title: inC-RNA-seq of L1210 single-cell derived colonies cultured in the presence of epigenetic drugs (CAGE_Colonies)

status: Public on Sep 11 2025

first: Ignas

last: Mazelis

address: 210 Longwood Avenue

department: System Biology

institute: Harvard Medical School

description: Library name: L1210_Clone_seq

data_processing:
BCL sequencing files received from Illumina BaseSpace portal were converted to raw FASTQ files for each of the 4 (R1, R2, R3, R4) sequencing reads without read trimming or masking by using bcl2fastq software (Illumina, v2.20.0.422). Raw FASTQ files were processed using a custom pipeline (available at https://github.com/AllonKleinLab/paper-data/tree/master/Mazelis2025_CAGEs). In brief, sequencing reads were demultiplexed based on Read1 index sequence (stored as read3) (index used: "Control_A_1":"ATAGAGAG", "Control_A_2":"AGAGGATA", "Control_A_3":"CTCCTTAC", "Control_A_4":"TATGCAGT", "Control_A_1":"TACTCCTT", "Control_A_2":"AGGCTTAG", "Control_A_3":"ATTAGACG", "Control_A_4":"CGGAGAGA", "Vorinostat1_1":"CTAGTCGA",  "Vorinostat1_2":"AGCTAGAA","Vorinostat1_3":"ACTCTAGG","Vorinostat1 4":"TCTTACGC","Vorinostat2_1":"CTTAATAG","Vorinostat2_2":"ATAGCCTT","Vorinostat2_3":"TAAGGCTC","Vorinostat2_4":"TCGCATAA","Decitabine1_1":"GTAACGTT","Decitabine1_2":"ACTGAGTT","Decitabine1_3":"ATACTCTT","Decitabine1_4":"GACAACTT","Decitabine2_1":"GAACGATT","Decitabine2_2":"AAGATTGT","Decitabine2_3":"AATCGGGT","Decitabine2_4":"TTGAGGGT","Azacytidine1_1":"AAGCTTCT", "Azacytidine1_2":"TATTGCCT","Azacytidine1_3":"CAGTCCCT","Azacytidine1_4":"ATGCGGAT","Azacytidine2_1":"CAAGTCAT","Azacytidine2_2":"ATATGCAT","Azacytidine2_3":"ATGGAAAT","Azacytidine2_4":"CTGCGTTG","Control_C_1":"AAGCGTAC", "Control_C_2":"TAGTGGAC","Control_C_3":"CGGACAAC","Control_C_4":"ATGGATTA","Control_C_1":"CCACATTA","Control_C_2":"GCAGGGTA","Control_C_3":"ATCCGCTA","Control_C_4":"TTCACATA","Control_B_1"…"TGAAATGA","Control_B_2":"AAACTCGA","Control_B_3":"ACCCACGA","Control_B_4":"CGACGTCA","Control_B_1":"TGTGCTCA","Control_B_2":"CTGGTGCA","Control_B_3":"TACCGGCA","Control_B_4":"ATGAAGCA"), and were filtered based on expected structure (all barcodes matching a barcode whitelist with hamming distance of 1). The demultiplexed reads were then processed using Trimmomatic (1) (with parameters: LEADING 28; SLIDINGWINDOW 4:20; MINLEN 20), followed by Poly-A length trim to 4 nt and selecting reads that are longer than MINLEN. For surviving reads, the fraction of length composed out of same base repeats (only considering > 5) was determined, rejecting reads whose fraction is greater than 0.5. Count matrices were generated using InDrops pipeline.
Count matrices were filtered by selecting barcodes with >2000 UMIs and fraction of mitochondrial counts being below 0.4. Mouse and human cells were filered based on gene expression. Read mapping and cell filtering based on counts and mitochondrial fraction were carried out as described above. Raw counts were then normalized to 10,000 counts per cell (CP10K). Highly variable genes were selected using Scanpy's implementation of the Seurat v3 approach (sc.pp.highly_variable_genes with flavor='seurat_v3'; 4,000 genes for K562 cells and 5,000 genes for L1210 cells; using unnormalized counts for variance calculations). Visualization by UMAP embedding. For visualization only, batch effects from library preparation and cell seeding were corrected using Harmony (Korsunsky et al., 2019) using the scanpy implementation, with the following non-default parameters: theta=4.0, lambda=10.0, and sigma=0.05. Harmony was applied to the 15 NMF program usages per cell. A nearest neighbor graph was constructed using the Harmony-corrected program usages with n_neighbors=10, and scanpy’s UMAP was then applied to the batch-corrected embedding with default parameters. Heatmaps of NMF gene loadings. For heatmaps of gene contributions to NMF programs, the NMF loading matrix (“H” matrix in scikit-learn) was normalized by dividing each gene's loading by its mean non-zero expression level (calculated as mean expression when expressed / fraction of cells expressing). The genes shown in the final heatmaps were filtered to remove mitochondrial genes and non-coding genes to improve interpretability, and ordered by descending normalized loading values. NMF usage means, CVs and Fano Factors. NMF program usage values were first normalized for each cell such that the sum of usages across all programs equaled 1. The mean, CV, and Fano factor of each program's usage across colonies was then calculated at each timepoint. To calculate mock colony CV and Fano factors, we corrected for systematic differences in means over time by regressing the CVs using the power law relationship observed between mean and CV. For comparisons across conditions, each metric was normalized to its value in control colonies at the same timepoint.
Assembly: Mixed Human GRCh38.101 and mouse GRCm.101 genome assembly
Supplementary files format and content: h5ad cell x genes matrices

