title: P3_361

value: keratinocyte


title: P3_352

status: Public on Feb 06 2026

type: SRA

city: Bethesda

first: Lingling

last: Miao

state: MD

address: 9000 Rockville Pike

department: NIAMS

country: USA

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
Sequencing reads were demultiplexed using Bcl2fastq. Adaptors were trimmed and 125bp sequencing reads were trimmed to 100bp using Trimmomatic. Reads were aligned to mouse reference genome Ensembl GRCm38.p6 using STAR 2.5.2b. Expression values for individual genes and transcripts were estimated and quantified with RSEM 1.3.0. Expression values of TPM (transcripts per million) were used for further analysis. 1057 cells passed quality control and were included in this study.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files at gene and transcript expression levels

molecule: total RNA

organism: Mus musculus

source_name: skin

extract_protocol:
Neonatal or postnatal epidermal cells and embryonic skin cells were disscociated from Sox2-GFP or Gfi1-GFP reporter mice. Cells were stained with DAPI for viability prior to cell sorting. Single GFP+ live cells were sorted into a 96 well plate preloaded with lysis buffer using Beckman MoFlo Astrios or BD Influx Cell Sorter. Lysis buffer was prepared following Smart-seq2 protocol (Picelli et al., 2014). Single GFP- live cells were sorted from the neonatal epidermal cells as controls.
Single-cell cDNA libraries were prepared following Smart-seq2 protocol (Picelli et al., 2014) with minor modifications. Briefly, single-cell RNA transcripts were reverse-transcribed using SuperScript II Reverse Transcriptase, following by pre-amplification of 21 cycles. cDNA concentration and quality were assessed using PicoGreen dsDNA Assay kit and Agilent bioanalyzer analysis with High sensitivity DNA kit, respectively. Single-cell cDNA libraries with high quality were selected for further processing. The cDNA was diluted and the concentration was normalized. 1152 single-cell cDNA libraries were generated using Illumina Nextera XT library preparation kit and were indexed using Illumina Nextera XT index kit v2.
cDNA libraries for each of the 384 cells was pooled together for sequencing in a way that each pooled library contained cells sourced from all different time points and both reporter mice. A total of three pooled cDNA libraries were prepared. Each pooled library was pair-end sequenced on 4 lanes of Hiseq3000 with 125bp or 100bp read length.

tag: cell type

value: dermal papilla cell

tag: tissue

value: skin

tag: strain

tag: age


title: P3_351


title: P3_347

value: hematopoietic cell


title: P3_345


title: P3_344

value: Merkel cell


title: P3_348


title: P3_346


title: P3_343


title: P3_341


title: P3_339


title: P3_335


title: P3_337


title: P3_338


title: P3_334


title: P3_332


title: P3_342


title: P3_330


title: P3_328


title: P3_326


title: P3_324


title: P3_325


title: P3_329


title: P3_340


title: P3_321


title: P3_319


title: P3_318


title: P3_323


title: P3_320


title: P3_327


title: P3_317


title: P3_331


title: P3_315


title: P3_313


title: P3_322


title: P3_312


title: P3_314


title: P3_333


title: P3_309


title: P3_308


title: P3_316


title: P3_310


title: P3_307


title: P3_306


title: P3_305


title: P3_299


title: P3_301


title: P3_298


title: P3_311


title: P3_303


title: P3_304


title: P3_291


title: P3_296


title: P3_297


title: P3_295


title: P3_292


title: P3_293


title: P3_289


title: P3_287


title: P3_302


title: P3_285


title: P3_284


title: P3_283


title: P3_278


title: P3_282


title: P3_280


title: P3_286


title: P3_274


title: P3_290


title: P3_294


title: P3_273


title: P3_272


title: P3_270


title: P3_269


title: P3_275


title: P3_267


title: P3_271


title: P3_266


title: P3_265


title: P3_263


title: P3_260


title: P3_262


title: P3_259


title: P3_256


title: P3_258


title: P3_261


title: P3_255


title: P3_268


title: P3_248


title: P3_250


title: P3_245


title: P3_253


title: P3_249


title: P3_254


title: P3_247


title: P3_246


title: P3_243


title: P3_242


title: P3_241


title: P3_237


title: P3_244


title: P3_239


title: P3_236


title: P3_235


title: P3_231


title: P3_230


title: P3_229


title: P3_234


title: P3_225


title: P3_226


title: P3_227


title: P3_222


title: P3_223


title: P3_224


title: P3_216


title: P3_218


title: P3_219


title: P3_217


title: P3_221


title: P3_232


title: P3_233


title: P3_211


title: P3_205


title: P3_220


title: P3_212


title: P3_209


title: P3_214


title: P3_204


title: P3_206


title: P3_215


title: P3_202


title: P3_199


title: P3_203


title: P3_200


title: P3_207


title: P3_208


title: P3_194


title: P3_195


title: P3_197


title: P3_196


title: P3_198


title: P3_201


title: P3_193


title: P3_190


title: P3_191


title: P3_192


title: P3_189


title: P3_188


title: P3_183


title: P3_181


title: P3_184


title: P3_187


title: P3_186


title: P3_175


title: P3_177


title: P3_176


title: P3_174


title: P3_180


title: P3_178


title: P3_182


title: P3_185


title: P3_172


title: P3_171


title: P3_210


title: P3_167


title: P3_173


title: P3_169


title: P3_166


title: P3_168


title: P3_164


title: P3_159


title: P3_160


title: P3_158


title: P3_170


title: P3_157


title: P3_156


title: P3_165


title: P3_161


title: P3_163


title: P3_151


title: P3_154


title: P3_162


title: P3_150


title: P3_155


title: P3_147


title: P3_148


title: P3_153


title: P3_149


title: P3_145


title: P3_152


title: P3_146


title: P3_141


title: P3_144


title: P3_137


title: P3_136


title: P3_139


title: P3_142


title: P3_140


title: P3_143


title: P3_138


title: P3_134


title: P3_132


title: P3_131


title: P3_130


title: P3_128


title: P3_127


title: P3_129


title: P3_135


title: P3_126


title: P3_123


title: P3_118


title: P3_124


title: P3_117


title: P3_120


title: P3_119


title: P3_116


title: P3_125


title: P3_133


title: P3_121


title: P3_113


title: P3_114


title: P3_112


title: P3_115


title: P3_111


title: P3_110


title: P3_108


title: P3_109


title: P3_107


title: P3_106


title: P3_103


title: P3_104


title: P3_102


title: P3_98


title: P3_101


title: P3_99


title: P3_95


title: P3_92


title: P3_94


title: P3_97


title: P3_105


title: P3_88


title: P3_85


title: P3_91


title: P3_90


title: P3_80


title: P3_89


title: P3_78


title: P3_82


title: P3_75


title: P3_79


title: P3_73


title: P3_77


title: P3_74


title: P3_100


title: P3_76


title: P3_71


title: P3_67


title: P3_68


title: P3_66


title: P3_64


title: P3_96


title: P3_65


title: P3_62


title: P3_59


title: P3_56


title: P3_70


title: P3_61


title: P3_57


title: P3_54


title: P3_53


title: P3_50


title: P3_52


title: P3_63


title: P3_45


title: P3_48


title: P3_49


title: P3_47


title: P3_51


title: P3_38


title: P3_42


title: P3_55


title: P3_35


title: P3_41


title: P3_44


title: P3_37


title: P3_43


title: P3_36


title: P3_34


title: P3_27


title: P3_33


title: P3_31


title: P3_30


title: P3_21


title: P3_23


title: P3_29


title: P3_25


title: P3_32


title: P3_26


title: P3_28


title: P3_9


title: P3_8


title: P3_19


title: P3_24


title: P3_12


title: P3_7


title: P3_15


title: P3_14


title: P3_17


title: P3_3


title: P3_18


title: P3_5


title: P3_11


title: P3_2


title: P3_13


title: P3_1


title: P3_4


title: P3_16


title: P2_382


title: P3_20


title: P3_6


title: P2_379


title: P2_376


title: P2_381


title: P2_377


title: P2_378


title: P2_374


title: P2_375


title: P2_372


title: P2_368


title: P2_373


title: P2_370


title: P2_367


title: P2_371


title: P2_365


title: P2_384


title: P2_369


title: P2_380


title: P2_364


title: P2_383


title: P2_361


title: P2_358


title: P2_360


title: P2_357


title: P2_354


title: P2_355


title: P2_353


title: P2_366


title: P2_363


title: P2_352


title: P2_362


title: P2_351


title: P2_350


title: P2_346


title: P2_347


title: P2_359


title: P2_348


title: P2_344


title: P2_342


title: P2_343


title: P2_356


title: P2_341


title: P2_339


title: P2_338


title: P2_340


title: P2_349


title: P2_332


title: P2_337


title: P2_333


title: P2_335


title: P2_336


title: P2_334


title: P2_330


title: P2_331


title: P2_345


title: P2_328


title: P2_325


title: P2_322


title: P2_329


title: P2_316


title: P2_323


title: P2_324


title: P2_320


title: P2_319


title: P2_315


title: P2_318


title: P2_326


title: P2_313


title: P2_312


title: P2_311


title: P2_317


title: P2_327


title: P2_309


title: P2_321


title: P2_308


title: P2_307


title: P2_305


title: P2_306


title: P2_304


title: P2_303


title: P2_302


title: P2_310


title: P2_301


title: P2_300


title: P2_299


title: P2_298


title: P2_296


title: P2_297


title: P2_294


title: P2_291


title: P2_293


title: P2_290


title: P2_295


title: P2_286


title: P2_289


title: P2_292


title: P2_288


title: P2_284


title: P2_281


title: P2_282


title: P2_279


title: P2_280


title: P2_278


title: P2_274


title: P2_272


title: P2_277


title: P2_276


title: P2_285


title: P2_283


title: P2_268


title: P2_267


title: P2_263


title: P2_275


title: P2_271


title: P2_262


title: P2_260


title: P2_261


title: P2_257


title: P2_264


title: P2_258


title: P2_270


title: P2_269


title: P2_251


title: P2_252


title: P2_256


title: P2_248


title: P2_259


title: P2_250


title: P2_246


title: P2_242


title: P2_244


title: P2_243


title: P2_249


title: P2_239


title: P2_237


title: P2_245


title: P2_238


title: P2_240


title: RWs17, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, ATAC

city: Atlanta

first: Felipe

last: ten Caten

state: Georgia

address: 1750 Haygood Road

department: Department of Pathology and Laboratory Medicine

institute: Emory University

description:
s13_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi

library_source: other

data_processing:
Barcode processing, gene counting and peak calling were made using Cell Ranger ARC Count v2.0.2 (gexExcludeIntrons: true, noBam: false, skipCompatibilityCheck: false)
Aggregation of multiple samples was performed with Cell Ranger ARC Aggr v2.0.2 (noSecondaryAnalysis: false, normalizationModeArc: none)
Assembly: Mmul_10 109
Supplementary files format and content: CellRanger aggr output files: aggr.csv, filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, atac_fragments.tsv.gz.tbi

molecule: other

organism: Macaca mulatta

source_name: lymph node

extract_protocol:
Lymph node mononuclear cells (LNMCs) nuclei were isolated according to the manufacturer’s instructions using Chromium Nuclei Isolation Kit (10x Genomics, Pleasanton, CA).
Single-cell Multiome ATAC and Gene Expression (GEX) libraries were prepared using the Chromium Single Cell Multiome ATAC + Gene Expression platform (10X Genomics). 8000 nuclei were used in each sample. Isolated nuclei were transposed and partitioned into Gel Beads-in-emulsion (GEMs) using the 10x Chromium Controller and Next GEM Chip J. ATAC and GEX libraries were generated from the same pool of pre-amplified transposed DNA/cDNA. Representative traces and quantitation of both libraries were determined using Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA).

