title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F9_MemorySeq010_S437

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F9_MemorySeq384_2_S129

status: Public on Feb 02 2022

type: SRA

city: Cambridge

first: Xiaojie

last: Qiu

state: MA

address: 455 Main St, Cambridge, MA

country: USA

institute: Whitehead Institute

description:
edge_df.csv
NovaSeq 5000

library_source: transcriptomic

data_processing:
Library strategy: SLAM-seq
For the HL60 10x dataset, we followed the standard pipeline of kb-python to quantify the total, spliced and unspliced RNA. For the HL60 metabolic labeling based scRNA-seq experiment with clone tracing, we used the NASC-seq pipeline (https://github.com/sandberg-lab/NASC-seq) developed in to quantify the new and total RNA read counts.
For the scNT-seq experiment of the human hematopoiesis, we developed dynast (https://github.com/aristoteleo/dynast-release), an inclusive and efficient command-line toolkit for preprocessing data from metabolic labeling–based scRNA-seq experiments and quantifying the following four types of mRNA species: unspliced, spliced, labeled (or new), and total RNAs (details will be reported elsewhere). Samples from days 4 and 7 were each subjected to standard dynast runs, using human genome hg38 as the alignment reference. The resultant objects were first filtered to keep only high quality cells and then merged to obtain in total about 2,000 high-quality cells. This merged object was then used for all downstream analyses.
Genome_build: hg38
Supplementary_files_format_and_content: file format is h5ad/csv. For h5ad files, they include the spliced, unspliced, labeled and total RNA counts for each gene in each cell from our scSLAM-seq and scNT-seq experiment. Only spliced and unspliced RNA counts for each gene in each cell are available for the 10x dataset. For the edge_df.csv file, it is the clone linkage information between different cells, processed from the static barcodes.

molecule: total RNA

organism: Homo sapiens

extract_protocol: To facilitate lineage tracing in scSLAM-seq libraries, cellular barcodes (GBCs) were introduced using a lentiviral transduction strategy (Adamson et al., 2016). Given that the success of this experiment critically depended on the uniqueness of barcode sequence to each cell at the start of the experiment, i.e. low barcode collision rate, and the capture of clone cells (clones with the same barcodes) across different days, we used an experimental scheme in which the starting population of the HL60 cells were infected at a low (2%) multiplicity of infection (MOI). This scheme has two benefits: first, we obtained a small number of barcoded single cells (~2000 in 1 ml of media in each well of a 24-well plate) so that we could capture clone cells via plate-based SLAM-seq (scRNA-seq augmented by metabolic labeling) characterized of low throughput; second, co-culturing the small number of infected cells with a large population of uninfected cells enabled us to differentiate infected cells more conveniently, as a small number of cells are difficult to grow and differentiate. Single cells carrying barcodes and expressing the blue fluorescent protein (BFP) reporter were sorted (Sony SH800) at five timepoints, days 0, 1, 2, 3, and 5, during differentiation in the presence of ATRA. cDNA from single cells was prepared in a 96-well format as previously described (Tabula Muris Consortium, 2020) following alkylation and RNA cleanup (Erhard et al., 2019; Hendriks et al., 2019). Sequencing libraries were either reformatted into a 384-well format and prepared using TTP Mosquito automated liquid handlers, or in a 96- well format using a multichannel pipette. GBC sequencing libraries were prepared by dual PCR amplification to enrich for GBC cDNA and to add Illumina adapters and dual indexes complimentary to that cell's transcriptome sequencing library indexes. GBC sequencing libraries were spiked into transcriptome libraries at 1:10 and sequenced on the NextSeq or MiSeq platform (Illumina). Transcriptome libraries were sequenced separately using a NovaSeq5000 S2 300-cycle kit.

