title: D14-OE-TMZ

city: tianjin

first: Kai

last: Huang

address: anshan roud

institute: tianjin medical university

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Data processing were performed as Shalem O et al., Science, 2014.
Raw FASTQ files were demultiplexed using FASTX-Toolkit and processed to only contain the unique sgRNA sequence.
The sgRNA reads were aligned to the designed sgRNA sequence library using Bowite2.
sgRNA counts were normaliezd using the formula: normalized sgRNA counts=(reads per sgRNA/total reads for all sgRNA in samples)*10^6+1
Genome_build: hg19
Supplementary_files_format_and_content: excel format files include sgRNA counts

source_name: U87 cell

growth_protocol: The cells were routinely maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% heat-inactivated fetal bovine serum (FBS, HyClone, Logan, UT, USA) in a humidified 5% CO2 atmosphere at 37℃.

extract_protocol:
Genomic DNA extraction were preformed by a ammonium acetate and alcohol precipitation precedures. 1*10^8 cells were homogenized in 15 mL 4 M guanidine thiocyanate with RNaseA, after incubated at 37 oC for 30 mins,15 mL 8 M ammonium acetate were added and mixing. To precipitate DNA, 15 mL isopanol were added and mixing vigorously, the DNA were hooked to a new tube and washed by 70% ethanol. DNA were dissolved in 3 mL TE and extacted by 2 round of choloform.
Two-step PCR amplification were performed on genomic DNA using Hifi DNA polymerase (Vazyme). The first PCR using  Outer-F(CTTGGCTTTATATATCTTGTGGAAAGGAC)and Outer-R(GGAAAAAGGCGGAGCCAGTACACGAC) to primeramplification the region containing sgRNA cassette. The second PCR included amplification to attach Illumina adaptors and to barcode samples(F:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTgtggaaaggacgaaacaccg, R:CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAGCCAGTACACGACATCACTTTCC).The samples were multiplexing and sequencing in a single HiSeq-X run.

treatment_protocol: U87 cell line was first transduced with vector or EGFRvIII-encoding lentivirus, followed by 7 days’ G-418 selection. Then cells were infected with the pooled GeCKOv2 human lentiviral library at an multiplicity of infection (MOI) of 0.3 to ensure that most cells receive only one stably integrated RNA guide. At day 2, puromycin was added to the cells to select the positive transduced cells. At day 9, cells were treated with 350 µM TMZ.

value: glioblastoma cells

value: U87 cells transduced with lentivirus encoding EGFRvIII


title: D14-NC-TMZ

status: Public on Jun 04 2020

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type

tag: cell line

tag: genotype

value: U87 cells transduced with lentivirus encoding vector


title: D14-NC-DMSO


title: D14-OE-DMSO


title: D7-OE-TMZ


title: sams-1(ww51)_rep2

status: Public on Jun 05 2020

city: Worcestor

first: Gabrielle

last: Giese

state: MA

address: 368 Plantation St.

department: Program in Systems Biology

country: USA

institute: University of Massachusetts Medical School

description:
grown on NGM + 20 nM vitamin B12 + E. coli OP50
ww51-2

library_source: transcriptomic

data_processing:
BGI internal software "SOAPnuke" was used to remove adaptors and low quality reads with parameters: -n 0.001 -l 20 -q 0.4 -A 0.25. Low quality reads are defined as having greater than 40% bases whose quality is less than 20.
Reads were aligned to the reference genome using Bowtie2 with default parameters.
RSEM was used for estimation of read counts with default parameters
The Deseq2 package in R 3.6.3 was used for differential expression analysis.
Genome_build: c_elegans.PRJNA13758 (WormBase WS271)
Supplementary_files_format_and_content: tab delimeted file containing TPM matrix for all samples and all genes

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Animals were maintained on NGM-agar with soy peptone and 0.64 nM vitamin B12 prior to experiment. They were synchronized by an 18 hour L1 arrest post-buffered bleach treatment.

extract_protocol:
A minumum of 200 staged animals were collected and washed thrice in M9 buffer. Total RNA was extracted via Trizol and BCP followed by Dnase I treatment. Zymo Direct-zol RNA miniprep kit was used for clean up.
BGI standard protocol

treatment_protocol: Synchronized animals were grown on NGM-agar containing 20 nM vitamin B12 and seeded with E. coli OP50.

tag: tissue

value: whole animal

tag: strain

tag: Stage


title: D7-OE-DMSO


title: D7-NC-TMZ


title: D7-NC-DMSO


title: AT4

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

data_processing:
The quality of the sequencing reads was evaluated using FastQC software (version 0.11.7). Read trimming was performed using Trim Galore software (version 0.4.4).
Reads were mapped to the latest bovine reference genome (ARS-UCD1.2) using Hisat2 sofware (version 2.1.0).
Transcript models were recontructed from read alignments using Cufflinks software (version 2.2.1).
The tool cuffmerge (Cufflinks) was used for merging together each of the assemblies with the reference bovine annotation file in order to combine novel isoforms with known isoforms.
The number of reads that mapped to each gene was obtained using the script htseq-count (mode intersection-nonempty).
Genome_build: Bovine genome assembly: (ARS-UCD1.2)
Supplementary_files_format_and_content: Tab-delimited text files including ensembl gene id and number of mapped reads

organism: Bos taurus

source_name: Adipose

extract_protocol:
RNA extraction was performed using RNeasy Mini Kit (Qiagen, Valencia, CA). RNA quantiy and quality were determined using Nanodrop™ (2000/2000c Spectrophotometers, Thermo Scientific). All samples had an A260/280 ratio > 1.8.
All the RNA-sequencing procedures were performed by Novogene Bioinformatics Technology Co., Ltd (Beijing, China). Sequencing libraries were prepared using a Poly-A tail capture method and sequenced with NovaSeq 6000.

value: Adipose

tag: breed

value: Holstein

tag: treatment

value: Control


title: D0-OE


title: D0-NC


title: AT1


title: MURSI3.ETMS018

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
CASAVA (v1.8.1) was used to demultiplex pooled samples and convert BCL to FASTQ.
RNA-Seq data were aligned to the human genome build hg19 by STAR-2.5.1b.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.1-beta), the code is available at https://github.com/itmat/Normalization
Genome_build: hg19 (ensemblv75)
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: blood

extract_protocol:
Whole blood, modified Trizol/ Cartridge isolation from Ambion.
Poly(A) selection by MicroPoly(A) Purist Kit AM1919 from Ambion.

treatment_protocol: PBMCs collected on Ambion LeukoLOCK filters bathed in RNAlater and frozen at -80 degrees

value: blood

tag: ethnicity

value: MURSI

tag: subsistence

value: Pastoralist


title: MURSI2.ETMS012


title: SANDAWE1.TZSW161

value: SANDAWE


title: WEYTO1.ETWE020

value: WEYTO

value: Hunter-Gatherer


title: SANDAWE4.TZSW193


title: MURSI1.ETMS008


title: SANDAWE3.TZSW188


title: SANDAWE2.TZSW174


title: DIZI2.ETDI037

value: DIZI

value: Agro-Pastoralist


title: DIZI1.ETDI022


title: AMHARA3.ETAM048

value: AMHARA

value: Agriculturalist


title: ARGOBBA2.ETAG035

value: ARGOBBA


title: AMHARA4.ETAM052


title: AMHARA1.ETAM046


title: ARGOBBA1.ETAG018


title: wox5_3: wox5-1 rep 3

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
Reads filtered using ea-utils
Reads aligned using Bowtie and Cufflinks
FPKM values obtained using Cufflinks
Genome_build: Tair10
Supplementary_files_format_and_content: FPKM values for each biological replicate

organism: Arabidopsis thaliana

source_name: Arabidopsis root tissue

growth_protocol: Seeds were vernalized and imbibed at 4C for 2 days, then plated on 1xMS, 1% sucrose and grown vertically in 16 hr light/8 hr dark for 5 days

extract_protocol: For AGL42:GFP roots, GFP positive and negative cells were collected in a solution of B-mercaptoethanol and RLT buffer using a MoFlo sorter. For the rest, approximately 3mm of root tissue was collected in a solution of of B-mercaptoethanol and RLT buffer

value: root

tag: genotype/variation

tag: age

value: 5 days


title: seu3_2: seu-3 rep 2


title: wox5_2: wox5-1 rep 2


title: wox5_1: wox5-1 rep 1


title: seu3_3: seu-3 rep 3


title: seu3_1: seu-3 rep 1


title: FreSH510_2

type: RNA

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

description: High replicate#2

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human Gene 2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC)

label: biotin-labeled with TdT

source_name: Human embryonic stem-cell (H9-hESC)-derived multipotent stem-cells (hES-MSCs)

label_protocol: Biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: hES-MSCs were grown in ECM Medium (Science Cell) on a collagen coated tissue culture plate at 37'C 5% CO2 conditions

extract_protocol: Total RNA from the FACS sorted cells was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN)

treatment_protocol: hES-MSCs were sorted by FACS Sorter (BD Bioscience FACSAria III) into GSHHigh and GSHLow fractions.

