title: C31_13_S173 [colonies_scRNA-seq]


title: C33_14_S178 [colonies_scRNA-seq]

status: Public on Feb 28 2019

type: SRA

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

country: USA

institute: Memorial Sloan Kettering

library_source: transcriptomic

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard two-pass approach.
Gene were quantified using the STAR --quantMode GeneCounts flag over the Gencode v19 annotation.
Processed bams were genotyped for mitochondria using a custom python script.
Samples were filtered based on the following criterion: 1) a cell had to have 500 genes detected with at least 2000 total counts and 2) minimum mean mitochondria coverage of 100x
Genome_build: hg19
Supplementary_files_format_and_content: Heteroplasmy for variants that separated colonies as well as single-cell gene expression counts for filtered genes and cells used in analysis

molecule: total RNA

organism: Homo sapiens

source_name: donor 2_CD34+ hematopoietic cells

growth_protocol: StemSpan II supplemented with CC100

extract_protocol:
Qiagen TCL lysis buffer
Smart-seq2; Single cell RNA-seq

tag: donor id

value: donor 2

tag: cell type

value: primary hematopoietic cells


title: C31_02_S102 [colonies_scRNA-seq]


title: C31_07_S137 [colonies_scRNA-seq]


title: C30_14_S172 [colonies_scRNA-seq]


title: C32_04_S116 [colonies_scRNA-seq]


title: C30_11_S159 [colonies_scRNA-seq]


title: C30_16_S184 [colonies_scRNA-seq]


title: C30_08_S136 [colonies_scRNA-seq]


title: C30_07_S135 [colonies_scRNA-seq]


title: C30_09_S147 [colonies_scRNA-seq]


title: C31_01_S101 [colonies_scRNA-seq]


title: C30_15_S183 [colonies_scRNA-seq]


title: C30_13_S171 [colonies_scRNA-seq]


title: C30_10_S148 [colonies_scRNA-seq]


title: C30_06_S124 [colonies_scRNA-seq]


title: C30_04_S112 [colonies_scRNA-seq]


title: C30_01_S99 [colonies_scRNA-seq]


title: C30_03_S111 [colonies_scRNA-seq]


title: C30_05_S123 [colonies_scRNA-seq]


title: C30_02_S100 [colonies_scRNA-seq]


title: C29_16_S182 [colonies_scRNA-seq]


title: C29_15_S181 [colonies_scRNA-seq]


title: C29_14_S170 [colonies_scRNA-seq]


title: C29_12_S158 [colonies_scRNA-seq]


title: C29_13_S169 [colonies_scRNA-seq]


title: C29_10_S146 [colonies_scRNA-seq]


title: C29_09_S145 [colonies_scRNA-seq]


title: C29_08_S134 [colonies_scRNA-seq]


title: C29_07_S133 [colonies_scRNA-seq]


title: C29_04_S110 [colonies_scRNA-seq]


title: C29_06_S122 [colonies_scRNA-seq]


title: C30_12_S160 [colonies_scRNA-seq]


title: C29_11_S157 [colonies_scRNA-seq]


title: C29_02_S98 [colonies_scRNA-seq]


title: C29_01_S97 [colonies_scRNA-seq]


title: C27_14_pos_S372 [colonies_scRNA-seq]


title: C27_11_S359 [colonies_scRNA-seq]


title: C29_03_S109 [colonies_scRNA-seq]


title: C27_15_S383 [colonies_scRNA-seq]


title: C27_16_neg_S384 [colonies_scRNA-seq]


title: C27_08_S336 [colonies_scRNA-seq]


title: C27_07_S335 [colonies_scRNA-seq]


title: C27_13_S371 [colonies_scRNA-seq]


title: C27_02_S300 [colonies_scRNA-seq]


title: C26_14_S370 [colonies_scRNA-seq]


title: C26_13_S369 [colonies_scRNA-seq]


title: C26_15_S381 [colonies_scRNA-seq]


title: C26_10_S346 [colonies_scRNA-seq]


title: C26_07_S333 [colonies_scRNA-seq]


title: C27_12_S360 [colonies_scRNA-seq]


title: C26_05_S321 [colonies_scRNA-seq]


title: C27_10_S348 [colonies_scRNA-seq]


title: C27_09_S347 [colonies_scRNA-seq]


title: C27_06_S324 [colonies_scRNA-seq]


title: C26_04_S310 [colonies_scRNA-seq]


title: C27_04_S312 [colonies_scRNA-seq]


title: C26_01_S297 [colonies_scRNA-seq]


title: C25_16_S380 [colonies_scRNA-seq]


title: C27_03_S311 [colonies_scRNA-seq]


title: C27_05_S323 [colonies_scRNA-seq]


title: C25_12_S356 [colonies_scRNA-seq]


title: C29_05_S121 [colonies_scRNA-seq]


title: C26_16_S382 [colonies_scRNA-seq]


title: C26_12_S358 [colonies_scRNA-seq]


title: C25_11_S355 [colonies_scRNA-seq]


title: C26_11_S357 [colonies_scRNA-seq]


title: C26_08_S334 [colonies_scRNA-seq]


title: C27_01_S299 [colonies_scRNA-seq]


title: C25_07_S331 [colonies_scRNA-seq]


title: C26_09_S345 [colonies_scRNA-seq]


title: C26_06_S322 [colonies_scRNA-seq]


title: C25_04_S308 [colonies_scRNA-seq]


title: C25_02_S296 [colonies_scRNA-seq]


title: C26_02_S298 [colonies_scRNA-seq]


title: C25_13_S367 [colonies_scRNA-seq]


title: C24_14_S366 [colonies_scRNA-seq]


title: C25_09_S343 [colonies_scRNA-seq]


title: C25_14_S368 [colonies_scRNA-seq]


title: C24_12_S354 [colonies_scRNA-seq]


title: C26_03_S309 [colonies_scRNA-seq]


title: C25_06_S320 [colonies_scRNA-seq]


title: C24_09_S341 [colonies_scRNA-seq]


title: C25_05_S319 [colonies_scRNA-seq]


title: C25_10_S344 [colonies_scRNA-seq]


title: C24_10_S342 [colonies_scRNA-seq]


title: C24_16_S378 [colonies_scRNA-seq]


title: C24_07_S329 [colonies_scRNA-seq]


title: C25_15_S379 [colonies_scRNA-seq]


title: C24_08_S330 [colonies_scRNA-seq]


title: C24_06_S318 [colonies_scRNA-seq]


title: C25_01_S295 [colonies_scRNA-seq]


title: C24_04_S306 [colonies_scRNA-seq]


title: C24_13_S365 [colonies_scRNA-seq]


title: C25_08_S332 [colonies_scRNA-seq]


title: C25_03_S307 [colonies_scRNA-seq]


title: C24_01_S293 [colonies_scRNA-seq]


title: C24_15_S377 [colonies_scRNA-seq]


title: C24_05_S317 [colonies_scRNA-seq]


title: C24_02_S294 [colonies_scRNA-seq]


title: C23_16_S376 [colonies_scRNA-seq]


title: C23_15_S375 [colonies_scRNA-seq]


title: C23_11_S351 [colonies_scRNA-seq]


title: C23_12_S352 [colonies_scRNA-seq]


title: C23_14_S364 [colonies_scRNA-seq]


title: C23_10_S340 [colonies_scRNA-seq]


title: C24_11_S353 [colonies_scRNA-seq]


title: C23_09_S339 [colonies_scRNA-seq]


title: C23_08_S328 [colonies_scRNA-seq]


title: C23_05_S315 [colonies_scRNA-seq]


title: C23_06_S316 [colonies_scRNA-seq]


title: C24_03_S305 [colonies_scRNA-seq]


title: C22_15_S373 [colonies_scRNA-seq]


title: C23_01_S291 [colonies_scRNA-seq]


title: C22_14_S362 [colonies_scRNA-seq]


title: C22_16_S374 [colonies_scRNA-seq]


title: C22_12_S350 [colonies_scRNA-seq]


title: C23_02_S292 [colonies_scRNA-seq]


title: C23_03_S303 [colonies_scRNA-seq]


title: C23_04_S304 [colonies_scRNA-seq]


title: C22_10_S338 [colonies_scRNA-seq]


title: C22_11_S349 [colonies_scRNA-seq]


title: C22_07_S325 [colonies_scRNA-seq]


title: C23_13_S363 [colonies_scRNA-seq]


title: C22_04_S302 [colonies_scRNA-seq]


title: C22_05_S313 [colonies_scRNA-seq]


title: C22_06_S314 [colonies_scRNA-seq]


title: C22_02_S290 [colonies_scRNA-seq]


title: C22_01_S289 [colonies_scRNA-seq]


title: C20_16_neg_S288 [colonies_scRNA-seq]


title: C20_15_S287 [colonies_scRNA-seq]


title: C23_07_S327 [colonies_scRNA-seq]


title: C20_14_pos_S276 [colonies_scRNA-seq]


title: C20_12_S264 [colonies_scRNA-seq]


title: C22_03_S301 [colonies_scRNA-seq]


title: C22_13_S361 [colonies_scRNA-seq]


title: C20_10_S252 [colonies_scRNA-seq]


title: C20_11_S263 [colonies_scRNA-seq]


title: C20_13_S275 [colonies_scRNA-seq]


title: C20_09_S251 [colonies_scRNA-seq]


title: C20_06_S228 [colonies_scRNA-seq]


title: C20_04_S216 [colonies_scRNA-seq]


title: C20_01_S203 [colonies_scRNA-seq]


title: C22_08_S326 [colonies_scRNA-seq]


title: C19_16_S286 [colonies_scRNA-seq]


title: C20_07_S239 [colonies_scRNA-seq]


title: C20_03_S215 [colonies_scRNA-seq]


title: C20_02_S204 [colonies_scRNA-seq]


title: C19_14_S274 [colonies_scRNA-seq]


title: C19_13_S273 [colonies_scRNA-seq]


title: C20_05_S227 [colonies_scRNA-seq]


title: C19_10_S250 [colonies_scRNA-seq]


title: C22_09_S337 [colonies_scRNA-seq]


title: C19_09_S249 [colonies_scRNA-seq]


title: C19_06_S226 [colonies_scRNA-seq]


title: C19_07_S237 [colonies_scRNA-seq]


title: C19_08_S238 [colonies_scRNA-seq]


title: C19_05_S225 [colonies_scRNA-seq]


title: C19_04_S214 [colonies_scRNA-seq]


title: C19_03_S213 [colonies_scRNA-seq]


title: C19_15_S285 [colonies_scRNA-seq]


title: C19_02_S202 [colonies_scRNA-seq]


title: C20_08_S240 [colonies_scRNA-seq]


title: C18_13_S271 [colonies_scRNA-seq]


title: C19_01_S201 [colonies_scRNA-seq]


title: C18_16_S284 [colonies_scRNA-seq]


title: C18_15_S283 [colonies_scRNA-seq]


title: C18_12_S260 [colonies_scRNA-seq]


title: C18_10_S248 [colonies_scRNA-seq]


title: C18_09_S247 [colonies_scRNA-seq]


title: C18_08_S236 [colonies_scRNA-seq]


title: C18_06_S224 [colonies_scRNA-seq]


title: C18_05_S223 [colonies_scRNA-seq]


title: C19_12_S262 [colonies_scRNA-seq]


title: C18_07_S235 [colonies_scRNA-seq]


title: C19_11_S261 [colonies_scRNA-seq]


title: C18_04_S212 [colonies_scRNA-seq]


title: C18_03_S211 [colonies_scRNA-seq]


title: C18_02_S200 [colonies_scRNA-seq]


title: C18_01_S199 [colonies_scRNA-seq]


title: C17_16_S282 [colonies_scRNA-seq]


title: C17_14_S270 [colonies_scRNA-seq]


title: C17_11_S257 [colonies_scRNA-seq]


title: C17_10_S246 [colonies_scRNA-seq]


title: C18_14_S272 [colonies_scRNA-seq]


title: C17_09_S245 [colonies_scRNA-seq]


title: C17_06_S222 [colonies_scRNA-seq]


title: C17_07_S233 [colonies_scRNA-seq]


title: C17_13_S269 [colonies_scRNA-seq]


title: C18_11_S259 [colonies_scRNA-seq]


title: C17_08_S234 [colonies_scRNA-seq]


title: C17_02_S198 [colonies_scRNA-seq]


title: C17_01_S197 [colonies_scRNA-seq]


title: C16_16_S280 [colonies_scRNA-seq]


title: C17_05_S221 [colonies_scRNA-seq]


title: C17_04_S210 [colonies_scRNA-seq]


title: C16_11_S255 [colonies_scRNA-seq]


title: C16_15_S279 [colonies_scRNA-seq]


title: C16_09_S243 [colonies_scRNA-seq]


title: C16_13_S267 [colonies_scRNA-seq]


title: C16_12_S256 [colonies_scRNA-seq]


title: C16_14_S268 [colonies_scRNA-seq]


title: C17_03_S209 [colonies_scRNA-seq]


title: C16_07_S231 [colonies_scRNA-seq]


title: C16_08_S232 [colonies_scRNA-seq]


title: C17_15_S281 [colonies_scRNA-seq]


title: C17_12_S258 [colonies_scRNA-seq]


title: C16_05_S219 [colonies_scRNA-seq]


title: C16_04_S208 [colonies_scRNA-seq]


title: C16_03_S207 [colonies_scRNA-seq]


title: C16_06_S220 [colonies_scRNA-seq]


title: C16_01_S195 [colonies_scRNA-seq]


title: C15_16_S278 [colonies_scRNA-seq]


title: C16_02_S196 [colonies_scRNA-seq]


title: C15_13_S265 [colonies_scRNA-seq]


title: C15_14_S266 [colonies_scRNA-seq]


