title: RBG23599_WT

value: WT


title: 5_S100B_87

status: Public on May 24 2023

type: SRA

city: New Haven

first: Thazin

middle: N

last: Aung

state: CT

address: 310 Cedar St

department: Pathology

country: USA

institute: Yale University

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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

tag: tissue

value: Melanoma

tag: cell type

tag: treatment

value: Immunotherapy

tag: roilabel


title: RBG23601_DKO

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

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.

organism: Mus musculus

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.

value: Bone marrow

tag: genotype

value: Aldh2 & Fancd2 double knock-outs


title: 51_S100B_179


title: RBG23596_p53KO

value: p53 knock-outs


title: RBG28638_Aldh2KO

value: Aldh2 knock-outs


title: RBG23597_WT


title: 13F_M_745

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

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

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: 5_S100B_45


title: 49_S100B_177


title: RBG23598_WT


title: RBG23595_p53KO


title: 13F_M_744


title: RBG28635_WT


title: 13F_M_743


title: 49_S100B_126


title: RBG23591_DKO


title: 48_S100B_44


title: RBG23592_DKO


title: RBG23593_DKO


title: RBG23590_DKO


title: RBG23594_p53KO


title: 13F_M_742


title: RBG23589_DKO


title: 48_S100B_176


title: RBG23587_WT


title: 47_S100B_86


title: 13F_M_741


title: 13F_M_740


title: 13F_M_746


title: RBG23588_DKO


title: RBG23585_WT


title: RBG23586_WT


title: RBG23583_p53KO


title: RBG23584_p53KO


title: RBG23582_p53KO


title: 13F_M_738


title: 47_S100B_125


title: 47_S100B_175


title: 13F_M_739


title: RBG23580_DKO


title: RBG23581_DKO


title: 13F_M_737


title: RBG23579_DKO


title: RBG23578_DKO


title: 13F_M_736


title: 46_S100B_42


title: 45_S100B_84


title: 13F_M_735


title: RBG23577_DKO


title: RBG23575_WT


title: 47_S100B_43


title: 13F_M_734


title: RBG23574_WT


title: RBG23573_WT


title: 13F_M_733


title: RBG23572_p53KO


title: RBG23571_p53KO


title: 45_S100B_41


title: 13F_M_732


title: 45_S100B_174


title: 45_S100B_124


title: RBG23570_p53KO


title: RBG23569_DKO


title: RBG23567_DKO


title: 46_S100B_85


title: 13F_M_730


title: RBG23568_DKO


title: 13F_M_731


title: RBG23566_DKO


title: 44_S100B_40


title: RBG23564_DKO


title: 43_S100B_173


title: 13F_M_729


title: RBG23576_DKO


title: RBG23563_WT


title: RBG23565_DKO


title: 13F_M_728


title: RBG23561_WT


title: RBG23560_p53KO


title: 43_S100B_123


title: RBG23558_p53KO


title: 13F_M_726


title: 42_S100B_172


title: RBG23559_p53KO


title: RBG23562_WT


title: 42_S100B_122


title: RBG23556_DKO


title: 44_S100B_83


title: 13F_M_725


title: RBG23555_DKO


title: RBG23557_DKO


title: 13F_M_724


title: RBG23554_DKO


title: 41_S100B_39


title: 13F_M_723


title: RBG23551_WT


title: 13F_M_727


title: RBG23553_DKO


title: RBG23550_WT


title: 40_S100B_81


title: RBG23549_WT


title: 13F_M_722


title: 40_S100B_121


title: RBG23548_p53KO


title: 4_S100B_80


title: RBG23547_p53KO


title: 13F_M_720


title: 4_S100B_38


title: RBG23545_DKO


title: RBG23546_p53KO


title: RBG23543_DKO


title: 13F_M_719


title: 41_S100B_82


title: RBG23542_DKO


title: 13F_M_718


title: 39_S100B_79


title: RBG23540_DKO


title: RBG23541_DKO


title: RBG23552_DKO


title: 39_S100B_37


title: 39_S100B_171


title: RBG23538_WT


title: RBG23539_WT


title: 13F_M_721


title: RBG23537_WT


title: 13F_M_714


title: RBG23535_p53KO


title: RBG23534_p53KO


title: 13F_M_715


title: RBG23536_p53KO


title: RBG23533_DKO


title: RBG23532_DKO


title: 39_S100B_120


title: RBG23531_DKO


title: 38_S100B_170


title: 38_S100B_36


title: 13F_M_712


title: 13F_M_717


title: RBG23530_DKO


title: RBG23529_DKO


title: 13F_M_711


title: RBG23528_DKO


title: 37_S100B_77


title: 13F_M_716


title: RBG23526_WT


title: RBG23527_WT


title: 13F_M_713


title: 13F_M_710


title: 38_S100B_78


title: 13F_M_709


title: RBG23524_p53KO


title: 37_S100B_35


title: RBG23523_p53KO


title: RBG23521_DKO


title: 37_S100B_118


title: 37_S100B_169


title: 13F_M_708


title: 38_S100B_119


title: RBG23519_DKO


title: RBG23515_WT


title: 13F_M_706


title: RBG23514_WT


title: RBG23516_DKO


title: RBG23520_DKO


title: RBG23517_DKO


title: RBG23513_WT


title: 36_S100B_34


title: 36_S100B_168


title: RBG23510_p53KO


title: 13F_M_704


title: RBG23508_WT


title: 36_S100B_117


title: RBG23511_p53KO


title: RBG23512_p53KO


title: 13F_M_705


title: 13F_M_703


title: 35_S100B_75


title: RBG23506_p53KO


title: RBG23507_WT


title: 13F_M_702


title: 13F_M_707


title: RBG23505_p53KO


title: 13F_M_701


title: 13F_M_700


title: RBG23501_DKO


title: RBG23503_DKO


title: 13F_M_697


title: RBG23504_p53KO


title: 36_S100B_76


title: 13F_M_699


title: 34_S100B_74


title: RBG23502_DKO


title: 35_S100B_116


title: RBG23495_WT


title: RBG23499_DKO


title: RBG23496_WT


title: RBG23498_DKO


title: 35_S100B_167


title: 13F_M_695


title: RBG23497_WT


title: 34_S100B_32


title: RBG23494_p53KO


title: 34_S100B_115


title: 13F_M_693


title: RBG23492_p53KO


title: RBG23493_p53KO


title: 13F_M_696


title: 35_S100B_33


title: RBG23500_DKO


title: 34_S100B_166


title: RBG23489_DKO


title: RBG23491_DKO


title: 33_S100B_31


title: RBG23490_DKO


title: 33_S100B_165


title: RBG23488_DKO


title: 13F_M_691


title: RBG23487_DKO


title: 13F_M_688


title: RBG23486_DKO


title: RBG23484_WT


title: 13F_M_686


title: RBG23481_p53KO


title: 13F_M_687


title: RBG23480_p53KO


title: 32_S100B_164


title: RBG23482_p53KO


title: 33_S100B_114


title: 32_S100B_72


title: 32_S100B_30


title: 13F_M_684


title: RBG23485_WT


title: RBG23478_DKO


title: RBG23483_WT


title: 13F_M_692


title: 33_S100B_73


title: 32_S100B_113


title: RBG23476_DKO


title: RBG23477_DKO


title: RBG23474_DKO


title: 31_S100B_163


title: RBG23479_DKO


title: 30_S100B_162


title: 13F_M_681


title: 13F_M_680


title: 13F_M_685


title: RBG23472_WT


title: RBG23473_WT


title: 3_S100B_71


title: RBG23469_p53KO


title: 13F_M_678


title: RBG23470_p53KO


title: RBG23471_WT


title: 13F_M_679


title: 30_S100B_112


title: 13F_M_677


title: 13F_M_676


title: RBG23466_DKO


title: RBG23467_DKO


title: RBG23465_DKO


title: RBG23464_DKO


title: RBG23475_DKO


title: 3_S100B_29


title: RBG23468_p53KO


title: RBG23463_DKO


title: 13F_M_675


title: 13F_M_683


title: 29_S100B_161


title: RBG23462_DKO


title: RBG23459_WT


title: RBG23461_WT


title: RBG23458_p53KO


title: 13F_M_673


title: RBG23457_p53KO


title: 29_S100B_28


title: RBG23456_p53KO


title: 29_S100B_70


title: 28_S100B_69


title: 13F_M_672


title: 13F_M_671


title: RBG23455_DKO


title: RBG23454_DKO


title: 13F_M_670


title: 29_S100B_111


title: 28_S100B_27


title: RBG23453_DKO


title: RBG23452_DKO


title: 28_S100B_160


title: 13F_M_669


title: 27_S100B_68


title: RBG23449_WT


title: RBG23451_DKO


title: RBG23448_WT


title: 13F_M_668


title: 27_S100B_26


title: RBG23447_WT


title: 13F_M_667


title: 27_S100B_110


title: RBG23443_DKO


title: RBG23525_WT


title: RBG23439_DKO


title: 26_S100B_109


title: 13F_M_665


title: RBG23442_DKO


title: RBG23440_DKO


title: 13F_M_664


title: 25_S100B_67


title: 26_S100B_158


title: RBG23435_WT


title: RBG23444_p53KO


title: 13F_M_666


title: RBG23436_WT


title: 13F_M_661


title: RBG23434_p53KO


title: 13F_M_663


title: 13F_M_662


title: 25_S100B_25


title: RBG23446_p53KO


title: RBG23437_WT


title: RBG23445_p53KO


title: RBG23433_p53KO


title: 13F_M_660


title: 24_S100B_66


title: RBG23432_p53KO


title: RBG23431_DKO


title: 27_S100B_159


title: RBG23441_DKO


title: 24_S100B_24


title: RBG23430_DKO


title: RBG23429_DKO


title: 13F_M_659


title: 23_S100B_65


title: RBG23428_DKO


title: 13F_M_658


title: 22_S100B_64


title: RBG23427_DKO


title: RBG23426_DKO


title: 22_S100B_23


title: RBG23425_WT


title: 13F_M_657


title: 13F_M_656


title: RBG23423_WT


title: RBG23422_p53KO


title: 22_S100B_157


title: RBG23421_p53KO


title: RBG23420_p53KO


title: 13F_M_655


title: RBG23419_DKO


title: 21_S100B_63


title: 13F_M_654


title: 13F_M_653


title: 21_S100B_22


title: 22_S100B_108


title: RBG23417_DKO


title: RBG23413_DKO


title: RBG23424_WT


