title: mRNA-seq ΔgcvB 10 mg/ml KSG

city: San Francisco

first: Yan

last: Zhang

state: CA

address: 600 16th Street

department: Microbiology and Immunology

institute: UC San Francisco

data_processing:
Library strategy: Ribo-seq
Raw reads were first filtered for quality and the linker sequence was removed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
The sequences were then mapped to the E. coli MG1655 genome (NC_000913.2.fna) obtained from the NCBI Reference Sequence Bank using Bowtie v. 1.2.3 (http://bowtie-bio.sourceforge.net/index.shtml) allowing for no more than two mismatches. Reads mapped to more than one locus were discarded. Ribo-seq reads were assigned to the 3’ end of the reads, and then adjusted by a shift of -12nt, so it reflects the location of the first base of A-site codon. RNA-seq reads were similarly mapped to E. coli MG1655 genome. Uniquely mapped reads were equally assigned to all the bases that each read covers. For example, for a RNA-seq read that is N-nt long, all the bases covered by the read were given a score of 1/N.
To calculate mRNA abundance, the number of mRNA-seq reads mapped to a gene was normalized by the length of the gene and the total number of reads that mapped to the genome.
The protein synthesis rate of individual ORFs was measured by the average Ribo-seq signal across the ORF body (excluding the first and last 6 amino acids to remove effect of translation initiation and termination), normalized by the total number of Ribo-seq reads that mapped to all ORF bodies across genome, and adjusted by the different overall translation level quantified by the rate of  [35S]-L methionine incorporation.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Wiggle files with two columns: first column containing chromosome positions and second column containing the number of reads mapped to the position.

molecule: polyA RNA

organism: Escherichia coli

source_name: Bacteria

growth_protocol: E. coli MG1655 ΔgcvB cells were grown overnight at 37˚C in MOPS rich defined medium lacking methionine (Teknova). The cultures were then diluted to an OD600 = 0.005 in fresh medium and grown until OD600 reached 0.35 (mid-log phase) at 37˚C.

extract_protocol:
200 mL of culture was rapidly filtered through a Whatman cellulose nitrate membrane with 220 nm pore size (GE Healthcare, 7182-009) and the cell pellet was flash-frozen in liquid nitrogen. Cells were pulverized in 10mL canisters pre-chilled in liquid nitrogen with 600 µL of frozen lysis buffer (10 mM MgCl2, 100mM NH4Cl, 20mM Tris-HCl pH 8.0, 0.1% NP-40, 0.4% Triton X-100, 100 U/mL DNase I, 1mM chloramphenicol) using QIAGEN TissueLyser II (5 cycles of 3 min at 15 Hz). Pulverized lysate was clarified by centrifugation at 16,000×g for 10 min at 4˚C. Clarified lysate containing 0.5 mg of RNA was digested for 1 h with 750 U of S7 micrococcal nuclease (Roche, 10107921001) at 25˚C. The reaction was quenched by adding EGTA to 6 mM and moved onto ice. Undigested lysate containing 0.14 mg of RNA was incubated without nuclease as control. The polysome profile of control samples was obtained by centrifugation through a 7%-47% sucrose gradient at 35,000 rpm for 2.5 hr at 4˚C. The monosome fraction in the digested samples was collected from the sucrose gradient and was purified by hot-phenol extraction. Ribosome-protected mRNA fragments were isolated by size excision on a Novex 15% TBE-Urea gel (Invitrogen, EC6885BOX). Fragments with size ranging from 25 to 35 nt were excised and extracted. For mRNA-seq performed in parallel with ribosome profiling, total RNA was phenol extracted from the same lysate. Short RNA molecules (sRNA and tRNA) and ribosomal RNA were removed from the total RNA with MEGAclear transcription clean-up kit (Invitrogen, AM1908) and MICROBExpress bacterial mRNA enrichment kit (Ambion, AM1905), respectively. mRNA was randomly fragmented using RNA Fragmentation Reagents (Ambion, AM8740) by incubating at 95˚C for 1 min 45 sec. The fragmented mRNA sample was size selected by running a Novex 15% TBE-Urea gel and excised between 25 and 45 nt.
RNA fragments were dephosphorylated using 20 U of T4 polynucleotide kinase (New England Biolabs, M0201S) at 37˚C for 1 hr. 20 pmol of RNA were ligated to 1 µL of 100 µM oligonucleotide Linker-1 (5’ rApp/CTGTAGGCACCATCAAT/3’ddC/) using truncated T4 RNA ligase 2 K277Q (New England Biolabs, M0351S) at 37˚C for 3 hr. The ligated products were isolated by size excision on a Novex 10% TBE-Urea polyacrylamide gel (Invitrogen, EC6875BOX). cDNA was generated by reverse transcription using Superscript III (Invitrogen, 18080093) at 50˚C for 30 min and the primer RT, and isolated by size excision on a 10% TBE-Urea polyacrylamide gel. Single-stranded cDNA was circularized with CircLigase ssDNA Ligase (Epicenter, CL4111K) at 60˚C for 2 hr. For ribosome profiling, circularized ssDNA molecules containing ribosomal RNA fragments were further removed using biotin-linked DNA oligos Biot-1 to Biot-4 and MyOne Streptavidin C1 Dynabeads (Invitrogen, 65001). The remaining circularized ssDNA was used as template for PCR amplification using Phusion High-Fidelity DNA polymerase (NEB, M0530S) with the universal primer Uniseq and indexing primers Index. After 8–10 rounds of PCR amplification, the library was size selected in a Novex 8% TBE gel (Invitrogen, EC62152BOX) and the target (168-178 bp for Ribo-seq and 168-188 bp for RNA-seq) products were eluted. The concentration and quality of the library was assessed using an Agilent High Sensitivity DNA Kit (Agilent, 5067-4626). Sequencing was performed on an Illumina HiSeq 4000 system.