value: lymph node

tag: Sex

value: male

tag: time

tag: group

value: CA-vDNAlo

tag: treatment

tag: library type

value: ATAC


title: P2_236


title: P2_234


title: P2_235


title: RBv17, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, ATAC

description:
s12_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi


title: P2_231


title: P2_225


title: P2_247


title: RBf17, LN, wk0postATI, aIL10_aPD1, CA-vDNAhi, ATAC

description:
s11_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi

value: CA-vDNAhi


title: P2_233


title: P2_228


title: P2_224


title: P2_230


title: RYm17, LN, wk0postATI, aIL10_aPD1, CA-vDNAhi, ATAC

description:
s8_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi


title: P2_232


title: RNy16, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, ATAC

description:
s9_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi


title: RWs17, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, GEX

description:
s13_mRNA
filtered_feature_bc_matrix.h5

molecule: nuclear RNA

value: mRNA


title: P2_223


title: P2_226


title: RRh17, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, ATAC

description:
s10_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi


title: P2_222


title: RBv17, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, GEX

description:
s12_mRNA
filtered_feature_bc_matrix.h5


title: P2_221


title: RRh17, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, GEX

description:
s10_mRNA
filtered_feature_bc_matrix.h5


title: P2_219


title: P2_217


title: RNy16, LN, wk0postATI, aIL10_aPD1, CA-vDNAlo, GEX

description:
s9_mRNA
filtered_feature_bc_matrix.h5


title: RBf17, LN, wk0postATI, aIL10_aPD1, CA-vDNAhi, GEX

description:
s11_mRNA
filtered_feature_bc_matrix.h5


title: RFl17, LN, wk0postATI, aIL10_aPD1, CA-vDNAhi, ATAC

description:
s7_atac
atac_fragments.tsv.gz
atac_fragments.tsv.gz.tbi


title: P2_218


title: RYm17, LN, wk0postATI, aIL10_aPD1, CA-vDNAhi, GEX

description:
s8_mRNA
filtered_feature_bc_matrix.h5


title: RFl17, LN, wk0postATI, aIL10_aPD1, CA-vDNAhi, GEX

description:
s7_mRNA
filtered_feature_bc_matrix.h5


title: RVi17, PBMC, Control, wk24postATI

library_source: transcriptomic

data_processing:
Reads were aligned to the reference using STAR v2.7.3 and read counts per gene were calculated internal to the STAR aligner.
Assembly: Mmul10 Ensembl release 100
Supplementary files format and content: tab-delimited text file inlcudes raw counts for each sample

source_name: peripheral blood mononuclear cell

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (QIAGEN, Hilden, Germany) with on-column DNase digestion.
mRNA purification was performed using magnetic beads with Oligo (dT). The mRNA was then mixed with a fragmentation buffer to generate short fragments. cDNA was synthesized using these mRNA fragments as templates. The short fragments were purified and resolved with EB buffer for end repair and single nucleotide A (adenine) addition. Adapters were ligated to the short fragments and suitable fragments were amplified via PCR. After quantification and qualification the sample libraries were pooled at equimolar concentrations and sequenced.

value: peripheral blood mononuclear cell

value: Control


title: P2_213


title: REq17, PBMC, Control, wk24postATI


title: P2_212


title: P2_214


title: P2_210


title: RZg17, PBMC, Control, wk24postATI


title: REu17, PBMC, Control, wk24postATI

value: female


title: RMl17, PBMC, Control, wk24postATI


title: P2_215


title: P2_216


title: P2_209


title: RTd17, PBMC, Control, wk24postATI


title: RVz16, PBMC, Control, wk24postATI


title: P2_207


title: P2_211


title: RWs17, PBMC, aIL10_aPD1, wk24postATI


title: P2_208


title: P2_204


title: RBe17, PBMC, Control, wk24postATI


title: RBv17, PBMC, aIL10_aPD1, wk24postATI


title: P2_205


title: P2_202


title: P2_203


title: P2_206


title: P2_201


title: P2_199


title: 34918, PBMC, aIL10_aPD1, wk24postATI


title: RIb17, PBMC, aIL10_aPD1, wk24postATI


title: P2_198


title: P2_200


title: RKq17, PBMC, aIL10_aPD1, wk24postATI


title: RBf17, PBMC, aIL10_aPD1, wk24postATI


title: RRh17, PBMC, aIL10_aPD1, wk24postATI


title: P2_197


title: RFl17, PBMC, aIL10_aPD1, wk24postATI


title: RNy16, PBMC, aIL10_aPD1, wk24postATI


title: P2_196


title: RZp17, PBMC, aIL10, wk24postATI


title: 34930, PBMC, aIL10, wk24postATI


title: P2_194


title: P2_193


title: 34920, PBMC, aIL10, wk24postATI


title: P2_195


title: P2_192


title: RVc17, PBMC, aIL10, wk24postATI


title: RYm17, PBMC, aIL10_aPD1, wk24postATI


title: RFn17, PBMC, aIL10, wk24postATI


title: P2_191


title: 34897, PBMC, aIL10, wk24postATI


title: P2_189


title: RVm17, PBMC, aIL10, wk24postATI


title: P2_190


title: P2_188


title: P2_186


title: RHm17, PBMC, aIL10, wk24postATI


title: REq17, PBMC, Control, wk0postATI


title: P2_187


title: RVi17, PBMC, Control, wk0postATI


title: RZg17, PBMC, Control, wk0postATI


title: RMl17, PBMC, Control, wk0postATI


title: P2_181


title: RYk17, PBMC, aIL10, wk24postATI


title: P2_183


title: REu17, PBMC, Control, wk0postATI


title: P2_182


title: P2_185


title: RBe17, PBMC, Control, wk0postATI


title: P2_179


title: P2_180


title: P2_178


title: RVz16, PBMC, Control, wk0postATI


title: RWs17, PBMC, aIL10_aPD1, wk0postATI


title: RTd17, PBMC, Control, wk0postATI


title: RKq17, PBMC, aIL10_aPD1, wk0postATI


title: P2_177


title: RBf17, PBMC, aIL10_aPD1, wk0postATI


title: RIb17, PBMC, aIL10_aPD1, wk0postATI


title: P2_173


title: RRh17, PBMC, aIL10_aPD1, wk0postATI


title: P2_176


title: 34918, PBMC, aIL10_aPD1, wk0postATI


title: P2_175


title: RYm17, PBMC, aIL10_aPD1, wk0postATI


title: P2_167


title: P2_169


title: P2_171


title: RZp17, PBMC, aIL10, wk0postATI


title: P2_172


title: RGr17, PBMC, aIL10, wk0postATI


title: RFl17, PBMC, aIL10_aPD1, wk0postATI


title: P2_168


title: RNy16, PBMC, aIL10_aPD1, wk0postATI


title: P2_166


title: RBv17, PBMC, aIL10_aPD1, wk0postATI


title: 34920, PBMC, aIL10, wk0postATI


title: P2_162


title: P2_163


title: 34930, PBMC, aIL10, wk0postATI


title: P2_160


title: RVm17, PBMC, aIL10, wk0postATI


title: P2_161


title: RVc17, PBMC, aIL10, wk0postATI


title: P2_165


title: RFn17, PBMC, aIL10, wk0postATI


title: P2_174


title: P2_159


title: P2_158


title: RHm17, PBMC, aIL10, wk0postATI


title: P2_156


title: 34897, PBMC, aIL10, wk0postATI


title: P2_157


title: P2_154


title: P2_152


title: P2_155


title: REu17, LN, Control, wk24postATI


title: REq17, LN, Control, wk24postATI


title: P2_151


title: RYk17, PBMC, aIL10, wk0postATI


title: P2_149


title: RMl17, LN, Control, wk24postATI


title: P2_148


title: P2_150


title: RBe17, LN, Control, wk24postATI


title: P2_144


title: RVz16, LN, Control, wk24postATI


title: RWs17, LN, aIL10_aPD1, wk24postATI


title: RKq17, LN, aIL10_aPD1, wk24postATI


title: RVi17, LN, Control, wk24postATI


title: RZg17, LN, Control, wk24postATI


title: P2_147


title: P2_146


title: 34918, LN, aIL10_aPD1, wk24postATI


title: RBf17, LN, aIL10_aPD1, wk24postATI


title: RIb17, LN, aIL10_aPD1, wk24postATI


title: P2_140


title: P2_142


title: RBv17, LN, aIL10_aPD1, wk24postATI


title: P2_143


title: RTd17, LN, Control, wk24postATI


title: RRh17, LN, aIL10_aPD1, wk24postATI


title: RYm17, LN, aIL10_aPD1, wk24postATI


title: RNy16, LN, aIL10_aPD1, wk24postATI


title: P2_137


title: P2_141


title: RFl17, LN, aIL10_aPD1, wk24postATI


title: P2_135


title: RZp17, LN, aIL10, wk24postATI


title: P2_133


title: P2_134


title: P2_132


title: RVc17, LN, aIL10, wk24postATI


title: P2_139


title: P2_138


title: RVm17, LN, aIL10, wk24postATI


title: 34920, LN, aIL10, wk24postATI


title: P2_131


title: RFn17, LN, aIL10, wk24postATI


title: P2_130


title: P2_128


title: 34930, LN, aIL10, wk24postATI


title: 34897, LN, aIL10, wk24postATI


title: P2_127


title: P2_129


title: P2_126


title: RYk17, LN, aIL10, wk24postATI


title: RHm17, LN, aIL10, wk24postATI


title: REq17, LN, Control, wk0postATI


title: RVi17, LN, Control, wk0postATI


title: P2_124


title: P2_119


title: RBe17, LN, Control, wk0postATI


title: P2_118


title: P2_121


title: P2_117


title: P2_125


title: P2_120


title: RTd17, LN, Control, wk0postATI


title: RVz16, LN, Control, wk0postATI


title: P2_116


title: P2_115


title: P2_114


title: RWs17, LN, aIL10_aPD1, wk0postATI


title: RMl17, LN, Control, wk0postATI


title: REu17, LN, Control, wk0postATI


title: RZg17, LN, Control, wk0postATI


title: 34918, LN, aIL10_aPD1, wk0postATI


title: RBf17, LN, aIL10_aPD1, wk0postATI


title: P2_112


title: P2_111


title: RBv17, LN, aIL10_aPD1, wk0postATI


title: P2_113


title: RKq17, LN, aIL10_aPD1, wk0postATI


title: RRh17, LN, aIL10_aPD1, wk0postATI


title: RNy16, LN, aIL10_aPD1, wk0postATI


title: P2_108


title: P2_109


title: RYm17, LN, aIL10_aPD1, wk0postATI


title: P2_107


title: RIb17, LN, aIL10_aPD1, wk0postATI


title: RFl17, LN, aIL10_aPD1, wk0postATI


title: P2_105


title: P2_102


title: P2_110


title: P2_104


title: P2_103


title: 34920, LN, aIL10, wk0postATI


title: P2_100


title: P2_101


title: RFn17, LN, aIL10, wk0postATI


title: RVm17, LN, aIL10, wk0postATI


title: RVc17, LN, aIL10, wk0postATI


title: P2_97


title: RZp17, LN, aIL10, wk0postATI


title: 34897, LN, aIL10, wk0postATI


title: P2_98


title: P2_99


title: P2_96


title: RHm17, LN, aIL10, wk0postATI


title: RYk17, LN, aIL10, wk0postATI


title: 34930, LN, aIL10, wk0postATI


title: P2_93


title: P2_94


title: P2_92


title: P2_91


title: RGr17, LN, aIL10, wk0postATI


title: P2_90


title: RAW264.7, LPS+Anti-CD36, rep1

city: Beijing

first: Weixuan

last: Wang

address: No. 38 Xueyuan Road, Haidian District

country: China

institute: Peking University

description:
Library name: LPS AntiCD36 1
14x Genomics

data_processing:
Illumina Casava2.19 software used for basecalling.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm39
Supplementary files format and content: FPKM

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen) and reverse transcribed into cDNA with GoScriptTM Reverse Transcription System (Promega). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

tag: cell line

tag: genotype

value: WT

value: LPS 50ng/ml, Anti-CD36 dilution 1:100


title: RAW264.7, LPS, rep3

description:
Library name: LPS 3
13x Genomics

value: LPS 50ng/ml


title: RAW264.7, LPS+Anti-CD36, rep2

description:
Library name: LPS AntiCD36 2
15x Genomics


title: RAW264.7, LPS, rep2

description:
Library name: LPS 2
12x Genomics


title: RAW264.7, LPS+Anti-CD36, rep3

description:
Library name: LPS AntiCD36 3
16x Genomics


title: P2_89

value: keratinocyte


title: P2_88


title: RAW264.7, LPS, rep1

description:
Library name: LPS 1
11x Genomics


title: P2_87


title: RAW264.7, Anti-CD36, rep2

description:
Library name: AntiCD36 2
10x Genomics

value: Anti-CD36 dilution 1:100


title: P2_85

value: skin


title: RAW264.7, untreat, rep2

description:
Library name: UT 2
10x Genomics

value: UT


title: P2_84


title: RAW264.7, Anti-CD36, rep1

description:
Library name: AntiCD36 1
10x Genomics


title: RAW264.7, untreat, rep1

description:
Library name: UT 1
10x Genomics


title: RAW264.7, Anti-CD36, rep3

description:
Library name: AntiCD36 3
10x Genomics


title: P2_86

value: Merkel cell


title: P2_81


title: RAW264.7, untreat, rep3

description:
Library name: UT 3
10x Genomics


title: P2_79


title: CUT&RUNseq - Mouse Cardiac tissue  68-weeks of age input

city: London

first: Joseph

last: Burgoyne

state: Please select...

