title: PBM_IgAN_19_065


title: PBM_IgAN_19_066

status: Public on Jul 06 2021

type: SRA

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
scRNA-Seq：Sequencing read pairs were split into single-cell RNA-seq read pairs according to the 8bp barcode of read2, followed by corresponding extraction of read1. Unique Molecular Identifiers (UMIs) were added to sequence identifier of read1 in order to correctly identify PCR duplicates later. We subsequently trimmed template switch oligo (TSO) sequence and ployA tail sequence in read1. After removing adapter contaminants and low-quality bases (N > 10%), we aligned clean reads to hg19 human reference genome from UCSC using TopHat (version 2.0.12). Then, the htseq-count script developed with HTSeq (version 0.6.0) was used to count uniquely aligned reads with genes. Transcripts of the same gene with identical UMIs were regarded as PCR duplicates and removed in this process.
Genome_build: hg19
Supplementary_files_format_and_content: A  comma-separated values (csv) file include UMI counts for each single cell RNA samples

molecule: polyA RNA

organism: Homo sapiens

source_name: monocytes from IgAN patients' peripheral blood

growth_protocol: Paracancerous tissues from renal carcinoma were diced and incubated with 0.5mg/ml type II (SIGMA, C6885) and 0.5mg/ml type IV (SIGMA, C5138) collagenase at 37℃ for 15 min. The glomeruli were transferred by pipetting to RPMI 1640 with 25 mM HEPES (Gibco, 22400-089) supplemented with 100 U/mL penicillin, 100 ug/mL streptomycin, 2 mM L-glutamine and 10% fetal bovine serum. After 7-10 days’ incubation, mesangial cells were seen at the edges of glomeruli that attached to the plate and passaged when confluent using 0.05% trypsin. Mesangial cells after 4~5 weeks of subculture still remains homogenous, the morphologically was characterized by phase contrast microscopy. Immunofluorescence staining of Desmin (Abcam, ab32362, 1:100) and Vimentin (Abcam, ab8978, 1:100) were used to identify mesangium. All experiments were performed using confluent mesangial cells from the 2nd to 4th passage. In an attempt to mimic the microenvironment around mesangial cells in vivo, mesangial cells were cultured with serum collected from normal volunteers or IgAN patients. In order to avoid influence of complement, all human serums were heat-inactivated by 56℃ water bath for 30 min before using.

extract_protocol:
Single-cell RNA sequencing was conducted using a modified high throughput STRT method. Single cell was transferred to lysis buffer containing a 25-bp RT primer that consists of poly T and a fragment of cell barcode and unique molecular identifier (UMI). The reverse transcription was then initiated by SSII, the synthesized cDNA was further amplified by 19 cycles of PCR to generate double-strand DNA. Then, the purified DNA was further amplified by another four cycles of PCR using a biotinylationed primer to add biotin modification to the 3’ terminal of the synthesized DNA. Subsequently, the modified double-strand DNA were fragmented to 300 bp by super sonication, the 3’ terminal fragments were then coupled to streptavidin C1 beads with one hour’s incubation. After washing by 2X B&W buffer, 3’ terminal of reverse transcribed DNA on C1 beads were used for library construction.
Preparation of library was based on the instruction of Kapa Hyper Prep Kit.
All sequencing data were generated by 150-bp pair-end sequencing through an Illumina Hiseq-4000 platform.

treatment_protocol: Sample collection procedure was approved by the Medicine Ethics Committee of the Chinese People’s Liberation Army General Hospital (S2017-102-01). 13 IgAN patients’ renal biopsies and 6 renal paracancerous tissue were collected. To capture cells inside glomerulus, renal biopsies were first cut into millimeter-sized pieces, the treated tissues were then transferred to 1ml 0.5mg/ml collagenase II and collagenase IV mixtures and digested for 5 min at 37°C with slight shaking. Digested tissues were then transferred to a 2 cm dish and diluted by 1 ml DMEM cell culture medium. Glomerulus were quickly picked using 100 µm inner-diameter mouth pipette and transferred to a 20 µl DPBS dro in 2 cm dish, after slightly treating with needle, the glomerulus were transferred to 200 µl mixtures containing 0.5mg/ml collagenase II, 0.5 mg/ml collagenase IV and 0.0125% tyrisin for 15 minutes’ digestion at 37°C with 900 rpm shaking. Meanwhile, the rest tissues were collected and centrifuged at 500g for 3min, after removing supernatant, tissues were resuspeded by 500 µl 0.5mg/ml collagenase II and collagenase IV mixtures and digested at 37°C with 900 rpm shaking for 10 min. After digestion, cells were centrifuged at 800g for 5min. For glomerulus cells, about 80~90 µl supernatant was discarded and resuspended by 200 µl DMEM culture medium. For the rest renal cells, all supernatant was removed and the pellets were then resuspended by 100 µl DMEM. To capture the major cell types, the non-glomerulus renal cells were first incubated with 100 µl buffer containing 10 µl CD14+ MicroBeads (Miltenyi, 130-050-021) for 15 min at 4°C. Cells were then washed by 1X DPBS and macrophages were isolated on magnetic rack using MS column, 300 µl DMEM was added to the column to flush out macrophages. The negative selected cells were then resuspended by 100 µl DMEM, after 15 min’s incubation with 100 µl buffer that contains 10 µl CD326 (EPCAM) beads at 4°C, epithelium were isolated using MS column on magnetic rack. To cover all the cell types, the last negative selected cells were also collected. All collected cells were diluted to 300 µl using DMEM. For monocytes collection, we took 5 ml peripheral blood from each of the 5 normal people and 5 of the 13 IgAN patients. Peripheral blood samples were collected into EDTA vacutainers. Peripheral blood monocytes were first isolated by Ficoll-Paque (Solarbio, P8680). The PBMC cell layer was collected and washed three times with PBS. After centrifugation with 800g for 5 min, cell pellets were resuspended in 300 µL buffer which contains 30 µl CD14+ beads and incubated for 15 min at 4℃. Cells were washed by PBS and monocytes were isolated using LS Column on MACS Separator (Miltenyi, 130-042-302). 5 mL of DMEM were added to the column to flush out positive cells using the plunger supplied with the column. Cell suspension was centrifuged and resuspended to 500 µl.