value: Mesenchyme

value: hES-MSC


title: Col_3: Col-0 rep 3


title: Col_2: Col-0 rep 2


title: FreSH580_2


title: FreSH580_3


title: FreSH510_1

description: High replicate#1


title: FreSH510_3

description: High replicate#3


title: AMHARA2.ETAM080


title: eCLIP no Flag control

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: eCLIP with no Flag as negative control

data_processing:
Library strategy: eCLIP
Takes output from raw files. Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6 -m 18 -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards --times 1 -e 0.1 -O 5 --quality-cutoff 6 -m 18 -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2. Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads. Command: STAR --runMode alignReads --runThreadN 16 --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within --outFilterMultimapNmax 30 --outFilterMultimapScoreRange 1 --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All --readFilesCommand zcat --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep. Maps unique reads to the human genome. Command: STAR --runMode alignReads --runThreadN 16 --genomeDir /path/to/STAR_database_file --genomeLoad LoadAndRemove --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1 /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2 --outSAMunmapped Within --outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted --outFilterType BySJout --outReadsUnmapped Fastx --outFilterScoreMin 10 --outSAMattrRGline ID:foo --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
Takes output from STAR genome mapping. Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE. Sorts resulting bam file for use downstream. Command: java -Xmx2048m -XX:+UseParallelOldGC -XX:ParallelGCThreads=4 -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Djava.io.tmpdir=/full/path/to/files/.queue/tmp -cp /path/to/gatk/dist/Queue.jar net.sf.picard.sam.SortSam INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam TMP_DIR=/full/path/to/files/.queue/tmp OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam VALIDATION_STRINGENCY=SILENT SO=coordinate CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream. Command: samtools index /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files. Merges the two technical replicates for further downstream analysis. Command: samtools merge /full/path/to/files/CombinedID.merged.bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream. Command: samtools index /full/path/to/files/CombinedID.merged.bam /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam. Only outputs the second read in each pair for use with single stranded peak caller. This is the final bam file to perform analysis on. Command: samtools view -hb -f 128 /full/path/to/files/CombinedID.merged.bam > /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view. Calls peaks on those files. Command: clipper -b /full/path/to/files/CombinedID.merged.r2.bam -s hg19 -o /full/path/to/files/CombinedID.merged.r2.peaks.bed --bonferroni --superlocal --threshold-method binomial --save-pickle
Genome_build: mm10

organism: Mus musculus

source_name: mouse emrbyonic stem cells

growth_protocol: Maintenance of mESCs was conducted in in 500 mL of High-glucose DMEM (ThermoScientific), 15% USDA certified fetal bovine serum (FBS - Biological Industries), 1 mM L-Glutamine (Biological Industries), 1% nonessential amino acids (Biological Industries), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Biological Industries), 1% Sodium-Pyruvate (Biological Industries), 10μg recombinant human LIF (Peprotech).

extract_protocol: Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes. After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

tag: mouse strain

value: mouse emrbyonic stem cells


title: 50618_wt5ssc_H11

city: St. Louis

first: Debabrata

last: Patra

state: MO

address: 425 S. Euclid Avenue

department: Orthopaedic Surgery

institute: Washington University School of Medicine

description: FACS-sorted SSC from WT5 mouse

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts in tab-delimited text format

source_name: Bone Marrow/crushed bones

growth_protocol: Not applicable

extract_protocol:
Single cells were collected directly (one cell/well) in to wells containing 10X lysis buffer (Clontech) plus Protector RNAse inhibitor (Roche).
The RNA in each well was primed with oligo dT primer that incorporates a unique 10 basepair barcode and Takara's SMART Sequence to the 3'ends  and reverse transcribed (RT) to yield cDNA using SMARTScribe RT enzyme (Takara) and a template switching oligo to incorporate the SMART sequence to 5'-ends. cDNAs from each well/96-well plate was combined, purified, and amplified for 16 cylces using an oligo for the SMART sequence. Full-length cDNAs were sheared and cDNAs blunt-ended, an A base added to the 3'-ends and Illumina sequencing adapters ligated to these ends.  Ligated fragments were then amplified for 16 cycles using standard i7 indexing primer and P5 primer that binds only to the 3’ ends of the cDNAs containing SMART sequences and barcodes.  Fragments were sequenced on an Illumina HiSeq-2500 using paired reads extending 26 bases for read one to read cell barcodes, and 98 bases for read two for mRNA data.  Each plate was represented by a unique index and each well is represented by unique barcode.

treatment_protocol: Not applicable

value: Postnatal 21 day old

value: Hindlimbs and forelimbs (Bone Marrow/crushed bones)

value: FACS-sorted SSC

value: WT


title: 50618_wt5ssc_H10

description: FACS-sorted SSC from WT5 mouse


title: Ythdf3 eCLIP mESCs

description: Ythdf3 eCLIP in mouse embryonic stem cells

value: V6.5 X2FLAG-mYthdf3-ires-puro polyclonal mouse ESC


title: 50618_wt5ssc_H9

description: FACS-sorted SSC from WT5 mouse


title: FreSH580_1


title: Ythdf2 eCLIP mESCs

description: Ythdf2 eCLIP in mouse embryonic stem cells

value: V6.5 X2FLAG-mYthdf2-ires-puro polyclonal mouse ESC


title: Ythdf1 eCLIP mESCs

description: Ythdf1 eCLIP in mouse embryonic stem cells

value: V6.5 X2FLAG-mYthdf1-ires-puro polyclonal mouse ESC


title: 50618_wt5ssc_H12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G6

description: FACS-sorted SSC from WT5 mouse


title: Col_1: Col-0 rep 1


title: 50618_wt5ssc_G4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_H6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_G11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_E4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_F8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_C2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B4

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B5

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_D7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B2

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A12

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_B1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A11

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A10

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A7

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A6

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A9

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A8

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A5

description: FACS-sorted SSC from WT5 mouse


title: 49521_cko4_H11

description: FACS-sorted SSC from Cko4 mouse

value: Cko


title: 49521_cko4_H10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H9

description: FACS-sorted SSC from Cko4 mouse


title: 50618_wt5ssc_A3

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A1

description: FACS-sorted SSC from WT5 mouse


title: 50618_wt5ssc_A2

description: FACS-sorted SSC from WT5 mouse


title: 49521_cko4_H4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H3

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G3

description: FACS-sorted SSC from Cko4 mouse


title: 50618_wt5ssc_A4

description: FACS-sorted SSC from WT5 mouse


title: 49521_cko4_G2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_H7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F3

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_G5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E3

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_E2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_F4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D3

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C3

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B7

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_D6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_C8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B2

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A9

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_B3

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A11

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A10

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A12

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A6

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A8

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A5

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A4

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A1

description: FACS-sorted SSC from Cko4 mouse


title: 49521_cko4_A2

description: FACS-sorted SSC from Cko4 mouse


title: 49518_wt3_H12

description: FACS-sorted SSC from WT3 mouse


title: 49521_cko4_A3

description: FACS-sorted SSC from Cko4 mouse


title: 49518_wt3_H9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H4

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H10

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H11

description: FACS-sorted SSC from WT3 mouse


title: 49521_cko4_A7

description: FACS-sorted SSC from Cko4 mouse


title: 49518_wt3_G11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G10

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G4

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_H3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F10

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F4

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E10

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_G3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E4

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_F1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D10

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D4

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C4

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_E3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_D2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B8

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B7

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_C12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B3

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A11

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A10

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B12

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A9

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_B2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A1

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A6

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A5

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A2

description: FACS-sorted SSC from WT3 mouse


title: 49518_wt3_A4

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_H12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H10

description: FACS-sorted SSC from Cko2 mouse


title: 49518_wt3_B10

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_H9

description: FACS-sorted SSC from Cko2 mouse


title: 49518_wt3_A7

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_H8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H7

description: FACS-sorted SSC from Cko2 mouse


title: 49518_wt3_A8

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_H3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H5

description: FACS-sorted SSC from Cko2 mouse


title: 49518_wt3_A3

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_H4

description: FACS-sorted SSC from Cko2 mouse


title: 49518_wt3_B4

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_G10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_H2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F7

description: FACS-sorted SSC from Cko2 mouse


title: 49518_wt3_C10

description: FACS-sorted SSC from WT3 mouse


title: 49517_cko2_F8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_G7

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D7

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_F6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_D1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C7

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E7

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_E8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B7

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A12

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A11

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_B1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A7

