title: 14A_M_733


title: 14A_M_732

status: Public on May 24 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

tag: age

tag: strain


title: 14A_M_724


title: 14A_M_730


title: 14A_M_722


title: 14A_M_728


title: 14A_M_731


title: 14A_M_729


title: 14A_M_725


title: 14A_M_727


title: 14A_M_721


title: 14A_M_726


title: RBG31761_WT

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Reads were mapped simultaneously to the Mus musculus genome (mm10) and the 92 ERCC sequences using STAR. FeatureCounts was used to count the number of reads mapped to each gene. Quality control was applied to exclude dead and dying cells as well as poor quality cells (using the parameters fGenes:Total > 12%, mit:mappedToGene < 20%, nNuclearReads > 150K, ercc:mapped < 20%). Data was pre-processed using the in-house pre-processing tool smqpp in Python analysed using Scanpy (1.7.1). Cells were normalised using the DESeq2 method and logged.
Assembly: mm10
Supplementary files format and content: a h5ad file that contains raw counts, metadata for each cell and gene annoataion information.

molecule: total RNA

source_name: Bone marrow

extract_protocol:
To harvest mouse bone marrow cells, spine, femurs, tibiae and pelvic bones were crushed with a pestle and mortar in 3 mL PBS + 2% FBS. Further 3 mL PBS + 2% FCS were used to wash the bones and the resulting cell suspension was filtered through a 0.75 uM filter. Cells were pelleted and resuspended in 3 mL PBS + 2% FBS. Red cell lysis was performed using cold ammonium chloride (StemCell Technologies cat. no 07800). PBS 2% FCS was added to dilute the red cell lysis buffer during subsequent centrifugation at 4 oC.   For lineage depletion, EasySep™ Mouse Hematopoietic Progenitor Cell Enrichment Kit from StemCell Technologies (cat no. 19816A) was used according to the manufacturer’s instructions but avoiding the use of rat serum. Samples were transferred into 5 ml polystyrene (352058) FACS tubes and incubated with 10 µl/ml EasySep mouse hematopoietic progenitor cell isolation cocktail labelled with biotin. 40 µl/ml of EasySep™ Streptavidin RapidSpheres were added and allowed to bind on ice for 10 minutes. The samples were subsequently diluted to 2.5 ml using PBS + 2% FBS and placed in the EasyStep magnet (StemCell Technologies cat no. 18000) for 3 minutes at room temperature. After incubation, samples were transferred into new tubes, spun down, and resuspended in 100 ul PBS + 2% FCS.   For antibody staining, a master mix was prepared as indicated in table 2 and cell suspensions were incubated on ice, in the dark for 30 minutes. After staining, cells were washed, pelleted, and resuspended in 100 ul PBS + 2% FCS. Were necessary, streptavidin conjugated antibody was added in a second step. Samples were pelleted and resuspended to a final volume of 500 ul PBS + 2% FCS. We used single colour, unstained, and full panel controls that were made using pooled BM cells from all mice before lineage depletion.
Primary single cells (LSK cells – Lin-Sca1+ckit+) were FACS index sorted into lysis buffer (0.2% Triton X-100 (Sigma), RNase inhibitor (SUPERase, Thermofisher), and nuclease-free water (Thermo Fisher)). scRNA sequencing was performed according to the Smart-Seq2 protocol.
Libraries were prepared using the Illumina nextera XT DNA preparation kit and sequenced on the Illumina Hi-Seq 2500.

