5_d2_450_2


title: SWI5_d2_450_1


title: SWI5_d2_500_2


title: SWI5_d2_400_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI5 Δ2 400 SV40 NLS MNase::kanMX


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad010

value: STR

value: female


title: SWI5_d2_400_1


title: SWI5_d2_400_3


title: SWI5_d2_200_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad008


title: SWI5_d2_200_5


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad012


title: SWI5_d2_200_4


title: SWI5_d2_200_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E1_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E12_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E12_ad010


title: SWI5_d2_450_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E12_ad007


title: SWI5_d2_200_1


title: SWI4_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI4 Δ37 155 MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E12_ad004


title: SWI4_nonDBD_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E12_ad002

value: male


title: SWI4_d901_1093_8

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI4 Δ901 1093 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E12_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E11_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E11_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E11_ad007


title: SWI4_d901_1093_5


title: SWI4_d475_1093_9

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI4 Δ475 1093 SV40 NLS MNase


title: SWI4_d701_1093_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI4 Δ701 1093 SV40 NLS MNase


title: SWI4_d475_1093_8


title: SWI4_d701_1093_4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E10_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E10_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E10_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E11_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E10_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E11_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_E10_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D9_ad012


title: SWI4_d475_1093_7


title: SWI4_d901_1093_7


title: SWI4_d475_1093_5


title: SWI4_d701_1093_3


title: SWI4_d475_1093_6


title: SWI4_d901_1093_6


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D9_ad010


title: SWI4_d301_1093_7

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI4 Δ301 1093 SV40 NLS MNase


title: SWI4_d475_1093_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D9_ad008


title: SWI4_d701_1093_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D9_ad006


title: SWI4_d301_1093_4

value: DBD


title: SWI4_d301_1093_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D9_ad004

value: HY


title: SWI4_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SWI4 MNase

value: TF


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D8_ad012

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D8_ad004

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D7_ad012

value: VTA


title: SWI4_4


title: SWI4_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D7_ad010


title: SUM1_d2_700_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0SUM1 Δ2 700 SV40 NLS MNase

value: Truncation


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D7_ad008

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D7_ad007


title: SUM1_d2_800_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ2 800 SV40 NLS MNase


title: SUM1_d2_500_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ2 500 SV40 NLS MNase


title: SUM1_d2_600_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ2 600 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D7_ad002

value: male


title: SUM1_d2_500_4


title: SUM1_d2_800_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D6_ad008


title: SUM1_d2_500_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D6_ad007


title: SUM1_d2_400_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ2 400 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D6_ad010

value: female


title: SUM1_d2_500_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D6_ad012


title: SUM1_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ2 100 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D9_ad007


title: SUM1_d2_400_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D6_ad006


title: SUM1_d2_100_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D5_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D5_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D5_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D5_ad002


title: SUM1_CT_del_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ524 1062 MNase

value: DBD


title: SUM1_CT_del_2


title: SUM1_AT_hook_del_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 Δ205 338 MNase

value: nonDBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D5_ad007

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D4_ad012


title: SUM1_AT_hook_del_3


title: SUM1_AT_hook_del_2


title: SUM1_AT_hook_del_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D4_ad010


title: SUM1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SUM1 MNase

value: TF


title: SUM1_1


title: STE12_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 STE12 Δ58 167 MNase


title: STE12_nonDBD_1

value: Truncation


title: SOK2_nonDBD_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ415 520 MNase


title: SOK2_idr350_585_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ2-349 Δ585-785 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D4_ad008

value: VTA

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D3_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D4_ad007

value: male


title: SOK2_idr350_585_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D4_ad004

value: HY

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D3_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D3_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D3_ad004

value: female


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D2_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D3_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D2_ad012


title: SOK2_d685_785_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ685 785 SV40 NLS MNase


title: SOK2_d685_785_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D2_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D2_ad008


title: SOK2_d585_785_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ585 785 SV40 NLS MNase


title: SOK2_d585_785_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D3_ad010


title: SOK2_idr350_585_1

value: DBD


title: SOK2_nonDBD_2

value: nonDBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D2_ad002

value: brain


title: SOK2_d521_785_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ521 785 SV40 NLS MNase


title: SOK2_d521_785_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad008


title: SOK2_idr350_585_2


title: SOK2_d415_785_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ415 785 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad007


title: SOK2_d521_785_1


title: SOK2_d415_785_4


title: SOK2_d415_785_5


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D1_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D2_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D12_ad012