title: C15_12_S254 [colonies_scRNA-seq]


title: C15_11_S253 [colonies_scRNA-seq]


title: C15_10_S242 [colonies_scRNA-seq]


title: C15_06_S218 [colonies_scRNA-seq]


title: C15_08_S230 [colonies_scRNA-seq]


title: C16_10_S244 [colonies_scRNA-seq]


title: C15_05_S217 [colonies_scRNA-seq]


title: C15_03_S205 [colonies_scRNA-seq]


title: C15_04_S206 [colonies_scRNA-seq]


title: C15_01_S193 [colonies_scRNA-seq]


title: C15_02_S194 [colonies_scRNA-seq]


title: C13_15_S191 [colonies_scRNA-seq]


title: C13_16_neg_S192 [colonies_scRNA-seq]


title: C13_14_pos_S180 [colonies_scRNA-seq]


title: C13_13_S179 [colonies_scRNA-seq]


title: C13_10_S156 [colonies_scRNA-seq]


title: C13_09_S155 [colonies_scRNA-seq]


title: C13_11_S167 [colonies_scRNA-seq]


title: C13_08_S144 [colonies_scRNA-seq]


title: C13_07_S143 [colonies_scRNA-seq]


title: C15_15_S277 [colonies_scRNA-seq]


title: C13_06_S132 [colonies_scRNA-seq]


title: C13_04_S120 [colonies_scRNA-seq]


title: C13_03_S119 [colonies_scRNA-seq]


title: C13_01_S107 [colonies_scRNA-seq]


title: C15_09_S241 [colonies_scRNA-seq]


title: C13_05_S131 [colonies_scRNA-seq]


title: C15_07_S229 [colonies_scRNA-seq]


title: C12_16_S190 [colonies_scRNA-seq]


title: C12_11_S165 [colonies_scRNA-seq]


title: C12_09_S153 [colonies_scRNA-seq]


title: C12_14_S178 [colonies_scRNA-seq]


title: C12_15_S189 [colonies_scRNA-seq]


title: C12_10_S154 [colonies_scRNA-seq]


title: C12_12_S166 [colonies_scRNA-seq]


title: C12_13_S177 [colonies_scRNA-seq]


title: C12_04_S118 [colonies_scRNA-seq]


title: C12_07_S141 [colonies_scRNA-seq]


title: C12_08_S142 [colonies_scRNA-seq]


title: C12_06_S130 [colonies_scRNA-seq]


title: C13_12_S168 [colonies_scRNA-seq]


title: C12_05_S129 [colonies_scRNA-seq]


title: C12_03_S117 [colonies_scRNA-seq]


title: C12_02_S106 [colonies_scRNA-seq]


title: C11_16_S188 [colonies_scRNA-seq]


title: C11_15_S187 [colonies_scRNA-seq]


title: C12_01_S105 [colonies_scRNA-seq]


title: C11_13_S175 [colonies_scRNA-seq]


title: C11_14_S176 [colonies_scRNA-seq]


title: C13_02_S108 [colonies_scRNA-seq]


title: C11_11_S163 [colonies_scRNA-seq]


title: C11_08_S140 [colonies_scRNA-seq]


title: C11_09_S151 [colonies_scRNA-seq]


title: C11_10_S152 [colonies_scRNA-seq]


title: C11_06_S128 [colonies_scRNA-seq]


title: C11_07_S139 [colonies_scRNA-seq]


title: C11_05_S127 [colonies_scRNA-seq]


title: C11_12_S164 [colonies_scRNA-seq]


title: C11_04_S116 [colonies_scRNA-seq]


title: C11_03_S115 [colonies_scRNA-seq]


title: C10_14_S174 [colonies_scRNA-seq]


title: C10_16_S186 [colonies_scRNA-seq]


title: C10_13_S173 [colonies_scRNA-seq]


title: C10_11_S161 [colonies_scRNA-seq]


title: C10_15_S185 [colonies_scRNA-seq]


title: C10_10_S150 [colonies_scRNA-seq]


title: C10_08_S138 [colonies_scRNA-seq]


title: C10_09_S149 [colonies_scRNA-seq]


title: C11_02_S104 [colonies_scRNA-seq]


title: C10_07_S137 [colonies_scRNA-seq]


title: C10_12_S162 [colonies_scRNA-seq]


title: C10_05_S125 [colonies_scRNA-seq]


title: C10_03_S113 [colonies_scRNA-seq]


title: C10_04_S114 [colonies_scRNA-seq]


title: C10_02_S102 [colonies_scRNA-seq]


title: C09_16_S184 [colonies_scRNA-seq]


title: C10_01_S101 [colonies_scRNA-seq]


title: C09_15_S183 [colonies_scRNA-seq]


title: C09_14_S172 [colonies_scRNA-seq]


title: C09_13_S171 [colonies_scRNA-seq]


title: C09_12_S160 [colonies_scRNA-seq]


title: C09_09_S147 [colonies_scRNA-seq]


title: C09_07_S135 [colonies_scRNA-seq]


title: C09_08_S136 [colonies_scRNA-seq]


title: C09_10_S148 [colonies_scRNA-seq]


title: C09_11_S159 [colonies_scRNA-seq]


title: C11_01_S103 [colonies_scRNA-seq]


title: AAVS1_A_MEFs

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

data_processing:
Sequencing was performed on an Illumina NextSeq 500 using 75 base pair single-end reads
Reads were trimmed to eliminate adaptor contamination using the Illumina bcl2fastq-conversion software (v2.20), and any reads shorter than 36bp after trimming were removed
Filtered reads were mapped to hg38/Gencode_v25 using STAR (v2.4.2a)
Filtered reads were also mapped to mm10/Gencode_vM12 using STAR (v2.4.2a)
Human and mouse BAM files were analyzed using XenofileR (v0.99.0) to remove contaminating mouse reads
Human filtered BAM files were summarized to read counts using HTSeq (v0.6.1)
Genome_build: hg38

source_name: H1 ESCs

growth_protocol: H1 cells (NIH code WA01, sex: male, RRID: CVCL_9771) were obtained from WiCell for research use. H1 wild-type and H1-iCas9 cells were maintained in one of two culture conditions:  “MEF culture” means culture on irradiated mouse embryonic fibroblasts (MEFs) in human embryonic stem cell (hESC) medium as described (Ditadi and Sturgeon, 2016). Briefly, hESC medium consists of DMEM/F12 (50:50; ThermoFisher) supplemented with 20% knockout serum replacement (KOSR) (Gibco), 1% penicillin/streptomycin (ThermoFisher), 2mM L-glutamine (ThermoFisher), 1% non-essential amino acids (NEAA) (ThermoFisher) and 55µM b-mercaptoethanol (Sigma). Immediately prior to use, hESC media was supplemented with 15ng/ml human basic fibroblast growth factor (hbFGF) (R&D Systems). Cells were passaged every 4-5 days using TrypLE Express (Gibco), and plated in presence of 10µM ROCK inhibitor Y-27632 (ROCKi) (Tocris) for 24 hours. Cells were cryopreserved in freezing media containing 50% hESC medium plus 40% FCS plus 10% DMSO. In feeder-free conditions, H1-iCas9 cells were maintained on tissue culture plates coated with recombinant human laminin at a concentration of 0.5mg/cm2 (rhLaminin-521, ThermoFisher; diluted in DPBS with Ca2+ and Mg2+, Gibco) or vitronectin at a concentration of 1.05mg/cm2 (STEMCELL, diluted in PBS) in mTeSR1 complete medium (STEMCELL). Cells were passaged every 4-5 days using ReLeSR enzyme-free dissociation reagent (STEMCELL) in the absence of ROCKi (only used for thawing and transduction), and cryopreserved in mFreSR medium (STEMCELL). H1 and H1-iCas9 cells were maintained in culture plates of 24-well to 10-cm size at individually optimized cell numbers. Growth media were changed daily with occasional “double-feeds” over two days. To generate the iCas9 targeting construct for the AAVS1 locus, humanized S. pyogenes Cas9 was amplified from pLCV2 (Addgene #52961) by PCR and, together with a BFP2 PCR product, was inserted into a target vector with AAVS1 homology arms (kindly provided by Ajamete Kaykas) via Gibson cloning (NEBuilder HiFi DNA Assembly Master Mix, NEB). The resulting all-in-one plasmid constitutively expresses the Tet-On 3G protein under a CAG promoter, and Cas9-P2A-BFP2 inducibly under a TRE3Gs promoter in the presence of doxycycline. Correct insertion into the AAVS1 locus yields expression of the promoterless P2A-Neomycin resistance gene fused to a splice acceptor site, resulting in cell survival upon G418 treatment.  The all-in-one plasmid was inserted into intron 1 of PPP1R12C (AAVS1 locus) of H1-hESCs by homologous recombination via co-electroporation (10-20ms, 1100/1200/1400V) with an AAVS1-targeting gRNA, similar to a previously described approach (González et al., 2014), and selected with 100µg/ml G418 for 7 days. AAVS1 T2 CRISPR in pX330 was a gift from Masato Kanemaki (Addgene plasmid #72833).  G418-resistant colonies were expanded for characterization. Sanger sequencing of clones that successfully underwent homologous recombination confirmed seamless integration of the construct at the 3’ and 5’ ends into the AAVS1 locus, and plasmid backbone-specific PCRs confirmed absence of random integration. Short tandem repeat (STR) profiles by PCR profiling of 9 regions plus Amelogenin for gender determination (GenePrint 10 System, Promega) and karyotype are consistent with parental H1 cells as determined by G-banding analysis of fixed cells. Sample preparation was performed as instructed (www.cuh.nhs.uk/sites/default/files/misc/ Tissue%20 Harvest%20Protocol%283%29.pdf) and karyotyping was performed by the Medical Genetics Service Cytogenics Laboratory, Cambridge, UK. STR profiling was performed at The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children (SickKids), Toronto, Canada.

extract_protocol:
Transduced and untransduced H1-iCas9 cells were lysed on ice using RLT Plus buffer, and total RNA was extracted with the RNeasy Plus Mini Kit (Qiagen). Following lysis, supernatant was transferred to a QIAShredder spin column (Qiagen) and centrifuged at maximum speed for 2 minutes. The supernatant was transferred to RNeasy spin columns and on-column DNase digestion was performed using the RNase-Free DNase set (Qiagen). RNA extraction procedure was continued according to manufacturer’s instructions. Samples were stored at -80ºC prior to sequencing. Total RNA was quantified using Qubit RNA BR Assay fluorescent chemistry (ThermoFisher Scientific) and diluted to 1ng/µl. 1µL of the dilution stock was used to obtain RNA Integrity Number (RIN) using the Agilent Bioanalyzer RNA 6000 Pico kit (Agilent). Lowest RIN was 8.4, median RIN score was 9.7.
750ng per sample was processed according to Illumina TruSeq Stranded mRNA sample preparation protocol (Part # 15031047 Rev. E). 1µL top stock of each purified final library was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip (Agilent). The libraries were quantified using Qubit dsDNA HS Assay Kit (ThermoFisher Scientific) and were pooled at equimolar ratios after size adjustment. The final pool was run on an Agilent Bioanalyzer dsDNA High Sensitivity chip and quantified using NEBNext Library Quant Kit for Illumina (NEB). The quantified pool was hybridized at a final concentration of 2.2pM and sequenced single-end on the Illumina NextSeq500 platform using high-output v2.5 75c chemistry.

treatment_protocol: gRNA transductions (DRICH1 = g15 and g16, AAVS = control) on MEF feeder cells were performed after induction with doxycycline (1.5µg/ml, Sigma) for 48 hours. Infected cells were selected with 0.5µg/ml puromycin (Sigma) for 48 hours. For gRNA experiments on laminin, H1-iCas9 cells were treated with doxycycline (1.5µg/ml, Sigma) 48 hours prior to infection with gRNAs. 24 hours prior to infection, cells were dissociated using ReLeSR and plated at optimized densities in 24-well plates in triplicate wells with 10µM ROCKi. Adherent doxycycline-treated cells were infected with target and control gRNAs with ROCKi. 24 hours post infection, mTeSR1 medium was replaced with fresh medium containing puromycin (0.5ug/ml) and cells were incubated for 48 hours. Cells were cultured on both MEFs and laminin until 4 days after infection (2 days after selection).

value: H1 ESCs

tag: transfection

value: sgRNA targeting AAVS1

tag: culture

value: MEFs

tag: replicate


title: WT_A_MEFs

source_name: Parental H1 ESCs


title: AAVS1_B_MEFs


title: 15A_MEFs

value: sgRNA #1 targeting DRICH1


title: g16_Laminin_2

value: sgRNA #2 targeting DRICH1

value: laminin


title: g16_Laminin_1


title: g15_Laminin_2


title: 16B_MEFs


title: 15B_MEFs


title: 16A_MEFs


title: C10_06_S126 [colonies_scRNA-seq]


title: g15_Laminin_1


title: WT_Laminin_2


title: AAVS1_Laminin_2


title: AAVS1_Laminin_1


title: WT_Laminin_1


title: p21_high_2E2_rep3

city: Boulder

first: Mingwei

last: Min

state: CO

address: 3415 Colorado Ave

institute: University of colorado-boulderB

description:
Sample 8
Cellswere sorted on high level of p21

data_processing:
RTA2 on Illumina NextSeq500 used for basecalling
Adaptor sequences were clipped using Trimmomative version 0.32 (Bolger et al., 2014). Reads were mapped to human genome (GRCh38) using HISAT2 version 2.0.3-beta (Kim et al., 2015).
Mapped fragments were counted using GenomicAlignments package in R (Lawrence et al., 2013).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: human epithelial cells

growth_protocol: MCF10A cells were maintained in DMEM/F12 (Gibco) supplemented with 5% (v/v) horse serum (Gibco), 20 ng/mL epidermal growth factor (EGF, Sigma-Aldrich), 0.5 mg/mL hydrocortisone (Sigma-Aldrich, St. Louis, MO), 100 ng/mL cholera toxin (Sigma-Aldrich), 10 μg/mL insulin (Thermo Fisher) and 1X penicillin/streptomycin. For serum starvation media, the horse serum, EGF, and insulin were removed, and 0.3% BSA was added. For live-cell time-lapse imaging, phenol-red free DMEM/F12 (Gibco) was used.