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A6

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A8

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A5

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A10

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A4

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A9

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A2

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A1

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_A3

description: FACS-sorted SSC from Cko2 mouse


title: 49517_cko2_C2

description: FACS-sorted SSC from Cko2 mouse


title: 48883_creGFP_H12

description: GFP-expressing cell from bone marrow pooled from Cko mouse 3 and 4

value: GFP-expressing cell


title: 48883_creGFP_H11


title: 49517_cko2_B8

description: FACS-sorted SSC from Cko2 mouse


title: 48883_creGFP_H10


title: 48883_creGFP_H9


title: 48883_creGFP_H8


title: 48883_creGFP_H7


title: 48883_creGFP_H6


title: 48883_creGFP_H4


title: 48883_creGFP_H3


title: 48883_creGFP_H1


title: 48883_creGFP_G12


title: 48883_creGFP_G11


title: 48883_creGFP_G7


title: 48883_creGFP_G10


title: 48883_creGFP_G8


title: 48883_creGFP_G9


title: 48883_creGFP_G4


title: 48883_creGFP_G6


title: 48883_creGFP_F11


title: 48883_creGFP_G2


title: 48883_creGFP_G1


title: 48883_creGFP_G3


title: 48883_creGFP_G5


title: 48883_creGFP_F12


title: 48883_creGFP_F9


title: 48883_creGFP_F10


title: 48883_creGFP_F8


title: 48883_creGFP_F6


title: 48883_creGFP_H5


title: 48883_creGFP_F3


title: 48883_creGFP_F4


title: 48883_creGFP_F1


title: 48883_creGFP_F5


title: 48883_creGFP_F7


title: 48883_creGFP_E12


title: 48883_creGFP_F2


title: 48883_creGFP_E10


title: 48883_creGFP_H2


title: 48883_creGFP_E11


title: 48883_creGFP_E9


title: 48883_creGFP_E6


title: 48883_creGFP_E5


title: 48883_creGFP_E7


title: 48883_creGFP_E3


title: 48883_creGFP_E4


title: 48883_creGFP_E1


title: 48883_creGFP_E2


title: 48883_creGFP_D11


title: 48883_creGFP_D7


title: 48883_creGFP_D9


title: 48883_creGFP_D5


title: 48883_creGFP_D10


title: 48883_creGFP_D4


title: 48883_creGFP_D6


title: 48883_creGFP_D3


title: 48883_creGFP_D1


title: 48883_creGFP_D8


title: 48883_creGFP_D2


title: 48883_creGFP_C12


title: 48883_creGFP_C11


title: 48883_creGFP_C10


title: 48883_creGFP_C8


title: 48883_creGFP_E8


title: 48883_creGFP_C9


title: 48883_creGFP_D12


title: 48883_creGFP_C4


title: 48883_creGFP_C5


title: 48883_creGFP_C3


title: 48883_creGFP_C1


title: 48883_creGFP_B10


title: 48883_creGFP_B12


title: 48883_creGFP_B8


title: 48883_creGFP_B9


title: 48883_creGFP_C2


title: 48883_creGFP_B7


title: 48883_creGFP_B5


title: 48883_creGFP_C6


title: 48883_creGFP_C7


title: 48883_creGFP_B6


title: 48883_creGFP_A12


title: 48883_creGFP_B3


title: 48883_creGFP_B2


title: 48883_creGFP_B4


title: 48883_creGFP_B1


title: 48883_creGFP_A8


title: 48883_creGFP_A9


title: 48883_creGFP_A6


title: 48883_creGFP_A10


title: 48883_creGFP_A5


title: 48883_creGFP_B11


title: 48883_creGFP_A4


title: 48883_creGFP_A3


title: 48342_creGFP_H12

description: GFP-expressing cell from bone marrow pooled from Cko mouse 1 and 2


title: 48883_creGFP_A2


title: 48883_creGFP_A1


title: 48342_creGFP_H8


title: 48342_creGFP_H10


title: 48342_creGFP_H7


title: 48342_creGFP_H4


title: 48342_creGFP_H5


title: 48883_creGFP_A11


title: 48342_creGFP_H3


title: 48342_creGFP_H2


title: 48342_creGFP_H6


title: 48342_creGFP_G10


title: 48342_creGFP_G12


title: 48342_creGFP_G11


title: 48883_creGFP_A7


title: 48342_creGFP_H1


title: 48342_creGFP_G8


title: 48342_creGFP_G7


title: 48342_creGFP_G6


title: 48342_creGFP_G3


title: 48342_creGFP_G4


title: 48342_creGFP_G1


title: 48342_creGFP_G2


title: 48342_creGFP_G9


title: 48342_creGFP_G5


title: 48342_creGFP_H9


title: 48342_creGFP_H11


title: 48342_creGFP_F12


title: 48342_creGFP_F7


title: 48342_creGFP_F8


title: 48342_creGFP_F10


title: 48342_creGFP_F9


title: 48342_creGFP_F11


title: 48342_creGFP_F5


title: 48342_creGFP_F4


title: 48342_creGFP_F6


title: 48342_creGFP_F2


title: 48342_creGFP_F3


title: 48342_creGFP_F1


title: 48342_creGFP_E12


title: 48342_creGFP_E7


title: 48342_creGFP_E10


title: 48342_creGFP_E6


title: 48342_creGFP_E9


title: 48342_creGFP_E5


title: 48342_creGFP_E4


title: 48342_creGFP_E3


title: 48342_creGFP_E1


title: 48342_creGFP_D10


title: 48342_creGFP_D8


title: 48342_creGFP_E2


title: 48342_creGFP_D12


title: 48342_creGFP_D9


title: 48342_creGFP_D7


title: 48342_creGFP_D6


title: 48342_creGFP_D4


title: 48342_creGFP_D2


title: 48342_creGFP_D5


title: 48342_creGFP_D1


title: 48342_creGFP_D3


title: 48342_creGFP_E11


title: 48342_creGFP_C11


title: 48342_creGFP_C8


title: 48342_creGFP_C10


title: 48342_creGFP_E8


title: 48342_creGFP_C7


title: 48342_creGFP_C9


title: 48342_creGFP_C6


title: 48342_creGFP_C5


title: 48342_creGFP_D11


title: 48342_creGFP_C3


title: 48342_creGFP_C1


title: 48342_creGFP_C2


title: 48342_creGFP_B8


title: 48342_creGFP_B5


title: 48342_creGFP_B4


title: 48342_creGFP_B1


title: 48342_creGFP_C12


title: 48342_creGFP_A11


title: 48342_creGFP_B10


title: 48342_creGFP_C4


title: 48342_creGFP_B11


title: 48342_creGFP_B6


title: 48342_creGFP_B3


title: 48342_creGFP_B9


title: 48342_creGFP_A7


title: 48342_creGFP_A10


title: 48342_creGFP_A9


title: 48342_creGFP_A8


title: 48342_creGFP_B12


title: 48342_creGFP_A5


title: 48342_creGFP_A4


title: Cko

data_processing:
Alignments and Gene quantifications were done with 10X Cell ranger software as per 10xgenomics.com
Genome_build: GRCm38
Supplementary_files_format_and_content: expression matrix

source_name: Bone Marrow Cells

extract_protocol:
Single non-RBC bone marrow cells (BMC) wre processed using the Chromium Controller as per instructions for 10x Genomics platform (www.10xgenomics.com).
Chromium Single Cell 3' library and Gel Bead Kit v2 and the manufacturer's recommended protocol was followed to make unique barcoded single cell RNA sequencing libraries.

value: Hindlimbs and forelimbs

value: bone marrow

value: S1P Cko


title: 48342_creGFP_A3


title: WT


title: 48342_creGFP_B7


title: 48342_creGFP_A6


title: 48342_creGFP_A1


title: 48342_creGFP_A2


title: 48342_creGFP_A12


title: 48342_creGFP_B2


title: ChIP-seq-delCsn1s2b-E-H3K27ac-L1-rep2

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
The ChIP-seq analysis worklow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed by the application of bowtie aligner (Langmead et al., Nature methods, 2012)  with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Deeptools (Ramírez et al., Nucleic Acids Research, 2016) was applied  for the generation of bedGraph files.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of ChIP-seq

source_name: Mammary gland

growth_protocol: Mouse mammary tissues were harvested at day one of lactation (L1), day 6 and day 18 of pregnancy (p6 and p18).

extract_protocol:
Mammary tissues from specific stages during pregnancy and lactation were harvested, and stored at -80°C. The frozen-stored tissues were ground into powder in liquid nitrogen. Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-1081 and sc-271542), GR (Thermo Fisher Scientific, PA1-511A), H3K27ac (Abcam, ab4729), NFIB (Santa Cruz Biotechnology, sc-5567) and V5 (Thermo Fisher Scientific, 46-0705). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 2500 instrument (Illumina).
Libraries for sequencing were prepared using standard Illumina protocols.

tag: strain/background

value: Lactation day 1

value: Mammary gland

tag: chip-antibody

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq-delCsn1s2b-E-Pol2-L1-rep2

value: RNA polymerase II (Abcam, ab5408)


title: ChIP-seq-delCsn1s2b-E-STAT5A-L1-rep2

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: ChIP-seq-delCsn1s2b-E-H3K27ac-L1-rep1


title: ChIP-seq-delCsn1s2b-E-Pol2-L1-rep1


title: ChIP-seq-delCsn1s2b-E-GR-L1-rep2

value: GR (Thermo Scientific, PA1-511A)


title: ChIP-seq-delCsn1s2b-E-GR-L1-rep1


title: ChIP-seq-delCsn3-PE-L1-Pol2-rep1


title: ChIP-seq-delCsn3-PE-L1-H3K27ac-rep1


title: ChIP-seq-delCsn3-PE-L1-STAT5A-rep1


title: ChIP-seq-delCsn3-PE-L1-H3K27ac-rep2


title: ChIP-seq-delCsn3-PE-L1-GR-rep2


title: ChIP-seq-delCsn1s2b-E-STAT5A-L1-rep1


title: ChIP-seq-delS1-4-p6-STAT5A-rep2

value: Pregnancy day 6


title: ChIP-seq-delCsn3-PE-L1-GR-rep1


title: ChIP-seq-delS1-4-p6-STAT5A-rep1


title: ChIP-seq-delS1-4-p6-H3K27ac-rep2


title: ChIP-seq-delS1-4-p6-GR-rep1


title: ChIP-seq-delS1-4-p6-H3K27ac-rep1


title: ChIP-seq-delS1-4-p6-GR-rep2


title: ChIP-seq-WT-p6-STAT5A-rep1

value: wild-type


title: ChIP-seq-WT-p6-STAT5A-rep2


title: ChIP-seq-WT-p6-MED1-rep2

value: MED1 (Bethyl Laboratory, A300-793A)