tag: patients

tag: disease state

value: IgAN

tag: cell type

value: monocytes


title: PBM_IgAN_19_064


title: PBM_IgAN_19_059


title: PBM_IgAN_19_060


title: PBM_IgAN_19_058


title: PBM_IgAN_19_056


title: PBM_IgAN_19_055


title: PBM_IgAN_19_061


title: PBM_IgAN_19_062


title: PBM_IgAN_19_053


title: PBM_IgAN_19_051


title: PBM_IgAN_19_054


title: PBM_IgAN_19_050


title: PBM_IgAN_19_057


title: PBM_IgAN_19_052


title: PBM_IgAN_19_048


title: PBM_IgAN_19_049


title: PBM_IgAN_19_044


title: PBM_IgAN_19_045


title: PBM_IgAN_19_047


title: PBM_IgAN_19_046


title: PBM_IgAN_19_042


title: PBM_IgAN_19_043


title: PBM_IgAN_19_063


title: PBM_IgAN_19_040


title: PBM_IgAN_19_039


title: PBM_IgAN_19_034


title: PBM_IgAN_19_033


title: PBM_IgAN_19_031


title: PBM_IgAN_19_029


title: PBM_IgAN_19_035


title: PBM_IgAN_19_038


title: PBM_IgAN_19_037


title: PBM_IgAN_19_024


title: PBM_IgAN_19_025


title: PBM_IgAN_19_036


title: PBM_IgAN_19_027


title: PBM_IgAN_19_023


title: PBM_IgAN_19_021


title: PBM_IgAN_19_022


title: PBM_IgAN_19_028


title: PBM_IgAN_19_020


title: PBM_IgAN_19_018


title: PBM_IgAN_19_016


title: PBM_IgAN_19_019


title: PBM_IgAN_19_041


title: PBM_IgAN_19_030


title: PBM_IgAN_19_032


title: PBM_IgAN_19_014


title: PBM_IgAN_19_015


title: PBM_IgAN_19_013


title: PBM_IgAN_19_012


title: PBM_IgAN_19_026


title: PBM_IgAN_19_011


title: PBM_IgAN_19_017


title: PBM_IgAN_19_010


title: PBM_IgAN_19_004


title: PBM_IgAN_19_006


title: PBM_IgAN_19_002


title: PBM_IgAN_19_009


title: PBM_IgAN_17_104


title: PBM_IgAN_19_001


title: PBM_IgAN_17_105


title: PBM_IgAN_17_108


title: PBM_IgAN_19_008


title: PBM_IgAN_19_003


title: PBM_IgAN_19_005


title: PBM_IgAN_19_007


title: PBM_IgAN_17_106


title: PBM_IgAN_17_107


title: PBM_IgAN_17_103


title: PBM_IgAN_17_102


title: PBM_IgAN_17_100


title: PBM_IgAN_17_099


title: PBM_IgAN_17_101


title: PBM_IgAN_17_098


title: PBM_IgAN_17_097


title: PBM_IgAN_17_095


title: PBM_IgAN_17_092


title: PBM_IgAN_17_096


title: PBM_IgAN_17_093


title: PBM_IgAN_17_094


title: PBM_IgAN_17_091


title: PBM_IgAN_17_090


title: PBM_IgAN_17_089


title: PBM_IgAN_17_087


title: PBM_IgAN_17_088


title: PBM_IgAN_17_086


title: PBM_IgAN_17_080


title: PBM_IgAN_17_085


title: PBM_IgAN_17_079


title: PBM_IgAN_17_077


title: PBM_IgAN_17_081


title: PBM_IgAN_17_082


title: PBM_IgAN_17_083


title: PBM_IgAN_17_078


title: PBM_IgAN_17_074


title: PBM_IgAN_17_070


title: PBM_IgAN_17_068


title: PBM_IgAN_17_075


title: PBM_IgAN_17_073


title: PBM_IgAN_17_072


title: PBM_IgAN_17_076


title: PBM_IgAN_17_071


title: PBM_IgAN_17_065


title: PBM_IgAN_17_067


title: PBM_IgAN_17_066


title: PBM_IgAN_17_063


title: PBM_IgAN_17_069


title: PBM_IgAN_17_062


title: PBM_IgAN_17_084


title: PBM_IgAN_17_061


title: PBM_IgAN_17_058


title: PBM_IgAN_17_059


title: PBM_IgAN_17_060


title: PBM_IgAN_17_057


title: PBM_IgAN_17_064


title: PBM_IgAN_17_053


title: PBM_IgAN_17_054


title: PBM_IgAN_17_051


title: PBM_IgAN_17_056


title: PBM_IgAN_17_050


title: PBM_IgAN_17_052


title: PBM_IgAN_17_049


title: PBM_IgAN_17_047


title: PBM_IgAN_17_048


title: PBM_IgAN_17_044


title: PBM_IgAN_17_046


title: PBM_IgAN_17_042


title: PBM_IgAN_17_045


title: PBM_IgAN_17_043


title: PBM_IgAN_17_041


title: PBM_IgAN_17_040


title: PBM_IgAN_17_039


title: PBM_IgAN_17_037


title: PBM_IgAN_17_038


title: PBM_IgAN_17_036


title: PBM_IgAN_17_034


title: PBM_IgAN_17_055


title: PBM_IgAN_17_033


title: PBM_IgAN_17_031


title: PBM_IgAN_17_032


title: PBM_IgAN_17_030


title: PBM_IgAN_17_029


title: PBM_IgAN_17_026


title: PBM_IgAN_17_028


title: PBM_IgAN_17_025


title: PBM_IgAN_17_021


title: PBM_IgAN_17_024


title: PBM_IgAN_17_023


title: PBM_IgAN_17_027


title: PBM_IgAN_17_022


title: PBM_IgAN_17_017


title: PBM_IgAN_17_035


title: PBM_IgAN_17_015


title: PBM_IgAN_17_011


title: PBM_IgAN_17_020


title: PBM_IgAN_17_013


title: PBM_IgAN_17_016


title: PBM_IgAN_17_010


title: PBM_IgAN_17_009


title: PBM_IgAN_17_008


title: PBM_IgAN_17_014


title: PBM_IgAN_17_018


title: PBM_IgAN_17_007


title: PBM_IgAN_17_012


title: PBM_IgAN_17_006


title: PBM_IgAN_17_005


title: PBM_IgAN_17_002


title: PBM_IgAN_17_003


title: PBM_IgAN_19_069


title: PBM_IgAN_17_019


title: PBM_IgAN_12_076


title: PBM_IgAN_12_074


title: PBM_IgAN_12_073


title: PBM_IgAN_12_070


title: PBM_IgAN_12_072


title: PBM_IgAN_12_075


title: PBM_IgAN_12_067


title: PBM_IgAN_12_064


title: PBM_IgAN_12_065


title: PBM_IgAN_12_068


title: PBM_IgAN_12_061


title: PBM_IgAN_12_060


title: PBM_IgAN_12_062


title: PBM_IgAN_12_066


title: PBM_IgAN_12_059


title: PBM_IgAN_12_055


title: PBM_IgAN_12_058


title: PBM_IgAN_12_056


title: PBM_IgAN_12_057


title: PBM_IgAN_12_063


title: PBM_IgAN_12_054


title: PBM_IgAN_17_004


title: PBM_IgAN_12_053


title: PBM_IgAN_12_071


title: PBM_IgAN_17_001


title: PBM_IgAN_12_069


title: PBM_IgAN_12_049


title: PBM_IgAN_12_050


title: PBM_IgAN_12_047


title: PBM_IgAN_12_043


title: PBM_IgAN_12_039


title: PBM_IgAN_12_042


title: PBM_IgAN_12_040


title: PBM_IgAN_12_038


title: PBM_IgAN_12_037


title: PBM_IgAN_12_035


title: PBM_IgAN_12_036


title: PBM_IgAN_12_034


title: PBM_IgAN_12_031


title: PBM_IgAN_12_033


title: PBM_IgAN_12_052


title: PBM_IgAN_12_029


title: PBM_IgAN_12_030


title: PBM_IgAN_12_051


title: PBM_IgAN_12_028


title: PBM_IgAN_12_026


title: PBM_IgAN_12_025


title: PBM_IgAN_12_024


title: PBM_IgAN_12_046


title: PBM_IgAN_12_027


title: PBM_IgAN_12_045


title: PBM_IgAN_12_048


title: PBM_IgAN_12_021


title: PBM_IgAN_12_020


title: PBM_IgAN_12_022


title: PBM_IgAN_12_044


title: PBM_IgAN_12_023


title: PBM_IgAN_12_019


title: PBM_IgAN_12_041


title: PBM_IgAN_12_018


title: PBM_IgAN_12_032


title: PBM_IgAN_12_017


title: PBM_IgAN_12_016


title: PBM_IgAN_12_013


title: PBM_IgAN_12_014


title: PBM_IgAN_12_015


title: PBM_IgAN_12_012


title: PBM_IgAN_12_011


title: PBM_IgAN_12_009


title: PBM_IgAN_12_010


title: PBM_IgAN_12_007


title: PBM_IgAN_12_006


title: PBM_IgAN_12_005


title: PBM_IgAN_12_004


title: PBM_IgAN_12_008


title: PBM_IgAN_12_003


title: PBM_IgAN_12_002


title: PBM_IgAN_10_220


title: PBM_IgAN_10_218


title: PBM_IgAN_10_217


title: PBM_IgAN_10_219


title: PBM_IgAN_12_001


title: PBM_IgAN_10_216


title: PBM_IgAN_10_212


title: PBM_IgAN_10_213


title: PBM_IgAN_10_211


title: PBM_IgAN_10_210


title: PBM_IgAN_10_209


title: PBM_IgAN_10_214


title: PBM_IgAN_10_207


title: PBM_IgAN_10_208


title: PBM_IgAN_10_201


title: PBM_IgAN_10_204


title: PBM_IgAN_10_199


title: PBM_IgAN_10_206


title: PBM_IgAN_10_203


title: PBM_IgAN_10_196


title: PBM_IgAN_10_195


title: PBM_IgAN_10_198


title: PBM_IgAN_10_194


title: PBM_IgAN_10_215


title: PBM_IgAN_10_193


title: PBM_IgAN_10_192


title: PBM_IgAN_10_191


title: PBM_IgAN_10_189


title: PBM_IgAN_10_190


title: PBM_IgAN_10_205


title: PBM_IgAN_10_202


title: PBM_IgAN_10_200


title: PBM_IgAN_10_197


title: IgAN_10_024

source_name: IgAN patients’ renal biopsies

tag: tissue

value: renal biopsies


title: IgAN_10_023


title: IgAN_10_026


title: IgAN_10_022


title: IgAN_10_025


title: IgAN_10_027


title: IgAN_10_020


title: IgAN_10_021


title: IgAN_10_017


title: IgAN_10_019


title: IgAN_10_018


title: IgAN_10_014


title: IgAN_10_011


title: IgAN_10_010


title: IgAN_10_009


title: IgAN_10_006


title: IgAN_10_007


title: IgAN_10_008


title: IgAN_10_016


title: IgAN_10_005


title: IgAN_10_004


title: IgAN_10_015


title: IgAN_10_012


title: IgAN_10_003


title: IgAN_10_001


title: IgAN_09_303


title: IgAN_10_002


title: IgAN_09_302


title: IgAN_10_013


title: IgAN_09_301


title: IgAN_09_299


title: IgAN_09_295


title: IgAN_09_296


title: IgAN_09_298


title: IgAN_09_290


title: IgAN_09_300


title: IgAN_09_297


title: IgAN_09_291


title: IgAN_09_286


title: IgAN_09_289


title: IgAN_09_294


title: IgAN_09_285


title: IgAN_09_293


title: IgAN_09_292


title: IgAN_09_287


title: IgAN_09_282


title: IgAN_09_283


title: IgAN_09_284


title: IgAN_09_288


title: IgAN_09_281


title: IgAN_09_279


title: IgAN_09_280


title: IgAN_09_276


title: IgAN_09_275


title: IgAN_09_274


title: IgAN_09_277


title: IgAN_09_273


title: IgAN_09_272


title: IgAN_09_271


title: IgAN_09_278


title: IgAN_09_270


title: IgAN_09_267


title: IgAN_09_269


title: IgAN_09_268


title: IgAN_09_265


title: IgAN_09_266


title: IgAN_09_261


title: IgAN_09_264


title: IgAN_09_263


title: IgAN_09_258


title: IgAN_09_254


title: IgAN_09_257


title: IgAN_09_256


title: IgAN_09_249


title: IgAN_09_252


title: IgAN_09_253


title: IgAN_09_251


title: IgAN_09_248


title: IgAN_09_246


title: IgAN_09_247


title: IgAN_09_245


title: IgAN_09_244


title: IgAN_09_262


title: IgAN_09_260


title: IgAN_09_243


title: IgAN_09_255


title: IgAN_09_259


title: IgAN_09_241


title: IgAN_09_242


title: IgAN_09_250


title: IgAN_09_236


title: IgAN_09_240


title: IgAN_09_237


title: IgAN_09_235


title: IgAN_09_239


title: IgAN_09_238


title: IgAN_09_234


title: IgAN_09_233


title: IgAN_09_231


title: IgAN_09_230


title: IgAN_09_229


title: IgAN_09_228


title: IgAN_09_226


title: IgAN_09_227


title: IgAN_09_225


title: IgAN_09_223


title: IgAN_09_221


title: IgAN_09_222


title: IgAN_09_219


title: IgAN_09_224


title: IgAN_09_217


title: IgAN_09_218


title: IgAN_09_220


title: IgAN_09_215


title: IgAN_09_216


title: IgAN_09_214


title: IgAN_09_213


title: IgAN_09_212


title: IgAN_09_209


title: IgAN_09_210


title: IgAN_09_211


title: IgAN_09_207


title: IgAN_09_208


title: IgAN_09_205


title: IgAN_09_203


title: IgAN_09_199


title: IgAN_09_206


title: IgAN_09_202


title: IgAN_09_200


title: IgAN_09_197


title: IgAN_09_198


title: IgAN_09_201


title: IgAN_09_196


title: IgAN_09_195


title: IgAN_09_188


title: IgAN_09_194


title: IgAN_09_193


title: IgAN_09_232


title: IgAN_09_191


title: IgAN_09_192


title: IgAN_09_190


title: IgAN_09_183


title: IgAN_09_189


title: IgAN_09_187


title: IgAN_09_185


title: IgAN_09_186


title: IgAN_09_169


title: IgAN_09_171


title: IgAN_09_204


title: IgAN_09_184


title: IgAN_09_182


title: IgAN_09_178


title: IgAN_09_179


title: IgAN_09_180


title: IgAN_09_164


title: IgAN_09_181


title: IgAN_09_176


title: IgAN_09_177


title: IgAN_09_163


title: IgAN_09_174


title: IgAN_09_173


title: IgAN_09_161


title: IgAN_09_170


title: IgAN_09_172


title: IgAN_09_158


title: IgAN_09_157


title: IgAN_09_156


title: IgAN_09_155


title: IgAN_09_154


title: IgAN_09_168


title: IgAN_09_167


title: IgAN_09_166


title: IgAN_09_150


title: IgAN_09_165


title: IgAN_09_151


title: IgAN_09_162


title: IgAN_09_146


title: IgAN_09_149


title: IgAN_09_159


title: IgAN_09_141


title: IgAN_09_142


title: IgAN_09_160


title: IgAN_09_175


title: IgAN_09_138


title: IgAN_09_137


title: IgAN_09_153


title: IgAN_09_152


title: IgAN_09_147


title: IgAN_09_134


title: IgAN_09_135