address: The Rayne Institute, St Thomas' Hospital

country: United Kingdom

institute: King's College London

description:
Library name: CR11
Used to compile Old_CL.csv
Old_CL.csv

library_source: genomic

data_processing:
RNAseq: sequencing reads were trimmed with Trimmomatic v.0.36 to remove possible adapter sequences and low-quality nucleotides. The trimmed reads were then aligned to the mouse genome (mm10) using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Differential gene expression was performed with DESeq2.
CUT&RUN: Raw sequencing reads were trimmed with TrimGalore (ver. 0.6.5) to remove adapters and low-quality reads. Trimmed fastq files were aligned to the mouse genome (GRmC39) using bowtie2 (ver. 2.4.2). Aligned bam files were sorted and indexed with samtools (ver. 1.14), and PCR duplicates were assessed using Picard tools (ver. 2.26.2). Peaks were called using MACS3 (ver. 3.0.0b1)
Assembly: Mouse mm10
Supplementary files format and content: RNAseq: text file with raw counts for each sample
Supplementary files format and content: CUT&RUN: csv file with peaks identified for each experimental group
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Heart

growth_protocol: C57BL/6 male mice maintained on standard chow diet

extract_protocol:
RNAseq: Total RNA was extracted from about 10 mg pulverised young and aged mouse cardiac tissue using a RNeasy mini kit. CUT&RUN: CUT&RUN was done using the CUT&RUN assay kit from Cell Signaling Technology (cat. #86652). 5 mg of powdered heart tissue from young and aged mice was used for each antibody reaction. The tissue was fixed in 0.1% formaldehyde methanol-free.
RNAseq libraries prepared by Genewiz. CUT&RUN: libraries generated using  the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, cat. #E7645) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, cat. #7335).

value: Heart

value: Male


title: CUT&RUNseq - Mouse Cardiac tissue  12-weeks of age input

description:
Library name: CR12
Used to compile Young_CL.csv
Young_CL.csv


title: P2_80


title: P2_77


title: CUT&RUNseq - Mouse Cardiac tissue  12-weeks of age 2

description:
Library name: CR9
Used to compile Young_CL.csv
Young_CL.csv


title: P2_82


title: CUT&RUNseq - Mouse Cardiac tissue  12-weeks of age 1

description:
Library name: CR8
Used to compile Young_CL.csv
Young_CL.csv


title: CUT&RUNseq - Mouse Cardiac tissue  68-weeks of age 2

description:
Library name: CR10
Used to compile Old_CL.csv
Old_CL.csv


title: P2_73


title: RNAseq - Mouse Cardiac tissue  68-weeks of age 4

description:
Library name: CLO12
Column name in raw_counts.csv: CLO12
raw_counts.csv

data_processing:
RNAseq: sequencing reads were trimmed with Trimmomatic v.0.36 to remove possible adapter sequences and low-quality nucleotides. The trimmed reads were then aligned to the mouse genome (mm10) using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2. Differential gene expression was performed with DESeq2.
CUT&RUN: Raw sequencing reads were trimmed with TrimGalore (ver. 0.6.5) to remove adapters and low-quality reads. Trimmed fastq files were aligned to the mouse genome (GRmC39) using bowtie2 (ver. 2.4.2). Aligned bam files were sorted and indexed with samtools (ver. 1.14), and PCR duplicates were assessed using Picard tools (ver. 2.26.2). Peaks were called using MACS3 (ver. 3.0.0b1)
Assembly: Mouse mm10
Supplementary files format and content: RNAseq: text file with raw counts for each sample
Supplementary files format and content: CUT&RUN: csv file with peaks identified for each experimental group


title: CUT&RUNseq - Mouse Cardiac tissue  68-weeks of age 1

description:
Library name: CR7
Used to compile Old_CL.csv
Old_CL.csv


title: P2_75


title: P2_76


title: P2_71


title: RNAseq - Mouse Cardiac tissue  68-weeks of age 2

description:
Library name: CLO10
Column name in raw_counts.csv: CLO10
raw_counts.csv


title: P2_68


title: P2_69


title: RNAseq - Mouse Cardiac tissue  68-weeks of age 3

description:
Library name: CLO11
Column name in raw_counts.csv: CLO11
raw_counts.csv


title: RNAseq - Mouse Cardiac tissue  68-weeks of age 1

description:
Library name: CLO9
Column name in raw_counts.csv: CLO9
raw_counts.csv


title: P2_66

value: hematopoietic cell


title: P2_67


title: RNAseq - Mouse Cardiac tissue  12-weeks of age 3

description:
Library name: CLY5
Column name in raw_counts.csv: CLY5
raw_counts.csv


title: RNAseq - Mouse Cardiac tissue  12-weeks of age 4

description:
Library name: CLY6
Column name in raw_counts.csv: CLY6
raw_counts.csv


title: P2_70


title: B16 cells, shAD4-2, Replicate 3

city: Changsha

first: Xiaolong

last: Tang

state: Select State

address: No. 106, Fubuhe Road, Yuelu district,

institute: Hunan University

description: Library name: SAMPLES 9

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

growth_protocol: B16 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
RNA-seq

value: B16 cells

value: Melanoma cells


title: RNAseq - Mouse Cardiac tissue  12-weeks of age 1

description:
Library name: CLY3
Column name in raw_counts.csv: CLY3
raw_counts.csv


title: RNAseq - Mouse Cardiac tissue  12-weeks of age 2

description:
Library name: CLY4
Column name in raw_counts.csv: CLY4
raw_counts.csv


title: P2_65


title: P2_63


title: P2_60


title: P2_61


title: P2_62


title: B16 cells, shAD4-1, Replicate 3

description: Library name: SAMPLES 6


title: P2_59


title: B16 cells, shAD4-1, Replicate 2

description: Library name: SAMPLES 5


title: B16 cells, shAD4-2, Replicate 2

description: Library name: SAMPLES 8


title: P2_58


title: B16 cells, shCotrol, Replicate 2

description: Library name: SAMPLES 2


title: B16 cells, shAD4-1, Replicate 1

description: Library name: SAMPLES 4


title: P2_54


title: B16 cells, shCotrol, Replicate 3

description: Library name: SAMPLES 3


title: P2_56


title: P2_51


title: VX, replicate 2, scRNAseq

city: Houston

first: Stephen

middle: Qi Rong

last: Wong

state: Texas

address: 6670 Bertner Ave

institute: Houston Methodist

description: Library name: Sample 8

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.1.0 including intons  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Femurs and tibia were dissected from tumor-bearing mice treated with either vehicle, GC Chemotherapy, GC Chemotherapy + Casp1i, or Casp1i for 2 cycles and kept on ice. Muscles were removed and bone marrow cells were collected by centrifugation at 13,000g for 15 seconds. Extracted bone marrow cells were treated with red blood cell removal buffer, for 5 min at room temperature. Lysis buffer was neutralized by the addition of 10X volumes of PBS and centrifuged at 300g at 4oC for 5 minutes. Centrifuged cells were resuspended in FACS buffer (0.5% BSA in PBS) and counted. Cells were then resuspended to a concentration of 10^7 cells/ml and hematopoietic progenitor cells were immuno-magnetically separated using the Hematopoietic Progenitor Isolation kit from Stem Cell Technologies following the manufacturer’s instructions (Cat# 19856). Isolated hematopoietic progenitor cells were then counted and resuspended in FACS buffer to a concentration of 1000 cells/μL. Samples were finally processed according to the 10x Genomics protocol for the 3’ v3.1 assay and were loaded to target 10,000 cell recovery.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, hematopoetic progenitor cells  were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone Marrow

value: FVB/NJ

value: 12-13 weeks old

value: VX


title: P2_46


title: P2_47


title: VXGC, replicate 2, scRNAseq

description: Library name: Sample 6

value: VXGC


title: VXGC, replicate 1, scRNAseq

description: Library name: Sample 5


title: P2_53


title: P2_44


title: P2_43


title: P2_49


title: B16 cells, shAD4-2, Replicate 1

description: Library name: SAMPLES 7


title: VX, replicate 1, scRNAseq

description: Library name: Sample 7


title: GC Ctx, replicate 2, scRNAseq

description: Library name: Sample 4

value: GC Ctx


title: Vehicle, replicate 2, scRNAseq

description: Library name: Sample 2

value: Vehicle


title: P2_42


title: P2_39


title: B16 cells, shCotrol, Replicate 1

description: Library name: SAMPLES 1


title: P2_45


title: KO, RS, 2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description:
Library name: sample11
KO_RS_2

data_processing:
Raw reads were trimmed to remove low-quality bases and adaptor sequences using Trim Galore v0.6.7. Reads were further mapped to the mouse (mm10) genomes using STAR v2.7.10a.
Uniquely mapped reads were applied for gene expression quantification using FeatureCounts v2.0.2.
The gene transcript abundance was further analyzed using the DESeq2 R package. An adjusted p-value of < 0.05, and fold change (FC) of APEXflox/+;Gdf9-Cre/WT > 2 were considered statistically significant to identify primordial follicle oocyte mRNAs.
Transcripts per million mapped reads (TPM) was calculated to validate gene expression and normalized to gene length and sequencing depth.
Assembly: mm10
Supplementary files format and content: countlist.xlsx includes raw counts for each sample

molecule: polyA RNA

source_name: sperm

extract_protocol:
The sperm collected by FACS was lysed and then RNA was enriched for sequencing.
RNAs were diluted to 0.2 ng/μL and 2.5 μL samples were performed library constructions. The samples were incubated with oligo(dT) primers (a deoxynucleoside triphosphate mixture) for 3 min at 72 °C, and cDNA pools were obtained by Smart-seq2 reverse transcription reactions. After the first-strand reaction, the cDNAs were pre-amplified with limited cycles (~ 12 cycles). Sequencing libraries were then constructed with 0.5 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503; Vazyme, Nanjing, China) according to the manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform in the 151 bp paired-end mode.

value: sperm


title: KO, RS, 3

description:
Library name: sample12
KO_RS_3


title: P2_38


title: P2_36


title: P2_37


title: WT, RS, 3

description:
Library name: sample9
WT_RS_3

value: wildtype


title: Vehicle, replicate 1, scRNAseq

description: Library name: Sample 1


title: WT, RS, 2

description:
Library name: sample8
WT_RS_2


title: KO, RS, 1

description:
Library name: sample10
KO_RS_1


title: P2_41

value: skin


title: GC Ctx, replicate 1, scRNAseq

description: Library name: Sample 3


title: P2_34


title: P2_35


title: WT, RS, 1

description:
Library name: sample7
WT_RS_1


title: P2_33


title: KO, MII, 3

description:
Library name: sample6
KO_MII_3


title: KO, MII, 1

description:
Library name: sample4
KO_MII_1


title: KO, MII, 2

description:
Library name: sample5
KO_MII_2


title: P2_32


title: WT, MII, 3

description:
Library name: sample3
WT_MII_3


title: WT, MII, 2

description:
Library name: sample2
WT_MII_2


title: P2_30

value: keratinocyte


title: P2_29

value: Merkel cell


title: P2_25


title: db/db_scATAC-seq_replicate 1

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

description: Library name: db/db

library_source: genomic single cell

data_processing:
The scATAC-seq data were preprocessed using the 10x Genomics pipeline (Cell Ranger ATAC v.1.2.0 using the mm10 genome and default parameters. Quality control measurements and filtering were conducted using ArchR (v.1.0.1). Briefly, we retained high-quality cells using the following filters: filterTSS=4, filterFrags=1000 and filtered doublets using filterDoublets in ArchR. scATAC-seq reads from all groups were combined at the single-cells level and then mapped to each 500-bp bin across the mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Processed data file per each sample: .h5 file (filtered_peak_bc_matrix).

source_name: Aorta

extract_protocol:
We pooled aortas from 8 mice into two replicates (4 mice per replicate) for each of the three groups. Aortas (4/group) were cut into ~1 mm pieces and placed into enzyme mixture containing Liberase DH (1Unit/aorta, 5401054001, Roche), Elastase (0.125 mg/aorta, E0127, Sigma) and DNase I (Kunitz unit/aorta, 79254, Qiagen) in M199 medium (10060CV, Corning). After incubating at 37°C for 45 minutes, cell suspensions were filtered through a 70-µm strainer and centrifuged at 500g for 5 min. The cell pellets were washed with Hank's balanced salt solution (HBSS) and FACS buffer (HBSS containing 2% FBS) and resuspended in 500 µL of FACS buffer and passed through 35-µm strainer. Cell viability was measured using the Acridine Orange/Propidium Iodide method (Cellometer, Nexcelom Biosciences).
Ten thousand nuclei were processed according to 10X Genomics’ standard protocol using Chromium Next GEM single cell ATAC reagent kits v1.1, Version CG000209 Rev F kit according to the manufacturer’s protocol.