title: ChIP-seq-WT-p6-GR-rep2


title: ChIP-seq-WT-p6-MED1-rep1


title: ChIP-seq-WT-L1-Pol2-rep1


title: ChIP-seq-WT-L1-H3K4me1-rep2

value: H3K4me1 (Active Motif, 39297)


title: ChIP-seq-delCsn3-DE-L1-H3K27ac-rep2

value: mammary gland


title: ChIP-seq-WT-L1-Pol2-rep2


title: ChIP-seq-delCsn3-DE-L1-H3K27ac-rep1


title: ChIP-seq-WT-L1-H3K4me1-rep1


title: ChIP-seq-delCsn3-DE-L1-GR-rep2


title: ChIP-seq-delCsn3-PE-L1-Pol2-rep2


title: ChIP-seq-delCsn3-DE-L1-GR-rep1


title: ChIP-seq-delCsn3-DE-L1-STAT5A-rep2

value: STAT5A (Santa Cruz Biotechnology, sc-1081)


title: ChIP-seq-delCsn3-DE-L1-STAT5A-rep1


title: E18.5 C1 Saline 11

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
Cell_36_index408_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt

data_processing:
Single cell suspensions were loaded onto a Fluidigm C1 10-17µ chip and captured according to the Manufacturer’s protocol.  Chambers (96) were microscopically examined and those with single cells recorded.  Cells were lysed for RNA isolation. RNA was dT primed for cDNA synthesis.  cDNA products were harvested, diluted, barcoded, and “tagmented” using Illumina Nextera, and sequenced on a single lane with Illumina HiSeq2500, generating approximately 250 million single end 50-100 base pair reads per 96 well plate as described in Extended Experimental Procedures.
Single cells with read count < 0.5 million and total number of genes expressed < 500 were removed from the analysis. Cells with co-highly-expressed selective markers of two distinct cell types were considered as doublets and were removed from the analysis.
Nextera adapter sequences were removed from the ATAC seq data using Trim Galore, then the paired end FASTQ files were aligned to the mm10 reference genome using Bowtie2 with parameters “–X 2000 and –k 1”. MACS2 algorithm was used to call peaks and Homer for peak annotation.
Sorted RNA reads were aligned from FASTQ files to mouse mm10 genome in TopHat2.  Quantification was performed with UCSC reference transcriptome using Partek E/M in Partek Flow. Samples were further processed via trimmed mean normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Text files including Read counts expression

source_name: E18.5 saline treated mouse lung single cell

growth_protocol: For bulk RNAseq, Twist2Cre;:Rosa26mT/mG and Rosa26mT/mG mice were time mated and pregnant dams were injected i.p. at E18.5 with 1mg/kg dexamethasone (DexaJect) or saline as a control; For scRNAseq, Wild type C57Bl6/J mice (8 week old) were time mated and dams were injected i.p. at E17.5 with 2mg/kg dexamethasone (DexaJect) or saline as a control.; For CD106+ ATACseq samples, Lungs were isolated from E16.5 and E18.5 C57Bl/6J mice and placed in DMEM.

extract_protocol:
For bulk RNAseq, lungs were removed, pooled by genotype, and minced in a petri dish on ice with a razor blade.  Minced lung tissue was incubated in 1.5% collagenase (Sigma) in TrypLE (Life Technologies) + 64U DNase I (Sigma) at 37C for 30min with occasion tituration.  The lung cell suspension was filtered successively through 100um, 40um and 20um filters, pelleted and resuspended in 20%FBS in DMEM/Hepes.  Cells were sorted on a BD FACSAria II sorter and gated for tdTomato-/GFP+ (Twist2Cre+ mesenchyme) cells.  Cells were collected, lysed in RLT+ buffer containing b-mercaptoethanol and RNA was isolated with the Nucleospin RNA Plus Kit (Macherey-Nagel).  RNAs were extracted from mesenchymal cells from Twist2Cre; For scRNAseq, Lungs were excised and placed in DMEM.  Lung lobes were diced into cubes with a microblade scapel under a dissecting microscope, placed in digest buffer (2mg/ml type2 collagenase (Worthington), 1mg/ml Pronase E (Sigma), 62.5 U/ml DNase I (Sigma), 5mM CaCl2 in PBS without calcium and magnesium) at 37C for 10min followed by gentle trituration.  Digested tissue was passed through a 23 gauge needle, filtered through a 40uM filter and cells pelleted.  Pellets were resuspended in red blood cell lysis buffer for 2 min at room temperature and washed with PBS/0.01% BSA.; For ATACseq samples, CD106+ cells were then isolated from the CD45-/CD31-/CD309- cell fraction using biotin-anti-mouse CD106 (clone 429, Miltenyi) and anti-biotin microbeads.  CD106+ cells were re-suspended in DMEM+10% FBS+25mM HEPES in Eppendorf tubes and treated with 100nM dexamethasone or saline for 4hrs at 37C.  Following treatment, cells were pelleted, counted and 50,000 cells per sample prepared for ATAC-seq.
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).

treatment_protocol: For bulk RNAseq, pups were harvested 2hrs post-injection and visually genotyped under a fluorescent microscope on the basis of red only fluorescence (Rosa26mT/mG) or green and red fluorescence (Twist2Cre;Rosa26mT/mG); For scRNAseq, Pups were harvested 24hrs after injection.; For ATACseq samples, CD106+ cells were isolated using negative selection followed by positive selection (CD45-/CD31-/CD309-/CD106+). Cells were pelleted, resuspended in MACS buffer, incubated with anti-biotin microbeads (Miltenyi) and passed over a LS column (Miltenyi) on a QuadroMACS separator.  Cells on the column were washed and eluted in MACS buffer and the flow-through was saved.

value: lung

value: saline


title: ChIP-seq-WT-p6-GR-rep1


title: E18.5 C1 Saline 4

description:
Cell_16_index809_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 1

description:
Cell_8_index808_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 7

description:
Cell_19_index305_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 3

description:
Cell_10_index203_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 6

description:
Cell_18_index204_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 8

description:
Cell_20_index406_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 2

description:
Cell_9_index102_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 9

description:
Cell_23_index709_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 14

description:
Bridges_Cell_81_index110_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt

source_name: E18.5 dex treated mouse lung single cell

value: 2mg/kg dexamethasone


title: E18.5 C1 Dex 15

description:
Bridges_Cell_85_index502_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 5

description:
Cell_17_index103_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 13

description:
Bridges_Cell_80_index804_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 12

description:
Bridges_Cell_79_index703_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 10

description:
Bridges_Cell_66_index209_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 9

description:
Bridges_Cell_62_index612_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 8

description:
Bridges_Cell_59_index309_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 11

description:
Bridges_Cell_74_index210_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 7

description:
Bridges_Cell_56_index801_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 6

description:
Bridges_Cell_55_index712_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 5

description:
Bridges_Cell_51_index308_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 3

description:
Bridges_Cell_37_index509_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Saline 10

description:
Cell_27_index306_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 4

description:
Bridges_Cell_44_index403_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 2

description:
Bridges_Cell_36_index408_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 C1 Dex 1

description:
Bridges_Cell_35_index307_1
scRNAseq
E18.5_c1_Dex_saline_counts.txt


title: E18.5 CD106+ Saline ATAC

description:
ATACseq
E18.broad_control_lambda.bw

source_name: E18.5 CD106+ sorted saline treated mouse lung


title: E16.5 CD106+ Dex ATAC

description:
ATACseq
E16.broad_treat_pileup.bw

source_name: E16.5 CD106+ sorted dex treated mouse lung


title: E16.5 CD106+ Saline ATAC

description:
ATACseq
E16.broad_control_lambda.bw

source_name: E16.5 CD106+ sorted saline treated mouse lung


title: E18.5 CD106- RNA 1

description:
1_CD106_neg_16105_R1
Bulk-RNAseq
Cd106+_Cd106-_bulk_RNAseq_counts.txt

source_name: E18.5 CD106- mouse lung


title: E18.5 Saline RNA 1

description:
saline1_16082
Bulk-RNAseq
E18.5_DexVsSaline_gene_counts.txt

source_name: E18.5 Twist2Cre Saline treated mouse lung


title: E18.5 Dex RNA 1

description:
Dex1_16078
Bulk-RNAseq
E18.5_DexVsSaline_gene_counts.txt

source_name: E18.5 Twist2Cre Dex treated mouse lung

value: 1mg/kg dexamethasone


title: E18.5 CD106+ RNA 1

description:
1_CD106_pos_16106_R1
Bulk-RNAseq
Cd106+_Cd106-_bulk_RNAseq_counts.txt

source_name: E18.5 CD106+ sorted mouse lung


title: E18.5 Dex RNA 4

description:
Dex4_16081
Bulk-RNAseq
E18.5_DexVsSaline_gene_counts.txt


title: E18.5 Dex RNA 3

description:
Dex3_16080
Bulk-RNAseq
E18.5_DexVsSaline_gene_counts.txt


title: gelatin_std_1

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
All reads are mapped to mm10 using TopHat (version 2.1.1)
FPKM are quantified using Cufflinks (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: genes.fpkm.csv and isoforms.fpkm.csv files include RPKM values at gene- and transcript-level, respectively

source_name: C57BL6/J WT mESC

growth_protocol: WT mESCs derived from inbred mouse (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA) were cultured on either LN511 or gelatin coated dish under either Std or 2i medium.