extract_protocol:
Total RNA was extracted from each sample using Quick-RNA MicroPrep kit from Zymo.
The Lexogen RiboCop rRNA Depletion Kit was used for ribosomal RNA removal and the Lexogen SENSE total RNA kit was used to prepare paired-end, stranded libraries.

tag: cell line

tag: clone


title: p21_low_2E2_rep4

description:
Sample 9
Cellswere sorted on low level of p21


title: p21_high_2E2_rep5

description:
Sample 5
Cellswere sorted on high level of p21


title: p21_high_2E2_rep4

description:
Sample 4
Cellswere sorted on high level of p21


title: p21_low_2E2_rep1

description:
Sample 6
Cellswere sorted on low level of p21


title: ContactIn_3B6_rep2

description: Sample 40


title: p21_low_2E2_rep2

description:
Sample 7
Cellswere sorted on low level of p21


title: p21_low_2E2_rep3

description:
Sample 3
Cellswere sorted on low level of p21


title: ContactIn_3B6_rep1

description: Sample 39


title: WT_B_MEFs


title: CDK46i_3B6_rep1

description: Sample 37


title: CDK46i_3B6_rep2

description: Sample 38


title: Meki_3B6_rep2

description: Sample 36


title: Meki_3B6_rep1

description: Sample 35


title: Control_3B6_rep2

description: Sample 32


title: SerumStarvation_3B6_rep1

description:
Sample 33
Starvation media: the horse serum, EGF, and insulin were removed, and 0.3% BSA was added.


title: SerumStarvation_3B6_rep2

description:
Sample 34
Starvation media: the horse serum, EGF, and insulin were removed, and 0.3% BSA was added.


title: CDK46i_2E2_rep2

description: Sample 28


title: CDK46i_2E2_rep1

description: Sample 27


title: ContactIn_2E2_rep1

description: Sample 29


title: p21_high_2E2_rep2

description:
Sample 2
Cellswere sorted on high level of p21


title: Meki_2E2_rep2

description: Sample 26


title: SerumStarvation_2E2_rep2

description:
Sample 24
Starvation media: the horse serum, EGF, and insulin were removed, and 0.3% BSA was added.


title: Control_2E2_rep2

description: Sample 22


title: SerumStarvation_2E2_rep1

description:
Sample 23
Starvation media: the horse serum, EGF, and insulin were removed, and 0.3% BSA was added.


title: Control_3B6_rep1

description: Sample 31


title: p21_low_3B6_rep4

description:
Sample 19
Cellswere sorted on low level of p21


title: p21_high_2E2_rep1

description:
Sample 1
Cellswere sorted on high level of p21


title: p21_low_3B6_rep3

description:
Sample 18
Cellswere sorted on low level of p21


title: Meki_2E2_rep1

description: Sample 25


title: p21_low_3B6_rep2

description:
Sample 17
Cellswere sorted on low level of p21


title: p21_high_3B6_rep5

description:
Sample 15
Cellswere sorted on high level of p21


title: p21_low_3B6_rep5

description:
Sample 20
Cellswere sorted on low level of p21


title: p21_low_3B6_rep1

description:
Sample 16
Cellswere sorted on low level of p21


title: p21_high_3B6_rep4

description:
Sample 14
Cellswere sorted on high level of p21


title: p21_high_3B6_rep1

description:
Sample 11
Cellswere sorted on high level of p21


title: p21_high_3B6_rep3

description:
Sample 13
Cellswere sorted on high level of p21


title: p21_low_2E2_rep5

description:
Sample 10
Cellswere sorted on low level of p21


title: p21_high_3B6_rep2

description:
Sample 12
Cellswere sorted on high level of p21


title: Adjacent healthy tissue 2

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script.
All samples/libraries passed QC (none were filtered in downstream analyses)
Genome_build: hg19
Supplementary_files_format_and_content: Heteroplasmy estimations for bulk populations assayed through ATAC-seq from three samples

molecule: genomic DNA

source_name: Adjacent healthy tissue

extract_protocol: NP 40 lysis

treatment_protocol: tissue dissociation and sorting based on EPCAM+ surface marker expression

value: primary cells

tag: tissue

value: colon

tag: disease state

value: colorectal adenocarcinoma


title: Adjacent healthy tissue 1


title: Colorectal cancer tissue 1

source_name: Colorectal cancer tissue


title: ContactIn_2E2_rep2

description: Sample 30


title: TumA_98_S194

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard two-pass approach.
Gene were quantified using the STAR --quantMode GeneCounts flag over the Gencode v19 annotation with a custom chromosome to map the lentiviral infected GFP+ random 30-mer barcode
Processed bams were genotyped for mitochondria using a custom python script.
Samples were filtered such that individual cells each had at least 100x coverage at heteroplasmic variants. No nuclear genome QC was performed.
Genome_build: hg19
Supplementary_files_format_and_content: High confidence mitochondrial variants and cluster annotations from derived clonotypes

source_name: human patient


title: TumA_99_S195


title: TumA_96_pos_S96


title: TumA_95_S95


title: TumA_94_S94


title: TumA_92_S92


title: TumA_91_S91


title: TumA_90_S90


title: Control_2E2_rep1

description: Sample 21


title: TumA_83_S83


title: TumA_87_S87


title: TumA_82_S82


title: TumA_93_S93


title: TumA_81_S81


title: TumA_80_S80


title: TumA_88_S88


title: TumA_86_S86


title: TumA_78_S78


title: TumA_84_S84


title: TumA_76_S76


title: TumA_75_S75


title: TumA_77_S77


title: TumA_85_S85


title: TumA_97_neg_S193


title: TumA_74_S74


title: TumA_70_S70


title: TumA_72_S72


title: TumA_69_S69


title: TumA_71_S71


title: TumA_68_S68


title: TumA_89_S89


title: TumA_73_S73


title: TumA_67_S67


title: TumA_65_S65


title: TumA_66_S66


title: TumA_62_S62


title: TumA_61_S61


title: TumA_60_S60


title: TumA_63_S63


title: TumA_59_S59


title: TumA_57_S57


title: TumA_58_S58


title: TumA_79_S79


title: TumA_56_S56


title: TumA_54_S54


title: TumA_53_S53


title: TumA_50_S50


title: TumA_49_S49


title: TumA_52_S52


title: TumA_46_S46


title: TumA_47_S47


title: TumA_44_S44


title: TumA_64_S64


title: TumA_39_S39


title: TumA_55_S55


title: TumA_40_S40


title: TumA_38_S38


title: TumA_41_S41


title: TumA_37_S37


title: TumA_45_S45


title: TumA_33_S33


title: TumA_36_S36


title: TumA_34_S34


title: TumA_42_S42


title: TumA_32_S32


title: TumA_29_S29


title: TumA_27_S27


title: TumA_51_S51


title: TumA_28_S28


title: TumA_35_S35


title: TumA_272_S368


title: TumA_270_S366


title: TumA_271_S367


title: TumA_26_S26


title: TumA_43_S43


title: TumA_267_S363


title: TumA_268_S364


title: TumA_48_S48


title: TumA_269_S365


title: TumA_266_S362


title: TumA_264_S360


title: TumA_263_S359


title: TumA_265_S361


title: TumA_262_S358


title: TumA_25_S25


title: TumA_31_S31


title: TumA_30_S30


title: TumA_260_S356


title: TumA_259_S355


title: TumA_258_S354


title: TumA_254_S350


title: TumA_255_S351


title: TumA_252_S348


title: TumA_251_S347


title: TumA_253_S349


title: TumA_24_S24


title: TumA_250_S346


title: TumA_247_S343


title: TumA_245_S341


title: TumA_241_S337


title: TumA_240_S336


title: TumA_244_S340


title: TumA_261_S357


title: TumA_23_S23


title: TumA_238_S334


title: TumA_243_S339


title: TumA_256_S352


title: TumA_237_S333


title: TumA_235_S331


title: TumA_239_S335


title: TumA_234_S330


title: TumA_231_S327


title: TumA_233_S329


title: TumA_257_S353


title: TumA_232_S328


title: TumA_248_S344


title: TumA_230_S326


title: TumA_22_S22


title: TumA_229_S325


title: TumA_228_S324


title: TumA_227_S323


title: TumA_224_S320


title: TumA_223_S319


title: TumA_222_S318


title: TumA_219_S315


title: TumA_21_S21


title: TumA_220_S316


title: TumA_221_S317


title: TumA_218_S314


title: TumA_216_S312


title: TumA_226_S322


title: TumA_215_S311


title: TumA_214_S310


title: TumA_208_S304


title: TumA_210_S306


title: TumA_20_S20


title: TumA_206_S302


title: TumA_249_S345


title: TumA_212_S308


title: TumA_205_S301


title: TumA_203_S299


title: TumA_204_S300


title: TumA_202_S298


title: TumA_217_S313


title: TumA_201_S297


title: TumA_199_S295


title: TumA_19_S19


title: TumA_211_S307


title: TumA_197_S293


title: TumA_200_S296


title: TumA_196_S292


title: TumA_213_S309


title: TumA_194_S290


title: TumA_209_S305


title: TumA_195_S291


title: TumA_198_S294


title: TumA_225_S321


title: TumA_193_neg_S289


title: TumA_207_S303


title: TumA_236_S332


title: TumA_190_S286


title: TumA_189_S285


title: TumA_18_S18


title: TumA_192_pos_S288


title: TumA_187_S283


title: TumA_191_S287


title: TumA_186_S282


title: TumA_188_S284


title: TumA_183_S279


title: TumA_184_S280


title: TumA_182_S278


title: TumA_180_S276


title: TumA_17_S17


title: TumA_177_S273


title: TumA_176_S272


title: TumA_171_S267


title: TumA_172_S268


title: TumA_170_S266


title: TumA_174_S270


title: TumA_165_S261


title: TumA_168_S264


title: TumA_16_S16


title: TumA_169_S265


title: TumA_181_S277


title: TumA_164_S260


title: TumA_163_S259


title: TumA_175_S271


title: TumA_185_S281


title: TumA_179_S275


title: TumA_166_S262


title: TumA_173_S269


title: TumA_15_S15


title: TumA_160_S256


title: TumA_159_S255


title: TumA_178_S274


title: TumA_157_S253


title: TumA_158_S254


title: TumA_156_S252


title: TumA_155_S251


title: TumA_154_S250


title: TumA_167_S263


title: TumA_153_S249


title: TumA_152_S248


title: TumA_151_S247


title: TumA_150_S246


title: TumA_161_S257


title: TumA_146_S242


title: TumA_148_S244


title: TumA_145_S241


title: TumA_162_S258


title: TumA_142_S238


title: TumA_149_S245


title: TumA_140_S236


title: TumA_147_S243


title: TumA_143_S239


title: TumA_13_S13


title: TumA_139_S235


title: TumA_14_S14


title: TumA_138_S234


title: TumA_144_S240


title: TumA_141_S237


title: TumA_136_S232


title: TumA_137_S233


title: TumA_134_S230


title: TumA_132_S228


title: TumA_131_S227


title: TumA_135_S231


title: TumA_130_S226


title: TumA_12_S12


title: TumA_128_S224


title: TumA_129_S225


title: TumA_126_S222


title: TumA_127_S223


title: TumA_123_S219


title: TumA_125_S221


title: TumA_122_S218


title: TumA_11_S11


title: TumA_124_S220


title: TumA_121_S217


title: TumA_117_S213


title: TumA_120_S216


title: TumA_119_S215


title: TumA_114_S210


title: TumA_118_S214


title: TumA_112_S208


title: TumA_115_S211


title: TumA_113_S209


title: TumA_111_S207


title: TumA_110_S206


title: TumA_10_S10


title: TumA_133_S229


title: TumA_108_S204


title: TumA_107_S203


title: TumA_105_S201


title: TumA_106_S202


title: TumA_116_S212


title: TumA_103_S199


title: TumA_09_S9


title: TumA_100_S196


title: TumA_104_S200


title: TumA_08_S8


title: TumA_07_S7


title: TumA_101_S197


title: TumA_04_S4


title: TumA_05_S5


title: TF_99_S99

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard two-pass approach.
Gene were quantified using the STAR --quantMode GeneCounts flag over the Gencode v19 annotation with a custom chromosome to map the lentiviral infected GFP+ random 30-mer barcode
Processed bams were genotyped for mitochondria using a custom python script.
Samples were filtered such that individual cells each had at least 100x coverage at heteroplasmic variants. No nuclear genome QC was performed. Samples were further filtered to ensure that each cell at least one unique barcode
Genome_build: hg19
Supplementary_files_format_and_content: High confidence mitochondrial variants for 3 clones assayed by 3 separate single cell technologies