tag: cell type

tag: tissue

value: Bone marrow

tag: genotype

value: WT


title: RBG31766_TKO

value: Aldh2 & Fancd2 & p53 triple knock-outs


title: RBG31765_TKO


title: RBG31764_TKO


title: RBG31762_TKO


title: RBG31760_WT


title: 14A_M_719


title: RBG31759_p53KO

value: p53 knock-outs


title: RBG31757_p53KO


title: 14A_M_720


title: 14A_M_717


title: RBG31767_DKO

value: Aldh2 & Fancd2 double knock-outs


title: 14A_M_716


title: 14A_M_718


title: 14A_M_715


title: RBG31763_TKO


title: RBG31756_DKO


title: RBG31754_TKO


title: 14A_M_710


title: 14A_M_709


title: RBG31755_DKO


title: 14A_M_714


title: RBG31758_p53KO


title: 14A_M_706


title: RBG31753_TKO


title: RBG31752_TKO


title: RBG31750_TKO


title: RBG31746_p53KO


title: 14A_M_711


title: RBG31751_TKO


title: RBG31749_WT


title: 14A_M_707


title: RBG31747_p53KO


title: RBG31743_DKO


title: RBG31745_p53KO


title: 14A_M_705


title: 14A_M_575


title: 14A_M_573


title: 14A_M_712


title: RBG31748_WT


title: 14A_M_574


title: 14A_M_708


title: RBG31742_TKO


title: RBG31744_DKO


title: 14A_M_704


title: 14A_M_713


title: 14A_M_572


title: RBG31741_TKO


title: RBG31740_TKO


title: RBG31739_TKO


title: 14A_M_569


title: RBG31738_TKO


title: 14A_M_571


title: 14A_M_570


title: 14A_M_568


title: RBG31737_WT


title: RBG31736_WT


title: 14A_M_565


title: RBG31735_p53KO


title: RBG31733_p53KO


title: 14A_M_567


title: 14A_M_562


title: 14A_M_563


title: RBG31731_DKO


title: 14A_M_561


title: RBG31730_TKO


title: RBG31728_TKO


title: RBG32687_WT


title: 14A_M_559


title: 14A_M_558


title: RBG32686_WT


title: 14A_M_557


title: 14A_M_566


title: RBG32683_WT


title: RBG32684_WT


title: 14A_M_564


title: RBG31732_DKO


title: RBG31734_p53KO


title: RBG32680_p53KO


title: RBG32685_WT


title: 14A_M_553


title: 14A_M_555


title: RBG32682_WT


title: 14A_M_550


title: 14A_M_551


title: 14A_M_560


title: 14A_M_554


title: RBG32679_p53KO


title: 14A_M_552


title: RBG32676_p53KO


title: RBG32677_p53KO


title: 14A_M_547


title: RBG32675_WT


title: 14A_M_548


title: 14A_M_546


title: 14A_M_545


title: RBG32674_WT


title: 14A_M_549


title: RBG32673_WT


title: RBG32681_p53KO


title: 14A_M_556


title: 14A_M_544


title: 14A_M_543


title: RBG32672_WT


title: RBG32670_WT


title: RBG32669_p53KO


title: 14A_M_541


title: 14A_M_540


title: 14A_M_542


title: RBG32668_p53KO


title: 14A_M_539


title: RBG32678_p53KO


title: RBG32666_p53KO


title: RBG32667_p53KO


title: RBG32664_p53KO


title: 14A_M_537


title: RBG32665_p53KO


title: 14A_M_536


title: 14A_M_535


title: RBG32661_WT


title: 14A_M_534


title: 14A_M_532


title: 14A_M_533


title: RBG32662_WT


title: RBG32663_WT


title: RBG32660_WT


title: RBG32658_WT


title: RBG32657_p53KO


title: 14A_M_530


title: 14A_M_529


title: RBG32656_p53KO


title: 14A_M_538


title: RBG32655_p53KO


title: 14A_M_528


title: 14A_M_527


title: RBG32654_p53KO


title: 14A_M_526


title: 14A_M_525


title: RBG32653_p53KO


title: RBG32650_WT


title: RBG32649_WT


title: RBG32659_WT


title: 14A_M_521


title: 14A_M_519


title: RBG32652_p53KO


title: RBG32648_WT


title: 14A_M_531


title: RBG32651_WT


title: 14A_M_522


title: 14A_M_520


title: RBG32644_p53KO


title: RBG32643_p53KO


title: RBG32645_p53KO


title: 14A_M_518


title: 14A_M_517


title: RBG32642_p53KO


title: 14A_M_516


title: RBG32641_p53KO


title: RBG32640_p53KO


title: 14A_M_524


title: 14A_M_523


title: 14A_M_514


title: 14A_M_513


title: 14A_M_512


title: RBG32637_WT


title: 14A_M_254


title: 14A_M_255


title: RBG32639_WT


title: RBG32635_WT


title: RBG32634_WT


title: RBG32633_p53KO


title: 14A_M_252


title: RBG32632_p53KO


title: 14A_M_253


title: 14A_M_250


title: RBG32631_p53KO


title: RBG32636_WT


title: RBG32630_p53KO


title: 14A_M_251


title: 14A_M_515


title: 14A_M_249


title: 14A_M_248


title: 14A_M_247


title: 14A_M_246


title: RBG32627_WT


title: RBG32628_p53KO


title: RBG32638_WT


title: 14A_M_245


title: RBG32626_WT


title: RBG32625_WT


title: 14A_M_243


title: 14A_M_244


title: RBG32624_WT


title: 14A_M_242


title: RBG32623_WT


title: RBG32622_WT


title: RBG32629_p53KO


title: 14A_M_241


title: RBG32621_p53KO


title: RBG32619_p53KO


title: 14A_M_237


title: RBG32618_p53KO


title: RBG32617_p53KO


title: 14A_M_236


title: 14A_M_235


title: 14A_M_240


title: 14A_M_234


title: RBG32616_p53KO


title: RBG32615_WT


title: RBG32620_p53KO


title: 14A_M_238


title: 14A_M_233


title: RBG32614_WT


title: RBG32613_WT


title: 14A_M_231


title: 14A_M_230


title: 14A_M_229


title: 14A_M_228


title: 14A_M_239


title: RBG32612_WT


title: RBG32609_p53KO


title: RBG32610_WT


title: RBG32611_WT


title: 14A_M_226


title: RBG32607_p53KO


title: RBG32608_p53KO


title: 14A_M_225


title: 14A_M_224


title: 14A_M_223


title: 14A_M_232


title: 14A_M_221


title: 14A_M_222


title: RBG32605_p53KO


title: 14A_M_220


title: RBG32602_WT


title: 14A_M_219


title: RBG32601_WT


title: RBG32600_WT


title: RBG32603_WT


title: 14A_M_217


title: 14A_M_218


title: RBG32599_WT


title: RBG32598_WT


title: 14A_M_216


title: 14A_M_227


title: RBG32596_p53KO


title: 14A_M_215


title: RBG32597_p53KO


title: 14A_M_213


title: RBG32595_p53KO


title: RBG32606_p53KO


title: RBG32594_p53KO


title: 14A_M_212


title: RBG32593_p53KO


title: RBG32592_p53KO


title: 14A_M_210


title: RBG31727_TKO


title: RBG32604_p53KO


title: RBG31726_TKO


title: 14A_M_208


title: 14A_M_211


title: RBG31723_TKO


title: 14A_M_207


title: RBG31724_TKO


title: 14A_M_205


title: RBG31722_DKO


title: 14A_M_204


title: 14A_M_203


title: 14A_M_206


title: RBG31721_DKO


title: 14A_M_202


title: RBG31719_p53KO


title: 14A_M_201


title: 14A_M_200


title: 14A_M_214


title: 14A_M_199


title: RBG31715_TKO


title: RBG31717_WT


title: RBG31716_WT


title: RBG31725_TKO


title: 14A_M_209


title: RBG31714_TKO


title: RBG31713_TKO


title: RBG31712_TKO


title: 14A_M_196


title: 14A_M_195


title: 14A_M_197


title: 14A_M_194


title: RBG31710_DKO


title: RBG31709_DKO


title: RBG31720_DKO


title: RBG31711_TKO


title: 14A_M_190


title: 14A_M_193


title: 14A_M_191


title: RBG31706_p53KO


title: RBG31707_p53KO


title: 14A_M_198


title: 14A_M_192


title: 14A_M_189


title: RBG31704_WT


title: RBG31708_DKO


title: RBG31703_TKO


title: RBG31702_TKO


title: 14A_M_187


title: 14A_M_185


title: 14A_M_188


title: RBG31705_WT


title: RBG31701_TKO


title: 14A_M_186


title: 14A_M_183


title: 14A_M_184


title: RBG31699_TKO


title: RBG31700_TKO


title: 14A_M_182


title: RBG31698_DKO


title: 14A_M_181


title: 14A_M_179


title: 14A_M_180


title: RBG31696_DKO


title: RBG31694_p53KO


title: 14A_M_178


title: RBG31691_TKO


title: RBG31690_TKO


title: 14A_M_174


title: 14A_M_173


title: 14A_M_177


title: RBG31693_WT


title: 14A_M_175


title: RBG31692_WT


title: 14A_M_176


title: RBG31688_TKO


title: RBG31687_TKO


title: 14A_M_171


title: RBG31689_TKO


title: RBG31686_DKO


title: 14A_M_172


title: RBG31697_DKO


title: RBG31683_p53KO


title: 14A_M_170


title: RBG31695_p53KO


title: RBG31682_p53KO


title: 14A_M_168


title: 14A_M_167


title: 14A_M_166


title: RBG31684_DKO


title: RBG31681_WT


title: 14A_M_165


title: 14A_M_164


title: RBG31678_TKO


title: RBG31677_TKO


title: 14A_M_163


title: 14A_M_162


title: RBG31675_TKO


title: 14A_M_160


title: RBG31676_TKO


title: 14A_M_161


title: 14A_M_159


title: 14A_M_158


title: RBG31674_DKO


title: 14A_M_169


title: RBG31672_p53KO


title: RBG31671_p53KO


title: RBG31669_WT


title: 14A_M_157


title: RBG31668_WT


title: RBG31667_TKO


title: 14A_M_156


title: 14A_M_155


title: 14A_M_153


title: 14A_M_152


title: RBG31679_TKO


title: RBG31664_TKO


title: RBG31666_TKO


title: 14A_M_154


title: 14A_M_151


title: RBG31665_TKO


title: 14A_M_150


title: RBG31663_TKO


title: RBG31662_DKO


title: RBG31661_DKO


title: 14A_M_149


title: 14A_M_147


title: RBG31659_p53KO


title: 14A_M_146


title: RBG31657_WT


title: RBG31656_WT


title: 14A_M_145


title: RBG31655_TKO


title: RBG31654_TKO


title: 14A_M_143


title: RBG31653_TKO


title: 14A_M_144


title: 14A_M_141


title: RBG31648_p53KO


title: 14A_M_138


title: RBG31650_DKO


title: RBG31652_TKO


title: RBG31647_p53KO


title: RBG31646_p53KO


title: 14A_M_137


title: RBG31644_WT


title: 14A_M_136


title: 14A_M_148


title: RBG31660_p53KO


title: RBG31643_TKO


title: 14A_M_134


title: RBG31642_TKO


title: RBG31641_TKO


title: 14A_M_133


title: 14A_M_131


title: RBG31639_TKO


title: RBG31640_TKO


title: 14A_M_142


title: RBG31638_DKO


title: 14A_M_139


title: 14A_M_130


title: 14A_M_62


title: 14A_M_129


title: 14A_M_63


title: 14A_M_135


title: RBG31637_DKO


title: RBG31635_p53KO


title: 14A_M_140


title: 14A_M_61


title: RBG31633_WT


title: 14A_M_60


title: 14A_M_59


title: RBG31636_p53KO


title: RBG31630_p53KO


title: 14A_M_128


title: RBG31631_p53KO


title: 14A_M_58


title: RBG31632_WT


title: 14A_M_132


title: RBG31627_DKO


title: 14A_M_56


title: 14A_M_57


title: 14A_M_55


title: RBG31626_WT


title: RBG31624_TKO


title: 14A_M_54


title: 14A_M_53


title: RBG31622_TKO


title: 14A_M_52


title: 14A_M_51


title: RBG31618_p53KO


title: RBG31617_p53KO


title: RBG31619_p53KO


title: RBG31620_TKO


title: 14A_M_50


title: 14A_M_49


title: RBG31629_p53KO


title: RBG31616_DKO


title: 14A_M_45


title: 14A_M_44


title: RBG31612_TKO


title: RBG31611_TKO


title: RBG31615_DKO


title: 14A_M_46


title: 14A_M_47


title: 14A_M_43


title: RBG31607_p53KO


title: 14A_M_42


title: RBG31625_WT


title: RBG31606_p53KO


title: RBG31608_TKO


title: 14A_M_41


title: 14A_M_40


title: 14A_M_39


title: RBG31603_DKO


title: 14A_M_48


title: 14A_M_37


title: 14A_M_36


title: RBG31600_TKO


title: RBG31601_WT


title: RBG31602_WT


title: 14A_M_33


title: 14A_M_35


title: 14A_M_32


title: RBG31594_p53KO


title: 14A_M_34


title: 14A_M_31


title: RBG31597_TKO


title: RBG31599_TKO


title: RBG31596_TKO


title: 14A_M_30


title: RBG31605_p53KO


title: RBG31592_DKO


title: RBG31591_DKO


title: 14A_M_27


title: RBG31590_WT


title: RBG31604_DKO


title: RBG31593_p53KO


title: 14A_M_28


title: 14A_M_25


title: 14A_M_26


title: RBG31588_TKO


title: 14A_M_38


title: RBG31587_TKO


title: RBG31595_p53KO


title: 14A_M_24


title: RBG31586_TKO


title: RBG31582_p53KO


title: 14A_M_22


title: 14A_M_23


title: RBG31585_TKO


title: RBG31583_p53KO


title: RBG31578_WT


title: RBG31576_TKO


title: 14A_M_29


title: RBG31577_WT


title: RBG31589_WT


title: 14A_M_20


title: 14A_M_17


title: 14A_M_21


title: 14A_M_18


title: RBG31581_DKO


title: 14A_M_19


title: 14A_M_15


title: 14A_M_16


title: RBG31580_DKO


title: 14A_M_13


title: 14A_M_14


title: RBG31573_TKO


title: RBG31574_TKO


title: RBG31572_TKO


title: 14A_M_12


title: 14A_M_11


title: RBG31571_p53KO


title: 14A_M_10


title: RBG31570_p53KO


title: 14A_M_9


title: RBG31568_DKO


title: RBG31569_DKO


title: 14A_M_7


title: 14A_M_6


title: RBG31567_DKO


title: 14A_M_5


title: RBG31564_TKO


title: RBG31566_WT


title: 14A_M_3


title: RBG31562_TKO


title: 14A_M_4


title: RBG31563_TKO


title: RBG31561_TKO


title: RBG31560_TKO


title: RBG31559_p53KO


title: RBG31558_p53KO


title: 14A_M_2


title: 13F_M_2996


title: 13F_M_2995


title: 13F_M_2997


title: RBG31556_DKO


title: RBG31557_DKO


title: 13F_M_2994


title: 14A_M_8


title: 13F_M_2993


title: RBG31555_DKO


title: RBG31565_WT


title: 13F_M_2991


title: 13F_M_2992


title: 14A_M_0


title: 13F_M_2989


title: 14A_M_1


title: 13F_M_2990


title: RBG31551_TKO


title: RBG31552_TKO


title: 13F_M_2986


title: RBG31550_TKO


title: RBG31548_TKO


title: 13F_M_2985


title: RBG31546_p53KO


title: RBG31549_TKO


title: 13F_M_2984


title: RBG31544_DKO


title: RBG31542_WT


title: RBG31545_DKO


title: 13F_M_2987


title: 13F_M_2988


title: RBG31547_p53KO


title: RBG31554_WT


title: RBG31541_WT


title: RBG31543_DKO


title: RBG31540_TKO


title: RBG31539_TKO


title: 13F_M_2981


title: 13F_M_2982


title: 13F_M_2980


title: 13F_M_2979


title: 13F_M_2978


title: 13F_M_2983


title: 13F_M_2977


title: RBG31538_TKO


title: 13F_M_2976


title: 13F_M_2975


title: RBG31537_TKO


title: RBG31536_TKO


title: 13F_M_2974


title: 13F_M_2973


title: RBG31534_WT


title: 13F_M_2972


title: RBG31530_TKO


title: RBG31529_TKO


title: 13F_M_2971


title: 13F_M_2970


title: RBG31526_TKO


title: 13F_M_2966


title: 13F_M_2964


title: 13F_M_2965


title: RBG31522_WT


title: 13F_M_2962


title: RBG31523_WT


title: 13F_M_2963


title: RBG31521_p53KO


title: RBG31520_p53KO


title: RBG31519_p53KO


title: RBG31535_WT


title: 13F_M_2961


title: RBG31525_DKO


title: RBG31518_TKO


title: RBG31517_TKO


title: 13F_M_2959


title: RBG31516_TKO


title: 13F_M_2960


title: 13F_M_2958


title: RBG31515_TKO


title: RBG31527_TKO


title: RBG31528_TKO


title: 13F_M_2957


title: 13F_M_2969


title: RBG31514_TKO


title: 13F_M_2968


title: 13F_M_2956


title: RBG31513_DKO


title: 13F_M_2955


title: RBG31511_WT


title: RBG31509_p53KO


title: 13F_M_2954


title: RBG31510_WT


title: 13F_M_2953


title: 13F_M_2950


title: RBG31507_p53KO


title: RBG31506_TKO


title: 13F_M_2952


title: RBG31504_TKO


title: 13F_M_2948


title: RBG31505_TKO


title: 13F_M_2949


title: 13F_M_2946


title: RBG31501_DKO


title: RBG31503_TKO


title: RBG31502_TKO


title: 13F_M_2947


title: RBG31499_WT


title: 13F_M_2944


title: RBG31497_p53KO


title: 13F_M_2943


title: 13F_M_2945


title: RBG31496_p53KO


title: 13F_M_2942


title: RBG31495_p53KO


title: 13F_M_2941


title: 13F_M_2940


title: 13F_M_2951


title: RBG31494_TKO


title: 13F_M_2967


title: 13F_M_2938


title: RBG31493_TKO


title: RBG31492_TKO


title: 13F_M_2939


title: 13F_M_2936


title: 13F_M_2937


title: 13F_M_2935


title: 13F_M_2934


title: RBG31491_TKO


title: RBG31498_WT


title: RBG31489_DKO


title: RBG31487_WT


title: 13F_M_2869


title: RBG31485_p53KO


title: RBG31484_p53KO


title: RBG31482_TKO


title: RBG31481_TKO


title: 13F_M_2864


title: 13F_M_2866


title: 13F_M_2867


title: 13F_M_2868


title: RBG31483_TKO


title: 13F_M_2865


title: 13F_M_2863


title: RBG31480_TKO


title: RBG31479_TKO


title: 13F_M_2861


title: RBG31490_TKO


title: RBG31478_DKO


title: 13F_M_2860


title: 13F_M_2862


title: 13F_M_2859


title: 13F_M_2858


title: 13F_M_2857


title: RBG31486_WT


title: RBG31472_p53KO


title: 13F_M_2856


title: RBG31474_WT


title: RBG31471_TKO


title: 13F_M_2855


title: RBG31477_DKO


title: 13F_M_2854


title: 13F_M_2853


title: RBG31468_TKO


title: RBG31469_TKO


title: RBG31467_TKO


title: RBG31466_DKO


title: 13F_M_2852


title: 13F_M_2851


title: 13F_M_2850


title: 13F_M_2849


title: RBG31465_DKO


title: RBG31463_WT


title: RBG31462_WT


title: 13F_M_2848


title: 13F_M_2847


title: RBG31473_p53KO


title: RBG31461_p53KO


title: RBG31460_p53KO


title: 13F_M_2845


title: RBG31470_TKO


title: RBG31458_TKO


title: RBG31459_TKO


title: RBG31457_TKO


title: RBG31456_TKO


title: RBG31455_TKO


title: 13F_M_2844


title: 13F_M_2841


title: 13F_M_2839


title: 13F_M_2838


title: RBG31452_DKO


title: 13F_M_2836


title: RBG31453_DKO


title: 13F_M_2837


title: RBG31450_WT


title: 13F_M_2835


title: RBG31451_WT


title: 13F_M_2834


title: 13F_M_2846


title: RBG31449_p53KO


title: 13F_M_2832


title: 13F_M_2831


title: RBG31447_TKO


title: RBG31448_p53KO


title: RBG31446_TKO


title: 13F_M_2833


title: 13F_M_2842


title: RBG31445_TKO


title: 13F_M_2843


title: 13F_M_2829


title: RBG31443_TKO


title: RBG31454_DKO


title: 13F_M_2830


title: 13F_M_2840


title: 13F_M_2828


title: RBG31442_DKO


title: 13F_M_2827


title: 13F_M_2825


title: RBG31440_DKO


title: RBG29497_WT


title: 13F_M_2824


title: RBG31441_DKO


title: RBG29496_WT


title: RBG29495_WT


title: RBG29494_WT


title: 13F_M_2821


title: RBG31444_TKO


title: 13F_M_2823


title: 13F_M_2822


title: RBG29489_Fancd2KO

value: Fancd2 knock-outs


title: RBG29490_Fancd2KO


title: RBG29492_Fancd2KO


title: 13F_M_2818


title: 13F_M_2817


title: RBG29491_Fancd2KO


title: 13F_M_2819


title: 13F_M_2820


title: RBG29488_Fancd2KO


title: RBG29487_Fancd2KO


title: RBG29486_Fancd2KO


title: 13F_M_2813


title: 13F_M_2816


title: 13F_M_2815


title: 13F_M_2826


title: 13F_M_2812


title: RBG29484_WT


title: 13F_M_2810


title: 13F_M_2811


title: RBG29483_WT


title: 13F_M_2809


title: RBG29493_Fancd2KO


title: RBG29481_Fancd2KO


title: RBG29480_Fancd2KO


title: 13F_M_2806


title: RBG29477_Fancd2KO


title: 13F_M_2805


title: RBG29485_WT


title: RBG29475_Fancd2KO


title: RBG29478_Fancd2KO


title: 13F_M_2800


title: 13F_M_2804


title: 13F_M_2801


title: RBG29473_WT


title: RBG29476_Fancd2KO


title: RBG29482_WT


title: RBG29472_WT


title: RBG29474_Fancd2KO


title: 13F_M_2808


title: 13F_M_2798


title: RBG29479_Fancd2KO


title: RBG29470_WT


title: RBG29471_WT


title: 13F_M_2796


title: RBG29469_Fancd2KO


title: 13F_M_2793


title: 13F_M_2807


title: RBG29468_Fancd2KO


title: 13F_M_2792


title: 13F_M_2791


title: RBG29467_Fancd2KO


title: 13F_M_2799


title: 13F_M_2790


title: RBG29465_Fancd2KO


title: 13F_M_2789


title: RBG29466_Fancd2KO


title: 13F_M_2788


title: 13F_M_2786


title: ESC-OB-GFP+(hi) -rep2

city: stanford

first: Hui

last: Zhu

address: 1651 Page Mill Road

institute: Stanford Universtiy

description:
Processed data ESC_OB_GFP+ and ESC.txt
ESC-OB GFP+ rep2

data_processing:
For RNA-seq, paired end sequencing reads (100bp) were generated and aligned to mouse reference sequence NCBI Build 37/mm9 with the STAR (v2.4.2a) algorithm.
For RNA-seq, normalization of RefSeq annotated genes, expression level and differential expression analysis were performed using the Bioconductor package DESeq2 in R (Version 3.2.2)
Genes with False Discovery Rate (FDR) <0.05 were defined as differentially expressed genes.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include normalized count values for each Sample

source_name: GFP+ (hi) differentiated from mouse ESCs

extract_protocol:
RNA was extracted by using PureLink® RNA Mini Kit. Poly-A mRNA was purified using Dynabeads® mRNA Purification Kit according to the manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

value: osteoblast

tag: treatment

value: osteogenic differentiation


title: 13F_M_2787


title: ESC-OB-GFP+(hi) -rep3

description:
Processed data ESC_OB_GFP+ and ESC.txt
ESC-OB GFP+ rep3

value: GFP+ (hi) differentiated from mouse ESCs


title: 13F_M_2794


title: ESC cells rep3

description:
Processed data ESC_OB_GFP+ and ESC.txt
ESC-rep3

source_name: mouse ESC cells

value: mouse ESC cells

value: embrionic stem cells


title: ESC-OB-GFP+(hi) -rep1

description:
Processed data ESC_OB_GFP+ and ESC.txt
ESC-OB GFP+ rep1


title: 13F_M_2785


title: ESC cells rep2

description:
Processed data ESC_OB_GFP+ and ESC.txt
ESC-rep2


title: ESC cells rep1

description:
Processed data ESC_OB_GFP+ and ESC.txt
ESC-rep1


title: 13F_M_2782


title: 13F_M_2781


title: 13F_M_2784


title: 13F_M_2780


title: Bone chip GFP+ (hi) - rep2

description:
Processed data bonechip-GFP+hi and GFP negative.txt
Bonechip-OB GFP+ rep2