extract_protocol:
C57BL/6J WT mESCs were conditioned on either gelatin or LN511 coated dish in either Std or 2i medium for 2 weeks.
Then, RNA was recovered from 1x106 cells using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany).

tag: strain background

value: Embryonic stem cell

tag: culture condition

value: gelatin coated dish under Std medium


title: gelatin_std_2

tag: cell type


title: E18.5 Dex RNA 2

description:
Dex2_16079
Bulk-RNAseq
E18.5_DexVsSaline_gene_counts.txt


title: E18.5 CD106- RNA 2

description:
2_CD106_neg_16107_R1
Bulk-RNAseq
Cd106+_Cd106-_bulk_RNAseq_counts.txt


title: LM511_std_1

value: LN511 coated dish under Std medium


title: GeCKO_mouse_library_A_plasmid

data_processing:
Cutadapt software (Martin, 2011) was used to trim adapter with the parameters “-g CGAAACACCG.”
MAGeCK (v0.5.5) (Li et al., 2014) count command was executed with the parameters “count -l FASTA_GeckoV2_Mouse_A.csv --trim-5 0 --norm-method total --control-sgrna FASTA_GeckoV2_Mouse_A_controlList.txt.”
Genome_build: FASTA_GeckoV2_Mouse_A.csv
Supplementary_files_format_and_content: FASTA_GeckoV2_Mouse_A.csv is a reference file used for alignment.; FASTA_GeckoV2_Mouse_A_controlList.txt containing a list of control sgRNAs is used in MAGeCK analysis.; gecko_low.count.txt is resulting count data.

source_name: GeCKO mouse library A in lentiCRISPR v2 plasmid

growth_protocol: We knocked in GFP and iRFP reporter separately into the two alleles for Nanog, Trim28 and Dnmt3L genes using WT mESC line (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA). Knockin mESC lines were cultured on Laminin-511 coated dish under  Std medium (StemSure D-MEM [Wako Pure Chemicals, Osaka, Japan], 15% of fetal bovine serum, 0.1 mM β-mercaptoethanol, 1x MEM nonessential amino acids [Wako Pure Chemicals], a 2 mM L-alanyl-L-glutamine solution [Wako Pure Chemicals], 1000 U/mL LIF [Wako Pure Chemicals], 20 mg/ mL gentamicin [Wako Pure Chemicals]).

extract_protocol:
After 3 days after the fourth sorting, 2 x 10^5 cells were collected and genomic DNA was extracted using Wizard Genomic DNA Purification kit (Promega).
PCR of the virally integrated guides was performed on sgDNA at the equivalent of approximately 2000 cells per guide in 48 parallel reactions using KOD-FX neo (TOYOBO, Japan) in a single-step reaction of 22 cycles. Primers are listed here: forward primer, AATGATACGGCGACCACCGAGATCTACACTCTTTC CCTACACGACGCTCTTCCGATCTNNNNNNNN(1–8-bp stagger) GTGGAAAGGACGAAACACCG; reverse primer, CAAGCAGAAGACGGCATACGAGATNNNNNNNN GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGTGGGCGATGTGCGCTCTG, 8-bp index read barcode indicated in italic. PCR products from all 48 reactions were pooled, purified using PCR purification kit (Qiagen, Hilden, Germany) and gel extracted using the Gel extraction kit (Qiagen, Hilden, Germany).
Resulting libraries were deep-sequenced on Illumina HiSeq platform with a total coverage of >8 million reads passing filter per library.

treatment_protocol: Nanog, Trim28, Dnmt3L knockin cells were transduced with the Mouse CRISPR Knockout Pooled Library (GeCKO v2) (Addgene, # 1000000052) (Sanjana et al., 2014) via spinfection as previously described. We used only Mouse library A gRNA. Briefly, 3x10^6 cells per well (a total of 1.2 x 10^7 cells) were plated into a LN511-coated 12 well plate in the standard media supplemented with 8 µg/ml polybrene (Sigma-Aldrich). Each well received a virus amount equal to MOI = 0.3. The 12-well plate was centrifuged at 1,000 g for 2 h at 37°C. After the spin, media was aspirated and fresh media (without polybrene) was added. Cells were incubated overnight. 24 h after spinfection, cells were detached with trypsin and were replated into 4 of LN511-coated 10 cm dishes with 0.5 µg/mL puromycin for 3 days. Media was refreshed daily. At 6 days after transduction, cells were treated with 25 µM BV. After 24 h, at least 1.75 × 10^5 cells showing GFP/iRFP expression ratio close to 1 were sorted by FACS, and plated on 12 well plates (LM 511/Std condition). Unsorted cells were passaged to 10 cm plates, 5 × 10^5 each. After expansion of these sorted cells for 1 week, cells with GFP/iRFP expression ratio were close to 1 were sorted again. These sorting and expansion procedures were repeated 4 times in total.

value: Plasmid


title: gelatin_2i_1

value: gelatin coated dish under 2i medium


title: gelatin_2i_2


title: LM511_std_2


title: GeCKO-Dnmt3L_SORT_T2

source_name: CRISPR-library-introduced Dnmt3L-GFP/iRFP KI mESC line derived from C57BL6/J mESC


title: ChIP-seq-delCsn3-PE-L1-STAT5A-rep2

value: Lactation day 1

value: Mammary gland

value: STAT5A (Santa Cruz Biotechnology, sc-271542)


title: GeCKO-Dnmt3L_UNSORT

value: Unsort


title: GeCKO-Trim28_SORT_T2

source_name: CRISPR-library-introduced Trim28-GFP/iRFP KI mESC line derived from C57BL6/J mESC


title: E18.5 CD106+ Dex ATAC

description:
ATACseq
E18.broad_treat_pileup.bw

source_name: E18.5 CD106+ sorted dex treated mouse lung


title: GeCKO-Dnmt3L_SORT_T1


title: LM511_2i_1

value: LN511 coated dish under 2i medium


title: GeCKO-Trim28_SORT_T1


title: E18.5 CD106+ Dex RNA

description:
Bulk-RNAseq
E18_Cd106+Dex_bulk_RNAseq_counts.txt


title: E18.5 CD106+ RNA 2

description:
2_CD106_pos_16108_R1
Bulk-RNAseq
Cd106+_Cd106-_bulk_RNAseq_counts.txt


title: E18.5 Saline RNA 2

description:
saline2_16083
Bulk-RNAseq
E18.5_DexVsSaline_gene_counts.txt


title: GeCKO-Trim28_UNSORT


title: GeCKO-Nanog_SORT_T2

source_name: CRISPR-library-introduced Nanog-GFP/iRFP KI mESC line derived from C57BL6/J mESC


title: GeCKO-Nanog_SORT_T1


title: GeCKO-Nanog_UNSORT


title: PDIS9063-475

data_processing:
library strategy: RamDA-seq (random displacement amplification sequencing)
129 and CAST genomes by incorporating SNPs and indels into reference genome and transcriptome was created by Seqnature (Munger et al., 2014).
Bowtie (version 1.1.2) was used to align scRamDA-seq reads against the diploid transcriptome with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: ASEcount_G1_129.txt and ASEcount_G1_CAST.txt include read count data derived from 129 and CAST alleles, respectively, for each cell.

source_name: 129/CAST hybrid mESC

growth_protocol: The hybrid mouse ES cell line F1-21.6 (129Sv-Cast/EiJ, female), a kind gift from Prof. Joost Gribnau, were grown on either Laminin-511 (LN511, BioLamina, Stockholm, Sweden) in  Std medium (15% fetal bovine serum [FBS] [Gibco], 0.1 mM β-mercaptoethanol [Wako Pure Chemicals, Osaka, Japan], 1000U/ml of leukemia inhibitory factor [LIF, Wako Pure Chemicals, Osaka, Japan]). This cell line was previously described in (Jonkers et al., 2009).

extract_protocol:
Single cells were collected in 1 μL of cell lysis buffer (1 U RNasein plus (Promega), 10% RealTime ready Cell Lysis Buffer (Roche), 0.3% NP40 (Thermo Fisher), and RNase-free water (TaKaRa)) in a 96-well PCR plate (BIOplastics). The cell lysates were denatured at 70 °C for 90 s and held at 4 °C until the next step. To eliminate genomic DNA contamination, 1 µL of genomic DNA digestion mix (0.5× PrimeScript Buffer, 0.2 U of DNase I Amplification Grade, 1: 5 000 000 ERCC RNA Spike-In Mix I (Thermo Fisher) in RNase-free water) was added to 1 µL of the denatured sample. The mixtures were agitated for 30 s at 2000 rpm using a ThermoMixer C at 4 °C, incubated in a C1000 thermal cycler at 30 °C for 5 min and held at 4 °C until the next step.
Library preparation for single-cell RamDA-Seq was performed as described previously (Hayashi et al., 2018).