title: IgAN_09_136


title: IgAN_09_145


title: IgAN_09_132


title: IgAN_09_133


title: IgAN_09_144


title: IgAN_09_143


title: IgAN_09_140


title: IgAN_09_130


title: IgAN_09_139


title: IgAN_09_148


title: IgAN_09_125


title: IgAN_09_124


title: IgAN_09_122


title: IgAN_09_121


title: IgAN_09_131


title: IgAN_09_129


title: IgAN_09_128


title: IgAN_09_116


title: IgAN_09_127


title: IgAN_09_126


title: IgAN_09_114


title: IgAN_09_109


title: IgAN_09_117


title: IgAN_09_120


title: IgAN_09_112


title: IgAN_09_113


title: IgAN_09_119


title: IgAN_09_118


title: IgAN_09_107


title: IgAN_09_115


title: IgAN_09_104


title: IgAN_09_106


title: IgAN_09_103


title: IgAN_09_111


title: IgAN_09_110


title: IgAN_09_123


title: IgAN_09_102


title: IgAN_09_098


title: IgAN_09_105


title: IgAN_09_096


title: IgAN_09_094


title: IgAN_09_092


title: IgAN_09_095


title: IgAN_09_093


title: IgAN_09_108


title: IgAN_09_101


title: IgAN_09_091


title: IgAN_09_090


title: IgAN_09_086


title: IgAN_09_084


title: IgAN_09_085


title: IgAN_09_083


title: IgAN_09_100


title: IgAN_09_082


title: IgAN_09_099


title: IgAN_09_077


title: IgAN_09_097


title: IgAN_09_076


title: IgAN_09_079


title: IgAN_09_078


title: IgAN_09_080


title: IgAN_09_075


title: IgAN_09_074


title: IgAN_09_089


title: IgAN_09_073


title: IgAN_09_088


title: IgAN_09_087


title: IgAN_09_071


title: IgAN_09_069


title: IgAN_09_065


title: IgAN_09_081


title: IgAN_09_061


title: IgAN_09_062


title: IgAN_09_060


title: IgAN_09_066


title: IgAN_09_058


title: IgAN_09_057


title: IgAN_09_056


title: IgAN_09_055


title: IgAN_09_054


title: IgAN_09_063


title: IgAN_09_053


title: IgAN_09_064


title: IgAN_09_072


title: IgAN_09_052


title: IgAN_09_059


title: IgAN_09_070


title: IgAN_09_068


title: IgAN_09_049


title: IgAN_09_051


title: IgAN_09_044


title: IgAN_09_045


title: IgAN_09_048


title: IgAN_09_046


title: IgAN_09_047


title: IgAN_09_067


title: IgAN_09_043


title: IgAN_09_042


title: IgAN_09_041


title: IgAN_09_040


title: IgAN_09_039


title: IgAN_09_050


title: IgAN_09_038


title: IgAN_09_037


title: IgAN_09_036


title: IgAN_09_032


title: IgAN_09_033


title: IgAN_09_034


title: IgAN_09_035


title: IgAN_09_031


title: IgAN_09_029


title: IgAN_09_030


title: IgAN_09_027


title: IgAN_09_022


title: IgAN_09_026


title: IgAN_09_023


title: IgAN_09_024


title: IgAN_09_028


title: IgAN_09_016


title: IgAN_09_020


title: IgAN_09_019


title: IgAN_09_015


title: IgAN_09_025


title: IgAN_09_012


title: IgAN_09_011


title: IgAN_09_010


title: IgAN_09_007


title: IgAN_09_006


title: IgAN_09_008


title: IgAN_09_002


title: IgAN_09_021


title: IgAN_09_004


title: IgAN_09_018


title: IgAN_09_017


title: IgAN_09_014


title: IgAN_09_005


title: IgAN_09_001


title: IgAN_09_009


title: IgAN_07_440


title: IgAN_07_439


title: IgAN_07_438


title: IgAN_07_437


title: IgAN_07_442


title: IgAN_07_441


title: IgAN_07_436


title: IgAN_09_013


title: IgAN_07_430


title: IgAN_07_432


title: IgAN_07_434


title: IgAN_07_435


title: IgAN_07_431


title: IgAN_09_003


title: IgAN_07_429


title: IgAN_07_428


title: IgAN_07_427


title: IgAN_07_425


title: IgAN_07_426


title: IgAN_07_424


title: IgAN_07_423


title: IgAN_07_422


title: IgAN_07_415


title: IgAN_07_419


title: IgAN_07_420


title: IgAN_07_418


title: IgAN_07_421


title: IgAN_07_433


title: IgAN_07_417


title: IgAN_07_416


title: IgAN_07_414


title: IgAN_07_411


title: IgAN_07_410


title: IgAN_07_413


title: IgAN_07_412


title: IgAN_07_407


title: IgAN_07_408


title: IgAN_07_405


title: IgAN_07_409


title: IgAN_07_406


title: IgAN_07_403


title: IgAN_07_404


title: IgAN_07_402


title: IgAN_07_401


title: IgAN_07_400


title: IgAN_07_399


title: IgAN_07_398


title: IgAN_07_396


title: IgAN_07_397


title: IgAN_07_394


title: IgAN_07_391


title: IgAN_07_390


title: IgAN_07_393


title: IgAN_07_389


title: IgAN_07_392


title: IgAN_07_380


title: IgAN_07_379


title: IgAN_07_378


title: IgAN_07_377


title: IgAN_07_384


title: IgAN_07_388


title: IgAN_07_387


title: IgAN_07_385


title: IgAN_07_381


title: IgAN_07_376


title: IgAN_07_375


title: IgAN_07_383


title: IgAN_07_395


title: IgAN_07_373


title: IgAN_07_372


title: IgAN_07_371


title: IgAN_07_370


title: IgAN_07_386


title: IgAN_07_369


title: IgAN_07_382


title: IgAN_07_364


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title: IgAN_07_366


title: IgAN_07_374


title: IgAN_07_363


title: IgAN_07_360


title: IgAN_07_361


title: IgAN_07_362


title: IgAN_07_359


title: IgAN_07_357


title: IgAN_07_356


title: IgAN_07_358


title: IgAN_07_351


title: IgAN_07_349


title: IgAN_07_350


title: IgAN_07_352


title: IgAN_07_355


title: IgAN_07_353


title: IgAN_07_348


title: IgAN_07_368


title: IgAN_07_367


title: IgAN_07_346


title: IgAN_07_354


title: IgAN_07_343


title: IgAN_07_341


title: IgAN_07_345


title: IgAN_07_339


title: IgAN_07_342


title: IgAN_07_340


title: IgAN_07_347


title: IgAN_07_338


title: IgAN_07_337


title: IgAN_07_334


title: IgAN_07_336


title: IgAN_07_332


title: IgAN_07_335


title: IgAN_07_333


title: IgAN_07_329


title: IgAN_07_331


title: IgAN_07_328


title: IgAN_07_327


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title: IgAN_07_322


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title: IgAN_07_318


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title: IgAN_07_307


title: IgAN_07_326


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title: IgAN_07_300


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title: IgAN_07_296


title: IgAN_07_295


title: IgAN_07_294


title: IgAN_07_293


title: IgAN_07_344


title: IgAN_07_289


title: IgAN_07_292


title: IgAN_07_291


title: IgAN_07_290


title: IgAN_07_315


title: IgAN_07_285


title: IgAN_07_287


title: IgAN_07_306


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title: IgAN_07_288


title: IgAN_07_302


title: IgAN_07_301


title: IgAN_07_283


title: IgAN_07_284


title: IgAN_07_317


title: IgAN_07_297


title: IgAN_07_281


title: IgAN_07_282


title: IgAN_07_313


title: IgAN_07_280


title: IgAN_07_278


title: IgAN_07_279


title: IgAN_07_276


title: IgAN_07_275


title: IgAN_07_277


title: IgAN_07_274


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title: IgAN_07_273


title: IgAN_07_265


title: IgAN_07_268


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title: IgAN_07_270


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title: IgAN_07_257


title: IgAN_07_263


title: IgAN_07_264


title: IgAN_07_252


title: IgAN_07_262


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title: IgAN_07_255


title: IgAN_07_254


title: IgAN_07_256


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title: IgAN_07_261


title: IgAN_07_250


title: IgAN_07_249


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title: IgAN_07_251


title: IgAN_07_246


title: IgAN_07_244


title: IgAN_07_245


title: IgAN_07_243


title: IgAN_07_267


title: IgAN_07_242


title: IgAN_07_241


title: IgAN_07_240


title: IgAN_07_239


title: IgAN_07_238


title: IgAN_07_237


title: IgAN_07_236


title: IgAN_07_234


title: IgAN_07_248


title: IgAN_07_247


title: IgAN_07_231


title: IgAN_07_233


title: IgAN_07_229


title: IgAN_07_228


title: IgAN_07_224


title: IgAN_07_223


title: IgAN_07_225


title: IgAN_07_227


title: IgAN_07_221


title: IgAN_07_219


title: IgAN_07_217


title: IgAN_07_220


title: IgAN_07_235


title: IgAN_07_226


title: IgAN_07_216


title: IgAN_07_215


title: IgAN_07_232


title: IgAN_07_230


title: IgAN_07_214


title: IgAN_07_208


title: IgAN_07_211


title: IgAN_07_212


title: IgAN_07_209


title: IgAN_07_210


title: IgAN_07_213


title: IgAN_07_207


title: IgAN_07_222


title: IgAN_07_205


title: IgAN_07_206


title: IgAN_07_204


title: IgAN_07_218


title: IgAN_07_203


title: IgAN_07_201


title: IgAN_07_202


title: IgAN_07_199


title: IgAN_07_197


title: IgAN_07_198


title: IgAN_07_200


title: IgAN_07_196


title: IgAN_07_193


title: IgAN_07_194


title: IgAN_07_189


title: IgAN_07_188


title: IgAN_07_187


title: IgAN_07_185


title: IgAN_07_183


title: IgAN_07_179


title: IgAN_07_178


title: IgAN_07_177


title: IgAN_07_176


title: IgAN_07_181


title: IgAN_07_175


title: IgAN_07_195


title: IgAN_07_174


title: IgAN_07_169


title: IgAN_07_171


title: IgAN_07_190


title: IgAN_07_192


title: IgAN_07_191


title: IgAN_07_167


title: IgAN_07_168


title: IgAN_07_166


title: IgAN_07_165


title: IgAN_07_186


title: IgAN_07_164


title: IgAN_07_182


title: IgAN_07_184


title: IgAN_07_180


title: IgAN_07_163


title: IgAN_07_162


title: IgAN_07_161


title: IgAN_07_160


title: IgAN_07_159


title: IgAN_07_170


title: IgAN_07_157


title: IgAN_07_172


title: IgAN_07_151


title: IgAN_07_156


title: IgAN_07_149


title: IgAN_07_148


title: IgAN_07_147


title: IgAN_07_144


title: IgAN_07_146


title: IgAN_07_150


title: IgAN_07_145


title: IgAN_07_155


title: IgAN_07_154


title: IgAN_07_152


title: IgAN_07_142


title: IgAN_07_139


title: IgAN_07_137


title: IgAN_07_138


title: IgAN_07_136


title: IgAN_07_141


title: IgAN_07_135


title: IgAN_07_134


title: IgAN_07_158


title: IgAN_07_133


title: IgAN_07_153


title: IgAN_07_173


title: IgAN_07_132


title: IgAN_07_131


title: IgAN_07_130


title: IgAN_07_129


title: IgAN_07_143


title: IgAN_07_128


title: IgAN_07_127


title: IgAN_07_140


title: IgAN_07_124


title: IgAN_07_126


title: IgAN_07_125


title: IgAN_07_119


title: IgAN_07_118


title: IgAN_07_123


title: IgAN_07_121


title: IgAN_07_122


title: IgAN_07_117


title: IgAN_07_114


title: IgAN_07_113


title: IgAN_07_109


title: IgAN_07_111


title: IgAN_07_108


title: IgAN_07_107


title: IgAN_07_106


title: IgAN_07_105


title: IgAN_07_120


title: IgAN_07_115


title: IgAN_07_104


title: IgAN_07_110


title: IgAN_07_112


title: IgAN_07_103


title: IgAN_07_102


title: IgAN_07_101


title: IgAN_07_096


title: IgAN_07_100


title: IgAN_07_098


title: IgAN_07_099


title: IgAN_07_116


title: IgAN_07_097


title: IgAN_07_095


title: IgAN_16_012


title: IgAN_16_014


title: IgAN_16_011


title: IgAN_07_094


title: IgAN_16_010


title: IgAN_16_009


title: IgAN_16_013


title: IgAN_07_091


title: IgAN_07_093


title: IgAN_07_092


title: IgAN_16_008


title: IgAN_16_007


title: IgAN_16_005


title: IgAN_16_004


title: IgAN_16_003


title: IgAN_15_220


title: IgAN_16_001


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title: IgAN_15_221


title: IgAN_16_002


title: IgAN_15_214


title: IgAN_15_213


title: IgAN_15_217


title: IgAN_15_216


title: IgAN_15_211


title: IgAN_15_218


title: IgAN_15_215


title: IgAN_15_210


title: IgAN_15_212


title: IgAN_15_206


title: IgAN_15_207


title: IgAN_16_006


title: IgAN_15_208


title: IgAN_15_209


title: IgAN_15_205


title: IgAN_15_200


title: IgAN_15_199


title: IgAN_15_204


