title: TM_HC_1274_F_202


title: TM_HC_1252_F_212

status: Public on May 20 2021

type: SRA

city: Nouzilly

first: Vincent

last: Coustham

address: INRAE Centre Val de Loire

country: France

institute: INRAE

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequenced reads were mapped to Coturnix japonica 2.0 genome using STAR with default arguments
Reads were counted using FeatureCounts with arguments -T 6 -s 2 -t exon -g gene and the annotation file GCF_001577835.1_Coturnix_japonica_2.0_genomic.gff
Biostatistical analysis was performed using the Bioconductor edgeR package (version 3.24.3); p-values were adjusted by controlling the false positive rate below 0.05 with a Benjamini-Hochberg correction
Genome_build: Coturnix japonica 2.0, GCA_001577835.1
Supplementary_files_format_and_content: tab-delimited text files including normalized counts and adjusted p-values
Supplementary_files_format_and_content: processed counts for all samples: S19041.processed.counts.txt
Supplementary_files_format_and_content: edgeR analysis for FCHC vs FCRT comparison: FCHCvsFCRT.complete.txt
Supplementary_files_format_and_content: edgeR analysis for FCHC vs FTMHC comparison: FCHCvsFTMHC.complete.txt
Supplementary_files_format_and_content: edgeR analysis for FCRT vs FTMRT comparison: FCRTvsFTMRT.complete.txt
Supplementary_files_format_and_content: edgeR analysis for FTMHC vs FTMRT comparison: FTMHCvsFTMRT.complete.txt
Supplementary_files_format_and_content: edgeR analysis for MCHC vs MCRT comparison: MCHCvsMCRT.complete.txt
Supplementary_files_format_and_content: edgeR analysis for MCHC vs MTMHC comparison: MCHCvsMTMHC.complete.txt
Supplementary_files_format_and_content: edgeR analysis for MCRT vs MTMRT comparison: MCRTvsMTMRT.complete.txt
Supplementary_files_format_and_content: edgeR analysis for MTMHC vs MTMRT comparison: MTMHCvsMTMRT.complete.txt

molecule: polyA RNA

organism: Coturnix japonica

source_name: Total RNA samples produced with Qiagen Allprep mini kit.

extract_protocol:
RNA extraction was performed using All Prep RNA/DNA Mini kit (Qiagen), according to the manufacturer’s instruction. RNA concentration was obtained on a Nanodrop ND-1000 UV-Vis Spectrophotometer. RNA integrity was verified by on an Agilent 2100 bioanalyzer with a RNA Nano kit (Agilent), according to the manufacturer’s instruction. All sample RIN was above 8.5.
RNA-Seq libraries were generated from 500ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Eggs of Cons DD Japanese quail line were dispatched between two embryonic treatments: Control incubation (C) or Thermo-Manipulated incubation (TM). C eggs were maintained at 37.8°C and 56% relative humidity (RH) during the whole incubation period. TM eggs were incubated at 39.5°C and 65% RH for 12 h/d from I0 to I13 and incubated at 37.8°C 56 % RH the rest of the time. At D35, half of the quails (same proportion of C and TM animals) was kept at room temperature (RT) while the other half was submitted to a heat challenge (HC - 36°C for 7 hours).

tag: tissue

value: hypothalamus

tag: strain

value: Cons DD

tag: Sex

value: Female

tag: incubation condition

value: TM

tag: challenge condition (at age day 35)

value: Heat challenge

tag: age

value: post natal day 35


title: s.NJA01501.N03

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

molecule: total RNA

organism: Mus musculus

growth_protocol: Small intestine and colon were removed from C57BL/J wild-type mice and kept on ice in phosphate buffered saline (PBS). Lumina of colon and small intestine were washed three times with PBS and adipose tissue connected to the exterior of the small intestine or colon was removed. Colon and small intestine were opened longitudinally, and any remaining mucous on covering the epithelial layer was gently rubbed off. Tissues were washed once in PBS before being cut into 0.5 - 1 mm long fragments. Colon fragments were immersed in 10mM EDTA-PBS and incubated for 105 minutes on ice, with shaking every 15 minutes. Small intestinal fragments were similarly immersed in 10mM EDTA-PBS on ice and shaken. After 15 minutes, small intestinal fragments were allowed to settle at the bottom and the supernatant was discarded and replaced with new 10mM EDTA-PBS and shaken vigorously. This procedure was repeated 1-2 times, with supernatant fractions investigated through light microscopy before discarding, in order to enrich for crypts. Small intestinal fragments were then incubated on ice for 45-60 minutes for a total of 105 minutes. Following EDTA-PBS treatment fractions were triturated 10-15 times. Colon fractions were strained through a 100 um filter while small intestinal fractions were strained through a 70 um filter. Fractions were centrifuged at 300g for 5 minutes and dissociated using TrypLE Express (Invitrogen) at 37°C for 15-20 minutes. Enzymatic dissociation was supervised using light microscopy during regular intervals to obtain an appropriate amount of single cells and multiplets. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's protocol before staining for FACS sorting was performed.

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

tag: facs cellnumber

value: Singlet

tag: age (days)


title: s.NJA01501.N02


title: s.NJA01501.N01


title: TM_RT_1247_M_197

value: Male

value: Room temperature


title: s.NJA01501.N14


title: TM_RT_1263_M_97


title: m.NJA01501.M22

value: Multiplet


title: TM_RT_1021_M_182


title: m.NJA01501.M24


title: TM_HC_1091_M_287


title: m.NJA01501.M20


title: m.NJA01501.M23


title: TM_HC_1265_M_282


title: TM_RT_1118_M_82


title: s.NJA01501.N08


title: m.NJA01501.M19


title: TM_RT_1231_M_87


title: TM_RT_1082_M_77


title: s.NJA01501.M18


title: TM_RT_1194_F_122


title: TM_RT_1159_F_117


title: s.NJA01501.M17


title: TM_RT_1098_F_107


title: s.NJA01501.M16


title: s.NJA01501.M15


title: s.NJA01501.M14


title: s.NJA01501.M12


title: s.NJA01501.M13


title: TM_RT_1027_F_102


title: TM_RT_1023_F_12


title: TM_RT_1239_F_2


title: s.NJA01501.M11


title: s.NJA01501.M07


title: ATAC-seq TP53 KO iPSC doxorubicin #2

city: Salt Lake City

first: Edward

middle: John

last: Grow

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

country: USA

institute: University of Utah

data_processing:
Paired-end, raw read files were first processed by Trim Galore (Babraham Institute) to trim low-quality reads and remove adapters.
Processed reads were then aligned to hg38 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant)
ATAC–seq peaks were called with MACS2 ‘callpeak’ (--B –nomodel –nolambda)
Genome_build: hg38
Supplementary_files_format_and_content: MACS2 peak file in BED format

organism: Homo sapiens

source_name: male FSHD iPSC

growth_protocol: Human PSC were maintained on Matrigel (BD Corning® Matrigel® Matrix, VWR 356231) coated plates using STEM-MACS IPSC-brew (Miltenyi Biotec Inc 130-104-368), passaged using ReLesr (STEMCELL Technologies 05872).

extract_protocol:
cells were processed immediately for ATACseq
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630), and the nuclei were pelleted and resus¬pended in transposase buffer. The Tn5 (Illumina FC-121-1030), and the transposition reaction was carried out for 30 min at 37 °C. After purifica¬tion, the Nextera libraries were amplified for 12 cycles with NEBnext PCR master mix and purified with a Qiagen PCR cleanup kit.

treatment_protocol: Cells were treated with 1uM doxorubicin or DMSO vehicle control for 6H

tag: genotype

value: TP53 KO

tag: cell type

value: iPSC

tag: agent

value: doxorubicin


title: s.NJA01501.M06


title: MDA-MB-231-LM2_rep2

city: Xuzhou

first: Chen-Long

last: Wang

state: Jiangsu

address: No. 209 Tongshan Rd.

country: China

institute: Xuzhou Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination, and then mapped to the hg19 whole genome using Tophat2 v2.0.13 with parameters --read_mismatches 2 --read_gap_length 2 --read_edit_dist 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values (trans.rpkm.txt) and counts (trans.count.txt) for each Sample.

source_name: breast cancer cells

growth_protocol: MDA-MB-231 was cultured in Leibovitz L-15 medium (Gibco) supplemented with 10% FBS, MDA-MB-231-LM2 was cultured in DMEM medium (Hyclone) supplemented with 10% FBS.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: metastatic ability

value: highly pulmonary metastatic


title: MDA-MB-231_rep1

value: parental


title: MDA-MB-231-LM2_rep1


title: MDA-MB-231_rep2


title: s.NJA01501.M09


title: ATAC-seq TP53 KO iPSC doxorubicin #1


title: s.NJA01501.M02


title: s.NJA01501.M01


title: s.NJA01501.M03


title: m.NJA01501.L23


title: ATAC-seq TP53 KO iPSC control #2

value: control


title: m.NJA01501.L20


title: ATAC-seq FSHD iPSC control #1

value: FSHD


title: ATAC-seq FSHD iPSC doxorubicin #2


title: m.NJA01501.L21


title: ATAC-seq FSHD iPSC doxorubicin #1


title: m.NJA01501.L24


title: ATAC-seq FSHD iPSC control #2


title: s.NJA01501.L17


title: s.NJA01501.L16


title: ATAC-seq TP53 KO iPSC control #1


title: s.NJA01501.L18


title: mESC_Nailseq_EH_Pol2-IAA_HU059_LY138d

city: Beijing

first: Chen

last: Ai

address: Yiheyuan Road No.5

institute: Peking University

description: nascent DNA strand

library_source: genomic

data_processing:
Library strategy: NAIL-seq
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
Mapping for NAIL-seq: R1 and R2 reads were stitched using PEAR [74] and the bridge adapter sequences were trimmed with custom scripts. The stitched reads were aligned to the human genome (assembly hg19) or mouse genome (assembly mm10) by BWA-MEM (-k 20). PCR duplicates were distinguished by random molecular barcodes (RMBs) and only one was kept. Then the reads with MAPQ (mapping quality) >= 30 were kept for further analysis. We used samtools to convert .sam files into .bam files.
To generate genome tracks, we converted the .bam files into .BigWig. For NAIL-seq or ORC2 ChIP-seq, files were generated by the bamCoverage (in deepTools) with the parameter --binSize 1000 --normalizeUsing RPKM. For MCM5 ChIP-seq, the fold change value of ChIP-ed samples over input was generated by bamCompare with parameter --binSize 1000, --normalizeUsing RPKM –operation ratio. The data was presented by IGV 2.4.14.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

source_name: mESC

growth_protocol:
K562/GM12878: GM12878 and K562 (3111C0001CCC000039, National Infrastructure of Cell line resource, China) cells were cultured in RPMI1640 media supplied with 15% FBS as described (Rao SS et al., 2014, Cell and Chiarle R. et al., 2011, Cell). For G1 arrest, GM12878 or K562 were incubated with 1 µM or 5 µM palbociclib (SelleckChem) for 36 hours, respectively.
mouse splenic B: The wild-type C57BL/6NCr mice at 6-8 weeks old were used for splenic B cell purification, following the manufacturer’s instructions (EasySep Mouse B cell isolation kit by STEMCELL). Both male and female mice were indiscriminately used in this study. Mice were housed and handled according to the standards set by Peking University laboratory animal center and all animal experiments were approved by the institutional animal care and use committee at Peking University. Naïve splenic B cells were isolated and activated with LPS (25 mg/mL; Sigma) and IL-4 (5 ng/mL; Sigma).
mESC: Murine embryonic stem V6.5 (mES-V6.5) cells were grown in 2i media containing 15% FBS, 1 µM PD0325901 (SelleckChem), 3 µM CHIR99021 (SelleckChem), 1000 U/mL mouse LIF (Millipore) and other described essential supplements. mES-V6.5 cells were always cultured on 0.2% gelatin (Sigma)-treated plates and synchronized by thymidine and nocodazole as described (Ballabeni A et al., 2011, PNAS).

extract_protocol:
Cells were harvested, washed with PBS, and applied to genomic DNA (gDNA) extraction with Proteinase K digestion as described previously.  Purified genomic DNA was subjected to Click reaction with 100 µM Biotin-PEG-azide, 2 mM CuSO4, 4 mM THPTA, and 10 mM Sodium ascorbate at 25℃ for 1 hour, followed by DNA precipitation. The copper in the click reaction hydrolyzes gDNA and fragments it into small fragments (around 200~400 bp in length), resulting in that each fragmented nascent DNA has little chance to contain both EdU and BrdU, simultaneously. Dissolved DNA was denatured at 95℃ for 5 min and phosphorylated by T4 PNK at 37℃ for 30 min.  For EdU/HU-labeled samples, T4 PNK-treated DNA was incubated with C1 beads alone. All of the enrichment steps were performed at room temperature for 4 hours.  Isolated EdU-labeled ssDNA were ligated on-beads with two types of bridge adapters (Bridge adapter -1 and -2, see the resource table for sequence details), simultaneously, at room temperature for at least 4 hours as follow: 1 µM Bridge adapters each, 1,600 U T4 DNA ligase and 15% PEG-8000.
After that, ligated DNA was harshly washed and tagged with Illumina P5-I5 and P7-I7 sequences as described (Yin J, et al., 2019, Cell Discov.).All the libraries were subjected to 2 × 150 bp Hiseq sequencing.