tag: cell line

tag: treatment

value: neutrophil lineage differentiation in the presence of  ATRA

tag: gender

value: female

tag: age

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F8_MemorySeq028_S928

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F8_MemorySeq384_2_S128

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F7_MemorySeq384_3_S607

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F7_MemorySeq010_S436

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F7_MemorySeq384_2_S127

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F6_MemorySeq384_3_S606

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F5_MemorySeq384_3_S605

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F5_MemorySeq384_2_S125

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, G10_MemorySeq384_2_S154

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F4_MemorySeq384_3_S604

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F5_MemorySeq010_S435

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F3_MemorySeq384_3_S603

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F6_MemorySeq028_S927

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F4_MemorySeq384_2_S124

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F3_MemorySeq384_2_S123

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F3_MemorySeq010_S434

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F2_MemorySeq384_2_S122

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F2_MemorySeq384_3_S602

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F24_MemorySeq384_3_S624

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F6_MemorySeq384_2_S126

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F24_MemorySeq384_2_S144

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F23_MemorySeq384_3_S623

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F23_MemorySeq384_2_S143

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F22_MemorySeq384_2_S142

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F21_MemorySeq384_3_S621

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F22_MemorySeq384_3_S622

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F23_MemorySeq010_S444

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F21_MemorySeq384_2_S141

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F19_MemorySeq010_S442

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F20_MemorySeq028_S934

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F19_MemorySeq384_2_S139

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F4_MemorySeq028_S926

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F20_MemorySeq384_3_S620

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F2_MemorySeq028_S925

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F21_MemorySeq010_S443

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F19_MemorySeq384_3_S619

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F1_MemorySeq384_3_S601

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F18_MemorySeq384_3_S618

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F17_MemorySeq384_2_S137

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F17_MemorySeq010_S441

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F18_MemorySeq384_2_S138

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F1_MemorySeq384_2_S121

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F18_MemorySeq028_S933

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F15_MemorySeq010_S440

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F16_MemorySeq384_3_S616

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F15_MemorySeq384_3_S615

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F16_MemorySeq384_2_S136

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F16_MemorySeq028_S932

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F12_MemorySeq384_2_S132

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F14_MemorySeq384_3_S614

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F15_MemorySeq384_2_S135

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F20_MemorySeq384_2_S140

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F12_MemorySeq028_S930

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F13_MemorySeq010_S439

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F14_MemorySeq028_S931

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F13_MemorySeq384_3_S613

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F11_MemorySeq010_S438

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F11_MemorySeq384_3_S611

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F14_MemorySeq384_2_S134

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F11_MemorySeq384_2_S131

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E9_MemorySeq384_3_S585

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F10_MemorySeq384_2_S130

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E9_MemorySeq010_S425

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E8_MemorySeq384_2_S104

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F12_MemorySeq384_3_S612

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E8_MemorySeq028_S916

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F10_MemorySeq028_S929

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E8_MemorySeq384_3_S584

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E7_MemorySeq384_2_S103

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F13_MemorySeq384_2_S133

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, F10_MemorySeq384_3_S610

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E7_MemorySeq010_S424

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E7_MemorySeq384_3_S583

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E5_MemorySeq384_3_S581

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E5_MemorySeq010_S423

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E4_MemorySeq384_2_S100

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E6_MemorySeq384_2_S102

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E6_MemorySeq384_3_S582

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E6_MemorySeq028_S915

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E5_MemorySeq384_2_S101

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E3_MemorySeq384_2_S99

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E4_MemorySeq384_3_S580

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E2_MemorySeq384_2_S98

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E4_MemorySeq028_S914

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E9_MemorySeq384_2_S105

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E23_MemorySeq010_S432

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E3_MemorySeq384_3_S579

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E2_MemorySeq028_S913

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E3_MemorySeq010_S422

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E21_MemorySeq010_S431

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E21_MemorySeq384_2_S117

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E23_MemorySeq384_2_S119

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E21_MemorySeq384_3_S597

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E1_MemorySeq384_2_S97

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E2_MemorySeq384_3_S578

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E23_MemorySeq384_3_S599

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E22_MemorySeq384_2_S118

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E1_MemorySeq010_S421

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E24_MemorySeq384_2_S120

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E24_MemorySeq384_3_S600

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E20_MemorySeq028_S922

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E20_MemorySeq384_3_S596

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E19_MemorySeq010_S430

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E20_MemorySeq384_2_S116

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E19_MemorySeq384_3_S595

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E19_MemorySeq384_2_S115

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E1_MemorySeq384_3_S577

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E18_MemorySeq384_3_S594

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E18_MemorySeq028_S921

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E17_MemorySeq010_S429

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E17_MemorySeq384_2_S113

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E16_MemorySeq384_2_S112

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E15_MemorySeq384_3_S591

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E15_MemorySeq010_S428

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E15_MemorySeq384_2_S111

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E17_MemorySeq384_3_S593

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E13_MemorySeq384_3_S589

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E14_MemorySeq384_3_S590

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E12_MemorySeq384_3_S588

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E12_MemorySeq384_2_S108

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E12_MemorySeq028_S918

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E16_MemorySeq028_S920

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E13_MemorySeq384_2_S109

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E13_MemorySeq010_S427

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E11_MemorySeq384_2_S107

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E11_MemorySeq384_3_S587

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E11_MemorySeq010_S426

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E10_MemorySeq384_3_S586

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D9_MemorySeq384_3_S561

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E10_MemorySeq028_S917

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D8_MemorySeq384_2_S80

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E10_MemorySeq384_2_S106

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E16_MemorySeq384_3_S592

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D7_MemorySeq384_3_S559

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D6_MemorySeq384_3_S558

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D8_MemorySeq384_3_S560

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E14_MemorySeq028_S919

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D7_MemorySeq010_S412

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, E14_MemorySeq384_2_S110

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D5_MemorySeq384_3_S557

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D6_MemorySeq384_2_S78

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D4_MemorySeq384_3_S556

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D5_MemorySeq010_S411