title: IgAN_15_198


title: IgAN_15_201


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title: IgAN_15_197


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title: IgAN_15_191


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title: IgAN_15_202


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title: IgAN_15_183


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title: IgAN_15_188


title: IgAN_15_179


title: IgAN_15_182


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title: IgAN_15_180


title: IgAN_15_181


title: IgAN_15_187


title: IgAN_15_195


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title: IgAN_15_175


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title: IgAN_15_193


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title: IgAN_15_171


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title: IgAN_15_169


title: IgAN_15_166


title: IgAN_15_165


title: IgAN_15_174


title: IgAN_15_163


title: IgAN_15_172


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title: IgAN_15_162


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title: IgAN_15_158


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title: IgAN_15_155


title: IgAN_15_153


title: IgAN_15_159


title: IgAN_15_167


title: IgAN_15_147


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title: IgAN_15_141


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title: IgAN_15_028


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title: IgAN_15_018


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title: IgAN_15_021


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title: IgAN_10_282


title: IgAN_10_283


title: IgAN_10_284


title: IgAN_10_280


title: IgAN_10_281


title: IgAN_10_279


title: IgAN_10_291


title: IgAN_10_278


title: IgAN_10_276


title: IgAN_10_275


title: IgAN_10_277


title: IgAN_10_297


title: IgAN_10_274


title: IgAN_10_273


title: IgAN_10_271


title: IgAN_10_272


title: IgAN_10_270


title: IgAN_10_269


title: IgAN_10_267


title: IgAN_10_268


title: IgAN_10_264


title: IgAN_10_265


title: IgAN_10_266


title: IgAN_10_260


title: IgAN_10_262


title: IgAN_10_261


title: IgAN_10_263


title: IgAN_10_259


title: IgAN_10_257


title: IgAN_10_258


title: IgAN_10_255


title: IgAN_10_254


title: IgAN_10_253


title: IgAN_10_256


title: IgAN_10_249


title: IgAN_10_251


title: IgAN_10_252


title: IgAN_10_248


title: IgAN_10_247


title: IgAN_10_246


title: IgAN_10_250


title: IgAN_10_244


title: IgAN_10_243


title: IgAN_10_245


title: IgAN_10_241


title: IgAN_10_242


title: IgAN_10_240


title: IgAN_10_239


title: IgAN_10_238


title: IgAN_10_235


title: IgAN_10_234


title: IgAN_10_233


title: IgAN_10_231


title: IgAN_10_230


title: IgAN_10_228


title: IgAN_10_229


title: IgAN_10_225


title: IgAN_10_222


title: IgAN_10_227


title: IgAN_10_223


title: IgAN_10_224


title: IgAN_10_226


title: IgAN_10_219


title: IgAN_10_221


title: IgAN_10_217


title: IgAN_10_218


title: IgAN_10_236


title: IgAN_10_237


title: IgAN_10_214


title: IgAN_10_215


title: IgAN_10_216


title: IgAN_10_232


title: IgAN_10_212


title: IgAN_10_211


title: IgAN_10_209


title: IgAN_10_210


title: IgAN_10_208


title: IgAN_10_220


title: IgAN_10_206


title: IgAN_10_202


title: IgAN_10_205


title: IgAN_10_207


title: IgAN_10_201


title: IgAN_10_200


title: IgAN_10_197


title: IgAN_10_203


title: IgAN_10_194


title: IgAN_10_199


title: IgAN_10_195


title: IgAN_10_196


title: IgAN_10_198


title: IgAN_10_213


title: IgAN_10_193


title: IgAN_10_191


title: IgAN_10_189


title: IgAN_10_188


title: IgAN_10_192


title: IgAN_10_190


title: IgAN_10_204


title: IgAN_10_187


title: IgAN_10_186


title: IgAN_10_185


title: IgAN_10_182


title: IgAN_10_181


title: IgAN_10_183


title: IgAN_10_184


title: IgAN_10_178


title: IgAN_10_179


title: IgAN_10_319


title: IgAN_10_180


title: RET215 (expression)

type: RNA

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

description: Gene expression data from fetal retina

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG,  Brainarray Custom CDF EntrezG version 23, Batch effects were corrected with the help of the bioconductor package SVA,

label: biotin

molecule: total RNA

source_name: fetal retina RET215

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

growth_protocol: Immediately following enucleation, a needle was inserted through the anterior chamber of the eye to extract a tumor sample by aspiration. The tumor specimen was placed in RPMI medium on ice, cells were re-suspended, counted and separated into two tubes (for DNA and RNA preparation). The tubes were then centrifuged to remove all media and snap frozen for later extraction.

extract_protocol: Tumor RNA was extracted using Qiazol (Qiagen, Courtaboeuf, France) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).

tag: geo dataset serie

value: SAMPLE 118

tag: batch

value: fetal retina


title: RB7_REP2 (expression)

description: Batch replicate - Gene expression data from retinoblastoma samples

source_name: retinoblastoma sample RB7_REP2

value: SAMPLE 6

value: retinoblastoma


title: BMpDCs treated with Oxymatrine

city: Toyama

first: Takeshi

last: Yamamoto

address: 2630 Sugitani

country: Japan

institute: University of Toyama

hyb_protocol: The fragmented and labeled single stranded cDNA was hybridized to Mouse Clariom S arrays for 16 h at 45°C and 60 rpm in an GeneChip Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an GeneChipTM Fluidics Station 450 according to GeneChipTM Hybridization, Wash and Stain Kit manual.

scan_protocol: Mouse Clariom S arrays were scanned using GeneChipTM Scanner 3000 7G

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Expression ConsoleTM Software 1.4.1

organism: Mus musculus

source_name: BMpDCs treated with Oxymatrine

label_protocol: Microarray and RNA quality check were performed at Takara Bio Inc. (Osaka, Japan). Biotinylated cRNA were prepared using the Affimetrix GeneChip™ WT PLUS Reagent Kit from total RNA.

extract_protocol: RNeasy Mini Kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: pDCs were generated from bone marrow cells isolated from the femurs and tibias of male BALB/c mice. For pDC differentiation, BMs were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 55 µM 2-mercaptoethanol, 100 units/mL penicillin, 140 μM streptomycin, 2 mM L-glutamine, and 100 ng/mL Flt3 ligand for 6 to 9 days. CpG oligodeoxynucleotides were used to induce BMpDC maturation. Mature BMpDCs sorted with a BD FACSAria SORP were used for RNA extraction. Mature BMpDCs were treated with Astragaloside IV or Oxymatrine for 12 hours, followed by induction with CCL21 for 1 hour at 37°C.

tag: genotype

value: WT

tag: gender

value: male

tag: strain

value: BALB/c

value: bone marrow

value: bone marrow-derived plasmacytoid dendritic cells

tag: age

value: 4-5 weeks


title: RB11_REP2 (expression)

source_name: retinoblastoma sample RB11_REP2

value: SAMPLE 9


title: RET1 (expression)

description: Gene expression data from fetal retina

source_name: fetal retina RET1

value: SAMPLE 116


title: IgAN_10_176


title: IgAN_10_177


title: IgAN_10_173


title: IgAN_10_175


title: Control BMpDCs

source_name: Control BMpDCs


title: IgAN_10_172


title: IgAN_10_170


title: RB224 (expression)

description: Gene expression data from retinoblastoma samples

source_name: retinoblastoma sample RB224

value: SAMPLE 81


title: BMpDCs treated with Astragaloside IV

source_name: BMpDCs treated with Astragaloside IV


title: RB42_REP2 (expression)

source_name: retinoblastoma sample RB42_REP2

value: SAMPLE 33


title: RB223 (expression)

source_name: retinoblastoma sample RB223

value: SAMPLE 80


title: RB225 (expression)

source_name: retinoblastoma sample RB225

value: SAMPLE 82


title: RB220 (expression)

source_name: retinoblastoma sample RB220

value: SAMPLE 77


title: IgAN_10_174

value: IgAN

value: renal biopsies


title: RET2 (expression)

description: Gene expression data from fetal retina

source_name: fetal retina RET2

value: SAMPLE 117

value: fetal retina


title: RB10_REP2 (expression)

source_name: retinoblastoma sample RB10_REP2

value: SAMPLE 8

value: retinoblastoma


title: RB219 (expression)

source_name: retinoblastoma sample RB219

value: SAMPLE 76


title: RB221 (expression)

source_name: retinoblastoma sample RB221

value: SAMPLE 78


title: RB222 (expression)

source_name: retinoblastoma sample RB222

value: SAMPLE 79


title: RB216 (expression)

source_name: retinoblastoma sample RB216

value: SAMPLE 73


title: RB212 (expression)

source_name: retinoblastoma sample RB212

value: SAMPLE 69


title: IgAN_10_171

source_name: IgAN patients’ renal biopsies


title: IgAN_10_169


title: IgAN_10_167


title: IgAN_10_166


title: IgAN_10_165


title: IgAN_10_168


title: RB213 (expression)

source_name: retinoblastoma sample RB213

value: SAMPLE 70


title: IgAN_10_163


title: IgAN_10_160


title: IgAN_10_159


title: IgAN_10_161


title: IgAN_10_158


title: IgAN_10_156


title: IgAN_10_157


title: IgAN_10_164


title: RB60 (expression)

source_name: retinoblastoma sample RB60

value: SAMPLE 50


title: RB63 (expression)

source_name: retinoblastoma sample RB63

value: SAMPLE 53


title: RB59 (expression)

source_name: retinoblastoma sample RB59

value: SAMPLE 49


title: RB56 (expression)

source_name: retinoblastoma sample RB56

value: SAMPLE 46


title: IgAN_10_162


title: RB217 (expression)

source_name: retinoblastoma sample RB217

value: SAMPLE 74


title: RB61 (expression)

source_name: retinoblastoma sample RB61

value: SAMPLE 51


title: RB57 (expression)

source_name: retinoblastoma sample RB57

value: SAMPLE 47


title: RB54 (expression)

source_name: retinoblastoma sample RB54

value: SAMPLE 44


title: RB58 (expression)

source_name: retinoblastoma sample RB58

value: SAMPLE 48


title: IgAN_10_155

value: IgAN

value: renal biopsies


title: RB51 (expression)

source_name: retinoblastoma sample RB51

value: SAMPLE 42

value: retinoblastoma


title: RB62 (expression)

source_name: retinoblastoma sample RB62

value: SAMPLE 52


title: RB211 (expression)

source_name: retinoblastoma sample RB211

value: SAMPLE 68


title: IgAN_10_154


title: IgAN_10_153


title: IgAN_10_152


title: RB50 (expression)

source_name: retinoblastoma sample RB50

value: SAMPLE 41


title: RB47 (expression)

source_name: retinoblastoma sample RB47

value: SAMPLE 38


title: RB46 (expression)

source_name: retinoblastoma sample RB46

value: SAMPLE 37


title: RB52 (expression)

source_name: retinoblastoma sample RB52

value: SAMPLE 43


title: RB49 (expression)

source_name: retinoblastoma sample RB49

value: SAMPLE 40


title: IgAN_10_149

source_name: IgAN patients’ renal biopsies


title: IgAN_10_148


title: RB44 (expression)

source_name: retinoblastoma sample RB44

value: SAMPLE 35


title: RB45 (expression)

source_name: retinoblastoma sample RB45

value: SAMPLE 36


title: IgAN_10_146


title: IgAN_10_143


title: IgAN_10_144


title: IgAN_10_145


title: RB42_REP1 (expression)