treatment_protocol: We randomly divided db/db mice into two groups, and treated them daily with either saline (db/db) or DAPA (db/dbDAPA) by oral gavage (n=12 per group). Initially, for four weeks we dosed db/db mice with 1 mg/kg/day DAPA, which is equvalent to the clinicaly recommended starting dose (5 mg/day oral) to reduce hyperglycemia in T2D patients. In the subsequent two weeks of treatment (4-6 weeks), we increased DAPA dose to 3 mg/kg/day for db/db mice to achieve additional glycemic control.

value: Aorta

value: db/db

tag: batch


title: P2_27


title: P2_24


title: P2_26


title: db/dbDAPA_scRNA-seq_replicate 2

description: Library name: db/dbDAPA_R2

data_processing:
Fastq files from each single cell library were aligned to reference genome mm10 (mm10-2020A) individually using CellRanger software (Cellranger-6.1.1, 10X Genomics). The aligned data sets were analyzed using the R software package Seurat version 3.5. We filtered out the cells with high mitochondrial reads (<7.5%) and hemoglobin contents (<5%). Potential doublets (individually assessed by counts) were filtered out. Seurat VlnPlot and DimPlot functions were used to generate violin and dot plots.
Assembly: mm10
Supplementary files format and content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

extract_protocol:
We pooled aortas from 8 mice into two replicates (4 mice per replicate) for each of the three groups. Aortas (4/group) were cut into ~1 mm pieces and placed into enzyme mixture containing Liberase DH (1Unit/aorta, 5401054001, Roche), Elastase (0.125 mg/aorta, E0127, Sigma) and DNase I (Kunitz unit/aorta, 79254, Qiagen) in M199 medium (10060CV, Corning). After incubating at 37°C for 45 minutes, cell suspensions were filtered through a 70-µm strainer and centrifuged at 500g for 5 min. The cell pellets were washed with Hank's balanced salt solution (HBSS) and FACS buffer (HBSS containing 2% FBS) and resuspended in 500 µL of FACS buffer and passed through 35-µm strainer. Cell viability was measured using the Acridine Orange/Propidium Iodide method (Cellometer, Nexcelom Biosciences).
Around 10,000 single cells were used for library preparation using the Chromium Next GEM single cell 3’ reagent kits v3.1 (Dual index), Version CG000315 Rev B (10X Genomics) following the manufacturer’s protocol.

value: DAPA treatment for 6 weeks


title: db/+_scATAC-seq_replicate 1

description: Library name: db/+

value: db/+


title: db/dbDAPA_scRNA-seq_replicate 1

description: Library name: db/dbDAPA_R1


title: P2_31


title: db/db_scRNA-seq_replicate 2

description: Library name: db/db_R2


title: P2_23


title: db/dbDAPA_scATAC-seq_replicate 1

description: Library name: db/dbDAPA


title: P2_22


title: P2_21


title: db/+_scRNA-seq_replicate 2

description: Library name: db/+_R2


title: db/+_scRNA-seq_replicate 1

description: Library name: db/+_R1


title: P2_19


title: P2_17


title: GMC_BL6J_ 5m_ET82_c2349_testis

city: Bonn

first: Dan

last: Ehninger

state: NRW

address: Venusberg-Campus 1/99

department: AG Ehninger

country: Germany

institute: DZNE

description: Library name: Sample 268

data_processing:
Demultiplexing and data transformation to generate fastq files was done using bcl2fastq2 (v2.20).
Sequencing reads were trimmed using Trim Galore (https://usegalaxy.org/) to remove adapter sequences. Trimmed reads were mapped to the mouse transcriptome (GRCm38, mm10) using HISAT2 (v2.1.0).
Bam files were indexed using Samtools and count matrices generated by Genomic Alignments in R. Gene count matrices were generated using annotation information from a Mus_musculus.GRCm38.102.chr.gtf file imported with the rtracklayer (Lawrence et al., 2009) package into R. All downstream analyses were performed using R (Version 3.5.1, https://cran.r-project.org/). Library normalization and expression differences between samples were quantified using the DESeq2 package (Love et al., 2014). A false discovery rate (FDR) < 0.05 was used as a cutoff in differential expression analyses.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: testis

extract_protocol:
Mouse tissues were harvested, flash frozen on dry ice and total RNA isolated from the tissues with TRI-Reagent. Total RNA was purified with the Monarch RNA Cleanup kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using a ligation mediated RNA sequencing protocol published by Huo et al. 2015