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D9_MemorySeq010_S413

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D4_MemorySeq384_2_S76

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D4_MemorySeq028_S902

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D2_MemorySeq384_3_S554

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D3_MemorySeq010_S410

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D2_MemorySeq384_2_S74

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D23_MemorySeq010_S420

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D3_MemorySeq384_3_S555

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D8_MemorySeq028_S904

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D24_MemorySeq384_2_S96

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D6_MemorySeq028_S903

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D22_MemorySeq384_3_S574

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D23_MemorySeq384_3_S575

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D21_MemorySeq384_3_S573

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D22_MemorySeq384_2_S94

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D20_MemorySeq028_S910

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D20_MemorySeq384_3_S572

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D1_MemorySeq010_S409

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D20_MemorySeq384_2_S92

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D19_MemorySeq010_S418

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D24_MemorySeq384_3_S576

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D18_MemorySeq384_2_S90

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D19_MemorySeq384_3_S571

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D16_MemorySeq384_3_S568

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D18_MemorySeq384_3_S570

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D17_MemorySeq384_3_S569

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D16_MemorySeq384_2_S88

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D16_MemorySeq028_S908

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D21_MemorySeq010_S419

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D15_MemorySeq010_S416

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D14_MemorySeq384_2_S86

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D13_MemorySeq010_S415

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D12_MemorySeq384_2_S84

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D11_MemorySeq384_3_S563

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D12_MemorySeq384_3_S564

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D14_MemorySeq384_3_S566

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D1_MemorySeq384_3_S553

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D14_MemorySeq028_S907

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D10_MemorySeq028_S905

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D10_MemorySeq384_3_S562

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D11_MemorySeq010_S414

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C9_MemorySeq384_2_S57

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D10_MemorySeq384_2_S82

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C9_MemorySeq384_3_S537

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C9_MemorySeq010_S401

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D15_MemorySeq384_3_S567

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D18_MemorySeq028_S909

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C7_MemorySeq384_3_S535

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C8_MemorySeq028_S892

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, D12_MemorySeq028_S906

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C6_MemorySeq384_2_S54

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C7_MemorySeq384_2_S55

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C6_MemorySeq384_3_S534

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C4_MemorySeq384_3_S532

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C4_MemorySeq384_2_S52

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C3_MemorySeq384_3_S531

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C8_MemorySeq384_2_S56

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C7_MemorySeq010_S400

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C5_MemorySeq384_2_S53

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C5_MemorySeq010_S399

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C2_MemorySeq384_2_S50

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C4_MemorySeq028_S890

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C3_MemorySeq384_2_S51

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C24_MemorySeq384_2_S72

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C23_MemorySeq010_S408

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C3_MemorySeq010_S398

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C2_MemorySeq384_3_S530

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C2_MemorySeq028_S889

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C5_MemorySeq384_3_S533

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C8_MemorySeq384_3_S536

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C21_MemorySeq384_2_S69

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C20_MemorySeq384_3_S548

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C23_MemorySeq384_3_S551

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C21_MemorySeq010_S407

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C22_MemorySeq384_3_S550

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C23_MemorySeq384_2_S71

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C20_MemorySeq028_S898

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C24_MemorySeq384_3_S552

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C1_MemorySeq384_3_S529

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C20_MemorySeq384_2_S68

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C19_MemorySeq384_2_S67

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C21_MemorySeq384_3_S549

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C1_MemorySeq010_S397

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C22_MemorySeq384_2_S70

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C19_MemorySeq384_3_S547

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C1_MemorySeq384_2_S49

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C19_MemorySeq010_S406

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C17_MemorySeq384_3_S545

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C18_MemorySeq384_3_S546

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C18_MemorySeq384_2_S66

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C18_MemorySeq028_S897

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C16_MemorySeq028_S896

description:
edge_df.csv
NovaSeq 5000


title: Oscillatory shear stress + Hypoxia + IL-1B + OxPAPC, rep2

type: RNA

city: Sao Paulo

first: Jose Eduardo

last: Krieger

state: Sao Paulo

address: 44 Av. Dr. Enéas de Carvalho Aguiar

department: Medical School

country: Brazil

institute: University of Sao Paulo

description: RNA extracted from primary cultured endothelial cells

hyb_protocol: Samples were hybridized with GeneChipTM    WT PLUS Reagent Kit (Affymetrix) and scanned at  GeneTitan ™ Microarray System

scan_protocol: The entire protocol for processing, running and scanning the samples followed the manufacturer's instruction [GeneChip ™ WT PLUS Reagent Kit Manual] at GeneTitan ™ Microarray System

data_processing: The CEL were analyzed using arrayQualityMetrics (R package) to identify abnormal signal intensities (saturation or noise), an average of the variance of the intensity of this signal and possible outliers. The differential expression analysis gene expression was performed with the limma (R package).

label: biotin

label_protocol: Samples were enzymatically fragmented and biotinylated using RNA samples for whole  transcriptome  expression analysis with GeneChipTM Whole Transcript (WT) Expression Arrays (appliedbiosystems)

growth_protocol: Human coronary artery endothelial cell (HCAEC) were acquired at LONZA. The cells were grown in EBM-2MV medium (LONZA) and incubate at 37ºC, 5% CO2. All experiments were carried out between passages 4 and 6

extract_protocol: We used the RNeasy Micro Kit (Qiagen) for total RNA isolation

treatment_protocol: The ECs were exposed to a unidirectional atheroprotective shear flow with 20 dynes/cm2 (LSS) and an atherogenic, bidirectional at 1 Hz (0 ~ ± 5 dynes/cm2) shear flow (OSS). Then, add the stimuli: IL-1β (10ng/ml), OxPAPC (50µg/ml), and CoCl2 (150µM) individually or combined to the perfusion set and integrated into the pump; iii) the ECs were subjected to either the LSS or OSS for 48 hours

tag: tissue

value: Coronary artery

tag: cell type

value: human coronary artery endothelial cell (HCAEC)

tag: stress


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C17_MemorySeq384_2_S65

description:
edge_df.csv
NovaSeq 5000


title: Oscillatory shear stress + Hypoxia + IL-1B + OxPAPC, rep4


title: Oscillatory shear stress + Hypoxia + IL-1B + OxPAPC, rep3


title: Oscillatory shear stress, OSS, rep4

value: Oscillatory shear stress


title: Oscillatory shear stress + Hypoxia + IL-1B + OxPAPC, rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C15_MemorySeq384_3_S543

description:
edge_df.csv
NovaSeq 5000


title: Oscillatory shear stress, OSS, rep3


title: Oscillatory shear stress, OSS, rep2


title: Oscillatory shear stress, OSS, rep1


title: Laminar shear stress + OxPAPC, rep3

value: Laminar shear stress + OxPAPC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C17_MemorySeq010_S405

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + IL-1B, rep4

value: Laminar shear stress + IL-1B


title: Laminar shear stress + IL-1B, rep3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C16_MemorySeq384_3_S544

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + OxPAPC, rep2


title: Laminar shear stress + OxPAPC, rep4


title: Laminar shear stress + IL-1B, rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C14_MemorySeq384_3_S542

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C15_MemorySeq384_2_S63

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + IL-1B, rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C14_MemorySeq028_S895

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C13_MemorySeq384_2_S61

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + Hypoxia, rep2

value: Laminar shear stress + Hypoxia


title: Laminar shear stress + Hypoxia, rep4


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C13_MemorySeq384_3_S541

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + OxPAPC, rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C12_MemorySeq384_3_S540