treatment_protocol: For KSG-treated samples, KSG powder was dissolved in medium and added to log-phase culture to final concentration of 1 mg/ml or 10 mg/ml. Cultures were kept shaking at 37˚C for 2.5 min.

value: MG1655 delta-gcvB

value: 10 mg/ml KSG for 2.5 min

tag: molecule subtype

value: mRNA


title: knrl/kni - control2

status: Public on Feb 02 2022

type: SRA

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

country: USA

institute: Princeton University

library_source: genomic

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

molecule: genomic DNA

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

tag: tissue

value: embryo

tag: genotype

value: yw


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A10_MemorySeq384_3_S490

city: Cambridge

first: Xiaojie

last: Qiu

state: MA

address: 455 Main St, Cambridge, MA

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: mRNA-seq ΔgcvB untreated

tag: strain


title: knrl/kni - knrl tethers replacement2

value: knrl-tether-del


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: PDGFRα- Replicate 2

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.

organism: Mus musculus

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.

tag: cell type

value: periosteal stromal cells

tag: pdgfra expression

value: PDGFRa-


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A10_MemorySeq028_S869

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, A10_MemorySeq384_2_S10

description:
edge_df.csv
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: SFL_1

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome astMex_2.0 with STAR aligner (version 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (version v1.3.0 )
Genome_build: Astyanax mexicanus 2.0
Supplementary_files_format_and_content: TPM gene expression in text file

organism: Astyanax mexicanus

source_name: 5 month old Surface liver

extract_protocol:
According to manufacturer's imstructions Qiagen RNeasy RNA mini kit.
RNA was extracted using Qiagen RNeasy kit according to manufacturer’s instructions. Libraries were generated from 250ng of high-quality total RNA, as assessed using the Bioanalyzer (Agilent).  Libraries were made according to the manufacturer’s directions using the TruSeq Stranded mRNA Library Prep kit (48 Samples) (Illumina, Cat. No. 20020594), and TruSeq RNA Single Indexes Sets A and B (Illumina Cat. No. 20020492 and 20020493). Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, quantified, and sequenced as 75bp single reads on a high-output flow cell using the Illumina NextSeq 500 instrument. Following sequencing, Illumina Primary Analysis version RTA 2.4.11 and bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.

value: Liver

tag: morphotype

value: Surface


title: Ribosome profiling ΔgcvB 1 mg/ml KSG

value: 1 mg/ml KSG for 2.5 min

value: Ribosome protected mRNA


title: mRNA-seq ΔgcvB 1 mg/ml KSG


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Ribosome profiling ΔgcvB 10 mg/ml KSG


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: CFL_2

source_name: 5 month old Pachón liver

value: Pachón


title: SFL_2


title: SFL_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: CFL_3


title: CFL_1


title: PN121-4: GDF5+ cells

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

data_processing:
Raw mRNA sequence reads were pre-processed using Cutadapt (v1.15) to remove bases with quality scores < 20 and adapter sequences, followed by alignment of clean RNA-seq reads to GRCh38.83 with STAR (v2.5.3a). Uniquely-mapped reads overlapping genes were counted by HTseq-count with default parameter using annotation from ENSEMBL v83. Gene normorlized reads count and RPKM value were calculated by DESeq2 and RSEM (v1.3.0).
Genome_build: RNA-seq: GRCh38.83
Supplementary_files_format_and_content: Merged file: tab-delimited text files include FPKM values for each Sample

source_name: H9 hESCs

growth_protocol: GDF5+ cells: The FACS-isolated KDR-/loPDGFR+ cells maintained in FSbC medium (i.e., SOX9+ cells) were passaged at 3 x 104 cells/cm2 and 3-15h later the medium was changed to CDM-AO2 supplemented with 15 ng/ml PDGF, 100 ng/ml noggin, and 2 µM CHIR99021 (PNC medium). The cells were passaged twice in PNC (approximately 7-10 days after the FSbC to PNC transfer). Between 3 and 15h after the second passage, the medium was changed to PN (PNC minus CHIR99021). The PN culture was maintained for another 3-6 days.