source_name: ATCC

growth_protocol: RPMI, 10%FBS, Pen/Strep, 2ng/ml GM-CSF

extract_protocol:
Qiagen TCL lysis buffer
Smart-seq2

value: TF1 hematopoietic cell line


title: TF_96_neg_S96


title: TF_98_S98


title: TF_97_pos_S97


title: TumA_03_S3


title: TumA_01_neg_S1


title: TumA_02_S2


title: TF_94_S94


title: TF_95_S95


title: TF_92_S92


title: TF_93_S93


title: TumA_109_S205


title: TF_90_S90


title: TumA_246_S342


title: TF_88_S88


title: TF_91_S91


title: TumA_102_S198


title: TF_89_S89


title: TF_84_S84


title: TF_85_S85


title: TF_87_S87


title: TF_86_S86


title: TF_83_S83


title: TF_82_S82


title: TF_80_S80


title: TF_79_S79


title: TF_78_S78


title: TF_76_S76


title: TF_77_S77


title: TF_75_S75


title: TF_74_S74


title: TF_73_S73


title: TF_71_S71


title: TF_72_S72


title: TF_70_S70


title: TF_69_S69


title: TF_68_S68


title: TF_67_S67


title: TF_66_S66


title: TF_65_S65


title: TF_64_S64


title: TF_63_S63


title: TF_81_S81


title: TF_59_S59


title: TF_58_S58


title: TF_57_S57


title: TF_56_S56


title: TF_54_S54


title: TF_62_S62


title: TF_52_S52


title: TF_61_S61


title: TF_50_S50


title: TF_49_S49


title: TF_51_S51


title: TF_47_S47


title: TF_46_S46


title: TF_45_S45


title: TF_43_S43


title: TF_44_S44


title: TF_55_S55


title: TF_48_S48


title: C09_06_S124 [colonies_scRNA-seq]


title: C09_05_S123 [colonies_scRNA-seq]


title: C09_03_S111 [colonies_scRNA-seq]


title: C09_02_S100 [colonies_scRNA-seq]


title: C09_04_S112 [colonies_scRNA-seq]


title: TF_60_S60


title: C08_16_S182 [colonies_scRNA-seq]


title: C09_01_S99 [colonies_scRNA-seq]


title: TumA_06_S6


title: TF_53_S53


title: C08_15_S181 [colonies_scRNA-seq]


title: C08_12_S158 [colonies_scRNA-seq]


title: C08_10_S146 [colonies_scRNA-seq]


title: C08_11_S157 [colonies_scRNA-seq]


title: C08_08_S134 [colonies_scRNA-seq]


title: C08_14_S170 [colonies_scRNA-seq]


title: C08_13_S169 [colonies_scRNA-seq]


title: C08_07_S133 [colonies_scRNA-seq]


title: C08_06_S122 [colonies_scRNA-seq]


title: C08_05_S121 [colonies_scRNA-seq]


title: C08_04_S110 [colonies_scRNA-seq]


title: C08_01_S97 [colonies_scRNA-seq]


title: C07_15_S95 [colonies_scRNA-seq]


title: C08_03_S109 [colonies_scRNA-seq]


title: C07_14_pos_S84 [colonies_scRNA-seq]


title: C07_13_S83 [colonies_scRNA-seq]


title: C08_02_S98 [colonies_scRNA-seq]


title: C07_12_S72 [colonies_scRNA-seq]


title: C07_11_S71 [colonies_scRNA-seq]


title: C07_10_S60 [colonies_scRNA-seq]


title: C07_09_S59 [colonies_scRNA-seq]


title: C07_08_S48 [colonies_scRNA-seq]


title: C07_06_S36 [colonies_scRNA-seq]


title: C07_07_S47 [colonies_scRNA-seq]


title: C07_04_S24 [colonies_scRNA-seq]


title: C07_03_S23 [colonies_scRNA-seq]


title: C07_01_S11 [colonies_scRNA-seq]


title: C07_02_S12 [colonies_scRNA-seq]


title: C08_09_S145 [colonies_scRNA-seq]


title: C06_16_S94 [colonies_scRNA-seq]


title: C06_15_S93 [colonies_scRNA-seq]


title: C06_14_S82 [colonies_scRNA-seq]


title: C06_11_S69 [colonies_scRNA-seq]


title: C06_08_S46 [colonies_scRNA-seq]


title: C07_16_neg_S96 [colonies_scRNA-seq]


title: C06_09_S57 [colonies_scRNA-seq]


title: C06_03_S21 [colonies_scRNA-seq]


title: C06_06_S34 [colonies_scRNA-seq]


title: C06_02_S10 [colonies_scRNA-seq]


title: C06_01_S9 [colonies_scRNA-seq]


title: C06_05_S33 [colonies_scRNA-seq]


title: C05_16_S92 [colonies_scRNA-seq]


title: C07_05_S35 [colonies_scRNA-seq]


title: C05_15_S91 [colonies_scRNA-seq]


title: C05_13_S79 [colonies_scRNA-seq]


title: C06_07_S45 [colonies_scRNA-seq]


title: C05_11_S67 [colonies_scRNA-seq]


title: C05_12_S68 [colonies_scRNA-seq]


title: C06_12_S70 [colonies_scRNA-seq]


title: C05_09_S55 [colonies_scRNA-seq]


title: C05_07_S43 [colonies_scRNA-seq]


title: C06_13_S81 [colonies_scRNA-seq]


title: C05_06_S32 [colonies_scRNA-seq]


title: C05_05_S31 [colonies_scRNA-seq]


title: C05_08_S44 [colonies_scRNA-seq]


title: C06_10_S58 [colonies_scRNA-seq]


title: C05_02_S8 [colonies_scRNA-seq]


title: C05_03_S19 [colonies_scRNA-seq]


title: C03_16_S90 [colonies_scRNA-seq]


title: C05_01_S7 [colonies_scRNA-seq]


title: C03_15_S89 [colonies_scRNA-seq]


title: C06_04_S22 [colonies_scRNA-seq]


title: C03_14_S78 [colonies_scRNA-seq]


title: C03_13_S77 [colonies_scRNA-seq]


title: C05_14_S80 [colonies_scRNA-seq]


title: C03_11_S65 [colonies_scRNA-seq]


title: C03_12_S66 [colonies_scRNA-seq]


title: C03_09_S53 [colonies_scRNA-seq]


title: C03_08_S42 [colonies_scRNA-seq]


title: C05_10_S56 [colonies_scRNA-seq]


title: C03_04_S18 [colonies_scRNA-seq]


title: C03_03_S17 [colonies_scRNA-seq]


title: C05_04_S20 [colonies_scRNA-seq]


title: C03_02_S6 [colonies_scRNA-seq]


title: C03_07_S41 [colonies_scRNA-seq]


title: C03_06_S30 [colonies_scRNA-seq]


title: C03_01_S5 [colonies_scRNA-seq]


title: C02_13_S75 [colonies_scRNA-seq]


title: C03_05_S29 [colonies_scRNA-seq]


title: C02_11_S63 [colonies_scRNA-seq]


title: C02_12_S64 [colonies_scRNA-seq]


title: C02_14_S76 [colonies_scRNA-seq]


title: C02_16_S88 [colonies_scRNA-seq]


title: C02_08_S40 [colonies_scRNA-seq]


title: C02_09_S51 [colonies_scRNA-seq]


title: C02_10_S52 [colonies_scRNA-seq]


title: C02_06_S28 [colonies_scRNA-seq]


title: C02_07_S39 [colonies_scRNA-seq]


title: C02_04_S16 [colonies_scRNA-seq]


title: TumA_242_S338


title: C02_05_S27 [colonies_scRNA-seq]


title: C03_10_S54 [colonies_scRNA-seq]


title: C02_01_S3 [colonies_scRNA-seq]


title: C02_02_S4 [colonies_scRNA-seq]


title: C01_16_S86 [colonies_scRNA-seq]


title: C01_15_S85 [colonies_scRNA-seq]


title: C01_14_S74 [colonies_scRNA-seq]


title: C01_13_S73 [colonies_scRNA-seq]


title: C01_12_S62 [colonies_scRNA-seq]


title: C01_09_S49 [colonies_scRNA-seq]


title: C01_10_S50 [colonies_scRNA-seq]


title: C01_06_S26 [colonies_scRNA-seq]


title: C01_05_S25 [colonies_scRNA-seq]


title: C01_11_S61 [colonies_scRNA-seq]


title: C01_04_S14 [colonies_scRNA-seq]


title: C01_03_S13 [colonies_scRNA-seq]


title: C01_08_S38 [colonies_scRNA-seq]


title: D12_C18_15_S263 [colonies_scRNA-seq]

source_name: donor 1_CD34+ hematopoietic cells

value: donor 1


title: D12_C18_13_S251 [colonies_scRNA-seq]


title: negative_S72 [colonies_scRNA-seq]


title: negative2_S264 [colonies_scRNA-seq]


title: C01_01_S1 [colonies_scRNA-seq]


title: C02_03_S15 [colonies_scRNA-seq]


title: C02_15_S87 [colonies_scRNA-seq]


title: C01_02_S2 [colonies_scRNA-seq]


title: D12_C18_11_S239 [colonies_scRNA-seq]


title: D12_C18_09_S227 [colonies_scRNA-seq]


title: D12_C18_08_S216 [colonies_scRNA-seq]


title: D12_C18_10_S228 [colonies_scRNA-seq]


title: D12_C18_05_S203 [colonies_scRNA-seq]


title: D12_C18_07_S215 [colonies_scRNA-seq]


title: C01_07_S37 [colonies_scRNA-seq]


title: D12_C18_04_S192 [colonies_scRNA-seq]


title: D12_C18_02_S180 [colonies_scRNA-seq]


title: D12_C18_03_S191 [colonies_scRNA-seq]


title: D12_C17_16_S262 [colonies_scRNA-seq]


title: D12_C18_01_S179 [colonies_scRNA-seq]


title: D12_C17_13_S249 [colonies_scRNA-seq]


title: D12_C17_15_S261 [colonies_scRNA-seq]


title: D12_C18_14_positive_S252 [colonies_scRNA-seq]


title: D12_C17_11_S237 [colonies_scRNA-seq]


title: D12_C17_14_S250 [colonies_scRNA-seq]


title: negative1_S168 [colonies_scRNA-seq]


title: D12_C18_12_S240 [colonies_scRNA-seq]


title: D12_C17_10_S226 [colonies_scRNA-seq]


title: D12_C17_07_S213 [colonies_scRNA-seq]


title: D12_C17_05_S201 [colonies_scRNA-seq]


title: D12_C17_06_S202 [colonies_scRNA-seq]


title: D12_C17_04_S190 [colonies_scRNA-seq]


title: D12_C17_03_S189 [colonies_scRNA-seq]


title: D12_C17_09_S225 [colonies_scRNA-seq]


title: D12_C17_01_S177 [colonies_scRNA-seq]


title: D12_C16_16_S260 [colonies_scRNA-seq]


title: D12_C17_02_S178 [colonies_scRNA-seq]


title: D12_C18_06_S204 [colonies_scRNA-seq]


title: D12_C16_12_S236 [colonies_scRNA-seq]


title: D12_C16_13_S247 [colonies_scRNA-seq]


title: D12_C16_14_S248 [colonies_scRNA-seq]


title: D12_C17_12_S238 [colonies_scRNA-seq]


title: D12_C16_10_S224 [colonies_scRNA-seq]


title: D12_C16_11_S235 [colonies_scRNA-seq]


title: D12_C16_08_S212 [colonies_scRNA-seq]


title: D12_C16_07_S211 [colonies_scRNA-seq]


title: D12_C16_09_S223 [colonies_scRNA-seq]


title: D12_C16_06_S200 [colonies_scRNA-seq]


title: D12_C16_04_S188 [colonies_scRNA-seq]


title: D12_C16_02_S176 [colonies_scRNA-seq]


title: D12_C16_03_S187 [colonies_scRNA-seq]


title: D12_C17_08_S214 [colonies_scRNA-seq]


title: D12_C15_15_S257 [colonies_scRNA-seq]


title: D12_C15_16_S258 [colonies_scRNA-seq]


title: D12_C15_13_S245 [colonies_scRNA-seq]


title: D12_C15_14_S246 [colonies_scRNA-seq]


title: D12_C15_09_S221 [colonies_scRNA-seq]


title: D12_C15_10_S222 [colonies_scRNA-seq]


title: D12_C15_08_S210 [colonies_scRNA-seq]


title: D12_C15_12_S234 [colonies_scRNA-seq]


title: D12_C16_15_S259 [colonies_scRNA-seq]


title: D12_C15_06_S198 [colonies_scRNA-seq]


title: D12_C15_07_S209 [colonies_scRNA-seq]


title: D12_C15_01_S173 [colonies_scRNA-seq]


title: D12_C15_04_S186 [colonies_scRNA-seq]


title: D12_C15_11_S233 [colonies_scRNA-seq]


title: D12_C15_03_S185 [colonies_scRNA-seq]


title: D12_C15_02_S174 [colonies_scRNA-seq]


title: D12_C15_05_S197 [colonies_scRNA-seq]


title: D12_C14_16_S256 [colonies_scRNA-seq]


title: D12_C16_05_S199 [colonies_scRNA-seq]


title: D12_C14_14_S244 [colonies_scRNA-seq]


title: D12_C14_15_S255 [colonies_scRNA-seq]


title: D12_C14_12_S232 [colonies_scRNA-seq]


title: D12_C14_13_S243 [colonies_scRNA-seq]


title: D12_C16_01_S175 [colonies_scRNA-seq]


title: D12_C14_09_S219 [colonies_scRNA-seq]


title: D12_C14_10_S220 [colonies_scRNA-seq]


title: D12_C14_08_S208 [colonies_scRNA-seq]


title: D12_C14_06_S196 [colonies_scRNA-seq]


title: D12_C14_07_S207 [colonies_scRNA-seq]


title: D12_C14_04_S184 [colonies_scRNA-seq]


title: D12_C14_05_S195 [colonies_scRNA-seq]


title: D12_C13_14_S242 [colonies_scRNA-seq]


title: D12_C14_01_S171 [colonies_scRNA-seq]


title: D12_C14_03_S183 [colonies_scRNA-seq]