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C14_MemorySeq384_2_S62

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress, LSS, rep4

value: Laminar shear stress


title: T. equiperdum STIB842 rep2

city: Guangzhou

first: Cai

last: Xiao-Li

state: Guangdong

address: Xingangxi Rd 135

department: School of Life Sciences

country: China

institute: Sun Yat-Sen University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated
Bowtie2 v2.2.3 was used for building the genome index, and clean Data was then aligned to the T. brucei genome using HISAT2  v2.1.0. (Parameter:--dta –t –p 4)
Reads count for each gene in each sample was counted by HTSeq v0.6.0
Genome_build: The reference genomes and the annotation file were downloaded from TritrypDB  database (https://tritrypdb.org/common/downloads/Current_Release/TbruceiTREU927/fasta/data/;https://tritrypdb.org/common/downloads/Current_Release/TbruceiTREU927/gff/data/ )
Supplementary_files_format_and_content:  Tab-delimited text file containing abundance measurements with the read counts

organism: Trypanosoma equiperdum

source_name: mouse blood

growth_protocol: mouse blood (in vivo)

extract_protocol:
Trypanosomes were purified from whole blood by passage through a DE52 column, and RNA was harvested using Trizol reagent. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) with a total amount of 2 μg RNA per sample following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: STIB 842

tag: condition

value: ascending C /high parasitemia

value: monomorphic


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C12_MemorySeq384_2_S60

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C11_MemorySeq384_3_S539

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C16_MemorySeq384_2_S64

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + Hypoxia, rep1


title: Laminar shear stress, LSS, rep3


title: T. equiperdum STIB841 rep1

value: STIB 841


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C13_MemorySeq010_S403

description:
edge_df.csv
NovaSeq 5000


title: T. equiperdum STIB818 rep2

value: STIB 818


title: T. equiperdum STIB842 rep3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C12_MemorySeq028_S894

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C10_MemorySeq384_2_S58

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C15_MemorySeq010_S404

description:
edge_df.csv
NovaSeq 5000


title: T. evansi CPOgz rep3

organism: Trypanosoma evansi

value: CPOgz


title: T. equiperdum STIB842 rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C11_MemorySeq384_2_S59

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B9_MemorySeq384_2_S33

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B9_MemorySeq384_3_S513

description:
edge_df.csv
NovaSeq 5000


title: T. equiperdum STIB818 rep3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C11_MemorySeq010_S402

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C10_MemorySeq384_3_S538

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress, LSS, rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, C10_MemorySeq028_S893

description:
edge_df.csv
NovaSeq 5000


title: T. equiperdum STIB841 rep3


title: T. equiperdum STIB841 rep2


title: Laminar shear stress, LSS, rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B8_MemorySeq028_S880

description:
edge_df.csv
NovaSeq 5000


title: Laminar shear stress + Hypoxia, rep3


title: T. evansi STIB805 rep3

value: STIB 805


title: T. evansi CPOgz rep1


title: T. evansi STIB816 rep3

value: STIB 816


title: T. equiperdum STIB818 rep1


title: T. evansi STIB805 rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B9_MemorySeq010_S389

description:
edge_df.csv
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B7_MemorySeq010_S388

description:
edge_df.csv
NovaSeq 5000

value: female


title: T. evansi STIB816 rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B5_MemorySeq384_3_S509

description:
edge_df.csv
NovaSeq 5000


title: T. evansi STIB816 rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B8_MemorySeq384_2_S32

description:
edge_df.csv
NovaSeq 5000


title: Ttf1_Input

city: Hangzhou

first: Yanqing

last: Zhu

state: Zhejiang

address: No.866, Road Yuhangtang

department: College of Animal Science

institute: Zhejiang University

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the Danio_rerio.GRCz10.88 genome assembly using bowtie2 -x Genome.fa –S sample.sam –N 1 -1 -2
Data were filtered using SAMtools V0.1.19 with configuration samtools depth BamFile > Sample.depth
Genome_build: Danio_rerio.GRCz10.88
Supplementary_files_format_and_content: peak text files

molecule: genomic DNA

organism: Danio rerio

source_name: embryo

growth_protocol: Fish were raised and maintained according to standard procedures.     Lo, J. et al. Genome research 13, 455-466 (2003).

extract_protocol:
Lysates were clarified from sonicated zebrafish embryo and Ttf1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. The DNA was sent to ANNOROAD (Beijing, China) for sequencing after precipitating and purify.

value: AB

tag: developmental stage

tag: antibody

value: input


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B8_MemorySeq384_3_S512

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B7_MemorySeq384_2_S31

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B4_MemorySeq384_2_S28

description:
edge_df.csv
NovaSeq 5000


title: T. evansi CPOgz rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B7_MemorySeq384_3_S511

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B6_MemorySeq384_2_S30

description:
edge_df.csv
NovaSeq 5000


title: Ttf1_IP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B6_MemorySeq028_S879

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B3_MemorySeq384_3_S507

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B4_MemorySeq384_3_S508

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B5_MemorySeq010_S387

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B5_MemorySeq384_2_S29

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B3_MemorySeq384_2_S27

description:
edge_df.csv
NovaSeq 5000


title: AB_EVs_rep1

city: Changsha

first: Zhenxing

last: Wang

address: Xiangya Road #87

institute: Xiangya hospital Central South University

description: microRNAs expression in AB-EVs

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

organism: Mus musculus

source_name: EVs collected from aged bone, replicate 1

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat #5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using SBI SeraMir Exosome RNA Amplification, following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US).

value: Male

value: 16 month

value: EVs collected from bone


title: AB_EVs_rep2

description: microRNAs expression in AB-EVs

source_name: EVs collected from aged bone, replicate 2


title: WT rep1

first: Chen

last: Wentao

address: No. 866 Yuhangtang Road

data_processing:
Paired-end sequencing of the library was performed on the HiSeq XTen sequencers (Illumina, San Diego, CA). FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36). Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default parameters. RSeQC (version 2.6.1) was used to run statistics on the alignment results. The homogeneity distribution and the genomic structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used for statistical analysis of the gene coverage ratio. Gene expression values of the transcripts were computed by StringTie (version 1.3.3b). The TPM eliminated the influence of gene lengths and sequencing discrepancies to enable direct comparison of gene expression between samples. DESeq2 (version 1.12.4) was used to determine differentially expressed genes (DEGs) between two samples. Genes were considered as significantly differentially expressed if q value < 0.05 and |log2foldchange| > 1.
Genome_build: scrofa.Sscrofa11.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Sus scrofa

source_name: Longissimus dorsi

extract_protocol:
 Total RNA was extracted from longissimus dorsi using the Total RNA Extractor (Trizol) kit and it was treated with RNase-free DNase I to remove genomic DNA contamination. The quality and  amount of  total RNA were determined by Nanodrop 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Longissimus dorsi muscle

tag: genotype

value: WT


title: YB_EVs_rep3

description: microRNAs expression in YB-EVs

source_name: EVs collected from young bone, replicate 3

value: 1 month


title: UCP1-KI rep3


title: UCP1-KI rep2


title: UCP1-KI rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B4_MemorySeq028_S878

description:
edge_df.csv
NovaSeq 5000


title: YB_EVs_rep1

description: microRNAs expression in YB-EVs

source_name: EVs collected from young bone, replicate 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B2_MemorySeq028_S877

description:
edge_df.csv
NovaSeq 5000


title: WT rep2


title: AB_EVs_rep3

description: microRNAs expression in AB-EVs

source_name: EVs collected from aged bone, replicate 3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B24_MemorySeq384_3_S528