value: testis

value: WT

tag: gender

value: male


title: WT, MII, 1

description:
Library name: sample1
WT_MII_1


title: P2_14


title: db/db_scRNA-seq_replicate 1

description: Library name: db/db_R1


title: GMC_BL6J_ 20M_ET0_c3580_testis

description: Library name: Sample 267


title: P2_13


title: P2_18


title: P2_11


title: GMC_BL6J_ 8M_ET1_c1457_testis

description: Library name: Sample 269


title: P2_20


title: GMC_BL6J_14M_ET20_c3841_testis

description: Library name: Sample 266


title: P2_10


title: P2_9


title: GMC_BL6J_ 14M_ET0_c2626_testis

description: Library name: Sample 270


title: GMC_BL6J_ 8M_ET2_c1383_testis

description: Library name: Sample 265


title: P2_8


title: GMC_BL6J_ 5M_ET32_c2346_testis

description: Library name: Sample 264


title: GMC_BL6J_ 3M_ET8_c1190_testis

description: Library name: Sample 263


title: GMC_BL6J_ 14M_ET30_c3840_testis

description: Library name: Sample 261


title: GMC_BL6J_ 20M_ET9_c1315_testis

description: Library name: Sample 262


title: P2_4


title: P2_7


title: P2_5


title: P2_3


title: P2_2


title: GMC_BL6J_ 8M_ET0_c3663_testis

description: Library name: Sample 260


title: GMC_BL6J_ 26M_ET30_c620_testis

description: Library name: Sample 257


title: P1_384

value: hematopoietic cell


title: GMC_BL6J_ 3M_ET30_c1164_testis

description: Library name: Sample 258


title: GMC_BL6J_ 14M_ET8_c2634_testis

description: Library name: Sample 255


title: P1_382


title: P1_383


title: P1_380


title: GMC_BL6J_ 8M_ET35_c1378_testis

description: Library name: Sample 254


title: GMC_BL6J_ 3M_ET3_c1114_testis

description: Library name: Sample 252


title: GMC_BL6J_ 5M_ET20_c2318_testis

description: Library name: Sample 259


title: P1_381


title: GMC_BL6J_ 5M_ET0_c3671_testis

description: Library name: Sample 253


title: P1_378

value: dermal papilla cell


title: P1_377


title: GMC_BL6J_ 20M_ET66_c3055_testis

description: Library name: Sample 250


title: GMC_BL6J_ 20M_ET3_c1312_testis

description: Library name: Sample 256


title: GMC_BL6J_ 26M_ET5_c2293_testis

description: Library name: Sample 251


title: GMC_BL6J_ 14M_ET3_c847_testis

description: Library name: Sample 249


title: P1_374


title: P1_376


title: P1_379


title: GMC_BL6J_ 5m_ET66_c2287_testis

description: Library name: Sample 246


title: P1_372


title: GMC_BL6J_ 14M_ET4_c755_testis

description: Library name: Sample 248


title: P1_375


title: GMC_BL6J_ 8M_ET6_c1364_testis

description: Library name: Sample 247


title: P1_371


title: GMC_BL6J_ 5M_ET30_c2254_testis

description: Library name: Sample 245


title: GMC_BL6J_ 3M_ET0_c2908_testis

description: Library name: Sample 244


title: P1_373


title: GMC_BL6J_ 26M_ET0_c3668_testis

description: Library name: Sample 243


title: P1_369


title: P1_370


title: GMC_BL6J_ 20M_ET60_c1300_testis

description: Library name: Sample 242


title: P1_367


title: P1_365


title: P1_364


title: GMC_BL6J_ 5M_ET24_c2275_testis

description: Library name: Sample 239


title: GMC_BL6J_14M_ET20_c636_testis

description: Library name: Sample 241


title: GMC_BL6J_ 8M_ET2_c1358_testis

description: Library name: Sample 240


title: P1_366


title: GMC_BL6J_ 3M_ET55_c1030_testis

description: Library name: Sample 238


title: P1_363


title: GMC_BL6J_ 8M_ET66_c2295_testis

description: Library name: Sample 234


title: P1_362


title: GMC_BL6J_20M_ET5_c3054_testis

description: Library name: Sample 236


title: P1_359


title: GMC_BL6J_14M_ET2_c568_testis

description: Library name: Sample 235


title: P1_361


title: P1_358


title: GMC_BL6J_ 26M_ET0_c3667_testis

description: Library name: Sample 237


title: P1_360


title: GMC_BL6J_5M_ET80_c2231_testis

description: Library name: Sample 233


title: GMC_BL6J_3M_ET2_c953_testis

description: Library name: Sample 232


title: P1_355


title: P1_356


title: P1_353


title: GMC_BL6J_20M_ET0_c2140_testis

description: Library name: Sample 230


title: GMC_BL6J_14M_ET0_c2600_testis

description: Library name: Sample 229


title: GMC_BL6J_26M_ET65_c3775_testis

description: Library name: Sample 231


title: P1_352


title: GMC_BL6J_3M_ET4_c940_testis

description: Library name: Sample 226


title: P1_357


title: P1_350


title: P1_349


title: GMC_BL6J_ 8M_ET1_c1457_skeletal-muscle

description: Library name: Sample 224

source_name: skeletal muscle

value: skeletal muscle


title: P1_348


title: GMC_BL6J_5M_ET6_c3670_testis

description: Library name: Sample 227


title: P1_351


title: GMC_BL6J_ 14M_ET0_c2626_skeletal-muscle

description: Library name: Sample 225


title: P1_347


title: GMC_BL6J_8M_ET0_c3662_testis

description: Library name: Sample 228


title: GMC_BL6J_ 5m_ET82_c2349_skeletal-muscle

description: Library name: Sample 223


title: P1_345


title: GMC_BL6J_14M_ET20_c3841_skeletal-muscle

description: Library name: Sample 221


title: P1_346


title: GMC_BL6J_ 5M_ET32_c2346_skeletal-muscle

description: Library name: Sample 219


title: GMC_BL6J_ 8M_ET2_c1383_skeletal-muscle

description: Library name: Sample 220


title: P1_344


title: P1_342


title: GMC_BL6J_ 20M_ET0_c3580_skeletal-muscle

description: Library name: Sample 222


title: P1_343


title: P1_341


title: GMC_BL6J_ 8M_ET0_c3663_skeletal-muscle

description: Library name: Sample 215


title: P1_339


title: GMC_BL6J_ 5M_ET20_c2318_skeletal-muscle

description: Library name: Sample 214


title: P1_340


title: GMC_BL6J_ 3M_ET8_c1190_skeletal-muscle

description: Library name: Sample 218


title: GMC_BL6J_ 20M_ET9_c1315_skeletal-muscle

description: Library name: Sample 217


title: GMC_BL6J_ 14M_ET30_c3840_skeletal-muscle

description: Library name: Sample 216


title: GMC_BL6J_ 26M_ET30_c620_skeletal-muscle

description: Library name: Sample 212


title: P1_336


title: GMC_BL6J_ 3M_ET30_c1164_skeletal-muscle

description: Library name: Sample 213


title: GMC_BL6J_ 14M_ET8_c2634_skeletal-muscle

description: Library name: Sample 210


title: P1_335


title: P1_331


title: GMC_BL6J_ 5M_ET0_c3671_skeletal-muscle

description: Library name: Sample 208


title: GMC_BL6J_ 8M_ET35_c1378_skeletal-muscle

description: Library name: Sample 209


title: P1_333


title: P1_330


title: GMC_BL6J_ 3M_ET3_c1114_skeletal-muscle

description: Library name: Sample 207


title: P1_329


title: GMC_BL6J_ 26M_ET5_c2293_skeletal-muscle

description: Library name: Sample 206


title: P1_338


title: P1_327


title: P1_328


title: GMC_BL6J_ 20M_ET3_c1312_skeletal-muscle

description: Library name: Sample 211


title: P1_334


title: GMC_BL6J_ 20M_ET66_c3055_skeletal-muscle

description: Library name: Sample 205


title: GMC_BL6J_ 14M_ET4_c755_skeletal-muscle

description: Library name: Sample 203


title: P1_326


title: GMC_BL6J_ 14M_ET3_c847_skeletal-muscle

description: Library name: Sample 204


title: GMC_BL6J_ 5m_ET66, c2287_skeletal-muscle

description: Library name: Sample 201


title: GMC_BL6J_ 8M_ET6_c1364_skeletal-muscle

description: Library name: Sample 202


title: P1_332


title: P1_325


title: P1_324


title: P1_322


title: P1_323


title: GMC_BL6J_ 26M_ET0_c3668_skeletal-muscle

description: Library name: Sample 198


title: GMC_BL6J_ 5M_ET30_c2254_skeletal-muscle

description: Library name: Sample 200


title: GMC_BL6J_ 3M_ET0_c2908_skeletal-muscle

description: Library name: Sample 199


title: GMC_BL6J_ 20M_ET60_c1300_skeletal-muscle

description: Library name: Sample 197


title: P1_321


title: GMC_BL6J_14M_ET20_c636_skeletal-muscle

description: Library name: Sample 196


title: GMC_BL6J_ 8M_ET2_c1358_skeletal-muscle

description: Library name: Sample 195


title: P1_319


title: P1_317


title: GMC_BL6J_ 26M_ET0_c3667_skeletal-muscle

description: Library name: Sample 192


title: P1_318


title: P1_315


title: GMC_BL6J_20M_ET5_c3054_skeletal-muscle

description: Library name: Sample 191


title: GMC_BL6J_ 5M_ET24_c2275_skeletal-muscle

description: Library name: Sample 194


title: P1_314


title: GMC_BL6J_ 3M_ET55_c1030_skeletal-muscle

description: Library name: Sample 193


title: P1_320


title: GMC_BL6J_14M_ET2_c568_skeletal-muscle

description: Library name: Sample 190


title: P1_313


title: P1_310


title: P1_311


title: P1_308


title: GMC_BL6J_20M_ET0_c2140_skeletal-muscle

description: Library name: Sample 185


title: P1_316


title: GMC_BL6J_8M_ET0_c3662_skeletal-muscle

description: Library name: Sample 183


title: GMC_BL6J_5M_ET80_c2231_skeletal-muscle

description: Library name: Sample 188


title: P1_307


title: GMC_BL6J_ 8M_ET66_c2295_skeletal-muscle

description: Library name: Sample 189


title: GMC_BL6J_26M_ET65_c3775_skeletal-muscle

description: Library name: Sample 186


title: P1_305


title: P1_303


title: P1_312


title: GMC_BL6J_5M_ET6_c3670_skeletal-muscle

description: Library name: Sample 182


title: GMC_BL6J_14M_ET0_c2600_skeletal-muscle

description: Library name: Sample 184


title: P1_306


title: GMC_BL6J_ 5m_ET82_c2349_lung

description: Library name: Sample 178

source_name: lung

value: lung


title: P1_302


title: P1_300


title: GMC_BL6J_3M_ET2_c953_skeletal-muscle

description: Library name: Sample 187


title: P1_304


title: GMC_BL6J_ 14M_ET0_c2626_lung

description: Library name: Sample 180


title: GMC_BL6J_ 8M_ET2_c1383_lung

description: Library name: Sample 175


title: GMC_BL6J_3M_ET4_c940_skeletal-muscle

description: Library name: Sample 181


title: P1_299


title: P1_309


title: GMC_BL6J_ 20M_ET0_c3580_lung

description: Library name: Sample 177


title: P1_301


title: GMC_BL6J_14M_ET20_c3841_lung

description: Library name: Sample 176


title: GMC_BL6J_ 3M_ET8_c1190_lung

description: Library name: Sample 173


title: P1_295


title: P1_297


title: GMC_BL6J_ 5M_ET20_c2318_lung

description: Library name: Sample 169


title: GMC_BL6J_ 8M_ET0_c3663_lung

description: Library name: Sample 170


title: P1_298


title: GMC_BL6J_ 20M_ET9_c1315_lung

description: Library name: Sample 172


title: P1_292


title: GMC_BL6J_ 5M_ET32_c2346_lung

description: Library name: Sample 174


title: P1_291


title: GMC_BL6J_ 26M_ET30_c620_lung

description: Library name: Sample 167


title: GMC_BL6J_ 14M_ET30_c3840_lung

description: Library name: Sample 171


title: P1_294


title: GMC_BL6J_ 8M_ET1_c1457_lung

description: Library name: Sample 179


title: P1_296


title: P1_286


title: P1_290


title: P1_289


title: GMC_BL6J_ 14M_ET8_c2634_lung

description: Library name: Sample 165


title: GMC_BL6J_ 5M_ET0_c3671_lung

description: Library name: Sample 163


title: GMC_BL6J_ 8M_ET35_c1378_lung

description: Library name: Sample 164


title: P1_288


title: GMC_BL6J_ 3M_ET30_c1164_lung

description: Library name: Sample 168


title: GMC_BL6J_ 3M_ET3_c1114_lung

description: Library name: Sample 162


title: GMC_BL6J_ 26M_ET5_c2293_lung

description: Library name: Sample 161


title: P1_293


title: GMC_BL6J_ 20M_ET3_c1312_lung

description: Library name: Sample 166


title: P1_285


title: P1_287


title: P1_284


title: P1_281


title: GMC_BL6J_ 14M_ET3_c847_lung

description: Library name: Sample 159


title: P1_283


title: P1_282


title: GMC_BL6J_ 8M_ET6_c1364_lung

description: Library name: Sample 157


title: P1_279


title: GMC_BL6J_ 14M_ET4_c755_lung

description: Library name: Sample 158


title: GMC_BL6J_ 20M_ET66_c3055_lung

description: Library name: Sample 160


title: GMC_BL6J_ 5m_ET66_c2287_lung

description: Library name: Sample 156


title: P1_278


title: P1_275


title: P1_276


title: P1_277


title: P1_280


title: P1_274


title: GMC_BL6J_ 5M_ET24_c2275_lung

description: Library name: Sample 149


title: GMC_BL6J_ 5M_ET30_c2254_lung

description: Library name: Sample 155


title: P1_273


title: GMC_BL6J_ 8M_ET2_c1358_lung

description: Library name: Sample 150


title: GMC_BL6J_ 3M_ET55_c1030_lung

description: Library name: Sample 148


title: P1_272


title: GMC_BL6J_14M_ET20_c636_lung

description: Library name: Sample 151


title: GMC_BL6J_ 26M_ET0_c3668_lung

description: Library name: Sample 153


title: GMC_BL6J_ 3M_ET0_c2908_lung

description: Library name: Sample 154


title: P1_270


title: GMC_BL6J_ 20M_ET60_c1300_lung

description: Library name: Sample 152


title: GMC_BL6J_ 26M_ET0_c3667_lung

description: Library name: Sample 147


title: P1_271


title: GMC_BL6J_20M_ET5_c3054_lung

description: Library name: Sample 146


title: P1_269


title: P1_266


title: GMC_BL6J_ 8M_ET66_c2295_lung

description: Library name: Sample 144


title: P1_267


title: GMC_BL6J_5M_ET80_c2231_lung

description: Library name: Sample 143


title: GMC_BL6J_14M_ET2_c568_lung

description: Library name: Sample 145


title: P1_268


title: P1_264


title: GMC_BL6J_3M_ET2_c953_lung

description: Library name: Sample 142


title: P1_260


title: GMC_BL6J_14M_ET0_c2600_lung

description: Library name: Sample 139


title: P1_259


title: GMC_BL6J_20M_ET0_c2140_lung

description: Library name: Sample 140


title: P1_263


title: GMC_BL6J_26M_ET65_c3775_lung

description: Library name: Sample 141


title: GMC_BL6J_8M_ET0_c3662_lung

description: Library name: Sample 138


title: P1_258


title: P1_262


title: GMC_BL6J_5M_ET6_c3670_lung

description: Library name: Sample 137


title: P1_256


title: GMC_BL6J_ 5m_ET82_c2349_liver

description: Library name: Sample 133

source_name: liver

value: liver


title: P1_254


title: P1_255


title: P1_257


title: P1_265


title: GMC_BL6J_ 14M_ET0_c2626_liver

description: Library name: Sample 135


title: GMC_BL6J_ 8M_ET1_c1457_liver

description: Library name: Sample 134


title: P1_253


title: GMC_BL6J_14M_ET20_c3841_liver

description: Library name: Sample 131


title: GMC_BL6J_3M_ET4_c940_lung

description: Library name: Sample 136


title: P1_252


title: GMC_BL6J_ 5M_ET32_c2346_liver

description: Library name: Sample 129


title: GMC_BL6J_ 8M_ET2_c1383_liver

description: Library name: Sample 130


title: GMC_BL6J_ 20M_ET0_c3580_liver

description: Library name: Sample 132


title: GMC_BL6J_ 3M_ET8_c1190_liver