treatment_protocol:
K562/GM12878: For EdU/HU treatment, G1-synchronized GM12878 or K562 cells were released into fresh media with 10 µM EdU plus 5 or 10 mM HU for 24 or 12 hours, respectively. The concentration of EdU is comparable with the endogenous dTTP [68], and EdU can be incorporated into nascent DNA in a very efficient way and 2 minutes are sufficient for EdU to label nascent Okazaki fragments in OK-seq . Moreover, the G1-released K562 cells requires additional 2.5 hours to reach the G1/S transition. Therefore, the initiation sites are hard to escape from EdU labelling in the EdU/HU assay. For ⍺-amanitin or DRB mediated-RNA polymerase II inhibition, G1-arrest K562 cells were released into fresh media containing indicated concentrations of ⍺-amanitin, or DRB, plus HU and EdU for 12 hours.
mouse splenic B:The B cells were treated with 10 mM HU and 10 µM EdU for 28 hours from activation. For ⍺-amanitin treatment, primary B cells were incubated with 10 mM HU, 10 µM EdU, and ⍺-amanitin for 28 hours once LPS and IL-4 were added.
mESC: Mitotically arrested cells were shaken off, washed by pre-warmed 2i media, cultured in fresh media for 1.5 hours. To reduce replication fork progression speed, M phase synchronized mES cells were released into fresh media and incubated with 4 mM HU and 50 µM EdU for 3 hours. For the degradation of RNA polymerase II, the homozygous mAID-tagged RNA polymerase II cells were synchronized as wild-type cells. 1 ug/mL Doxycycline (Dox) was added to induce the production of OsTIR1. 500 uM IAA was added at 1 hour before releasing from nocodazole to induce the degradation of RNA polymerase II. The nocodazole-arrested cells were then cultured in the presence of Dox, IAA, EdU, and HU for 3 hours before harvesting.

value: mouse embryonic stem cells

tag: technique

value: NAIL-seq

tag: nail-seq labeling strategy

value: EdU/HU

tag: treatment

value: Pol2-mAID IAA treated

tag: cell phase

value: S

tag: purified antibody/biotin

value: EdU

tag: protocol

value: Protocol 2:NAIL-seq EdU/HU


title: s.NJA01501.L15

tag: strain

tag: tissue

value: Singlet


title: s.NJA01501.L11


title: mESC_Nailseq_EH_WT_HU037_LY096h

description: nascent DNA strand

value: WT


title: mESC_Nailseq_EH_Pol2_HU059_LY138c

description: nascent DNA strand

value: Pol2-mAID untreated


title: mESC_Nailseq_EH_WT-IAA_HU059_LY138b

description: nascent DNA strand

value: WT IAA treated


title: s.NJA01501.L09


title: mouseSB_Nailseq_EH_ama2_HU020_LY069e

description: nascent DNA strand

source_name: mouseSB

value: mouse spleenic primary B cells

value: WT ama 2ug/mL


title: s.NJA01501.L12


title: mouseSB_Nailseq_EH_ama1_HU020_LY069d

description: nascent DNA strand

value: WT ama 1ug/mL


title: mouseSB_Nailseq_EH_ama0.5_HU020_LY069c

description: nascent DNA strand

value: WT ama 0.5ug/mL


title: s.NJA01501.L08


title: mouseSB_Nailseq_EH_EdUHU_HU037_LY096b

description: nascent DNA strand

value: WT untreated


title: s.NJA01501.L10


title: mouseSB_Nailseq_EH_ama0_HU020_LY069b

description: nascent DNA strand


title: NCAM-1 WT VM3

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Genome_build: mm10
Supplementary_files_format_and_content: Count Tables (.txt)  BigWig files (.bw)

extract_protocol:
PicoPure RNA Isolation Kit
RNA from adult mouse hearts was extracted from cells captured onto thermoplastic film using the PicoPure RNA Isolation Kit (Arcturus Engineering, Mountain View, CA). RNA from NRVMs was extracted using silica-membrane spin columns from the RNeasy Plus Mini Kit (Qiagen, Netherlands). For RNA-seq, RNA from sorted Purkinje cells and Ventricular Myocytes cells, was amplified and libraries prepared using the Automated Nugen Ovation Trio Low input RNA (Nugen). RNAseq experiments were done at the NYU School of Medicine Genome Technology center. Samples from were sequenced 50 bp paired-ended at 10 million to 20 million reads per replicate on an Illumina HiSeq2500 instrument. All the reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.5.0c). Alignments were guided by a Gene Transfer File (GTF, version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard/). The read count tables were generated using HTSeq (v0.6.0) and normalized based on their library size factors using DESeq2 (v3.0) and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4), and downstream statistical analyses and generating plots were performed in R environment (v3.1.1) (http://www.r-project.org/).

treatment_protocol: Ventricular cardiomyocytes and Purkinje cells were dissociated from Ncam-1 WT and Ncam-1 KO crossed with Cntn2-EGFP mice. Hearts were Langendorff perfused and enzymatically digested. Tetramethylrhodamine methyl ester perchlorate (TMRM, Invitrogen) mitochondrial dye was used to identify cardiomyocytes and sort them into RFP+ population. Dissociated ventricular cardiomyocytes were incubated with 50 nM TMRM for 15 minutes and purified using the On-Chip microfluidic cell sorter using a 150m-wide sorting chip into PC (RFP+GFP+) and VM (RFP+GFPâ€“) populations.

value: NCAM-1 WT


title: s.NJA01501.L07


title: NCAM-1 WT VM2


title: NCAM-1 WT VM1


title: m.NJA01501.L19

value: Multiplet


title: s.NJA01501.L06


title: s.NJA01501.L04


title: m.NJA01501.K23


title: m.NJA01501.K22


title: NCAM-1 WT PC1


title: NCAM-1 WT PC2


title: s.NJA01501.L02


title: NCAM-1 KO VM2

value: NCAM-1 KO


title: NCAM-1 KO VM3


title: m.NJA01501.K21


title: NCAM-1 WT PC3


title: NCAM-1 KO VM1


title: m.NJA01501.K19


title: s.NJA01501.K17


title: NCAM-1 KO PC2


title: m.NJA01501.K20


title: NCAM-1 KO PC3


title: s.NJA01501.K16


title: NCAM-1 KO PC1


title: s.NJA01501.K15


title: s.NJA01501.K13


title: CAG-Dmrt1 ATAC-seq rep 1 (6 DPTx)

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
processed data file:
CAGDmrt1_Granulosa_Cells_ATACseq_6_DPTx.bigWig
Supplementary_Table_2.xlsx

data_processing:
For each of the experiments, reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). STAR (v2.7.2a), BWA mem (v0.7.12) and HiC-Pro (v2.11.4) were used to map transcriptomic (RNA-seq), genomic (ChIP-seq, ATAC-seq) and 3D (Hi-C) trimmed reads to the GRCm38 (mm10) genome respectively
The GENCODE M23 gene annotation set was used to estimate strand-specific gene expression data in the RNA-seq data with the Bioconductor package RSubread (v1.28.1) and to assign the locations of nearby genes in the ATAC-seq datasets. For ChIP-seq and ATAC-seq experiments, duplicated reads were removed with Picard MarkDuplicates (v2.17.10) and low quality reads (MAPQ < 55) or reads that mapped to the mitochondrial genome were removed with SAMtools (v1.0).
MACS2 (v2.1.1.20160309) was used to call peaks in the ChIP-seq and ATAC-seq datasets using the parameters ‘-call-summits -m 2 20’ and ‘--nomodel –broad’ respectively
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tables of expression values and fold changes in gene expression, bigWig Coverage files and called peaks.

source_name: Cultured Granulosa Cells

extract_protocol: ATAC-seq was performed using 50,000 freshly isolated cells.  Transposition and library prep were performed as described in PMID: 25559105.

treatment_protocol: Tamoxifen treatments began on day 2 of culture (24 hr after plating).  Immediately prior to treatment, 2 mM 4-hydroxytamoxifen (in ethanol; Sigma H7904) was diluted to 2 uM in serum-free McCoy 5A with 0.1% BSA, 1X ITSS supplement (Sigma I1884) and 1X Pen/Strep. Cells were tamoxifen-treated for 48 hours before replacing media with complete media. Thereafter, media was changed every 2-3 days until the indicated timepoint.

tag: genoype

value: CAG-Stopflox-Dmrt1-eGfp;  UBC-CreERT2

tag: strain background

value: Mixed 129Sv and C57Bl/6J

tag: tamoxifen time point

value: 6 DPTx

tag: antibody


title: CAG-Dmrt1 ATAC-seq rep 3 (6 DPTx)

tag: age


title: CAG-Dmrt1 ATAC-seq rep 2 (6 DPTx)


title: Control for CAG-Dmrt1 ATAC-seq rep 2 (6 DPTx)

description:
processed data file:
Control_for_CAGDmrt1_Granulosa_Cells_ATACseq_6_DPTx.bigWig
Supplementary_Table_2.xlsx


title: s.NJA01501.L03

tag: facs cellnumber

tag: age (days)


title: s.NJA01501.K09


title: s.NJA01501.K08


title: CAG-Dmrt1 α-SOX9 ChIP-seq (6 DPTx)

description:
processed data file:
Supplementary_Table_2.xlsx

extract_protocol: Cells were fixed with 1% methanol-free formaldehyde in PBS (Thermo scientific #28906) for five minutes at RT with rotation.  Fixation was stopped by addition of glycine to 0.125M and rotation at RT for 10 min.  After pelleting, cells were washed in PBS and stored at -80o C until use.  Sertoli cell ChIP was performed with about 2.5 million cells and granulosa cell ChIP with about 1 million cells.  Nuclei were prepared from the fixed cells and chromatin was sheared to an average size of 300-400 bp in a Covaris S220 according to the manufacturer’s recommendations.  After shearing, the lysate was diluted 1:3 with complete DOC RIPA (37) and the sample was centrifuged at 21,000g for ten minutes at 4o C to pellet any insoluble material.  The supernatant was transferred to a fresh siliconized tube and the ChIP was initiated with the addition of ~1 ug of the relevant antibody and rotated at 4o C overnight.  Samples were then spun at 21,000g for 10 min. to pellet insoluble material and supernatant was mixed with 20 ul Protein A Dynabeads (Invitrogen, 10002D) previously blocked with BSA and yeast tRNA to inhibit non-specific binding.  After incubation at 4o C for 60 min. with rotation to allow association of protein A with the antibody, beads were applied to a magnet and washed sequentially as described previously (37).  After elution and cross link reversal, sequencing libraries were prepared using the Hyper Prep Kit (KAPA Biosystems, KK8502). Whole gonad ChIP-seq was performed essentially the same as for primary cells ChIP-seq except gonads from 2-3 animals were pooled and fixed in 1% paraformaldehyde (Electron Microscopy Sciences #15710) for 10 min. (ESR2 and FOXL2) or fixed in 2 mM disuccinimidyl glutarate (DSG, ThermoFisher Scientific #20593) at RT for 45 min. followed by 1% paraformaldehyde fixation at RT for 15 minutes (SOX9).  After quenching the fix with 0.125M glycine, chromatin was sheared to an average size of 300-500 bp using a tip sonicator.


title: s.NJA01501.K07


title: CAG-Dmrt1 α-DMRT1 ChIP-seq (6 DPTx)


title: s.NJA01501.K04


title: CAG-Sox9 α-SOX9 ChIP-seq  (6 DPTx)

value: CAG-mRFP1 floxed-Sox9-eGFP; UBC-CreERT2


title: XX Gonad CAG-Dmrt1 α-SOX9 ChIP-seq (8w)

source_name: Ovary

value: 8 weeks


title: XX Gonad CAG-Dmrt1 α-DMRT1 ChIP-seq (8w)


title: s.NJA01501.K01

value: Singlet


title: s.NJA01501.K02


title: s.NJA01501.K03


title: Testis Input Dmrt1 flox/flox; Dhh-Cre (P9)

source_name: Testis

value: Dmrt1 flox/flox; Dhh-Cre

value: 9 days


title: Testis α-H3K27ac ChIP-seq Dmrt1 flox/flox; Dhh-Cre (P9)

value: Abcam ab4729


title: s.NJA01501.K12


title: Testis α-H3K27ac ChIP-seq Dmrt1 flox/flox (P9)

value: Dmrt1 flox/flox


title: m.NJA01501.J23


title: Control for CAG-Dmrt1 ATAC-seq rep 3 (6 DPTx)


title: m.NJA01501.J24


title: m.NJA01501.J21


title: Sertoli α-DMRT1 ChIP-seq rep 1 (P7)

description:
processed data file:
Sertoli_DMRT1_ChIPseq_P7.bigWig
Supplementary_Table_2.xlsx

source_name: Sertoli Cells

value: CAG-Stopflox-tdTomato; Dhh-Cre

value: 7 days


title: CAG-Sox9 2 DPTx rep3

description:
processed data file:
Supplementary_Table_3.xlsx
Supplementary_Table_4.xlsx

extract_protocol: Cells or tissues were harvested into 1 ml Trizol reagent and stored at -80o C.  Total RNA was prepared according to Trizol reagent manufacturer’s protocols and further cleaned up using RNAeasy kit protocols and reagents (Qiagen).  RNA was quantified via Qubit RNA assay, and 500 ng total RNA per sample were used in stranded mRNA-seq library preparation (KAPA Biosystems, KK8481) for Illumina sequencing.