value: 129/CAST hybrid F1


title: PDIS9063-479


title: PDIS9063-476


title: LM511_2i_2


title: PDIS9063-474


title: PDIS9063-470


title: PDIS9063-473


title: PDIS9063-477


title: PDIS9063-471


title: PDIS9063-467


title: PDIS9063-469


title: PDIS9063-466


title: PDIS9063-465


title: PDIS9063-464


title: PDIS9063-461


title: PDIS9063-462


title: PDIS9063-460


title: PDIS9063-463


title: PDIS9063-459


title: PDIS9063-458


title: PDIS9063-457


title: PDIS9063-456


title: PDIS9063-452


title: PDIS9063-453


title: PDIS9063-455


title: PDIS9063-454


title: PDIS9063-451


title: PDIS9063-447


title: PDIS9063-448


title: PDIS9063-445


title: PDIS9063-446


title: PDIS9063-443


title: PDIS9063-441


title: PDIS9063-440


title: PDIS9063-439


title: PDIS9063-442


title: PDIS9063-444


title: PDIS9063-438


title: PDIS9063-436


title: PDIS9063-434


title: PDIS9063-433


title: PDIS9063-432


title: PDIS9063-437


title: PDIS9063-431


title: PDIS9063-429


title: PDIS9063-428


title: PDIS9063-427


title: PDIS9063-430


title: PDIS9063-426


title: PDIS9063-425


title: PDIS9063-449


title: PDIS9063-423


title: PDIS9063-420


title: PDIS9063-421


title: PDIS9063-424


title: PDIS9063-422


title: PDIS9063-418


title: PDIS9063-419


title: PDIS9063-435


title: PDIS9063-416


title: PDIS9063-412


title: PDIS9063-407


title: PDIS9063-406


title: PDIS9063-413


title: PDIS9063-409


title: PDIS9063-402


title: PDIS9063-417


title: PDIS9063-405


title: PDIS9063-403


title: PDIS9063-414


title: PDIS9063-399


title: PDIS9063-397


title: PDIS9063-395


title: PDIS9063-398


title: PDIS9063-400


title: PDIS9063-404


title: PDIS9063-408


title: PDIS9063-392


title: PDIS9063-394


title: PDIS9063-391


title: PDIS9063-390


title: PDIS9063-389


title: PDIS9063-386


title: PDIS9063-385


title: PDIS9063-388


title: PDIS9063-410


title: PDIS9063-382


title: PDIS9063-381


title: PDIS9063-379


title: PDIS9063-375


title: PDIS9063-378


title: PDIS9063-377


title: PDIS9063-401


title: PDIS9063-367


title: PDIS9063-370


title: PDIS9063-371


title: PDIS9063-365


title: PDIS9063-366


title: PDIS9063-369


title: PDIS9063-359


title: PDIS9063-364


title: PDIS9063-356


title: PDIS9063-362


title: PDIS9063-355


title: PDIS9063-357


title: PDIS9063-351


title: PDIS9063-350


title: PDIS9063-353


title: PDIS9063-380


title: PDIS9063-348


title: PDIS9063-349


title: PDIS9063-373


title: PDIS9063-347


title: P2H2WT_SS16_f

city: Dresden

first: Ben

last: Wielockx

address: Fetscherstr. 74

country: Germany

institute: Institut für Klinische Chemie und Laboratoriumsmedizin

description: wild type

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star v2.5.3a with parameters --runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate  --readFilesCommand zcat
Raw gene counts were generated using htseq-count with parameters  -f bam -s reverse -m union -a   and annotation file of gencode.vM12.annotation.gtf
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bones

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

value: bones

value: 8-12 weeks


title: PDIS9063-368


title: P2H2WT_SS14_m

description: wild type


title: P2H2WT_SS13_m

description: wild type


title: P2H2WT_SS18_m

description: wild type


title: PDIS9063-344


title: PDIS9063-358


title: P2H2KO_SS17_f

description: Vav:cre-PHD2/HIF2ff/ff (cKO P2H2)


title: PDIS9063-343


title: P2H2KO_SS15_f

description: Vav:cre-PHD2/HIF2ff/ff (cKO P2H2)


title: PDIS9063-352


title: P2H2KO_SS12_m

description: Vav:cre-PHD2/HIF2ff/ff (cKO P2H2)


title: PDIS9063-340


title: PDIS9063-335


title: P2WT_SS7_f

description: wild type


title: P2WT_SS4_m

description: wild type


title: PDIS9063-334


title: PDIS9063-341


title: PDIS9063-332


title: P2WT_SS10_f

description: wild type


title: PDIS9063-339


title: PDIS9063-346


title: PDIS9063-331


title: PDIS9063-333


title: PDIS9063-345


title: P2KO_SS9_f

description: Vav:cre-PHD2f/f (cKO P2)


title: P2KO_SS6_m

description: Vav:cre-PHD2f/f (cKO P2)


title: PDIS9063-330


title: PDIS9063-328


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 8h after actinomycin D treatment [10h_Triple_KO_8_repB]

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were aligned to mouse genome version mm10 with Bowtie2 software using its default parameters.
Gene expression levels were estimated using ESAT software (Derr et al. 2016), with parameters  -minMappingQuality 0 -singleEnd -maxIntoGene 1000, for mm10 RefSeq genes.
Gene expression levels were normalized by library size of each sample (FPM, fragments per million reads).
Genome_build: mm10
Supplementary_files_format_and_content: ESAT output

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using Trizol, followed by ethanol precipitation.
3’ Poly A-RNA-seq library preparation was done as previously described (Geula, 2015).

treatment_protocol: For RNA stability assay 5x105 cells of each cell type were plated on a gelatin-coated 6 cm plate. 48 hours later, the media was replaced with fresh media containing 5 μM Actinomycin-D for the inhibition of mRNA transcription. Cell samples were harvested at the indicated time points (0, 4 and 8 hours).

tag: cell line

value: mouse Embryonic Stem Cells (mESCs)

tag: treatment/time point

value: 8h after actinomycin D treatment

tag: replicate

value: B

tag: library strategy

value: 3'UTR RNA-seq


title: PDIS9063-329

value: Embryonic stem cell


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 8h after actinomycin D treatment [10g_Triple_KO_8_repB]

tag: genotype


title: P2WT_SS3_m

description: wild type

tag: strain

tag: tissue


title: PDIS9063-342


title: P2KO_SS1_m

description: Vav:cre-PHD2f/f (cKO P2)


title: PDIS9063-327


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 4h after actinomycin D treatment [10f_Triple_KO_4_repB]

value: 4h after actinomycin D treatment


title: P2KO_SS5_m

description: Vav:cre-PHD2f/f (cKO P2)


title: PDIS9063-326


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 0h after actinomycin D treatment [10e_Triple_KO_0_repB]

value: 0h after actinomycin D treatment


title: P2H2KO_SS11_m

description: Vav:cre-PHD2/HIF2ff/ff (cKO P2H2)


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 0h after actinomycin D treatment [10d_Triple_KO_0_repB]


title: PDIS9063-325


title: PDIS9063-324


title: PDIS9063-323


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 8h after actinomycin D treatment [9g_Triple_KO_8_repA]

value: A


title: PDIS9063-322


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 8h after actinomycin D treatment [9h_Triple_KO_8_repA]


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 4h after actinomycin D treatment [9f_Triple_KO_4_repA]


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 0h after actinomycin D treatment [9e_Triple_KO_0_repA]


title: PDIS9063-321


title: Ythdf1-/-Ythdf2-/-Ythdf3-/- mESCs, 0h after actinomycin D treatment [9d_Triple_KO_0_repA]


title: PDIS9063-320


title: PDIS9063-319


title: Abf1 90 min input Replicate 3

city: Utrecht

first: Wim

middle: J

last: de Jonge

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

description: Input of Abf1-aa-V5 cells 90 minutes after induction of nuclear depletion

data_processing:
Paired-end reads were aligned to the sacCer3 genome assembly (February 2011) using HISAT2 v2.0.5 (Kim et al, 2015) using the settings “--add-chrname -X 1000 --score-min L,0,-0.2 -k 1 --no-spliced-alignment -5 12 -3 6”
The bam files were filtered to keep only fragments with a unique combination of UMIs using the custom scripts “addumis2bam.sh” and “uniqify-umis.pl” available from https://github.com/wdejonge/DIVORSEQ.
Peaks were called using MACS2 v2.1.1.20160309 (Zhang et al, 2008) with the settings “-f BAMPE -g 1.25e7 --keep-dup all --mfold 5 2000 --call-summits -q 0.001 --fe-cutoff 2” using all three replicate t=0 time points (no depletion) versus their corresponding inputs,
To fit the exponential decay model, the bam files were centred and smoothed with a 101bp window, as described in (de Jonge et al, 2017). Subsequently, all samples were scaled to 1 million reads using genomecov from the bedtools2 suite v2.27 (Quinlan & Hall, 2010) which makes sure that total coverage across the genome is the same for all samples (1.01 x 10e8 bases).
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig files contain the binding of Abf1 (or WT) without depletion or after nuclear depletion for the indicated time. For all read pairs the center of the fragment was taken and extended 50 bp on both sides such that all fragments are 101 bp. The bw files were scaled to 1 million reads such that the genome coverage between all samples is the same (101 million bases).
Supplementary_files_format_and_content: The combined peak calls of all three 0 min samples versus their corresponding inputs are provided, with a fold enrichment cutoff of 2 and a q-value cutoff of 0.001. The broad peaks are provided in narrowPeak format (peaks + summits) and the summits are also provided in bed format.