source_name: retinoblastoma sample RB42_REP1

value: SAMPLE 33


title: IgAN_10_151


title: IgAN_10_140


title: IgAN_10_142


title: IgAN_10_141


title: IgAN_10_150


title: IgAN_10_139


title: RB41 (expression)

source_name: retinoblastoma sample RB41

value: SAMPLE 32


title: RB38 (expression)

source_name: retinoblastoma sample RB38

value: SAMPLE 29


title: RB39 (expression)

source_name: retinoblastoma sample RB39

value: SAMPLE 30


title: IgAN_10_147

value: IgAN


title: RB37 (expression)

source_name: retinoblastoma sample RB37

value: SAMPLE 28


title: RB35 (expression)

source_name: retinoblastoma sample RB35

value: SAMPLE 27


title: IgAN_10_138

value: renal biopsies


title: RB43 (expression)

source_name: retinoblastoma sample RB43

value: SAMPLE 34

value: retinoblastoma


title: RB32 (expression)

source_name: retinoblastoma sample RB32

value: SAMPLE 24


title: RB34 (expression)

source_name: retinoblastoma sample RB34

value: SAMPLE 26


title: IgAN_10_137


title: IgAN_10_136


title: IgAN_10_134


title: RB40 (expression)

source_name: retinoblastoma sample RB40

value: SAMPLE 31


title: IgAN_10_135


title: IgAN_10_132


title: RB28 (expression)

source_name: retinoblastoma sample RB28

value: SAMPLE 20


title: IgAN_10_133


title: RB33 (expression)

source_name: retinoblastoma sample RB33

value: SAMPLE 25


title: RB27 (expression)

source_name: retinoblastoma sample RB27

value: SAMPLE 19


title: IgAN_10_131


title: IgAN_10_130


title: RB23 (expression)

source_name: retinoblastoma sample RB23

value: SAMPLE 16


title: RB25 (expression)

source_name: retinoblastoma sample RB25

value: SAMPLE 18


title: RB31 (expression)

source_name: retinoblastoma sample RB31

value: SAMPLE 23


title: IgAN_10_129

source_name: IgAN patients’ renal biopsies


title: IgAN_10_127


title: IgAN_10_125


title: IgAN_10_126


title: IgAN_10_128


title: RB24 (expression)

source_name: retinoblastoma sample RB24

value: SAMPLE 17


title: RB15 (expression)

source_name: retinoblastoma sample RB15

value: SAMPLE 13


title: RB14 (expression)

source_name: retinoblastoma sample RB14

value: SAMPLE 12


title: RB21 (expression)

source_name: retinoblastoma sample RB21

value: SAMPLE 14


title: IgAN_10_124

value: IgAN


title: RB22 (expression)

source_name: retinoblastoma sample RB22

value: SAMPLE 15


title: IgAN_10_123

value: renal biopsies


title: RB7_REP1 (expression)

source_name: retinoblastoma sample RB7_REP1

value: SAMPLE 6

value: retinoblastoma


title: IgAN_10_121


title: IgAN_10_119


title: IgAN_10_118


title: RB10_REP1 (expression)

source_name: retinoblastoma sample RB10_REP1

value: SAMPLE 8


title: IgAN_10_117


title: RB6 (expression)

source_name: retinoblastoma sample RB6

value: SAMPLE 5


title: IgAN_10_120


title: RB9 (expression)

source_name: retinoblastoma sample RB9

value: SAMPLE 7


title: RB11_REP1 (expression)

source_name: retinoblastoma sample RB11_REP1

value: SAMPLE 9


title: RB2 (expression)

source_name: retinoblastoma sample RB2

value: SAMPLE 2


title: RB4 (expression)

source_name: retinoblastoma sample RB4

value: SAMPLE 4


title: IgAN_10_115


title: RB1 (expression)

source_name: retinoblastoma sample RB1

value: SAMPLE 1


title: IgAN_10_116


title: IgAN_10_114


title: IgAN_10_122


title: IgAN_10_113


title: Kidney_KifKD_4weeks_rep7

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

hyb_protocol: 15 µg labelled cRNA were hybridized onto Mouse 4302 arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor using Single-Channel Array Normalization (SCAN), (Picolo et al., Genomics 2012).

label: Biotin

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: Raptor fl/fl or Kif fl/fl mice (used as controls), Raptor fl/fl*KspCre, Kif3a fl/fl*KspCre and Raptor fl/fl*Kif3a fl/fl*KspCre animals were sacrificed at 1 day, 1 week, 2 and 4 weeks (n>=7).

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Kidneys were split in half and immediately snap frozen in liquid nitrogen.

tag: strain background

value: C57BL/6 N

tag: genotype/variation

value: Kif3a fl/fl*KspCre

value: male

value: 4 weeks

value: kidney


title: Kidney_KifKD_4weeks_rep10

value: female


title: Kidney_KifKD_4weeks_rep9


title: Kidney_KifKD_4weeks_rep8


title: Kidney_KifKD_4weeks_rep6


title: Kidney_KifKD_4weeks_rep4


title: IgAN_10_108

value: IgAN


title: IgAN_10_107

value: renal biopsies


title: IgAN_10_112


title: IgAN_10_111


title: IgAN_10_106


title: Kidney_KifKD_4weeks_rep5


title: IgAN_10_110


title: Kidney_KifKD_4weeks_rep3


title: Kidney_KifKD_4weeks_rep1


title: Kidney_KifKD_4weeks_rep2


title: IgAN_10_105


title: IgAN_10_104


title: Kidney_RapKifKD_4weeks_rep14

value: Raptor fl/fl*Kif3a fl/fl*KspCre


title: Kidney_RapKifKD_4weeks_rep12


title: Kidney_RapKifKD_4weeks_rep10


title: Kidney_RapKifKD_4weeks_rep11


title: Kidney_RapKifKD_4weeks_rep13


title: IgAN_10_103


title: Kidney_RapKifKD_4weeks_rep8


title: Kidney_RapKifKD_4weeks_rep7


title: Kidney_RapKifKD_4weeks_rep9


title: IgAN_10_100


title: IgAN_10_096


title: IgAN_10_099


title: IgAN_10_095


title: IgAN_10_101


title: IgAN_10_109


title: IgAN_10_098


title: IgAN_10_093


title: IgAN_10_102


title: IgAN_10_094


title: IgAN_10_097


title: Kidney_RapKifKD_4weeks_rep4


title: IgAN_10_091


title: IgAN_10_092


title: IgAN_10_090


title: Kidney_RapKifKD_4weeks_rep5


title: Kidney_RapKifKD_4weeks_rep3


title: Kidney_RapKifKD_4weeks_rep2


title: Kidney_RapKifKD_4weeks_rep6


title: Kidney_RapKD_4weeks_rep5

value: Raptor fl/fl*KspCre


title: IgAN_10_089


title: Kidney_RapKD_4weeks_rep3


title: Kidney_RapKD_4weeks_rep4


title: Kidney_RapKD_4weeks_rep7


title: IgAN_10_088


title: IgAN_10_086


title: IgAN_10_087


title: Kidney_RapKifKD_4weeks_rep1


title: Kidney_RapKD_4weeks_rep1


title: Kidney_RapKD_4weeks_rep2


title: Kidney_RapKD_4weeks_rep6


title: IgAN_10_085


title: IgAN_10_084


title: RB48 (expression)