value: 2 DPTx


title: s.NJA01501.K10


title: m.NJA01501.J22


title: Testis Input Dmrt1 flox/flox (P9)


title: Control for CAG-Dmrt1 ATAC-seq rep 1 (6 DPTx)


title: CAG-Dmrt1 1 DPTx rep4

value: 1 DPTx


title: m.NJA01501.J19


title: m.NJA01501.J20


title: CAG-Dmrt1 2 DPTx rep4


title: s.NJA01501.K05


title: s.NJA01501.J16


title: s.NJA01501.J15


title: s.NJA01501.J14


title: CAG-Dmrt1 1 DPTx rep3


title: s.NJA01501.J13


title: Sertoli Input rep 1 (P7)


title: Control 2 DPTx rep5


title: s.NJA01501.J12


title: Control 1 DPTx rep5


title: Control 6 DPTx rep6


title: Control 0 DPTx rep6

value: CAG-mRFP1 floxed-Sox9-eGFP

value: 0 DPTx


title: s.NJA01501.J09


title: s.NJA01501.J10


title: CAG-Dmrt1 2 DPTx rep3


title: CAG-Dmrt1 6 DPTx rep4


title: s.NJA01501.J08


title: CAG-Dmrt1 0 DPTx rep3


title: s.NJA01501.J07


title: CAG-Sox9 1 DPTx rep3


title: s.NJA01501.J17


title: s.NJA01501.J18


title: s.NJA01501.J06


title: CAG-Sox9 1 DPTx rep2


title: Control 1 DPTx rep4


title: s.NJA01501.J04


title: Control 0 DPTx rep5


title: s.NJA01501.J02


title: s.NJA01501.J03


title: CAG-Sox9 1 DPTx rep1


title: CAG-Sox9 6 DPTx rep4


title: m.NJA01501.I24

value: Multiplet


title: s.NJA01501.J11


title: m.NJA01501.I23


title: Control 6 DPTx rep5


title: m.NJA01501.I22


title: m.NJA01501.I21


title: Control 0 DPTx rep4


title: CAG-Sox9 6 DPTx rep3


title: CAG-Sox9 0 DPTx rep2


title: m.NJA01501.I20


title: CAG-Sox9 6 DPTx rep2


title: m.NJA01501.I19


title: CAG-Sox9 0 DPTx rep3


title: CAG-Dmrt1 6 DPTx rep3

value: CAG-Stopflox-Dmrt1-eGfp;  UBC-CreERT2


title: s.NJA01501.I18


title: s.NJA01501.I17


title: CAG-Dmrt1 1 DPTx rep2

value: Mixed 129Sv and C57Bl/6J


title: s.NJA01501.I16


title: s.NJA01501.I15


title: Control 1 DPTx rep3


title: Control 2 DPTx rep4


title: Control 2 DPTx rep3


title: CAG-Sox9 2 DPTx rep2


title: s.NJA01501.I14


title: CAG-Sox9 2 DPTx rep1


title: s.NJA01501.I13


title: CAG-Dmrt1 6 DPTx rep2

value: 6 DPTx


title: s.NJA01501.I12


title: s.NJA01501.I11


title: s.NJA01501.I07


title: s.NJA01501.I06


title: Control 6 DPTx rep4


title: s.NJA01501.I04


title: Control 0 DPTx rep3


title: CAG-Sox9 6 DPTx rep1

value: CAG-mRFP1 floxed-Sox9-eGFP; UBC-CreERT2


title: s.NJA01501.I01


title: s.NJA01501.I02


title: CAG-Dmrt1 2 DPTx rep2


title: s.NJA01501.I03


title: Control 6 DPTx rep3


title: m.NJA01501.H22


title: s.NJA01501.I08


title: Control 6 DPTx rep2


title: m.NJA01501.H21


title: CAG-Sox9 0 DPTx rep1


title: CAG-Dmrt1 0 DPTx rep2


title: Control 0 DPTx rep2


title: Control 1 DPTx rep2


title: m.NJA01501.H19


title: s.NJA01501.H17


title: s.NJA01501.H18


title: Control 6 DPTx rep1


title: s.NJA01501.H16


title: CAG-Dmrt1 6 DPTx rep1


title: Control 2 DPTx rep2


title: Control 2 DPTx rep1


title: s.NJA01501.H15


title: CAG-Dmrt1 2 DPTx rep1


title: CAG-Dmrt1 1 DPTx rep1


title: s.NJA01501.H14


title: Control 1 DPTx rep1


title: s.NJA01501.H12


title: CAG-Dmrt1 0 DPTx rep1


title: m.NJA01501.H24


title: Control 0 DPTx rep1


title: s.NJA01501.H10


title: s.NJA01501.H11


title: s.NJA01501.H08


title: s.NJA01501.H07


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 Ovary rep6

value: Adult


title: s.NJA01501.H05

value: Singlet


title: Sox8+/-;Sox9-/-;CAG-Dmrt1 Ovary rep2


title: s.NJA01501.H03


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 Ovary rep5


title: s.NJA01501.H09


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 Ovary rep4


title: s.NJA01501.H02


title: Sox8+/-;Sox9+/-;CAG-Dmrt1 Ovary rep2


title: s.NJA01501.H01


title: m.NJA01501.G24


title: Sox8+/-;Sox9+/-;CAG-Dmrt1 Ovary rep1


title: m.NJA01501.G23


title: Sox8-/-;Sox9+/-;CAG-Dmrt1 Ovary rep2


title: Sox8-/-;Sox9+/-;CAG-Dmrt1 Ovary rep3


title: m.NJA01501.G22


title: Sox8-/-;Sox9-/- Ovary rep1


title: m.NJA01501.G20


title: Sox8-/-;Sox9-/- Ovary rep2


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 Ovary rep3


title: m.NJA01501.G19


title: Sox8+/+;Sox9-/-;CAG-Dmrt1 Ovary rep1


title: s.NJA01501.G17


title: s.NJA01501.G15


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 Ovary rep2


title: CAG-Dmrt1 Ovary Rep2


title: s.NJA01501.G14


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 Ovary rep1


title: s.NJA01501.G13


title: Wild Type Ovary Rep2

value: wild type


title: s.NJA01501.G12


title: Sox8-/-;Sox9+/-;CAG-Dmrt1 Ovary rep1


title: Wild Type Ovary Rep1


title: Freshly Isolated Sertoli Cells Rep2


title: s.NJA01501.G11


title: s.NJA01501.G10


title: m.NJA01501.G21


title: Freshly Isolated Sertoli Cells Rep1


title: Sox8+/-;Sox9-/-;CAG-Dmrt1 Ovary rep1


title: s.NJA01501.G08


title: s.NJA01501.G07


title: s.NJA01501.G06


title: s.NJA01501.G05


title: s.NJA01501.G09


title: 15208x14: H3K9me3 ChIP-seq, vehicle control rep #2

data_processing:
bbduk v36.38 read trimming
Processed reads were then aligned to mm10 with Bowtie2 (v2.2.6) with the following parameters (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant)
Peaks were called using combined 2 biological replicates with MACS2 2.2.5 'callpeak' (--f BAMPE --B --SPMR)
Genome_build: mm10+Dux contig
Supplementary_files_format_and_content: Bedfile of peaks

growth_protocol: Mycoplasma-free E14 mESCs were cultured on gelatin in 2i+LIF medium containing Gibco KO-DMEM with nonessential amino acids, 2-mercaptoethanol, and dipeptide glutamine, and were supplemented with 15% ES-grade FBS, leukemia inhibitory factor (LIF) (Thermo Fisher), 1 mM PD0325901 (Sigma-Aldrich), and 3 mM CHIR99021 (Sigma-Aldrich). Stable cell lines were selected using puromycin (Thermo Fisher Scientific A11138-03) at 0.5-1 ug/mL, Geneticin (Life Technologies 10131-035) at 100-200ug/mL, or Blasticidin (Fisher Scientific B12150-0.1) at 1.5-3ug/mL.

extract_protocol:
ChIP assays were performed from approximately 107 cells per experiment, according to previously described protocol with slight modifications (Rada-Igelsias, Nature 2010).  Briefly, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and formaldehyde was quenched by addition of glycine to a final concentration of 0.125 M. Chromatin was sonicated to an average size of 100-600 bp, using Bioruptor Pico (Diagenode). 50–75 µl of protein G dynal beads (Invitrogen) were used to capture 3–5 µg of antibody in phosphate citrate buffer pH 5.0 (2.4 mM citric acid, 5.16 mM Na2HPO4) for 30 min at 27 °C. Antibody bead complexes were rinsed two times with PBS and added to sonicated chromatin and rotated at 4 °C overnight. Ten per cent of chromatin was reserved as ‘input’ DNA. Magnetic beads were washed 5 times with 500mM LiCl wash buffer and once with 50mM NaCl+TE and chromatin eluted, followed by reversal of the crosslinkings and DNA purification. Resultant ChIP DNA was dissolved in TE.fter reversal of cross-links, libraries were prepared with an NEBnext DNA Library Prep kit (NEB, E7370L). Adaptor-ligated DNA was then size-selected and purified with AMPure XP beads (Beckman Coulter) and PCR amplified as above (see RNA-seq library prep). HA epitope tag (for p53-HA) abcam ab91110; H3K9me3 (active motif 39161); H3K27ac (abcam 4729).
After reversal of cross-links, libraries were prepared with an NEBnext DNA Library Prep kit (NEB, E7370L). Adaptor-ligated DNA was then size-selected and purified with AMPure XP beads (Beckman Coulter) and PCR amplified as above (see RNA-seq library prep).

treatment_protocol: mESC were treated with 1uM doxorubicin for 6 hours and then media was replaced with non-drug containing media. Control cells were treated with DMSO vehicle control for 6 hours and then media was replaced. 6-hour washout was performed and cells were harvested at 12H after onset of doxR/veh treatment

tag: cell type

value: mESC

tag: chip antibody

value: H3K9me3 control ChIP


title: CAG-Dmrt1 Ovary Rep1


title: 15208x13: H3K9me3 ChIP-seq, vehicle control rep #1


title: 15209X11: H3K27ac ChIP-seq, doxorubicin treated rep #1

value: H3K27ac doxrubicin ChIP


title: s.NJA01501.G02


title: m.NJA01501.F24


title: 15209X12: H3K27ac ChIP-seq, doxorubicin treated rep #2


title: m.NJA01501.F22


title: 15209X09: H3K27ac ChIP-seq, vehicle control rep #1

value: H3K27ac control ChIP


title: 15208x15: H3K9me3 ChIP-seq, doxorubicin treated rep #1

value: H3K9me3 doxorubicin ChIP


title: 15209X10: H3K27ac ChIP-seq, vehicle control rep #2


title: s.NJA01501.G16


title: m.NJA01501.F23


title: 15209X08: p53 (HA IP) ChIP-seq rep #1

value: HA-p53 ChIP


title: Freshly Isolated Granulosa Cells Rep1

source_name: Granulosa Cells


title: m.NJA01501.F21


title: 15209X07: p53 (HA IP) ChIP-seq rep #1


title: 15208x16: H3K9me3 ChIP-seq, doxorubicin treated rep #2


title: 15209X06: HA no tag control ChIP rep #2

value: HA control ChIP


title: m.NJA01501.F20


title: m.NJA01501.F19


title: s.NJA01501.F18


title: s.NJA01501.F17


title: 15209X04: input control rep #2, doxorubicin treated

value: input control


title: s.NJA01501.G03


title: mESC vehicle treated control #2

data_processing:
bbduk v36.38 read trimming
Processed reads were then aligned to mm10 with Bowtie2 (v2.2.6) with the following parameters (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant)
Peaks were called using combined 2 biological replicates with MACS2 2.2.5 'callpeak' (--f BAMPE --B --SPMR)
Genome_build: mm10+dux contig
Supplementary_files_format_and_content: Bed file