description: Library name: Sample 128


title: P1_248


title: GMC_BL6J_ 5M_ET20_c2318_liver

description: Library name: Sample 124


title: P1_249


title: GMC_BL6J_ 8M_ET0_c3663_liver

description: Library name: Sample 125


title: P1_244


title: GMC_BL6J_ 14M_ET30_c3840_liver

description: Library name: Sample 126


title: GMC_BL6J_ 3M_ET30_c1164_liver

description: Library name: Sample 123


title: P1_247


title: GMC_BL6J_ 20M_ET9_c1315_liver

description: Library name: Sample 127


title: P1_242


title: GMC_BL6J_ 26M_ET30_c620_liver

description: Library name: Sample 122


title: P1_245


title: GMC_BL6J_ 8M_ET35_c1378_liver

description: Library name: Sample 119


title: P1_251


title: P1_240


title: GMC_BL6J_ 14M_ET8_c2634_liver

description: Library name: Sample 120


title: GMC_BL6J_ 5M_ET0_c3671_liver

description: Library name: Sample 118


title: P1_239


title: P1_243


title: GMC_BL6J_ 20M_ET3_c1312_liver

description: Library name: Sample 121


title: GMC_BL6J_ 3M_ET3_c1114_liver

description: Library name: Sample 117


title: P1_237


title: P1_246


title: GMC_BL6J_ 20M_ET66_c3055_liver

description: Library name: Sample 115


title: P1_236


title: GMC_BL6J_ 26M_ET5_c2293_liver

description: Library name: Sample 116


title: P1_235


title: GMC_BL6J_ 14M_ET3_c847_liver

description: Library name: Sample 114


title: P1_234


title: P1_233


title: GMC_BL6J_ 14M_ET4_c755_liver

description: Library name: Sample 113


title: GMC_BL6J_ 8M_ET6_c1364_liver

description: Library name: Sample 112


title: P1_232


title: GMC_BL6J_ 5M_ET30_c2254_liver

description: Library name: Sample 110


title: GMC_BL6J_ 3M_ET0_c2908_liver

description: Library name: Sample 109


title: P1_229


title: P1_231


title: P1_230


title: GMC_BL6J_ 26M_ET0_c3668_liver

description: Library name: Sample 108


title: P1_228


title: GMC_BL6J_ 20M_ET60_c1300_liver

description: Library name: Sample 107


title: P1_223


title: GMC_BL6J_14M_ET20_c636_liver

description: Library name: Sample 106


title: GMC_BL6J_ 3M_ET55_c1030_liver

description: Library name: Sample 103


title: P1_221


title: P1_224


title: GMC_BL6J_ 26M_ET0_c3667_liver

description: Library name: Sample 102


title: GMC_BL6J_ 8M_ET2_c1358_liver

description: Library name: Sample 105


title: GMC_BL6J_ 5m_ET66_c2287_liver

description: Library name: Sample 111


title: P1_225


title: GMC_BL6J_20M_ET5_c3054_liver

description: Library name: Sample 101


title: P1_220


title: P1_218


title: GMC_BL6J_14M_ET2_c568_liver

description: Library name: Sample 100


title: P1_217


title: GMC_BL6J_ 8M_ET66_c2295_liver

description: Library name: Sample 99


title: P1_216


title: P1_222


title: P1_215


title: GMC_BL6J_3M_ET2_c953_liver

description: Library name: Sample 97


title: GMC_BL6J_ 5M_ET24_c2275_liver

description: Library name: Sample 104


title: GMC_BL6J_5M_ET80_c2231_liver

description: Library name: Sample 98


title: P1_219


title: GMC_BL6J_26M_ET65_c3775_liver

description: Library name: Sample 96


title: GMC_BL6J_20M_ET0_c2140_liver

description: Library name: Sample 95


title: P1_212


title: P1_211


title: GMC_BL6J_14M_ET0_c2600_liver

description: Library name: Sample 94


title: GMC_BL6J_8M_ET0_c3662_liver

description: Library name: Sample 93


title: P1_210


title: P1_208


title: GMC_BL6J_5M_ET6_c3670_liver

description: Library name: Sample 92


title: P1_209


title: P1_207


title: P1_213


title: P1_206


title: GMC_BL6J_ 8M_ET1_c1457_kidney

description: Library name: Sample 89

source_name: kidney

value: kidney


title: P1_205


title: GMC_BL6J_3M_ET4_c940_liver

description: Library name: Sample 91


title: P1_204


title: GMC_BL6J_ 5m_ET82_c2349_kidney

description: Library name: Sample 88


title: GMC_BL6J_ 14M_ET0_c2626_kidney

description: Library name: Sample 90


title: P1_203


title: GMC_BL6J_ 20M_ET0_c3580_kidney

description: Library name: Sample 87


title: GMC_BL6J_14M_ET20_c3841_kidney

description: Library name: Sample 86


title: P1_201


title: GMC_BL6J_ 8M_ET2_c1383_kidney

description: Library name: Sample 85


title: P1_199


title: P1_200


title: GMC_BL6J_ 3M_ET8_c1190_kidney

description: Library name: Sample 83


title: GMC_BL6J_ 5M_ET32_c2346_kidney

description: Library name: Sample 84


title: GMC_BL6J_ 14M_ET30_c3840_kidney

description: Library name: Sample 81


title: GMC_BL6J_ 20M_ET9_c1315_kidney

description: Library name: Sample 82


title: P1_196


title: P1_197


title: P1_195


title: GMC_BL6J_ 8M_ET0_c3663_kidney

description: Library name: Sample 80


title: GMC_BL6J_ 5M_ET20_c2318_kidney

description: Library name: Sample 79


title: P1_192


title: P1_191


title: P1_198


title: GMC_BL6J_ 3M_ET30_c1164_kidney

description: Library name: Sample 78


title: GMC_BL6J_ 26M_ET30_c620_kidney

description: Library name: Sample 77


title: GMC_BL6J_ 20M_ET3_c1312_kidney

description: Library name: Sample 76


title: GMC_BL6J_ 8M_ET35_c1378_kidney

description: Library name: Sample 74


title: P1_190


title: P1_189


title: GMC_BL6J_ 14M_ET8_c2634_kidney

description: Library name: Sample 75


title: GMC_BL6J_ 5M_ET0_c3671_kidney

description: Library name: Sample 73


title: P1_187


title: P1_188


title: P1_186


title: GMC_BL6J_ 26M_ET5_c2293_kidney

description: Library name: Sample 71


title: GMC_BL6J_ 3M_ET3_c1114_kidney

description: Library name: Sample 72


title: P1_185


title: GMC_BL6J_ 14M_ET4_c755_kidney

description: Library name: Sample 68


title: GMC_BL6J_ 20M_ET66_c3055_kidney

description: Library name: Sample 70


title: P1_183


title: GMC_BL6J_ 5m_ET66_c2287_kidney

description: Library name: Sample 66


title: GMC_BL6J_ 8M_ET6_c1364_kidney

description: Library name: Sample 67


title: P1_182


title: P1_184


title: GMC_BL6J_ 26M_ET0_c3668_kidney

description: Library name: Sample 63


title: P1_177


title: GMC_BL6J_ 14M_ET3_c847_kidney

description: Library name: Sample 69


title: GMC_BL6J_ 20M_ET60_c1300_kidney

description: Library name: Sample 62


title: GMC_BL6J_ 8M_ET2_c1358_kidney

description: Library name: Sample 60


title: P1_179


title: P1_180


title: GMC_BL6J_ 5M_ET30_c2254_kidney

description: Library name: Sample 65


title: GMC_BL6J_ 3M_ET0_c2908_kidney

description: Library name: Sample 64


title: P1_172


title: P1_170


title: P1_176


title: P1_181


title: P1_178


title: P1_175


title: GMC_BL6J_14M_ET2_c568_kidney

description: Library name: Sample 55


title: GMC_BL6J_14M_ET20_c636_kidney

description: Library name: Sample 61


title: P1_174


title: GMC_BL6J_ 3M_ET55_c1030_kidney

description: Library name: Sample 58


title: P1_173


title: GMC_BL6J_ 5M_ET24_c2275_kidney

description: Library name: Sample 59


title: GMC_BL6J_3M_ET2_c953_kidney

description: Library name: Sample 52


title: P1_166


title: GMC_BL6J_20M_ET5_c3054_kidney

description: Library name: Sample 56


title: P1_169


title: GMC_BL6J_20M_ET0_c2140_kidney

description: Library name: Sample 50


title: GMC_BL6J_ 26M_ET0_c3667_kidney

description: Library name: Sample 57


title: P1_171


title: GMC_BL6J_ 8M_ET66_c2295_kidney

description: Library name: Sample 54


title: P1_162


title: P1_168


title: P1_161


title: GMC_BL6J_26M_ET65_c3775_kidney

description: Library name: Sample 51


title: GMC_BL6J_14M_ET0_c2600_kidney

description: Library name: Sample 49


title: P1_165


title: P1_163


title: P1_164


title: GMC_BL6J_5M_ET6_c3670_kidney

description: Library name: Sample 47


title: P1_160


title: GMC_BL6J_3M_ET4_c940_kidney

description: Library name: Sample 46


title: GMC_BL6J_5M_ET80_c2231_kidney

description: Library name: Sample 53


title: GMC_BL6J_ 14M_ET0_c2626_heart

description: Library name: Sample 45

source_name: heart

value: heart


title: P1_159

value: skin


title: GMC_BL6J_ 8M_ET1_c1457_heart

description: Library name: Sample 44


title: P1_157

value: keratinocyte


title: P1_156


title: GMC_BL6J_8M_ET0_c3662_kidney

description: Library name: Sample 48


title: GMC_BL6J_ 5m_ET82_c2349_heart

description: Library name: Sample 43


title: P1_167


title: GMC_BL6J_ 20M_ET0_c3580_heart

description: Library name: Sample 42


title: GMC_BL6J_14M_ET20_c3841_heart

description: Library name: Sample 41


title: P1_155


title: P1_154


title: GMC_BL6J_ 8M_ET2_c1383_heart

description: Library name: Sample 40


title: GMC_BL6J_ 3M_ET8_c1190_heart

description: Library name: Sample 38


title: P1_151

value: Merkel cell


title: P1_152


title: P1_153


title: P1_158


title: GMC_BL6J_ 20M_ET9_c1315_heart

description: Library name: Sample 37


title: GMC_BL6J_ 5M_ET32_c2346_heart

description: Library name: Sample 39


title: P1_149


title: GMC_BL6J_ 8M_ET0_c3663_heart

description: Library name: Sample 35


title: GMC_BL6J_ 14M_ET30_c3840_heart

description: Library name: Sample 36


title: GMC_BL6J_ 5M_ET20_c2318_heart

description: Library name: Sample 34


title: P1_148


title: P1_144


title: P1_143


title: GMC_BL6J_ 20M_ET3_c1312_heart

description: Library name: Sample 31


title: P1_145


title: GMC_BL6J_ 14M_ET8_c2634_heart

description: Library name: Sample 30


title: P1_150


title: GMC_BL6J_ 8M_ET35_c1378_heart

description: Library name: Sample 29


title: P1_142


title: GMC_BL6J_ 3M_ET30_c1164_heart

description: Library name: Sample 33


title: GMC_BL6J_ 5M_ET0_c3671_heart

description: Library name: Sample 28


title: P1_140


title: P1_146


title: P1_139


title: GMC_BL6J_ 26M_ET30_c620_heart

description: Library name: Sample 32


title: GMC_BL6J_ 3M_ET3_c1114_heart

description: Library name: Sample 27


title: GMC_BL6J_ 14M_ET4_c755_heart

description: Library name: Sample 23


title: GMC_BL6J_ 14M_ET3_c847_heart

description: Library name: Sample 24


title: P1_137


title: P1_141


title: P1_135


title: GMC_BL6J_ 26M_ET5_c2293_heart

description: Library name: Sample 26


title: P1_132


title: P1_138


title: GMC_BL6J_ 8M_ET6_c1364_heart

description: Library name: Sample 22


title: GMC_BL6J_ 5M_ET30_c2254_heart

description: Library name: Sample 20


title: GMC_BL6J_ 20M_ET66_c3055_heart

description: Library name: Sample 25


title: P1_134


title: GMC_BL6J_ 3M_ET0_c2908_heart

description: Library name: Sample 19


title: P1_136


title: GMC_BL6J_ 5m_ET66_c2287_heart

description: Library name: Sample 21


title: GMC_BL6J_ 20M_ET60_c1300_heart

description: Library name: Sample 17


title: P1_129


title: GMC_BL6J_ 8M_ET2_c1358_heart

description: Library name: Sample 15


title: P1_127


title: GMC_BL6J_14M_ET20_c636_heart

description: Library name: Sample 16


title: P1_126


title: P1_122


title: P1_125


title: GMC_BL6J_ 5M_ET24_c2275_heart

description: Library name: Sample 14


title: GMC_BL6J_ 3M_ET55_c1030_heart

description: Library name: Sample 13


title: P1_128


title: GMC_BL6J_ 26M_ET0_c3668_heart

description: Library name: Sample 18


title: P1_124


title: P1_130


title: P1_131


title: GMC_BL6J_20M_ET5_c3054_heart

description: Library name: Sample 11


title: P1_117


title: P1_118


title: GMC_BL6J_14M_ET2_c568_heart

description: Library name: Sample 10


title: GMC_BL6J_ 8M_ET66_c2295_heart

description: Library name: Sample 9


title: P1_119


title: GMC_BL6J_5M_ET80_c2231_heart

description: Library name: Sample 8


title: GMC_BL6J_ 26M_ET0_c3667_heart

description: Library name: Sample 12


title: GMC_BL6J_14M_ET0_c2600_heart

description: Library name: Sample 4


title: P1_116


title: P1_120


title: GMC_BL6J_20M_ET0_c2140_heart

description: Library name: Sample 5


title: P1_114


title: GMC_BL6J_3M_ET2_c953_heart

description: Library name: Sample 7


title: GMC_BL6J_8M_ET0_c3662_heart

description: Library name: Sample 3


title: P1_115


title: P1_113


title: GMC_BL6J_3M_ET4_c940_heart

description: Library name: Sample 1


title: P1_112


title: P1_111


title: GMC_BL6J_26M_ET65_c3775_heart

description: Library name: Sample 6


title: GMC_BL6J_5M_ET6_c3670_heart

description: Library name: Sample 2


title: P1_108


title: P1_107


title: F1 - Smad1fl/fl+BMP4 #1

city: Bronx

first: Silvia

middle: C

last: Hernandez

state: New York

address: 1300 Morris Park Avenue

department: Medicine-Cardiology

institute: Albert Einstein College of Medicine

description: Library name: F1

data_processing:
Adapter, poly-N and low-quality reads from the raw data were excluded to purify the data analysis. Quality Phred Scores, Q20%, Q30% and GC contents of the clean data were calculated, showing high accuracy of reads (>99%, with 0.02 error rate).
Filtered reads were aligned to the C57BL/6J reference genome (mm10; GRCm38.p6) using TopHat2 algorithm alignment program v.2.0.9.
Mapped reads were assembled using both Scripture (beta2) and Cufflinks v.2.1.1 algorithm.
HTSeq software v.0.6.1[22]  was used to count the number of reads mapped to each gene.
Read count of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) was used to calculate gene expression level, which considered the effects of both sequencing depth and gene length.
Assembly: mm10
Supplementary files format and content: Excel files including raw readcounts for every gene and every sample
Supplementary files format and content: Excel files including FPKM values for every gene and every sample
Supplementary files format and content: Excel files including gene description for every gene

growth_protocol: Tibial BMMs were obtained from 2-3-month-old Smad1fl/fl mice and MyS1KO mice. Briefly, bone marrow cells were incubated for 24 h in α+ MEM medium supplemented with 15% fetal calf serum (GIBCO), 10% WEHI-3 conditioned media, as a source of interleukin-3, and 12 ng/ml CSF-1 (R&D systems). Non-adherent primitive mononuclear phagocytes were reseeded in media containing 15% fetal calf serum and CSF-1 (120 ng/ml) for 48 hours, in order to allow their differentiation to adherent macrophages. Cells used for experiments were cultured until confluent, starved in media without serum for approximately 16 hours, and then stimulated  or no for 4 hours.