title: RBG23416_DKO


title: 21_S100B_156


title: 13F_M_651


title: RBG23410_WT


title: RBG23412_DKO


title: RBG23411_DKO


title: 13F_M_650


title: 21_S100B_107


title: RBG23409_WT


title: 13F_M_649


title: 13F_M_648


title: RBG23407_p53KO


title: RBG23408_WT


title: RBG23418_DKO


title: RBG23406_p53KO


title: RBG23404_DKO


title: RBG23405_p53KO


title: 13F_M_652


title: 20_S100B_62


title: 20_S100B_21


title: RBG23414_DKO


title: 13F_M_644


title: 20_S100B_155


title: RBG23402_DKO


title: 20_S100B_106


title: RBG23401_DKO


title: RBG23400_DKO


title: 13F_M_643


title: 2_S100B_20


title: 13F_M_641


title: RBG23398_WT


title: RBG23399_DKO


title: 13F_M_640


title: 13F_M_647


title: 19_S100B_154


title: RBG23396_WT


title: 19_S100B_105


title: RBG23395_p53KO


title: 13F_M_639


title: RBG23394_p53KO


title: RBG23393_p53KO


title: RBG23403_DKO


title: 13F_M_638


title: RBG23391_DKO


title: 18_S100B_104


title: 17_S100B_60


title: RBG23389_DKO


title: 13F_M_637


title: 18_S100B_153


title: RBG23392_DKO


title: 13F_M_380


title: RBG23390_DKO


title: RBG23387_DKO


title: RBG23388_DKO


title: 13F_M_379


title: 17_S100B_152


title: RBG23386_WT


title: 17_S100B_19


title: RBG23397_WT


title: 17_S100B_103


title: RBG23384_WT


title: 13F_M_378


title: RBG23382_p53KO


title: RBG23381_p53KO


title: RBG23383_p53KO


title: 13F_M_376


title: 13F_M_377


title: RBG23380_DKO


title: 13F_M_375


title: 16_S100B_18


title: RBG23376_DKO


title: 16_S100B_151


title: 13F_M_374


title: RBG23377_DKO


title: 16_S100B_102


title: RBG23373_WT


title: 13F_M_373


title: RBG23374_WT


title: RBG23385_WT


title: RBG23372_WT


title: 15_S100B_58


title: RBG23371_p53KO


title: 15_S100B_17


title: 13F_M_372


title: 16_S100B_59


title: RBG23369_p53KO


title: 2_S100B_61


title: RBG23368_DKO


title: 13F_M_371


title: RBG23366_DKO


title: RBG23365_DKO


title: 15_S100B_101


title: 13F_M_370


title: RBG23364_DKO


title: RBG23363_DKO


title: 14_S100B_57


title: 13F_M_369


title: 13F_M_368


title: RBG23375_DKO


title: 14_S100B_16


title: RBG23361_WT


title: RBG23360_WT


title: RBG23359_p53KO


title: RBG23362_WT


title: 13F_M_367


title: RBG23370_p53KO


title: RBG23358_p53KO


title: 13F_M_366


title: 14_S100B_149


title: 14_S100B_100


title: RBG23356_DKO


title: RBG23367_DKO


title: 15_S100B_150


title: 13F_M_365


title: 13_S100B_99


title: RBG23355_DKO


title: RBG23353_DKO


title: RBG23352_DKO


title: 13F_M_364


title: RBG23354_DKO


title: 13F_M_363


title: RBG23351_DKO


title: 13_S100B_15


title: RBG23349_WT


title: 13F_M_362


title: 13F_M_361


title: RBG23350_WT


title: 13_S100B_148


title: RBG23357_p53KO


title: 13F_M_360


title: RBG23346_p53KO


title: 13F_M_359


title: 12_S100B_98


title: 12_S100B_55


title: RBG23347_p53KO


title: RBG23348_WT


title: RBG23345_p53KO


title: RBG23344_DKO


title: RBG23343_DKO


title: 12_S100B_147


title: RBG23341_DKO


title: 13F_M_358


title: 13_S100B_56


title: RBG23340_DKO


title: 12_S100B_14


title: 11_S100B_97


title: RBG23338_WT


title: RBG23339_DKO


title: 13F_M_357


title: 13F_M_356


title: 11_S100B_54


title: 13F_M_355


title: RBG23335_p53KO


title: RBG23334_p53KO


title: 11_S100B_146


title: 13F_M_354


title: RBG23333_p53KO


title: RBG23332_DKO


title: RBG23331_DKO


title: 10_S100B_96


title: 13F_M_353


title: RBG23330_DKO


title: RBG23329_DKO


title: RBG23327_DKO


title: 13F_M_351


title: 10_S100B_53


title: RBG23328_DKO


title: RBG23326_WT


title: 10_S100B_145


title: RBG23324_WT


title: 13F_M_349


title: 10_S100B_12


title: RBG23336_WT


title: RBG23337_WT


title: RBG23322_p53KO


title: RBG23323_p53KO


title: 1_S100B_52


title: RBG23321_p53KO


title: 006_S100B_95


title: 11_S100B_13


title: 13F_M_346


title: RBG23319_DKO


title: RBG23320_DKO


title: 006_S100B_144


title: 13F_M_347


title: 13F_M_352


title: 005_S100B_94


title: RBG23317_p53KO


title: RBG23318_DKO


title: 13F_M_345


title: RBG23325_WT


title: RBG23316_p53KO


title: RBG23315_p53KO


title: RBG23314_DKO


title: 005_S100B_143


title: 13F_M_344


title: RBG23313_DKO


title: 13F_M_343


title: 004_S100B_93


title: RBG23312_DKO


title: RBG23311_DKO


title: 13F_M_348


title: RBG23310_DKO


title: 004_S100B_142


title: RBG23309_DKO


title: 003_S100B_92


title: 13F_M_341


title: RBG23307_WT


title: 13F_M_340


title: 13F_M_339


title: 003_S100B_141


title: 002_S100B_91


title: RBG23304_p53KO


title: 13F_M_338


title: RBG23303_p53KO


title: RBG23302_DKO


title: RBG23305_p53KO


title: RBG23300_DKO


title: RBG23301_DKO


title: 001_S100B_90


title: 13F_M_336


title: 001_S100B_51


title: 13F_M_337


title: RBG23299_DKO


title: 002_S100B_140


title: 13F_M_342


title: RBG23296_WT


title: 001_S100B_139


title: 13F_M_335


title: RBG23295_WT


title: 13F_M_334


title: RBG23308_WT


title: RBG23293_p53KO


title: 001_S100B_11


title: RBG23306_WT


title: RBG23292_p53KO


title: RBG23291_p53KO


title: 13F_M_333


title: RBG23290_DKO


title: 8_CD68_66


title: 13F_M_332


title: RBG23289_DKO


title: RBG23288_DKO


title: RBG23287_DKO


title: RBG23285_DKO


title: 13F_M_330


title: 70_CD68_7


title: RBG23286_DKO


title: 13F_M_331


title: 69_CD68_6


title: 72_CD68_8


title: RBG23297_DKO


title: 13F_M_329


title: RBG23284_WT


title: RBG23283_WT


title: 13F_M_328


title: RBG23280_p53KO


title: RBG23281_p53KO


title: RBG23282_WT


title: 65_CD68_5


title: RBG23279_p53KO


title: 64_CD68_4


title: 13F_M_327


title: 64_CD68_164


title: RBG23278_DKO


title: RBG23277_DKO


title: RBG23276_DKO


title: RBG23274_DKO


title: 63_CD68_115


title: RBG23273_DKO


title: 13F_M_324


title: RBG23272_WT


title: 62_CD68_3


title: RBG23271_WT


title: 13F_M_323


title: RBG23268_p53KO


title: 13F_M_322


title: 62_CD68_114


title: 13F_M_326


title: 13F_M_321


title: 60_CD68_113


title: RBG23265_DKO


title: RBG23266_DKO


title: 64_CD68_116


title: RBG23263_DKO


title: RBG23267_p53KO


title: 60_CD68_163


title: 13F_M_319


title: 13F_M_320


title: RBG23264_DKO


title: RBG23261_DKO


title: RBG23262_DKO


title: 13F_M_325


title: 59_CD68_162


title: RBG23260_WT


title: 59_CD68_112


title: 13F_M_318


title: RBG23258_WT


title: RBG23259_WT


title: 13F_M_317


title: RBG23269_p53KO


title: 60_CD68_2


title: 58_CD68_161


title: RBG23256_p53KO


title: 58_CD68_111


title: RBG23253_DKO


title: RBG23252_DKO


title: RBG23275_DKO


title: 13F_M_314


title: 58_CD68_1


title: RBG23250_DKO


title: 13F_M_312


title: RBG23251_DKO


title: RBG23248_WT


title: 57_CD68_110


title: 57_CD68_160


title: RBG23249_DKO


title: RBG23247_WT


title: RBG23257_p53KO


title: RBG23255_p53KO


title: 13F_M_316


title: RBG23245_p53KO


title: RBG23244_p53KO


title: 56_CD68_38


title: 57_CD68_39


title: 13F_M_311


title: RBG23254_DKO


title: RBG23243_p53KO


title: 13F_M_309


title: 56_CD68_159


title: RBG23242_DKO


title: RBG23241_DKO


title: 56_CD68_109


title: 13F_M_308


title: 55_CD68_108


title: RBG23240_DKO


title: RBG23238_DKO


title: RBG23237_DKO


title: 54_CD68_158


title: RBG23239_DKO


title: 13F_M_307


title: RBG23236_WT


title: RBG23246_WT


title: 54_CD68_107


title: 13F_M_310


title: RBG23235_WT


title: RBG23234_WT


title: 53_CD68_157


title: RBG23232_p53KO


title: 13F_M_304


title: RBG23233_p53KO


title: 53_CD68_37


title: 13F_M_305


title: RBG23231_p53KO


title: RBG23230_DKO


title: RBG23229_DKO


title: RBG23228_DKO


title: 53_CD68_106


title: 13F_M_303


title: 13F_M_302


title: 52_CD68_36


title: 13F_M_306


title: RBG23227_DKO


title: RBG23225_DKO


title: 52_CD68_105


title: 52_CD68_156


title: RBG23224_WT


title: 13F_M_301


title: RBG23223_WT


title: RBG23222_WT


title: 13F_M_300


title: RBG25432_WT


title: 13F_M_298


title: RBG25430_WT


title: RBG25429_WT


title: 51_CD68_155


title: RBG25428_WT


title: 13F_M_297


title: 50_CD68_154


title: RBG25427_WT


title: RBG25426_DKO


title: RBG25425_DKO


title: 13F_M_296


title: 13F_M_295


title: 50_CD68_103


title: RBG23226_DKO


title: RBG25424_DKO


title: 5_CD68_35


title: 13F_M_299


title: RBG25422_WT


title: RBG25420_WT


title: 49_CD68_153


title: 13F_M_294


title: RBG25418_WT


title: 51_CD68_104


title: RBG25423_WT


title: 13F_M_293


title: RBG25419_WT


title: 13F_M_292


title: 48_CD68_34