source_name: retinoblastoma sample RB48

value: SAMPLE 39

value: retinoblastoma


title: Kidney_Ctl_4weeks_rep6

value: Control


title: Kidney_Ctl_4weeks_rep7


title: IgAN_10_083


title: IgAN_10_082


title: Kidney_Ctl_4weeks_rep9


title: Kidney_Ctl_4weeks_rep8


title: Kidney_Ctl_4weeks_rep5


title: IgAN_10_081


title: IgAN_10_080


title: IgAN_10_079


title: Kidney_Ctl_4weeks_rep3


title: IgAN_10_078


title: Kidney_RapKD_4weeks_rep8


title: IgAN_10_076


title: Kidney_Ctl_4weeks_rep2


title: IgAN_10_077


title: IgAN_10_073


title: IgAN_10_074


title: IgAN_10_075


title: Kidney_Ctl_4weeks_rep1


title: IgAN_10_072


title: Kidney_KifKD_2weeks_rep6

value: 2 weeks


title: Kidney_KifKD_2weeks_rep3


title: Kidney_KifKD_2weeks_rep8


title: Kidney_KifKD_2weeks_rep4


title: IgAN_10_070


title: Kidney_KifKD_2weeks_rep2


title: IgAN_10_069


title: Kidney_KifKD_2weeks_rep1


title: IgAN_10_068


title: IgAN_10_071


title: Kidney_KifKD_2weeks_rep7


title: Kidney_RapKifKD_2weeks_rep7


title: IgAN_10_067


title: IgAN_10_065


title: Kidney_RapKifKD_2weeks_rep8


title: Kidney_KifKD_2weeks_rep5


title: Kidney_RapKifKD_2weeks_rep4


title: IgAN_10_062


title: Kidney_RapKifKD_2weeks_rep5


title: IgAN_10_066


title: IgAN_10_063


title: IgAN_10_060


title: IgAN_10_058


title: IgAN_10_061


title: IgAN_10_059


title: Kidney_RapKifKD_2weeks_rep3


title: Kidney_RapKifKD_2weeks_rep6


title: Kidney_RapKifKD_2weeks_rep2


title: IgAN_10_057


title: IgAN_10_056


title: IgAN_10_064


title: IgAN_10_055


title: Kidney_RapKD_2weeks_rep4


title: Kidney_RapKD_2weeks_rep7


title: IgAN_10_054


title: Kidney_RapKD_2weeks_rep8


title: Kidney_RapKD_2weeks_rep6


title: Kidney_RapKD_2weeks_rep3


title: IgAN_10_053


title: Kidney_RapKifKD_2weeks_rep1


title: Kidney_RapKD_2weeks_rep5


title: Kidney_RapKD_2weeks_rep2


title: IgAN_10_052


title: Kidney_Ctl_2weeks_rep10


title: IgAN_10_051


title: Kidney_Ctl_2weeks_rep11


title: IgAN_10_050


title: Kidney_Ctl_2weeks_rep9


title: IgAN_10_049


title: IgAN_10_048


title: IgAN_10_047


title: Kidney_Ctl_2weeks_rep6


title: IgAN_10_046


title: Kidney_Ctl_2weeks_rep8


title: Kidney_RapKD_2weeks_rep1


title: IgAN_10_044


title: IgAN_10_045


title: IgAN_10_042


title: IgAN_10_041


title: Kidney_Ctl_2weeks_rep5


title: IgAN_10_040


title: Kidney_Ctl_2weeks_rep3


title: Kidney_Ctl_2weeks_rep2


title: Kidney_Ctl_2weeks_rep1


title: Kidney_KifKD_1week_rep5

value: 1 week


title: IgAN_10_039


title: IgAN_10_037


title: IgAN_10_036


title: IgAN_10_035


title: IgAN_10_043


title: IgAN_10_034


title: Kidney_KifKD_1week_rep6


title: Kidney_Ctl_2weeks_rep7


title: Kidney_Ctl_2weeks_rep4


title: Kidney_KifKD_1week_rep7


title: IgAN_10_033


title: Kidney_KifKD_1week_rep3


title: Kidney_KifKD_1week_rep2


title: Kidney_RapKifKD_1week_rep8


title: Kidney_RapKifKD_1week_rep7


title: Kidney_RapKifKD_1week_rep9


title: Kidney_RapKifKD_1week_rep6


title: IgAN_10_032


title: Kidney_KifKD_1week_rep4


title: Kidney_RapKifKD_1week_rep5


title: IgAN_10_038


title: IgAN_10_030


title: Kidney_RapKifKD_1week_rep4


title: Kidney_RapKifKD_1week_rep3


title: IgAN_10_028


title: IgAN_07_090


title: IgAN_07_089


title: IgAN_10_029


title: IgAN_07_088


title: IgAN_10_031


title: Kidney_KifKD_1week_rep1


title: IgAN_07_087


title: Kidney_RapKifKD_1week_rep1


title: IgAN_07_085


title: IgAN_07_084


title: Kidney_RapKifKD_1week_rep2


title: IgAN_07_083


title: IgAN_07_086


title: Kidney_RapKD_1week_rep7


title: IgAN_07_082


title: Kidney_RapKD_1week_rep4


title: Kidney_RapKD_1week_rep5


title: Kidney_RapKD_1week_rep6


title: Kidney_Ctl_1week_rep7


title: Kidney_Ctl_1week_rep8


title: Kidney_Ctl_1week_rep9


title: Kidney_Ctl_1week_rep6


title: Kidney_Ctl_4weeks_rep4


title: Kidney_RapKD_1week_rep2


title: Kidney_RapKD_1week_rep1


title: Kidney_Ctl_1week_rep5


title: Kidney_RapKD_1week_rep3


title: IgAN_07_077


title: IgAN_07_078


title: IgAN_07_074


title: IgAN_07_079


title: IgAN_07_076


title: IgAN_07_075


title: IgAN_07_072


title: IgAN_07_080


title: IgAN_07_073


title: IgAN_07_081


title: Kidney_Ctl_1week_rep3


title: Kidney_Ctl_1week_rep2


title: Kidney_KifKD_1day_rep6

value: 1 day


title: Kidney_KifKD_1day_rep7


title: Kidney_Ctl_1week_rep1


title: Kidney_KifKD_1day_rep5


title: IgAN_07_071


title: IgAN_07_069


title: IgAN_07_068


title: IgAN_07_070


title: IgAN_07_067


title: IgAN_07_066


title: Kidney_Ctl_1week_rep4


title: IgAN_07_065


title: IgAN_07_064


title: Kidney_KifKD_1day_rep1


title: Kidney_KifKD_1day_rep3


title: Kidney_RapKifKD_1day_rep8


title: Kidney_KifKD_1day_rep8


title: IgAN_07_063


title: IgAN_07_062


title: IgAN_07_061


title: Kidney_RapKifKD_1day_rep6


title: IgAN_07_060


title: IgAN_07_058


title: IgAN_07_055


title: Kidney_RapKifKD_1day_rep4


title: Kidney_RapKifKD_1day_rep5


title: Kidney_KifKD_1day_rep4


title: IgAN_07_054


title: IgAN_07_053


title: Kidney_KifKD_1day_rep2


title: Kidney_RapKifKD_1day_rep1


title: Kidney_RapKifKD_1day_rep7


title: IgAN_07_057


title: IgAN_07_056


title: Kidney_RapKD_1day_rep9


title: Kidney_RapKD_1day_rep7


title: IgAN_07_050


title: IgAN_07_049


title: IgAN_07_059


title: Kidney_RapKD_1day_rep8


title: Kidney_RapKD_1day_rep10


title: IgAN_07_051


title: IgAN_07_052


title: Kidney_RapKifKD_1day_rep3


title: Kidney_RapKifKD_1day_rep2


title: Kidney_RapKD_1day_rep11


title: Kidney_RapKD_1day_rep3


title: Kidney_RapKD_1day_rep6


title: IgAN_07_048


title: Kidney_RapKD_1day_rep5


title: Kidney_RapKD_1day_rep1


title: Kidney_RapKD_1day_rep4


title: Kidney_RapKD_1day_rep2


title: IgAN_07_046


title: IgAN_07_047


title: IgAN_07_045


title: IgAN_07_044


title: IgAN_07_043


title: IgAN_07_040


title: IgAN_07_041


title: IgAN_07_042


title: control_wild-type_E12.5_replicate1

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

country: Canada

institute: University of Lethbridge

description:
microdissected dorsal telencephalon
sE12_5Wt1_S11

data_processing:
Basecalling and demultiplexing: CASAVA 1.9
Initial quality control: FastQC 0.11.8
Read mapping: hisat2 v.2.2.1
SAM to BAM conversion, sorting and indexing: samtools 1.9
Generating bigwigs (RPKM normalized): deeptools bamCoverage v.3.3.0
Genome_build: GRCm38 Ensembl
Supplementary_files_format_and_content: bigwig

source_name: Mouse embryonic brain

growth_protocol: Mouse primary cells from wild-type, L3mbtl3 het and KO were used

extract_protocol:
Total RNA were prepared using MagMAX™-96 Total RNA Isolation Kit AM1830 according to manufacturer's protocol. The sequencing libraries were prepared using Truseq Stranded mRNA kit. The fragment libraries were sequenced using Illumina NEXTSEQ500 for 75 cycles.
Single-end; 75 bp; Truseq mRNA stranded with polyA selection

value: embryonic day 12

value: wild-type

value: dorsal telencephalon


title: L3mbtl3 KO_E12.5_replicate1

description:
microdissected dorsal telencephalon
sE12_5Mbt1_KO1_S14

value: L3mbtl3 -/-


title: L3mbtl3 KO_E12.5_replicate2

description:
microdissected dorsal telencephalon
sE12_5Mbt1_KO2_S15


title: Kidney_Ctl_1day_rep7

value: C57BL/6 N


title: Kidney_Ctl_1day_rep6

value: kidney


title: Kidney_Ctl_1day_rep3

value: male


title: Kidney_Ctl_1day_rep4

value: female


title: IgAN_07_039

value: IgAN

value: renal biopsies


title: IgAN_07_038


title: Kidney_Ctl_1day_rep5


title: control_L3mbtl3 het_E12.5_ replicate1

description:
microdissected dorsal telencephalon
sE12_5Het1_S12

value: L3mbtl3 +/-


title: IgAN_07_037


title: IgAN_07_036


title: L3mbtl3_Gain-of-function_ replicate3

description:
GFP+ cells isolated by FACS after in utero electroporation of pCIG2-L3mbtl3 from E12.5 to E15.5
sMbt1_GoF_3_S10

value: embryonic day 15

value: wild-type with electoporation of pCIG2-L3mbtl3

value: GFP+ brain cells


title: control_L3mbtl3 het_ E12.5_replicate2

description:
microdissected dorsal telencephalon
sE12_5Het2_S13


title: IgAN_07_035


title: L3mbtl3_Gain-of-function_ replicate1

description:
GFP+ cells isolated by FACS after in utero electroporation of pCIG2-L3mbtl3 from E12.5 to E15.5
sMbt1_GoF_1_S8


title: L3mbtl3_Gain-of-function_ replicate2

description:
GFP+ cells isolated by FACS after in utero electroporation of pCIG2-L3mbtl3 from E12.5 to E15.5
sMbt1_GoF_2_S9


title: Kidney_Ctl_1day_rep1

value: Control


title: Kidney_Ctl_1day_rep2


title: IgAN_07_033


title: IgAN_07_032


title: Control_Gain-of-function_replicate3

description:
GFP+ cells isolated by FACS after in utero electroporation of pCIG2 from E12.5 to E15.5
sCtrl_GoF_3_S7

value: wild-type with electoporation of pCIG2


title: Control_Gain-of-function_replicate2

description:
GFP+ cells isolated by FACS after in utero electroporation of pCIG2 from E12.5 to E15.5
sCtrl_GoF_2_S6


title: Control_Gain-of-function_replicate1

description:
GFP+ cells isolated by FACS after in utero electroporation of pCIG2 from E12.5 to E15.5
sCtrl_GoF_1_S5


title: IgAN_07_031


title: IgAN_07_030


title: IgAN_07_028


title: IgAN_07_029


title: NKs 5OPRU + B16 1

city: Melbourne

first: Paul

last: Beavis

state: Victoria

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The RNA sequencing reads were trimmed using cutadapt(v1.7) to remove poor quality ends.
Read data was then aligned using Hisat2 to the human reference genome (hg19)
Read counting was performed with featureCounts from the subread package (v1.6.4)
Genome_build: mm10
Supplementary_files_format_and_content: count file generated by featureCounts

source_name: 5-OP-RU- treated and B16F10 challenged lungs

growth_protocol: After harvesting lungs were digested with 1 mg/mL collagenase and 0.01mg/ml Dnase for 30 minutes at 37deg celcius for 30mins. RBCs were lysed with ACK lysis buffer.

extract_protocol:
Total RNA extracted from Flow cytometry sorted NK or MAIT cells using RNAeasy (Qiagen) kit as per manufacturers instructions
Quant-seq 3′ mRNA-seq Library Prep Kit for Illumina (Lexogen) as per manufacturer’s instructions.

treatment_protocol: Cells were labeled with  live dead stain, CD45.2-ApCCy7, CD19-BV650, TCRb-FITC, NK1.1-BV785, MR!-5-OP-RU tetramer -PE and sorted on either NK cells or MAIT cells

value: NK cell

value: B6-MAITcast MR1 WT

tag: tumour bearing

value: B16F10 melanoma

tag: drug treatment

tag: treatment schedule

value: 50 ul of 233mM 5-OP-RU intranasal Day 0, 1, 2, 4. B16F10 i.v. tumor cells Day 5. Harvest lungs day 6


title: IgAN_07_034

source_name: IgAN patients’ renal biopsies


title: MAITs: 5OPRU 2

source_name: 5-OP-RU- treated lungs

value: MAIT cell

value: No tumour

value: 50 ul of 233mM 5-OP-RU intranasal Day 0, 1, 2, 4. Harvest lungs day 6


title: IgAN_07_027


title: NKs 5OPRU + B16 2


title: IgAN_07_026


title: NKs: 5OPRU 2


title: NKs: 5OPRU 1


title: IgAN_07_025


title: Nks: PBS + B16 2

source_name: PBS treated and B16F10 challenged lungs

value: PBS

value: 50 ul PBS intranasal Day 0, 1, 2, 4. B16F10 i.v. tumor cells Day 5. Harvest lungs day 6


title: Nks: PBS + B16 1


title: MAITs: PBS 1

source_name: PBS treated lungs

value: 50 ul PBS intranasal Day 0, 1, 2, 4. Harvest lungs day 6


title: IgAN_07_024

value: IgAN

value: renal biopsies


title: MAITs: PBS 2


title: NKs: PBS 2


title: IgAN_07_021


title: IgAN_07_023


title: IgAN_07_020


title: IgAN_07_022


title: IgAN_07_019


title: NKs: PBS 1


title: IgAN_07_018


title: IgAN_07_017


title: MAITs: 5OPRU 1


title: Mixed WT, A06

city: Amsterdam

first: Saskia

middle: JE

last: Suijkerbuijk

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
Sample 6
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv
results_WTmix_Wtpure.csv

data_processing:
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode. After quality control and adaptor removal, read 2 was aligned to the m10 RefSeq transcriptome using BWA (Li and Durbin, 2010). Reads that mapped equally well to multiple locations were discarded.
Reads were quantified with featureCounts to generate read counts for each gene based on the gene annotation from Ensemble.
Differential gene expression was analyzed, based on featureCounts results, using DEseq2 version 1.22.2 (Love et al., 2014).
Fastq files were generated by paired-end sequencing following the mRNA bulk sequencing protocol based on the CEL-seq method as described in Simmini et al. Nat. Comm 2014 (https://www.nature.com/articles/ncomms6728?origin=ppub).The resulting, multiplexed, fastq files were demultiplexed based on CEL-seq barcode. Barcode information from these demultiplexed read1 fastq files was placed in the header of read 2 fastq files.
Read1 contained 8bp of Sample barcode and then 4bp UMI. This information was copied to the header of read 2. The rest of read1 is poly-A stretches from the mRNA's poly-A tail and can be ignored.
In Read2, the cell barcode and umi are indicated in the header by the following nomenclature; CB -> Cell barcode, RX-> UMI. Example: CB:CATCACGC;QT:aaaaaeee;RX:GGAT
To map the data, only these merged fastqfiles need to be mapped.
Genome_build: MM10
Supplementary_files_format_and_content: Matrix table with raw read/barcode/transcript counts for every gene and every sample
Supplementary_files_format_and_content: Comparison of gene expression in WT samples

source_name: wild-type small intestine organoids

growth_protocol: All lines were cultured in drops of Cultrex PathClear Reduced Growth Factor Basement Membrane Extract Type 2 (Amsbio, 3533-005-02) in murine small intestinal organoids medium containing advanced DMEM/F12 medium (adDMEM/F12; Thermo Fisher Scientific, cat. no. 12634-010), GlutaMAX 1% (Thermo Fisher Scientific, cat. no. 35050-068), HEPES 10mM (Thermo Fisher Scientific, cat. no. 15630-056), 1x Penicillin/streptomycin (10,000 U/ml; Thermo Fisher Scientific, cat. no. 15140-122). B27 2% (Thermo Fisher Scientific, cat. no. 17504-044), N-acetylcysteine 1.25 mM (Sigma-Aldrich, cat. no. A9165), mEGF 50ng/ml (Peprotech, cat. no. 315-09), Noggin and R-spondin1 both 10% (conditioned medium prepared in house).