extract_protocol:
Cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630), and the nuclei were pelleted and resuspended in transposase buffer. The Tn5 (Illumina FC-121-1030), and the transposition reaction was carried out for 30 min at 37 °C. After purification, the Nextera libraries were amplified for 12 cycles with NEBnext PCR master mix and purified with a Qiagen PCR cleanup kit.
PCR with NEB phusion master mix, 12-15 PCR cycles


title: s.NJA01501.F16


title: Freshly Isolated Granulosa Cells Rep2


title: mESC vehicle treated control #1


title: s.NJA01501.F15


title: s.NJA01501.G04


title: 15209X05: HA no tag control ChIP rep #1


title: s.NJA01501.F14


title: mESC 12 hours doxorubicin treated rep #2


title: mESC 12 hours doxorubicin treated rep #1


title: s.NJA01501.F11


title: mESC 6 hours doxorubicin treated rep #2


title: mESC 6 hours doxorubicin treated rep #1


title: s.NJA01501.F10


title: s.NJA01501.F09


title: s.NJA01501.F08


title: IL-17D KO_ILC3

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Clean reads were aligned to mm10 by bowtie2 with default parameters
Uniquely mapping reads were summarized by featureCounts(from Subread package)
RPKM (Reads Per Kilobase of exon model per Million mapped reads) were calculated using edgeR TMM normalization
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05 using Deseq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited xlsx files include gene symbol and gene expression (or read count) for each sample

source_name: small intestine

growth_protocol: Cell suspension were cultured for 12hrs without any stimulation before the sorting of CD93+ and CD93- ILC3

extract_protocol: The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions

tag: state

value: steady state

value: small intestine

tag: genotype


title: CD93-positive

tag: sorting


title: s.NJA01501.F07


title: s.NJA01501.F06


title: F2138_sftpc-GFP_adult

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
Fastq files were aligned to the mm9 reference genome using STAR and default parameters
Ensmebl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: mm9
Supplementary_files_format_and_content: Voom transformed abundance measurements

source_name: Lung

growth_protocol: Sftpc-eGFP and Hopx-3XFLAG-GFP mice were bred to wild-type animals to generate heterozygous offspring at embryonic day 15.5, embryonic day 18.5, postnatal day 4, and postnatal day 42. The date of plug was considered embryonic day 0.5, and the date of birth considered postnatal day 0. Two mice of each genotype at each developmental time point were harvested, lungs dissociated into single cell suspensions, and sorted using FACS to yield enriched populations of AT1 and AT2 cells. RNA was extracted from these populations, analyzed by BioA pico chips and sent for library preparation and sequencing.

extract_protocol: Distal lung lobule dissociation with dispase, collagenase, and DNAse, followed by single cell suspension and fluorescece-activated cell sorting. Isolated cells were frozen in trizol, and RNA was prepared using standard methods and cleaned up over a column followed by library preparation

value: Lung

value: Sftpc-GFP Transgene

value: Mixed background; CD-1


title: 15209X03: input control rep #1, doxorubicin treated


title: WT_ILC3

value: Wild type


title: M2136_sftpc-GFP_adult

value: enriched populations of AT1 and AT2 cells

value: Adult


title: s.NJA01501.F05

value: Singlet


title: F0033-02_sftpc-GFP_P4


title: s.NJA01501.F04


title: s.NJA01501.F01


title: m.NJA01501.E24

value: Multiplet


title: s.NJA01501.F12


title: F8401-3_sftpc-GFP_e18.5


title: F8401-2_sftpc-GFP_e18.5


title: s.NJA01501.F03


title: m.NJA01501.E23


title: m.NJA01501.E22


title: s.NJA01501.F13


title: F0003_sftpc-GFP_e15.5


title: F0140_Hopx-GFP_adult


title: F0011_bright_sftpc-GFP_e15.5


title: CD93-negative


title: M0029_Hopx-GFP_adult


title: m.NJA01501.E20


title: m.NJA01501.E19


title: m.NJA01501.E21


title: F8402-02_Hopx-GFP_e18.5


title: s.NJA01501.E18


title: s.NJA01501.E17


title: F8402-01_Hopx-GFP_e18.5


title: F0033-01_sftpc-GFP_P4


title: s.NJA01501.E16


title: F0012-01_Hopx-GFP_e18.5


title: s.NJA01501.E14


title: F0012-02_Hopx-GFP_e18.5


title: F0008_Hopx-GFP_e15.5


title: s.NJA01501.E15


title: s.NJA01501.E13


title: s.NJA01501.E09


title: F0027_Hopx-GFP_e15.5


title: s.NJA01501.E11


title: s.NJA01501.E08


title: SLE3

city: Jackson

first: Kurt

middle: C

last: Showmaker

state: MS

address: 2500 North State St.

department: Pharmacology and Toxicology

institute: UMMC

data_processing:
Basecalling with cellranger-3.1.0 mkfastq function and bcl2fastq2-v2.20 with cellranger default parameters.
Cell counting cellranger-3.1.0 count function with cellranger default parameters.
Aggregate samples with the cellranger-3.1.0  aggr function with cellranger default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5/h5) file was generated with cellranger-3.1.0 and contains per-molecule information for all molecules that contain a valid barcode and valid UMI and were assigned with high confidence to a gene or Feature Barcode. This HDF5 file contains data corresponding to the observed molecules, as well as data about the libraries and feature set(s) used.
Supplementary_files_format_and_content: aggregation.csv is the aggregation CSV that reflects the order of samples used in the cellranger aggergation.
Supplementary_files_format_and_content: barcode tsv files contain the 10 genomic GEW data output by the cellranger aggergation data processing step.
Supplementary_files_format_and_content: features tsv contain the gene features counted in the analysis output by the cellranger aggergation data processing step.
Supplementary_files_format_and_content: matrix mtx files contatin the counts for the data output by the cellranger aggergation data processing step.

growth_protocol: Seven-to-eight-week-old female New Zealand Black (NZB), New Zealand White (NZW), and New Zealand Black-White F1 (NZBWF1) mice (n = 3) were purchased from The Jackson Laboratory, and were delivered at the same time.  Animals were maintained on a 12-hour day/night cycle and allowed to feed (standard chow) and drink ad libitum until they reached 9 - 10 weeks of age to conduct the study.

extract_protocol:
RNA extraction was conduced with the 10x Chromium Single Cell 3’ v3.1 Reagent Kit (10x Genomics Product Code 1000268).
Libraries were constructed with the 10x Chromium Single Cell 3’ v3.1 Reagent Kit (10x Genomics Product Code 1000268).

tag: Sex

value: female

tag: developmental stage

value: adult

value: femur bone marrow


title: SLE2


title: NZW3

value: New Zealand White


title: NZW1


title: NZB3

value: New Zealand Black


title: s.NJA01501.E05


title: NZB2


title: SLE1


title: s.NJA01501.E10


title: NZW2


title: s.NJA01501.E06


title: s.NJA01501.E07


title: s.NJA01501.E04


title: NZB1


title: s.NJA01501.E03


title: m.NJA01501.D23


title: s.NJA01501.E02


title: Treg.VAT.IL-33.invitro#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Treg

extract_protocol:
1,000 Cells were double-sorted by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: For the HFD dataset, 12-week-old vTreg53 TCR tg mice were fed with NCD or HFD for 2, 4, 8, or 16 weeks. The clonotype+ Tregs from the spleen and VAT of recipient mice were double sorted and processed for RNA-seq. For the in vitro dataset, 8-10-week-old PPARγ-tdT Foxp3-GFP mice were injected with two doses of IL-33 in a week to expand VAT-Treg cells, and PPARγ(tdT)+ VAT-Treg cells were sorted and cultured in the presence of 10ng/ml IL-33, 2000U/ml IL-2, with or without 50ng/ml IFNa for 3 days. Foxp3/GFP+ Treg cells were sorted and processed for RNA-Seq.

value: visceral adipose tissue

value: PPARgamma-tdT KI/KI Foxp3-GFP KI/y


title: m.NJA01501.D20


title: Treg.VAT.IL-33+IFNa.invitro#1


title: m.NJA01501.D21


title: Treg.VAT.IL-33.invitro#1


title: Treg.VAT.IL-33+IFNa.invitro#2


title: Tg+.HFD.W16.VAT.Treg#3

value: vTreg53 Tg+

tag: time point

tag: diet

value: HFD


title: m.NJA01501.D19

tag: strain

tag: tissue


title: Tg+.HFD.W16.VAT.Treg#1


title: Tg+.HFD.W16.VAT.Treg#2


title: s.NJA01501.D17


title: s.NJA01501.D18


title: s.NJA01501.D14


title: s.NJA01501.D16


title: Tg+.HFD.W8.VAT.Treg#3


title: s.NJA01501.D15


title: Tg+.HFD.W8.VAT.Treg#1


title: Tg+.HFD.W8.VAT.Treg#2


title: s.NJA01501.D12


title: s.NJA01501.D11


title: s.NJA01501.D13


title: Tg+.HFD.W4.VAT.Treg#2


title: Tg+.HFD.W2.VAT.Treg#3


title: s.NJA01501.D09


title: Tg+.HFD.W4.VAT.Treg#3


title: s.NJA01501.D07


title: s.NJA01501.D10


title: Tg+.HFD.W2.VAT.Treg#2


title: Tg+.HFD.W2.VAT.Treg#1


title: Tg+.NCD.W16.VAT.Treg#2

value: NCD


title: Tg+.NCD.W16.VAT.Treg#3


title: s.NJA01501.D05


title: Treg.VAT.IL-33.invitro#2


title: Tg+.NCD.W8.VAT.Treg#3


title: s.NJA01501.D06


title: Tg+.NCD.W8.VAT.Treg#2


title: s.NJA01501.D04


title: s.NJA01501.D03


title: m.NJA01501.C23


title: Tg+.NCD.W4.VAT.Treg#1


title: Tg+.NCD.W4.VAT.Treg#2


title: Tg+.NCD.W2.VAT.Treg#3


title: m.NJA01501.C21


title: s.NJA01501.D02


title: Tg+.NCD.W4.VAT.Treg#3


title: m.NJA01501.C24


title: m.NJA01501.C22


title: m.NJA01501.C19


title: m.NJA01501.C20


title: Tg+.W0.VAT.Treg#2


title: Tg+.NCD.W2.VAT.Treg#2


title: Tg+.NCD.W2.VAT.Treg#1


title: Tg+.W0.VAT.Treg#3


title: Tg+.HFD.W16.Sp.Treg#2


title: s.NJA01501.C15


title: s.NJA01501.C16


title: s.NJA01501.C18


title: s.NJA01501.C14


title: Tg+.W0.VAT.Treg#1


title: Tg+.NCD.W8.VAT.Treg#1


title: s.NJA01501.C17


title: Tg+.HFD.W16.Sp.Treg#3


title: Tg+.HFD.W8.Sp.Treg#3


title: s.NJA01501.D01


title: Tg+.HFD.W16.Sp.Treg#1


title: s.NJA01501.C12


title: Tg+.HFD.W4.Sp.Treg#3


title: Tg+.HFD.W8.Sp.Treg#1


title: s.NJA01501.C11


title: Tg+.HFD.W4.Sp.Treg#1


title: s.NJA01501.C10


title: Tg+.HFD.W4.Sp.Treg#2


title: s.NJA01501.C08


title: s.NJA01501.C07


title: Tg+.HFD.W2.Sp.Treg#2


title: Tg+.HFD.W2.Sp.Treg#1


title: Tg+.HFD.W8.Sp.Treg#2


title: Tg+.NCD.W16.Sp.Treg#2


title: Tg+.NCD.W16.Sp.Treg#1


title: s.NJA01501.C13


title: s.NJA01501.C03


title: s.NJA01501.C01


title: s.NJA01501.C02


title: Tg+.NCD.W8.Sp.Treg#2


title: m.NJA01501.B23


title: Tg+.NCD.W4.Sp.Treg#2


title: m.NJA01501.B22


title: Tg+.NCD.W4.Sp.Treg#1


title: Tg+.HFD.W2.Sp.Treg#3


title: m.NJA01501.B21


title: m.NJA01501.B20


title: s.NJA01501.C09


title: Tg+.NCD.W2.Sp.Treg#1


title: Tg+.NCD.W2.Sp.Treg#3


title: Tg+.NCD.W2.Sp.Treg#2


title: s.NJA01501.C05


title: s.NJA01501.C06


title: Tg+.NCD.W16.Sp.Treg#3


title: m.NJA01501.B19


title: s.NJA01501.B18


title: s.NJA01501.B17


title: Tg+.W0.Sp.Treg#3


title: s.NJA01501.C04


title: Tg+.NCD.W8.Sp.Treg#3


title: Tg+.NCD.W8.Sp.Treg#1


title: Tg+.W0.Sp.Treg#2


title: s.NJA01501.B15


title: s.NJA01501.B13


title: ATAC-Seq_NB508_shEVI1

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference mouse (mm9) genome assembly using Bowtie2 allowing two-mismatches for only unique alignment. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net). HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using makeBigwig.pl script of HOMER suite.