title: 49_CD68_102


title: RBG25416_WT


title: 13F_M_291


title: RBG25415_WT


title: 13F_M_315


title: 13F_M_290


title: RBG25412_DKO


title: 13F_M_289


title: RBG25414_DKO


title: RBG25411_WT


title: RBG25410_WT


title: 47_CD68_65


title: 13F_M_288


title: 47_CD68_33


title: RBG25408_WT


title: RBG25407_WT


title: 13F_M_287


title: RBG25409_WT


title: RBG25406_WT


title: RBG25417_WT


title: RBG25405_WT


title: 48_CD68_152


title: RBG25404_WT


title: 46_CD68_32


title: RBG25400_DKO


title: RBG25402_DKO


title: 47_CD68_101


title: 13F_M_284


title: RBG25399_WT


title: 13F_M_286


title: 45_CD68_64


title: 45_CD68_31


title: RBG25398_WT


title: RBG25397_WT


title: 13F_M_283


title: 47_CD68_151


title: RBG25395_WT


title: 45_CD68_100


title: 13F_M_282


title: RBG25396_WT


title: RBG25394_WT


title: 13F_M_281


title: RBG25393_WT


title: 44_CD68_30


title: 13F_M_280


title: 13F_M_285


title: RBG25391_WT


title: 43_CD68_99


title: RBG25392_WT


title: RBG25390_DKO


title: RBG25403_WT


title: RBG25388_DKO


title: 45_CD68_150


title: 13F_M_278


title: RBG25387_WT


title: RBG25389_DKO


title: 13F_M_279


title: RBG25386_WT


title: 13F_M_277


title: RBG25384_WT


title: 13F_M_276


title: RBG25383_WT


title: 41_CD68_63


title: 42_CD68_98


title: 43_CD68_149


title: 13F_M_275


title: RBG25381_WT


title: 13F_M_274


title: RBG25379_WT


title: 40_CD68_97


title: 40_CD68_62


title: RBG25378_DKO


title: 13F_M_273


title: RBG25382_WT


title: RBG25377_DKO


title: RBG25376_DKO


title: RBG25385_WT


title: RBG25374_WT


title: RBG25373_WT


title: 42_CD68_148


title: RBG25372_WT


title: RBG25371_WT


title: RBG25380_WT


title: 4_CD68_29


title: RBG25370_WT


title: RBG25369_WT


title: 39_CD68_96


title: 38_CD68_95


title: RBG25368_WT


title: 13F_M_270


title: 13F_M_272


title: 38_CD68_61


title: 13F_M_271


title: 13F_M_313


title: 13F_M_268


title: 39_CD68_147


title: RBG25367_WT


title: RBG25366_DKO


title: RBG25375_WT


title: RBG25363_WT


title: 13F_M_267


title: 38_CD68_146


title: 13F_M_266


title: RBG25365_DKO


title: RBG25362_WT


title: RBG25361_WT


title: RBG25360_WT


title: 13F_M_269


title: 37_CD68_60


title: RBG25359_WT


title: 37_CD68_28


title: 13F_M_265


title: 13F_M_264


title: RBG25358_WT


title: RBG25357_WT


title: 13F_M_263


title: RBG25355_WT


title: 37_CD68_145


title: RBG25354_DKO


title: 13F_M_262


title: 13F_M_261


title: RBG25356_WT


title: 37_CD68_94


title: RBG25351_WT


title: 13F_M_260


title: RBG25349_WT


title: RBG25352_DKO


title: RBG25350_WT


title: 36_CD68_27


title: 13F_M_259


title: RBG25348_WT


title: RBG25344_WT


title: RBG25346_WT


title: RBG25345_WT


title: 36_CD68_93


title: 36_CD68_59


title: 13F_M_257


title: 35_CD68_58


title: RBG25353_DKO


title: 13F_M_258


title: RBG25340_DKO


title: 13F_M_191


title: 36_CD68_144


title: RBG25343_WT


title: RBG25341_DKO


title: 13F_M_256


title: 13F_M_190


title: 34_CD68_25


title: RBG25338_WT


title: 34_CD68_92


title: 35_CD68_26


title: RBG25337_WT


title: RBG25336_WT


title: 33_CD68_91


title: 13F_M_189


title: 34_CD68_143


title: RBG25339_WT


title: 33_CD68_57


title: RBG25347_WT


title: RBG25335_WT


title: RBG25333_DKO


title: RBG25334_WT


title: RBG25342_DKO


title: RBG25332_DKO


title: 33_CD68_24


title: 13F_M_188


title: RBG25330_WT


title: 13F_M_187


title: 33_CD68_142


title: 32_CD68_90


title: 13F_M_185


title: RBG25328_WT


title: RBG25329_WT


title: 32_CD68_23


title: 13F_M_186


title: 13F_M_184


title: RBG25327_WT


title: 13F_M_183


title: RBG25323_WT


title: RBG25326_WT


title: RBG25324_WT


title: RBG25321_DKO


title: RBG25319_DKO


title: RBG25322_WT


title: 13F_M_181


title: 13F_M_182


title: 31_CD68_140


title: 30_CD68_89


title: 32_CD68_141


title: RBG25317_WT


title: RBG25316_WT


title: RBG25315_WT


title: RBG25318_WT


title: RBG25325_WT


title: 13F_M_180


title: RBG25314_WT


title: 13F_M_179


title: RBG25310_WT


title: 13F_M_177


title: RBG25311_WT


title: RBG25309_DKO


title: 29_CD68_55


title: 13F_M_176


title: 29_CD68_88


title: 13F_M_178


title: 28_CD68_21


title: 28_CD68_138


title: RBG25306_WT


title: 13F_M_175


title: RBG25308_DKO


title: RBG25307_DKO


title: RBG25305_WT


title: RBG25304_WT


title: 13F_M_174


title: 3_CD68_56


title: 30_CD68_139


title: RBG25303_WT


title: RBG25313_WT


title: 27_CD68_87


title: RBG25312_WT


title: 27_CD68_54


title: RBG25302_WT


title: RBG25301_WT


title: 13F_M_173


title: 3_CD68_22


title: RBG25299_WT


title: RBG25300_WT


title: 13F_M_171


title: RBG25298_WT


title: RBG25296_DKO


title: 26_CD68_86


title: 13F_M_170


title: 13F_M_172


title: RBG25297_DKO


title: 26_CD68_137


title: RBG25294_WT


title: RBG25295_DKO


title: 13F_M_169


title: RBG25293_WT


title: RBG25292_WT


title: 13F_M_168


title: 25_CD68_19


title: 25_CD68_53


title: RBG25291_WT


title: RBG25290_WT


title: 13F_M_167


title: 24_CD68_52


title: RBG25289_WT


title: 27_CD68_20


title: RBG25288_WT


title: 13F_M_166


title: 13F_M_165


title: RBG25286_WT


title: 24_CD68_18


title: RBG25285_DKO


title: RBG25284_DKO


title: 13F_M_164


title: 23_CD68_51


title: RBG25283_DKO


title: RBG25281_WT


title: 13F_M_162


title: RBG25279_WT


title: RBG25280_WT


title: 13F_M_161


title: RBG25278_WT


title: 23_CD68_136


title: 23_CD68_17


title: 22_CD68_84


title: RBG25287_WT


title: RBG25276_WT


title: RBG25277_WT


title: RBG25275_WT


title: 13F_M_160


title: RBG25274_WT


title: 13F_M_159


title: 22_CD68_16


title: 22_CD68_135


title: RBG25273_DKO


title: 21_CD68_83


title: 23_CD68_85


title: RBG25272_DKO


title: 13F_M_163


title: RBG25271_DKO


title: 13F_M_158


title: RBG25270_WT


title: 13F_M_157


title: RBG25282_WT


title: 13F_M_156


title: RBG25269_WT


title: 21_CD68_50


title: 21_CD68_134


title: 20_CD68_82


title: RBG25265_WT


title: 13F_M_154


title: RBG25264_WT


title: RBG25266_WT


title: RBG25262_WT


title: 13F_M_153


title: RBG25263_WT


title: 20_CD68_49


title: RBG25260_DKO


title: 20_CD68_133


title: RBG25259_DKO


title: 13F_M_152


title: RBG25257_WT


title: 20_CD68_15


title: RBG25268_WT


title: RBG25267_WT


title: RBG25256_WT


title: 2_CD68_48


title: RBG25258_WT


title: 19_CD68_81


title: RBG25254_WT


title: 13F_M_150


title: 13F_M_155


title: RBG25255_WT


title: RBG25252_WT


title: 13F_M_148


title: 13F_M_151


title: RBG25251_WT


title: RBG25250_WT


title: 13F_M_147


title: 19_CD68_132


title: RBG25253_WT


title: RBG25247_DKO


title: RBG25246_WT


title: RBG25249_DKO


title: 17_CD68_79


title: RBG25245_WT


title: 18_CD68_131


title: RBG25244_WT


title: RBG25243_WT


title: 13F_M_145


title: 17_CD68_14


title: RBG25242_WT


title: 17_CD68_47


title: 13F_M_144


title: RBG25241_WT


title: 13F_M_142


title: RBG25237_WT


title: 18_CD68_80


title: RBG25238_WT


title: RBG25240_WT


title: RBG25239_WT


title: 17_CD68_130


title: RBG25236_WT


title: 16_CD68_78


title: RBG25235_WT


title: 13F_M_141


title: 13F_M_146


title: 16_CD68_13


title: RBG25233_WT


title: 13F_M_140


title: RBG25234_WT


title: 13F_M_139


title: 13F_M_143


title: RBG25232_WT


title: RBG25231_DKO


title: RBG25229_DKO


title: RBG25228_WT


title: RBG25227_WT


title: 13F_M_138


title: 13F_M_137


title: 13F_M_135


title: 14_CD68_76


title: RBG25226_WT


title: 16_CD68_129


title: 15_CD68_128


title: RBG25225_WT


title: 16_CD68_46


title: 15_CD68_77


title: 13F_M_136


title: 13F_M_134


title: RBG25230_DKO


title: 14_CD68_127


title: 13_CD68_75


title: RBG25224_WT


title: 13F_M_133


title: 13F_M_132


title: 13F_M_130


title: RBG25213_WT


title: RBG25221_WT


title: RBG25220_WT


title: RBG25215_WT


title: RBG25217_DKO


title: 13F_M_128


title: RBG25218_DKO


title: 13_CD68_45


title: 12_CD68_125


title: 12_CD68_44


title: 12_CD68_11


title: 13_CD68_126


title: 13F_M_131


title: RBG25216_WT


title: 13_CD68_12


title: RBG25223_WT


title: RBG25209_WT


title: MYC-input

city: Hefei

first: wang

last: jin

state: Anhui

address: Shushan District

department: School of Basic Medicine

institute: Anhui Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Mus using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
bigWig files were generated using deepTools.
Supplementary files format and content: bigWig