extract_protocol:
Total RNAs from four independent sets of FSbC-expanded SOX9+ cells (passage 4 to 6, derived from H9 hESCs), and four independent sets of PNC/PN-treated GDF5+ cells were extracted with an RNeasy mini kit (Qiagen), followed by DNaseI treatment, and then RNA purification
Poly (A)-tailed messenger RNA was enriched and the RNA-seq library was prepared in the UTHealth Cancer Genomics Core by following the instructions of KAPA mRNA HyperPrep Kit (KK8581, Roche Holding AG, Switzerland) and KAPA Unique Dual-indexed Adapter kit (KK8727, Roche).
RNA-seq was performed using the Illumina Nextseq550 system with the 75 bp pair-ended running mode

tag: Sex

value: F

value: human joint progenitor-like cells


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: PN121-3: GDF5+ cells


title: Ribosome profiling ΔgcvB untreated

value: MG1655 delta-gcvB


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: PN121-1: GDF5+ cells


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: FSbC-4: SOX9+ cells

growth_protocol: SOX9+ cells: The FACS-isolated KDR-/loPDGFR+ progeny of hPSCs were cultured on a gelatin-fibronectin coated plate in CDM supplemented with 2.5 g/ml catalase and 2 g/ml heparin (Sigma) (i.e., CDM-AO2), and protein and small molecule factors: 10 ng/ml FGF2, 5 ng/ml PDGF, 5-7.5 M SB431542 and 2 µM CHIR99021 (FPSbC medium), at 37oC under 5% CO2 /4-5% O2 and passaged every 2-3 days at 3 x 104 cells/cm2 using TrypLE Select. At passage 1, the expanded cells were either stored in liquid nitrogen, or continued in culture to passage 2 when the medium was changed to FSbC (i.e., FPSbC minus PDGF).

value: human embryonic chondroprogenitors


title: FSbC-3: SOX9+ cells


title: FSbC-2: SOX9+ cells


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: FSbC-1: SOX9+ cells


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: PN121-2: GDF5+ cells


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_WDR77_TAM_1

city: Boston

first: Kevin

last: Struhl

address: 240 Longwood Ave

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

data_processing:
base-calling performed by Illumina Hiseq 2000
trimmed adapter sequences, ambiguous ‘N’ nucleotides (the ratio of “N” > 5%), and low-quality tags (quality score < 20)
aligned trimmed reads against the GENCODE v30 reference transcriptome using STAR
Counts were normalized to TPM (transcripts per million RNA molecules) using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression quantification

source_name: Breast cell line

growth_protocol: MCF-10A-ER-Src cells (Iliopoulos et al., 2009; Iliopoulos et al., 2010) were grown in DMEM/F12 without phenol red (Thermo Fisher Scientific, 11039-047) + 5% charcoal stripped FBS (Sigma, F6765) + 1% pen/strep (Thermo Fisher Scientific, 15140122)+20 ng/ml EGF (Peprotech, AF-100-15) + 0.5 μg/ml Hydrocortisone (Sigma, H-0888) + 0.1 μg/ml cholera toxin (Sigma, C-8052) + 10 μg/ml insulin (Sigma, 10516).

extract_protocol:
RNA was prepared used mRNeasy Mini Kit (Qiagen, No. 217004).
RNA-seq libraries were generated using TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).

treatment_protocol: 1-0.4 μM Tamoxifen (Sigma, H7904) + 2-4 μM AZD0530 (Selleck Chemicals, S1006) were used to induce the transformation.

value: MCF10A ER-Src cells

tag: transformation status

value: transformed


title: RNA-seq_WDR77_ETH_1

value: non-transformed


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: RNA-seq_TCF4_TAM_1


title: RNA-seq_TCF4_TAM_2


title: RNA-seq_TCF4_ETH_1


title: RNA-seq_WDR77_TAM_2


title: RNA-seq_WDR77_ETH_2


title: RNA-seq_TCF4_ETH_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_MAFB_TAM_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_MAFB_ETH_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_MAFB_ETH_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_ß-catenin_TAM_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_ß-catenin_ETH_2


title: RNA-seq_ß-catenin_TAM_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_MAFB_TAM_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: LEF_TAM_rep2

data_processing:
base-calling performed by Illumina Hiseq 2000
FASTQ reads were aligned to the human reference genome (GRCh38) using Bowtie2
samtools with MAPQ threshold 30 was used to remove low quality reads and picard-tools was used to remove PCR duplicates.
SPP was used with --cap-num-peak 300000 to call peaks and IDR with --soft-idr-threshold 0.05 was used to identify peaks conserved across replicates. If only one replicate passed quality control, pseudo-replicates were generated by randomly splitting the data in half for further processing.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak file

extract_protocol:
Cells were dual cross-linking with a mixture of 2 mM each of ethylene glycol bis (succinimidyl succinate) (EGS) and disuccinimidyl glutarate (DSG) and 1% formaldehyde. Chromatin was digested with 60 units MNase (New England Biolabs, M0247S) at 37 0C for 10 minutes and then sonicated using Branson Microtip Sonifier 450 (4X15 second at output 4.5 and duty cycle 60%) to the sizes mostly between 150-500 bp.
50 μg chromatin, antibodies for transcription factors (listed in Table S6), and 15 μl Dynabead protein G (Thermo Fisher Scientific, 10004D) was used for the chromatin immunoprecipitation (ChIP)