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_91

city: SAINT LOUIS

first: Qihao

last: Ren

state: MO

address: 425 South Euclid Avenue, BJC-IH, Rm 7303, Washington University in St Louis

department: Cell Biology and Physiology

institute: Washington University in St Louis

data_processing:
Libraries were pooled and paired-end sequenced (150-bp reads) on Illumina NextSeq500 on a high-throughput mode
Illumina sequence adapters were trimmed and reads were aligned to a modified version of the GRCm38/mm10 mouse genome (supplemented with ERCC, mApple, eGFP, luciferase, PyMT oncogene sequences) using the STAR aligner.
Summarized gene transcript counts and TPMs were generated using RSEM.
All subsequent normalization and differential expression analysis were performed using the BASiCS package.
Genome_build: GRCm38/mm10 mouse genome (supplemented with ERCC, mApple, eGFP, luciferase, PyMT oncogene sequences)

source_name: Single PyMT-Bo1 cells from bone

growth_protocol: PyMT-Bo1 breast cancer cells were labelled with Vybrant DiD dye (Invitrogen) and injected into wild-type C57BL6 mice by intracardiac injection.

extract_protocol:
PyMT-Bo1 cells were first labelled with membrane DiD dye before injected into mice. Femur and tibia were isolated and pooled together from 5 IC injected mice. 32 dormant (DiD+) and 28 proliferative (DiD-) cells were isolated by FACS sorting for single cell RNA sequencing (scRNA-seq).
Single‐cell cDNA was generated using the SMARTer Ultra Low RNA Kit v4 (Takara) with modifications. 1:2,500,000 dilution of ERCC spike-in controls (Ambion) were incorporated during first-strand cDNA synthesis and subsequent steps were performed according to the manufacturer's instructions at half-reaction volumes. cDNA amplification was performed at 18 cycles and its quality was assessed using the Bioanalyzer HS DNA chip (Agilent Technologies) according to the manufacturer's instructions. Sequencing libraries were generated using 1 ng of input material using the Nextera XT Kit (Illumina) according to the manufacturer's protocol at half-reaction volumes.

tag: did intensity

value: Low

tag: cancer type

value: Breast

tag: animal model

value: intracardiac injection


title: WT rep3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B23_MemorySeq010_S396