growth_protocol: It was cultured in DMEM basal medium (319-005-CL, WISENTINC) supplemented with 10% fetal bovine serum (EVERY GREEN) at 37°C in a humidified environment with 5% CO2,

extract_protocol:
The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature by a vacuum pump, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tissue was then collected and frozen in liquid nitrogen, and grinded by tissue lyser. The grinded powder was treated with lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-H3K27me3 antibody（#9733, CST）and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: When GC-1 cells were grown at 75% density, replaced with fresh DMEM consisting of all supplements, and after 30 min, Lipofectamine 3000 reagent was mixed with plasmids by incubating them at room temperature for 15 min in proportion to the manufacturer's instructions and adding them to the medium. fresh DMEM containing all supplements was replaced after 12 h, and after 24 h fresh DMEM was replaced with puromycin (1000 ng /ml) to screen TET1,MYC lentiviral vector-stabilized cell clones. single cell clones were isolated after one week of dilution culture and amplified for the next experiments

tag: cell line

value: male germ cell

tag: antibody


title: TET1-input


title: RBG25222_WT


title: RBG25214_WT


title: 13F_M_129


title: 12_CD68_74


title: RBG25208_WT


title: npr-8_D9_25C_S05

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
Cuffquant from Cufflinks v2.2.1 was used to quantify genes and transcripts.
Cuffdiff from Cufflinks v2.2.1 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans was cultured at 20⁰C or 25⁰ and fed E. coli strain OP50.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: C. elegans was cultured at 20⁰C or 25⁰ for at least two generations and was collected at day 0 young-adult stage or day 9.

tag: developmental stage

value: 9-day old adult

tag: protocol

value: propagated at 25degreeC


title: RBG25212_WT


title: TET1-IP


title: RBG25207_DKO


title: MYC-IP


title: 10_CD68_72


title: cerebral cortex, 10 month, recovered, Brapflox/floxEmx1Cre, bio rep 4

city: Chicago

first: Jayasri

last: Nanduri

state: IL

address: 5841 S. Maryland Avenue

institute: University of Chicago

data_processing:
Quasi-mapping and quantification: salmon 1.5.2
Assembly: GRCm38.primary_GencodeM25
Supplementary files format and content: gene level raw abdunance in TSV format

molecule: polyA RNA

source_name: whole cerebral cortex

extract_protocol:
Cerebral cortices were removed, flash frozen in liquid nitrogen, and RNA was extracted and purified using Trizol reagent followed by treatment with TURBO DNase.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole cerebral cortex

value: 10 month

tag: phenotype

value: recovered


title: RBG25211_WT


title: A_3

type: RNA

city: Hangzhou

first: Di

last: Wu

state: Zhejiang

address: No. 268, Kaixuan Road

institute: Zhejiang University

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Clariom D Arrays, mouse (Affymetrix, 902931). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Foxp3-Cre mice, older than 18-months-old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained in SPF condition.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Peripheral lymph nodes and spleens were harvested from mice, and grinded into single cells, then the CD4+-T cells were isolated by Mouse CD4 T Lymphocyte Enrichment Set-DM (BD Biosciences, 558131), followed with FACS sorting (SONY Cell Sorter, SH800S) to purify CD4+YFP+ Treg cells with purities >99%.

value: peripheral lymph nodes and spleens from mice

value: Treg

tag: Sex

value: female


title: B_KO_1

value: Bim-deficient

value: 8-10 weeks


title: A_1

value: WT


title: A_2


title: 11_CD68_73

value: Melanoma

value: Immunotherapy


title: B_KO_2


title: WT2

source_name: Foxp3-Cre mice, 8-10-weeks-old


title: 13F_M_149


title: B_KO_3


title: npr-8_D9_25C_S02


title: 1_CD68_41


title: cerebral cortex, 10 month, recovered, Brapflox/floxEmx1Cre, bio rep 2


title: RBG25210_WT

value: Bone marrow


title: 11_CD68_43


title: 11_CD68_124


title: cerebral cortex, 10 month, recovered, Brapflox/floxEmx1Cre, bio rep 6


title: 006_CD68_71


title: 006_CD68_122


title: RBG25201_WT


title: cerebral cortex, 10 month, recovered, Brapflox/floxEmx1Cre, bio rep 5


title: npr-8_D9_25C_S03


title: RBG25202_WT


title: 10_CD68_42


title: RBG25206_DKO

value: Aldh2 & Fancd2 double knock-outs


title: cerebral cortex, 10 month, NA, Brapflox/wt Cre-, biol rep 4

value: Brapflox/wt Cre-


title: cerebral cortex, 10 month, recovered, Brapflox/floxEmx1Cre, bio rep 3


title: 005_CD68_70


title: 11_CD68_10


title: WT4


title: WT_D9_25C_S03

value: wild-type N2


title: WT3


title: 005_CD68_121


title: RBG25205_DKO


title: 10_CD68_123


title: npr-8_D9_25C_S04

value: 9-day old adult


title: RBG25204_WT


title: npr-8_D9_25C_S01

value: propagated at 25degreeC


title: WT_D9_25C_S01


title: cerebral cortex, 3 month, mild, Brapflox/floxTie2Cre, biol rep 4

value: whole cerebral cortex

value: 3 month

value: mild


title: RBG25198_WT


title: RBG25203_WT


title: WT_D9_25C_S05


title: npr-8_D0_25C_S04

value: 0-day old young adult


title: WT_D9_25C_S04


title: cerebral cortex, 10 month, NA, Brapflox/wt Cre-, biol rep 3

value: 10 month


title: cerebral cortex, 10 month, NA, Brapflox/wt Cre-, biol rep 2


title: 003_CD68_68


title: RBG25200_WT


title: cerebral cortex, 10 month, recovered, Brapflox/floxEmx1Cre, bio rep 1

value: recovered


title: npr-8_D0_25C_S03


title: 003_CD68_119


title: cerebral cortex, 3 month, mild, Brapflox/floxTie2Cre, biol rep 2


title: WT_D9_25C_S02


title: RBG25195_DKO


title: cerebral cortex, 10 month, NA, Brapflox/wt Cre-, biol rep 1


title: cerebral cortex, 3 month, mild, Brapflox/floxTie2Cre, biol rep 1


title: RBG25194_DKO


title: 004_CD68_69


title: RBG25199_WT


title: cerebral cortex, 3 month, mild, Brapflox/floxTie2Cre, biol rep 5


title: 002_CD68_118


title: npr-8_D0_25C_S01


title: RBG25197_WT


title: RBG25192_WT


title: cerebral cortex, 3 month, strong, Brapflox/floxThy1Cre, biol rep 2

value: strong


title: WT_D0_25C_S03


title: RBG25196_WT


title: 002_CD68_67


title: npr-8_D0_25C_S02


title: 004_CD68_120


title: 001_CD68_117


title: cerebral cortex, 3 month, strong, Brapflox/floxThy1Cre, biol rep 3


title: 9_CD45_47


title: cerebral cortex, 3 month, mild, Brapflox/floxTie2Cre, biol rep 3


title: npr-8_D0_25C_S05


title: RBG25189_WT


title: RBG25193_DKO


title: cerebral cortex, 3 month, strong, Brapflox/floxThy1Cre, biol rep 5


title: 001_CD68_40


title: 001_CD68_9


title: WT_D0_25C_S05


title: RBG25187_WT


title: cerebral cortex, 3 month, strong, Brapflox/floxThy1Cre, biol rep 4


title: 70_CD45_5


title: RBG25186_WT


title: npr-8_D9_20C_S03

value: propagated at 20degreeC


title: npr-8_D9_20C_S04


title: WT_D0_25C_S04


title: RBG25191_WT

value: WT


title: npr-8_D9_20C_S02


title: WT_D0_25C_S02


title: RBG25190_WT


title: cerebral cortex, 3 month, strong, Brapflox/floxEmx1Cre, biol rep 1


title: cerebral cortex, 3 month, strong, Brapflox/floxThy1Cre, biol rep 1


title: 8_CD45_7

value: Melanoma


title: cerebral cortex, 3 month, strong, Brapflox/floxEmx1Cre, biol rep 6


title: WT_D0_25C_S01


title: 64_CD45_3

value: Immunotherapy


title: 63_CD45_79


title: RBG25188_WT

value: Bone marrow


title: cerebral cortex, 3 month, NA, Brapflox/wt Cre-, biol rep 4


title: WT_D9_20C_S04


title: cerebral cortex, 3 month, NA, Brapflox/wt Cre-, biol rep 3


title: 72_CD45_6


title: npr-8_D9_20C_S05


title: cerebral cortex, 3 month, strong, Brapflox/floxEmx1Cre, biol rep 5


title: 65_CD45_4


title: cerebral cortex, 3 month, strong, Brapflox/floxEmx1Cre, biol rep 4


title: RBG25185_WT


title: 64_CD45_80


title: cerebral cortex, 3 month, NA, Brapflox/wt Cre-, biol rep 2


title: 60_CD45_2


title: WT_D9_20C_S05


title: WT_D9_20C_S02


title: cerebral cortex, 3 month, NA, Brapflox/wt Cre-, biol rep 1


title: RBG25178_WT


title: npr-8_D9_20C_S01


title: cerebral cortex, 3 month, strong, Brapflox/floxEmx1Cre, biol rep 2


title: 59_CD45_76


title: RBG25184_WT


title: RBG25183_DKO

value: Aldh2 & Fancd2 double knock-outs


title: cerebral cortex, 3 month, strong, Brapflox/floxEmx1Cre, biol rep 3


title: RBG25182_DKO


title: RBG25181_DKO


title: RBG25177_WT


title: RBG25176_WT


title: 60_CD45_77


title: WT_D9_20C_S03


title: RBG25180_WT


title: RBG25179_WT


title: 58_CD45_1


title: 62_CD45_78


title: npr-8_D0_20C_S02


title: RBG25175_WT


title: Lewis cells, 10% FBS, rep1

city: Wuhan, China

first: Xiao

last: Yang

state: 湖北省

address: 武汉市江汉区马场路109号协和医院肿瘤中心

institute: Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using NGSQC (v2.3.3)
The clean reads were then aligned to the reference genome using HISAT2 (v2.1.0) with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome.
The gene expression analyses were performed with StringTie (v1.3.3b). DESeq(v1.28.0) was used to analyze the DEGs between samples.
Assembly: mm10
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: Lewis

growth_protocol: Lewis cells were maintained in DMEM supplemented with 10% serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and Qubit Fluorometer (Invitrogen).
The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.