extract_protocol:
RNA was isolated using TRIzol reagent (Qiagen, #79306) according to manufacterer's instructions.
RNA samples were sent to Novogene (Sacramento, California) to construct a total of eight cDNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). Briefly, libraries were prepared using at least 1ug high quality total RNA input per sample. mRNA purification and enrichmes was preformed using oligo(dt)-attached magnetic beads. After fragmentation, double stranded cDNA synthesis was preformed. Sequencing adaptors were ligated and cDNA fragmets were selected (150-200bp), amplified and purified. Library concentration and quality were assessed using a Bioanalyzer 2100 system (Agilent). These librarys were sequenced on Illumina NovaSeq 6000 devices, generating 150 bp paired-end reads.

treatment_protocol: A group of samples (n=3) from each genotype group was treated with TGF-β1 (10 ng/ml) or BMP4 (50 ng/ml) for 4 hours. After this incubation time samples were collected for RNA isolation.

value: Bone Marrow

value: Bone Marrow Macrophages

value: Smad1 fl/fl

value: BMP4 (50 ng/ml) stimulation for 4 hours


title: F2 - Smad1fl/fl+BMP4 #2

description: Library name: F2


title: P1_110


title: E3 - Smad1fl/fl+TGFβ1 #3

description: Library name: E3

value: TGF-β1 (10 ng/ml) stimulation for 4 hours


title: P1_106


title: P1_109


title: E2 - Smad1fl/fl+TGFβ1 #2

description: Library name: E2


title: P1_105


title: E1 - Smad1fl/fl+TGFβ1 #1

description: Library name: E1


title: D3 - Smad1fl/fl Ctrl #3

description: Library name: D3

value: untreated


title: F3 - Smad1fl/fl+BMP4 #3

description: Library name: F3


title: P1_103


title: D2 - Smad1fl/fl Ctrl #2

description: Library name: D2


title: P1_102


title: D1 - Smad1fl/fl Ctrl #1

description: Library name: D1


title: C3 - Smad1KO+BMP4 #3

description: Library name: C3

value: Smad1 fl/fl + LyzM-Cre (MyS1KO)


title: P1_101


title: C1 - Smad1KO+BMP4 #1

description: Library name: C1


title: C2 - Smad1KO+BMP4 #2

description: Library name: C2


title: P1_99


title: B3 - Smad1KO+TGFβ1 #3

description: Library name: B3


title: P1_97


title: B2 - Smad1KO+TGFβ1 #2

description: Library name: B2


title: B1 - Smad1KO+TGFβ1 #1

description: Library name: B1


title: P1_98


title: P1_95


title: P1_96

value: hematopoietic cell


title: A2 - Smad1KO Ctrl #2

description: Library name: A2


title: A3 - Smad1KO Ctrl #3

description: Library name: A3


title: P1_92


title: P1_100


title: P1_91


title: P1_104


title: P1_94


title: P1_90


title: Control_mCrypt_HTO_2_S2_TotalSeqA_GEX

city: Hoboken

first: ansu

last: perekatt

state: NJ

address: 507 River street

department: CCB

institute: Stevens Institute of Technology

description: Library name: S2_gex

data_processing:
cellranger count
Assembly: mm10
Supplementary files format and content: Filtered h5 matrices

source_name: duodenum crypt_ epithelium

extract_protocol: 10X scRNA 3prime with hash tags

value: duodenum crypt_ epithelium

value: Wildtype

value: Control crypt


title: P1_93


title: P1_88


title: Control_mCrypt_HTO_2_S2_TotalSeqA_tag

description: Library name: S2_htos

tag: htos

value: TotalSeq™-A0302 anti-mouse Hashtag 1 Antibody

value: Control crypt_tag


title: A1 - Smad1KO Ctrl #1

description: Library name: A1


title: P1_86


title: P1_87


title: Control_mVilli_HTO_1_S1_TotalSeqB_Gex

description: Library name: S1_gex

source_name: duodenum villi_epithelium

value: duodenum villi_epithelium

value: Control villi


title: Tpo_PT 1,scRNAseq

city: Aachen

first: Ivan

middle: Gesteira

last: Costa

state: Northrhine-Westphalia

address: Pauwelsstr. 19

department: Joint Research Center for Computational Biomedicine

institute: UKA RWTH Aachen

description: Library name: PTSF_BB_DMSO_PT_TPO

data_processing:
The Cell Ranger Software (version 2.1.1,6.0.2,8.0.)as used for processing sequencing information.
Seurat was used to integrate the singlecell RNA-seq data.
Assembly: mm10 with tdTom transcript cDNA and mm10
Supplementary files format and content: Rds

extract_protocol:
Murine bone marrow from long bones and spine was crushed, flushed, RBC lysed, and MACS-depleted for CD11b, Gr1, Ter119, CD4, CD8, B220, CD45, and CD71, and subsequently combined with the digested bone chip fraction, after which the samples were FACS-sorted for lineage-, tdTom+ viable cells for sequencing
All protocols to generate scRNA-seq data on the 10x Chromium platform, including sample prep, library prep, instrument and sequencing settings, are available here:https://support.10xgenomics.com/single-cell-gene-expression

value: MACS-depleted for CD11b, Gr1, Ter119, CD4, CD8, B220, and CD71, sorted for alive, lin- CD71- cKit+Sca1+ (LSK) fraction, and lin-CD71-GFP-CD45- stromal fraction

value: PT


title: Tpo 1,scRNAseq

description: Library name: SF_BB_DMSO_TPO

source_name: Murine bone marrow from long bones and spine

value: TPO


title: Control_mVilli__HTO_1_S1_TotalSeqB_Tag

description: Library name: S1_htos

value: TotalSeqTM-B 0301 anti-mouse Hashtag 1

value: Control villi_tag


title: P1_85

value: Merkel cell

value: skin


title: P1_84

value: keratinocyte


title: P1_89


title: P1_82


title: 7-day_double mutant_RFP and CD44_Crypts

description: Library name: Crypts

data_processing:
cellranger count
Assembly: mm10
Supplementary files format and content: raw h5 matrix

source_name: duodenum crypt epithelium

extract_protocol: 10X 3' GEX

value: duodenum crypt epithelium

value: 4 days of tamoxifen and harvest at 7 days post induction


title: replicate 2,Visium10x

description: Library name: AB72

value: Murine bone marrow from long bones and spine

value: not applicable as visium work-up

value: EV,TPO,PT


title: replicate 3,Visium10x

description: Library name: AB73


title: P1_79

source_name: skin


title: Pdgfrb,replicate 3,scRNAseq

description: Library name: PT

value: MACS-depleted for CD11b, Gr1, Ter119, CD4, CD8, B220, CD45, and CD71, sorted for alive, lin neg tdTom+ singlets


title: 7-day_double mutant_all Villi cells

description: Library name: Villi

source_name: duodenum villi epithelium

value: duodenum villi epithelium


title: P1_78


title: replicate 1,Visium10x

description: Library name: AB71


title: Pdgfrb,replicate 2,scRNAseq

description: Library name: PE

value: EV


title: P1_80


title: Grem1,replicate 4,scRNAseq

description: Library name: Gremlin

value: Homeo


title: P1_73

value: dermal papilla cell


title: P1_76


title: Grem1,replicate 2,scRNAseq

description: Library name: Bella_68


title: P1_74


title: Grem1,replicate 1,scRNAseq

description: Library name: Bella_67


title: P1_70


title: P1_72


title: Pdgfrb,replicate 1,scRNAseq

description: Library name: Bella_1


title: Gli1,replicate 4,scRNAseq

description: Library name: Bella_GE


title: P1_69


title: Gli1,replicate 2,scRNAseq

description: Library name: FP59


title: Gli1,replicate 5,scRNAseq

description: Library name: Bella_GT


title: Gli1,replicate 3,scRNAseq

description: Library name: Homeo


title: P1_71


title: P1_67


title: Gli1,replicate 1,scRNAseq

description: Library name: FP58


title: P1_68


title: P1_66


title: P1_64


title: P1_65


title: Grem1,replicate 3,scRNAseq

description: Library name: GrH


title: carm-fib cells rep3

city: Chongqing

first: Wen

last: Zeng

address: Gaotanyan street

department: Department of Cell Biology

institute: Army Medical University

data_processing:
reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2.2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each Sample
Supplementary files format and content: Excel file includes TPM values for each Sample

source_name: macrophage

growth_protocol: carm and carm-fib cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The CAR-M group was cultured under normal conditions, while the CAR-M-Fib group was co-cultured with fibroblasts for 24 hours.

value: macrophage

value: culture with fibroblast


title: carm-fib cells rep2


title: P1_63

data_processing:
Sequencing reads were demultiplexed using Bcl2fastq. Adaptors were trimmed and 125bp sequencing reads were trimmed to 100bp using Trimmomatic. Reads were aligned to mouse reference genome Ensembl GRCm38.p6 using STAR 2.5.2b. Expression values for individual genes and transcripts were estimated and quantified with RSEM 1.3.0. Expression values of TPM (transcripts per million) were used for further analysis. 1057 cells passed quality control and were included in this study.
Assembly: mm10
Supplementary files format and content: Tab-separated matrix files at gene and transcript expression levels


title: carm cells, rep2

value: no treatment


title: P1_61


title: carm cells, rep3


title: carm cells, rep1


title: carm-fib cells rep1


title: P1_83


title: P1_59


title: P1_58


title: P1_57


title: GF_replicate_2_S_GFp21F_S

first: Lanlan

last: Shen

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
The WGBS reads were mapped to mouse genome (mm10) using BSMAP 2.90 with default parameters.
The methylation levels of these genomic features(promoters/gene-bodies/CpG islands/transposon) were calculated using the ‘avgmod’ module in BASALkit (https://www.github.com/JiejunShi/BASAL)
Differentially methylated regions (DMRs) are identified by Metilene v0.2-862 in ‘de novo’ mode with the option of ‘-m 5’ to get regions of at least 5 CpGs.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: colonic stem cell

extract_protocol:
Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (QIAGEN).
Approximately 250 ng genomic DNA was fragmented and used for xGen Methyl-Seq Library Preparation (Integrated DNA Technologies), according to the manufacturer's instructions. Bisulfite treatment was performed using the EZ DNA Methylation-Direct kit (Zymo Research).

value: colonic stem cell

tag: stain

value: Female

value: 3 wks

value: GF


title: GF_replicate_2_D_GFp21F_D

source_name: colonic differentiated cell

value: colonic differentiated cell


title: SPF_replicate_2_D_LD058245D

value: SPF


title: P1_62

extract_protocol:
Neonatal or postnatal epidermal cells and embryonic skin cells were disscociated from Sox2-GFP or Gfi1-GFP reporter mice. Cells were stained with DAPI for viability prior to cell sorting. Single GFP+ live cells were sorted into a 96 well plate preloaded with lysis buffer using Beckman MoFlo Astrios or BD Influx Cell Sorter. Lysis buffer was prepared following Smart-seq2 protocol (Picelli et al., 2014). Single GFP- live cells were sorted from the neonatal epidermal cells as controls.
Single-cell cDNA libraries were prepared following Smart-seq2 protocol (Picelli et al., 2014) with minor modifications. Briefly, single-cell RNA transcripts were reverse-transcribed using SuperScript II Reverse Transcriptase, following by pre-amplification of 21 cycles. cDNA concentration and quality were assessed using PicoGreen dsDNA Assay kit and Agilent bioanalyzer analysis with High sensitivity DNA kit, respectively. Single-cell cDNA libraries with high quality were selected for further processing. The cDNA was diluted and the concentration was normalized. 1152 single-cell cDNA libraries were generated using Illumina Nextera XT library preparation kit and were indexed using Illumina Nextera XT index kit v2.
cDNA libraries for each of the 384 cells was pooled together for sequencing in a way that each pooled library contained cells sourced from all different time points and both reporter mice. A total of three pooled cDNA libraries were prepared. Each pooled library was pair-end sequenced on 4 lanes of Hiseq3000 with 125bp or 100bp read length.