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B2_MemorySeq384_3_S506

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B3_MemorySeq010_S386

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B22_MemorySeq384_3_S526

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B2_MemorySeq384_2_S26

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B23_MemorySeq384_2_S47

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_87

value: High


title: YB_EVs_rep2

description: microRNAs expression in YB-EVs

source_name: EVs collected from young bone, replicate 2


title: T. evansi STIB805 rep2

value: ascending C /high parasitemia

value: monomorphic


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B22_MemorySeq384_2_S46

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_84


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B21_MemorySeq384_3_S525

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B24_MemorySeq384_2_S48

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_82


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B20_MemorySeq384_3_S524

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B23_MemorySeq384_3_S527

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_90


title: WashU_Pymt_79


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B1_MemorySeq010_S385

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_77


title: WashU_Pymt_76


title: WashU_Pymt_86


title: WashU_Pymt_88


title: WashU_Pymt_89


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B21_MemorySeq384_2_S45

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B18_MemorySeq384_2_S42

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B21_MemorySeq010_S395

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_92


title: WashU_Pymt_80


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B20_MemorySeq384_2_S44

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_78


title: WashU_Pymt_71


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B17_MemorySeq384_3_S521

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_81


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B20_MemorySeq028_S886

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_85


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B19_MemorySeq384_3_S523

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_70


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B1_MemorySeq384_2_S25

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B19_MemorySeq384_2_S43

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_74


title: WashU_Pymt_75


title: WashU_Pymt_68


title: WashU_Pymt_67


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B16_MemorySeq384_2_S40

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_72


title: WashU_Pymt_83


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B16_MemorySeq028_S884

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B18_MemorySeq384_3_S522

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B19_MemorySeq010_S394

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B17_MemorySeq384_2_S41

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_63


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B15_MemorySeq384_3_S519

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_73


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B18_MemorySeq028_S885

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B17_MemorySeq010_S393

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B16_MemorySeq384_3_S520

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_65


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B15_MemorySeq384_2_S39

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B14_MemorySeq384_3_S518

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_69


title: WashU_Pymt_64


title: WashU_Pymt_45


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B12_MemorySeq384_3_S516

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B13_MemorySeq010_S391

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B15_MemorySeq010_S392

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_46


title: WashU_Pymt_43


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B14_MemorySeq028_S883

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B14_MemorySeq384_2_S38

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_42


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B13_MemorySeq384_2_S37

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B12_MemorySeq028_S882

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_39


title: WashU_Pymt_44


title: WashU_Pymt_66


title: WashU_Pymt_40


title: WashU_Pymt_41


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B13_MemorySeq384_3_S517

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_38


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B11_MemorySeq384_3_S515

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B10_MemorySeq384_3_S514

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_33


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B10_MemorySeq384_2_S34

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_36


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B11_MemorySeq010_S390

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A9_MemorySeq384_3_S489

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B11_MemorySeq384_2_S35

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_32


title: WashU_Pymt_31


title: WashU_Pymt_37


title: WashU_Pymt_35


title: WashU_Pymt_28


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A9_MemorySeq384_2_S9

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A8_MemorySeq384_2_S8

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A7_MemorySeq384_2_S7

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A8_MemorySeq028_S868

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_25


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B12_MemorySeq384_2_S36

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_34


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, B10_MemorySeq028_S881

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A6_MemorySeq028_S867

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A8_MemorySeq384_3_S488

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_30


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A5_MemorySeq384_3_S485

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_19


title: WashU_Pymt_20


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A5_MemorySeq384_2_S5

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A3_MemorySeq384_3_S483

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A4_MemorySeq384_3_S484

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A7_MemorySeq384_3_S487

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A6_MemorySeq384_3_S486

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_26


title: WashU_Pymt_23


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A4_MemorySeq384_2_S4

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_27


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A6_MemorySeq384_2_S6

description:
edge_df.csv
NovaSeq 5000


title: WashU_Pymt_24


title: Brain_ctl

city: Newark

first: Yun-juan

last: Chang

state: NJ

address: 185 South Orange Ave.

department: OARC

institute: Rutgers University

data_processing:
Cell Ranger (v3.0.2) mkfastq used to convert Illumnia BCLs to FASTQ files with bcl2fastq v2.20
Cell Ranger (v3.0.2) Count used to generate count matrix from FASTQ files
Seurat (v.3.0.2) function Read10X() was used to import count matrix data generated by cellranger pipeline
To filter out low-quality cells,  only those cells that had a mitochondrial read rate < 5% and expressed more than 500 and less than 3000 genes were selected for downstream analysis.
Genome_build: mm10 (Ensemble release 93)
Supplementary_files_format_and_content: compressed count matrix data_directory in file format .tar.gz, containing tsv and matrix files of barcodes.tsv.gz,  features.tsv.gz,  and matrix.mtx.gz,  generated by the cellranger pipeline v. 3.0.2
Supplementary_files_format_and_content: HDF5 file containing UMI counts, feature-barcode matrix data, generated by the cellranger pipeline v. 3.0.2

source_name: Brain tissue

extract_protocol:
O4+ cells were isolated from acutely dissociated brain and spinal cord samples by Miltenyl magnetic columns and used immediately for scRNA-Seq
Chromium Single Cell 3’ Library (v2 chemistry) by 10X genomics

treatment_protocol: Control (mTORfl/fl) and mTOR conditional knockout (CNP-Cre;mTORfl/fl) mice at postnatal day 14 (brain samples) or postnatal day 10 (spinal cord samples)

value: Wildtype  Brain

tag: experimental id

value: mTOR fl/fl

value: postnatal day 14


title: WashU_Pymt_18


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A2_MemorySeq028_S865

description:
edge_df.csv
NovaSeq 5000

tag: cell line

value: neutrophil lineage differentiation in the presence of  ATRA

value: female


title: Brain_KO

value: mTOR KO  Brain

value: CNP-Cre; mTOR fl/fl


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A3_MemorySeq384_2_S3

description:
edge_df.csv
NovaSeq 5000

tag: treatment


title: Spinal_ctl

source_name: Spinal cord

value: Wildtype  Spinal

value: postnatal day 10


title: WashU_Pymt_22


title: WashU_Pymt_17


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A2_MemorySeq384_3_S482

description:
edge_df.csv
NovaSeq 5000

tag: gender


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A2_MemorySeq384_2_S2

description:
edge_df.csv
NovaSeq 5000

tag: age


title: WashU_Pymt_21


title: WashU_Pymt_29


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A24_MemorySeq384_2_S24

description:
edge_df.csv
NovaSeq 5000

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A23_MemorySeq384_3_S503

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A24_MemorySeq384_3_S504

description:
edge_df.csv
NovaSeq 5000


title: Spinal_KO

value: mTOR KO  Spinal


title: Cup1

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

data_processing:
[data processing step 10x Genomics samples]  Cellranger version 3.0.0
[data processing step Bulk alignment]  Hisat v0.1.5
[data processing step Bulk sorting reads]  samtools v1.2
[data processing step Bulk counting reads]  HTSeq v0.6.1
Genome_build: Bulk GRCh37, human SC GRCh38, mouse SC GRCm38
Supplementary_files_format_and_content: Countfiles with raw counts per sample (bulk) or droplet barcode (single-cell)

source_name: brain

extract_protocol:
[Macrophage isolation human]  Mechanical tissue dissociation followed by percoll gradient centrifugation. FACS sorting for CD45posCD11Bpos cells.
[Macrophage isolation mouse]  Enzymatic isolation at 4C using protease from Bacillus lichenformis and L-cysteine. FACS sorted on tdTomato Red cells.
Qiagen Rneasy lipid mini kit
3’ Quantseq FWD kit from Lexogen for bulk RNAseq. 3’ single cell RNAseq v2 from 10x Genomics for single cell.

treatment_protocol: [diet protocol mice]  Mice were fed 0.2% cuprizone in their diet ad libitum. Control animals received similarly prepared chow but without cuprizone

tag: group

value: 3 weeks cuprizone

value: macrophages

tag: postmortem delay

tag: rin

value: M

tag: cell isolation

value: enzymatic

tag: rna isolation

tag: sequencing method

value: 3’ single cell RNAseq 10x Genomics v2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A22_MemorySeq384_2_S22

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A21_MemorySeq384_3_S501

description:
edge_df.csv
NovaSeq 5000


title: Corneal endothelium KO 3

city: Bloomington

first: Joseph

middle: A.