treatment_protocol: Lewis cells were cultured in 10% or 2% serum medium for 72 h.

value: Lewis

value: Lung Carcinoma Cell Lines

value: 10% FBS

tag: time


title: Lewis cells, 10% FBS, rep3

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: Lewis cells, 2% FBS, rep3

address: 武汉市江汉区马场路109号协和医院肿瘤中心

value: 2% FBS


title: Lewis cells, 10% FBS, rep2

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: npr-8_D0_20C_S01


title: 58_CD45_95


title: RBG25174_WT


title: RBG25173_WT


title: WT_D0_20C_S05

value: wild-type N2


title: 56_CD45_30


title: npr-8_D0_20C_S05


title: npr-8_D0_20C_S04


title: 58_CD45_75


title: RBG25172_WT


title: WT_D0_20C_S04


title: npr-8_D0_20C_S03


title: WT_D9_20C_S01

value: 9-day old adult


title: 57_CD45_74


title: RBG25170_DKO


title: Lewis cells, 2% FBS, rep2

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: RBG25169_DKO


title: 53_CD45_70


title: 52_CD45_29


title: 56_CD45_73


title: RBG25167_WT


title: Lewis cells, 2% FBS, rep1

address: 武汉市江汉区马场路109号协和医院肿瘤中心


title: Mouse, Tet2 cKO-3, 2-month

city: Su zhou

first: Xingyun

last: Xu

address: Ren ai Street

institute: Soochow University

data_processing:
The quality evaluation of sequencing data is analyzed using software FastQC (v0.10.1)
Filter sequencing data using software Cutadapt (version 1.9.1)
Using Hisat2 (v2.0.1) software for short reads comparison
We compared the results of each sample with the reference genome and used samtools (v0.1.19) software for mpileup processing to obtain possible SNV results for each sample. Then, we used  Annotate separately using the annovar (v2013.02.11) software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: habenular

growth_protocol: Mice used in this study were housed under specific-pathogen-free conditions.

extract_protocol:
The habenular of Tet2 cKO mice and WT mice were removed, flash frozen in liquid nitrogen, and total RNA was harvested using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: habenular

value: Tet2 cKO


title: Mouse, WT-1, 2-month


title: 55_CD45_72


title: 51_CD45_93


title: RBG25166_WT


title: 51_CD45_69


title: 54_CD45_94


title: RBG25165_WT


title: WT_D0_20C_S03

value: 0-day old young adult


title: Mouse, Tet2 cKO-1, 2-month


title: 54_CD45_71


title: 47_CD45_91


title: WT_D0_20C_S02


title: Mouse, WT-3, 2-month


title: WT_D0_20C_S01


title: Mouse, WT-2, 2-month


title: RBG25168_WT


title: RBG25161_WT


title: Tumor immune cells, HashTag Library

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description:
10X Genomics
Monocytes_raw_feature_bc_matrix.h5
clvi_2021.rds
clvi_2021_info.md

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software (cellranger-6.0.0, 10x Genomics).
scanpy, see for more details clvi_2021_info.md
seurat, see for more details clvi_2021_info.md
hashtag details, see for more details 230422 hashtag info AB.xlsx
Assembly: mm10, refdata-cellranger-mm10-3.0.0
Supplementary files format and content: matrix file (h5, 10X Genomics), rds file (seurat object)

molecule: protein

extract_protocol:
3 individual tumors per group were harvested and processed into single suspensions. CD45+ cells were enriched using a positive selection kit (Miltenyi). Next, individual samples were hashtagged with unique TotalSeq-B hashtag antibodies B0301-B0302, B0304-B0310 (Biolegend) and subsequently stained with  fluorescently labelled antibodies. CD45+CD11b+Ly6G- cells were sorted with an Aria III fluorescence activated cell sorter (BD).
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3'v3.1 + Cell Surface Protein (Dual Index), 10x Genomics). Cellular mRNA and hashtag oligos (HTO) were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol.
scRNA-seq (gene expression with feature barcoding)

value: Myeloid immune cells

value: treated with TRP-1 TCRtg CD4+ T-cells or untreated

tag: sort marker

tag: hashtag

value: HashTagOligo (see  "230422 hashtag info AB.xlsx")


title: Tumor immune cells, 3GEX Library

library_source: transcriptomic single cell

tag: tissue


title: RBG25160_WT

tag: cell type

value: WT


title: 45_CD45_90

value: Melanoma

tag: treatment


title: RBG25171_DKO


title: Mouse, Tet2 cKO-2, 2-month


title: Blood_749_317

first: Adam

last: Williams

state: Ilinois

address: 240 East Huron

department: Department of Medicine, Allergy and Immunology

institute: Northwestern University

data_processing:
Quality control of the fastq files was performed using FASTQC.
BBDuk was used to remove hemoglobin contamination from the blood samples.
The reads were mapped to gencode.v38 release (GRCh38.p13 Release 38) using Salmon.
R version 4.1.2 was used for the statistical analysis. R packages DESeq2 (1.32.0), tximport (1.20.0), Salmon (version 1.5.2) and WGCNA (1.4.1717) were used for quantification and analysis of the RNA-sequencing data.
Assembly: GRCh38.p13 Release 38
Supplementary files format and content: xls files containing TPM values

growth_protocol: Hypertonic saline was used to induced sputum in healthy subjects with chronic tobacco exposure

extract_protocol:
RNA from sputum and blood was analyzed on an Agilent TapeStation 4200 (Agilent Technologies) using the RNA High Sensitivity assay.
RNA samples were prepared for mRNA-Sequencing by the University of Connecticut Genomic Core Facility (Institute for System Genomics) using the Illumina TruSeq. Stranded mRNA Sample Preparation kit, following the manufacturer’s protocol

treatment_protocol: Cigarettes, e-cigs, and non users.

value: Blood

value: Control


title: Blood_749_226

value: E-cigarette


title: Blood_749_320


title: Blood_749_308


title: Blood_749_235


title: Blood_749_316


title: RBG25159_DKO

value: Bone marrow

value: Aldh2 & Fancd2 double knock-outs


title: SLX18935_SIGAH3

description: 10x Genomics

data_processing:
Barcode processing, mapping and gene counting were performed using the Cell Ranger pipeline v6.0.1
Assembly: mm10
Supplementary files format and content: h5 files that contains fitlered raw counts as Cellranger output

source_name: bone marrow

extract_protocol:
Mouse bone marrow cells were collected from the femurs, tibiae and iliac crest and depleted of red blood cells by an ammonium chloride lysis step (STEMCELL Technologies). The cells were stained with the fluorophore-conjugated monoclonal antibodies and lineage− c-Kit+ (LK) cells were then isolated using an LSRII Fortessa (BD).
Single-cell sequencing libraries were generated using 10x Chromium (10x Genomics, Pleasanton, CA) reagent kit v3 according to the manufacturer’s protocol.

value: bone marrow

value: LK

value: M

value: 88 weeks


title: Blood_749_234


title: Blood_749_220


title: RBG25158_DKO


title: RBG25163_WT


title: RBG25162_WT


title: 48_CD45_92

value: Immunotherapy

tag: roilabel


title: SLX18935_SIGAA7

description: 10x Genomics

value: F

value: 16 weeks

tag: genotype


title: 43_CD45_89


title: H2B FAST H2B

city: Rehovot

first: Yonatan

last: Stelzer

state: Israel

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
Paired-end reads were aligned to the mm10 genome assembly downloaded from the UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest using bowtie2 with default options.
Aligned files were then imported into R with readGAlignments function from GenomicAlignments package (Lawrence et al., 2013), requiring minimum mapping quality of 10.
Assembly: mm10
Supplementary files format and content: bw
Supplementary files format and content: bw fille was created using bamCoverage command from deepTools package with the following options: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --maxFragmentLength 300

source_name: mESC

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Crosslinked pellet was re-suspended in 20ul of cell lysis buffer (50mM Tris pH8.0, 150mM NaCl, 1%TritonX-100, 0.1%sodium deoxycholate, 5 mM CaCl2, EDTA-free protease inhibitor cocktail and incubated on ice for 15 minutes. Cells were centrifuged at 3000RPM for 10 minutes at 4°C. The supernatant was discarded, and pellet was re-suspended in 10ul of lysis buffer supplemented with 17.5 units of micrococcal nuclease (Worthington MNase, LS004798) and chilled on ice for 10 minutes. Samples were incubated at 37°C for 15 minutes. To stop reaction, 20mM EDTA was added and samples were vortexed and placed on ice for 30 minutes. Cell lysate was then centrifuged at max speed (20,000xg) for 10 minutes at 4°C and supernatant moved to a separate tube. Reaction volume was increased to 180ul with RIPA buffer (10mM Tris pH8.0, 140mM NaCl, 1mM EDTA, 0.1%SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail), and reaction was then split into two separate wells of 96-well LoBind Eppendorf plate. ~5ug of anti-HA (12CA5) and anti-myc (9E10) antibodies was added to the separate wells and incubated at 4°C for 2 hours with rotations. Both antibody stocks were the supernatant of the respective hybridoma cell cultures grown in miniPERM bioreactors in-house by the Weizmann Institute Core Facility Antibody Unit. All subsequent steps were carried out as described in (Gutin et al., 2018).
SLIM-Chip, as per Gutin et al, Cell Reports 2019

tag: chip antibody

value: mESC

tag: sensor type

value: cleavable H2B


title: 40_CD45_67


title: RBG25155_WT


title: 45_CD45_68


title: 47_CD45_28


title: Blood_749_216


title: 46_CD45_27


title: SLX18935_SIGAE3

description: 10x Genomics

tag: age

value: 68 weeks


title: Hepatocytes H3.1 K27ac

data_processing:
Paired-end reads were aligned to the mm10 genome assembly downloaded from the UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest using bowtie2 with default options.
Aligned files were then imported into R with readGAlignments function from GenomicAlignments package (Lawrence et al., 2013), requiring minimum mapping quality of 10.
Assembly: mm10
Supplementary files format and content: bw fille was created using bamCoverage command from deepTools package with the following options: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --maxFragmentLength 300