source_name: KPC mouse

growth_protocol: Mouse PDA cell lines were cultured in conditions as described in this study.

extract_protocol:
Nuclear extract were prepared from 50,000 single cell dissociated of cell lines, incubated with Tn5 transposase, and purified with Qiagen MinElute kit for library construction.
Sequencing libraries were constructed using the Illumina Nextera DNA Sample prep kit, as described in Corces et al, 2017 (PMID: 28846090).

treatment_protocol: (for Tet-ON system only) treated with doxycycline (1 uM) as indicated.

tag: cell line

value: NB508 cells

tag: transgene

tag: treatment


title: s.NJA01501.B14


title: ATAC-Seq_T3-2D_Tet-EVI1_Dox48h

value: T3-2D cells

value: Doxycycline, 48 hr


title: ATAC-Seq_T3-2D_Tet-EVI1_Dox72h

value: Doxycycline, 72 hr


title: s.NJA01501.B12


title: ATAC-Seq_T3-2D_Tet-EVI1_Dox24h

value: Doxycycline, 24 hr


title: s.NJA01501.B10

value: Singlet


title: s.NJA01501.B11


title: ATAC-Seq_T3-2D_Tet-EVI1_Dox0h

value: Doxycycline, 0 hr


title: Tg+.W0.Sp.Treg#1


title: s.NJA01501.B07


title: s.NJA01501.B09


title: s.NJA01501.B16


title: ATAC-Seq_T3-2D_emp

value: PiG/empty


title: ATAC-Seq_T3-2D_EVI1


title: s.NJA01501.B05


title: s.NJA01501.B06


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox72h_K4me1

growth_protocol: Mouse PDA organoids or cell lines were cultured in conditions as described in this study.

extract_protocol:
Lysates were prepared from ~5 millon single cell dissociated of organoid cultures or monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared using the NEXTflex ChIP-seq kit (Cat# NOVA-5143-02;  PerkinElmer) according to the manufacturer's instructions.

value: H3K4me1 (ab8895, Abcam)


title: s.NJA01501.B04


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox48h_K4me1


title: s.NJA01501.B03


title: s.NJA01501.B02


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox0h_K4me1


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox72h_K27ac

value: H3K27ac (ab4729, Abcam)


title: m.NJA01501.A24

value: Multiplet


title: ATAC-Seq_NB508_shRen

value: LEPG/shRen


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox48h_K27ac


title: m.NJA01501.A22


title: m.NJA01501.A23


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox24h_K27ac


title: ChIP-Seq_NB508_shEVI1_K4me1


title: m.NJA01501.A21


title: s.NJA01501.A18


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox0h_K27ac


title: m.NJA01501.A20


title: ChIP-Seq_T3-2D_Tet-EVI1_Dox24h_K4me1


title: ChIP-Seq_NB508_shRen_K27ac


title: m.NJA01501.A19


title: ChIP-Seq_NB508_shRen_K4me1


title: ChIP-Seq_NB508_shEVI1_K27ac


title: s.NJA01501.A17


title: s.NJA01501.A16


title: s.NJA01501.A15


title: ChIP-Seq_T3-2D_emp_K4me1


title: s.NJA01501.A13


title: ChIP-Seq_T3-2D_EVI1_K4me1


title: s.NJA01501.A14


title: ChIP-Seq_M3P-org_BRD4

value: mouse PDA M3P organoid


title: ChIP-Seq_T3-2D_EVI1_K27ac


title: s.NJA01501.A08


title: ChIP-Seq_T3-2D_EVI1_Flag

value: Flag (F1804, Sigma)


title: s.NJA01501.A09


title: ChIP-Seq_T6-org_BRD4

value: mouse PDA T6 organoid


title: s.NJA01501.A07


title: s.NJA01501.A04


title: RNA-Seq_T3-2D_Tet-shEVI1.shRen_Dox24h_ScatterPlot

description: processed data file: RNA-Seq_T3-2D_Dox24hr_ScatterPlot.txt

data_processing:
Raw reads were mapped to the reference genome assembly mm10 using STAR mapping tool (Dobin et al, 2013l; PMID: 23104886).
Genome_build: mm9
Supplementary_files_format_and_content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

tag: biological replicate


title: s.NJA01501.A11

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

tag: facs cellnumber


title: s.NJA01501.A05

tag: age (days)


title: RNA-Seq_T3-2D_Tet-shEVI1.3604_Dox24h_ScatterPlot


title: s.NJA01501.A06


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox72h_rep2

description: processed data file: RNA-Seq_T3-2D_Tet-shEVI1_DoxTimeCourse.txt


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox72h_rep1


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox48h_rep1


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox48h_rep2


title: s.NJA01501.A02


title: s.NJA01501.A03


title: s.NJA01501.A01


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox24h_rep1


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox24h_rep2


title: m.NJA01503.P22

source_name: colon

value: colon


title: ChIP-Seq_T3-2D_emp_K27ac


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox72h_rep2

description: processed data file: RNA-Seq_T3-2D_Tet-EVI1_DoxTimeCourse.txt


title: m.NJA01503.P20


title: m.NJA01503.P19


title: s.NJA01503.P17


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox72h_rep1


title: s.NJA01503.P16


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox48h_rep2


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox0h_rep2


title: s.NJA01503.P12


title: RNA-Seq_T3-2D_Tet-shEVI1_TimeCourseDox0h_rep1


title: s.NJA01503.P13


title: s.NJA01503.P15


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox48h_rep1


title: s.NJA01503.P14


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox24h_rep2


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox24h_rep1


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox0h_rep2


title: s.NJA01503.P09


title: RNA-Seq_NB508_shEVI1.4327

description: processed data file: RNA-Seq_NB508_LOF.txt


title: s.NJA01503.P07


title: RNA-Seq_NB508_shEVI1.3604


title: s.NJA01503.P06


title: RNA-Seq_NB508_shRen_rep2


title: s.NJA01503.P05


title: s.NJA01503.P18


title: s.NJA01503.P04


title: RNA-Seq_NB508_shRen_rep1


title: RNA-Seq_T3-2D_Tet-EVI1_TimeCourseDox0h_rep1


title: RNA-Seq_T3-2D_shEVI1.4327

description: processed data file: RNA-Seq_T3-2D_LOF.txt


title: s.NJA01503.P02


title: RNA-Seq_T3-2D_shRen_rep1


title: RNA-Seq_T3-2D_shRen_rep2


title: s.NJA01503.P01


title: m.NJA01503.O23


title: m.NJA01503.O24


title: RNA-Seq_T3-2D_EVI1_rep1

description: processed data file: RNA-Seq_T3-2D_GOF.txt


title: RNA-Seq_T3-2D_emp_rep2


title: RNA-Seq_T3-2D_emp_rep1


title: m.NJA01503.O21


title: m.NJA01503.O20


title: m.NJA01503.O19


title: s.NJA01503.O18


title: Adult AT1 Yap/Taz KO

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.  Genome_build: mm10  Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

source_name: Lung epithelium, FACS-prepped

extract_protocol: Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) and scATAC scATAC sequencing library was prepared on the 10X Genomics Chromium platform following the manufacturer's protocol (10X Genomics 1000110). The isolated nuclei suspension was diluted and then incubated with transposition mix for a targeted nuclei recovery of 10,000 cells. NextSeq500 with 2 × 75 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

value: Hopx-creERT2/+;Yap1 fl/fl; Wwtr1 (Taz) fl/fl;eYFP/+

tag: age

value: control


title: s.NJA01503.O17


title: Adult Control Lung Epithelium


title: s.NJA01503.O16


title: s.NJA01503.P03


title: s.NJA01503.O15


title: Pink1Snca double mutant mouse Aged 5  replicate 1

city: Frankfurt

first: Irmgard

last: Tegeder

state: Hessen

address: Theodor Stern Kai 7

department: Clinical Pharmacology

country: Germany

institute: Goethe University Frankfurt

data_processing:
Sample quality was assessed with demultiplexed fastq.gz files and subsequently the alignment was performed with SeqMan NGen 16 (Lasergene) using the reference genome mm10 provided from UCSC (GRCm38) as template, a minimum read length of 35 bp and automatic adapter trimming.
Results were displayed with ArrayStar 16 (Lasergene) including the amount of mapped reads, target length, source length and position, strand, genes and gene IDs, annotated according to the mm10 assembly, and reads were normalized according to RPKM.
Normalized reads were analyzed with ArrayStar, which uses general linear models to assess differential expression.
Genes were filtered for at least 7 valid values out of 17 samples with normalized reads > 0.015 to exclude low expression genes. Data were log2 transformed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include feature counts for each sample, target length and coordinates, tab-delimited text file with normalized counts of valid genes including gene IDs
Supplementary_files_format_and_content: RawCounts_allgenes_replicates: tab delimited txt file with raw counts of all genes of each replicate (2 replicates per mouse)
Supplementary_files_format_and_content: LinRPKM_permouse_filteredgenes: tab delimited txt file with linear RPKM normalized counts per mouse of filtered valid genes
Supplementary_files_format_and_content: GeneIDs_allgenes.txt: tab delimited txt file of gene IDs

source_name: Dorsal root ganglia (DRG)

growth_protocol: does not apply

extract_protocol:
DRGs were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (TruSeq Total RNA with Ribo-Zero rRNA depletion) was used with 1 µg of total RNA for the construction of sequencing libraries. Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: naive mice, no treatment

value: DRG

value: 41 wks

tag: gender

value: female

value: Pink1-/-, SNCA A53T Double mutant


title: Pink1Snca double mutant mouse Aged 5  replicate 2


title: m.NJA01503.O22


title: s.NJA01503.O12

value: Singlet


title: s.NJA01503.O13


title: s.NJA01503.O14


title: Pink1Snca double mutant mouse Aged 4  replicate 1


title: Pink1Snca double mutant mouse Aged 3  replicate 2

value: 60 wks


title: s.NJA01503.O11


title: s.NJA01503.O10


title: Pink1Snca double mutant mouse Aged 2  replicate 2


title: RNA-Seq_T3-2D_EVI1_rep2

value: T3-2D cells


title: s.NJA01503.O09


title: RNA-Seq_T3-2D_shEVI1.3604


title: s.NJA01503.O08


title: Adult scATAC

source_name: Lung epithelium

value: wildtype


title: s.NJA01503.O07


title: Pink1Snca double mutant mouse Aged 3  replicate 1


title: s.NJA01503.O05


title: s.NJA01503.O04


title: Pink1Snca double mutant mouse Old 6  replicate 1


title: Pink1Snca double mutant mouse Aged 2  replicate 1


title: Pink1Snca double mutant mouse Aged 4  replicate 2


title: Pink1Snca double mutant mouse Aged 1  replicate 2


title: Pink1Snca double mutant mouse Aged 1  replicate 1


title: Pink1Snca double mutant mouse Old 5  replicate 2


title: s.NJA01503.O03


title: s.NJA01503.O02


title: s.NJA01503.O01


title: Pink1Snca double mutant mouse Old 5  replicate 1


title: m.NJA01503.N24


title: Pink1Snca double mutant mouse Old 4  replicate 1


title: Pink1Snca double mutant mouse Old 4  replicate 2


title: Pink1Snca double mutant mouse Old 1 replicate 2


title: Pink1Snca double mutant mouse Old 1 replicate 1


title: m.NJA01503.N21


title: m.NJA01503.N22


title: Wildtype FVBSv129 mouse Aged 4 replicate 1

value: wildtye control (WT)


title: m.NJA01503.N19

value: Multiplet


title: Wildtype FVBSv129 mouse Aged 3 replicate 2


title: m.NJA01503.N20


title: Wildtype FVBSv129 mouse Aged 3 replicate 1


title: Pink1Snca double mutant mouse Old 6  replicate 2


title: s.NJA01503.N17


title: s.NJA01503.N16


title: Wildtype FVBSv129 mouse Aged 2 replicate 2

value: 62 wks


title: Wildtype FVBSv129 mouse Aged 1 replicate 2


title: s.NJA01503.N14


title: Wildtype FVBSv129 mouse Old 6 replicate 1


title: Wildtype FVBSv129 mouse Old 6 replicate 2


title: s.NJA01503.N13


title: s.NJA01503.N15


title: Wildtype FVBSv129 mouse Aged 1 replicate 1


title: Wildtype FVBSv129 mouse Aged 2 replicate 1


title: s.NJA01503.N12


title: s.NJA01503.N11


title: s.NJA01503.N09


title: Wildtype FVBSv129 mouse Old 4 replicate 2


title: Wildtype FVBSv129 mouse Old 4 replicate 1


title: Wildtype FVBSv129 mouse Aged 4 replicate 2


title: Wildtype FVBSv129 mouse Old 3 replicate 2


title: m.NJA01503.N23


title: s.NJA01503.N06


title: s.NJA01503.N05


title: s.NJA01503.N03


title: Wildtype FVBSv129 mouse Old 1 replicate 1


title: s.NJA01503.N02


title: Wildtype FVBSv129 mouse Old 3 replicate 1


title: s.NJA01503.N18


title: Wildtype FVBSv129 mouse Old 1 replicate 2


title: rep2_YM155_Tabloid

city: Heidelberg

first: Lukas

last: Mathur

address: Meyerhofstraße 1

department: Genome Biology

institute: EMBL

data_processing:
CASANA software was used for basecalling
Read1 (Barcode) was used to demultiplex read 2 according to treatment conditions using Je Debarcode version 2.0.beta allowing a maximum of 6 mismatches per barcode sequence
Sequences were aligned to Homo_sapiens.GRCh38.84. using STAR version 2.4.2a
Created matrix with all alignments (treatment conditions) and remove genes with 0 read counts in all samples
Supplementary_files_format_and_content: Matrix containing read counts for all samples (replicate 1 to 3)

source_name: K562 cells

growth_protocol: K562 cells were cultures in DMEM media supplemented with 10% BSA and 1% Penicillin Streptomycin

extract_protocol:
Cells were lysed and the released mRNA was reversed transcribed using barcoded poly-dT primers.
Biotin on the poly-dT primer was used to purify cDNA. Priming sites introduced over the poly-dT primers and the template switching oligonucleotide were used to amplify the cDNA. Subsequently, cDNA was fragmented using a hyperactive Tn5 transposase.