extract_protocol:
Pure and mixed cells were cultured in 6-well plates and FACS sorted 3 days after mixing on a FACS Jazz system (BD). After a FSC/SSC gate doublets were excluded, live cells (DAPI negative) were sorted based on mTomato (wild-type cells) and Dendra2 (cancer cells) expression. Total RNA was extracted using the standard TRIzol (Invitrogen) protocol and used for library preparation and sequencing.
mRNA was processed as described previously, following an adapted version of the single-cell mRNA seq protocol of CEL-Seq (Hashimshony et al., 2012; Simmini et al., 2014). In brief, samples were barcoded with CEL-seq primers during a reverse transcription protocol and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. Paired-end sequencing was performed on the Illumina Nextseq500 platform.
Bulk RNA-seq

treatment_protocol: 3D mixed organoid cultures were prepared as follows; suspensions of small clumps of cells were generated from organoids by mechanical disruption and divided over Eppendorf vials in a 2:1 ratio (WT:cancer). Cells were concentrated by mild centrifugation, the pellet as resuspended in a small volume of murine small intestinal organoids medium and incubated at 37C for 30 minutes. Cell aggregates were plated in BME2 and cultured in murine small intestinal organoids medium.

tag: transgenic

value: mTmG

value: wild-type small intestine organoids

tag: isolated from

value: mixed cultures


title: IgAN_07_016

tag: patients


title: Pure WT, A05

description:
Sample 5
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv
results_WTmix_Wtpure.csv

value: pure cultures


title: Mixed Cancer, A08

description:
Sample 8
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv

source_name: cancer small intestine organoids

value: cancer small intestine organoids


title: IgAN_07_015

tag: disease state


title: IgAN_07_014


title: Pure Cancer, A03

description:
Sample 3
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv


title: IgAN_07_012


title: IgAN_07_013


title: IgAN_07_011


title: Pure WT, A01

description:
Sample 1
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv
results_WTmix_Wtpure.csv


title: iTreg_DFMO_JMJD3CKO3

city: Berkeley

first: Allon

last: Wagner

state: CA

address: 378 Stanley Hall

country: USA

institute: UC Berkeley

data_processing:
Reads were pseudoaligned and estimated counts quantified with Kallisto
Non-protein-coding genes were excluded
Genome_build: GRCm38.96
Supplementary_files_format_and_content: Two csv tables: a) expected read counts; and b) TPMs, quantified by Kallisto

source_name: Spleen CD4+ T cells

growth_protocol: Naïve CD4+CD44-CD62L+CD25-T cells were sorted using BD FACSAria sorter and activated with plate-bound anti-CD3 (1µg/ml) and antiCD28 antibodies (1µg/ml) in the presence of cytokines at a concentration of 0.5 x 10^6 cells/ml. For T cell differentiations the following combinations of cytokines were used: pathogenic Th17: 25ng/ml rmIL-6, 20ng/ml rmIL-1b (both Miltenyi Biotec) and 20ng/ml rmIL-23 (R&D systems); non-pathogenic Th17: 25ng/ml rmIL-6 and 2ng/ml of rhTGFb1 (Miltenyi Biotec); iTreg: 2ng/ml of rhTGFb1;

extract_protocol:
in vitro differentiated T-cells were sorted for live cells and lysed with RLT Plus buffer. RNA was extracted using SPRI paramagenetic beads (Beckman) as previously described (Singer et al., Cell 2016).
Full-length RNA-seq libraries were prepared as previously described (Singer et al., Cell 2016) and paired-end sequenced (75 bp × 2) with a 150 cycle Nextseq 500 high output V2 kit.

treatment_protocol: cells were harvested at 68 hours and were performed in the presence or absence of 100µM DFMO (Sigma)

tag: differentiation

value: iTreg

tag: treatment

value: DFMO


title: Th17n_DFMO_JMJD3CKO3


title: IgAN_07_010

tag: tissue


title: IgAN_07_008


title: Pure Cancer, A07

description:
Sample 7
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv


title: IgAN_07_007


title: Th17n_DFMO_JMJD3CKO2


title: iTreg_DFMO_JMJD3CKO2


title: iTreg_DFMO_JMJD3CKO1


title: iTreg_DFMO_WT4

value: WT


title: IgAN_07_004


title: IgAN_07_009


title: IgAN_07_006


title: IgAN_07_003


title: iTreg_DFMO_WT3


title: Th17n_DFMO_WT4


title: Mixed WT, A02

description:
Sample 2
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv
results_WTmix_Wtpure.csv


title: Mixed Cancer, A04

description:
Sample 4
Readcounts.tsv
Barcodecounts.tsv
Transcriptcounts.tsv


title: Th17n_DFMO_JMJD3CKO1


title: IgAN_07_002


title: iTreg_DFMO_WT2


title: Th17n_DFMO_WT3


title: IgAN_06_018


title: iTreg_DFMO_WT1


title: IgAN_06_017


title: Th17n_DFMO_WT2


title: Th17n_DFMO_WT1


title: IgAN_07_005


title: IgAN_06_014


title: iTreg_ctrl_JMJD3CKO3

value: ctrl


title: Th17n_ctrl_JMJD3CKO3


title: IgAN_07_001


title: IgAN_06_013


title: IgAN_06_011


title: iTreg_ctrl_JMJD3CKO1


title: Th17n_ctrl_JMJD3CKO2


title: iTreg_ctrl_JMJD3CKO2


title: IgAN_06_015


title: IgAN_06_016


title: IgAN_06_012


title: Th17n_ctrl_JMJD3CKO1


title: IgAN_06_009


title: IgAN_06_008


title: iTreg_ctrl_WT3


title: IgAN_06_010


title: IgAN_06_007


title: iTreg_ctrl_WT4


title: Th17n_ctrl_WT4


title: IgAN_06_005


title: IgAN_06_006


title: IgAN_06_004


title: Th17n_ctrl_WT3


title: iTreg_ctrl_WT2


title: iTreg_ctrl_WT1


title: IgAN_06_003


title: IgAN_06_002


title: IgAN_06_001


title: Th17n_ctrl_WT1


title: iTreg_DFMO_WT3_run2

data_processing:
Read were aligned with Bowtie2
Expected read counts and TPM expression were quantified with RSEM
Non-protein-coding genes were discarded
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: Expected read counts and TPMs (csv tables)

tag: cell type


title: IgAN_01_137


title: IgAN_01_136


title: iTreg_DFMO_WT3_run1


title: Th17n_DFMO_WT3_run2


title: IgAN_01_134


title: IgAN_01_135


title: Th17n_DFMO_WT3_run1


title: Th17p_DFMO_WT3_run2


title: iTreg_Vehicle_WT3_run2

value: Vehicle


title: Th17p_DFMO_WT3_run1


title: iTreg_Vehicle_WT3_run1


title: IgAN_01_131


title: Th17n_Vehicle_WT3_run2


title: IgAN_01_129


title: Th17n_Vehicle_WT3_run1


title: IgAN_01_130


title: IgAN_01_128


title: Th17p_Vehicle_WT3_run2


title: Th17n_ctrl_WT2

tag: genotype


title: IgAN_01_127


title: iTreg_DFMO_WT2_run2


title: Th17p_Vehicle_WT3_run1


title: IgAN_01_125


title: IgAN_01_124


title: iTreg_DFMO_WT2_run1


title: Th17n_DFMO_WT2_run2


title: IgAN_01_123


title: Th17n_DFMO_WT2_run1


title: IgAN_01_122


title: Th17p_DFMO_WT2_run2


title: IgAN_01_133


title: IgAN_01_120


title: IgAN_01_121


title: Th17p_DFMO_WT2_run1


title: IgAN_01_132


title: IgAN_01_117


title: IgAN_01_126


title: iTreg_Vehicle_WT2_run2


title: Th17p_Vehicle_WT2_run2


title: Th17n_Vehicle_WT2_run1


title: Th17n_Vehicle_WT2_run2


title: IgAN_01_113


title: IgAN_01_116


title: IgAN_01_115


title: Th17p_Vehicle_WT2_run1


title: IgAN_01_119


title: IgAN_01_118


title: iTreg_Vehicle_WT2_run1


title: iTreg_DFMO_WT1_run1


title: IgAN_01_114


title: Th17n_DFMO_WT1_run2


title: iTreg_DFMO_WT1_run2


title: IgAN_01_111


title: IgAN_01_110


title: Th17p_DFMO_WT1_run2


title: IgAN_01_109


title: Th17p_DFMO_WT1_run1


title: IgAN_01_108


title: iTreg_Vehicle_WT1_run2


title: IgAN_01_107


title: iTreg_Vehicle_WT1_run1


title: Th17n_Vehicle_WT1_run2


title: IgAN_01_106


title: IgAN_01_105


title: Th17n_Vehicle_WT1_run1


title: IgAN_01_112


title: IgAN_01_103


title: Th17n_DFMO_WT1_run1


title: Th17p_Vehicle_WT1_run2


title: Th17p_Vehicle_WT1_run1


title: IgAN_01_104


title: IgAN_01_101


title: CML TKI HSC rep3

city: Boston

first: Mahmoud

middle: Adel

last: Bassal

state: Massachusetts

address: 3 Blackfan Circle

department: Hematology and Oncology

institute: Beth Israel Deaconess Medical Center

data_processing:
Basecalls performed using Partek Flow software, version 8.0
For Bulk RNA-seq: double-ended sequencing reads were aligned to the mouse (mm10) or human (hg38) using Spliced Transcripts Alignment to a Reference (STAR 2.6.1d). Aligned reads were then quantified to the transcriptome (RefSeq Transcripts 92) and normalized
Genome_build: mm10

source_name: Sorted Lin-Sca1+cKit+Flt3-CD150-CD48+

extract_protocol:
RNA was isolated using the RNeasy Plus mini kit (Qiagen) for bulk RNA-seq
Libraries were prepared according to Illumina's Nextera XT instructions

treatment_protocol: mice were treated with 400mg/kg of imatinib was administered by gavage every alternate day for 30 days

value: Stem cells

tag: organ

value: Bone marrow

tag: murine strain

value: 400mg/kg imatinib every alternate days for 4 weeks

value: CML mice tretaed with TKI


title: CML TKI HSC rep4


title: IgAN_01_100


title: IgAN_01_102


title: CML TKI HSC rep1


title: 20190806_MGC-KT-1920_EP008_11

hyb_protocol: As per manufacturer's instructions

scan_protocol: As per manufacturer's instructions

data_processing: nSolver 4.0

label: NanoString

source_name: 5-OP-RU treated lungs

label_protocol: As per manufacturer's instructions

extract_protocol: RNA was extracted from processed lungs using RNAeasy (Qiagen) kit as per manufacturers instructions.