source_name: GFP+ (hi) sorted from bone chip culture

value: GFP+ (hi) sorted from bone chip culture


title: 13F_M_2783


title: Bone chip GFP+ (hi) - rep3

description:
Processed data bonechip-GFP+hi and GFP negative.txt
Bonechip-OB GFP+ rep3


title: 13F_M_2779


title: Bone chip GFP+ (hi) - rep1

description:
Processed data bonechip-GFP+hi and GFP negative.txt
Bonechip-OB GFP+ rep1


title: 13F_M_2778


title: Bone chip GFPneg-rep3

description:
Processed data bonechip-GFP+hi and GFP negative.txt
bonechip-OB GFPneg-rep3

source_name: GFP- sorted from bone chip culture

value: GFP- sorted from bone chip culture

value: heterogeneous GFP negative population


title: Bone chip GFPneg-rep2

description:
Processed data bonechip-GFP+hi and GFP negative.txt
bonechip-OB GFPneg-rep2


title: 13F_M_2777


title: mouse bone GFPneg- rep3

description:
Processed data mosue_bone_GFP_hi and GFP neg.txt
Mice bone GFPneg-rep3

source_name: GFP- freshly sorted from mouse long bone


title: 13F_M_2776


title: Bone chip GFPneg-rep1

description:
Processed data bonechip-GFP+hi and GFP negative.txt
bonechip-OB GFPneg-rep1


title: 13F_M_2775


title: mouse bone GFPneg- rep2

description:
Processed data mosue_bone_GFP_hi and GFP neg.txt
Mice bone GFPneg-rep2

value: GFP- freshly sorted from mouse long bone


title: 13F_M_2773


title: 13F_M_2772


title: CT26 sgPhf8+Phf8_3

city: China

first: Yanan

last: Liu

address: 500 Dongchuan Road, Minhang District, Shanghai, China

department: School of Life Sciences

institute: East China Normal University

data_processing:
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome; We selected Hisat2 as the mapping tool; Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level; featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10 (CT26) and hg38 (PANC28)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: colorectal cancer

value: CT26 sgPhf8+Phf8, replicate3

tag: time

value: CT26 Phf8 knockout and transduced with Phf8 vector cell


title: 13F_M_2771


title: CT26 sgPhf8+Phf8_2

value: Phf8 knockout and  transduced with Phf8 vector

value: CT26 sgPhf8+Phf8, replicate2


title: 13F_M_2770


title: 13F_M_2769


title: CT26 sgPhf8_3

value: Phf8 knockout

value: CT26 sgPhf8, replicate3

value: CT26 Phf8 knockout cell


title: 13F_M_2768


title: CT26 sg con_3

value: WT

value: CT26 cells, replicate3

value: CT26 cells


title: CT26 sgPhf8_1

value: CT26 sgPhf8, replicate1


title: CT26 sg con_1

value: CT26 cells, replicate1


title: 13F_M_2767


title: 13F_M_2765


title: 13F_M_2764


title: 13F_M_2763


title: CT26 sh2_8

value: Phf8 knockdown

value: CT26 Phf8 sh2 tumor tissues

value: Day 18 after CT26 Phf8 sh2 cells injection


title: CT26 sh2_7


title: CT26 sh2_6


title: mouse bone GFPneg- rep1

description:
Processed data mosue_bone_GFP_hi and GFP neg.txt
Mice bone GFPneg-rep1