title: SOK2_d415_785_2


title: SOK2_d415_785_3


title: SOK2_d415_785_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D12_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D12_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D12_ad002


title: SOK2_d2_350_7

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ2 350 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D12_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad012


title: SOK2_d2_350_6

value: Truncation


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D12_ad001


title: SOK2_d2_350_4


title: SOK2_d521_785_2


title: SOK2_d2_350_3


title: SOK2_d2_350_2


title: SOK2_d2_350_5


title: SOK2_d2_350_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad008


title: SOK2_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 MNase

value: TF


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad007

value: VTA


title: SOK2_1


title: SOK2_d2_300_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SOK2 Δ2 300 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad002

value: male


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D10_ad012

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D10_ad010


title: SOK2_d2_350_8


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad006

value: HY

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D10_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D10_ad001


title: SMP1_d301_452_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SMP1 Δ301 452 SV40 NLS MNase


title: SMP1_d301_452_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C9_ad010

value: female


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C9_ad008


title: SMP1_d101_452_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SMP1 Δ101 452 SV40 NLS MNase

value: DBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C9_ad007

value: brain


title: SMP1_d101_452_1


title: SKO1_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ420 453 MNase::kanMX

value: nonDBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D11_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C8_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_D10_ad008


title: SOK2_d2_300_1


title: SKO1_nonDBD_1


title: SKO1_d551_647_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ551 647 SV40 NLS MNase::kanMX


title: SKO1_d483_647_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ483 647 SV40 NLS MNase::kanMX

value: Truncation


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C8_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C8_ad004


title: SKO1_d551_647_1


title: SMP1_d401_452_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SMP1 Δ401 452 SV40 NLS MNase


title: SKO1_d2_50_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ2 50 SV40 NLS MNase::kanMX


title: SMP1_d401_452_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C7_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C7_ad008

value: VTA


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C8_ad010


title: SKO1_d2_50_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C7_ad007

value: male


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad012

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C7_ad001

value: HY


title: SKO1_d2_419_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ2 419 SV40 NLS MNase::kanMX


title: SKO1_d2_350_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ2 350 SV40 NLS MNase::kanMX


title: SKO1_d2_350_3


title: SKO1_d2_419_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad010

value: female


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad006

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C7_ad012


title: SKO1_d483_647_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C5_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad002


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C5_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C5_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C5_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C5_ad002


title: SKO1_d2_150_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ2 150 SV40 NLS MNase::kanMX


title: SKO1_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ2 200 SV40 NLS MNase::kanMX


title: SKO1_d2_200_1


title: SKO1_d2_150_2


title: SKO1_d2_200_3


title: SKO1_d2_350_1


title: SKO1_d2_350_2


title: SKO1_d2_200_4


title: SKN7_d401_622_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKN7 Δ401 622 SV40 NLS MNase::kanMX


title: SKO1_d2_100_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKO1 Δ2 100 SV40 NLS MNase::kanMX


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C4_ad008

value: brain


title: SKO1_d2_100_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C6_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C7_ad010


title: SKN7_d401_622_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C4_ad007


title: SKN7_d301_622_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKN7 Δ301 622 SV40 NLS MNase::kanMX


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C4_ad001


title: SKN7_d201_622_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SKN7 Δ201 622 SV40 NLS MNase::kanMX

value: DBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C3_ad012


title: SKN7_d201_622_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C3_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C3_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C4_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C3_ad004


title: SFL1_nonDBD_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SFL1 Δ65 205 MNase

value: nonDBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C4_ad010

value: VTA


title: SKN7_d301_622_4

value: Truncation


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C3_ad001

value: HY

value: male


title: SFL1_d651_766_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SFL1 Δ651 766 SV40 NLS MNase


title: SFL1_nonDBD_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C3_ad002


title: SFL1_d567_766_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SFL1 Δ567 766 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C2_ad012

value: STR

value: female


title: SFL1_d451_766_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SFL1 Δ451 766 SV40 NLS MNase


title: SFL1_d567_766_1


title: SFL1_d451_766_6


title: SFL1_d451_766_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C2_ad004

value: MY


title: SFL1_d451_766_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C1_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C1_ad012


title: SFL1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 SFL1 MNase

value: TF


title: SFL1_1


title: SFL1_nonDBD_4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C2_ad006