organism: Saccharomyces cerevisiae

source_name: Cell culture

growth_protocol: Strains were streaked from -80oC stocks onto appropriate selection plates and grown for 3 days. Liquid cultures were inoculated with independent colonies and grown overnight (O/N) in Synthetic Complete (SC) medium: 2 gr/L Drop out mix Complete and 6.71 gr/L Yeast Nitrogen Base without AA, Carbohydrate & w/AS (YNB) from US Biologicals (Swampscott, USA) with 2% D-glucose. The following day O/N cultures were used to inoculate 100 ml cultures of SC media at OD595=0.20 and were grown for two doublings. All growth was done at 30oC.

extract_protocol:
ChIP was carried out a described (de Jonge et al., STAR protocols 2020: https://star-protocols.cell.com/protocols/71). All samples were cross-linked using a final concentration of 2% formaldehyde for 5 minutes and subsequently quenched with a final concentration of 1.5M Tris pH=8.0 for 1 minute.
Sequencing libraries were created from the purified DNA using a combination of the Nextflex Rapid DNA-Seq Kit (Bioo Scientific) and the NEXTflex Rapid Directional qRNA-Seq Kit (Bioo Scientific) using a modified protocol.

treatment_protocol: Abf1 was depleted from the nucleus using the anchor-away system by adding rapamycin, dissolved in DMSO, to a final concentration of 7.5 µM for the time indicated. For the t=0 timepoints no rapamycin but the same amount of DMSO was added for 90 minutes.

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: MATalpha

tag: treatment

value: 90 minutes depletion (7.5µM rapamycin)

tag: chip antibody

value: anti-V5, Life Technologies, #R96025


title: Ythdf3-/- mESCs, 8h after actinomycin D treatment [8h_Ythdf3_KO_8_repB]


title: Abf1 90 min input Replicate 1


title: Abf1 90 min input Replicate 2


title: Ythdf3-/- mESCs, 0h after actinomycin D treatment [8d_Ythdf3_KO_0_repB]


title: Ythdf3-/- mESCs, 8h after actinomycin D treatment [8g_Ythdf3_KO_8_repB]


title: PDIS9063-317


title: Ythdf3-/- mESCs, 4h after actinomycin D treatment [8f_Ythdf3_KO_4_repB]


title: Ythdf3-/- mESCs, 8h after actinomycin D treatment [7h_Ythdf3_KO_8_repA]


title: PDIS9063-318


title: Abf1 75 min input Replicate 3

description: Input of Abf1-aa-V5 cells 75 minutes after induction of nuclear depletion

value: 75 minutes depletion (7.5µM rapamycin)


title: Abf1 75 min input Replicate 2


title: PDIS9063-316


title: Ythdf3-/- mESCs, 0h after actinomycin D treatment [7e_Ythdf3_KO_0_repA]


title: Ythdf3-/- mESCs, 4h after actinomycin D treatment [7f_Ythdf3_KO_4_repA]


title: Ythdf3-/- mESCs, 0h after actinomycin D treatment [7d_Ythdf3_KO_0_repA]


title: Ythdf2-/- mESCs, 8h after actinomycin D treatment [6h_Ythdf2_KO_8_repB]


title: Ythdf2-/- mESCs, 8h after actinomycin D treatment [6g_Ythdf2_KO_8_repB]


title: PDIS9063-315


title: Ythdf2-/- mESCs, 4h after actinomycin D treatment [6f_Ythdf2_KO_4_repB]


title: Abf1 60 min input Replicate 3

description: Input of Abf1-aa-V5 cells 60 minutes after induction of nuclear depletion

value: 60 minutes depletion (7.5µM rapamycin)


title: PDIS9063-313

value: 129/CAST hybrid F1


title: Ythdf2-/- mESCs, 0h after actinomycin D treatment [6d_Ythdf2_KO_0_repB]


title: Ythdf3-/- mESCs, 0h after actinomycin D treatment [8e_Ythdf3_KO_0_repB]


title: Ythdf2-/- mESCs, 0h after actinomycin D treatment [6e_Ythdf2_KO_0_repB]


title: Abf1 60 min input Replicate 2


title: Abf1 60 min input Replicate 1


title: Ythdf2-/- mESCs, 8h after actinomycin D treatment [5g_Ythdf2_KO_8_repA]


title: Ythdf2-/- mESCs, 4h after actinomycin D treatment [5f_Ythdf2_KO_4_repA]


title: Abf1 50 min input Replicate 3

description: Input of Abf1-aa-V5 cells 50 minutes after induction of nuclear depletion

value: 50 minutes depletion (7.5µM rapamycin)


title: PDIS9063-312


title: Ythdf1-/- mESCs, 4h after actinomycin D treatment [4h_Ythdf1_KO_4_repB]


title: Ythdf2-/- mESCs, 8h after actinomycin D treatment [5h_Ythdf2_KO_8_repA]


title: Abf1 50 min input Replicate 2


title: Abf1 75 min input Replicate 1


title: Ythdf1-/- mESCs, 0h after actinomycin D treatment [4g_Ythdf1_KO_0_repB]


title: PDIS9063-314


title: Abf1 50 min input Replicate 1


title: Ythdf3-/- mESCs, 8h after actinomycin D treatment [7g_Ythdf3_KO_8_repA]


title: PDIS9063-311


title: Ythdf2-/- mESCs, 0h after actinomycin D treatment [5e_Ythdf2_KO_0_repA]


title: Ythdf1-/- mESCs, 4h after actinomycin D treatment [3h_Ythdf1_KO_4_repA]


title: Ythdf1-/- mESCs, 8h after actinomycin D treatment [4d_Ythdf1_KO_8_repB]


title: PDIS9063-309


title: PDIS9063-310


title: Abf1 40 min input Replicate 2

description: Input of Abf1-aa-V5 cells 40 minutes after induction of nuclear depletion

value: 40 minutes depletion (7.5µM rapamycin)


title: Ythdf1-/- mESCs, 0h after actinomycin D treatment [3g_Ythdf1_KO_0_repA]

value: mouse Embryonic Stem Cells (mESCs)


title: PDIS9063-308


title: PDIS9063-305


title: PDIS9063-306


title: Ythdf2-/- mESCs, 0h after actinomycin D treatment [5d_Ythdf2_KO_0_repA]


title: Ythdf1-/- mESCs, 8h after actinomycin D treatment [3e_Ythdf1_KO_8_repA]

value: 8h after actinomycin D treatment


title: Ythdf1-/- mESCs, 0h after actinomycin D treatment [3f_Ythdf1_KO_0_repA]


title: WT mESCs, 4h after actinomycin D treatment [2h_KH2_WT_4_repB]

value: WT

value: B


title: WT mESCs, 0h after actinomycin D treatment [2g_KH2_WT_0_repB]

value: 3'UTR RNA-seq


title: PDIS9063-303

value: Embryonic stem cell


title: PDIS9063-304


title: Abf1 30 min input Replicate 3

description: Input of Abf1-aa-V5 cells 30 minutes after induction of nuclear depletion

value: 30 minutes depletion (7.5µM rapamycin)


title: Ythdf1-/- mESCs, 8h after actinomycin D treatment [3d_Ythdf1_KO_8_repA]

value: A


title: Abf1 30 min input Replicate 2

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4


title: Abf1 40 min input Replicate 3

value: MATalpha


title: WT mESCs, 8h after actinomycin D treatment [2d_KH2_WT_8_repB]


title: WT mESCs, 8h after actinomycin D treatment [2e_KH2_WT_8_repB]


title: WT mESCs, 0h after actinomycin D treatment [2f_KH2_WT_0_repB]

value: 0h after actinomycin D treatment


title: Abf1 30 min input Replicate 1

value: anti-V5, Life Technologies, #R96025


title: Ythdf1-/- mESCs, 0h after actinomycin D treatment [4f_Ythdf1_KO_0_repB]


title: PDIS9063-302


title: WT mESCs, 8h after actinomycin D treatment [1h_KH2_WT_8_repA]


title: WT mESCs, 4h after actinomycin D treatment [1f_KH2_WT_4_repA]

value: 4h after actinomycin D treatment


title: Abf1 20 min input Replicate 2

description: Input of Abf1-aa-V5 cells 20 minutes after induction of nuclear depletion

value: 20 minutes depletion (7.5µM rapamycin)


title: PDIS9063-301

value: 129/CAST hybrid F1


title: PDIS9063-299


title: Abf1 40 min input Replicate 1


title: WT mESCs, 0h after actinomycin D treatment [1d_KH2_WT_0_repA]


title: Abf1 20 min input Replicate 3


title: Ythdf1-/- mESCs, 8h after actinomycin D treatment [4e_Ythdf1_KO_8_repB]


title: WT mESCs, 8h after actinomycin D treatment [1g_KH2_WT_8_repA]


title: WT mESCs, 0h after actinomycin D treatment [1e_KH2_WT_0_repA]


title: PDIS9063-297


title: Abf1 15 min input Replicate 3

description: Input of Abf1-aa-V5 cells 15 minutes after induction of nuclear depletion

value: 15 minutes depletion (7.5µM rapamycin)


title: PDIS9063-296


title: Abf1 15 min input Replicate 2


title: PDIS9063-295


title: Abf1 15 min input Replicate 1


title: PDIS9063-294


title: Colon_DC_cKO_rep3

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

description: Litter mate 4

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was analyzed using Partek Genomics Suite software. Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization. Prbes and annotation files used are - MoGene-1_0-st-v1.r4.pgf and  MoGene-1_0-st-v1.na31.mm9.transcript.csv

label: Biotin

source_name: cecum

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse RM and CD11b+ DC freshly isolated from colon and FACS sorted.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions, which included a DNase step.