value: GFP- freshly sorted from mouse long bone

value: heterogeneous GFP negative population


title: 13F_M_2762


title: 13F_M_2761


title: 13F_M_2774


title: CT26 sh2_5

value: colorectal cancer


title: 13F_M_2760


title: CT26 sgPhf8+Phf8_1

value: CT26 sgPhf8+Phf8, replicate1

value: CT26 Phf8 knockout and transduced with Phf8 vector cell


title: CT26 sh2_4


title: CT26 sgPhf8_2

value: CT26 sgPhf8, replicate2


title: 13F_M_2759


title: 13F_M_2758


title: 13F_M_2757


title: 13F_M_2754


title: CT26 sg con_2

value: CT26 cells, replicate2


title: CT26 sh2_1


title: CT26 sh1_7

value: CT26 Phf8 sh1 tumor tissues

value: Day 18 after CT26 Phf8 sh1 cells injection


title: 13F_M_2756


title: 13F_M_2766


title: CT26 sh2_3


title: CT26 sh1_6


title: 13F_M_2753


title: CT26 sh1_8


title: CT26 sh2_2


title: CT26 sh1_5


title: 13F_M_2752


title: 13F_M_2751


title: CT26 sh1_3


title: CT26 sh1_4


title: 13F_M_2749


title: CT26 sh1_1


title: 13F_M_2746


title: 13F_M_2745


title: 13F_M_2748


title: CT26 sh1_2


title: 13F_M_2814


title: CT26 sh con_8

value: WT

value: CT26 tumor tissues

value: Day 18 after CT26 cells injection


title: 13F_M_2744


title: 13F_M_2743


title: CT26 sh con_7


title: CT26 sh con_6


title: CT26 sh con_4


title: CT26 sh con_5


title: CT26 sh con_3


title: 13F_M_2742


title: CT26 sh con_2


title: 13F_M_2740


title: 13F_M_2741


title: RBG32589_p53KO

value: Bone marrow

value: p53 knock-outs


title: RBG32588_p53KO


title: RBG32587_p53KO


title: RBG32584_WT


title: RBG32585_WT


title: RBG32586_p53KO


title: 13F_M_2739


title: 13F_M_2733


title: 13F_M_2735


title: 13F_M_2734


title: 13F_M_2736


title: 13F_M_2730


title: 13F_M_2729


title: RBG32583_WT


title: 13F_M_2731


title: 13F_M_2732


title: CT26 sh con_1


title: RBG32582_WT


title: RBG32590_p53KO


title: 13F_M_2738


title: RBG32591_p53KO


title: 13F_M_2728


title: 13F_M_2737


title: RBG32581_WT


title: 13F_M_2727


title: RBG32580_WT


title: 13F_M_2726


title: RBG32579_p53KO


title: 13F_M_2725


title: 13F_M_2724


title: RBG32578_p53KO


title: 13F_M_2723


title: RBG32577_p53KO


title: RBG32576_p53KO


title: 13F_M_2720


title: 13F_M_2721


title: RBG32575_p53KO


title: RBG32573_WT


title: RBG32571_WT


title: RBG32574_p53KO


title: 13F_M_2719


title: 13F_M_2722


title: RBG32570_WT


title: RBG32572_WT


title: RBG32568_WT


title: RBG32567_p53KO


title: 13F_M_2715


title: 13F_M_2717


title: RBG32569_WT


title: RBG32566_p53KO


title: RBG32565_p53KO


title: 13F_M_2716


title: 13F_M_2718


title: 13F_M_2713


title: 13F_M_2711


title: 13F_M_2714


title: RBG32564_p53KO


title: 13F_M_2709


title: RBG32561_WT


title: RBG32562_p53KO


title: RBG32560_WT


title: 13F_M_2708


title: RBG32559_WT


title: RBG32558_WT


title: 13F_M_2707


title: 13F_M_2704


title: 13F_M_2706


title: 13F_M_2712


title: 13F_M_2703


title: RBG32555_p53KO


title: RBG32557_WT


title: RBG32554_p53KO


title: 13F_M_2710


title: RBG32553_p53KO


title: 13F_M_2700


title: 13F_M_2699


title: 13F_M_2698


title: RBG32551_p53KO


title: 13F_M_2701


title: 13F_M_2697


title: RBG32549_WT


title: RBG32550_p53KO


title: RBG32548_WT


title: 13F_M_2695


title: RBG32547_WT


title: 13F_M_2694


title: 13F_M_2696


title: RBG32546_WT


title: 13F_M_2693


title: 13F_M_2702


title: 13F_M_2692


title: 13F_M_2691


title: RBG32545_WT


title: RBG32543_p53KO


title: 13F_M_2690


title: RBG32541_p53KO


title: 13F_M_2689


title: RBG32540_p53KO


title: 13F_M_2687


title: RBG32539_p53KO


title: RBG32535_WT


title: RBG32537_WT


title: 13F_M_2686


title: 13F_M_2684


title: 13F_M_2688


title: RBG32536_WT


title: RBG32534_WT


title: 13F_M_2683


title: RBG32533_WT


title: RBG32532_WT


title: 13F_M_2682


title: 13F_M_2681


title: 13F_M_2680


title: 13F_M_2685


title: 13F_M_2679


title: RBG32544_WT


title: 13F_M_2678


title: RBG32542_p53KO


title: RBG32529_p53KO


title: 13F_M_2677


title: RBG32527_p53KO


title: RBG32528_p53KO


title: 13F_M_2676


title: RBG32526_p53KO


title: 13F_M_2675


title: 13F_M_2673


title: 13F_M_2671


title: 13F_M_2672


title: RBG32525_WT


title: 13F_M_2670


title: RBG32524_WT


title: RBG32522_WT


title: RBG32521_WT


title: RBG32530_p53KO


title: 13F_M_2668


title: 13F_M_2667


title: RBG32531_p53KO


title: RBG32518_p53KO


title: 13F_M_2669


title: 13F_M_2666


title: RBG32517_p53KO


title: 13F_M_2665


title: RBG32520_WT


title: 13F_M_2663


title: RBG32515_p53KO


title: RBG32516_p53KO


title: 13F_M_2664


title: RBG32513_WT


title: RBG32514_p53KO


title: 13F_M_2674


title: RBG32523_WT


title: 13F_M_2661


title: RBG32512_WT


title: RBG32511_WT


title: 13F_M_2660


title: 13F_M_2659


title: RBG32510_WT


title: 13F_M_2658


title: RBG32519_p53KO


title: 13F_M_2657


title: RBG32508_WT


title: RBG32509_WT


title: 13F_M_2656


title: RBG32507_WT


title: RBG32506_WT


title: RBG32504_WT


title: RBG32505_WT


title: 13F_M_2655


title: 13F_M_2662


title: 13F_M_2652


title: RBG32503_WT


title: 13F_M_2650


title: RBG32500_WT


title: 13F_M_2653


title: RBG32499_WT


title: 13F_M_2648


title: 13F_M_2651


title: RBG32498_WT


title: RBG32497_WT


title: 13F_M_2647


title: RBG32495_WT


title: RBG32496_WT


title: 13F_M_2646


title: 13F_M_2643


title: 13F_M_2644


title: RBG32493_WT


title: 13F_M_2654


title: 13F_M_2642


title: RBG32494_WT


title: 13F_M_2641


title: 13F_M_2640


title: RBG32492_WT


title: RBG32491_WT


title: RBG32490_WT


title: RBG32489_p53KO


title: RBG32501_WT


title: 13F_M_2649


title: 13F_M_2639


title: 13F_M_2637


title: 13F_M_2638


title: 13F_M_2636


title: RBG32487_p53KO


title: 13F_M_2635


title: 13F_M_2634


title: RBG32486_p53KO


title: RBG32485_p53KO


title: 13F_M_2633


title: 13F_M_2632


title: RBG32482_WT


title: RBG32483_WT


title: 13F_M_2631


title: RBG32480_WT


title: 13F_M_2628


title: RBG32481_WT


title: 13F_M_2630


title: RBG32479_WT


title: 13F_M_2629


title: RBG32477_p53KO


title: 13F_M_2626


title: 13F_M_2627


title: RBG32475_p53KO


title: RBG32476_p53KO


title: RBG32474_p53KO


title: RBG32478_WT


title: 13F_M_2624


title: RBG32488_p53KO


title: 13F_M_2621


title: RBG32473_p53KO


title: 13F_M_2620


title: 13F_M_2622


title: RBG32472_p53KO


title: 13F_M_2623


title: RBG32484_p53KO


title: 13F_M_2619


title: RBG32470_WT


title: RBG32469_WT


title: 13F_M_2618


title: 13F_M_2616


title: RBG32468_WT


title: 13F_M_2625


title: 13F_M_2617


title: RBG32464_p53KO


title: RBG32467_WT


title: RBG32466_WT


title: RBG32465_p53KO


title: 13F_M_2614


title: 13F_M_2549


title: 13F_M_2548


title: RBG32463_p53KO


title: RBG32462_p53KO


title: RBG32471_WT


title: 13F_M_2615


title: RBG32461_p53KO


title: 13F_M_2545


title: RBG32460_p53KO


title: 13F_M_2546


title: 13F_M_2547


title: 13F_M_2544


title: 13F_M_2543


title: RBG32459_WT


title: RBG32458_WT


title: RBG32457_WT


title: RBG32456_WT


title: 13F_M_2540


title: RBG32455_WT


title: RBG32453_p53KO


title: RBG32454_WT


title: 13F_M_2539


title: 13F_M_2538


title: RBG32452_p53KO


title: 13F_M_2537


title: 13F_M_2535


title: RBG32449_p53KO


title: RBG32450_p53KO


title: 13F_M_2542


title: 13F_M_2533


title: 13F_M_2532


title: RBG32447_WT


title: 13F_M_2531


title: RBG32448_p53KO


title: RBG32446_WT


title: 13F_M_2529


title: RBG32444_WT


title: RBG32445_WT


title: 13F_M_2541


title: 13F_M_2528


title: 13F_M_2527


title: RBG32442_WT


title: RBG32440_p53KO


title: 13F_M_2525


title: 13F_M_2526


title: RBG32441_p53KO


title: 13F_M_2524


title: 13F_M_2536


title: RBG32439_p53KO


title: RBG32438_p53KO


title: 13F_M_2534


title: 13F_M_2523


title: RBG32451_p53KO


title: 13F_M_2530


title: 13F_M_2522


title: RBG32436_p53KO


title: 13F_M_2519


title: RBG32434_WT


title: 13F_M_2520


title: RBG32443_WT


title: RBG32437_p53KO


title: 13F_M_2517


title: RBG32432_WT


title: RBG32435_WT


title: 13F_M_2518


title: RBG32431_WT


title: 13F_M_2521


title: RBG32430_WT


title: 13F_M_2516


title: 13F_M_2514


title: RBG32433_WT


title: 13F_M_2515


title: RBG32429_p53KO


title: 13F_M_2512


title: RBG32427_p53KO


title: 13F_M_2511


title: RBG32426_p53KO


title: RBG32425_p53KO


title: 13F_M_2510


title: RBG32424_p53KO


title: 13F_M_2508


title: RBG32423_WT


title: 13F_M_2507


title: 13F_M_2506


title: 13F_M_2505


title: RBG32422_WT


title: RBG32420_WT


title: 13F_M_2504


title: RBG32421_WT


title: 13F_M_2501


title: 13F_M_2500


title: 13F_M_2502


title: 13F_M_2513


title: RBG32417_p53KO


title: RBG32418_WT


title: RBG32428_p53KO


title: RBG32415_p53KO


title: RBG32416_p53KO


title: RBG32414_p53KO


title: RBG32413_p53KO


title: 13F_M_2509


title: 13F_M_2499


title: 13F_M_2497


title: 13F_M_2498


title: 13F_M_2496


title: RBG32410_WT


title: 13F_M_2495


title: RBG32409_WT


title: RBG32411_WT


title: 13F_M_2493


title: RBG32419_WT


title: 13F_M_2503


title: 13F_M_2492


title: RBG32407_WT


title: RBG32406_WT


title: RBG32405_p53KO


title: 13F_M_2490


title: 13F_M_2491


title: RBG32408_WT


title: 13F_M_2489


title: RBG32404_p53KO


title: 13F_M_2488


title: RBG32403_p53KO


title: RBG32402_p53KO


title: 13F_M_2487


title: 13F_M_2486


title: RBG32401_p53KO


title: 13F_M_2485


title: RBG32398_DKO

value: Aldh2 & Fancd2 double knock-outs


title: 13F_M_2481


title: 13F_M_2484


title: RBG32397_DKO


title: 13F_M_2483


title: RBG32396_TKO

value: Aldh2 & Fancd2 & p53 triple knock-outs


title: RBG32395_TKO


title: 13F_M_2480


title: 13F_M_2479


title: RBG32394_TKO


title: RBG32393_TKO


title: 13F_M_2478


title: RBG32392_TKO


title: 13F_M_2477


title: 13F_M_2475


title: RBG32387_DKO


title: 13F_M_2476


title: 13F_M_2474


title: RBG32400_p53KO


title: RBG32386_DKO


title: RBG32385_DKO


title: 13F_M_2473


title: RBG32384_TKO


title: 13F_M_2471


title: 13F_M_2472


title: 13F_M_2482


title: 13F_M_2470


title: RBG32399_DKO


title: RBG32382_TKO


title: RBG32383_TKO


title: RBG32381_TKO


title: 13F_M_2468


title: RBG32380_TKO


title: 13F_M_2469


title: 13F_M_2467


title: RBG32379_WT


title: 13F_M_2466


title: RBG32378_WT


title: 13F_M_2465


title: RBG32391_WT


title: RBG32377_p53KO


title: 13F_M_2464


title: 13F_M_2463


title: RBG32375_DKO


title: 13F_M_2462


title: RBG32374_DKO


title: 13F_M_2460


title: 13F_M_2461


title: RBG32372_TKO


title: RBG32371_TKO


title: 13F_M_2458


title: 13F_M_2459


title: 13F_M_2457


title: RBG32368_TKO


title: RBG32369_TKO


title: RBG32366_WT


title: 13F_M_2456


title: RBG32365_p53KO


title: RBG32367_WT


title: 13F_M_2452


title: RBG32362_DKO


title: RBG32363_DKO


title: RBG32370_TKO


title: RBG32373_DKO


title: 13F_M_2451


title: RBG32361_DKO


title: 13F_M_2450


title: RBG32360_TKO


title: RBG32359_TKO


title: 13F_M_2449


title: RBG32358_TKO


title: 13F_M_2454


title: 13F_M_2446


title: RBG32356_TKO


title: 13F_M_2448


title: 13F_M_2447


title: 13F_M_2445


title: RBG32355_WT


title: 13F_M_2443


title: 13F_M_2455


title: 13F_M_2444


title: 13F_M_2453


title: RBG32354_WT


title: RBG32353_p53KO


title: RBG32352_p53KO


title: 13F_M_2442


title: RBG32351_DKO


title: RBG32350_DKO


title: RBG32346_TKO


title: RBG32347_TKO


title: RBG32357_TKO


title: RBG32345_TKO


title: 13F_M_2439


title: 13F_M_2438


title: 13F_M_2436


title: 13F_M_2435


title: 13F_M_2437


title: 13F_M_2440


title: 13F_M_2434


title: RBG32344_WT


title: RBG32343_WT


title: 13F_M_2432


title: 13F_M_2433


title: RBG32342_p53KO


title: 13F_M_2431


title: 13F_M_2441


title: 13F_M_2430


title: RBG32340_p53KO


title: RBG32349_TKO


title: 13F_M_2429


title: RBG32339_DKO


title: RBG32348_TKO


title: 13F_M_2428


title: RBG32338_DKO


title: RBG32337_TKO


title: RBG32336_TKO


title: RBG32334_TKO


title: 13F_M_2426


title: 13F_M_2424


title: 13F_M_2425


title: 13F_M_2423


title: RBG32335_TKO


title: 13F_M_2422


title: RBG32331_WT


title: RBG32333_TKO


title: 13F_M_2421


title: RBG32329_p53KO


title: 13F_M_2418


title: RBG32341_p53KO


title: 13F_M_2420


title: RBG32332_WT


title: 13F_M_2417


title: RBG32328_p53KO


title: RBG32327_DKO


title: RBG32326_DKO


title: 13F_M_2427


title: 13F_M_2416


title: RBG32324_TKO


title: 13F_M_2415


title: 13F_M_2413


title: RBG32323_TKO


title: 13F_M_2412


title: RBG32325_TKO


title: 13F_M_2419


title: RBG32330_p53KO


title: RBG32322_TKO


title: 13F_M_2410


title: RBG32321_TKO


title: 13F_M_2411


title: RBG32320_WT


title: RBG32319_WT


title: 13F_M_2414


title: 13F_M_2408


title: RBG32317_p53KO


title: 13F_M_2407


title: 13F_M_2409


title: 13F_M_2406


title: RBG32316_p53KO


title: RBG32314_DKO


title: 13F_M_2404


title: RBG32313_TKO


title: 13F_M_2403


title: 13F_M_2402


title: RBG32312_TKO


title: RBG32311_TKO


title: 13F_M_2401


title: RBG32310_TKO