last: Bonanno

state: IN

address: 800 E Atwater Ave. , OPT 220

institute: Indiana University School of Optometry

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.6.4 which utilized cutadapt version 2.4 with parameters "--paired --length 17 --retain_unpaired --max_n 0", then mapped to GRCm38.p6 using Hisat2 version 2.1.0 with parameters "-q --rna-strandness F -mm".
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes using featureCounts tool of subread package version 1.6.4 with parameters "-O -M –primary -p –largetOverlap -s 2 -p -B" using Gencode M21 as the annotation.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Raw counts of reads mapped to genes using Gencode M21 as the annotation

source_name: Corneal endothelium

extract_protocol:
Corneal endothelial peelings corresponding to 6 eyes of 3 animal (6 peelings) were pooled in each sample. RNA was iolated with RNAeasy Plus Micro Kit (Qiagen #74034). The RNAseq libraries were generated using the TruSeq Stranded mRNA kit protocol. In brief, first the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were used for library preparation. The mRNA was purified from 100ng of total RNA for each sample, after cDNA synthesis and adapter ligation, the library was amplified with 12 rounds of PCR cycles.  The enriched and cleaned libraries were pooled and loaded on the sequencer.
First, the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were processed using the following steps. From each sample, 100ng of total RNA was used for library preparation following the Illumina TruSeq Stranded mRNA library preparation kit protocol. The cleaned adapter ligated libraries were pooled and loaded on the NextSeq 500 with a 75 cycle sequencing module to generate paired-end reads.

tag: strain

tag: tissue

value: Corneal endothelium

value: post natal week 12


title: Cup7

value: control

tag: cell type


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A23_MemorySeq384_2_S23

description:
edge_df.csv
NovaSeq 5000


title: Cup3

value: 5 weeks cuprizone


title: Corneal endothelium WT 4

tag: genotype


title: Corneal endothelium KO 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A1_MemorySeq384_2_S1

description:
edge_df.csv
NovaSeq 5000


title: Corneal endothelium KO 4


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A1_MemorySeq384_3_S481

description:
edge_df.csv
NovaSeq 5000


title: Cup5

value: 2 weeks remyelination


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A19_MemorySeq384_3_S499

description:
edge_df.csv
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: Corneal endothelium KO 5


title: Corneal endothelium WT 3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A20_MemorySeq384_3_S500

description:
edge_df.csv
NovaSeq 5000

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A18_MemorySeq384_3_S498

description:
edge_df.csv
NovaSeq 5000


title: Corneal endothelium WT 1


title: A009_ 2.2_7_dko

city: Helsinki

first: Satu

last: kUURE

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
UB samples: Demultiplexed and quality filtered reads were aligned to reference using STAR
UB samples: Gene counts were generated from alignments using featureCounts from subread-package
NP samples: Demultiplexed and quality filtered reads were aligned to reference using HISAT2
NP samples: Gene counts were generated from alignments using HTSeq.
After gene counts, both UB and NP data were normalized and differentially expressed genes were called using DESeq2 R-package.
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalized gene expression matrices for both UB and NP samples as .xlsx

source_name: E13.5 NP MAPK/ERK-deficient 3

growth_protocol: in vivo - normal growth

extract_protocol:
RNA was isolated from FAC-sorted cells by a standard protocol for chloroform/isopropanol extraction (Thermo Fisher Scientific – 04/2016, rev. B.00)
NuGen Ovation Solo

treatment_protocol: genetic modification

tag: cell type - genotype

value: MM - Six2-TGC;Mek1fl/fl;Mek2-/-

tag: background strain

value: mixed C57BL6/Rcc -129/SvEv


title: Corneal endothelium WT 5


title: Corneal endothelium KO 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A19_MemorySeq384_2_S19

description:
edge_df.csv
NovaSeq 5000

tag: cell line


title: Corneal endothelium WT 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A22_MemorySeq384_3_S502

description:
edge_df.csv
NovaSeq 5000

tag: treatment


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A21_MemorySeq384_2_S21

description:
edge_df.csv
NovaSeq 5000

tag: gender


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A18_MemorySeq028_S873

description:
edge_df.csv
NovaSeq 5000

tag: age


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A18_MemorySeq384_2_S18

description:
edge_df.csv
NovaSeq 5000

tag: ethnicity


title: A001_15.1_1_ctrl

source_name: E13.5 NP control 1

value: MM - Six2-TGC;Mek1fl/+;Mek2+/+


title: A013_30.9_8_dko

source_name: E12.5 UB MAPK/ERK-deficient 4

value: UB - HoxB7Cre-GFP;Mek1fl/fl;Mek2-/-


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A16_MemorySeq384_3_S496

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A16_MemorySeq384_2_S16

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A16_MemorySeq028_S872

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A15_MemorySeq384_3_S495

description:
edge_df.csv
NovaSeq 5000


title: A012_20.2_9_dko

source_name: E12.5 UB MAPK/ERK-deficient 3


title: A007_25.1_13_dko

source_name: E13.5 NP MAPK/ERK-deficient 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A17_MemorySeq384_3_S497

description:
edge_df.csv
NovaSeq 5000


title: A002_15.1_2_ctrl

source_name: E13.5 NP control 2


title: A018_ 25.3_6_ctrl

source_name: E12.5 UB control 4

value: UB - HoxB7Cre-GFP;Mek1fl/+;Mek2+/-


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A14_MemorySeq384_2_S14

description:
edge_df.csv
NovaSeq 5000


title: A004_24.2_6_ctrl

source_name: E13.5 NP control 3


title: A011_31.1_7_dko

source_name: E12.5 UB MAPK/ERK-deficient 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A15_MemorySeq384_2_S15

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A14_MemorySeq028_S871

description:
edge_df.csv
NovaSeq 5000


title: A008_ 25.1_5_dko

source_name: E13.5 NP MAPK/ERK-deficient 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A12_MemorySeq028_S870

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A17_MemorySeq384_2_S17

description:
edge_df.csv
NovaSeq 5000


title: PDGFRα- Replicate 1

city: Baltimore

first: Aaron

middle: W

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

description: The cells were isolated from mouse periosteum in PDGFRα-mTmG mice and expaned for 1 passage. Then, cells were devided into PDGFRα- and PDGFRα+ by FACS.

data_processing:
Paired-end 75nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to Mus musculus sequence GRCm38_p6 May-19, with CLCGenomicsServer 9.1.3 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 9.1.3 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: Mus musculus sequence GRCm38_p6 May-19
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples.