treatment_protocol: Cells were encapsulated into picoliter sized droplts along with 420 unique combinatorial treatment conditions. Droplets with cells were incubated for 12h at 37 degrees Celsius

tag: cell type

value: Myelogenous leukemia cells

value: Tabloid

value: bcr:abl fusion gene


title: s.NJA01503.N01

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

value: colon


title: rep3_YM155_Streptozotocin

value: Streptozotocin

tag: genotype


title: m.NJA01503.M24


title: m.NJA01503.M22


title: rep2_YM155_Streptozotocin


title: rep1_YM155_Streptozotocin


title: m.NJA01503.M20


title: s.NJA01503.N08


title: rep2_YM155_Sonolisib

value: Sonolisib


title: m.NJA01503.M21


title: rep3_YM155_Sonolisib


title: m.NJA01503.M19


title: rep1_YM155_Tabloid


title: m.NJA01503.M23


title: rep3_YM155_SF1126


title: rep1_YM155_Sonolisib


title: s.NJA01503.M14


title: s.NJA01503.M17


title: s.NJA01503.M11


title: rep1_YM155_Olomucin

value: Olomucin


title: s.NJA01503.M16


title: rep3_YM155_NMS1286937


title: rep2_YM155_SF1126


title: s.NJA01503.M15


title: rep1_YM155_SF1126


title: rep3_YM155_Olomucin


title: s.NJA01503.M13


title: s.NJA01503.M12


title: rep2_YM155_Olomucin


title: rep2_YM155_NMS1286937


title: s.NJA01503.M07


title: s.NJA01503.M05


title: s.NJA01503.M06


title: s.NJA01503.M10


title: s.NJA01503.M08


title: rep3_YM155_Methotrexate

value: Methotrexate


title: rep1_YM155_NMS1286937


title: s.NJA01503.M03


title: rep1_YM155_Methotrexate


title: rep2_YM155_Mitomycin

value: Mitomycin


title: rep3_YM155_Mitomycin


title: s.NJA01503.M02


title: s.NJA01503.M09


title: rep3_YM155_Imatininb

value: Imatininb


title: rep1_YM155_Mitomycin


title: rep2_YM155_Methotrexate


title: m.NJA01503.L22


title: rep2_YM155_Imatininb


title: m.NJA01503.L20


title: rep3_YM155_Hymenialdisine

value: Hymenialdisine


title: s.NJA01503.M01

value: Singlet


title: rep1_YM155_Imatininb


title: rep2_YM155_Hymenialdisine


title: s.NJA01503.L18


title: s.NJA01503.L17


title: rep1_YM155_Hymenialdisine


title: m.NJA01503.L19


title: rep3_YM155_Hematoxylin

value: Hematoxylin


title: s.NJA01503.L16


title: s.NJA01503.M04


title: s.NJA01503.L15


title: rep2_YM155_Hematoxylin


title: rep1_YM155_Hematoxylin


title: rep3_YM155_Fluoruracil

value: Fluoruracil


title: s.NJA01503.L14


title: s.NJA01503.L13


title: s.NJA01503.L12


title: rep1_YM155_Fluoruracil


title: s.NJA01503.L11


title: rep2_YM155_Fluoruracil


title: rep3_YM155_EPIRUBICIN

value: EPIRUBICIN


title: s.NJA01503.L08


title: rep2_YM155_EPIRUBICIN


title: s.NJA01503.L07


title: rep2_YM155_DMSO

value: DMSO


title: rep3_YM155_DMSO


title: s.NJA01503.L05


title: rep1_YM155_DMSO


title: s.NJA01503.L03


title: s.NJA01503.L04


title: s.NJA01503.L02


title: rep3_YM155_Decitabine

value: Decitabine


title: rep1_YM155_Decitabine

value: Myelogenous leukemia cells


title: rep2_YM155_Decitabine


title: s.NJA01503.L01


title: rep3_YM155_Dacarbazine

value: Dacarbazine


title: m.NJA01503.K24

value: Multiplet


title: m.NJA01503.K23

value: colon


title: rep2_YM155_Dacarbazine

value: bcr:abl fusion gene


title: m.NJA01503.K22


title: rep1_YM155_Dacarbazine


title: m.NJA01503.K21


title: rep3_YM155_Cytarabine

value: Cytarabine


title: rep1_YM155_EPIRUBICIN


title: s.NJA01503.L10


title: rep1_YM155_Cytarabine


title: rep3_YM155_Blebbistatin

value: Blebbistatin


title: rep3_YM155_AT9283


title: rep1_YM155_Blebbistatin


title: rep2_YM155_AT9283


title: rep2_YM155_Blebbistatin


title: rep2_YM155_Cytarabine


title: rep1_YM155_AT9283


title: s.NJA01503.K14


title: s.NJA01503.K12


title: s.NJA01503.K11


title: rep3_Wortmannin_YM155

value: Wortmannin


title: s.NJA01503.K13


title: rep1_Wortmannin_YM155


title: s.NJA01503.K10


title: m.NJA01503.K20


title: s.NJA01503.K18


title: s.NJA01503.K07


title: rep2_Wortmannin_Trametinib

value: Trametinib


title: s.NJA01503.K17


title: s.NJA01503.K06


title: s.NJA01503.K09


title: m.NJA01503.K19


title: rep1_Wortmannin_Tabloid

value: Tabloid


title: rep3_Wortmannin_Tabloid


title: s.NJA01503.K05


title: s.NJA01503.K03


title: s.NJA01503.K15


title: rep2_Wortmannin_Tabloid


title: s.NJA01503.K04


title: s.NJA01503.K01


title: rep3_Wortmannin_Sonolisib

value: Sonolisib


title: m.NJA01503.J22


title: rep1_Wortmannin_Streptozotocin

description: rep1_Wortmannin_StreptozotocinReadsPerGene

value: Streptozotocin


title: s.NJA01503.K08

value: Singlet


title: rep2_Wortmannin_Streptozotocin

description: rep2_Wortmannin_StreptozotocinReadsPerGene


title: s.NJA01503.K16


title: rep1_Wortmannin_Trametinib


title: rep3_Wortmannin_Trametinib


title: m.NJA01503.J21


title: rep2_Wortmannin_Sonolisib


title: s.NJA01503.J18


title: rep3_Wortmannin_SF1126


title: rep1_Wortmannin_Sonolisib


title: m.NJA01503.J19


title: rep2_Wortmannin_YM155


title: s.NJA01503.J17


title: rep1_Wortmannin_SF1126


title: s.NJA01503.K02


title: rep3_Wortmannin_Streptozotocin

description: rep3_Wortmannin_StreptozotocinReadsPerGene


title: s.NJA01503.J16


title: rep2_Wortmannin_SF1126


title: s.NJA01503.J15


title: m.NJA01503.J24


title: rep3_Wortmannin_NMS1286937


title: s.NJA01503.J13


title: rep3_Wortmannin_Olomucin

value: Olomucin


title: s.NJA01503.J14


title: s.NJA01503.J11


title: rep1_Wortmannin_Olomucin


title: rep1_Wortmannin_NMS1286937


title: s.NJA01503.J12


title: rep3_Wortmannin_Mitomycin

value: Mitomycin


title: rep2_Wortmannin_NMS1286937


title: rep2_Wortmannin_Mitomycin


title: s.NJA01503.J08


title: rep1_Wortmannin_Mitomycin


title: rep3_Wortmannin_Methotrexate

description: rep3_Wortmannin_MethotrexateReadsPerGene

value: Methotrexate


title: s.NJA01503.J09


title: s.NJA01503.J07


title: s.NJA01503.J06


title: rep2_Wortmannin_Methotrexate

description: rep2_Wortmannin_MethotrexateReadsPerGene


title: rep1_Wortmannin_Methotrexate

description: rep1_Wortmannin_MethotrexateReadsPerGene


title: s.NJA01503.J04


title: s.NJA01503.J05


title: rep3_Wortmannin_Imatininb

value: Imatininb


title: s.NJA01503.J02


title: rep1_Wortmannin_Imatininb

value: Myelogenous leukemia cells


title: rep2_Wortmannin_Olomucin


title: s.NJA01503.J03


title: rep2_Wortmannin_Imatininb


title: s.NJA01503.J01


title: m.NJA01503.I24


title: rep3_Wortmannin_Hymenialdisine

description: rep3_Wortmannin_HymenialdisineReadsPerGene

value: Hymenialdisine


title: m.NJA01503.I22

value: Multiplet


title: rep2_Wortmannin_Hematoxylin

value: Hematoxylin


title: s.NJA01503.J10

value: colon


title: rep1_Wortmannin_Hematoxylin

value: bcr:abl fusion gene


title: rep3_Wortmannin_Hematoxylin


title: m.NJA01503.I23


title: rep2_Wortmannin_Hymenialdisine

description: rep2_Wortmannin_HymenialdisineReadsPerGene


title: s.NJA01503.I17


title: s.NJA01503.I18


title: rep2_Wortmannin_Fluoruracil

value: Fluoruracil


title: s.NJA01503.I16


title: rep3_Wortmannin_Fluoruracil

value: Wortmannin


title: rep1_Wortmannin_Fluoruracil


title: rep3_Wortmannin_EPIRUBICIN

value: EPIRUBICIN


title: m.NJA01503.I20


title: s.NJA01503.I15


title: s.NJA01503.I14


title: rep2_Wortmannin_EPIRUBICIN


title: s.NJA01503.I13


title: rep1_Wortmannin_EPIRUBICIN


title: s.NJA01503.I10


title: s.NJA01503.I12


title: rep2_Wortmannin_DMSO

value: DMSO


title: s.NJA01503.I09


title: rep3_Wortmannin_DMSO


title: rep1_Wortmannin_DMSO


title: s.NJA01503.I07


title: rep1_Wortmannin_Hymenialdisine

description: rep1_Wortmannin_HymenialdisineReadsPerGene


title: rep3_Wortmannin_Decitabine

value: Decitabine


title: s.NJA01503.I11


title: s.NJA01503.I08


title: s.NJA01503.I04


title: s.NJA01503.I05


title: rep2_Wortmannin_Decitabine


title: rep2_Wortmannin_Dacarbazine

value: Dacarbazine


title: s.NJA01503.I02

value: Singlet


title: s.NJA01503.I01


title: rep1_Wortmannin_Dacarbazine


title: rep3_Wortmannin_Cytarabine

value: Cytarabine


title: s.NJA01503.I06


title: rep2_Wortmannin_Cytarabine


title: m.NJA01503.H23


title: rep2_Wortmannin_Blebbistatin

description: rep2_Wortmannin_BlebbistatinReadsPerGene

value: Blebbistatin


title: rep3_Wortmannin_Blebbistatin

description: rep3_Wortmannin_BlebbistatinReadsPerGene


title: rep1_Wortmannin_Cytarabine


title: m.NJA01503.H21


title: m.NJA01503.H20


title: rep1_Wortmannin_Blebbistatin

description: rep1_Wortmannin_BlebbistatinReadsPerGene


title: m.NJA01503.H19


title: rep3_Wortmannin_AT9283


title: rep1_Wortmannin_Decitabine


title: rep2_Wortmannin_AT9283


title: s.NJA01503.H18


title: s.NJA01503.H17


title: s.NJA01503.H16


title: rep3_Triciribine_YM155

value: Triciribine


title: rep1_Wortmannin_AT9283


title: s.NJA01503.I03


title: s.NJA01503.H15


title: s.NJA01503.H13


title: s.NJA01503.H14


title: m.NJA01503.H22


title: rep2_Triciribine_YM155


title: rep3_Triciribine_Trametinib

value: Trametinib


title: s.NJA01503.H11


title: s.NJA01503.H10


title: rep1_Triciribine_Trametinib

value: Myelogenous leukemia cells


title: rep2_Triciribine_Trametinib


title: rep3_Triciribine_Tabloid

value: Tabloid


title: s.NJA01503.H09


title: rep2_Triciribine_Tabloid


title: s.NJA01503.H08


title: rep1_Triciribine_Tabloid


title: rep1_Triciribine_YM155


title: rep3_Triciribine_Streptozotocin

description: rep3_Triciribine_StreptozotocinReadsPerGene

value: Streptozotocin


title: s.NJA01503.H05


title: s.NJA01503.H06


title: s.NJA01503.H07


title: rep1_Triciribine_Streptozotocin

description: rep1_Triciribine_StreptozotocinReadsPerGene


title: rep2_Triciribine_Streptozotocin

description: rep2_Triciribine_StreptozotocinReadsPerGene