title: RBG32309_TKO


title: RBG32318_p53KO


title: 13F_M_2399


title: RBG32308_WT


title: 13F_M_2396


title: RBG32305_p53KO


title: 13F_M_2400


title: RBG32306_p53KO


title: RBG32304_p53KO


title: 13F_M_2394


title: 13F_M_2405


title: 13F_M_2398


title: 13F_M_2395


title: 13F_M_2397


title: 13F_M_2393


title: RBG32307_WT


title: RBG32303_TKO


title: RBG32298_p53KO


title: 13F_M_2391


title: 13F_M_2392


title: RBG32299_WT


title: RBG32301_TKO


title: 13F_M_2389


title: 13F_M_2390


title: 13F_M_2388


title: RBG32302_TKO


title: 13F_M_2386


title: RBG32286_p53KO


title: RBG32290_TKO


title: RBG32297_p53KO


title: RBG32283_DKO


title: RBG32285_p53KO


title: RBG32289_TKO


title: RBG32288_WT


title: RBG32292_TKO


title: RBG32296_DKO


title: RBG32284_DKO


title: RBG32287_WT


title: RBG32291_TKO


title: RBG32281_TKO


title: RBG32280_TKO


title: RBG32279_TKO


title: 13F_M_2387


title: 13F_M_2385


title: 13F_M_2383


title: 13F_M_2380


title: 13F_M_2376


title: 13F_M_2374


title: 13F_M_2379


title: 13F_M_2382


title: 13F_M_2375


title: 13F_M_2378


title: 13F_M_2384


title: 13F_M_2381


title: 13F_M_2377


title: RBG32278_TKO


title: RBG32276_WT


title: RBG32275_WT


title: RBG32273_p53KO


title: RBG32270_DKO


title: RBG32269_TKO


title: 13F_M_2372


title: 13F_M_2367


title: 13F_M_2368


title: 13F_M_2369


title: 13F_M_2371


title: RBG32268_TKO


title: 13F_M_2366


title: 13F_M_2365


title: 13F_M_2373


title: RBG32264_WT


title: 13F_M_2361


title: 13F_M_2360


title: 13F_M_2359


title: RBG32265_TKO


title: RBG32266_TKO


title: 13F_M_2363


title: 13F_M_2364


title: 13F_M_2362


title: RBG32262_p53KO


title: RBG32272_DKO


title: 13F_M_2370


title: RBG32261_p53KO


title: 13F_M_2358


title: RBG32274_p53KO


title: RBG32260_DKO


title: 13F_M_2357


title: 13F_M_2353


title: RBG32258_DKO


title: RBG32257_TKO


title: 13F_M_2355


title: 13F_M_2356


title: RBG32256_TKO


title: 13F_M_2354


title: RBG32267_TKO


title: RBG32263_WT


title: 13F_M_2352


title: RBG32253_WT


title: RBG32250_p53KO


title: RBG32252_WT


title: RBG32251_p53KO


title: 13F_M_2350


title: 13F_M_2349


title: 13F_M_2351


title: RBG32247_DKO


title: RBG32249_p53KO


title: 13F_M_2348


title: 13F_M_2346


title: 13F_M_2347


title: RBG32248_DKO


title: 13F_M_2345


title: RBG32246_TKO


title: RBG32254_TKO


title: 13F_M_2344


title: RBG32255_TKO


title: 13F_M_2343


title: 13F_M_2342


title: RBG32245_TKO


title: RBG32243_TKO


title: RBG32242_TKO


title: 13F_M_2340


title: 13F_M_2341


title: 13F_M_2339


title: 13F_M_2338


title: RBG32239_p53KO


title: RBG32240_WT


title: RBG32241_WT


title: 13F_M_2336


title: RBG32237_p53KO


title: RBG32236_DKO


title: RBG32238_p53KO


title: 13F_M_2337


title: 13F_M_2335


title: RBG32234_TKO


title: RBG32232_TKO


title: RBG32231_TKO


title: RBG32233_TKO


title: 13F_M_2331


title: 13F_M_2334


title: 13F_M_2332


title: 13F_M_2330


title: RBG32230_TKO


title: 13F_M_2327


title: 13F_M_2329


title: RBG32229_WT


title: RBG32227_p53KO


title: RBG32228_WT


title: 13F_M_2328


title: RBG32226_p53KO


title: 13F_M_2324


title: RBG32224_DKO


title: 13F_M_2323


title: 13F_M_2326


title: RBG32225_p53KO


title: RBG32223_DKO


title: RBG32235_DKO


title: RBG32222_TKO


title: 13F_M_2322


title: 13F_M_2333


title: 13F_M_2325


title: 13F_M_2320


title: 13F_M_2321


title: RBG32221_TKO


title: 13F_M_2317


title: 13F_M_2316


title: 13F_M_2319


title: 13F_M_2318


title: RBG32216_WT


title: RBG32219_TKO


title: RBG32215_p53KO


title: 13F_M_2315


title: 13F_M_2313


title: RBG32213_p53KO


title: RBG32218_TKO


title: 13F_M_2312


title: RBG32210_TKO


title: 13F_M_2310


title: RBG32211_DKO


title: 13F_M_2311


title: RBG32209_TKO


title: RBG32207_TKO


title: RBG32206_TKO


title: RBG32208_TKO


title: 13F_M_2308


title: 13F_M_2309


title: 13F_M_2307


title: 13F_M_2305


title: RBG32220_TKO


title: RBG32204_TKO


title: RBG32217_WT


title: RBG32205_TKO


title: RBG32203_TKO


title: 13F_M_2304


title: 13F_M_2303


title: 13F_M_2306


title: 13F_M_2314


title: RBG32214_p53KO


title: RBG32202_DKO


title: 13F_M_2298


title: RBG32199_p53KO


title: 13F_M_2299


title: 13F_M_2300


title: RBG32201_DKO


title: RBG32198_p53KO


title: 13F_M_2302


title: 13F_M_2301


title: RBG32200_DKO


title: RBG32192_TKO


title: 13F_M_2295


title: RBG32195_TKO


title: RBG32194_TKO


title: RBG32193_TKO


title: 13F_M_2297


title: 13F_M_2291


title: 13F_M_2294


title: 13F_M_2292


title: RBG32190_DKO


title: 13F_M_2289


title: 13F_M_2290


title: RBG32187_p53KO


title: RBG32191_TKO


title: RBG32188_DKO


title: RBG32189_DKO


title: 13F_M_2288


title: RBG32186_p53KO


title: 13F_M_2296


title: RBG32185_WT


title: 13F_M_2287


title: 13F_M_2286


title: 13F_M_2285


title: RBG32182_TKO


title: RBG32183_TKO


title: 13F_M_2293


title: 13F_M_2284


title: 13F_M_2282


title: 13F_M_2283


title: 13F_M_2281


title: RBG32178_DKO


title: RBG32177_DKO


title: RBG32176_DKO


title: RBG32174_p53KO


title: 13F_M_2278


title: RBG32175_p53KO


title: 13F_M_2279


title: RBG32171_TKO


title: RBG32172_WT


title: 13F_M_2277


title: 13F_M_2274


title: 13F_M_2275


title: 13F_M_2276


title: RBG32181_TKO


title: RBG32169_TKO


title: RBG32168_TKO


title: RBG32179_TKO


title: RBG32170_TKO


title: RBG32167_TKO


title: RBG32166_DKO


title: 13F_M_2270


title: RBG32165_DKO


title: 13F_M_2272


title: 13F_M_2273


title: 13F_M_2280


title: RBG32173_WT


title: RBG32164_DKO


title: 13F_M_2269


title: 13F_M_2268


title: RBG32163_p53KO


title: RBG32162_p53KO


title: 13F_M_2267


title: RBG32161_WT


title: RBG32159_TKO


title: RBG32158_TKO


title: 13F_M_2263


title: 13F_M_2264


title: 13F_M_2262


title: RBG32157_TKO


title: 13F_M_2266


title: 13F_M_2265


title: 13F_M_2261


title: 13F_M_2271


title: RBG32156_TKO


title: RBG32155_TKO


title: RBG32154_DKO


title: RBG32152_p53KO


title: 13F_M_2257


title: 13F_M_2255


title: RBG32153_DKO


title: 13F_M_2258


title: RBG32151_p53KO


title: RBG32160_WT


title: 13F_M_2253


title: 13F_M_2252


title: 13F_M_2251


title: RBG32149_WT


title: 13F_M_2254


title: 13F_M_2250


title: 13F_M_2260


title: RBG32148_WT


title: RBG32147_TKO


title: RBG32144_TKO


title: RBG32146_TKO


title: 13F_M_2247


title: 13F_M_2246


title: 13F_M_2249


title: 13F_M_2256


title: 13F_M_2248


title: RBG32145_TKO


title: 13F_M_2245


title: RBG32150_p53KO


title: RBG32143_TKO


title: RBG32142_DKO


title: RBG32141_DKO


title: 13F_M_2242


title: 13F_M_2244


title: 13F_M_2243


title: 13F_M_2241


title: RBG32139_p53KO


title: RBG32138_p53KO


title: 13F_M_2240


title: RBG32137_WT


title: RBG32136_WT


title: RBG32135_TKO


title: 13F_M_2239


title: RBG32134_TKO


title: 13F_M_2238


title: 13F_M_2237


title: RBG32133_TKO


title: 13F_M_2236


title: RBG32132_TKO


title: 13F_M_2235


title: 13F_M_2234


title: 13F_M_2233


title: RBG32140_p53KO


title: RBG32129_DKO


title: RBG32130_DKO


title: RBG32131_TKO


title: RBG32128_p53KO


title: RBG32127_p53KO


title: 13F_M_2229


title: 13F_M_2230


title: 13F_M_2231


title: RBG32126_p53KO


title: RBG32125_WT


title: RBG32124_WT


title: 13F_M_2227


title: RBG32123_TKO


title: 13F_M_2226


title: 13F_M_2224


title: 13F_M_2223


title: RBG32120_TKO


title: RBG32122_TKO


title: RBG32119_TKO


title: 13F_M_2222


title: RBG32118_DKO


title: 13F_M_2221


title: RBG32117_DKO


title: 13F_M_2232


title: 13F_M_2220


title: 13F_M_2219


title: RBG32116_p53KO


title: RBG32115_p53KO


title: 13F_M_2228


title: 13F_M_2218


title: RBG32114_p53KO


title: 13F_M_2217


title: RBG32113_WT


title: RBG32112_WT


title: 13F_M_2215


title: 13F_M_2214


title: 13F_M_2216


title: RBG32111_p53KO


title: RBG32121_TKO


title: RBG32110_p53KO


title: 13F_M_2225


title: RBG32109_p53KO


title: 13F_M_2213


title: 13F_M_2211


title: 13F_M_2212


title: RBG32105_WT


title: 13F_M_2209


title: 13F_M_2210


title: RBG32108_DKO


title: 13F_M_2208


title: 13F_M_2207


title: RBG32103_TKO


title: RBG32102_TKO


title: RBG32099_p53KO


title: RBG32106_WT


title: 13F_M_2205


title: 13F_M_2206


title: 13F_M_2203


title: 13F_M_2204


title: RBG32098_p53KO


title: 13F_M_2202


title: 13F_M_2201


title: 13F_M_2200


title: RBG32095_DKO


title: RBG32094_WT


title: RBG32107_DKO


title: RBG32092_TKO


title: 13F_M_2197


title: 13F_M_2198


title: 13F_M_2196


title: RBG32093_WT


title: RBG32090_TKO


title: 13F_M_2195


title: 13F_M_2193


title: 13F_M_2192


title: RBG32086_p53KO


title: 13F_M_2191


title: RBG32096_DKO


title: RBG32097_p53KO


title: RBG32085_p53KO


title: RBG32084_DKO


title: 13F_M_2188


title: RBG32083_DKO


title: 13F_M_2187


title: 13F_M_2190


title: RBG32080_TKO


title: 13F_M_2189


title: RBG32081_WT


title: 13F_M_2184


title: 13F_M_2182


title: RBG32077_TKO


title: RBG32078_TKO


title: RBG32088_TKO


title: 13F_M_2185


title: RBG32091_TKO


title: 13F_M_2181


title: RBG32076_TKO


title: RBG32079_TKO


title: RBG32075_p53KO


title: 13F_M_2179


title: 13F_M_2180


title: RBG32074_p53KO


title: RBG32087_p53KO


title: 13F_M_2178


title: RBG32073_p53KO


title: RBG32072_DKO


title: 13F_M_2186


title: RBG32082_WT


title: 13F_M_2176


title: 13F_M_2177


title: RBG32069_WT


title: RBG32068_TKO


title: 13F_M_2173


title: RBG32070_WT


title: 13F_M_2172


title: RBG32067_TKO


title: 13F_M_2171


title: RBG32065_TKO


title: 13F_M_2174


title: 13F_M_2169


title: RBG32064_TKO


title: 13F_M_2103


title: 13F_M_2170


title: RBG32062_p53KO


title: RBG32061_DKO


title: 13F_M_2168


title: RBG32060_DKO


title: RBG32063_p53KO


title: RBG32058_WT


title: 13F_M_2098


title: 13F_M_2102


title: 13F_M_2101


title: RBG32056_TKO


title: 13F_M_2097


title: RBG32057_WT


title: 13F_M_2096


title: RBG32055_TKO


title: RBG32054_TKO


title: 13F_M_2095


title: 13F_M_2094


title: RBG32053_TKO


title: 13F_M_2092


title: 13F_M_2093


title: RBG32051_p53KO


title: RBG32052_TKO


title: 13F_M_2091


title: RBG32059_DKO


title: RBG32048_DKO


title: 13F_M_2090


title: RBG32050_p53KO


title: 13F_M_2088


title: 13F_M_2089


title: 13F_M_2086


title: 13F_M_2099


title: 13F_M_2087


title: RBG32047_DKO


title: RBG32044_TKO


title: RBG32046_WT


title: 13F_M_2085


title: 13F_M_2083


title: RBG32042_TKO


title: 13F_M_2084


title: RBG32043_TKO


title: 13F_M_2082


title: RBG32040_TKO


title: 13F_M_2081


title: RBG32039_p53KO


title: 13F_M_2080


title: RBG32038_p53KO


title: RBG32045_WT


title: RBG32036_DKO


title: 13F_M_2077


title: 13F_M_2078


title: RBG32034_WT


title: 13F_M_2076


title: RBG32037_DKO


title: 13F_M_2074


title: 13F_M_2075


title: RBG32035_DKO


title: RBG32033_WT


title: 13F_M_2073


title: RBG32031_TKO


title: RBG32030_TKO


title: RBG32041_TKO


title: 13F_M_2071


title: RBG32028_TKO


title: 13F_M_2070


title: RBG32029_TKO


title: 13F_M_2069


title: RBG32027_p53KO


title: 13F_M_2068


title: RBG32026_p53KO


title: RBG32024_DKO


title: 13F_M_2067


title: 13F_M_2079


title: RBG32025_DKO


title: RBG32023_DKO


title: RBG32021_WT


title: RBG32020_TKO


title: RBG32022_WT


title: 13F_M_2064


title: 13F_M_2066


title: 13F_M_2065


title: 13F_M_2063


title: 13F_M_2062


title: 13F_M_2072


title: RBG32019_TKO


title: RBG32016_TKO


title: RBG32018_TKO


title: RBG32017_TKO


title: 13F_M_2059


title: 13F_M_2060


title: 13F_M_2058


title: RBG32783_p53KO


title: 13F_M_2057


title: 13F_M_2056


title: RBG32781_p53KO


title: 13F_M_2055


title: RBG32782_p53KO


title: RBG32780_p53KO


title: 13F_M_2053


title: RBG32778_p53KO


title: RBG32779_p53KO


title: RBG32777_WT


title: 13F_M_2061


title: RBG32775_WT


title: RBG32774_WT


title: RBG32773_WT


title: 13F_M_2048


title: 13F_M_2049


title: 13F_M_2047


title: 13F_M_2051


title: 13F_M_2046


title: RBG32771_p53KO


title: RBG32770_p53KO


title: 13F_M_2044


title: 13F_M_2043


title: 13F_M_2042


title: RBG32768_p53KO


title: RBG32769_p53KO


title: 13F_M_2054


title: RBG32767_p53KO


title: 13F_M_2052


title: 13F_M_1976


title: 13F_M_2041


title: 13F_M_1975


title: RBG32766_p53KO


title: RBG32765_WT


title: 13F_M_1974


title: RBG32776_WT


title: 13F_M_2050


title: RBG32764_WT


title: 13F_M_1972


title: RBG32772_WT


title: RBG32762_WT


title: RBG32763_WT


title: 13F_M_1973


title: 13F_M_1971


title: RBG32761_WT


title: RBG32760_WT


title: RBG32759_p53KO


title: RBG32758_p53KO


title: 13F_M_1967


title: RBG32757_p53KO


title: 13F_M_1970


title: 13F_M_1968


title: RBG32756_p53KO


title: 13F_M_1966


title: RBG32754_p53KO


title: RBG32753_WT


title: 13F_M_1965


title: RBG32755_p53KO


title: RBG32752_WT


title: 13F_M_1962


title: 13F_M_1963


title: 13F_M_1961


title: RBG32751_WT


title: 13F_M_1959


title: RBG32750_WT


title: RBG32749_WT