title: D12_C14_02_S172 [colonies_scRNA-seq]


title: D12_C13_16_S254 [colonies_scRNA-seq]


title: D12_C13_13_S241 [colonies_scRNA-seq]


title: D12_C13_10_S218 [colonies_scRNA-seq]


title: D12_C13_07_S205 [colonies_scRNA-seq]


title: D12_C13_08_S206 [colonies_scRNA-seq]


title: D12_C13_12_S230 [colonies_scRNA-seq]


title: D12_C13_11_S229 [colonies_scRNA-seq]


title: D12_C13_09_S217 [colonies_scRNA-seq]


title: D12_C13_05_S193 [colonies_scRNA-seq]


title: D12_C14_11_S231 [colonies_scRNA-seq]


title: D12_C13_03_S181 [colonies_scRNA-seq]


title: D12_C13_04_S182 [colonies_scRNA-seq]


title: D12_C13_01_S169 [colonies_scRNA-seq]


title: D12_C13_02_S170 [colonies_scRNA-seq]


title: C13_15_S167 [colonies_scRNA-seq]


title: C13_13_S155 [colonies_scRNA-seq]


title: C13_11_S143 [colonies_scRNA-seq]


title: C13_12_S144 [colonies_scRNA-seq]


title: C13_14_positive_S156 [colonies_scRNA-seq]


title: C13_10_S132 [colonies_scRNA-seq]


title: C13_08_S120 [colonies_scRNA-seq]


title: C13_07_S119 [colonies_scRNA-seq]


title: C13_09_S131 [colonies_scRNA-seq]


title: D12_C13_15_S253 [colonies_scRNA-seq]


title: C13_06_S108 [colonies_scRNA-seq]


title: C13_05_S107 [colonies_scRNA-seq]


title: C13_04_S96 [colonies_scRNA-seq]


title: C13_02_S84 [colonies_scRNA-seq]


title: C13_01_S83 [colonies_scRNA-seq]


title: C13_03_S95 [colonies_scRNA-seq]


title: C12_15_S165 [colonies_scRNA-seq]


title: C12_12_S142 [colonies_scRNA-seq]


title: C12_11_S141 [colonies_scRNA-seq]


title: C12_08_S118 [colonies_scRNA-seq]


title: C12_16_S166 [colonies_scRNA-seq]


title: D12_C13_06_S194 [colonies_scRNA-seq]


title: C12_14_S154 [colonies_scRNA-seq]


title: C12_13_S153 [colonies_scRNA-seq]


title: C12_05_S105 [colonies_scRNA-seq]


title: C12_10_S130 [colonies_scRNA-seq]


title: C12_07_S117 [colonies_scRNA-seq]


title: C12_06_S106 [colonies_scRNA-seq]


title: C12_03_S93 [colonies_scRNA-seq]


title: C12_02_S82 [colonies_scRNA-seq]


title: C12_04_S94 [colonies_scRNA-seq]


title: C11_16_S164 [colonies_scRNA-seq]


title: C12_01_S81 [colonies_scRNA-seq]


title: C11_15_S163 [colonies_scRNA-seq]


title: C11_13_S151 [colonies_scRNA-seq]


title: C11_11_S139 [colonies_scRNA-seq]


title: C11_12_S140 [colonies_scRNA-seq]


title: C11_10_S128 [colonies_scRNA-seq]


title: C11_08_S116 [colonies_scRNA-seq]


title: C11_14_S152 [colonies_scRNA-seq]


title: C11_09_S127 [colonies_scRNA-seq]


title: C11_07_S115 [colonies_scRNA-seq]


title: C11_03_S91 [colonies_scRNA-seq]


title: C12_09_S129 [colonies_scRNA-seq]


title: C11_02_S80 [colonies_scRNA-seq]


title: C11_01_S79 [colonies_scRNA-seq]


title: C10_16_S162 [colonies_scRNA-seq]


title: C11_05_S103 [colonies_scRNA-seq]


title: C11_04_S92 [colonies_scRNA-seq]


title: C10_14_S150 [colonies_scRNA-seq]


title: C10_13_S149 [colonies_scRNA-seq]


title: C10_12_S138 [colonies_scRNA-seq]


title: C10_11_S137 [colonies_scRNA-seq]


title: C10_07_S113 [colonies_scRNA-seq]


title: C10_10_S126 [colonies_scRNA-seq]


title: C10_06_S102 [colonies_scRNA-seq]


title: C10_05_S101 [colonies_scRNA-seq]


title: C10_04_S90 [colonies_scRNA-seq]


title: C10_09_S125 [colonies_scRNA-seq]


title: C10_03_S89 [colonies_scRNA-seq]


title: C10_15_S161 [colonies_scRNA-seq]


title: C10_08_S114 [colonies_scRNA-seq]


title: C09_16_S160 [colonies_scRNA-seq]


title: C09_14_S148 [colonies_scRNA-seq]


title: C10_02_S78 [colonies_scRNA-seq]


title: C11_06_S104 [colonies_scRNA-seq]


title: C10_01_S77 [colonies_scRNA-seq]


title: C09_15_S159 [colonies_scRNA-seq]


title: C09_11_S135 [colonies_scRNA-seq]


title: C09_10_S124 [colonies_scRNA-seq]


title: C09_08_S112 [colonies_scRNA-seq]


title: C09_09_S123 [colonies_scRNA-seq]


title: C09_13_S147 [colonies_scRNA-seq]


title: C09_12_S136 [colonies_scRNA-seq]


title: C09_05_S99 [colonies_scRNA-seq]


title: C09_07_S111 [colonies_scRNA-seq]


title: C09_04_S88 [colonies_scRNA-seq]


title: C09_06_S100 [colonies_scRNA-seq]


title: C09_02_S76 [colonies_scRNA-seq]


title: C08_15_S157 [colonies_scRNA-seq]


title: C09_01_S75 [colonies_scRNA-seq]


title: C08_16_S158 [colonies_scRNA-seq]


title: C08_13_S145 [colonies_scRNA-seq]


title: C08_07_S109 [colonies_scRNA-seq]


title: C08_12_S134 [colonies_scRNA-seq]


title: C08_14_S146 [colonies_scRNA-seq]


title: C08_09_S121 [colonies_scRNA-seq]


title: C08_06_S98 [colonies_scRNA-seq]


title: C08_05_S97 [colonies_scRNA-seq]


title: C08_04_S86 [colonies_scRNA-seq]


title: C08_03_S85 [colonies_scRNA-seq]


title: C08_11_S133 [colonies_scRNA-seq]


title: C08_02_S74 [colonies_scRNA-seq]


title: C07_15_S71 [colonies_scRNA-seq]


title: C08_01_S73 [colonies_scRNA-seq]


title: C07_13_S62 [colonies_scRNA-seq]


title: C07_14_positive_S63 [colonies_scRNA-seq]


title: C08_08_S110 [colonies_scRNA-seq]


title: C09_03_S87 [colonies_scRNA-seq]


title: C07_10_S45 [colonies_scRNA-seq]


title: C07_11_S53 [colonies_scRNA-seq]


title: C07_12_S54 [colonies_scRNA-seq]


title: C07_04_S18 [colonies_scRNA-seq]


title: C07_06_S27 [colonies_scRNA-seq]


title: C07_09_S44 [colonies_scRNA-seq]


title: C07_05_S26 [colonies_scRNA-seq]


title: C07_07_S35 [colonies_scRNA-seq]


title: C07_03_S17 [colonies_scRNA-seq]


title: C07_01_S8 [colonies_scRNA-seq]


title: C07_02_S9 [colonies_scRNA-seq]


title: C06_16_S70 [colonies_scRNA-seq]


title: C06_15_S69 [colonies_scRNA-seq]


title: C06_12_S52 [colonies_scRNA-seq]


title: C06_14_S61 [colonies_scRNA-seq]


title: C06_13_S60 [colonies_scRNA-seq]


title: C06_11_S51 [colonies_scRNA-seq]


title: C08_10_S122 [colonies_scRNA-seq]


title: C06_08_S34 [colonies_scRNA-seq]


title: C06_05_S24 [colonies_scRNA-seq]


title: C06_07_S33 [colonies_scRNA-seq]


title: C06_04_S16 [colonies_scRNA-seq]


title: C06_09_S42 [colonies_scRNA-seq]


title: C06_10_S43 [colonies_scRNA-seq]


title: C06_06_S25 [colonies_scRNA-seq]


title: C07_08_S36 [colonies_scRNA-seq]


title: C06_01_S6 [colonies_scRNA-seq]


title: C06_02_S7 [colonies_scRNA-seq]


title: C05_06_S50 [colonies_scRNA-seq]


title: C06_03_S15 [colonies_scRNA-seq]


title: C05_05_S41 [colonies_scRNA-seq]


title: C05_04_S32 [colonies_scRNA-seq]


title: C05_08_S68 [colonies_scRNA-seq]


title: C05_03_S23 [colonies_scRNA-seq]


title: C05_02_S14 [colonies_scRNA-seq]


title: C04_13_S57 [colonies_scRNA-seq]


title: C04_09_S39 [colonies_scRNA-seq]


title: C04_05_S21 [colonies_scRNA-seq]


title: C05_01_S5 [colonies_scRNA-seq]


title: C05_07_S59 [colonies_scRNA-seq]


title: C04_04_S13 [colonies_scRNA-seq]


title: C03_15_S64 [colonies_scRNA-seq]


title: C04_12_S49 [colonies_scRNA-seq]


title: C04_16_S67 [colonies_scRNA-seq]


title: C03_16_S65 [colonies_scRNA-seq]


title: C04_03_S12 [colonies_scRNA-seq]


title: C04_01_S3 [colonies_scRNA-seq]


title: C03_09_S37 [colonies_scRNA-seq]


title: C03_12_S47 [colonies_scRNA-seq]


title: C04_15_S66 [colonies_scRNA-seq]


title: C03_06_S20 [colonies_scRNA-seq]


title: C04_14_S58 [colonies_scRNA-seq]


title: C04_11_S48 [colonies_scRNA-seq]


title: C04_08_S31 [colonies_scRNA-seq]


title: C04_07_S30 [colonies_scRNA-seq]


title: C04_10_S40 [colonies_scRNA-seq]


title: C04_02_S4 [colonies_scRNA-seq]


title: C03_03_S10 [colonies_scRNA-seq]


title: C03_14_S56 [colonies_scRNA-seq]


title: C04_06_S22 [colonies_scRNA-seq]


title: C03_10_S38 [colonies_scRNA-seq]


title: negative_S176 [colonies_scRNA-seq]


title: single_cell_RNAseq Young10X2

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

data_processing:
The Cell Ranger Software (Ver. 2.0.0) provided by 10X Genomics was used to map the reads (provided as fastq files) to the mouse reference genome (ENSEMBL Release 78/GRCm38.p3) for each sample individually and the two samples were merged according to the Cell Ranger manual.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of all genes for all cells in zipped MEX format

organism: Mus musculus

growth_protocol: C57BL/6 male mice of 2 and 22 months of age were used for all experiments. Male C57BL/6 mice were purchased from Janvier or bred in house at the DKFZ Center for Preclinical Research facility. Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Animals were sacrificed by cervical dislocation and their brains immediately placed on ice. The lateral SVZ was microdissected as a whole mount as previously described. Pooled SVZ tissue from 4 mice of 2 and 8 mice of 22 months of age were pulled for each library. Tissue was digested with trypsin and DNAse according to the Neural Tissue Dissociation kit in a Gentle MACS dissociator (Miltenyi) to maximize cell viability and recovery. Cells were stained for 20 minutes on ice in DPBS (without Ca and Mg) supplemented with 10% fetal calf serum. Combinations of the following antibodies were used:  Ter119 APC-Cy7 (Biolegend, 1:100), O4 APC-Cy7 (Miltenyi, 1:50), CD45 APC-Cy7 (BD, 1:200) , GLAST(ACSA-1)-PE (Miltenyi, 1:20). Sytox Blue (Life Technologies, 1/1000) was added to the cell suspension prior to sorting. Stained cell suspensions were sorted in a FACS AriaII (BD) using a 100um nozzle at 20psi. Cells were collected in ice-cold Neurobasal medium supplemented with L-Glutamine, B27. To ensure that there is enough starting material for the 10x platform, we did a negative selection for O4, Ter119 and CD45 and we positively selected for GLAST. 8000 FACS events underwent the downstream process according to the manufacturer’s details.
Libraries were prepared according to Chromium™ Single Cell 3' Reagent Kit.

tag: age

value: 2 MO

value: SVZ

tag: gender

value: Male

tag: strain


title: C03_07_S28 [colonies_scRNA-seq]


title: C32_15_S271 [colonies_scRNA-seq]


title: C03_08_S29 [colonies_scRNA-seq]


title: C03_11_S46 [colonies_scRNA-seq]


title: negative2_S272 [colonies_scRNA-seq]


title: C32_13_S259 [colonies_scRNA-seq]


title: C32_12_S248 [colonies_scRNA-seq]


title: single_cell_RNAseq Old10X2

value: 22 MO


title: C03_05_S19 [colonies_scRNA-seq]


title: C32_14_positive_S260 [colonies_scRNA-seq]


title: C32_11_S247 [colonies_scRNA-seq]


title: C03_13_S55 [colonies_scRNA-seq]


title: C03_04_S11 [colonies_scRNA-seq]


title: Y211D

city: Beijing

first: bo

last: peng

address: Zhongguanchun street

department: School of Medicine

country: China

institute: Tsinghua University

data_processing:
Basecal was performed using CASAVA 1.8
clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads.
Tophat (v2.0.12) was used for pair-end reads alignment to reference genome hg38 with no more than 2 mismatches.
Gene expression level were quantified by using HTSeq (v0.6.1), and DEGSeq (1.12.0) was also used for further differential expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: Excel file contains quantified gene expression level as FPKM.