source_name: Mouse CD31-CD45-Ter119-PDGFRα- periosteal stromal cells

growth_protocol: Male 2-month-old Pdgfrα-mTmG mice were administered Tamoxifen (150 mg/kg/d for 5 d). Hind limbs were dissected and soft tissues surrounding the bones were meticulously removed 14 days after last Tamoxifen injection. Bilateral femurs and tibias were washed in PBS twice and digested with 2 mg/mL collagenase P (Roche, Basel, Switzerland) in Dulbecco's Modified Eagle's Medium (DMEM) (Gibco, Grand Island, NY), containing 0.5% bovine serum albumin (Sigma-Aldrich) at 37°C for 10 min (6 times). Digestion solution were filtered at 40 μm and centrifuged. Cells from the third to sixth digestion were pooled and resuspended in αMEM (Gibco) containing 15% FBS (Gibco), 1% penicillin/streptomycin (Gibco), and 10 ng/mL basic fibroblast growth factor (bFGF) (PeproTech, Rocky Hill, NJ). N=3-6 male 9-10 weeks old mice were used to yield a single cell population. After one passage, fluorescence activated cell sorting (FACS) and flow cytometry analysis was performed.

extract_protocol:
Total RNA was extract from cells by Trizol (Life technologies corporation, Gaitherburg, MD, USA).
RNA libraries were prepared for sequencing using standard stranded Illumina paired-end protocols

treatment_protocol: Cells were incubated with anti-CD31-allophycocyanin, anti-CD45-allophycocyanin, and anti-Ter119-allophycocyanin (BD Pharmingen, San Diego, CA) for 20 min on ice. For cell viability, propidium iodide (BD Pharmingen) was added. FACS was next performed using Beckman MoFlo (Beckman, Indianapolis, IN) and analyzed using Summit Software (PrismHR, Hopkinton, MA). Gating strategies were performed to isolate either PDGFRα- (CD31-CD45-Ter119-mTdtomato+) or PDGFRα+ (CD31-CD45-Ter119-mGFP+) cells. Cells were resuspended in Trizol (Life technologies corporation, Gaitherburg, MD, USA) for RNA isolation.

value: periosteal stromal cells

tag: pdgfra expression

value: PDGFRa-


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A13_MemorySeq384_2_S13

description:
edge_df.csv
NovaSeq 5000


title: A010_31.1_2_dko

source_name: E12.5 UB MAPK/ERK-deficient 1


title: A015_ 25.3_1_ctrl

source_name: E12.5 UB control 2

value: UB - HoxB7Cre-GFP;Mek1fl/+;Mek2+/+


title: scyl tethers replacement2

city: Princeton

first: Mike

last: Levine

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
Library strategy: Micro-C
Micro-C data was analyzed using the 4D Nucleome Hi-C analysis pipeline. Briefly, paired-end reads were mapped to the dm6 reference genome using BWA v0.7.17 [Li and Durbin, 2009], and alignments were filtered using pairtools v0.2.2 to retain only uniquely-mapping reads with alignment quality ≥3. Reads were assigned to 100bp genomic bins, and “inward”/”outward” reads assigned to adjacent bins (separated by less than 50bp) were removed. Matrix aggregation and normalization were performed using Cooler v0.8.3 [Abdennur and Mirny 2019], using the built-in ICE balancing method. Matrices were visualized using HiGlass [Kerpedjiev et al. 2018]. Visual inspection of contact matrices showed high concordance between biological duplicates, which were therefore pooled to generate final high-coverage contact matrices for each genotype.
Genome_build: dm6
Supplementary_files_format_and_content: cool,validpairs

organism: Drosophila melanogaster

source_name: nc14 embryo

growth_protocol: Embryos were collected on yeasted apple juice plates at 25˚C. Following two 1-hour pre-lays, embryos were collected for 45 mins and subsequently incubated at 25˚C for 2 hours to enrich for nc14 embryos.

extract_protocol:
Chromatin was digested with a pre-determined amount of Micrococcal Nuclease (Worthington Biochem) to yield a 90% mononucleosome / 10% dinucleosome ratio given the appropriate number of embryos.
Micro-C libraries were constructed as previously described [Hsieh et al. 2020], with the following modifications.
Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100nt Flowcell (read length 50 bases per mate, 6-base index read).

treatment_protocol: Embryos were collected in nylon mesh sieves, dechorionated for 3 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass scintillation vials containing 6 mL PBST (0.1% Triton-X in PBS), 7.5 mL N-heptane, and 1.5 mL fresh 16% formaldehyde. Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 5.5 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction. Embryos were washed twice with >15mL PBST and stored at 4˚C while an additional 2-3 collection rounds were carried out (45 mins each). Pooled embryos were subjected to a secondary crosslinking in 15 mL DSG+EGS (ThermoFisher, 3 mM each) at room temperature for 45 mins on a rotating mixer. Following quenching by addition of 5.5 mL 2M Tris-HCl pH7.5 and rotation for 5 mins, the embryos were washed twice with PBST and stored at 4˚C overnight. Samples were hand-sorted the following day under a dissection microscope to remove inappropriately staged embryos, snap-frozen in liquid nitrogen and stored at -80˚C.

tag: developmental stage

value: embryo

value: scyl-tethers-del


title: scyl/chrb - control2

value: yw


title: PDGFRα+ Replicate  1

source_name: Mouse CD31-CD45-Ter119-PDGFRα+ periosteal stromal cells

value: PDGFRa+


title: A014_ 22.12_2_ctrl

source_name: E12.5 UB control 1


title: PDGFRα+ Replicate 2


title: A016_ 25.3_3_ctrl

source_name: E12.5 UB control 3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A12_MemorySeq384_3_S492

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: knrl/kni - control1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A11_MemorySeq384_3_S491

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A12_MemorySeq384_2_S12

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A11_MemorySeq384_2_S11

description:
edge_df.csv
NovaSeq 5000