treatment_protocol: Mice received either 50 ul of PBS or 233 uM 5-OP-RU intranasally on Day 0, 1, 2 and 4. Lungs were harvested day 6.

tag: gender

value: Female

tag: strain

value: B6-MAITcast MR1 WT

value: Lungs

tag: drug scheduling

value: 50 ul of 233uM 5-OP-RU intranasal Day 0, 1, 2, 4. Harvest lungs day 6


title: CML HSC rep4

value: Untreated

tag: genotype/variation

value: CML


title: 20190806_MGC-KT-1920_EP007_12

tag: drug treatment


title: IgAN_01_099

value: IgAN

value: renal biopsies


title: 20190806_MGC-KT-1920_EP005_05


title: 20190806_MGC-KT-1920_EP004_04

description: Excluded from final anaysis as tube was cracked and readings are inacccurate.

value: PBS

value: 50 ul PBS intranasal Day 0, 1, 2, 4. Harvest lungs day 6


title: IgAN_01_098


title: 20190806_MGC-KT-1920_EP006_06


title: PC9/GR-sh2-HUNT-3

city: harbin

first: shoubin

last: sun

address: baojian road 157

institute: harbin medical university

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) [1] by (1) Removing reads   containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) [2]. Bowtie2 (v2.2.5) [3] was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12) [4] . The heatmap was drawn by pheatmap (v1.0.8) [5] according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)[6] with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni [7] .
Genome_build: GCF_000001405.39
Supplementary_files_format_and_content: Excel files including FPKM of each sample

source_name: gefitinib-resistant lung adenocarcinoma cell lines（PC9/GR）

growth_protocol: The cells were cultured in RPMI 1640 medium with 10% fetal bovine serum (FBS) at 37 °C in the presence of 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: PC9/GR-sh1-HUMT and PC9/GR-sh2-HUMT were designed to knockdown HUMT in PC9/GR. PC9/GR-shNC was control.

value: HUMT-specific sh2-HUMT were designed to knockdown HUMT in PC9/GR


title: PC9/GR-sh2-HUNT-2


title: 20190806_MGC-KT-1920_EP001_01

description: Excluded from final anaysis as reads were below threshold.


title: 20190806_MGC-KT-1920_EP002_02


title: 20190806_MGC-KT-1920_EP003_03


title: PC9/GR-sh2-HUNT-1


title: PC9/GR-sh1-HUNT-3

value: HUMT-specific sh1-HUMT were designed to knockdown HUMT in PC9/GR


title: CML HSC rep2


title: IgAN_01_096


title: PC9/GR-sh1-HUNT-2


title: PC9/GR-sh1-HUMT-1


title: CML TKI HSC rep2


title: CML HSC rep1


title: IgAN_01_095


title: IgAN_01_094


title: PC9/GR-shNC-1

value: HUMT-specific shNC were designed in PC9/GR


title: IgAN_01_097


title: MDA-MB-231/PTX-si2-BCLIN25-3

treatment_protocol: MDA-MB-231/PTX-si1-BCLIN25 and MDA-MB-231/PTX-si2-BCLIN25 were designed to knockdown BCLIN25 in MDA-MB-231/PTX. PMDA-MB-231/PTX-siNC was control.


title: IgAN_01_093


title: MDA-MB-231/PTX-si2-BCLIN25-2


title: IgAN_01_092


title: CML TKI LSK [ChIP-seq]

description: STAT3 ChIP-seq on sorted LSK from WT mice, CML mice and CML mice treated with TKI

library_source: genomic

data_processing:
Basecalls performed using Partek Flow software, version 8.0
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
peaks were called using Partek Flow with the following setting: ChIP threshold (0.2), Enrichment Fold (2)
Transcription factors binding site analysis was performed on pSTAT3 peaks using Centdist68 with both Jaspar STAT3 (MA0144.1) and Transfac vertebrate databases
Potential binding sites were identified using a custom Perl script based on the TFBS library
Genome_build: mm10

molecule: genomic DNA

source_name: Sorted Lin-Sca1+cKti+

extract_protocol:
Cells were cross-linked and sheared for ChIP with IgG and pSTAT3-Y705 (#9131, Cell Signaling)
Libraries were constructed using Index Illumina library construction

value: Stem and progenitor cells

value: 200mg/kg imatinib every alternate days for 4 weeks

tag: antibody

value: pSTAT3-Y705 (#9131, Cell Signaling)

tag: genotype/variaton


title: MDA-MB-231/PTX-si1-BCLIN25-3


title: WT LSK [ChIP-seq]

value: Bone marrow

value: WT


title: MDA-MB-231/PTX-si1-BCLIN25-2


title: CML HSC rep3

value: Stem cells


title: CML LSK [ChIP-seq]


title: MDA-MB-231/PTX-si2-BCLIN25-1


title: MDA-MB-231/PTX-si1-BCLIN25-1


title: MDA-MB-231/PTX-si-NC-3


title: IgAN_01_090


title: MDA-MB-231/PTX-si-NC-2


title: PC9/GR-shNC-3


title: MDA-MB-231/PTX-si-NC-1


title: Input [ChIP-seq]

description: Input ChIP-seq on sorted LSK from WT mice, CML mice and CML mice treated with TKI

value: IgG


title: IgAN_01_089


title: RB307 (SNP_370K)

type: genomic

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 44

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
The B allele frequency  and log-ratio signals were smoothes and analyzed using the Geneome Alteration Print (GAP) algorithm (Popova et al., 2009).
1.Raw data file :
X raw and Y raw : raw coordinates ; X and Y: normalized coordinates
1.Processed  data file :
score: GenomeStudio score; Theta: GenomeStudio genotype metric; R: GenomeStudio intensity metric; B allele frequency: GenomeStudio B allele frequency estimate; Log R ratio: GenomeStudio signal intensity estimate

source_name: retinblastoma sample RB307

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A.  DNA was then extracted using a standard phenol-chloroform protocol

tag: geo dataset

value: SAMPLE 89

tag: batch name

value: retinoblastoma


title: RB305 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 43

source_name: retinblastoma sample RB305

value: SAMPLE 88


title: IgAN_01_088

tag: patients

tag: disease state

value: IgAN


title: PC9/GR-shNC-2

tag: treatment


title: RB304 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 42

source_name: retinblastoma sample RB304

value: SAMPLE 87

tag: tissue


title: IgAN_01_091

value: renal biopsies


title: IgAN_01_087


title: RB303 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 41

source_name: retinblastoma sample RB303

value: SAMPLE 86


title: RB301 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 39

source_name: retinblastoma sample RB301

value: SAMPLE 84


title: rag2∆/∆, il2rga-/- zebrafish kidney marrow animal 1

city: Cambridge

first: Qian

last: Qin

state: MA

address: 24 Peabody Terrace, Unit 2002

department: Molecular Pathology Unit

institute: Massachusetts General Hospital

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
rag2il2rga_rep1_run1_CTCCTTAC

data_processing:
bcl2fastq2-v2.17.1 was used to convert BCL into FASTQ
indrops pipeline (https://github.com/indrops/indrops) was used to demultiplex, align, sort and quantify the gene expression of barcoded cells.
indrops sort output fastq.gz was uploaded
Seurat was used for downstream analysis
the preprocessing and analysis script is at https://github.com/qinqian/zebrafish_indrop/.
Genome_build: GRCz10
Supplementary_files_format_and_content: indrop..counts.tsv.gz

organism: Danio rerio

growth_protocol: WT, rag2∆/∆ and rag2∆/∆, il2rga-/- immunocompromised zebrafish are sacrificed at approximately 2 month post fertilisation and kidney marrow extracted

extract_protocol:
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 standard Illumina protocols

treatment_protocol: Extracted kidney marrow are dissociated into single cell suspension and subjected to indrop single cell sequencing

value: Kidney marrow

tag: cell type

value: Immune cells

value: rag2{delta}/{delta}, il2rga-/-


title: IgAN_01_086


title: rag2∆/∆ zebrafish kidney marrow animal 2

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
rag2_rep2_run1_AGAGGATA

source_name: rag2∆/∆ zebrafish kidney marrow

tag: genotype


title: rag2∆/∆, il2rga-/- zebrafish kidney marrow animal 3

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
rag2il2rga_rep3_run1_TACTCCTT


title: RB300 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 38

source_name: retinblastoma sample RB300

value: SAMPLE 83


title: RB302 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 40

source_name: retinblastoma sample RB302

value: SAMPLE 85


title: rag2∆/∆, il2rga-/- zebrafish kidney marrow animal 2

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
rag2il2rga_rep2_run1_TATGCAGT


title: RB225 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 37

source_name: retinblastoma sample RB225

value: SAMPLE 82


title: IgAN_01_085

source_name: IgAN patients’ renal biopsies


title: RB223 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 35

source_name: retinblastoma sample RB223

value: SAMPLE 80


title: RB224 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 36

source_name: retinblastoma sample RB224

value: SAMPLE 81


title: IgAN_01_084


title: rag2∆/∆ zebrafish kidney marrow animal 1

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
rag2_rep1_run1_ATAGAGAG


title: WT zebrafish kidney marrow sample animal 3

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
WT_rep3_run1_CTAGTCGA

source_name: WT zebrafish kidney marrow

value: Wild type


title: IgAN_01_083


title: RB220 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 33

source_name: retinblastoma sample RB220

value: SAMPLE 77


title: WT zebrafish kidney marrow sample animal 2

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
WT_rep2_run1_CGGAGAGA


title: IgAN_01_080


title: RB219 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 32

source_name: retinblastoma sample RB219

value: SAMPLE 76

value: retinoblastoma


title: rag2∆/∆ zebrafish kidney marrow animal 3

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
rag2_rep3_run1_ATTAGACG


title: IgAN_01_082

value: IgAN


title: WT zebrafish kidney marrow sample animal 1

description:
InDrop single-cell sequencing was completed on adult zebrafish kidney marrow as previously described (Tang et al., 2017). Briefly, 2-month-old zebrafish were sacrificed, marrow extracted, and made into single-cell suspension for microfluidic encapsulation. Library construction was performed by the Harvard ICCB Single Cell Core using methods outlined in Klein et al. (Klein et al., 2015). Libraries were sequenced using the Nextseq 500 High Output V2 Kit. tSNE visualization used combined samples from three fish per genotype (wild type, n=4,654 cells; rag2∆/∆, n=9,418 cells; and rag2∆/∆, il2rga-/-, n=8,790 cells).
WT_rep1_run1_AGGCTTAG


title: RB215 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 30

source_name: retinblastoma sample RB215

value: SAMPLE 72


title: IgAN_01_081

value: renal biopsies


title: RB209 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 26

source_name: retinblastoma sample RB209

value: SAMPLE 66


title: IgAN_01_078


title: RB222 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 34

source_name: retinblastoma sample RB222

value: SAMPLE 79


title: RB211 (SNP_370K)

description:
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 28

source_name: retinblastoma sample RB211

value: SAMPLE 68