source_name: Cervical cancer cells

growth_protocol: Cells were cultured in DMEM with 10% FBS at 37˚C in a humidified atmosphere with 5% (vol/vol) CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Adding 1ug/ml Doxycycline to induce Flag-PCNA expression for four days

value: cervix

tag: protein tag

value: Flag

tag: genotype

value: Flag-PCNA(YD)/-


title: PCNA_WT

value: Flag-PCNA(WT)/-


title: C32_09_S235 [colonies_scRNA-seq]

value: primary hematopoietic cells


title: C32_08_S224 [colonies_scRNA-seq]


title: Y211F

value: Flag-PCNA(YF)/-


title: HeLa

value: wild type


title: C32_07_S223 [colonies_scRNA-seq]


title: C03_01_S1 [colonies_scRNA-seq]


title: C03_02_S2 [colonies_scRNA-seq]


title: C32_06_S212 [colonies_scRNA-seq]


title: C32_04_S200 [colonies_scRNA-seq]


title: C32_02_S188 [colonies_scRNA-seq]


title: C32_05_S211 [colonies_scRNA-seq]


title: C32_01_S187 [colonies_scRNA-seq]


title: BCBL-1_Dox_negative_rep1

type: RNA

city: Kumamoto

first: Seiji

last: Okada

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: Gene expression without Dox for 48 hr in BCBL-1

hyb_protocol: 0.6 ug of Cy3-labelled cRNA  was fragmented at 60°C for 30 minute using 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human Gene Expression 8x60K v3 Microarray Kit (G4851C) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE１_1010_Sep10 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BCBL-1, Dox, negative, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from cells using RNAiso plus (Takara Bio) according to the manufacturer’s instructions.

treatment_protocol: BCBL-1 cells were mainteined in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.   The cultures were incubated with or without Dox for 48 hours at 37 ºC in a humidified incubator with 5% CO2.


title: C31_16_S270 [colonies_scRNA-seq]


title: C31_13_S257 [colonies_scRNA-seq]


title: C31_15_S269 [colonies_scRNA-seq]


title: H1_S2 (2 organoid slices pooled)

city: Cambridge

first: Lea

middle: Marion Denise

last: Wenger

address: Robinson Way

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

description:
org75_seuratdata.txt
Sample 3

data_processing:
Samples were pooled together and sequenced on an Illumina HiSeq4000 RTA platform, and then converted to the standard fastq format by bcl2fastq. The "Cellranger count" code was run in CellRanger 2.1.1 using the GRCh38 human reference genome. STAR was utilized to align the reads.
Quality of reads have shown 87.2% fraction reads in cells. Low quality ends were disregarded during the mapping process. Only reads that were uniquely mapped to the transcriptome were used for UMI counting in CellRanger.
The three datasets were merged for analysis using the CellRanger function "cellranger aggr".
Data was loaded into Seurat and cells were filtered for a minimum (200) and maximum number (5,000) of genes expressed and for a maximum of 15% mitochondrial genes.
The data was normalized through Log normalization using Seurat's NormalizeData function (scale factor of 10,000).
After performing FIndVariableGenes, the data was scaled using the function ScaleData.
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file containing the gene names as rows and the cell names (barcode-sample#) as columns

source_name: Embryonic Stem Cell (ESC)-derived cerebral organoid

growth_protocol:
H1 and H9 human embryonic stem cell-derived cerebral organoids were generated and grown as slice cultures as described in Giandomenico et al., 2018.
Organoids were supplemented with serum-free slice culture medium (SFSCM): Neurobasal (Invitrogen, cat. #21103049), 1:50 (v/v) B27+A (Invitrogen, cat. #17504044), 0.5% (w/v) glucose, 1X (v/v) Glutamax supplemented with Antibiotic-Antimycotic (ThermoFisher, cat. #15240062). The cultures were maintained in SFSCM at 37 °C and 5% CO2 with daily media changes.

extract_protocol:
Dissociation of the slices was achieved by Accumax (Sigma, A7089) using the gentleMACS Octo Dissociator. The cell suspension was run through a 70μm strainer prior to processing through the 10X Genomics platform. scRNA-seq libraries were prepared for sequencing using the 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit (10X Genomics, 120237) workflow.
The cell suspension (34μl with a total of 7000 cells) was loaded onto a 10X Genomics Chromium Single Cell 3’ Chip with the appropriate amount of Mastermix. RNA extraction was performed following the same 10X Genomics Chromium workflow.
The reverse transcriptase reaction and subsequent amplification was carried out in a C1000 Touch Thermal Cycler (Biorad), with the cDNA being amplified for 12 cycles. Before sequencing, libraries were quality tested using the 2100 Bioanalyzer Instrument (Agilent) and their concentration was measured by qPCR.

value: embryonic stem cell line H1

value: organoid

value: 75 days


title: H1_S1 (2 organoid slices pooled)

description:
org75_seuratdata.txt
Sample 2


title: BCBL-1_Dox_positive_rep1

description: Gene expression with Dox for 48 hr in BCBL-1

source_name: BCBL-1, Dox, positive, replicate 1


title: C32_10_S236 [colonies_scRNA-seq]


title: C31_14_S258 [colonies_scRNA-seq]


title: C31_12_S246 [colonies_scRNA-seq]


title: C31_10_S234 [colonies_scRNA-seq]


title: C31_11_S245 [colonies_scRNA-seq]


title: C31_08_S222 [colonies_scRNA-seq]


title: C31_05_S209 [colonies_scRNA-seq]


title: C31_06_S210 [colonies_scRNA-seq]


title: C31_09_S233 [colonies_scRNA-seq]


title: C31_04_S198 [colonies_scRNA-seq]


title: H9_S1 (2 organoid slices pooled)

description:
org75_seuratdata.txt
Sample 1

value: embryonic stem cell line H9


title: C31_02_S186 [colonies_scRNA-seq]


title: C31_03_S197 [colonies_scRNA-seq]


title: C31_01_S185 [colonies_scRNA-seq]


title: C30_16_S268 [colonies_scRNA-seq]


title: C32_03_S199 [colonies_scRNA-seq]


title: C30_15_S267 [colonies_scRNA-seq]


title: C30_10_S232 [colonies_scRNA-seq]


title: C30_14_S256 [colonies_scRNA-seq]


title: C30_12_S244 [colonies_scRNA-seq]


title: C30_13_S255 [colonies_scRNA-seq]


title: C30_08_S220 [colonies_scRNA-seq]


title: C30_09_S231 [colonies_scRNA-seq]


title: C30_04_S196 [colonies_scRNA-seq]


title: C30_07_S219 [colonies_scRNA-seq]


title: C30_02_S184 [colonies_scRNA-seq]


title: C30_03_S195 [colonies_scRNA-seq]


title: C31_07_S221 [colonies_scRNA-seq]


title: C29_16_S266 [colonies_scRNA-seq]


title: C30_01_S183 [colonies_scRNA-seq]


title: C29_07_S217 [colonies_scRNA-seq]


title: C29_12_S242 [colonies_scRNA-seq]


title: C29_11_S241 [colonies_scRNA-seq]


title: C29_09_S229 [colonies_scRNA-seq]


title: C30_05_S207 [colonies_scRNA-seq]


title: C30_06_S208 [colonies_scRNA-seq]


title: C29_03_S193 [colonies_scRNA-seq]


title: C29_15_S265 [colonies_scRNA-seq]


title: C29_10_S230 [colonies_scRNA-seq]


title: C29_08_S218 [colonies_scRNA-seq]


title: C28_16_S264 [colonies_scRNA-seq]


title: C28_15_S263 [colonies_scRNA-seq]


title: C28_13_S251 [colonies_scRNA-seq]


title: C29_13_S253 [colonies_scRNA-seq]


title: C28_14_S252 [colonies_scRNA-seq]


title: C28_12_S240 [colonies_scRNA-seq]


title: C29_05_S205 [colonies_scRNA-seq]


title: C28_09_S227 [colonies_scRNA-seq]


title: C30_11_S243 [colonies_scRNA-seq]


title: C29_04_S194 [colonies_scRNA-seq]


title: C29_06_S206 [colonies_scRNA-seq]


title: C29_02_S182 [colonies_scRNA-seq]


title: C28_08_S216 [colonies_scRNA-seq]


title: C29_14_S254 [colonies_scRNA-seq]


title: C28_07_S215 [colonies_scRNA-seq]


title: C28_11_S239 [colonies_scRNA-seq]


title: C28_06_S204 [colonies_scRNA-seq]


title: C28_05_S203 [colonies_scRNA-seq]


title: C29_01_S181 [colonies_scRNA-seq]


title: C28_03_S191 [colonies_scRNA-seq]


title: C28_02_S180 [colonies_scRNA-seq]


title: C27_15_S261 [colonies_scRNA-seq]


title: C27_14_S250 [colonies_scRNA-seq]


title: C27_13_S249 [colonies_scRNA-seq]


title: C27_12_S238 [colonies_scRNA-seq]


title: C27_11_S237 [colonies_scRNA-seq]


title: C27_10_S226 [colonies_scRNA-seq]


title: C27_09_S225 [colonies_scRNA-seq]


title: C27_08_S214 [colonies_scRNA-seq]


title: C27_07_S213 [colonies_scRNA-seq]


title: C27_06_S202 [colonies_scRNA-seq]


title: C27_04_S190 [colonies_scRNA-seq]


title: C27_03_S189 [colonies_scRNA-seq]


title: C27_05_S201 [colonies_scRNA-seq]


title: C27_02_S178 [colonies_scRNA-seq]


title: C27_01_S177 [colonies_scRNA-seq]


title: C28_10_S228 [colonies_scRNA-seq]


title: C26_15_S79 [colonies_scRNA-seq]


title: C26_16_S80 [colonies_scRNA-seq]


title: C28_04_S192 [colonies_scRNA-seq]


title: C26_13_S69 [colonies_scRNA-seq]


title: C26_12_S60 [colonies_scRNA-seq]


title: C28_01_S179 [colonies_scRNA-seq]


title: C26_11_S59 [colonies_scRNA-seq]


title: C26_09_S49 [colonies_scRNA-seq]


title: C27_16_S262 [colonies_scRNA-seq]


title: C26_08_S40 [colonies_scRNA-seq]


title: C26_10_S50 [colonies_scRNA-seq]


title: C26_05_S29 [colonies_scRNA-seq]


title: C26_03_S19 [colonies_scRNA-seq]


title: C26_04_S20 [colonies_scRNA-seq]


title: C26_02_S10 [colonies_scRNA-seq]


title: C24_16_S78 [colonies_scRNA-seq]


title: C24_15_S77 [colonies_scRNA-seq]


title: C26_01_S9 [colonies_scRNA-seq]


title: C24_14_S68 [colonies_scRNA-seq]


title: C24_12_S58 [colonies_scRNA-seq]


title: C24_10_S48 [colonies_scRNA-seq]


title: C24_11_S57 [colonies_scRNA-seq]


title: C26_14_S70 [colonies_scRNA-seq]


title: C24_13_S67 [colonies_scRNA-seq]


title: C24_09_S47 [colonies_scRNA-seq]


title: C24_08_S38 [colonies_scRNA-seq]


title: C24_04_S18 [colonies_scRNA-seq]


title: C24_05_S27 [colonies_scRNA-seq]


title: C24_07_S37 [colonies_scRNA-seq]


title: C26_07_S39 [colonies_scRNA-seq]


title: C26_06_S30 [colonies_scRNA-seq]


title: C24_06_S28 [colonies_scRNA-seq]


title: C24_02_S8 [colonies_scRNA-seq]


title: C23_08_S76 [colonies_scRNA-seq]


title: C24_03_S17 [colonies_scRNA-seq]


title: C23_07_S66 [colonies_scRNA-seq]


title: C23_05_S46 [colonies_scRNA-seq]


title: C24_01_S7 [colonies_scRNA-seq]


title: C23_06_S56 [colonies_scRNA-seq]


title: C23_03_S26 [colonies_scRNA-seq]


title: C23_02_S16 [colonies_scRNA-seq]


title: C23_04_S36 [colonies_scRNA-seq]


title: C23_01_S6 [colonies_scRNA-seq]


title: C22_06_S55 [colonies_scRNA-seq]


title: C22_08_S75 [colonies_scRNA-seq]


title: C22_04_S35 [colonies_scRNA-seq]


title: C22_07_S65 [colonies_scRNA-seq]


title: C22_03_S25 [colonies_scRNA-seq]


title: C22_01_S5 [colonies_scRNA-seq]


title: C21_16_S74 [colonies_scRNA-seq]


title: C21_15_S73 [colonies_scRNA-seq]


title: C22_02_S15 [colonies_scRNA-seq]


title: C21_14_S64 [colonies_scRNA-seq]


title: C21_12_S54 [colonies_scRNA-seq]


title: C21_11_S53 [colonies_scRNA-seq]


title: C21_10_S44 [colonies_scRNA-seq]


title: C21_09_S43 [colonies_scRNA-seq]


title: C21_06_S24 [colonies_scRNA-seq]


title: C21_07_S33 [colonies_scRNA-seq]


title: C21_04_S14 [colonies_scRNA-seq]


title: C21_05_S23 [colonies_scRNA-seq]


title: C21_08_S34 [colonies_scRNA-seq]


title: C21_01_S3 [colonies_scRNA-seq]


title: C21_02_S4 [colonies_scRNA-seq]


title: C21_03_S13 [colonies_scRNA-seq]


title: C20_16_S72 [colonies_scRNA-seq]


title: C20_14_S62 [colonies_scRNA-seq]


title: C20_11_S51 [colonies_scRNA-seq]