tag: chip antibody

value: LEF1 (Cell Signaling, Cat. #76010)


title: LEF_TAM_rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WDR77_TAM_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: TCF4_ETH_1

value: TCF4/TCF7L2 (Cell Signaling, Cat. #2569)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: LEF_ETH_rep1


title: TCF4_TAM_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: RNA-seq_ß-catenin_ETH_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: LEF_ETH_rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, P12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: ß-catenin_TAM

value: Beta-catenin (Cell Signaling, Cat#9581)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WDR77_TAM_1


title: MAFB_TAM_2

value: MafB (SCBT, Cat# sc-10022)


title: TYKnu_Azacitidine carboplatin_flowcell 2

city: New Lambton Heights

first: Michelle

last: Brown

state: New South Wales

address: Hunter Medical Research Institute, Lot 1 Kookaburra Circuit

country: Australia

institute: University of Newcastle

data_processing:
Reads trimmed with Cutadapt to remove adapter sequences, primers, poly-A tails and low quality reads.
.Reads aligned to a reference genome GRCh37/hg19 using the sequence alignment tool HISAT2
Differential expression analysis between the untreated and treatment groups performed using DESeq2 package v3.12.
Genome_build: GRCh37/hg19

source_name: ovarian cancer cell line

growth_protocol: Cell lines grown in DMEM supplemented by 10% FCS, and supplemented with penicillin (100units/mL), streptomycin (100µg/mL), L-glutamine (2mM), HEPES (10µM), and sodium bicarbonate (0.075%)

extract_protocol:
Cell lines  were trypsinised from flasks and RNA was extracted using Trizol reagent. Illumina TruSeq Stranded Total RNA Gold (Cat# 20020598) was used with at least 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Australian Genome Research Facility (AGRF), Australia

treatment_protocol: Cell lines  were incubated at 37c in 5% CO2 and grown to 30-40% confluence  before treatment with 0.5 µM azacitidine every 24hr for 72hr, followed by 20µM carboplatin for 48hr.

value: TYKnu

value: Female

tag: tp53 mutation

value: TP53c.524G>A;  p.Arg175His

tag: kinase mutation

value: NRAS c.35G>A; p.Gly12Asp   NRAS c.181C>A; p.Gln61Lys

value: Treated with 5µM azacitidine and 20µM carboplatin


title: ß-catenin_ETH


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: TCF4_TAM_1


title: TCF4_ETH_2


title: MAFB_ETH_2


title: WDR77_ETH_1


title: OVCAR4_Azacitidine carboplatin_flowcell 2

value: TP53 c.388C>G; p.Leu130Val


title: OAW28_Azacitidine carboplatin_flowcell 2

value: TP53 c.455delC; p.Pro152Argfs*18


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: TYKnu_Untreated_flowcell 2

value: Untreated


title: OVCAR4_Untreated_flowcell 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: MAFB_ETH_1

value: MCF10A ER-Src cells


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: WDR77_ETH_2


title: MAFB_TAM_1

value: transformed


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: COV362_Azacitidine carboplatin_flowcell 2

tag: brca mutation

value: TP53 c.659A>G; p.Tyr220Cys


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
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, O2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: OAW28_Untreated_flowcell 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: OVCAR4_Azacitidine carboplatin_flowcell 1


title: OVCAR4_Baseline_flowcell 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: OAW28_Baseline_flowcell 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: OAW28_Azacitidine carboplatin_flowcell 1


title: TYKnu_Baseline_flowcell 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: COV362_Baseline_flowcell 1


title: COV362_Untreated_flowcell 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: COV362_Azacitidine carboplatin_flowcell 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: TYKnu_Azacitidine carboplatin_flowcell 1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_33PSU_1

type: RNA

city: Sopot

first: Magdalena

last: Malachowicz

address: Powstańców Warszawy

country: Poland

institute: Institute of Oceanology Polish Academy of Sciences

hyb_protocol: Hybridized according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned in an Agilent Technologies Scanner G2505C US10353831, according to the manufacturer’s protocol GE2_1010_Sep10

data_processing: Data were extracted using the Agilent Feature Extraction software (version 10.10.1.1) following the Agilent protocol GE2_1010_Sep10. Arrays normalization was performed using the Limma package in R. The raw mean signal (gMeanSignal) was background corrected (normexp method). Next lowess and quantile normalization were performed.

organism: Gadus morhua

source_name: Gills of cod from Kiel Bight

label_protocol: Amplified and labeled according to Agilent Two-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: RNA was isolated using the ISOLATE II RNA Mini Kit (Bioline). Concentration of extracted RNA was determined at 260 nm on microplate using the Epoch Microplate Spectrophotometer (BioTek Instruments). The RNA integrity was verified using an Agilent Bioanalyser (Agilent Technologies)

treatment_protocol: Fish were transported in containers with sea water to the Marine Station of the University of Gdansk in Hel for the experiment. Briefly, fish were divided into two tanks, termed here as salinity reference: GDA 8PSU and KIEL 18PSU and acclimated for 14 days in 10°C, in recirculated water with natural salinities of the geographic origin. Next, fish from each localization were divided and transferred to separate nine tanks and again acclimated. Two of the nine tanks represented controls (salinity reference) for fish from Gdansk Bay and Kiel Bight. In other tanks salinity was reduced or elevated. In all tanks, salinity was changed gradually (1PSU per hour) in order to minimize acute stress response.