title: 13F_M_1960


title: RBG32748_WT


title: 13F_M_1957


title: 13F_M_1969


title: RBG32747_p53KO


title: 13F_M_1958


title: RBG32746_p53KO


title: 13F_M_1964


title: RBG32744_p53KO


title: RBG32742_p53KO


title: 13F_M_1955


title: 13F_M_1953


title: 13F_M_1951


title: 13F_M_1952


title: 13F_M_1954


title: RBG32741_WT


title: RBG32740_WT


title: RBG32739_WT


title: 13F_M_1949


title: 13F_M_1948


title: RBG32738_WT


title: 13F_M_1950


title: 13F_M_1956


title: RBG32737_WT


title: 13F_M_1946


title: RBG32736_WT


title: 13F_M_1945


title: RBG32745_p53KO


title: RBG32735_p53KO


title: 13F_M_1943


title: 13F_M_1944


title: RBG32734_p53KO


title: RBG32733_p53KO


title: RBG32732_p53KO


title: 13F_M_1942


title: 13F_M_1941


title: RBG32743_p53KO


title: RBG32731_p53KO


title: RBG32729_WT


title: 13F_M_1937


title: 13F_M_1939


title: RBG32730_p53KO


title: RBG32727_WT


title: 13F_M_1947


title: 13F_M_1938


title: RBG32728_WT


title: RBG32725_WT


title: 13F_M_1935


title: RBG32726_WT


title: RBG29464_Fancd2KO

value: Fancd2 knock-outs


title: 13F_M_1934


title: 13F_M_1936


title: RBG29463_Fancd2KO


title: 13F_M_1933


title: RBG29462_Fancd2KO


title: 13F_M_1932


title: RBG29461_WT


title: 13F_M_1930


title: 13F_M_1931


title: RBG29460_WT


title: 13F_M_1929


title: 13F_M_1940


title: RBG29458_WT


title: RBG29457_Fancd2KO


title: 13F_M_1927


title: 13F_M_1926


title: 13F_M_1925


title: RBG29455_Fancd2KO


title: RBG29453_Fancd2KO


title: RBG29454_Fancd2KO


title: 13F_M_1923


title: 13F_M_1924


title: 13F_M_1922


title: RBG29450_Fancd2KO


title: RBG29452_Fancd2KO


title: RBG29449_WT


title: 13F_M_1921


title: 13F_M_1928


title: RBG29451_Fancd2KO


title: 13F_M_1918


title: 13F_M_1920


title: RBG29459_WT


title: 13F_M_1919


title: 13F_M_1917


title: RBG29446_WT


title: RBG29447_WT


title: 13F_M_1916


title: 13F_M_1915


title: RBG29445_Fancd2KO


title: RBG29456_Fancd2KO


title: RBG29444_Fancd2KO


title: RBG29443_Fancd2KO


title: 13F_M_1913


title: 13F_M_1914


title: 13F_M_1912


title: RBG29442_Fancd2KO


title: 13F_M_1910


title: 13F_M_1911


title: RBG29440_Fancd2KO


title: RBG29441_Fancd2KO


title: RBG29439_Fancd2KO


title: RBG29448_WT


title: 13F_M_1909


title: 13F_M_1908


title: RBG29438_Fancd2KO


title: RBG29436_WT


title: RBG29437_WT


title: RBG29435_WT


title: 13F_M_1903


title: 13F_M_1904


title: 13F_M_1905


title: 13F_M_1902


title: 13F_M_1901


title: 13F_M_1900


title: RBG29432_Fancd2KO


title: RBG29433_Fancd2KO


title: RBG29431_Fancd2KO


title: RBG29430_Fancd2KO


title: 13F_M_1899


title: 13F_M_1898


title: RBG29429_Fancd2KO


title: RBG29428_Fancd2KO


title: 13F_M_1897


title: 13F_M_1896


title: RBG29427_Fancd2KO


title: 13F_M_1907


title: 13F_M_1894


title: RBG29426_Fancd2KO


title: RBG29424_WT


title: 13F_M_1893


title: RBG29434_WT


title: RBG29421_Fancd2KO


title: 13F_M_1890


title: 13F_M_1889


title: 13F_M_1891


title: RBG29420_Fancd2KO


title: 13F_M_1888


title: 13F_M_1886


title: 13F_M_1887


title: RBG29419_Fancd2KO


title: RBG29418_Fancd2KO


title: RBG29417_Fancd2KO


title: RBG29415_Fancd2KO


title: 13F_M_1895


title: 13F_M_1884


title: 13F_M_1885


title: RBG29412_WT


title: 13F_M_1882


title: RBG29414_Fancd2KO


title: 13F_M_1880


title: RBG29425_WT


title: RBG29411_WT


title: 13F_M_1892


title: 13F_M_1881


title: 13F_M_1883


title: RBG29413_WT


title: RBG29423_WT


title: RBG29422_WT


title: RBG29410_WT


title: 13F_M_1879


title: RBG29409_Fancd2KO


title: 13F_M_1878


title: 13F_M_1877


title: RBG29408_Fancd2KO


title: 13F_M_1876


title: RBG29405_Fancd2KO


title: RBG29407_Fancd2KO


title: 13F_M_1874


title: 13F_M_1875


title: RBG29406_Fancd2KO


title: RBG29416_Fancd2KO


title: 13F_M_1873


title: RBG29404_Fancd2KO


title: RBG29403_Fancd2KO


title: 13F_M_1872


title: RBG29401_Fancd2KO


title: 13F_M_1871


title: 13F_M_1868


title: 13F_M_1870


title: RBG29400_Fancd2KO


title: RBG29399_Fancd2KO


title: 13F_M_1867


title: 13F_M_1866


title: 13F_M_1869


title: 13F_M_1865


title: RBG29395_WT


title: RBG29397_WT


title: RBG29396_WT


title: 13F_M_1864


title: RBG29394_WT


title: RBG29393_Fancd2KO


title: 13F_M_1863


title: 13F_M_1862


title: 13F_M_1861


title: RBG29392_Fancd2KO


title: RBG29402_Fancd2KO


title: 13F_M_1858


title: RBG29390_Fancd2KO


title: 13F_M_1860


title: RBG29391_Fancd2KO


title: RBG29389_Fancd2KO


title: RBG29398_Fancd2KO


title: RBG29386_Fancd2KO


title: RBG29387_Fancd2KO


title: 13F_M_1855


title: 13F_M_1854


title: 13F_M_1853


title: 13F_M_1856


title: 13F_M_1852


title: RBG29385_WT


title: RBG29382_WT


title: RBG29383_WT


title: RBG29381_Fancd2KO


title: 13F_M_1850


title: 13F_M_1851


title: 13F_M_1857


title: RBG29380_Fancd2KO


title: RBG29379_Fancd2KO


title: 13F_M_1784


title: 13F_M_1859


title: RBG29378_Fancd2KO


title: 13F_M_1783


title: RBG29388_Fancd2KO


title: 13F_M_1782


title: 13F_M_1781


title: RBG29384_WT


title: RBG29377_Fancd2KO


title: RBG29376_Fancd2KO


title: 13F_M_1780


title: RBG29374_Fancd2KO


title: RBG29375_Fancd2KO


title: 13F_M_1779


title: RBG29372_WT


title: 13F_M_1849


title: 13F_M_1776


title: 13F_M_1778


title: RBG29371_WT


title: 13F_M_1777


title: RBG29370_WT


title: RBG29369_Fancd2KO


title: 13F_M_1773


title: 13F_M_1775


title: 13F_M_1772


title: RBG29368_Fancd2KO


title: 13F_M_1774


title: RBG29367_Fancd2KO


title: 13F_M_1771


title: RBG29366_Fancd2KO


title: 13F_M_1770


title: RBG29373_WT


title: 13F_M_1769


title: 13F_M_1768


title: RBG29364_Fancd2KO


title: 13F_M_1767


title: 13F_M_1766


title: RBG29363_Fancd2KO


title: RBG29365_Fancd2KO


title: RBG29360_WT


title: 13F_M_1763


title: RBG29361_WT


title: RBG29358_WT


title: 13F_M_1761


title: 13F_M_1764


title: RBG29357_Fancd2KO


title: RBG29356_Fancd2KO


title: 13F_M_1760


title: 13F_M_1759


title: RBG29353_Fancd2KO


title: RBG29354_Fancd2KO


title: 13F_M_1762


title: 13F_M_1758


title: RBG29352_Fancd2KO


title: RBG29355_Fancd2KO


title: 13F_M_1757


title: 13F_M_1756


title: RBG29362_Fancd2KO


title: RBG29350_Fancd2KO


title: RBG29349_WT


title: 13F_M_1754


title: 13F_M_1755


title: RBG29348_WT


title: 13F_M_1765


title: 13F_M_1753


title: 13F_M_1752


title: RBG29344_Fancd2KO


title: 13F_M_1750


title: RBG29343_Fancd2KO


title: RBG29345_Fancd2KO


title: 13F_M_1749


title: 13F_M_1751


title: RBG29342_Fancd2KO


title: RBG29341_Fancd2KO


title: 13F_M_1746


title: 13F_M_1748


title: RBG29339_Fancd2KO


title: RBG29340_Fancd2KO


title: 13F_M_1747


title: RBG29351_Fancd2KO


title: 13F_M_1744


title: 13F_M_1743


title: RBG29338_Fancd2KO


title: RBG29337_WT


title: RBG29347_WT


title: RBG29336_WT


title: 13F_M_1740


title: RBG29334_WT


title: RBG29346_WT


title: 13F_M_1739


title: 13F_M_1742


title: RBG29333_Fancd2KO


title: 13F_M_1738


title: RBG29335_WT


title: RBG29330_Fancd2KO


title: RBG29331_Fancd2KO


title: RBG29332_Fancd2KO


title: 13F_M_1736


title: 13F_M_1745


title: 13F_M_1737


title: 13F_M_1734


title: 13F_M_1732


title: 13F_M_1735


title: RBG29329_Fancd2KO


title: 13F_M_1731


title: 13F_M_1733


title: 13F_M_1741


title: 13F_M_1730


title: RBG29326_Fancd2KO


title: RBG29325_WT


title: RBG29324_WT


title: RBG29323_WT


title: 13F_M_1729


title: 13F_M_1728


title: 13F_M_1727


title: RBG29322_WT


title: 13F_M_1726


title: RBG29321_Fancd2KO


title: 13F_M_1725


title: RBG29320_Fancd2KO


title: 13F_M_1724


title: RBG29328_Fancd2KO


title: RBG29319_Fancd2KO


title: RBG29318_Fancd2KO


title: RBG29317_Fancd2KO


title: RBG29327_Fancd2KO


title: RBG29316_Fancd2KO


title: RBG29315_Fancd2KO


title: 13F_M_1204


title: 13F_M_1722


title: 13F_M_1723


title: RBG29313_WT


title: 13F_M_1202


title: RBG29311_WT


title: RBG29312_WT


title: 13F_M_1200


title: 13F_M_1201


title: RBG29310_WT


title: 13F_M_1198


title: RBG29309_Fancd2KO


title: 13F_M_1199


title: 13F_M_1197


title: 13F_M_1196


title: RBG29308_Fancd2KO


title: RBG29307_Fancd2KO


title: RBG29306_Fancd2KO


title: 13F_M_1195


title: 13F_M_1194


title: RBG29305_Fancd2KO


title: 13F_M_1205


title: RBG29314_Fancd2KO


title: 13F_M_1203


title: RBG29304_Fancd2KO


title: RBG29303_Fancd2KO


title: RBG29302_Fancd2KO


title: 13F_M_1189


title: 13F_M_1193


title: 13F_M_1188


title: RBG29301_Fancd2KO


title: 13F_M_1191


title: 13F_M_1187


title: RBG29300_Fancd2KO


title: RBG29298_Fancd2KO


title: 13F_M_1185


title: 13F_M_1192


title: 13F_M_1183


title: 13F_M_1186


title: RBG29296_WT


title: 13F_M_1182


title: RBG29292_Fancd2KO


title: RBG29293_Fancd2KO


title: RBG29295_WT


title: 13F_M_1181


title: RBG29291_Fancd2KO


title: RBG29290_Fancd2KO


title: 13F_M_1180


title: 13F_M_1179


title: RBG29289_Fancd2KO


title: RBG29288_Fancd2KO


title: 13F_M_1178


title: RBG29299_Fancd2KO


title: 13F_M_1177


title: 13F_M_1173


title: RBG29286_Fancd2KO


title: 13F_M_1172


title: RBG29287_Fancd2KO


title: 13F_M_1184


title: RBG29297_WT


title: 13F_M_1169


title: 13F_M_1170


title: RBG29283_WT


title: RBG29285_WT


title: RBG29281_Fancd2KO


title: RBG29282_WT


title: 13F_M_1168


title: RBG29280_Fancd2KO


title: 13F_M_1164


title: 13F_M_1163


title: RBG29277_Fancd2KO


title: RBG29279_Fancd2KO


title: RBG29278_Fancd2KO


title: 13F_M_1167


title: 13F_M_1165


title: 13F_M_1166


title: RBG29276_Fancd2KO


title: 13F_M_1162


title: 13F_M_1157


title: RBG29274_Fancd2KO


title: RBG29284_WT


title: RBG29273_WT


title: 13F_M_1156


title: RBG29272_WT


title: 13F_M_1153


title: 13F_M_1154


title: RBG29271_WT


title: 13F_M_1152


title: 13F_M_1151


title: RBG29269_Fancd2KO


title: RBG29268_Fancd2KO


title: RBG29267_Fancd2KO


title: 13F_M_1147


title: 13F_M_1149


title: RBG29270_WT


title: RBG29266_Fancd2KO


title: RBG29275_Fancd2KO


title: RBG29264_Fancd2KO


title: 13F_M_1138


title: 13F_M_1146


title: 13F_M_1137


title: RBG29263_Fancd2KO


title: 13F_M_1141


title: RBG29262_Fancd2KO


title: 13F_M_1148


title: RBG29260_WT


title: RBG29257_Fancd2KO


title: 13F_M_1155


title: 13F_M_1134


title: 13F_M_1133


title: 13F_M_1132


title: 13F_M_1126


title: 13F_M_1150


title: RBG29258_WT


title: RBG29265_Fancd2KO


title: RBG29259_WT


title: RBG29254_Fancd2KO


title: 13F_M_1129


title: RBG29253_Fancd2KO


title: RBG29252_Fancd2KO


title: 13F_M_1122


title: 13F_M_1123


title: RBG29250_Fancd2KO


title: 13F_M_1130


title: 13F_M_1124


title: 13F_M_1120


title: 13F_M_1121


title: RBG29249_WT


title: RBG29248_WT


title: 13F_M_1119


title: 13F_M_1118


title: RBG29256_Fancd2KO


title: RBG29246_WT


title: 13F_M_1117


title: RBG29245_Fancd2KO


title: RBG29244_Fancd2KO


title: 13F_M_1116


title: 13F_M_1115


title: RBG29243_Fancd2KO


title: RBG29242_Fancd2KO


title: RBG29255_Fancd2KO


title: 13F_M_1113


title: 13F_M_1125


title: 13F_M_1114


title: 13F_M_1112


title: RBG29240_Fancd2KO


title: 13F_M_1111


title: RBG29241_Fancd2KO


title: RBG29237_WT


title: RBG29235_WT


title: RBG29236_WT


title: RBG29261_WT


title: RBG29239_Fancd2KO


title: RBG29247_WT


title: RBG29234_WT


title: 13F_M_1108


title: 13F_M_1107


title: 13F_M_1106


title: 13F_M_1105


title: RBG29238_Fancd2KO


title: 13F_M_1103


title: 13F_M_1104


title: RBG29232_Fancd2KO


title: 13F_M_1102


title: RBG29231_Fancd2KO


title: RBG29233_Fancd2KO


title: 13F_M_1100


title: RBG29230_Fancd2KO


title: 13F_M_1101


title: RBG29229_Fancd2KO


title: RBG29228_Fancd2KO


title: 13F_M_1097


title: 13F_M_1098


title: RBG29227_Fancd2KO


title: RBG29226_Fancd2KO


title: 13F_M_1094


title: RBG29225_WT


title: RBG29224_WT


title: 13F_M_1093


title: 13F_M_1091


title: 13F_M_1090


title: RBG29222_WT


title: 13F_M_1088


title: RBG29220_Fancd2KO


title: RBG29219_Fancd2KO


title: RBG29221_Fancd2KO


title: 13F_M_1089


title: 13F_M_1086


title: 13F_M_1099


title: RBG29218_Fancd2KO


title: C2C12 cells, MCI2

city: Fayetteville

first: Francielly

last: Morena da Silva

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

data_processing:
Standard 150 bp paired-end sequencing was performed and read counts were >20 million
Raw counts from RNA-sequencing were used as inputs into Partek Flow
Alignment was performed using STAR with mmu39
After filtering low-expressed genes, DESeq2 (Version 1.34.0) was used for normalization and differential analyses to identify differentially expressed genes (DEGs) with pairwise comparisons
DEGs were identified with a false discovery rate (FDR, step-up procedure) adjusted p-value<0.05
Assembly: mm9
Supplementary files format and content: Normalized counts, DEG

growth_protocol: C2C12 murine myoblasts were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Fisher Scientific). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA-sequencing was performed by NovoGene.