title: C22_05_S45 [colonies_scRNA-seq]


title: C20_10_S42 [colonies_scRNA-seq]


title: C20_08_S32 [colonies_scRNA-seq]


title: C20_09_S41 [colonies_scRNA-seq]


title: C20_07_S31 [colonies_scRNA-seq]


title: C20_12_S52 [colonies_scRNA-seq]


title: C20_05_S21 [colonies_scRNA-seq]


title: C20_04_S12 [colonies_scRNA-seq]


title: C20_02_S2 [colonies_scRNA-seq]


title: C19_15_S175 [colonies_scRNA-seq]


title: C21_13_S63 [colonies_scRNA-seq]


title: C20_01_S1 [colonies_scRNA-seq]


title: C20_03_S11 [colonies_scRNA-seq]


title: C19_11_S151 [colonies_scRNA-seq]


title: C19_12_S152 [colonies_scRNA-seq]


title: C19_14_positive_S164 [colonies_scRNA-seq]


title: C19_13_S163 [colonies_scRNA-seq]


title: C19_09_S139 [colonies_scRNA-seq]


title: C19_10_S140 [colonies_scRNA-seq]


title: C19_08_S128 [colonies_scRNA-seq]


title: C19_07_S127 [colonies_scRNA-seq]


title: C19_05_S115 [colonies_scRNA-seq]


title: C19_06_S116 [colonies_scRNA-seq]


title: C19_04_S104 [colonies_scRNA-seq]


title: C20_15_S71 [colonies_scRNA-seq]


title: C18_16_S174 [colonies_scRNA-seq]


title: C19_02_S92 [colonies_scRNA-seq]


title: C18_15_S173 [colonies_scRNA-seq]


title: C20_13_S61 [colonies_scRNA-seq]


title: C20_06_S22 [colonies_scRNA-seq]


title: C19_01_S91 [colonies_scRNA-seq]


title: C18_14_S162 [colonies_scRNA-seq]


title: C19_03_S103 [colonies_scRNA-seq]


title: C18_13_S161 [colonies_scRNA-seq]


title: C18_10_S138 [colonies_scRNA-seq]


title: C18_03_S101 [colonies_scRNA-seq]


title: C18_12_S150 [colonies_scRNA-seq]


title: C17_15_S171 [colonies_scRNA-seq]


title: C18_09_S137 [colonies_scRNA-seq]


title: C18_01_S89 [colonies_scRNA-seq]


title: C18_08_S126 [colonies_scRNA-seq]


title: C18_11_S149 [colonies_scRNA-seq]


title: C18_06_S114 [colonies_scRNA-seq]


title: C18_05_S113 [colonies_scRNA-seq]


title: C18_04_S102 [colonies_scRNA-seq]


title: C18_07_S125 [colonies_scRNA-seq]


title: C17_16_S172 [colonies_scRNA-seq]


title: C17_10_S136 [colonies_scRNA-seq]


title: C18_02_S90 [colonies_scRNA-seq]


title: C17_13_S159 [colonies_scRNA-seq]


title: C17_14_S160 [colonies_scRNA-seq]


title: C17_09_S135 [colonies_scRNA-seq]


title: C17_07_S123 [colonies_scRNA-seq]


title: C17_04_S100 [colonies_scRNA-seq]


title: C17_12_S148 [colonies_scRNA-seq]


title: C17_11_S147 [colonies_scRNA-seq]


title: C17_08_S124 [colonies_scRNA-seq]


title: C16_15_S169 [colonies_scRNA-seq]


title: C16_16_S170 [colonies_scRNA-seq]


title: C17_02_S88 [colonies_scRNA-seq]


title: C17_06_S112 [colonies_scRNA-seq]


title: C16_13_S157 [colonies_scRNA-seq]


title: C16_12_S146 [colonies_scRNA-seq]


title: C17_05_S111 [colonies_scRNA-seq]


title: C16_09_S133 [colonies_scRNA-seq]


title: C17_01_S87 [colonies_scRNA-seq]


title: C16_10_S134 [colonies_scRNA-seq]


title: C16_06_S110 [colonies_scRNA-seq]


title: C16_14_S158 [colonies_scRNA-seq]


title: C16_03_S97 [colonies_scRNA-seq]


title: C17_03_S99 [colonies_scRNA-seq]


title: C16_05_S109 [colonies_scRNA-seq]


title: C16_04_S98 [colonies_scRNA-seq]


title: C16_01_S85 [colonies_scRNA-seq]


title: C16_11_S145 [colonies_scRNA-seq]


title: C16_07_S121 [colonies_scRNA-seq]


title: C15_16_S168 [colonies_scRNA-seq]


title: C15_14_S156 [colonies_scRNA-seq]


title: C16_02_S86 [colonies_scRNA-seq]


title: C15_13_S155 [colonies_scRNA-seq]


title: C15_12_S144 [colonies_scRNA-seq]


title: C15_15_S167 [colonies_scRNA-seq]


title: C15_10_S132 [colonies_scRNA-seq]


title: C15_09_S131 [colonies_scRNA-seq]


title: C15_08_S120 [colonies_scRNA-seq]


title: C15_11_S143 [colonies_scRNA-seq]


title: C15_06_S108 [colonies_scRNA-seq]


title: C15_07_S119 [colonies_scRNA-seq]


title: C15_05_S107 [colonies_scRNA-seq]


title: C15_04_S96 [colonies_scRNA-seq]


title: C15_03_S95 [colonies_scRNA-seq]


title: C16_08_S122 [colonies_scRNA-seq]


title: C15_02_S84 [colonies_scRNA-seq]


title: C14_16_S166 [colonies_scRNA-seq]


title: C14_15_S165 [colonies_scRNA-seq]


title: C14_13_S153 [colonies_scRNA-seq]


title: C14_12_S142 [colonies_scRNA-seq]


title: C14_11_S141 [colonies_scRNA-seq]


title: C14_08_S118 [colonies_scRNA-seq]


title: C14_09_S129 [colonies_scRNA-seq]


title: C14_07_S117 [colonies_scRNA-seq]


title: C14_10_S130 [colonies_scRNA-seq]


title: C14_06_S106 [colonies_scRNA-seq]


title: C14_03_S93 [colonies_scRNA-seq]


title: C14_01_S81 [colonies_scRNA-seq]


title: C14_05_S105 [colonies_scRNA-seq]


title: C14_04_S94 [colonies_scRNA-seq]


title: BulkATAC-NextSeq-19-S41

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. We used MACS2 to call all  ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues.
For all subsequent analysis we discarded peaks falling within these regions. Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script.
All samples/libraries passed QC (none were filtered in downstream analyses)
Genome_build: hg19
Supplementary_files_format_and_content: Heteroplasmy for variants specific to individual colonies

source_name: donor 4_CD34+ hematopoietic cells

growth_protocol: MethoCult H4034 Optimum culture

extract_protocol:
NP 40 lysis
ATAC-seq

value: donor 4


title: BulkATAC-NextSeq-18-S40


title: BulkATAC-NextSeq-20-S42


title: BulkATAC-NextSeq-16-S38


title: C14_02_S82 [colonies_scRNA-seq]

value: donor 1


title: BulkATAC-NextSeq-15-S37


title: C15_01_S83 [colonies_scRNA-seq]


title: BulkATAC-NextSeq-13-S35


title: BulkATAC-NextSeq-11-S33


title: BulkATAC-NextSeq-09-S31


title: BulkATAC-NextSeq-08-S30


title: BulkATAC-NextSeq-10-S32


title: C14_14_S154 [colonies_scRNA-seq]


title: BulkATAC-NextSeq-07-S29


title: BulkATAC-NextSeq-04-S26


title: BulkATAC-NextSeq-05-S27


title: BulkATAC-NextSeq-03-S25


title: BulkATAC-NextSeq-01-S23


title: BulkATAC-NextSeq-02-S24


title: BulkATAC-NextSeq-06-S28


title: BulkATAC-NextSeq-14-S36


title: BulkATAC-NextSeq-17-S39


title: TF1_G10_26_S274 [TF_clones_scMito]

data_processing:
Paired-end reads were aligned to hg19 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script
Samples were filtered such that individual cells each had at least 100x coverage at 9 established heteroplasmic variants
Genome_build: hg19
Supplementary_files_format_and_content: High confidence mitochondrial variants for 3 clones assayed by 3 separate single cell technologies

extract_protocol:
Qiagen TCL lysis buffer
Qiagen Mito-RepliG
Single cell mitochondrial DNA-seq, Nextera

value: hematopoietic cell line

tag: clone id


title: TF1_G10_31_S287 [TF_clones_scMito]


title: TF1_G10_27_S275 [TF_clones_scMito]


title: TF1_G10_24_S264 [TF_clones_scMito]


title: TF1_G10_29_S285 [TF_clones_scMito]


title: TF1_G10_23_S263 [TF_clones_scMito]


title: TF1_G10_25_S273 [TF_clones_scMito]


title: BulkATAC-NextSeq-12-S34


title: TF1_G10_21_S261 [TF_clones_scMito]


title: TF1_G10_22_S262 [TF_clones_scMito]


title: TF1_G10_30_S286 [TF_clones_scMito]


title: TF1_G10_19_S251 [TF_clones_scMito]


title: TF1_G10_17_S249 [TF_clones_scMito]


title: TF1_G10_18_S250 [TF_clones_scMito]


title: TF1_G10_16_S240 [TF_clones_scMito]


title: TF1_G10_11_S227 [TF_clones_scMito]


title: TF1_G10_10_S226 [TF_clones_scMito]


title: TF1_G10_08_S216 [TF_clones_scMito]


title: TF1_G10_14_S238 [TF_clones_scMito]


title: TF1_G10_07_S215 [TF_clones_scMito]


title: TF1_G10_05_S213 [TF_clones_scMito]


title: TF1_G10_12_S228 [TF_clones_scMito]


title: TF1_G10_04_S204 [TF_clones_scMito]


title: TF1_G10_03_S203 [TF_clones_scMito]


title: TF1_G10_02_S202 [TF_clones_scMito]


title: TF1_G10_20_S252 [TF_clones_scMito]


title: TF1_D6_32_S284 [TF_clones_scMito]


title: TF1_G10_01_S201 [TF_clones_scMito]


title: TF1_D6_31_S283 [TF_clones_scMito]


title: TF1_D6_29_S281 [TF_clones_scMito]


title: TF1_D6_28_S272 [TF_clones_scMito]


title: TF1_D6_26_S270 [TF_clones_scMito]


title: TF1_D6_25_S269 [TF_clones_scMito]


title: TF1_G10_15_S239 [TF_clones_scMito]


title: TF1_D6_24_S260 [TF_clones_scMito]


title: TF1_G10_13_S237 [TF_clones_scMito]


title: TF1_G10_09_S225 [TF_clones_scMito]


title: TF1_D6_21_S257 [TF_clones_scMito]


title: TF1_D6_20_S248 [TF_clones_scMito]


title: TF1_D6_23_S259 [TF_clones_scMito]


title: TF1_G10_06_S214 [TF_clones_scMito]


title: TF1_D6_15_S235 [TF_clones_scMito]


title: TF1_D6_18_S246 [TF_clones_scMito]


title: TF1_D6_16_S236 [TF_clones_scMito]


title: TF1_D6_17_S245 [TF_clones_scMito]


title: TF1_D6_14_S234 [TF_clones_scMito]


title: TF1_D6_30_S282 [TF_clones_scMito]


title: TF1_D6_13_S233 [TF_clones_scMito]


title: TF1_D6_12_S224 [TF_clones_scMito]


title: TF1_D6_27_S271 [TF_clones_scMito]


title: TF1_D6_08_S212 [TF_clones_scMito]


title: TF1_D6_09_S221 [TF_clones_scMito]


title: TF1_D6_19_S247 [TF_clones_scMito]


title: TF1_D6_06_S210 [TF_clones_scMito]


title: TF1_D6_05_S209 [TF_clones_scMito]


title: TF1_D6_22_S258 [TF_clones_scMito]


title: TF1_D6_07_S211 [TF_clones_scMito]


title: TF1_D6_02_S198 [TF_clones_scMito]


title: TF1_D6_01_S197 [TF_clones_scMito]


title: TF1_C9_32_S280 [TF_clones_scMito]


title: TF1_D6_04_S200 [TF_clones_scMito]


title: TF1_D6_10_S222 [TF_clones_scMito]


title: TF1_D6_03_S199 [TF_clones_scMito]


title: TF1_C9_31_S279 [TF_clones_scMito]


title: TF1_C9_30_S278 [TF_clones_scMito]


title: TF1_C9_28_S268 [TF_clones_scMito]


title: TF1_C9_29_S277 [TF_clones_scMito]


title: TF1_C9_27_S267 [TF_clones_scMito]


title: TF1_C9_26_S266 [TF_clones_scMito]


title: TF1_C9_25_S265 [TF_clones_scMito]


title: TF1_D6_11_S223 [TF_clones_scMito]


title: TF1_C9_18_S242 [TF_clones_scMito]


title: TF1_C9_24_S256 [TF_clones_scMito]


title: TF1_C9_22_S254 [TF_clones_scMito]


title: TF1_C9_23_S255 [TF_clones_scMito]


title: TF1_C9_19_S243 [TF_clones_scMito]


title: TF1_C9_11_S219 [TF_clones_scMito]


title: TF1_C9_14_S230 [TF_clones_scMito]


title: TF1_C9_13_S229 [TF_clones_scMito]


title: TF1_C9_07_S207 [TF_clones_scMito]


title: TF1_C9_08_S208 [TF_clones_scMito]


title: TF1_C9_16_S232 [TF_clones_scMito]


title: TF1_C9_06_S206 [TF_clones_scMito]


title: TF1_C9_10_S218 [TF_clones_scMito]


title: C1_G10_92_S103 [TF1_clones_scATAC]