value: cleavable H3.1

value: WT


title: Blood_749_233

value: Blood


title: 45_CD45_26

value: Melanoma


title: MEF H3.1 myc

value: myc


title: Hepatocytes H3.1 HA

value: HA


title: Hepatocytes H3.3 HA

value: cleavable H3.3


title: Hepatocytes H3.3 myc


title: 39_CD45_44


title: MEF H3.1 K27ac


title: 37_CD45_42


title: Blood_749_219

value: E-cigarette


title: MEF H3.1 HA


title: RBG25157_DKO

value: Bone marrow

value: Aldh2 & Fancd2 double knock-outs


title: Blood_749_124

value: Cigarette


title: Blood_749_122


title: RBG25156_WT


title: Blood_749_207


title: 41_CD45_46

value: Immunotherapy


title: RBG25149_WT


title: Hepatocytes H3.3 K27ac


title: Blood_749_206


title: 36_CD45_65


title: RBG25154_WT


title: Hepatocytes H3.1 myc


title: Blood_749_203


title: RBG25147_DKO


title: IL-2 treated Lymph node, excised, replicate 1

first: Spencer

last: Brightman

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
The single-end reads that passed Illumina filters were subsequently filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were aligned with the GRCm38.p4.gencode.rM9 reference genome using STAR (v 2.6.1) and the RefSeq gene annotation downloaded from the University of California - Santa Cruz Genome Bioinformatics site.
DUST scores were calculated with PRINSEQ Lite (v 0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
The alignment results were parsed via the SAMtools  to generate SAM files.
Read counts to each genomic feature were obtained with the featureCounts (v 1.6.5) using the default option along with a minimum quality cut off (Phred > 10)
After removing absent features (zero counts in all samples), the raw counts were imported to R/Bioconductor package DESeq2 (v1.24.0)
Assembly: GRCm38.p4.gencode.rM9
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: lymph node

extract_protocol:
Animals were sacrificed by CO2 asphyxiation and inguinal lymph nodes and corresponding subcutaneous tumors were surgically excised. Tumors and lymph nodes were minced into 2mm pieces and digested enzymatically with 20 ug/mL Liberase and DNAse I for 30 minutes. Tissue pieces were manually pressed through a 70 uM cell strainer to obtain single cell suspensions for fluorescence activated cell sorting. Viable CD90.1+CD4+ cells were sorted for each condition
Libraries were constructed with SMART-seq2 protocol

value: lymph node

tag: strain

tag: gender

value: female

value: CD4 T cells


title: RBG25153_WT


title: 39_CD45_66


title: Blood_749_202


title: RBG25152_WT


title: Blood_749_112


title: RBG25151_WT


title: Blood_749_127


title: 40_CD45_45


title: IL-7 and IL-15 treated tumor, excised, replicate 1

source_name: squamous cell carcinoma

value: squamous cell carcinoma

value: IL-7 and IL-15


title: 38_CD45_43


title: 35_CD45_88


title: Blood_749_126


title: RBG25150_WT


title: IL-2 treated tumor, excised, replicate 1


title: IL-7 and IL-15 treated tumor, excised, replicate 2


title: IL-2 treated Lymph node, excised, replicate 2


title: 37_CD45_25


title: RBG25148_WT


title: 35_CD45_23


title: 35_CD45_41


title: Blood_749_121


title: Spt_316

value: Sputum

value: Control


title: 34_CD45_87


title: 35_CD45_64


title: Blood_749_110

value: Blood


title: IL-7 and IL-15 treated Lymph node, excised, replicate 2

value: WT


title: 36_CD45_24

value: Melanoma


title: RBG25146_DKO


title: Blood_749_109


title: RBG25145_DKO


title: IL-2 treated tumor, excised, replicate 2


title: RBG25144_WT


title: Sample_458, Imm.LERKO, Liver

city: College Station

first: Kartik

last: Shankar

email: kartik.shankar@cuanschutz.edu, kartikster@gmail.com, kartik.shankar@usda.gov, kartik.shankar@ag.tamu.edu

state: TX

address: 498 Olsen Blvd TAMU 2250 TAMU 2250

department: RAFSRU

institute: USDA ARS

data_processing:
All reads were trimmed for adapters, filtered based on quality score using FASTP and aligned to the mouse genome (mm10) using the STAR aligner using default settings. Resulting read alignments for each sample were imported in Seqmonk for gene level quantification as counts mapping to annotated genes. Gene counts were imported into R (v4.05) and analysis of differential expression between groups was done using the limma-voom pipeline
Supplementary files format and content: Processed data are provided as data matrix where rows are gene level quantitation (counts) and columns include samples. A single file is included for all samples.

source_name: Liver

extract_protocol:
RNA was extracted from liver tissue from individual mice in four groups (sexullay immature and mature, LERKO and flox mice, n = 4 per group) using the RNeasy Mini Kit per manufacturer’s instructions including on-column DNase digestion. Total RNA was quantified using a Qubit RNA BR Assay Kit and RNA integrity was assessed on an RNA ScreenTape.
mRNA-seq libraries (n = 4 per group) were prepared using a TruSeq Stranded RNA HT Sample Prep Kit (Illumina, Cat. No. RS-122-2303) on a Perkin Elmer Sciclone G3 platform. An additional standard 1.0x manual bead cleanup was performed using AMPure XP Beads (Beckman Coulter, A63881) after the libraries were completed to remove primer-dimers. Qubit dsDNA BR Assay kit was used to determine the concentration of the completed library and a Fragment Analyzer Standard Sensitivity NGS Fragment Kit
Paired-end, opposing strand directional libraries

value: Liver

tag: Stage

value: immature

tag: cre

value: yes

value: LERKO

tag: group


title: Sample_448, Imm.Con, Liver

value: no

value: Con


title: IL-7 and IL-15 treated Lymph node, excised, replicate 1


title: RBG25143_WT

value: Bone marrow


title: Sample_470, Imm.LERKO, Liver


title: Spt_317


title: RBG25142_WT


title: Sample_461, Imm.Con, Liver


title: RBG25141_DKO

value: Aldh2 & Fancd2 double knock-outs


title: RBG25138_WT


title: 32_CD45_21

value: Immunotherapy


title: 34_CD45_63


title: RBG25137_WT


title: RBG25136_WT


title: 30_CD45_62


title: Sample_435, Imm.Con, Liver


title: Spt_308


title: RBG25140_DKO


title: Spt_320


title: Sample_429, Imm.LERKO, Liver


title: Spt_235

value: E-cigarette


title: RBG25139_DKO


title: RBG25135_WT


title: 33_CD45_22


title: Spt_234


title: Sample_360, Mat.LERKO, Liver

value: mature


title: 29_CD45_40


title: Spt_216


title: RBG25134_WT


title: Spt_219


title: Sample_351, Mat.LERKO, Liver


title: Spt_233


title: 28_CD45_19


title: Sample_440, Imm.Con, Liver


title: Sample_436, Imm.LERKO, Liver


title: Spt_226


title: 31_CD45_85


title: RBG25132_WT


title: Spt_220


title: Sample_349, Mat.Con, Liver


title: Spt_206


title: 33_CD45_86


title: RBG25131_WT


title: Sample_339, Mat.LERKO, Liver


title: RBG25133_WT


title: Sample_333, Mat.LERKO, Liver


title: 29_CD45_20


title: 26_CD45_61


title: Spt_202


title: RBG25129_DKO


title: Spt_207


title: 24_CD45_39


title: Spt_127

value: Cigarette


title: Sample_331, Mat.Con, Liver


title: 27_CD45_18


title: 26_CD45_84


title: 23_CD45_60


title: Spt_203

value: Sputum


title: Spt_126


title: RBG25127_DKO


title: Sample_340, Mat.Con, Liver


title: RBG25128_DKO


title: RBG25126_WT


title: 23_CD45_38


title: RBG25130_WT


title: Sample_330, Mat.Con, Liver


title: CIA + soyasaponin Bb treatment (CIA treated), scRNA-seq

city: Baltimore

first: Kathleen

last: Noller

state: MD

address: 3400 N. Charles Street

institute: Johns Hopkins University

description: 10x Genomics

data_processing:
CellRanger (version 5.0.1) was used to perform initial processing of sequencing reads and alignment to the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow, femur

extract_protocol:
GemCode Single Cell platform (10X genomics) was used to determine the transcriptome of single cells. A single-cell suspension was obtained from the flushed bone marrow mixture of the mice femur (n = 3 mice from each sample group (CIA, CIA treated, and DBA control)) and subjected to Ficoll gradient centrifugation to enrich for mononuclear cells . Samples were profiled based on viability and amount and a range of 81-85% viability was achieved. A total of 10,000 cells were recorded for each run, followed by GEM-RT and cDNA amplification.
Single-cell library preparation was performed by the Johns Hopkins School of Medicine for Genomics and Bioinformatics (Core facility) and the quality of cDNA samples was examined by an Agilent 2100 Expert High Sensitivity DNA Assay. Single-cell libraries were constructed by attaching P5 and P7 primer sites and sample indices to the cDNA. ScRNA-seq was performed on the Illumina NovaSeq 6000 S2 Flow Cell according to the manufacturer’s protocol to a depth ranging from 315 to 377 million reads per sample.

treatment_protocol: DBA/1J mice were purchased from the Jackson Laboratory (strain number: 000670). The collagen-induced arthritis (CIA) model was established by injecting chicken type II collagen subcutaneously into the mouse tail of female DBA/1J mice at the 6-week of age. In brief, we prepared the collagen emulsion by homogenizing a chicken type II collagen solution (Chondrex) with Complete Freund’s Adjuvant (Chondrex) at high speed (15,000 rpm) following the manufacturer’s instructions. We injected 100 μg of the collagen emulsion into the tail subcutaneously, followed by a booster injection (100 μg collagen emulsified with Incomplete Freund’s Adjuvant [Chondrex]) at day 21 post-immunization. For the prophylactic treatment studies, the CIA mice were administrated with either vehicle (PBS) or soyasaponin Bb (10 mg/kg) intragastrically once per day for two months from the first day of collagen immunization. The mice were killed for further analysis at two months after the first immunization by using an overdose of isoflurane.