tag: location

value: Kiel Bight

tag: tissue

value: gill

tag: salinity

source_name: mix of all samples


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: cell line

tag: treatment


title: KIEL_gill_33PSU_6

tag: gender


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: age

tag: ethnicity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_33PSU_5


title: KIEL_gill_33PSU_3

value: male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_33PSU_2


title: KIEL_gill_33PSU_4


title: KIEL_gill_33PSU_7


title: KIEL_gill_28PSU_9


title: KIEL_gill_28PSU_11


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_28PSU_10


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_28PSU_5


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_28PSU_8


title: KIEL_gill_28PSU_7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_28PSU_4


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, O11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_8PSU_11


title: KIEL_gill_8PSU_7


title: KIEL_gill_8PSU_6


title: KIEL_gill_28PSU_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_8PSU_9


title: KIEL_gill_28PSU_2


title: KIEL_gill_28PSU_12


title: KIEL_gill_28PSU_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_28PSU_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_8PSU_10


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_3PSU_7


title: KIEL_gill_8PSU_2


title: KIEL_gill_8PSU_8


title: KIEL_gill_8PSU_3


title: KIEL_gill_8PSU_1


title: KIEL_gill_8PSU_4


title: KIEL_gill_8PSU_5


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_3PSU_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_3PSU_2


title: KIEL_gill_3PSU_8


title: KIEL_gill_3PSU_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_3PSU_5


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_3PSU_4


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_5


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_9


title: AK-co

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

country: China

institute: Institute of hydrobiology, CAS

description: AK-co

data_processing:
Adaptors of raw reads were trimmed by Trim-Galore (version 0.4.0)
mRNA-Seq data processing: Trimmed-reads were mapped to the Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads) using TopHat (version 2.0.9).Genes expression values were quantify to the number of fragments per kilobase of exon per million fragments mapped (FPKM) using Cuffdiff (version 2.1.1).
Genome_build: Tetrahymena themophila MAC genome (version 2014: http://ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: Reads counts table matrix

organism: Tetrahymena thermophila

source_name: Cells

growth_protocol: Tetrahymena thermophila cells were grown in SPP medium at 30°C.  For conjugation, log-phase growing cells (~200k cells/ml) of two different mating types were washed, starved (~16 hrs) and mixed in 10 mM Tris buffer at 30°C. For costimulation, cells were mixed in 9:1 ratio.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols. First strand specific libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kit (RS-122-2101). The Poly-A tailed mRNA as purified using the Sera‐Mag Magnetic Oligo(dT) Beads. The mRNA fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, A tailing, adaptor ligation and PCR amplification were performed according to the stranded mRNA sample preparation guide of the kit.  Sequencing (Single-end (52X1) for C3 and C6, Paired-end (101x2) FOR C10) was performed using an Illumina HiSeq 2000 sequencer (DNA Sequencing Core of University of Michigan).

tag: strain

tag: genotype

value: MTA knockout

tag: Stage

value: costimulation


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_4


title: BK-S

description: BK-S

value: MTB knockout

value: Starvation


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_3


title: KIEL_gill_control_8


title: BK-co

description: BK-co


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_3PSU_1


title: Wildtype-S

description: WT-S

value: WT


title: KIEL_gill_control_1


title: AK-S

description: AK-S


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 3D7_AP2-EXP2-GFP_S_input

city: Shanghai

first: Mei

last: Jiang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

data_processing:
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
Trimmed ChIP-seq reads were mapped to the P. falciparum 3D7 reference genome (release 47) using Bowtie2 v2.4.2 and default parameters.
Peaks were identified using the callpeak function of MACS2 v2.2.7.1 and a q-value cutoff of 0.05. The option --call-summits was applied to the detection of transcription factor binding peaks. Normalized signal tracks of log2-transformed ChIP/input fold enrichment were generated with MACS2 bdgcmp function.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: bigWig files of log2-transformed ChIP/input fold enrichment
Supplementary_files_format_and_content: BED files of peak summits

organism: Plasmodium falciparum

source_name: schizont (40–45 hpi)

growth_protocol: Parasites were cultured in fresh O-type human erythrocytes in complete RPMI 1640 medium (Gibco) with 0.5% Albumax I (Invitrogen) and a gas phase maintained under 5% CO2, 5% O2 and 90% N2 at 37°C.