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C1_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C1_ad006


title: RTG3_d2_250_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RTG3 Δ2 250 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C1_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C2_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C12_ad010


title: RTG3_d2_250_1

value: DBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C2_ad008


title: SFL1_d651_766_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C12_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C12_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C12_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C12_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad008


title: RTG3_d2_150_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RTG3 Δ2 150 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad012


title: RTG3_d2_150_3


title: RTG3_d2_150_1


title: RTG3_d2_150_5


title: RTG3_d2_150_6


title: RTG3_d2_150_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad007


title: RPN4_nonDBD_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RPN4 Δ433 511 MNase::kanMX

value: nonDBD


title: RTG1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RTG1 MNase


title: RTG1_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C11_ad002

value: HY


title: RPN4_nonDBD_1


title: RPH1_d2_700_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RPH1 Δ2 700 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C10_ad008

value: VTA

value: male


title: RPH1_d2_700_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C10_ad007

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C10_ad006

value: female


title: RPH1_d2_600_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RPH1 Δ2 600 SV40 NLS MNase

value: Truncation


title: RTG3_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RTG3 MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C10_ad001

value: MY


title: RTG3_1

value: TF


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C10_ad002

value: brain


title: RPH1_d2_600_2


title: RPH1_d2_600_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B9_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B9_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B9_ad006


title: RPH1_d2_600_1


title: RPH1_d2_500_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RPH1 Δ2 500 SV40 NLS MNase


title: RPH1_d2_400_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RPH1 Δ2 400 SV40 NLS MNase


title: RPH1_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RPH1 Δ2 200 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B9_ad008


title: RLM1_d601_676_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RLM1 Δ601 676 SV40 NLS MNase


title: RLM1_d601_676_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B9_ad004


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad012


title: RLM1_d501_676_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RLM1 Δ501 676 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_C10_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad006

value: HY


title: RLM1_d501_676_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad004


title: RLM1_d101_676_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RLM1 Δ101 676 SV40 NLS MNase

value: DBD


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad007

value: VTA

value: male


title: RPH1_d2_500_1


title: RLM1_d201_676_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RLM1 Δ201 676 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad001


title: RLM1_d101_676_1


title: RPH1_d2_200_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B7_ad012

value: STR

value: female


title: RFX1_d501_811_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RFX1 Δ501 811 SV40 NLS MNase

value: Truncation


title: RFX1_d401_811_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RFX1 Δ401 811 SV40 NLS MNase


title: RFX1_d401_811_5


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B7_ad010

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B7_ad008


title: RFX1_d401_811_4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B7_ad002

value: MY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B7_ad007


title: RFX1_d401_811_3


title: RFX1_d401_811_2


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B8_ad008


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B6_ad012


title: RFX1_d401_811_1


title: RFX1_d2_250_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RFX1 Δ2 250 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B6_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B6_ad007


title: RFX1_d2_250_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B5_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B5_ad008


title: RFX1_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 RFX1 MNase

value: TF


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B5_ad007


title: PHO4_d2_200_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO4 Δ2 200 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B5_ad004

value: HY


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B5_ad002


title: PHO4_d2_200_1


title: PHO4_d2_100_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO4 Δ2 100 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad012


title: RFX1_2


title: PHO4_d2_100_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad010


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B7_ad001


title: PHO4_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO4 MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad008

value: VTA


title: PHO4_1


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad004


title: PHO2_d451_559_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO2 Δ451 559 SV40 NLS MNase


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad007

value: male


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad001


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B3_ad012

value: STR


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B3_ad010

value: female


title: PHO2_d451_559_3


title: RFX1_4


title: PHO2_d451_559_2


title: PHO2_d201_559_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO2 Δ201 559 SV40 NLS MNase