value: Mononuclear cells

value: Bone marrow, femur

value: DBA/1J , CIA model + soyasaponin Bb treatment

value: 14 weeks old


title: Spt_124


title: DBA control, scRNA-seq

description: 10x Genomics

value: DBA/1J , control


title: 23_CD45_17

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

value: Melanoma


title: Collagen-induced arthritis (CIA), scRNA-seq

description: 10x Genomics

value: DBA/1J , collagen-induced arthritis (CIA) model


title: Spt_110


title: 21_CD45_58


title: Lm_ST_3

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: Peritoneal cells, suboptimal temperature-housed mouse, L.major injected IP

data_processing:
The quality of sequence reads was assessed using the FastQC tool (Babraham Bioinformatics). Overrepresented sequences (Illumina TruSeq Adapters) were removed by palindrome trimming with Trimmomatic V.0.36. Low-quality bases (phred score < 33) were also removed. The high quality of trimmed sequence reads was validated by FastQC.
The sequence reads were then mapped to the mouse mm10 UCSC GRCm38 reference assembly using HISAT2 v2.2.0 with parameters -k 1 to avoid multi-mapped reads and --rna-strandness FR for strand-specific information. The files containing mapped reads were converted from SAM to BAM format and then sorted using Samtools. FastQC reports of trimmed sequence reads showed high frequency of duplicates in the samples, which were filtered out using PicardTools (MarkDuplicates) and then indexed using Samtools.
Gene expression was quantified by counting the number of uniquely mapped reads using featureCounts with the -s parameter to perform strand-specific read counting. Reads mapped to rRNAs were removed to resolve any biases from incomplete ribodepletion. Genes with a minimum expression level of five counts per million (CPM) reads in at least 3 of the samples were retained. TMM normalization was applied with the edgeR Bioconductor package, and pairwise differential gene expression analyses were performed for the TT and ST samples comparing the endotoxin-free PBS with L. major-infected or nHz samples. One PBS-treated sample at TT was excluded from the analysis due to very low coverage. Genes with ≥|2| fold-change (FC) in expression and Benjamini-Hochberg adjusted p-values ≤ 0.001 were considered significant.
For data visualization, bigwigs were generated using genomeCoverageBed and wigToBigWig tools (UCSC, USA) for visualization using the Integrative Genomics Viewer. Bigwigs were scaled per million reads mapped to exons excluding the remaining rRNA reads.
Assembly: mm10
Supplementary files format and content: bw files contains normalized sequence coverage tracks in a bigwig format
Supplementary files format and content: txt files contains the raw read counts for each sample

source_name: peritoneal cells

growth_protocol: 6–8 week-old female C57BL/6 mice were housed at either sub-optimal (ST) or thermoneutral (TT) temperatures.

extract_protocol:
Total RNA was extracted using RNeasy columns coupled with on-column DNase I digestion (Qiagen) from PEC lavages. The RNA integrity was assessed on a TapeStation (Agilent, Santa Clara, CA, USA).
The RNA-seq libraries were prepared using the TruSeq ribodepleted mRNA stranded kit (Illumina, San Diego, CA, USA) and sequenced on a NovaSeq 6000 (Illumina) using a paired-end 100bp configuration aiming for 60 million paired reads per sample.

treatment_protocol: ST and TT housed mice were intraperitoneally injected with 200µl of endotoxin-free PBS (negative control), nHZ or 108 L. major promastigotes (positive control); three mice per group. 5ml of cold PBS was injected into the peritoneal cavity after six hours, and immune cells were collected by lavage.

value: peritoneal cells

tag: Sex

value: female

tag: housing condition

value: suboptimal temperature


title: Spt_122


title: 20_CD45_57

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


title: RBG25121_WT

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.

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.

value: Bone marrow

value: WT


title: 22_CD45_83

value: Immunotherapy


title: RBG25125_WT


title: Spt_121


title: 20_CD45_37


title: PANC28 sgPHF8_2

city: China

first: Yanan

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: pancreatic cancer

value: PHF8 knockout

value: PANC28 PHF8 knockout cell, replicate2

tag: time

value: PANC28 PHF8 knockout cell


title: Spt_109

tag: tissue

value: Sputum

value: Cigarette


title: 20_CD45_16

first: Thazin

institute: Yale University

tag: cell type


title: RBG25119_WT

first: Xiaonan

institute: Shanghai Jiao Tong University School of Medicine


title: RBG25124_WT


title: HZ_ST_2

description: Peritoneal cells, suboptimal temperature-housed mouse, nHZ injected IP

tag: treatment

value: nHZ


title: PANC28 sgPHF8_1

value: PANC28 PHF8 knockout cell, replicate1


title: 22_CD45_59

tag: roilabel


title: Spt_112


title: PANC28 sgcon_3

tag: genotype

value: PANC28 cell, replicate3

value: PANC28 cell


title: RBG25123_WT


title: PANC28 sgcon_2

value: PANC28 cell, replicate2


title: 18_CD45_55

value: Melanoma


title: PBS_ST_2

description: Peritoneal cells, suboptimal temperature-housed mouse, PBS injected IP

value: peritoneal cells

value: female

value: PBS


title: 17_CD45_14


title: PANC28 sgcon_1

value: WT

value: PANC28 cell, replicate1


title: Lm_ST_2

value: suboptimal temperature


title: RBG25122_WT

value: Bone marrow


title: HZ_ST_1


title: Lm_ST_1


title: RBG25114_WT


title: Lm_TT_3

description: Peritoneal cells, Thermoneutral-housed mouse, L.major injected IP

value: thermoneutral


title: RBG25113_WT


title: PANC28 sgPHF8_3

value: pancreatic cancer

value: PHF8 knockout

value: PANC28 PHF8 knockout cell, replicate3

value: PANC28 PHF8 knockout cell


title: HZ_ST_3

value: nHZ


title: Lm_TT_1


title: RBG25120_WT


title: 15_CD45_82

value: Immunotherapy


title: TEST 7

city: Tromsø

first: Wei

last: Meng

address: MH bygget

department: Faculty of Health Sciences

country: Norway

institute: University of Tromsø

data_processing: DESeq2 log normalization+1

source_name: mucosal biopsy

extract_protocol:
Total RNA was isolated using the Allprep DNA/ RNA Mini Kit from Qiagen(catalogue number 80204)
Whole transcriptome libraries of UC remission samples were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (catalogue number RS-122–2203).

tag: remission status

value: Unknown

tag: remission duration

value: mucosal biopsy


title: RBG25111_WT


title: HZ_TT_3

description: Peritoneal cells, Thermoneutral-housed mouse, nHZ injected IP


title: 2_CD45_15

last: Aung

address: 310 Cedar St

source_name: Melanoma

value: Melanoma


title: RBG25118_WT

last: Wang

address: 227 Chongqing South Road

source_name: Bone marrow


title: 19_CD45_56


title: 14_CD45_35


title: TEST 2


title: 16_CD45_13


title: TEST 5


title: TEST 6


title: PBS_ST_3

value: peritoneal cells


title: HZ_TT_1

value: female


title: RBG25106_WT


title: PBS_ST_1

value: PBS


title: RBG25115_DKO

value: Aldh2 & Fancd2 double knock-outs


title: RBG25116_DKO


title: 16_CD45_54


title: 13_CD45_34


title: PBS_TT_1

description: Peritoneal cells, Thermoneutral-housed mouse, PBS injected IP


title: RBG25105_DKO


title: 9_ATP6_T2A_3

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

description:
WES_NIH/3T3 cells transfected with the tandem version of the Atp6 construct from the mitoKO library
mitoKO.xlsx

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38)
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Assembly: GRChm38

source_name: NIH-3T3 cells

growth_protocol: Cells were cultured at 37 °C under 5 % (vol/vol) CO2 in complete Dulbecco's Modified Eagle Medium (DMEM) (4.5 g/L glucose 2 mM glutamine, 110 mg/ml sodium pyruvate), supplemented with 10% calf bovine serum with iron, 5% penicillin/streptomycin (all from Gibco) and 50 µg/ml uridine (Sigma, cn. U3750). The Atp6 animals were maintained in a temperature- and humidity-controlled animal care facility with a 12-h light/12-h dark cycle and free access to water and food, and they were sacrificed by cervical dislocation.

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse ear biopsies was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT

treatment_protocol: NIH/3T3 mouse cells plated in 6-well tissue culture plates at a confluency of 70% were transfected with 3200 ng of each monomer (L and H - see pairID), or 6400 ng of plasmid DNA when using Tandem architectures in a single plasmid (L + H), with 16 µl of FuGENE-HD (Promega), following manufacturer´s guidelines.

tag: ddcbe pair id used

tag: days after transfection

tag: target

value: Whole genome off-target


title: Lm_TT_2


title: 16_CD45_36

city: New Haven


title: NN 14

value: not applicable


title: RBG25112_WT

city: Shanghai

value: Bone marrow

value: WT


title: TEST 4


title: TEST 3


title: HZ_TT_2

value: thermoneutral


title: 15_CD45_53


title: RBG25110_WT


title: NN 13


title: RBG25103_DKO


title: 7_ATP6_T2A_1


title: NN 11


title: NN 12


title: 12_CD45_33


title: RBG25102_WT


title: TEST 1


title: RBG25109_WT


title: 14_CD45_12


title: PBS_TT_2


title: 11_CD45_9


title: RBG25100_WT


title: RBG25107_WT


title: 11_CD45_50


title: 13_CD45_52


title: RBG25099_WT


title: NN 16


title: NN 15


title: NN 8


title: 13_CD45_11


title: RBG25098_WT


title: 2_ATP6_control_2

description:
WES_NIH/3T3 cells transfected with empty plasmid (WT-control)
mitoKO.xlsx

value: empty


title: 8_ATP6_T2A_2


title: NN 7


title: 1_ATP6_control_1


title: RBG25097_WT


title: 6_ATP6_H_L_3

description:
WES_NIH/3T3 cells transfected with the 2-plasmid version of the Atp6 construct from the mitoKO library
mitoKO.xlsx


title: 12_CD45_10


title: 5_ATP6_H_L_2


title: RBG25104_DKO


title: NN 6


title: RBG25101_WT


title: RBG25117_DKO


title: NN 5


title: NN 10


title: 12_CD45_51


title: NN 9


title: 4_ATP6_H_L_1


title: 001_CD45_8


title: 3_ATP6_control_3


title: RBG25093_DKO


title: Paternal_DCHP rep3

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample ...