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools for reads uniquely mapping to the nuclear genome.
Reads were subsequently filtered for alignment quality of >Q20 and were required to be properly paired. We used MACS2 to call all  ATAC-seq peaks. MACS2 was used with the following parameters (--nomodel --nolambda --keep-dup all --call-summits). Peaks were filtered using the consensus excludable ENCODE blacklist (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/) and a custom blacklist, designed to remove high-signal causing repeats and mitochondrial homologues.
For all subsequent analysis we discarded peaks falling within these regions. Mitochondrial genotypes were inferred for each ATAC-seq sample using a custom python script.
Samples were filtered such that individual cells each had at least 100x coverage at 9 established heteroplasmic variants. No nuclear genome QC was performed
Genome_build: hg19
Supplementary_files_format_and_content: High confidence mitochondrial variants for 3 clones assayed by 3 separate single cell technologies

extract_protocol:
NP40 lysis
Single cell ATAC-seq (C1 Fluidigm)


title: TF1_C9_17_S241 [TF_clones_scMito]


title: C1_G10_93_S104 [TF1_clones_scATAC]


title: C1_G10_87_S98 [TF1_clones_scATAC]


title: TF1_C9_01_S193 [TF_clones_scMito]


title: TF1_C9_09_S217 [TF_clones_scMito]


title: C1_G10_91_S102 [TF1_clones_scATAC]


title: TF1_C9_02_S194 [TF_clones_scMito]


title: TF1_C9_12_S220 [TF_clones_scMito]


title: C1_G10_86_S97 [TF1_clones_scATAC]


title: TF1_C9_05_S205 [TF_clones_scMito]


title: TF1_C9_15_S231 [TF_clones_scMito]


title: C1_G10_85_S96 [TF1_clones_scATAC]


title: TF1_C9_20_S244 [TF_clones_scMito]


title: C1_G10_80_S91 [TF1_clones_scATAC]


title: C1_G10_79_S90 [TF1_clones_scATAC]


title: TF1_C9_21_S253 [TF_clones_scMito]


title: C1_G10_81_S92 [TF1_clones_scATAC]


title: C1_G10_74_S85 [TF1_clones_scATAC]


title: C1_G10_75_S86 [TF1_clones_scATAC]


title: TF1_C9_04_S196 [TF_clones_scMito]


title: TF1_C9_03_S195 [TF_clones_scMito]


title: C1_G10_69_S80 [TF1_clones_scATAC]


title: C1_G10_63_S74 [TF1_clones_scATAC]


title: C1_G10_62_S73 [TF1_clones_scATAC]


title: C1_G10_73_S84 [TF1_clones_scATAC]


title: C1_G10_50_S61 [TF1_clones_scATAC]


title: C1_G10_56_S67 [TF1_clones_scATAC]


title: C1_G10_61_S72 [TF1_clones_scATAC]


title: C1_G10_49_S60 [TF1_clones_scATAC]


title: C1_G10_68_S79 [TF1_clones_scATAC]


title: C1_G10_44_S55 [TF1_clones_scATAC]


title: C1_G10_43_S54 [TF1_clones_scATAC]


title: C1_G10_57_S68 [TF1_clones_scATAC]


title: C1_G10_51_S62 [TF1_clones_scATAC]


title: C1_G10_38_S49 [TF1_clones_scATAC]


title: C1_G10_67_S78 [TF1_clones_scATAC]


title: C1_G10_31_S42 [TF1_clones_scATAC]


title: C1_G10_26_S37 [TF1_clones_scATAC]


title: C1_G10_33_S44 [TF1_clones_scATAC]


title: C1_G10_27_S38 [TF1_clones_scATAC]


title: C1_G10_19_S30 [TF1_clones_scATAC]


title: C1_G10_25_S36 [TF1_clones_scATAC]


title: C1_G10_32_S43 [TF1_clones_scATAC]


title: C1_G10_20_S31 [TF1_clones_scATAC]


title: C1_G10_15_S26 [TF1_clones_scATAC]


title: C1_G10_14_S25 [TF1_clones_scATAC]


title: C1_G10_55_S66 [TF1_clones_scATAC]


title: C1_G10_09_S20 [TF1_clones_scATAC]


title: C1_G10_13_S24 [TF1_clones_scATAC]


title: C1_G10_45_S56 [TF1_clones_scATAC]


title: C1_G10_39_S50 [TF1_clones_scATAC]


title: C1_G10_37_S48 [TF1_clones_scATAC]


title: C1_G10_01_S12 [TF1_clones_scATAC]


title: C1_C9-D6_48_S155 [TF1_clones_scATAC]


title: C1_G10_08_S19 [TF1_clones_scATAC]


title: C1_C9-D6_42_S149 [TF1_clones_scATAC]


title: C1_C9-D6_43_S150 [TF1_clones_scATAC]


title: C1_G10_03_S14 [TF1_clones_scATAC]


title: C1_C9-D6_44_S151 [TF1_clones_scATAC]


title: C1_C9-D6_47_S154 [TF1_clones_scATAC]


title: C1_C9-D6_41_S148 [TF1_clones_scATAC]


title: C1_C9-D6_46_S153 [TF1_clones_scATAC]


title: C1_G10_02_S13 [TF1_clones_scATAC]


title: C1_C9-D6_40_S147 [TF1_clones_scATAC]


title: C1_G10_21_S32 [TF1_clones_scATAC]


title: C1_C9-D6_36_S143 [TF1_clones_scATAC]


title: C1_C9-D6_37_S144 [TF1_clones_scATAC]


title: C1_C9-D6_35_S142 [TF1_clones_scATAC]


title: C1_C9-D6_38_S145 [TF1_clones_scATAC]


title: C1_C9-D6_39_S146 [TF1_clones_scATAC]


title: C1_G10_07_S18 [TF1_clones_scATAC]


title: C1_C9-D6_34_S141 [TF1_clones_scATAC]


title: C1_C9-D6_33_S140 [TF1_clones_scATAC]


title: C1_C9-D6_45_S152 [TF1_clones_scATAC]


title: C1_C9-D6_32_S139 [TF1_clones_scATAC]


title: CluGFP- [H07_Plate4]

first: Bibaswan

last: Ghoshal

address: 600 University Avenue

institute: Lunenfeld Tanenbaum Research Institute

description:
H07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv

data_processing:
Reads obtained from each cell were then aligned to the mm10 mouse genome using the STAR RNAseq aligner. A combined count matrix was generated from all 192 cells using the featurecounts function.
Data is read into Seurat with 1 minimum cell and 200 minimum genes and subsequently converted in scater for quality control and filtering based on library size, feature size and percentage of mitochondrial genes. Furthermore, normalization steps are performed and then the normalized data is transported back to Seurat. In Seurat, data is scaled and dimension reduction, cluster identification, PCA and tSNE are performed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_data.csv: Comma-separated text files contain the raw data from the 192 cells and the normalized expression data from the filtered 166 cells that are finally used for analysis and visualization.

source_name: Intestinal Epithelium

extract_protocol:
Full length scRNA-seq was performed by SMART-seq2 upon enrichment of Clu+ rSCs using BAC-CluGFP transgenic mice. In short, approximately 2000 GFP+ and GFP- FACS-isolated cells in less than 10 mL were directly processed on a Fluidigm C1 platform and 96 GFP+ and 96 GFP- healthy cells were selected and subjected to RNA extraction, library preparation and deep sequencing using the SMART-Seq_V4 Ultra Low Input RNA Kit for Sequencing as described in the manual.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: FACS sorted intestinal epithelial cells

tag: treatment

value: EpCAM+ CluGFP-


title: CluGFP- [H10_Plate4]

description:
H10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H12_Plate4]

description:
H12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H09_Plate4]

description:
H09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H11_Plate4]

description:
H11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H08_Plate4]

description:
H08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H04_Plate4]

description:
H04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H05_Plate4]

description:
H05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H06_Plate4]

description:
H06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H03_Plate4]

description:
H03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [G12_Plate4]

description:
G12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [G10_Plate4]

description:
G10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_31_S138 [TF1_clones_scATAC]


title: CluGFP- [H02_Plate4]

description:
H02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [H01_Plate4]

description:
H01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [G06_Plate4]

description:
G06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_29_S136 [TF1_clones_scATAC]


title: C1_C9-D6_30_S137 [TF1_clones_scATAC]


title: CluGFP- [G09_Plate4]

description:
G09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [G08_Plate4]

description:
G08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_28_S135 [TF1_clones_scATAC]


title: CluGFP- [G07_Plate4]

description:
G07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_27_S134 [TF1_clones_scATAC]


title: C1_C9-D6_26_S133 [TF1_clones_scATAC]


title: CluGFP- [G04_Plate4]

description:
G04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_25_S132 [TF1_clones_scATAC]


title: CluGFP- [G02_Plate4]

description:
G02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [G11_Plate4]

description:
G11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_24_S131 [TF1_clones_scATAC]


title: CluGFP- [G03_Plate4]

description:
G03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F12_Plate4]

description:
F12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [G01_Plate4]

description:
G01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_23_S130 [TF1_clones_scATAC]


title: C1_C9-D6_22_S129 [TF1_clones_scATAC]


title: CluGFP- [F09_Plate4]

description:
F09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_20_S127 [TF1_clones_scATAC]


title: CluGFP- [F10_Plate4]

description:
F10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F08_Plate4]

description:
F08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F06_Plate4]

description:
F06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F07_Plate4]

description:
F07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F04_Plate4]

description:
F04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F03_Plate4]

description:
F03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_21_S128 [TF1_clones_scATAC]


title: CluGFP- [G05_Plate4]

description:
G05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F11_Plate4]

description:
F11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F01_Plate4]

description:
F01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F02_Plate4]

description:
F02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [E12_Plate4]

description:
E12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [F05_Plate4]

description:
F05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_18_S125 [TF1_clones_scATAC]


title: CluGFP- [E11_Plate4]

description:
E11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_17_S124 [TF1_clones_scATAC]


title: CluGFP- [E10_Plate4]

description:
E10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [E09_Plate4]

description:
E09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_16_S123 [TF1_clones_scATAC]


title: CluGFP- [E08_Plate4]

description:
E08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [E07_Plate4]

description:
E07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_15_S122 [TF1_clones_scATAC]


title: CluGFP- [E06_Plate4]

description:
E06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_14_S121 [TF1_clones_scATAC]


title: CluGFP- [E05_Plate4]

description:
E05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_13_S120 [TF1_clones_scATAC]


title: CluGFP- [E03_Plate4]

description:
E03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_12_S119 [TF1_clones_scATAC]


title: C1_C9-D6_19_S126 [TF1_clones_scATAC]


title: CluGFP- [E02_Plate4]

description:
E02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D12_Plate4]

description:
D12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [E04_Plate4]

description:
E04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [E01_Plate4]

description:
E01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D10_Plate4]

description:
D10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D09_Plate4]

description:
D09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D11_Plate4]

description:
D11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_10_S117 [TF1_clones_scATAC]


title: CluGFP- [D08_Plate4]

description:
D08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D06_Plate4]

description:
D06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_09_S116 [TF1_clones_scATAC]


title: CluGFP- [D05_Plate4]

description:
D05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_08_S115 [TF1_clones_scATAC]


title: CluGFP- [D07_Plate4]

description:
D07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D04_Plate4]

description:
D04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D03_Plate4]

description:
D03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_07_S114 [TF1_clones_scATAC]


title: C1_C9-D6_06_S113 [TF1_clones_scATAC]


title: C1_C9-D6_05_S112 [TF1_clones_scATAC]


title: CluGFP- [D01_Plate4]

description:
D01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [D02_Plate4]

description:
D02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C12_Plate4]

description:
C12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C11_Plate4]

description:
C11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_11_S118 [TF1_clones_scATAC]


title: CluGFP- [C10_Plate4]

description:
C10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_03_S110 [TF1_clones_scATAC]


title: CluGFP- [C06_Plate4]

description:
C06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C05_Plate4]

description:
C05_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C07_Plate4]

description:
C07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_04_S111 [TF1_clones_scATAC]


title: CluGFP- [C08_Plate4]

description:
C08_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C04_Plate4]

description:
C04_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: C1_C9-D6_02_S109 [TF1_clones_scATAC]


title: C1_C9-D6_01_S108 [TF1_clones_scATAC]


title: CluGFP- [C03_Plate4]

description:
C03_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C02_Plate4]

description:
C02_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1081_G10_G10_G001 [TF1_clones_scRNA-seq]

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh37/hg19) using STAR using standard two-pass approach.
Gene were quantified using the STAR --quantMode GeneCounts flag over the Gencode v19 annotation.
Processed bams were genotyped for mitochondria using a custom python script.
Samples were filtered such that individual cells each had at least 100x coverage at 9 established heteroplasmic variants. No nuclear genome QC was performed
Genome_build: hg19
Supplementary_files_format_and_content: High confidence mitochondrial variants for 3 clones assayed by 3 separate single cell technologies

extract_protocol:
Qiagen TCL lysis buffer
Smart-seq2
Single cell RNA-seq


title: CluGFP- [B11_Plate4]

description:
B11_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1080_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP- [B10_Plate4]

description:
B10_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [B12_Plate4]

description:
B12_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [C01_Plate4]

description:
C01_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [B09_Plate4]

description:
B09_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: CluGFP- [B07_Plate4]

description:
B07_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1078_G10_G10_G001 [TF1_clones_scRNA-seq]


title: CluGFP- [B06_Plate4]

description:
B06_Plate4
Single cell RNA-seq
processed data file: raw_data.csv
processed data file: processed_data.csv


title: S1077_G10_G10_G001 [TF1_clones_scRNA-seq]