treatment_protocol: Sorted RM and CD11b+ defined as CD45+CD11c+MHCII+CD11b+F4/80+Ly6c- and as CD45+CD11c+MHCII+CD11b+F4/80-Ly6c- respectively.

value: Cecum

value: CD11b+ dendritic cells

tag: Sex

value: pooled male and female

value: Runx3 -/-

value: 6-8 weeks


title: Colon_DC_cKO_rep1

description: Litter mate 1

tag: age


title: Colon_DC_cKO_rep2

description: Litter mate 3


title: Colon_DC_WT_rep1

description: Litter mate 2

value: Runx3 +/+


title: Colon_DC_WT_rep2

description: Litter mate 3


title: Colon_RM_cKO_rep4

description: Litter mate 4

value: resident macrophages


title: PDIS9063-298

value: Embryonic stem cell


title: Abf1 20 min input Replicate 1


title: Abf1 10 min input Replicate 3

description: Input of Abf1-aa-V5 cells 10 minutes after induction of nuclear depletion

value: 10 minutes depletion (7.5µM rapamycin)


title: Abf1 5 min input Replicate 2

description: Input of Abf1-aa-V5 cells 5 minutes after induction of nuclear depletion

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: 5 minutes depletion (7.5µM rapamycin)


title: PDIS9063-293


title: PDIS9063-288


title: e4a9_4fd6-PBMC

type: genomic

city: Chicago

first: Carole

last: Ober

state: IL

address: 920 E 58TH ST

department: Human Genetics

institute: The University of Chicago

description:
Sample e4a9_4fd6, age 7
Measured on EPIC array

hyb_protocol: Illumina Infinium

scan_protocol: Illumina IScan

data_processing:
1.) Remove probes with SNPs whose MAF is >= 0.05 in Africans, Americans or Europeans. 2.) Remove cross hybridizing probes; remove probes on sex chromosomes; remove probes with a detection pvalue >= 0.01 in more than 25% of the samples. 3.) Samples 7804_4bab-CBMC, a60f_493d-CBMC, f86d_4016-PBMC failed QC and were removed from downstream analysis. 4.) Normalize methylated and unmethylated probe intensities separately with normalize.quantile.450k(<Methylset_Object>, method = "quantile1"); this is from ENmix package, version 1.14.0. 5.) Remove probe-type bias with preprocessSWAN from the minfi package, version 1.24.0. 6.) Calculate M-values as log2(Processed unmethylated intensity + 100) - log2(Processed methylated intensity + 100). M-values were used in all downstream analyses.
Normalized Beta-value, calculated as (Normalized methylated intensity + 100)/{(Normalized methylated intensity + 100) + (Normalized unmethylated intensity + 100)}. The offset of 100 was recommended by Du et al., 2010

label: Cy3, Cy5

source_name: Human PBMCs at age 7

label_protocol: Illumina Infinium

extract_protocol: DNA for methylation studies was extracted from thawed CBMCs and PBMCs using the Qiagen AllPrep kit (QIAGEN, Valencia, CA)

value: PBMCs

value: age 7

tag: methylationplatenumber

tag: selfreportedrace

value: Black

value: Female

tag: samplecollectionsite

value: St. Louis


title: Abf1 5 min input Replicate 3

value: MATalpha

value: anti-V5, Life Technologies, #R96025


title: PDIS9063-292

tag: strain background

value: 129/CAST hybrid F1


title: Abf1 10 min input Replicate 2


title: PDIS9063-290


title: 4da9_4107-PBMC

description:
Sample 4da9_4107, age 7
Measured on EPIC array


title: PDIS9063-287


title: Abf1 5 min input Replicate 1


title: 540b_41ce-PBMC

description:
Sample 540b_41ce, age 7
Measured on EPIC array

value: Male


title: 540b_41ce-CBMC

description:
Sample 540b_41ce, birth
Measured on EPIC array

source_name: Human cord blood at birth

value: Cord blood

value: birth


title: e4a9_4fd6-CBMC

description:
Sample e4a9_4fd6, birth
Measured on EPIC array


title: 4da9_4107-CBMC

description:
Sample 4da9_4107, birth
Measured on EPIC array


title: Abf1 0 min input Replicate 3

description: Input of Abf1-aa-V5 cells without nuclear depletion

value: no depletion (90 min DMSO)


title: 364a_4d08-PBMC

description:
Sample 364a_4d08, age 7
Measured on EPIC array


title: 364a_4d08-CBMC

description:
Sample 364a_4d08, birth
Measured on EPIC array


title: Abf1 0 min input Replicate 2


title: PDIS9063-286


title: PDIS9063-285


title: Colon_RM_cKO_rep3

description: Litter mate 3

value: Cecum

value: resident macrophages

value: pooled male and female

value: Runx3 -/-

value: 6-8 weeks


title: 63e4_47b2-PBMC

description:
Sample 63e4_47b2, age 7
Measured on EPIC array

value: PBMCs


title: Colon_RM_WT_rep3

description: Litter mate 3

value: Runx3 +/+


title: Abf1 0 min input Replicate 1

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4


title: Colon_RM_WT_rep2

description: Litter mate 2


title: Colon_RM_cKO_rep1

description: Litter mate 1


title: 63e4_47b2-CBMC

description:
Sample 63e4_47b2, birth
Measured on EPIC array

value: Black


title: 26b7_45c4-PBMC

description:
Sample 26b7_45c4, age 7
Measured on EPIC array

value: age 7

value: St. Louis


title: be1d_425d-PBMC

description:
Sample be1d_425d, age 7
Measured on EPIC array


title: PDIS9063-284

value: Embryonic stem cell


title: PDIS9063-283

value: 129/CAST hybrid F1


title: Colon_RM_WT_rep1

description: Litter mate 1


title: WT 90 min input Replicate 2

description: Input of WT cells treated with rapamycin (90 min)

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT

value: MATalpha

value: 90 minutes rapamycin (7.5µM rapamycin)

value: anti-V5, Life Technologies, #R96025


title: 227d_4725-PBMC

description:
Sample 227d_4725, age 7
Measured on EPIC array

value: Male


title: WT 90 min input Replicate 3


title: PDIS9063-280


title: Colon_RM_cKO_rep2

description: Litter mate 2

value: Cecum

value: resident macrophages


title: 227d_4725-CBMC

description:
Sample 227d_4725, birth
Measured on EPIC array

value: Cord blood

value: birth


title: WT 90 min input Replicate 1


title: PDIS9063-279


title: be1d_425d-CBMC

description:
Sample be1d_425d, birth
Measured on EPIC array


title: a8e4_4c4a-CBMC

description:
Sample a8e4_4c4a, birth
Measured on EPIC array

value: Female


title: 26b7_45c4-CBMC

description:
Sample 26b7_45c4, birth
Measured on EPIC array


title: WT 0 min input Replicate 3

description: Input of WT cells treated with DMSO

value: no rapamycin (90 min DMSO)


title: e9b1_4987-PBMC

description:
Sample e9b1_4987, age 7
Measured on EPIC array

value: PBMCs


title: e9b1_4987-CBMC

description:
Sample e9b1_4987, birth
Measured on EPIC array

value: Black


title: PDIS9063-276


title: 49a4_4e39-CBMC

description:
Sample 49a4_4e39, birth
Measured on EPIC array


title: 49a4_4e39-PBMC

description:
Sample 49a4_4e39, age 7
Measured on EPIC array

value: age 7


title: 770d_4553-PBMC

description:
Sample 770d_4553, age 7
Measured on EPIC array

value: St. Louis


title: f972_4900-PBMC

description:
Sample f972_4900, age 7
Measured on EPIC array


title: WT 0 min input Replicate 1

description: Input of WT cells treated with DMSO


title: PDIS9063-275

value: Embryonic stem cell


title: Abf1 90 min IP Replicate 3

description: ChIP of Abf1-aa-V5 cells 90 minutes after induction of nuclear depletion

value: BY4742 tor1-1; fpr1del; RPL13A-FKBP12-NAT; Abf1-FRB-yEGFP-3V5-hphMX4

value: 90 minutes depletion (7.5µM rapamycin)


title: 01c8_4451-PBMC

description:
Sample 01c8_4451, age 7
Measured on EPIC array


title: 01c8_4451-CBMC

description:
Sample 01c8_4451, birth
Measured on EPIC array


title: PDIS9063-274

value: 129/CAST hybrid F1


title: 8dab_416d-PBMC

description:
Sample 8dab_416d, age 7
Measured on EPIC array


title: 770d_4553-CBMC

description:
Sample 770d_4553, birth
Measured on EPIC array


title: Abf1 90 min IP Replicate 2

value: MATalpha


title: PDIS9063-272


title: PDIS9063-273


title: Abf1 90 min IP Replicate 1

value: anti-V5, Life Technologies, #R96025