treatment_protocol: Plasmid DNA (1 μg) for miR-16-1 (miR-16-5p) and empty vector control (pCMVmiR) were transfected for 5 hours at 37C with 5% CO2

value: Myoblasts

value: miR-16 knockdown

value: 5 hours


title: C2C12 cells, MCI1


title: RBG29216_Fancd2KO


title: RBG29215_Fancd2KO


title: C2C12 cells, MCC3

value: empty vector control


title: RBG29214_Fancd2KO


title: 13F_M_1085


title: 13F_M_1083


title: 13F_M_1096


title: RBG29213_WT


title: 13F_M_1082


title: RBG29212_WT


title: C2C12 cells, MCC2


title: RBG29223_WT


title: RBG29211_WT


title: C2C12 cells, MCC1


title: 13F_M_1081


title: 13F_M_1087


title: RBG28921_WT


title: RBG28920_WT


title: 13F_M_1080


title: RBG29217_Fancd2KO


title: RBG28919_WT


title: 13F_M_1079


title: RBG28918_WT


title: genomic DNA from biopsies of common warts_12

type: genomic

city: Abha

first: Mansour

middle: Abdullah

last: Alghamdi

state: Aseer

address: Guraiger Campus

department: Medicine

country: Saudi Arabia

institute: King Khalid University

description: skin warts sample

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

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

data_processing:
BeadStudio software v3.2
processed data file contains mean Average Beta for each group and diffmeth.p.val

organism: Homo sapiens

source_name: Biopsies of warts

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from normal skin and warts samples using Qiagen DNeasy Kit according to standard instructions

value: warts

tag: gender

value: male

tag: sample type

value: skin biopsies

tag: disease state


title: genomic DNA from biopsies of common warts_11

description: skin warts sample


title: RBG28917_Aldh2KO

value: Aldh2 knock-outs


title: RBG28916_Aldh2KO


title: 13F_M_1078


title: RBG28915_Aldh2KO


title: 13F_M_1077


title: genomic DNA from biopsies of common warts_10

description: skin warts sample


title: genomic DNA from biopsies of common warts_9

description: skin warts sample


title: RBG28913_Aldh2KO


title: genomic DNA from biopsies of common warts_8

description: skin warts sample


title: RBG28912_Aldh2KO


title: 13F_M_1076


title: RBG28911_Aldh2KO


title: 13F_M_1075


title: RBG29210_WT


title: genomic DNA from biopsies of common warts_7

description: skin warts sample


title: RBG28914_Aldh2KO


title: RBG28909_WT


title: genomic DNA from biopsies of common warts_6

description: skin warts sample


title: 13F_M_1074


title: RBG28908_WT


title: RBG28907_WT


title: RBG28905_Aldh2KO


title: RBG28906_WT


title: RBG28904_Aldh2KO


title: 13F_M_1072


title: genomic DNA from biopsies of common warts_4

description: skin warts sample


title: genomic DNA from biopsies of common warts_5

description: skin warts sample


title: genomic DNA from biopsies of common warts_3

description: skin warts sample


title: RBG28902_Aldh2KO


title: RBG28903_Aldh2KO


title: 13F_M_1071


title: RBG28901_Aldh2KO


title: genomic DNA from biopsies of common warts_2

description: skin warts sample


title: RBG28910_Aldh2KO


title: RBG28899_Aldh2KO


title: RBG28897_WT


title: RBG28900_Aldh2KO


title: genomic DNA from biopsies of adjacent normal skin_12

description: normal skin sample

source_name: Biopsies of normal skin

value: normal skin

value: normal


title: RBG28896_WT

value: WT


title: RBG28898_Aldh2KO


title: 13F_M_1069


title: 13F_M_1068


title: genomic DNA from biopsies of common warts_1

description: skin warts sample


title: RBG28895_WT


title: RBG28894_WT


title: 13F_M_1066


title: 13F_M_1067


title: 13F_M_1073


title: genomic DNA from biopsies of adjacent normal skin_11

description: normal skin sample


title: genomic DNA from biopsies of adjacent normal skin_10

description: normal skin sample


title: RBG28892_Aldh2KO


title: 13F_M_1065


title: genomic DNA from biopsies of adjacent normal skin_9

description: normal skin sample


title: 13F_M_1070


title: RBG28888_Aldh2KO


title: RBG28890_Aldh2KO


title: RBG28889_Aldh2KO


title: genomic DNA from biopsies of adjacent normal skin_8

description: normal skin sample


title: 13F_M_1064


title: genomic DNA from biopsies of adjacent normal skin_7

description: normal skin sample


title: 13F_M_1063


title: 13F_M_1062


title: RBG28886_Aldh2KO


title: RBG28885_WT


title: RBG28884_WT


title: RBG28883_WT


title: genomic DNA from biopsies of adjacent normal skin_6

description: normal skin sample


title: genomic DNA from biopsies of adjacent normal skin_5

description: normal skin sample


title: RBG28882_WT


title: 13F_M_1061


title: RBG28893_Aldh2KO


title: genomic DNA from biopsies of adjacent normal skin_4

description: normal skin sample


title: 13F_M_1060


title: RBG28891_Aldh2KO


title: 13F_M_1059


title: RBG28880_Aldh2KO


title: RBG28879_Aldh2KO


title: genomic DNA from biopsies of adjacent normal skin_3

description: normal skin sample


title: RBG28877_Aldh2KO


title: RBG28887_Aldh2KO


title: 13F_M_1058


title: genomic DNA from biopsies of adjacent normal skin_2

description: normal skin sample


title: RBG28878_Aldh2KO


title: 13F_M_1057


title: genomic DNA from biopsies of adjacent normal skin_1

description: normal skin sample


title: RBG28876_Aldh2KO


title: RBG28874_Aldh2KO


title: RBG28873_WT


title: RBG28872_WT


title: PBMC, Neuro-PASC CL2

city: Chicago

first: Lavanya

last: Visvabharathy

state: IL

address: 5812 S. Ellis Ave.

department: Surgery

institute: University of Chicago

data_processing:
Processed data generated through ImmunoSEQ Analyzer, Adaptive Biotechnologies
Supplementary files format and content: .tsv files; CDR3 region nucleotide/aa sequence, length; VDJ gene identifiers,deletions,insertions

source_name: PBMC

extract_protocol:
Qiagen DNEasy kit
Conducted by Adaptive  Biotechnologies

value: PBMC

value: Neuro-PASC

value: Post-COVID


title: PBMC, Neuro-PASC CN70


title: RBG28870_WT

value: Bone marrow


title: RBG28881_Aldh2KO


title: 13F_M_1056


title: RBG28868_Aldh2KO


title: 13F_M_1055


title: RBG28869_Aldh2KO


title: RBG28867_Aldh2KO


title: PBMC, Neuro-PASC CN55


title: 13F_M_1053


title: 13F_M_1054


title: RBG28864_Aldh2KO


title: RBG28875_Aldh2KO


title: RBG28865_Aldh2KO


title: PBMC, Neuro-PASC CN77


title: 13F_M_1052


title: RBG28863_Aldh2KO


title: PBMC, Neuro-PASC CN65


title: 13F_M_1051


title: RBG28862_Aldh2KO


title: PBMC, Neuro-PASC CN46


title: 13F_M_1050


title: RBG28860_WT


title: RBG28858_WT


title: RBG28859_WT


title: PBMC, Neuro-PASC CN60


title: PBMC, Neuro-PASC CN96


title: 13F_M_1049


title: 13F_M_1048


title: PBMC, Neuro-PASC CN67


title: RBG28866_Aldh2KO


title: RBG28855_Aldh2KO


title: RBG28856_Aldh2KO


title: PBMC, Neuro-PASC CN75


title: RBG28854_Aldh2KO


title: RBG28852_Aldh2KO


title: RBG28857_Aldh2KO


title: 13F_M_1047


title: RBG28861_WT


title: PBMC, Neuro-PASC CN52


title: 13F_M_1046


title: RBG28851_Aldh2KO


title: RBG28850_Aldh2KO


title: 13F_M_1045


title: PBMC, Neuro-PASC CN66


title: 13F_M_1044


title: PBMC, Neuro-PASC CN76


title: RBG28849_WT


title: RBG28847_WT


title: RBG28848_WT


title: PBMC, Neuro-PASC CN94


title: 13F_M_1042


title: RBG28853_Aldh2KO


title: PBMC, Neuro-PASC CN34


title: 13F_M_1041


title: RBG28843_Aldh2KO


title: RBG28844_Aldh2KO


title: RBG28841_Aldh2KO


title: 13F_M_1040


title: RBG28842_Aldh2KO


title: RBG28840_Aldh2KO


title: PBMC, Neuro-PASC CN115


title: PBMC, Neuro-PASC CN20


title: 13F_M_1039


title: 13F_M_1038


title: RBG28837_WT


title: RBG28839_Aldh2KO


title: RBG28838_Aldh2KO


title: RBG28834_WT


title: RBG28835_WT


title: RBG28836_WT


title: RBG28845_Aldh2KO


title: RBG28833_Aldh2KO


title: PBMC, Neuro-PASC CN108


title: 13F_M_1043


title: PBMC, Neuro-PASC CN121


title: 13F_M_1036


title: RBG28846_WT


title: RBG28831_Aldh2KO


title: PBMC, Neuro-PASC CN64


title: PBMC, Neuro-PASC CN23


title: PBMC, Neuro-PASC CN106


title: RBG28830_Aldh2KO


title: RBG28829_Aldh2KO


title: 13F_M_1034


title: PBMC, Neuro-PASC CN107


title: 13F_M_1035


title: RBG28828_Aldh2KO


title: RBG28827_Aldh2KO


title: RBG28826_Aldh2KO


title: RBG28825_Aldh2KO


title: PBMC, Neuro-PASC CN62


title: 13F_M_1037


title: RBG28823_Aldh2KO


title: RBG28832_Aldh2KO


title: 13F_M_1032


title: 13F_M_1030


title: PBMC, Neuro-PASC CN72


title: RBG28822_Aldh2KO


title: PBMC, Neuro-PASC CN126


title: RBG28824_Aldh2KO


title: RBG28821_WT


title: RBG28820_WT


title: RBG28819_WT


title: PBMC, Neuro-PASC CN9


title: 13F_M_1029


title: 13F_M_1031


title: RBG28817_Aldh2KO


title: RBG28818_WT


title: PBMC, Neuro-PASC CN74


title: RBG28816_Aldh2KO


title: PBMC, COVID convalescent CC48

value: COVID convalescent


title: 13F_M_1027


title: PBMC, COVID convalescent CC31


title: 13F_M_1028


title: RBG28813_Aldh2KO


title: RBG28814_Aldh2KO


title: 13F_M_1033


title: 13F_M_1026


title: RBG28812_Aldh2KO


title: RBG28811_Aldh2KO


title: PBMC, COVID convalescent CC49


title: RBG28810_Aldh2KO


title: PBMC, COVID convalescent CC36


title: RBG28809_WT


title: 13F_M_1025


title: RBG28808_WT


title: RBG28807_WT


title: PBMC, COVID convalescent CC27


title: PBMC, COVID convalescent CC33


title: 13F_M_1022


title: RBG28815_Aldh2KO


title: RBG28804_Aldh2KO


title: RBG28805_Aldh2KO


title: RBG28806_WT


title: RBG28803_Aldh2KO


title: RBG28802_Aldh2KO


title: 13F_M_1021


title: PBMC, COVID convalescent CC34


title: PBMC, COVID convalescent CC35


title: 13F_M_1020


title: RBG28800_Aldh2KO


title: RBG28798_Aldh2KO


title: 13F_M_1019


title: PBMC, COVID convalescent CC47


title: 13F_M_1018


title: RBG28795_WT


title: RBG28796_WT


title: RBG28797_WT


title: 13F_M_1024


title: PBMC, COVID convalescent CC37


title: 13F_M_1023


title: 13F_M_827


title: RBG28794_WT


title: RBG28793_Aldh2KO


title: RBG28792_Aldh2KO


title: RBG28801_Aldh2KO


title: RBG28790_Aldh2KO


title: RBG28789_Aldh2KO


title: RBG28791_Aldh2KO


title: 13F_M_825


title: RBG28799_Aldh2KO


title: RBG28786_Aldh2KO


title: RBG28787_Aldh2KO


title: 13F_M_824


title: RBG28788_Aldh2KO


title: hMSC, HA-EWSR1-SSX1, R1

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

data_processing:
RNA seq reads were aligned the humangenome assembly hg19 and FPKM count matrix was generated using featureCounts
Assembly: hg19

source_name: ASC52telo, hTERT immortalized adipose derived Mesenchymal stem cells

growth_protocol: MesenPRO RSTM Medium (Gibco, 12746- 012) supplemented with L-glutamine (Sigma-Aldrich, G7513-100ML) at a final concentration of 2 mM.

extract_protocol: RNA libraries were prepared at the DKFZ Genomics and Proteomics Core Facility and wassequenced on a NovaSeq 6K Paired-End 100 S4.

treatment_protocol: RNA was prepared using RNeasy mini kit (QIAGEN) according to the manufacturer’s protocoland including the DNaseI (QIAGEN) treatment.

value: mesenchymal stem cells

value: puromycin selection

value: Day 7


title: hMSC, HA-MN1-SSX1, R1

value: ASC52telo, hTERT immortalized adipose derived Mesenchymal stem cells


title: hMSC, HA-MN1-SSX1, R2


title: hMSC, HA-EWSR1-SSX1, R2


title: hMSC, HA-SS18-SSX1, R2


title: hMSC, HA-SS18-SSX1, R1


title: 13F_M_823


title: RBG28785_WT


title: 13F_M_822


title: RBG28783_WT


title: RBG28782_WT


title: RBG28784_WT


title: 13F_M_821


title: hMSC, HA-EWSR1-FLI1, R2


title: RBG28781_Aldh2KO


title: hMSC, HA-EWSR1-FLI1, R1


title: RBG28780_Aldh2KO


title: 13F_M_826


title: 13F_M_820


title: RBG28779_Aldh2KO


title: hMSC, HA-SS18-NEDD4, R2


title: RBG28778_Aldh2KO


title: RBG28777_Aldh2KO


title: hMSC, HA-SS18-NEDD4, R1


title: 13F_M_819


title: RBG28776_Aldh2KO


title: 13F_M_817


title: 13F_M_815


title: hMSC, empty vector, R1

value: empty vector


title: RBG28770_WT


title: 13F_M_814


title: HSSY, sgPCGF1, input, R3

description: 50bp Paired-End reads

data_processing:
Sequenced reads were mapped using Bowtie 2 to the human genome build T2T-CHM13 using options --local --very-sensitive-local, and to dm6 genome (drosophila). PCR duplicates were removed using Rmdup tool.
Down-sampling of reads for each sample was done based on the formula from Fursova et al. 2019.
The down-sampled replicates were then combined using the pileup function from MACS2 (q-value 0.05) and bigWig files were generated with ucsc-wigtobigwig tool.
To visualize ChIP-Seq tracks, normalized bigWig files were generated with ucsc-wigtobigwig tool
Assembly: T2T
Supplementary files format and content: bigWig

source_name: HS-SY-II

growth_protocol: DMEM, 10% fetal bovine serum and cultured at 37C at 5% CO2.

extract_protocol:
The experiment was performed in biological triplicate. Drosophila cell line SG-4 was used as the spike-in cell line. HSSY-II were transduced with either the empty vector plasmid or with sgRNA targeting the PCGF1 gene. The cells were cultured for 10 days and after that 10*10^6 cells were harvested; 2*10^6 SG-4 cells were mixed with the harvested cells. The cells were washed with ice-cold lysis buffer (10 mM Tris-HCl at pH 8, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 5 mM sodium butyrate, 5 mM N-ethylmaleimide) to extract the nuclei. The nuclei were then digested using 100U of MNase (Fermentas EN0191) at 37°C for 5 minutes in MNase digestion buffer (10 mM Tris-HCl at pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.25 M sucrose, 3 mM CaCl2, 10 mM sodium butyrate, 10 mM N-ethylmaleimide, 1× PIC (Roche) followed by an addition of 4 mM EDTA to stop the digestion. All the buffers were supplemented with protease inhibitor and NEM (inhibitor of de-ubiquitinase enzymes). After centrifugation, the supernatant was retained and incubated overnight at 4°C with 5 μL of anti-H2AK119ub1 (Cell Signaling Technology, D27C4). Next, 30ul protein A/G magnetic beads (Thermofisher) were added for the pull down and incubated for 2h at 4°C. To elute the DNA, beads were incubated in 1% SDS, 0.1M NaHCO3 for 30 minutes at 24°C. DNA was purified using ZymoResearch ChIP DNA clean and concentrator kit.
DNA fragments obtained after ChIP were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). 5ng of DNA was used for libraries preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), SPRIselect beads (Beckman Coulter, #B23317) and NEBNext Multiplex Oligos for Illumina (NEB, Set 1 #E7335S, Set 2 #E7500S). ChIP libraries were done following NEB’s guidelines (NEB, E7645S)

treatment_protocol: Cell were transduced with Cas9 and sgRNA, ChIP was performed following puromycin selection and collected 10 days following transduction.