title: PHO2_d451_559_1

value: Truncation


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B3_ad006


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B2_ad012


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B2_ad010


title: PHO2_d151_559_4

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO2 Δ151 559 SV40 NLS MNase

value: DBD


title: PHO2_d151_559_3


title: PHO2_d201_559_1


title: PHO2_d151_559_2


title: PHO4_4


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B2_ad008

value: brain


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B2_ad007


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B4_ad006

value: MY


title: PHO2_d151_559_1


title: PHO2_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHO2 MNase


title: Liver, MetRNA, LCMV, Rep19

city: Grand Rapids

first: Zach

middle: B

last: Madaj

state: MI

address: 333 Bostwick Ave NE

department: Bioinformatics and Biostatistics Core

institute: Van Andel Research Institute

data_processing:
RNA libraries were normalized, pooled, and sequenced on Illumina NovaSeq S1 flow cell using paired end, 50 base pair reads to an average depth of 50 M reads per sample
Base calling was performed by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0
Adapters and low-quality bases (Phred>30) were trimmed from raw reads using Trim_Galore
Trimmed reads were then aligned to the GRCm38 reference genome using the STAR aligner v2.7
Aligned read counts were imported into edgeR wherein library sizes were normalized using the trimmed mean of M values method and pairwise comparisons for differential expression were performed using the quasi-likelihood approach
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts and ENSEMBL gene IDs. Each column is a replicate, where matching numbers in the column names indicate matched liver samples fomr the same animal.

source_name: Hepatic

extract_protocol:
RNA was isolated directly from frozen liver tissue (RNA) or from post-metabolite extracted liver tissue (MetRNA). Samples were pulverized using QIAzol Lysis Reagent and a Tissue Lyser II. RNA was then purified from the lysates using RNeasy Plus Universal Mini Kit column-based isolation per manufacturers’ instructions. Isolated RNA was quantified by Promega Quantus and measured for integrity using Agilent Bioanalyzer.
Stranded RNA libraries were prepared from 500 ng RNA using the KAPA - mRNA Hyper Prep (08098140702, Roche)

treatment_protocol:
At eleven weeks of age, mice were randomly selected to receive an intraperitoneal injection of lymphocytic choriomeningitis virus (LCMV) (Armstrong strain, 2x105 PFU by intravenous injection) or PBS vehicle (Veh). 2.5 days post-infection, mice were anesthetized with an isoflurane vaporizer. While anesthetized, the liver was removed and snap-frozen in liquid N2 for later processing.
Frozen livers were pulverized to a fine powder using a mortar and pestle pre-chilled in liquid N2. Being careful to avoid thawing of powdered liver, two roughly 30 mg aliquots of each liver were rapidly weighed into liquid N2 chilled tubes. One aliquot was weighed into a liquid N2 chilled 1.5 mL Eppendorf tube for later RNA extraction. The other aliquot was weighed in to a 2.0 mL Omni Bead Ruptor (19-627, Omni) tube for metabolite extraction. Precise weights were then recorded, and samples were stored at –80°C until processing.

value: Hepatic

tag: fraction

value: MetRNA

value: LCMV


title: Liver, RNA, LCMV, Rep20

value: RNA


title: Liver, RNA, LCMV, Rep19


title: Liver, MetRNA, LCMV, Rep20


title: Liver, RNA, LCMV, Rep18


title: PHD1_d2_100_6

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHD1 Δ2 100 SV40 NLS MNase


title: PHO2_1

value: TF


title: PHD1_d2_100_2


title: PDX_tumor

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: hg19
Supplementary files format and content: txt

source_name: tumor from the PDX model

growth_protocol: We used four-week-old female NSG mice that were housed in a pathogen-free, temperature-controlled environment with a 12-hour light/dark cycle. The mice were fed autoclaved water and irradiated food.

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).
cDNA libraries preparation and sequencing  were performed by Rarevariant, Inc. (Tokyo, Japan) using DNBSEQ-G400RS platform (MGI tech).

value: tumor from the PDX model


title: PHD1_d2_100_5


title: PHD1_d2_100_3


title: 200221_CEMBA_mm_P56_P63_RS2_Pool96_P5_Pool96_P6_B3_ad008

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: VTA

value: male


title: Liver, MetRNA, LCMV, Rep18


title: PHD1_2

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PHD1 MNase


title: PHD1_1


title: Original_tumor

source_name: ovarian tumor

value: ovarian tumor


title: Liver, RNA, LCMV, Rep17


title: PDR3_1

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PDR3 MNase


title: PDR1_nonDBD_3

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PDR1 Δ45 81 MNase

value: nonDBD


title: PDR3_2


title: PHD1_d2_100_1

value: Truncation


title: Liver, RNA, Veh, Rep16

value: Veh


title: PDR1_nonDBD_2


title: Liver, MetRNA, Veh, Rep16


title: PDC2_nonDBD_5

value: MATa his3Δ0 leu2Δ0 met15Δ0 ura3Δ0 PDC2 Δ72 138 MNase


title: PDR1_nonDBD_1