extract_protocol:
Synchronized parasites were harvested at the schizont stage (40-45 hpi) and crosslinked immediately with 1% paraformaldehyde (Sigma) by rotating for 10 minutes at 37°C, which was then quenched with 0.125 M glycine for 5 minutes on ice. Parasite nuclei released from infected red blood cells were sheared for 20-30 minutes using an M220 sonicator (Covaris) at 5% duty cycle, 200 cycles per burst, and 75 W of peak incident power to generate 100-500 bp fragments in length. 20 µL of the sheared chromatin was reserved as the input control. Chromatin was subsequently immunoprecipitated overnight at 4°C using 0.5 µg of antibodies against GFP (Abcam, ab290) and protein A/G magnetic beads (ThermoFisher Scientific, 26162). After extensive washes, the immunoprecipitated materials were eluted with elution buffer. Then crosslinking was reversed by overnight incubation at 45°C, followed by treatments of RNase A at 37°C for 30 minutes and Proteinase K at 45°C for two hours. The ChIPped DNA was finally purified according to the MinElute PCR purification kit (Qiagen, 28006) instructions.
1.5 ng of ChIP-DNA was subjected to end-repair (Epicentre, ER81050), 3' adenylation (NEB, M0212L), and adapter ligation (NEB, M2200L). Then after purification with Agencourt AMPure XP beads (Beckman Coulter), libraries were amplified using the KAPA HiFi PCR Kit (KAPA Biosystems, KB2500) under the following conditions: 1 minute of initial denaturation at 98°C, 12 cycles of 10 seconds at 98°C and 1 minute at 65°C, and 5 minutes of final extension at 65°C.

treatment_protocol: Ring stage cultures were regularly synchronized by treatments of 5% sorbitol.

value: whole body

tag: developmental stage

value: schizont (40-45 hpi)

value: Pf 3D7

tag: host

value: Homo sapiens


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 3D7_AP2-EXP2-GFP_S_AP2-EXP2_ChIP-seq, Rep2

tag: chip antibody

value: anti-GFP (Abcam, ab290)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Wildtype-co

description: WT-co


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Wildtype-C0.5

value: Conjugation 0.5h


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: KIEL_gill_control_10


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_33PSU_8

source_name: Gills of cod from Gdansk Bay

value: Gdansk Bay


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: neutrophil lineage differentiation in the presence of  ATRA


title: 3D7_AP2-EXP2-KD(-)GlcN_S_RNA-seq, Rep2

description: Parasites were not treated with glucosamine (GlcN)

data_processing:
To remove residual adapters and low-quality bases, sliding window trimming was performed on reads with Trimmomatic v0.39 using a window size of 4 and average quality of the window above 15. A minimum read length of 50 bp and average read quality above 20 were required after read clipping.
HISAT2 v2.2.1 was employed to align trimmed RNA-seq reads to the P. falciparum 3D7 reference genome (release 47) with the guide by the gene annotation, using default parameters except --max-intronlen 5000 --dta --rna-strandness RF.
StringTie v2.1.2 was used to count reads mapped to each gene.
Genome_build: Pf 3D7 v47
Supplementary_files_format_and_content: matrix table with raw gene counts for every gene and every sample

extract_protocol:
Highly synchronous parasites were collected in TRIzol at the ring (10–15 hpi), trophozoite (25–30 hpi), and schizont (40–45 hpi) stages from the next cycle, respectively. Total RNA purification was conducted with the Direct-zol RNA Kit (Zymo Research).
Libraries were prepared for strand-specific RNA sequencing by poly(A) selection with the KAPA mRNA Capture Beads (KAPA Biosystems) first and then RNA fragmentation to a size of 300–400 nucleotides. Subsequent library preparation steps followed the protocol of the KAPA Stranded mRNA-Seq Kit Illumina platform (KAPA Biosystems, KK8421).

treatment_protocol: Parasites were tightly synchronized to a 5-hour window by isolating schizonts over a 40% and 70% Percoll-sorbitol gradient followed by sorbitol treatment 5 hours post re-invasion. Synchronized ring-stage parasites were diluted at 0.5% parasitemia with 2% hematocrit and cultured in the presence or absence of 5 mM glucosamine.


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: 3D7_AP2-EXP2-KD(-)GlcN_S_RNA-seq, Rep3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_33PSU_5


title: GDA_gill_33PSU_6


title: GDA_gill_33PSU_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_33PSU_7

value: female/male


title: KIEL_gill_control_2

value: Kiel Bight

value: gill


title: 3D7_AP2-EXP2-GFP_S_AP2-EXP2_ChIP-seq, Rep1


title: 3D7_AP2-EXP2-KD(-)GlcN_S_RNA-seq, Rep1


title: 3D7_AP2-EXP2-KD(-)GlcN_T_RNA-seq, Rep2

source_name: trophozoite (25–30 hpi)

value: trophozoite (25-30 hpi)


title: GDA_gill_33PSU_3

value: male


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_33PSU_4


title: 3D7_AP2-EXP2-KD(+)GlcN_S_RNA-seq, Rep3

description: Parasites were treated with glucosamine (GlcN), and PfAP2-EXP2 protein level was dramatically reduced


title: 3D7_AP2-EXP2-KD(+)GlcN_S_RNA-seq, Rep2


title: GDA_gill_33PSU_1


title: 3D7_AP2-EXP2-KD(-)GlcN_R_RNA-seq, Rep1

source_name: ring (10–15 hpi)

value: ring (10-15 hpi)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, N10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 3D7_AP2-EXP2-KD(-)GlcN_T_RNA-seq, Rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_18PSU_9