value: HS-SY-II

value: Human synovial sarcoma cells

tag: chip antibody

value: SS18-SSX, Cas9, sgPCGF1


title: RBG28764_Aldh2KO

value: Aldh2 knock-outs


title: RBG28763_Aldh2KO


title: RBG28762_Aldh2KO


title: RBG28761_WT


title: RBG28773_WT


title: 13F_M_813


title: HSSY, sgPCGF1, H2Aub, R2

description: 50bp Paired-End reads

value: H2AK119ub1 Cell Signaling #8240


title: RBG28769_Aldh2KO


title: HSSY, sgPCGF1, H2Aub, R3

description: 50bp Paired-End reads


title: RBG28765_Aldh2KO


title: RBG28774_Aldh2KO


title: 13F_M_818


title: 13F_M_811


title: RBG28767_Aldh2KO


title: RBG28775_Aldh2KO


title: RBG28771_WT


title: RBG28772_WT


title: 13F_M_812


title: 13F_M_816


title: hMSC, HA-eGFP-SSX-C, R1

value: HA-eGFP-SSX-C


title: hMSC, HA-eGFP-SSX-C, R2


title: hMSC, empty vector, R2


title: RBG28760_WT

value: WT


title: 13F_M_810


title: RBG28768_Aldh2KO


title: HSSY, sgPCGF1, input, R2

description: 50bp Paired-End reads


title: HSSY, sgPCGF1, H2Aub, R1

description: 50bp Paired-End reads


title: RBG28766_Aldh2KO


title: 13F_M_809


title: RBG28758_WT


title: RBG28757_Aldh2KO


title: RBG28759_WT


title: HSSY, sgPCGF1, input, R1

description: 50bp Paired-End reads


title: 13F_M_808


title: RBG28756_Aldh2KO


title: RBG28755_Aldh2KO


title: HSSY, EV, H2Aub, R3

description: 50bp Paired-End reads

value: SS18-SSX, Cas9


title: HSSY, EV, input, R3

description: 50bp Paired-End reads


title: 13F_M_807


title: RBG28754_Aldh2KO


title: RBG28752_Aldh2KO


title: HSSY, EV, H2Aub, R2

description: 50bp Paired-End reads


title: HSSY, EV, input, R2

description: 50bp Paired-End reads


title: 13F_M_806


title: HSSY, EV, H2Aub, R1

description: 50bp Paired-End reads


title: RBG28747_WT


title: RBG28753_Aldh2KO


title: RBG28745_Aldh2KO


title: RBG28751_Aldh2KO


title: RBG28744_Aldh2KO


title: RBG28749_WT


title: 13F_M_802


title: 13F_M_804


title: 13F_M_803


title: HSSY, EV, input, R1

description: 50bp Paired-End reads


title: RBG28746_WT


title: RBG28750_Aldh2KO


title: RBG28742_Aldh2KO


title: KHOS, EV, SSX-C, HA

data_processing:
Paired-end reads were aligned to the newly released human genome build T2T-CHM13 and E.coli K12, MG1655 reference genome using Bowtie 2 (with options for T2T-CHM13: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 and for K12 --end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700).
To internally calibrate our CUT&RUN experiments, we used the exogenous60  E.coli genome to quantitatively compare the genomic profiles as previously described. We first calculated the percentage of spike-in reads in total reads that align uniquely (Nx). We then normalized the samples using a scaling factor so that E. coli spike-in signal is set to be equal across all samples. We used the sample displaying to smallest percentage of E.coli reads (Nmin) to downscale all the other conditions using the same constant to calculate our scaling factor: Scaling factor for sample x = 𝑁𝑚𝑖𝑛/𝑁𝑥.
Genome coverage files were generated using bamCoverage with 50bp bins, no normalisation and scaled (--scaleFactor).
Assembly: T2T
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

extract_protocol:
Chromatin profiles of endogenous SS18-SSX1/2, H2AK119ub1 in human synovial sarcoma cells and HA occupancy in osteosarcoma or synovial sarcoma cells expressing MSCV-HA-eGFP-SS18-PGK-Puro, MSCV-HA-eGFP-SS18-SSX1-PGK-Puro and MSCV-HA-eGFP- SSX-C-PGK-Puro was assayed using CUTANA ChIC/CUT&RUN Kit (EpiCypher, 14-1048)following manufacturer’s protocol. Briefly, 1 million cells (HS-SY-II, SYO-I or KHOS-240S)were harvested per sample and bound to activated Concanavalin A magnetic beads. Beads werethen incubated at 4 ̊C overnight with 1:50 dilution of antibodies per sample. Chromatin digestion was performed for 2 hours at 4 ̊C. Digestion is then stopped by chelating Ca++ ionsin a buffer containing E.coli DNA for Spike-in. DNA Fragments are then released in solution after a 10 min incubation at 37 ̊C on a ThermoMixer at 500 rpm. DNA Fragments were then purified using CUTANA DNA Purification Kit (EpiCypher).
DNA fragments obtained after CUT&RUN were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). 5ng of DNA was used for libraries preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), SPRIselect beads (Beckman Coulter, #B23317) and NEBNext Multiplex Oligos for Illumina (NEB, Set 1 #E7335S, Set 2 #E7500S). ChIP libraries were done following NEB’s guidelines (NEB, E7645S), CUT&RUN libraries were done following CUTANA ChIC/CUT&RUN Kit (EpiCypher, 14-1048) adapted protocol CUT&RUN libraries were sequenced as 75 bp Paired-End reads on Illumina NextSeq 550 platform Mid-Output.

value: Human Osteosarcoma

value: HA


title: 13F_M_801


title: RBG28741_Aldh2KO

value: Bone marrow


title: KHOS, EV, SS18-SSX1, HA


title: RBG28748_WT


title: KHOS, EV, SS18, HA


title: 13F_M_805


title: RBG28740_Aldh2KO


title: 13F_M_800


title: RBG28738_Aldh2KO


title: 13F_M_799


title: RBG28739_Aldh2KO


title: RBG28743_Aldh2KO


title: KHOS, EV, HA


title: KHOS, EV, IgG

value: IgG


title: HSSY, IgG, NoDox, SSX-C, HA

value: SS18-SSX1, shSS18-SSX


title: 13F_M_796


title: 13F_M_798


title: 13F_M_794


title: HSSY, IgG, Dox, SS18-SSX knockdown, SSX-C, HA


title: 13F_M_795


title: 13F_M_793


title: RBG28727_Aldh2KO


title: RBG28730_Aldh2KO


title: RBG28729_Aldh2KO


title: RBG28726_Aldh2KO


title: RBG28733_Aldh2KO


title: RBG28737_WT


title: RBG28724_Aldh2KO


title: RBG28723_Aldh2KO


title: Ctrl3, control 3

first: Bingjie

last: Guan

address: 85 Wujin Road

institute: Shanghai General Hospital

data_processing:
The quality information of raw data in FASTQ format was calculated and then the raw data was filtered using Cutadapt(v1.15) software.
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
The gene read count value was counted using HTSeq(v0.9.1) as the original expression level of the gene.
FPKM(fragments per kilobaseof exon per million fragments mapped) is used to normalize the expression.
Assembly: hg38
Supplementary files format and content: a single Excel file containing FPKM values for each Sample:processed data.xlsx

source_name: colon cancer

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). 3.0 ug of total RNA was used for the construction of sequencing libraries.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: colon cancer

value: RKO

value: colon cancer cells

value: cocultured with PBS-treated FHC cells


title: 13F_M_792


title: Ctrl2, control 2


title: RBG28728_Aldh2KO


title: RBG28731_Aldh2KO


title: RBG28732_Aldh2KO


title: RBG28735_WT


title: RBG28736_WT


title: Ctrl1, control 1


title: 13F_M_797


title: RBG28721_WT


title: RBG28734_WT


title: RBG28722_Aldh2KO


title: HSSY, IgG, NoDox

value: HS-SY-II


title: RBG28719_WT


title: RBG28720_WT


title: CC3, treated 3

value: cocultured with EV-stimulated FHC cells


title: 13F_M_789


title: 13F_M_791


title: CC1, treated 1


title: RBG28718_WT


title: 13F_M_788


title: RBG28717_Aldh2KO


title: 13F_M_786


title: RBG28711_Aldh2KO


title: 13F_M_787


title: RBG28708_WT


title: RBG28707_WT


title: RBG28705_Aldh2KO


title: RBG28714_Aldh2KO


title: RBG28706_WT


title: RBG28704_Aldh2KO


title: 13F_M_783


title: RBG28716_Aldh2KO


title: RBG28710_Aldh2KO


title: 13F_M_784


title: 13F_M_785


title: 9_S100B_89

city: New Haven

first: Thazin

middle: N

last: Aung

state: CT

address: 310 Cedar St

department: Pathology

institute: Yale University

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx®-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered/counted as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses

source_name: Melanoma

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx®-DSP protocol (MAN-10150-01).Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5/666 nm, excitation 645/19 nm, emission 683/30 nm), CD45 for lymphocyte compartment (Texas Red/615 nm, excitation 588/19 nm, emission 623/30 nm), S100B (Cy3/568 nm, excitation 538/19 nm, emission 564/15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx®-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx®-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

value: Melanoma

value: Immunotherapy

tag: roilabel


title: 8_S100B_9


title: 9_S100B_10


title: CC2, treated 2


title: RBG28702_Aldh2KO

value: Aldh2 knock-outs


title: 72_S100B_8


title: RBG28703_Aldh2KO


title: 13F_M_782


title: RBG28712_Aldh2KO


title: 13F_M_781


title: 8_S100B_88


title: 71_S100B_7


title: 13F_M_780


title: 70_S100B_6


title: 69_S100B_5


title: RBG28699_Aldh2KO


title: 13F_M_779


title: RBG28696_WT


title: RBG28695_WT


title: RBG28697_WT


title: RBG28698_Aldh2KO


title: 68_S100B_4


title: 13F_M_778


title: 64_S100B_3


title: 13F_M_777


title: RBG28694_WT


title: RBG28693_Aldh2KO


title: RBG28692_Aldh2KO


title: RBG28691_Aldh2KO


title: RBG28701_Aldh2KO


title: 64_S100B_188


title: RBG28690_Aldh2KO


title: 13F_M_776


title: RBG28689_Aldh2KO


title: RBG28688_Aldh2KO


title: RBG28687_Aldh2KO


title: RBG28700_Aldh2KO


title: 13F_M_774


title: RBG28686_Aldh2KO


title: RBG28685_WT


title: 63_S100B_2


title: 13F_M_773


title: 63_S100B_137


title: RBG28683_WT


title: RBG28682_WT


title: 13F_M_772


title: RBG28681_Aldh2KO


title: RBG28680_Aldh2KO


title: 13F_M_771


title: 13F_M_770


title: RBG28677_Aldh2KO


title: 64_S100B_138


title: RBG28678_Aldh2KO


title: 60_S100B_135


title: RBG28676_Aldh2KO


title: 60_S100B_1


title: 13F_M_769


title: RBG28675_Aldh2KO


title: RBG28673_WT


title: RBG28674_Aldh2KO


title: 13F_M_768


title: RBG28679_Aldh2KO


title: RBG28684_WT


title: 62_S100B_136


title: 59_S100B_134


title: RBG28672_WT


title: 60_S100B_187


title: RBG28670_WT


title: RBG28671_WT


title: 13F_M_775


title: 13F_M_766


title: RBG28669_Aldh2KO


title: 58_S100B_185


title: RBG28668_Aldh2KO


title: 58_S100B_50


title: 59_S100B_186


title: RBG28667_Aldh2KO


title: 13F_M_764


title: 58_S100B_133


title: 13F_M_765


title: RBG28665_Aldh2KO


title: RBG28664_Aldh2KO


title: 57_S100B_49


title: RBG28663_Aldh2KO


title: 13F_M_762


title: RBG28662_Aldh2KO


title: RBG28661_WT


title: 57_S100B_184


title: 13F_M_763


title: RBG28660_WT


title: 13F_M_767


title: 57_S100B_132


title: RBG28659_WT


title: RBG28658_WT


title: 13F_M_761


title: 56_S100B_48


title: 13F_M_760


title: RBG28657_Aldh2KO


title: RBG28666_Aldh2KO


title: 56_S100B_183


title: 13F_M_759


title: RBG28656_Aldh2KO


title: 56_S100B_131


title: RBG28655_Aldh2KO


title: RBG28654_Aldh2KO


title: 13F_M_758


title: RBG28651_Aldh2KO


title: RBG28652_Aldh2KO


title: RBG28653_Aldh2KO


title: 13F_M_757


title: RBG28650_Aldh2KO


title: 54_S100B_182


title: 54_S100B_130


title: RBG28648_WT


title: RBG28649_WT


title: 53_S100B_47


title: RBG28647_WT


title: 13F_M_755


title: RBG28646_WT


title: 13F_M_754


title: RBG28645_Aldh2KO


title: 53_S100B_181


title: RBG28644_Aldh2KO


title: 52_S100B_180


title: 13F_M_753


title: 13F_M_752


title: 13F_M_751


title: RBG28640_Aldh2KO


title: 52_S100B_129


title: RBG28642_Aldh2KO


title: RBG28643_Aldh2KO


title: 52_S100B_46


title: RBG28637_WT


title: 13F_M_750


title: 13F_M_756


title: 51_S100B_128


title: RBG28636_WT


title: 13F_M_749


title: RBG28634_WT


title: RBG23605_DKO

value: Aldh2 & Fancd2 double knock-outs


title: RBG23604_DKO


title: 13F_M_747


title: 50_S100B_178


title: 50_S100B_127


title: 13F_M_748


title: RBG28641_Aldh2KO


title: RBG28639_Aldh2KO