title: rep3_Triciribine_Sonolisib

value: Sonolisib


title: rep1_Triciribine_Sonolisib


title: s.NJA01503.H12

value: colon


title: s.NJA01503.H02


title: s.NJA01503.H04


title: s.NJA01503.H03


title: rep2_Triciribine_Sonolisib

value: bcr:abl fusion gene


title: rep2_Triciribine_Olomucin

value: Olomucin


title: m.NJA01503.G20

value: Multiplet


title: m.NJA01503.G24


title: rep3_Wortmannin_Dacarbazine

value: Wortmannin


title: m.NJA01503.G23


title: rep2_Triciribine_SF1126


title: rep3_Triciribine_Olomucin


title: m.NJA01503.G19


title: m.NJA01503.G21


title: s.NJA01503.G16


title: rep1_Triciribine_Olomucin


title: s.NJA01503.G14


title: s.NJA01503.G18


title: rep1_Triciribine_NMS1286937


title: rep2_Triciribine_Mitomycin

value: Mitomycin


title: rep3_Triciribine_NMS1286937


title: s.NJA01503.G11


title: rep3_Triciribine_Methotrexate

description: rep3_Triciribine_MethotrexateReadsPerGene

value: Methotrexate


title: rep2_Triciribine_NMS1286937


title: rep3_Triciribine_SF1126


title: s.NJA01503.G15


title: rep3_Triciribine_Mitomycin


title: m.NJA01503.G22


title: rep1_Triciribine_SF1126


title: s.NJA01503.G13


title: rep1_Triciribine_Mitomycin


title: s.NJA01503.G08


title: rep2_Triciribine_Methotrexate

description: rep2_Triciribine_MethotrexateReadsPerGene


title: s.NJA01503.G10


title: rep3_Triciribine_Hymenialdisine

description: rep3_Triciribine_HymenialdisineReadsPerGene

value: Hymenialdisine


title: rep2_Triciribine_Imatininb

value: Imatininb


title: s.NJA01503.G12

value: Singlet


title: s.NJA01503.G06


title: rep1_Triciribine_Imatininb


title: s.NJA01503.G04


title: rep2_Triciribine_Hymenialdisine

description: rep2_Triciribine_HymenialdisineReadsPerGene


title: s.NJA01503.G03


title: s.NJA01503.G09


title: rep3_Triciribine_Hematoxylin

description: rep3_Triciribine_HematoxylinReadsPerGene

value: Hematoxylin


title: s.NJA01503.G01


title: s.NJA01503.G02


title: rep1_Triciribine_Hymenialdisine

description: rep1_Triciribine_HymenialdisineReadsPerGene

value: Triciribine


title: rep1_Triciribine_Hematoxylin

description: rep1_Triciribine_HematoxylinReadsPerGene


title: rep2_Triciribine_Hematoxylin

description: rep2_Triciribine_HematoxylinReadsPerGene


title: m.NJA01503.F24


title: rep3_Triciribine_Imatininb


title: rep2_Triciribine_Fluoruracil

description: rep2_Triciribine_FluoruracilReadsPerGene

value: Fluoruracil


title: m.NJA01503.F21


title: rep3_Triciribine_Fluoruracil

description: rep3_Triciribine_FluoruracilReadsPerGene

value: Myelogenous leukemia cells


title: s.NJA01503.G07


title: m.NJA01503.F22


title: m.NJA01503.F20


title: m.NJA01503.F23


title: rep1_Triciribine_Methotrexate

description: rep1_Triciribine_MethotrexateReadsPerGene


title: rep3_Triciribine_EPIRUBICIN

value: EPIRUBICIN


title: s.NJA01503.G05


title: m.NJA01503.F19


title: rep1_Triciribine_Fluoruracil

description: rep1_Triciribine_FluoruracilReadsPerGene


title: rep2_Triciribine_EPIRUBICIN


title: s.NJA01503.F18


title: s.NJA01503.F16


title: rep1_Triciribine_EPIRUBICIN


title: rep3_Triciribine_DMSO

value: DMSO


title: rep2_Triciribine_DMSO


title: s.NJA01503.F15


title: s.NJA01503.F14


title: rep1_Triciribine_DMSO


title: rep1_Triciribine_Decitabine

value: Decitabine


title: rep2_Triciribine_Decitabine


title: s.NJA01503.F12

value: colon


title: s.NJA01503.F11


title: rep3_Triciribine_Dacarbazine

description: rep3_Triciribine_DacarbazineReadsPerGene

value: Dacarbazine

value: bcr:abl fusion gene


title: s.NJA01503.F17


title: rep2_Triciribine_Dacarbazine

description: rep2_Triciribine_DacarbazineReadsPerGene


title: s.NJA01503.F07


title: s.NJA01503.F06


title: s.NJA01503.F08


title: rep3_Triciribine_Decitabine


title: rep2_Triciribine_Cytarabine

value: Cytarabine


title: rep1_Triciribine_Dacarbazine

description: rep1_Triciribine_DacarbazineReadsPerGene


title: rep3_Triciribine_Blebbistatin

description: rep3_Triciribine_BlebbistatinReadsPerGene

value: Blebbistatin


title: rep3_Triciribine_Cytarabine


title: s.NJA01503.F13


title: s.NJA01503.F10


title: rep1_Triciribine_Cytarabine


title: s.NJA01503.F05


title: rep2_Triciribine_Blebbistatin

description: rep2_Triciribine_BlebbistatinReadsPerGene


title: s.NJA01503.F03


title: s.NJA01503.F09


title: s.NJA01503.F02


title: rep1_Triciribine_Blebbistatin

description: rep1_Triciribine_BlebbistatinReadsPerGene


title: rep3_Triciribine_AT9283


title: rep1_Triciribine_AT9283


title: m.NJA01503.E22

value: Multiplet


title: m.NJA01503.E21


title: rep2_Trametinib_YM155

value: Trametinib


title: s.NJA01503.F01


title: m.NJA01503.E24


title: rep3_Trametinib_YM155


title: rep1_Trametinib_YM155


title: m.NJA01503.E20


title: m.NJA01503.E19


title: rep1_Trametinib_Trametinib


title: rep2_Trametinib_Trametinib


title: s.NJA01503.E15


title: rep3_Trametinib_Tabloid

value: Tabloid


title: s.NJA01503.E16


title: rep3_Trametinib_Trametinib


title: s.NJA01503.E17


title: s.NJA01503.E18


title: rep1_Trametinib_Tabloid


title: s.NJA01503.E10


title: rep3_Trametinib_Streptozotocin

description: rep3_Trametinib_StreptozotocinReadsPerGene

value: Streptozotocin


title: s.NJA01503.E09

value: Singlet


title: rep2_Trametinib_Tabloid


title: s.NJA01503.E11


title: s.NJA01503.E14


title: rep2_Triciribine_AT9283


title: rep1_Trametinib_Streptozotocin

description: rep1_Trametinib_StreptozotocinReadsPerGene


title: s.NJA01503.E08


title: rep2_Trametinib_Streptozotocin

description: rep2_Trametinib_StreptozotocinReadsPerGene


title: s.NJA01503.E07


title: rep3_Trametinib_Sonolisib

value: Sonolisib


title: s.NJA01503.E06


title: rep2_Trametinib_Sonolisib


title: s.NJA01503.E05


title: s.NJA01503.E04


title: rep1_Trametinib_Sonolisib


title: s.NJA01503.E02


title: s.NJA01503.E03


title: rep3_Trametinib_SF1126


title: m.NJA01503.D23


title: rep1_Trametinib_SF1126


title: m.NJA01503.D22


title: rep3_Trametinib_Olomucin

value: Olomucin


title: rep1_Trametinib_Olomucin


title: m.NJA01503.D21


title: rep3_Trametinib_NMS1286937


title: rep2_Trametinib_Olomucin


title: m.NJA01503.D19


title: m.NJA01503.D20


title: rep2_Trametinib_NMS1286937


title: s.NJA01503.D17


title: s.NJA01503.D16


title: rep3_Trametinib_Mitomycin

value: Mitomycin


title: rep1_Trametinib_NMS1286937

value: Myelogenous leukemia cells


title: s.NJA01503.D15


title: rep1_Trametinib_Mitomycin


title: rep3_Trametinib_Methotrexate

description: rep3_Trametinib_MethotrexateReadsPerGene

value: Methotrexate


title: s.NJA01503.D14


title: rep2_Trametinib_SF1126


title: s.NJA01503.D13


title: s.NJA01503.D12


title: s.NJA01503.D11


title: rep3_Trametinib_Imatininb

value: Imatininb


title: rep1_Trametinib_Methotrexate

description: rep1_Trametinib_MethotrexateReadsPerGene


title: rep2_Trametinib_Methotrexate

description: rep2_Trametinib_MethotrexateReadsPerGene


title: s.NJA01503.D10


title: rep2_Trametinib_Imatininb


title: s.NJA01503.D18


title: rep1_Trametinib_Imatininb


title: s.NJA01503.D09


title: s.NJA01503.D08


title: s.NJA01503.D07


title: s.NJA01503.D05


title: rep2_Trametinib_Hymenialdisine

description: rep2_Trametinib_HymenialdisineReadsPerGene

value: Hymenialdisine


title: rep2_Trametinib_Mitomycin


title: rep1_Trametinib_Hymenialdisine

description: rep1_Trametinib_HymenialdisineReadsPerGene


title: s.NJA01503.D04

value: colon


title: rep3_Trametinib_Hematoxylin

value: Hematoxylin


title: s.NJA01503.D02


title: rep2_Trametinib_Hematoxylin

value: bcr:abl fusion gene


title: m.NJA01503.C23


title: rep1_Trametinib_Hematoxylin


title: m.NJA01503.C22


title: m.NJA01503.C21


title: rep1_Trametinib_Fluoruracil

value: Fluoruracil


title: rep3_Trametinib_EPIRUBICIN

value: EPIRUBICIN


title: rep3_Trametinib_Hymenialdisine

description: rep3_Trametinib_HymenialdisineReadsPerGene


title: rep1_Trametinib_EPIRUBICIN


title: rep3_Trametinib_DMSO

value: DMSO


title: rep2_Trametinib_EPIRUBICIN

value: Trametinib


title: s.NJA01503.D03


title: rep2_Trametinib_DMSO


title: s.NJA01503.C16


title: s.NJA01503.C17


title: s.NJA01503.C15


title: s.NJA01503.C13


title: rep3_Trametinib_Decitabine

value: Decitabine


title: rep1_Trametinib_Decitabine


title: s.NJA01503.C14


title: rep2_Trametinib_Decitabine


title: rep3_Trametinib_Fluoruracil


title: rep3_Trametinib_Dacarbazine

value: Dacarbazine


title: rep2_Trametinib_Fluoruracil


title: s.NJA01503.C11

value: Singlet


title: rep1_Trametinib_Dacarbazine


title: s.NJA01503.C10


title: m.NJA01503.C20

value: Multiplet


title: s.NJA01503.C08


title: s.NJA01503.C09


title: rep3_Trametinib_Cytarabine

value: Cytarabine


title: m.NJA01503.C19


title: s.NJA01503.C18


title: rep1_Trametinib_DMSO


title: rep2_Trametinib_Cytarabine


title: s.NJA01503.C07


title: rep1_Trametinib_Cytarabine


title: rep3_Trametinib_Blebbistatin

description: rep3_Trametinib_BlebbistatinReadsPerGene

value: Blebbistatin


title: s.NJA01503.C04


title: s.NJA01503.C06


title: s.NJA01503.C03


title: s.NJA01503.C12


title: rep1_Trametinib_Blebbistatin

description: rep1_Trametinib_BlebbistatinReadsPerGene

value: Myelogenous leukemia cells


title: s.NJA01503.C05


title: rep2_Trametinib_Blebbistatin

description: rep2_Trametinib_BlebbistatinReadsPerGene


title: rep2_Trametinib_Dacarbazine


title: rep2_Trametinib_AT9283


title: m.NJA01503.B24


title: s.NJA01503.C01


title: rep1_Trametinib_AT9283


title: m.NJA01503.B21


title: s.NJA01503.C02


title: m.NJA01503.B23


title: rep3_Sunitinib_YM155

value: Sunitinib


title: rep2_Sunitinib_YM155


title: rep1_Sunitinib_YM155