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 3D7_AP2-EXP2-KD(+)GlcN_S_RNA-seq, Rep1


title: 3D7_AP2-EXP2-KD(+)GlcN_T_RNA-seq, Rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_18PSU_7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_18PSU_4


title: GDA_gill_18PSU_6


title: GDA_gill_18PSU_8


title: GDA_gill_18PSU_3


title: GDA_gill_18PSU_5


title: 3D7_AP2-EXP2-KD(+)GlcN_T_RNA-seq, Rep2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: 3D7_AP2-EXP2-KD(+)GlcN_R_RNA-seq, Rep1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: treated 3

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

department: Animal Science

institute: Michigan State University

data_processing:
The library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Clean data (clean reads) were obtained by removing reads containing adapter, reads  containing ploy-N and low quality reads from raw data.
Index of the reference genome (GRCm38 - mm10) was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And  then FPKM of each gene was calculated based on the length of the gene and reads count  mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Genome_build:   GRCm38 - mm10
Supplementary_files_format_and_content: Gene_count, Gene_fpkm (excel sheets)

source_name: Oocytes

growth_protocol: In vivo work, mice colony were maintained on Teklad normal food pellet and autoclaved water ad libitum

extract_protocol:
Total RNA was extracted from fresh frozen oocytes using SMARTV4 kit followed by the manufacturer’s instructions by Novogene.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: 21 day old pre-pubertal C57BL/6J mice (Jackson Laboratory) were subjected to daily intraperitoneal (IP) injection of AMH (300ng; Recombinant Mouse Mullerian-inhibiting factor (Amh) expressed in E.coli

value: AMH treated

tag: cell type

value: Oocytes

value: 6-7 weeks


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: treated 1


title: treated 2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: control 2

value: Control


title: control 1


title: control 3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_10


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_9


title: S35-LOFDSP

first: Hyun-Hwan

last: Jeong

state: TX

address: 7000 Fannin St

data_processing:
FASTQC was used for the quality control check.
STAR was used to process the sequence alignment to the Musmusculus genome (Genome . STAR generated read counts for each gene.
DESeq2 was used to identify differentially expressed genes.
Genome_build: mm10 (Gencode version M25)
Supplementary_files_format_and_content: text file with raw gene read counts

source_name: Cardiomyocyte

extract_protocol:
Total RNA was extracted from mouse ventricular cardiac myocytes using the miRNeasy Mini Kit (Qiagen, Cat # 217004).
RNA extracts with an RNA Integrity Number (RIN) value of >8, determined using an Agilent Bioanalyzer RNA chip, were used to construct sequencing libraries. Strand-specific ribosomal RNA depleted sequencing libraries were generated using TruSeq stranded total RNA library preparation kit (Illumina Inc. Cat # 20020596). The libraries were sequenced as 75bp paired-end reads on an Illumina HiSeq 4000 instrument.
Ribosomal RNA depleted Total RNA seq  (Paired end)

value: LOFDSP (Myh6-MCM:DspF/F:Ctnnb1LoF)

value: C57BL/6 (mixed)


title: GDA_gill_18PSU_1


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_7


title: GDA_gill_18PSU_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_4


title: GDA_gill_3PSU_8


title: S33-GOFDSP

value: GOFDSP (Myh6-MCM:DspF/F:Ctnnb1GoF)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_6


title: S34-LOFDSP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S32-GOFDSP


title: S31-LOFDSP


title: S30-LOFDSP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_2


title: S29-LOFDSP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_1


title: S28-DSP

value: DSP (Myh6-MCM:DspF/F)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_3PSU_5

value: Gdansk Bay


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
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, M13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

value: female


title: S27-DSP


title: GDA_gill_control_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_control_4


title: GDA_gill_control_3


title: NU1539iMNC

city: La Jolla

first: Erika

last: Lin

address: 9500 Gilman Dr,

department: Pediatrics

institute: University of California, San DIego

data_processing:
Sequencing output was processed using Ceto (NGS analysis system put together in a collaboration between the Bartom computational Lab, the Shilatifard lab, and other scientists at Northwestern University)
Aligned data was normalized and transformed using EdgeR.
Differentially expressed genes were assessed using DeSeq2.
Output files were visualized in the Morpheus browser. Hierarchical clustering of samples was performed and K-means clustering of genes were generated using 1000 iterations  was performed within the browser
WGCNA analysis was performed using the CEMiTool.
Filtered counts tables were normalized using VST.
Gene list output from K-means clustering the WGCNA was then used as input for GOrilla to search for significant gene ontology (GO) terms for biological processes, function, and components
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Umbilical cord blood

extract_protocol:
Umbilical venous cord blood collected at birth into a cord blood bag or EDTA tube. We stored cord blood  specimens at 4ºC and performed monocyte isolation within 36 hours of delivery.
RNA libraries were prepared for sequencing using standard Illumina protocols (NextSeq 500/550 High Output v2  kit)

tag: cell population

value: iMNC

value: Umbilical cord

tag: gestational age


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S24-GOFDSP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S26-DSP