growth_protocol: 8 week male WT mice were exposed to DCHP by oral gavage for 4 weeks, 3 week old F1 male mice were fed with HFD for 9 weeks

extract_protocol:
Total RNA was isolated from the liver with TRIzol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: male

value: Paternal DCHP

value: 4 weeks


title: NN 2


title: RBG25096_WT


title: Paternal_DCHP rep6


title: RBG25092_DKO


title: 1_CD45_31

value: Immunotherapy


title: 10_CD45_32


title: NN 4

value: mucosal biopsy


title: RBG25095_WT


title: Paternal_DCHP rep4


title: 002_CD45_48

value: Melanoma


title: RBG25094_WT


title: 006_CD45_49


title: UC 14


title: Paternal_DCHP rep5


title: UC 13


title: Paternal_DCHP rep2


title: NN 1


title: 002_CD45_81


title: RBG25089_WT


title: Paternal_DCHP rep1


title: human CD8 T cells, BATF3, day10 [BATF3-D4]

city: Durham

first: Sean

last: McCutcheon

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

data_processing:
Consistent quality validation using FastQC v0.11.2 (Babraham Institute).
Raw reads were trimmed to remove adapters and bases with average quality score (Q; Phred33) of 20 using a 4-bp sliding window (SlidingWindow:4:20) with Trimmomatic v0.32 (Bolger et al., 2014).
Trimmed reads were aligned to the primary assembly of the GRCh38 human reference genome using STAR v2.4.1a removing alignments containing noncanonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical).
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using featureCounts (v1.4.6-p4) with default settings.
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (single table) including TPM values and ENSEMBL IDs for all samples and genes in Gencode v22

source_name: CD8 T cells

growth_protocol: CD8 T cells were cultured in PRIME-XV T cell expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed), 100 units/mL of penicilllin, 100 units/mL of streptomycin, and 100 units/mL human IL-2 (Peprotech).

extract_protocol:
RNA was harvested using Norgen's Total RNA Purification Kit.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences.

treatment_protocol:
Cells were activated with 3:1 ratio of CD3/CD28 dynabeads to cells. 24 hours post-activation, cells were transduced with lentivirus encoding for either BATF3 or GFP.
T cells were maintained at a concentration of 1-2e6 per mL for 10 days before RNA-sequencing.

value: CD8 T cells

value: CD3/CD28 dynabead activation

value: day 10


title: human CD8 T cells, GFP control, day10 [GFP-D4]

value: GFP


title: human CD8 T cells, BATF3, day10 [BATF3-D5]


title: UC 12


title: HEL Ita 48h - 2

city: St. Louis

first: Tim

last: Kong

state: MO

address: CSRB 8838

institute: Washington University School of Medicine

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.
TMM normalization size factors in EdgeR were calculated to adjust for samples for differences in library size.
Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.
Assembly: GrCh38
Supplementary files format and content: TSV of raw counts.

source_name: HEL

extract_protocol:
Total RNA from cell lines was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: HEL

value: Itacitinib


title: Paternal_control rep 6

value: Paternal control


title: RBG25091_DKO

value: Bone marrow

value: Aldh2 & Fancd2 double knock-outs


title: Paternal_control rep 4

value: WT


title: human CD8 T cells, GFP control, day10 [GFP-D5]


title: NN 3

value: not applicable


title: RBG25087_WT


title: UC 10


title: Paternal_control rep 5

value: Liver

value: male


title: HEL Pac 48h - 2

value: Pacritinib


title: RBG25090_WT


title: UC 9


title: RBG25084_WT


title: HEL Mmb 48h - 1

value: Momelotinib


title: Paternal_control rep 1

value: 4 weeks


title: UC 7

value: mucosal biopsy


title: week16_lib2, mRNA-derived cDNA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Read mapping: cDNA reads were aligned to ‘mm10’ genome using Ensembl 102 gene models with the STARsolo tool (v2.7.9a). ADT libraries were also processed using the STARsolo tool
Quality filtering: Cells were considered as high-quality cells if they had at least 2000 UMI counts, which is the threshold derived from the distribution of UMI counts across cells, forming a data set of 9953 cells.
Normalization and clustering: Multiple Bioconductor (v3.14) packages including DropletUtils (v1.14.2), scDblFinder (v1.8.0), scran (v1.22.1), scater (v1.22.0), scuttle (1.4.0) and batchelor (v1.10.0) were applied for the further analysis of the data set mostly following the steps of the workflow presented at https://bioconductor.org/books/release/OSCA/. Raw counts were normalized by deconvolution (Lun, Bach, and Marioni 2016). The function ‘computeDoubletDensity’ pointed at 66 potential doublets, which were removed from the further analysis. The normalized gene expression of remaining cells was used to construct a shared nearest-neighbour (SNN) graph (k=10) (Xu and Su 2015), which nodes, i.e. cells, were clustered by ‘cluster_louvain’ method from the R igraph package (Blondel et al. 2008). Counts reflecting the ADT abundance in cells were also log-normalized and clustered in a similar manner.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including counts of cDNA reads per cell and per gene (cDNA_counts.tsv.gz), counts of reads per cell and ADT (ADT_counts.txt.gz) and ADT sequences (ADT_sequences.txt.gz).
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Thymus

extract_protocol:
Isolated thymi were cleaned from adipose tissue, separated into the two lobes, and subsequently subjected to three rounds of enzymatic digestion with Liberase (2.5 mg/ml, Roche) and DNaseI (10 mg/ml, Roche) diluted in PBS (Sigma) at 37°C. After filtration through a 100 μm cell strainer and resuspension in FACS buffer (PBS supplemented with 2% FBS (Sigma)), cell number was determined using a CASY cell counter (Innovatis).
cDNA library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics).
For ADT library the following i7 primer 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ (Illumina) was used, N-sequence stands for the sample index.
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for CITE-seq library amplification.
Sequencing was performed on one lane of Illumina NovaSeq 6000 instrument with a mix of 90% cDNA library and 10% ADT library resulting in 151nt-long paired-end reads.

value: Thymus

value: Thymic epithelial cells

tag: library type

value: mRNA

tag: antibodies/tags


title: UC 11


title: HEL Ita 48h - 1


title: RBG25082_WT


title: RBG25088_WT


title: HEL Fed 48h - 1

value: Fedratinib


title: Paternal_control rep 3


title: Paternal_control rep 2


title: RBG25081_DKO


title: HEL Mmb 48h - 2

value: HEL


title: RBG25086_WT


title: week1_lib2, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

value: ADT

value: Totalseq-A:anti-CD9, anti-CD40, anti-CD49a, anti-CD54, anti-CD63, anti-CD73, anti-CD83, anti-CD117, anti-CD146, anti-CD200, anti-CD274, anti-HVEM, anti-Ly6D, anti-Ly6C/Ly6G (Gr1), anti-MadCAM1, anti-Podoplanin, anti-CD80, anti-CD86, anti-MHCII, anti-Sca1, anti-CD31, anti-EpCAM1, anti-CD36, anti-CD133, anti-CD157, anti-CD300LG, UEA1-bio SAV-PE-Totalseq


title: RBG25080_DKO

value: Bone marrow


title: week16_lib2, ADT-derived cDNA


title: HEL Pac 48h - 1


title: week16_lib1, ADT-derived cDNA


title: HEL Fed 48h - 2


title: UC 3


title: UC 5


title: RBG25078_WT


title: RBG25077_WT


title: week1_lib1, mRNA-derived cDNA


title: HEL DMSO 48h - 1

value: DMSO


title: RR 19

value: Non-relapsed


title: RBG25075_WT

value: WT


title: RR 18


title: week16_lib1, mRNA-derived cDNA


title: UC 1

value: not applicable


title: UC 4


title: RBG25085_WT


title: HEL Rux 48h - 2

value: Ruxolitinib


title: HEL Rux 48h - 1


title: UC 8


title: H3.3_cleavable_HIR_KO_1_I_myc

data_processing:
Paired-end reads were aligned to the mm10 genome assembly downloaded from the UCSC browser https://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/latest using bowtie2 with default options.
Aligned files were then imported into R with readGAlignments function from GenomicAlignments package (Lawrence et al., 2013), requiring minimum mapping quality of 10.
bw fille was created using bamCoverage command from deepTools package with the following options: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --maxFragmentLength 300
Assembly: mm10
Supplementary files format and content: bw

tag: chip antibody

value: myc

value: mESC

tag: sensor type

value: cleavable H3.3

value: HIRA KO


title: RR 16

value: mucosal biopsy


title: UC 6


title: RBG25072_WT


title: RBG25083_WT


title: week1_lib2, mRNA-derived cDNA

value: Thymus

value: Thymic epithelial cells


title: RBG25073_WT


title: HEL DMSO 48h - 2


title: UC 2


title: week1_lib1, ADT-derived cDNA


title: RBG25076_WT


title: HEL Ita 4h - 2

value: Itacitinib


title: HEL Mmb 4h - 2

value: HEL

value: Momelotinib


title: RBG25071_WT


title: H3.3_cleavable_HIR_KO_2_I_myc


title: RR 14


title: H3.3_cleavable_II_myc


title: HEL Mmb 4h - 1


title: H3.3_cleavable_HIR_KO_2_I_HA

value: HA


title: HEL Ita 4h - 1


title: HEL Pac 4h - 2

value: Pacritinib


title: RBG25074_WT

value: Bone marrow


title: RR 17

value: Non-relapsed


title: H3.3_cleavable_I_myc

value: WT


title: H3.3_cleavable_HIR_KO_1_I_HA


title: RBG25069_DKO

value: Aldh2 & Fancd2 double knock-outs


title: HEL Rux 4h - 2

value: Ruxolitinib


title: H3.3_cleavable_I_HA


title: RR 11


title: RR 15


title: RR 13


title: HEL Rux 4h - 1


title: HEL Fed 4h - 2

value: Fedratinib


title: H3.3_cleavable_II_HA

value: mESC


title: RBG25070_WT


title: HEL Fed 4h - 1


title: HEL Pac 4h - 1


title: H3.3_NC_I_myc

value: myc

value: non-cleavable H3.3


title: H3.1_cleavable_HIR_KO_2_II_myc

value: cleavable H3.1

value: HIRA KO


title: RBG25068_DKO


title: RR 10

value: mucosal biopsy


title: RBG25067_DKO


title: H3.3_NC_I_HA


title: H3.1_cleavable_HIR_KO_2_II_HA


title: RBG25065_WT


title: RBG25063_WT


title: HEL DMSO 4h - 1

value: DMSO


title: HEL DMSO 4h - 2

value: HEL


title: RBG25064_WT


title: RR 8

value: Relapsed


title: 205 – PN7

city: Vienna

first: Natalia

last: Alkon

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 6.1.2; 10x Genomics).
Assembly: GRCh38
Supplementary files format and content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Single cell suspensions from full thickness skin punch biopsies were generated using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
These cells were immediately processed for scRNA-seq by using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kit v1.1 (10X Genomics, Pleasanton, CA), following the manufacturer’s suggestions. T-cell receptor (TCR) sequences were enriched from cDNA using the respective reagents, and according to the instructions of the VDJ Kit workflow by 10X Genomics. Sequencing was performed using the Illumina NovaSeq platform and the 150bp paired-end configuration.

value: Skin Biopsy

tag: serum ige (kiu/l)

tag: diagnosis

value: Prurigo Nodularis