value: Merkel cell

value: skin


title: GF_replicate_1_D_GFp21M_D

value: Male


title: SPF_replicate_1_D_LD060124D


title: P1_55


title: GF_replicate_1_S_GFp21M_S


title: P1_60

value: keratinocyte


title: P1_54


title: SPF_replicate_1_S_LD060124


title: P1_52


title: GF_replicate_4_D_GFp100F_D

value: 15 wks


title: P1_49


title: P1_56


title: P1_50


title: GF_replicate_3_D_GFp100M_D


title: P1_53


title: GF_replicate_2_D_86712DCo


title: SPF_replicate_2_S_LD058245


title: GF_replicate_4_S_GFp100F_S


title: P1_51


title: P1_48


title: GF_replicate_1_D_328329DCo


title: P1_46


title: P1_45


title: GF_replicate_2_S_7349Co


title: GF_replicate_1_S_62636Co


title: P1_47


title: GF_replicate_3_S_GFp100M_S


title: SPF_replicate_1_D_LDf98DCo


title: SPF_replicate_2_D_LDf8595DCo


title: P1_44


title: P1_43


title: P1_40


title: P1_38


title: SPF_replicate_2_S_LDf42Co


title: Mouse embryos, siComb, Replicate 3

city: Barcelona

first: Agustín

middle: Sánchez

last: Belmonte

state: Barcelona

address: Nazaret 115 -117

department: Systems Oncology Program

country: Spain

institute: Vall d ́Hebron Institute of Oncology (VHIO)

description: Embryos were microinjected with the indicated siRNAs in the cytoplasm at the E0.5 zygote stage, and were cultured in vitro until E2.75 for transcriptomic analysis

data_processing:
Sequencing quality control was performed using multiqc preprocessing (v1.18), and adapters were removed with BBDuk (v39.01).
We performed read alignment to the mm10 version of GRCh38 mouse reference genome using STAR (v2.7.11a) and quantification using featureCounts from Subread package (v2.0.6; (Liao et al, 2019)) and count matrices were used for downstream analysis in scanpy v. 1.8.2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample, txt file

source_name: Mouse embryos

growth_protocol: Embryos of the indicated stages were cultured in vitro in KSOM medium until the morula stage (E2.75)

extract_protocol:
15-20 embryos were collected per sample and resuspended in 8 uL of low input lysis buffer of the NEBNext Single Cell/Low input cDNA Synthesis & Amplification module (#E6421S).
Whole cells were processed with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. Double stranded cDNA production was performed by limited-cycle PCR. Sequencing libraries were completed with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805) and subsequently analysed on an Illumina instrument by following manufacturer's protocols.
ultra-low input RNA-seq

treatment_protocol: Embryos were microinjected with siRNAs for the indicated targets at E0.5 or treated with the indicated small molecule inhibitors at E2.5. All embryos were harvested for bulk transcriptomic analysis at E2.75.

value: Mouse embryos

value: morula blastomeres

value: Wildtype

value: siComb


title: Mouse embryos, siComb, Replicate 2


title: P1_42


title: Mouse embryos, siComb, Replicate 1


title: P1_36


title: P1_34


title: Mouse embryos, siKat6b, Replicate 3


title: P1_37


title: Mouse embryos, siKat6b, Replicate 1


title: P1_33


title: SPF_replicate_1_S_LDf80Co


title: Mouse embryos, siKat6b, Replicate 2


title: Mouse embryos, siKat6a, Replicate 2


title: P1_28


title: Mouse embryos, siKat6a, Replicate 1


title: P1_32


title: P1_29


title: Mouse embryos, siP300, Replicate 3


title: Mouse embryos, siKat6a, Replicate 3


title: P1_39


title: P1_27


title: P1_31


title: P1_26


title: Mouse embryos, siP300, Replicate 1


title: Mouse embryos, siControl, Replicate 3

value: siControl


title: Mouse embryos, siP300, Replicate 2


title: P1_23


title: P1_22


title: Mouse embryos, siControl, Replicate 2


title: Mouse embryos, siControl, Replicate 1


title: P1_24


title: P1_25


title: P1_20


title: Mouse embryos, TSA, Replicate 1

description: Embryos were subjected to the indicated treatment from E2.5 to E2.75 in vitro

value: TSA inhibitor


title: Mouse embryos, TSA, Replicate 3


title: P1_21


title: Mouse embryos, TSA, Replicate 2


title: P1_19


title: Mouse embryos, A485, Replicate 2

value: A485 inhibitor


title: Mouse embryos, A485, Replicate 3


title: P1_17


title: P1_16


title: Mouse embryos, SAHA, Replicate 2

value: SAHA inhibitor


title: P1_18


title: Mouse embryos, SAHA, Replicate 3


title: P1_14


title: Mouse embryos, A485, Replicate 1


title: P1_15


title: Mouse embryos, SAHA, Replicate 1


title: P1_13


title: Mouse embryos, Vehicle, Replicate 3

value: Vehicle


title: Mouse embryos, Vehicle, Replicate 2


title: Treatment group

description: scRNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
Kidney tissue was minced and cells were dissociated using enzyme mixture (2.5 ml RPMI (no serum), 2 mg/ml collagen protease, 2 mg/ml dispertase and 0.05 mg/ml DNA enzyme I). Single cell suspension was stained in FACS buffer (PBS, 1% BSA, sc-46656, Santa Cruz biotechnology) antibody with fluorescent dye-labeled CD10 (0.05% sodium azide) and sorted with Aria sorp and cell sorter (BD Biosciences, USA). Cell debris was excluded by FSC and SSC parameters, cell adhesion by SSC or FSC W and H parameters, and dead cells by 7-AAD and calcein AM to select cells with good viability. The CD 10-positive cells were then sorted. CD10 + cells and Cd 10-cells were separately sorted from kidney samples and mixed at a 1:2 ratio.
The 10X Genomics 3' transcriptome uses short read long sequencing and microfluidic technology for simultaneous transcriptome expression profiling of 500-10,000 cells per sample. The cDNA digestion was first broken into fragments of approximately 200 to 300 bp, plus the traditional second-generation sequencing process of sequencing connector P5 and sequencing primer R1, and finally amplified by PCR to obtain the DNA library. Library sequencing was performed at high throughput using the two-end sequencing mode of the Illumina sequencing platform. At the Read 1 end, 16 bp of barcode information and 10 bp of UMI information were used to determine cells and expression quantification; at the Read 2 end, the cDNA fragment was used to identify the genes corresponding to the mRNA.

treatment_protocol: The sham group underwent unilateral ureteral separation, the fibrotic group underwent unilateral ureteral ligation, and the treatment group mice underwent unilateral ureteral ligation after CAR-M2 hydrogel renal capsule injection.

value: Kidney


title: P1_10


title: Mouse embryos, Vehicle, Replicate 1


title: P1_12


title: P1_9


title: Fibrotic group

description: scRNA-seq


title: Cisplatin_3,PD7

data_processing:
Raw reads were trimmed to remove low-quality bases and adaptor sequences using Trim Galore v0.6.7. Reads were further mapped to the mouse (mm9) genomes using STAR v2.7.10a.
Uniquely mapped reads were applied for gene expression quantification using FeatureCounts v2.0.2.
Biotinylated gene transcript abundance was further analyzed using the DESeq2 R package. An adjusted p-value of < 0.05, and fold change (FC) of APEXflox/+;Gdf9-Cre/WT > 2 were considered statistically significant to identify primordial follicle oocyte mRNAs.
Transcripts per million mapped reads (TPM) was calculated to validate gene expression and normalized to gene length and sequencing depth.
Assembly: mm9
Supplementary files format and content: countlist.xlsx includes raw counts for each sample

source_name: ovary

extract_protocol:
The whole ovary was lysed and then RNA was enriched for sequencing.
RNAs were diluted to 0.2 ng/μL and 2.5 μL samples were performed library constructions. The samples were incubated with oligo(dT) primers (a deoxynucleoside triphosphate mixture) for 3 min at 72 °C, and cDNA pools were obtained by Smart-seq2 reverse transcription reactions. After the first-strand reaction, the cDNAs were pre-amplified with limited cycles (~ 12 cycles). Sequencing libraries were then constructed with 0.5 ng cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina (TD503; Vazyme, Nanjing, China) according to the manufacturer’s instructions. Barcoded libraries were pooled and sequenced on the Illumina NovaSeq 6000 platform in the 151 bp paired-end mode.

value: ovary


title: P1_8


title: P1_7


title: P1_11


title: scRNA-seq after miR-18a KO 1

city: Tianjin

first: Wanyi

last: Xiao

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District Tianjin

institute: Tianjin Medical University Cancer Institute and Hospital

description: Library name: scRNA_KO_1

data_processing:
Raw sequencing data were processed using Cell Ranger for alignment and gene counting. Downstream quality control, normalization, dimensionality reduction, clustering, and differential expression analyses were performed using Seurat.
Assembly: hg19
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Homo sapiens

extract_protocol:
Single-cell suspensions were prepared from cultured cells with viability greater than 90% prior to loading onto the 10x Genomics Chromium platform.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ library preparation kit according to the manufacturer’s instructions.


title: scRNA-seq, VR

description: Library name: scRNA_VR


title: P1_5


title: Cisplatin_2,PD7


title: Single-cell sequencing WT 7

description: Library name: WT_scRNA_7


title: P1_4


title: P1_6


title: scRNA-seq after miR-18a KO 2

description: Library name: scRNA_KO_2


title: Single-cell sequencing WT 5

description: Library name: WT_scRNA_5


title: Sham group

description: scRNA-seq


title: Single-cell sequencing WT 4

description: Library name: WT_scRNA_4


title: Single-cell sequencing WT 3

description: Library name: WT_scRNA_3


title: scRNA-seq, TR

description: Library name: scRNA_TR


title: P1_2


title: Single-cell sequencing WT 8

description: Library name: WT_scRNA_8


title: Cisplatin_1,PD7


title: Apex_3,PD7


title: Apex_1,PD7


title: Single-cell sequencing WT 6

description: Library name: WT_scRNA_6


title: P1_3


title: WT_3,PD7


title: Apex_2,PD7


title: MII_smRNA-seq_5

city: Shanghai

first: Fengjuan

last: Zhang

state: Shanghai

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description:
Library name: Sample 46
MII stage oocyte (MII)

data_processing:
For small RNA-seq, raw read1 sequences were processed using the fastx_toolkit (v.0.0.14) for quality filtering and adapters trimming. Reads lacking the 3’ adapter sequence or shorter than 17 bp post-trimming were discarded. Reads of 17-40 bp were mapped to the human genome (hg19) using Bowtie (v.1.2) with parameters --k=100 --v=0.
For long RNA-seq, raw pair-end reads were processed using TrimGalore (v.0.5.0) for adapter trimming and quality filtering. The remaining reads were mapped to the human genome (hg19) and representative TE sequences using STAR (v2.7.1a) with parameters --winAnchorMultimapNmax 10000 --outFilterMultimapNmax 10000. Gene abundance was quantified using RSEM (v.1.2.31) with default settings.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include useful reads count of smRNAs and each gene count.

source_name: oocyte

extract_protocol:
Total RNAs were extracted from mouse oocytes and cultured cells using TRIzol reagent (Ambion), respectively. The quantity of isolated RNA was measured with Qubit 2.0 Fluorometer (Invitrogen).
Lysates from the single oocyte were incubated at 72 °C for 3 minutes to release and unfold the small RNAs. After 3′ adapter ligation, 5 U of lambda exonuclease and 25 U of 5′ deadenylates were used to remove the excess 3′ adapter. Subsequently, 5′ adapter was ligated, followed by reverse transcription and pre-amplification. For final amplification, 1 μL of the pre-amplified product was used as a template. Libraries were size-selected by electrophoresis on a 6% polyacrylamide gel, and 130–160 bp DNA fragments were extracted to recover small RNA libraries. Single-oocyte mRNA was captured and amplified using Smart-seq2, as previously described, 69. 2 ng of purified cDNA was subjected to a tagmentation reaction with Tn5 transposase70.

treatment_protocol: Human follicles were isolated from fresh ovarian cortex obtained from patients undergoing ovarian cyst or cystic teratoma resection, following previously described procedures67. Briefly, ovarian cortical tissues were fragmented into pieces measuring 30–600 μm and digested with 1 mg/mL collagenase type IA (Sigma-Aldrich) and 8 IU/mL DNase I (Sigma-Aldrich) in 10 mL of M199 medium (Gibco) at 37°C for 30 minutes with gentle agitation. Follicles were subsequently isolated and evaluated under a stereomicroscope (Nikon SMZ 1000), and their diameters were measured using an inverted microscope (Nikon Ti2). Ovarian stimulation and oocyte collection was performed as previously describe39, 67. GV and MI stage oocytes were collected following stimulation. MII stage oocytes were obtained after overnight incubation to facilitate maturation, conforming by the presence of a distinct first polar body under microscope observation. Granulosa cells were removed via incubation with trypsin-EDTA solution (Gibco) and 1 mg/mL hyaluronidase. The zona pellucida was eliminated using Acidic Tyrode's Solution (Millipore), yielding denuded oocytes which were then washed and transferred to PCR tubes containing 4 μL of cell lysis buffer (0.2% Triton X-100, Sigma; 1 U/μL RiboLock RNase inhibitor, Thermo Fisher). The oocytes were stored at -80°C until further processing.

value: oocyte

value: wild type


title: WT_2,PD7


title: MII_smRNA-seq_3

description:
Library name: Sample 44
MII stage oocyte (MII)


title: P1_1

first: Lingling

last: Miao

address: 9000 Rockville Pike

institute: National Institutes of Health

value: Merkel cell

value: skin