title: m.NJA01503.B20


title: m.NJA01503.B19


title: rep2_Sunitinib_Trametinib


title: s.NJA01503.B18


title: s.NJA01503.B17


title: rep1_Sunitinib_Trametinib


title: rep3_Sunitinib_Tabloid

value: Tabloid


title: s.NJA01503.B15


title: rep2_Sunitinib_Tabloid


title: s.NJA01503.B16


title: rep1_Sunitinib_Tabloid


title: rep3_Trametinib_AT9283


title: rep3_Sunitinib_Streptozotocin

description: rep3_Sunitinib_StreptozotocinReadsPerGene

value: Streptozotocin


title: s.NJA01503.B14

value: colon


title: s.NJA01503.B13


title: rep1_Sunitinib_Streptozotocin

description: rep1_Sunitinib_StreptozotocinReadsPerGene


title: rep3_Sunitinib_Sonolisib

value: Sonolisib


title: rep2_Sunitinib_Sonolisib

value: bcr:abl fusion gene


title: s.NJA01503.B11


title: s.NJA01503.B09


title: s.NJA01503.B08


title: s.NJA01503.B07


title: rep3_Sunitinib_SF1126


title: rep1_Sunitinib_Sonolisib


title: rep3_Sunitinib_Trametinib


title: rep2_Sunitinib_SF1126


title: rep3_Sunitinib_Olomucin

value: Olomucin


title: s.NJA01503.B03


title: rep2_Sunitinib_Olomucin


title: s.NJA01503.B12


title: s.NJA01503.B02


title: m.NJA01503.A24


title: rep3_Sunitinib_NMS1286937


title: rep2_Sunitinib_Streptozotocin

description: rep2_Sunitinib_StreptozotocinReadsPerGene


title: rep2_Sunitinib_NMS1286937


title: m.NJA01503.A22


title: m.NJA01503.A20


title: rep1_Sunitinib_NMS1286937


title: m.NJA01503.A21


title: rep2_Sunitinib_Mitomycin

value: Mitomycin


title: m.NJA01503.A19


title: rep3_Sunitinib_Mitomycin


title: rep1_Sunitinib_Mitomycin


title: s.NJA01503.B10


title: s.NJA01503.A18


title: rep3_Sunitinib_Methotrexate

value: Methotrexate


title: s.NJA01503.A17


title: s.NJA01503.B06


title: s.NJA01503.A15


title: s.NJA01503.A16


title: s.NJA01503.B05


title: rep3_Sunitinib_Imatininb

value: Imatininb


title: rep1_Sunitinib_Olomucin


title: s.NJA01503.A14


title: rep2_Sunitinib_Imatininb


title: s.NJA01503.A13


title: rep1_Sunitinib_Imatininb


title: rep3_Sunitinib_Hymenialdisine

description: rep3_Sunitinib_HymenialdisineReadsPerGene

value: Hymenialdisine


title: s.NJA01503.A11


title: s.NJA01503.A10


title: s.NJA01503.A09


title: s.NJA01503.A08


title: rep1_Sunitinib_Hymenialdisine

description: rep1_Sunitinib_HymenialdisineReadsPerGene


title: s.NJA01503.A07


title: rep2_Sunitinib_Hematoxylin

value: Hematoxylin


title: rep3_Sunitinib_Hematoxylin


title: rep2_Sunitinib_Methotrexate


title: rep3_Sunitinib_Fluoruracil

value: Fluoruracil


title: rep1_Sunitinib_Hematoxylin


title: s.NJA01503.A05

value: Singlet


title: s.NJA01503.A06


title: rep2_Sunitinib_Fluoruracil


title: s.NJA01503.A04


title: s.NJA01503.A02


title: rep3_Sunitinib_EPIRUBICIN

value: EPIRUBICIN


title: s.NJA01503.A03


title: rep1_Sunitinib_Fluoruracil


title: rep2_Sunitinib_EPIRUBICIN


title: s.NJA01503.A12


title: m.NJA01205.P05

value: Multiplet


title: rep1_Sunitinib_EPIRUBICIN

value: Myelogenous leukemia cells


title: rep2_Sunitinib_Hymenialdisine

description: rep2_Sunitinib_HymenialdisineReadsPerGene

value: Sunitinib


title: s.NJA01205.P03


title: rep3_Sunitinib_DMSO

value: DMSO


title: s.NJA01205.P04


title: rep2_Sunitinib_DMSO


title: s.NJA01205.P01


title: rep1_Sunitinib_DMSO


title: m.NJA01205.P06


title: rep3_Sunitinib_Decitabine

value: Decitabine


title: m.NJA01205.O05

value: colon


title: rep2_Sunitinib_Decitabine


title: s.NJA01205.O04


title: rep1_Sunitinib_Decitabine


title: s.NJA01205.O03


title: rep3_Sunitinib_Dacarbazine

value: Dacarbazine


title: s.NJA01205.O02


title: rep2_Sunitinib_Dacarbazine

value: bcr:abl fusion gene


title: m.NJA01205.N06


title: rep3_Sunitinib_Cytarabine

value: Cytarabine


title: m.NJA01205.N05


title: rep1_Sunitinib_Dacarbazine


title: rep1_Sunitinib_Cytarabine


title: rep2_Sunitinib_Cytarabine


title: s.NJA01205.N03


title: rep1_Sunitinib_Methotrexate


title: rep3_Sunitinib_Blebbistatin

value: Blebbistatin


title: s.NJA01205.N04


title: rep2_Sunitinib_Blebbistatin


title: m.NJA01205.O06


title: rep1_Sunitinib_Blebbistatin


title: s.NJA01205.N02


title: s.NJA01205.N01


title: rep2_Sunitinib_AT9283


title: rep3_Sunitinib_AT9283


title: rep1_Sunitinib_AT9283


title: rep3_SB747651_YM155


title: s.NJA01205.O01


title: s.NJA01205.M04


title: rep2_SB747651_YM155


title: s.NJA01205.M03


title: s.NJA01205.M02


title: s.NJA01205.M01


title: m.NJA01205.L05


title: rep3_SB747651_Trametinib

value: Trametinib


title: rep2_SB747651_Trametinib


title: s.NJA01205.L04


title: rep1_SB747651_Trametinib


title: rep2_SB747651_Tabloid

value: Tabloid


title: rep3_SB747651_Tabloid


title: s.NJA01205.L01


title: m.NJA01205.M05


title: rep1_SB747651_Tabloid


title: m.NJA01205.K06


title: m.NJA01205.K05


title: rep3_SB747651_Streptozotocin

description: rep3_SB747651_StreptozotocinReadsPerGene

value: Streptozotocin


title: rep2_SB747651_Streptozotocin

description: rep2_SB747651_StreptozotocinReadsPerGene


title: s.NJA01205.K03


title: s.NJA01205.K04


title: s.NJA01205.K02


title: rep1_SB747651_Streptozotocin

description: rep1_SB747651_StreptozotocinReadsPerGene


title: rep3_SB747651_Sonolisib

value: Sonolisib


title: rep1_Sunitinib_SF1126


title: m.NJA01205.L06


title: rep2_SB747651_Sonolisib


title: rep1_SB747651_YM155


title: s.NJA01205.L02


title: m.NJA01205.J06


title: s.NJA01205.K01


title: s.NJA01205.L03


title: rep1_SB747651_Sonolisib


title: rep3_SB747651_SF1126


title: s.NJA01205.J04


title: rep1_SB747651_SF1126


title: s.NJA01205.J02


title: s.NJA01205.J03


title: rep3_SB747651_Olomucin

value: Olomucin


title: s.NJA01205.J01

value: Singlet


title: rep2_SB747651_Olomucin


title: m.NJA01205.I06


title: rep1_SB747651_Olomucin


title: rep3_SB747651_NMS1286937


title: s.NJA01205.I02


title: s.NJA01205.I03


title: rep2_SB747651_NMS1286937


title: s.NJA01205.I01


title: rep3_SB747651_Mitomycin

value: Mitomycin


title: m.NJA01205.H05

value: Multiplet


title: rep3_SB747651_Methotrexate

value: Myelogenous leukemia cells

value: Methotrexate


title: rep1_SB747651_Mitomycin


title: rep2_SB747651_Mitomycin


title: s.NJA01205.H01


title: s.NJA01205.H02


title: m.NJA01205.J05


title: rep2_SB747651_SF1126


title: s.NJA01205.H03


title: rep1_SB747651_Methotrexate


title: m.NJA01205.G05


title: m.NJA01205.G06


title: rep3_SB747651_Imatininb

value: Imatininb


title: rep2_SB747651_Methotrexate


title: rep2_SB747651_Imatininb


title: s.NJA01205.G04


title: rep1_SB747651_Imatininb


title: rep3_SB747651_Hymenialdisine

description: rep3_SB747651_HymenialdisineReadsPerGene

value: Hymenialdisine


title: s.NJA01205.G01

value: colon


title: s.NJA01205.G02


title: s.NJA01205.G03


title: rep2_SB747651_Hymenialdisine

description: rep2_SB747651_HymenialdisineReadsPerGene


title: rep1_SB747651_NMS1286937


title: s.NJA01205.H04


title: m.NJA01205.F05


title: rep1_SB747651_Hymenialdisine

description: rep1_SB747651_HymenialdisineReadsPerGene


title: rep2_SB747651_Hematoxylin

value: Hematoxylin


title: s.NJA01205.F02


title: rep1_SB747651_Hematoxylin

value: bcr:abl fusion gene


title: s.NJA01205.F01


title: rep3_SB747651_Fluoruracil

value: Fluoruracil


title: s.NJA01205.F03


title: s.NJA01205.F04


title: rep3_SB747651_Hematoxylin


title: rep2_SB747651_Fluoruracil


title: m.NJA01205.E05


title: rep1_SB747651_Fluoruracil


title: s.NJA01205.E04


title: rep3_SB747651_EPIRUBICIN

value: EPIRUBICIN


title: s.NJA01205.E03


title: rep1_SB747651_EPIRUBICIN


title: s.NJA01205.E02


title: s.NJA01205.E01


title: rep3_SB747651_DMSO

value: DMSO


title: m.NJA01205.E06


title: s.NJA01503.B04


title: m.NJA01205.D05


title: s.NJA01205.D04


title: rep2_SB747651_DMSO


title: rep1_SB747651_DMSO


title: s.NJA01205.D03


title: rep3_SB747651_Decitabine

value: Decitabine


title: s.NJA01205.D02


title: s.NJA01205.D01


title: rep1_SB747651_Decitabine


title: m.NJA01205.C06


title: rep2_SB747651_Dacarbazine

value: Dacarbazine


title: rep3_SB747651_Dacarbazine


title: rep1_SB747651_Dacarbazine


title: m.NJA01205.C05


title: s.NJA01205.C04


title: s.NJA01205.C03


title: s.NJA01205.C02


title: rep2_SB747651_EPIRUBICIN


title: rep3_SB747651_Cytarabine

value: Cytarabine


title: s.NJA01205.C01


title: rep3_SB747651_Blebbistatin

value: Blebbistatin


title: rep1_SB747651_Cytarabine


title: rep2_SB747651_Blebbistatin


title: s.NJA01205.B04

value: Singlet


title: rep1_SB747651_Blebbistatin


title: m.NJA01205.B05


title: s.NJA01205.B02


title: s.NJA01205.B01


title: rep3_SB747651_AT9283


title: s.NJA01205.B03


title: rep2_SB747651_AT9283


title: rep2_SB747651_Decitabine


title: m.NJA01205.A06


title: m.NJA01205.A05


title: s.NJA01205.A04


title: rep3_Razoxane_YM155

value: Razoxane


title: rep1_Razoxane_YM155


title: s.NJA01205.A02


title: rep2_SB747651_Cytarabine


title: s.NJA01205.A03


title: rep3_Razoxane_Trametinib

value: Trametinib


title: s.NJA01205.A01


title: rep2_Razoxane_Trametinib

value: Myelogenous leukemia cells


title: rep1_Razoxane_Trametinib


title: rep3_Razoxane_Tabloid

value: Tabloid


title: m.NJA01401.P21

value: Multiplet


title: m.NJA01401.P19


title: rep1_Razoxane_Tabloid


title: s.NJA01401.P18


title: rep3_Razoxane_Streptozotocin

description: rep3_Razoxane_StreptozotocinReadsPerGene

value: Streptozotocin


title: rep1_SB747651_AT9283


title: s.NJA01401.P17

value: colon


title: s.NJA01401.P16


title: rep2_Razoxane_Streptozotocin

description: rep2_Razoxane_StreptozotocinReadsPerGene


title: s.NJA01401.P15


title: rep3_Razoxane_Sonolisib

value: Sonolisib


title: s.NJA01401.P13