title: GDA_gill_control_5

tag: location

value: gill


title: S25-GOFDSP


title: S23-GOFDSP


title: NU1497iMNC

tag: tissue


title: S22-DSP


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S21-LOF

value: LOF (Myh6-MCM:Ctnnb1LoF)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1521iMNC


title: NU1497cMNC

value: cMNC


title: GDA_gill_control_1

value: male

tag: salinity


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: cell line


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: treatment


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: gender


title: S19-DSP


title: NU1521cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: age


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000

tag: ethnicity


title: NU1539cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: GDA_gill_control_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, M19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1243iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1492cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S20-GOF

value: GOF (Myh6-MCM:Ctnnb1GoF)

tag: strain


title: NU1492iMNC


title: S15-LOF

tag: genotype


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S18-LOF


title: NU1393iMNC


title: S17-LOF


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S16-LOF


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1393cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1198iMNC


title: NU1243cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1242iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S14-CRE

value: CRE (Myh6-MCM)


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1241iMNC


title: S13-GOF


title: S11-GOF


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1242cMNC


title: S10-GOF


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1241cMNC


title: NU1198cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S8-CRE


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S9-CRE


title: S7-CRE


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1183iMNC


title: NU1152iMNC


title: S12-GOF


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1183cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1144cMNC


title: NU1152cMNC


title: S2-WT

value: WT


title: NU1144iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S5-WT


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K9_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S3-WT


title: S6-CRE


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S4-WT


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 904d - ind_15

city: Ankara

first: Mehmet

last: Somel

address: Dumlupınar Bulvarı No:1

department: Biology

country: Turkey

institute: Middle East Technical University

data_processing:
Raw sequencing reads were filtered with Trimmomatic to remove adaptor content with parameters: PE ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:1:0:8:true, SLIDINGWINDOW:4:15, MINLEN:25
Remaining high quality reads were aligned to reference genome GRCm38 using STAR-2.5.3 with parameters:  --sjdbOverhang 99 --outSAMattrIHstart 0 --outSAMstrandfield intronMotif --sjdbGTFfile GRCm38.gtf
Uniquely aligned reads were retrieved using: samtools -q 255
Expression levels were calculated as FPKM using cufflinks, yielding 51608 genes in total. Only the protein-coding genes were included in the analysis (using biotype feature of biomaRt) and the genes which are not detected (zero FPKM) in 25% or more of the samples (15/63) were excluded from the analysis, resulting in 15063 protein-coding genes in total.
FPKM values were 1+log2 transformed and quantile normalized using all the samples together.
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated files contain ENSEMBL gene ids and normalized expression levels for each sample

source_name: Skeletal Muscle

extract_protocol:
RNA sequencing was performed as previously described (Liu et al. 2016)  with slight modifications. Total RNA was extracted using Trizol reagent (Invitrogen).
For sequencing library construction, all samples were randomized first and prepared with TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instruction. Libraries were sequenced on the Illumina Hi-seq 4000 system in three lanes within one flow-cell, using the 150-bp paired-end module

value: Skeletal Muscle

tag: individual


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1142cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, L10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 654d - ind_14


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: S1-WT


title: Skeletal Muscle - 904d - ind_16


title: NU1138iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1138cMNC


title: Skeletal Muscle - 303d - ind_12


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K2_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K3_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 232d - ind_11


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K6_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 649d - ind_13


title: NU1139iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K3_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1142iMNC


title: NU1139cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K24_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1137iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K24_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 93d - ind_9


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K2_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1133cMNC


title: Skeletal Muscle - 93d - ind_8


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K23_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 61d - ind_7


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K4_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1132iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K22_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K23_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K21_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K22_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1133iMNC


title: Skeletal Muscle - 144d - ind_10


title: NU1137cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K4_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K20_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K20_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1123cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K1_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K1_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 11d - ind_4


title: Skeletal Muscle - 20d - ind_5


title: Skeletal Muscle - 5d - ind_3


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K18_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K18_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1123iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K17_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 32d - ind_6


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K16_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 2d - ind_2


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K21_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1121iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K17_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1132cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K15_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K19_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1121cMNC


title: Liver - 904d - ind_16

source_name: Liver

value: Liver


title: Liver - 904d - ind_15


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K16_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1097iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K19_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1122iMNC


title: NU1097cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K14_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K14_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Skeletal Muscle - 2d - ind_1


title: Liver - 654d - ind_14


title: NU1122cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K13_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Liver - 649d - ind_13


title: NU1094iMNC


title: NU1094cMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K12_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K15_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K12_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K13_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1084iMNC


title: Liver - 232d - ind_11


title: Liver - 303d - ind_12


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K11_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1084cMNC


title: NU1067cMNC


title: NU1067iMNC


title: Liver - 144d - ind_10


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J9_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K10_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K10_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Liver - 93d - ind_9


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J8_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J8_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J7_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J7_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1058iMNC


title: Liver - 93d - ind_8


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J6_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Liver - 32d - ind_6


title: NU1045iMNC


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J5_MemorySeq384_2

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Liver - 20d - ind_5


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, J5_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: Sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, K11_MemorySeq384_3

description:
HL60_memory_seq.h5ad
NovaSeq 5000


title: NU1045cMNC