source_name: Blood cell line

growth_protocol: K562 and L1210 cells were pre-treated with drugs separately by seeding 150,000 (L1210) and 200,000 (K562) cells into 6-well plate wells (Corning). Cells were grown in 2mL of IMDM with 10% FBS, 1X Pen/Strep in the presence of 0.05 μM Dec, 0.7μM Aza, 0.4μM Vor (MedChemExpress) or no drugs (3 repeats) for 48 hours. Next, cells were collected and K562 and L1210 cell-lines were pooled based on the drug condition at a 1:1 ratio. Cell suspensions were encapsulated into CAGEs using a final cell concentration of 1.4e6 cells/mL. Each drug condition was encapsulated for 2 hours, collecting the droplets into four 30 min fractions. One fraction of each condition was sampled instantly by lysing the cells inside the CAGEs and freezing the lysate containing CAGEs at -80ºC in 3X SSCI with 10% DMSO and 0.05U/μL Murine RNAse Inhibitor. Remaining fractions of packed hydrogel CAGEs were seeded into a different 24-well plate well into 1mL of IMDM with 10% FBS and 1x Pen/Strep, 0.1% F127 and 0.1% L31 with appropriate drug. 10,000 K562 and L1210 cells from appropriate drug conditions were seeded outside the CAGEs for the first two days. Every two days, media was exchanged with fresh media with appropriate drugs and one well of each condition was sampled for inC-RNA-seq by lysing the cells and freezing at -80ºC as described above.

extract_protocol:
After all the time points were collected, CAGEs were thawed, washed, and treated with Turbo DNAse I and Proteinase K. Finally, CAGEs were washed three times with 3X SSCI buffer and three times with HI10. Resulting CAGEs were subjected to the inC-RNA-seq protocol.  Reverse-transcription reaction was set on ice and performed in PCR strip tubes. A standard 100μL reaction was composed out of 60.5μL of packed capsules, 2.5μL of 10μM RT poly(T) primer housing a 10nt UMI and 6nt barcode (Table S3, RT), 3μL of 10% Igepal CA-630 (Millipore Sigma, I8896-50ML), 20μL of 5X SMARTseq3 RT buffer (100mM Tris pH 8.3, 150mM NaCl, 12.5mM MgCl2, 5mM GTP, 40mM DTT), 0.5μL of 10mM dNTPs (NEB, N0447L), 2.5μL of 40U/μL Recombinant RNase Inhibitor (Takara Bio, 2313A), 1.5μL of 50μM TSO, 5μL of Maxima H- reverse transcriptase (ThermoFisher, EP0753). Different timepoints were pooled and were kept separate from other timepoints. Reaction volumes were scaled according to the amount of capsules used and number of reactions performed. To set up the reaction, capsules, RT primer and Igepal CA-630 (Millipore Sigma, I8896-50ML) were mixed on ice in a PCR tube, with each housing a different RT barcode. Capsules were incubated on ice for 10 min to allow the RT primer to diffuse in, followed by heating at 70ºC for 5 min and cooling down on ice. Next, RT master mix, composed out of the remaining reagents was added to each tube, ensuring a thought mixing of capsules with pipetting. Tubes were incubated on ice for 5 min and the reaction was carried out at 42ºC for 90 min, followed by cycling between 50ºC and 42ºC incubation of 2 mins for 15 cycles. Reactions were left at room temperature overnight and processed the next day. After the RT reaction, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with ice-cold TI100 (pH 8.0) with 2 min incubations on ice. Finally capsules were washed twice with TI10 (pH 8.0). Next, Capsule dU PCR was performed to carry out cDNA amplification. After the cDNA amplification, capsules were washed three times with TI100 (pH 8.0), twice with TIbS (pH 8.0), three times with TI100 (pH 8.0), twice with TI10 (pH 8.0). Washed capsules were subjected to tree rounds of split-and-pool barcoding. Following split-and-pool barcoding, capsules were split into 8 tubes and were dissolved  using 10M NaOH. DNA was purified using MinElute PCR purification kit and barcoded cDNA was eluted into 20μL of the elution buffer. Barcoded and purified DNA was amplified using PCR. After the reaction, amplified barcoded cDNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and was eluted into a 15μL Elution Buffer.
To construct Illumina sequencing libraries, 50 ng of barcoded and amplified cDNA was fragmented, blunted and dA-tailed by mixing it with 3.5 μL of NEBNext Ultra II FS Reaction buffer (NEB), 1 μL of fully mixed NEBNext Ultra II FS Enzyme mix (NEB) and nuclease free water to a final volume of 17.5 μL. The reaction mix was vortexed for 10 s, spanned down and placed into a preheated PCR machine for incubation at 37°C for 10 min; 65°C for 30 min; hold 4°C (lid at 75ºC). Fragmented DNA was purified using 0.8X AMPure XP beads (Beckman Coulter, A63881) and eluted into 16μL of water. Single-stranded DNA adapter, containing Illumina’s TruSeq read 1 (Adp. TruSeq R1 FW and RV) sequences were annealed together at the final concentration of 1.5 μM by mixing 1.5 μL of forward ligation primer and reverse ligation primer (each at 100 μM) with 97 μL of nuclease-free water and heating the solution to 95°C for 2 min and cooling it at room temperature for 5 min. 16 μL of the purified fragmented DNA was mixed with 1.25 μL of 1.5 μM annealed adapters, 1.5μL of 10X T4 DNA ligase buffer, 15 μL of NEBNext Ultra II Ligation Master Mix (NEB, E7805S kit) and 0.5 μL of NEBNext Ultra II Ligation Master Enhancer (NEB, E7805S kit). The ligation reaction was carried out by incubating in the thermocycler for 15 min at 20°C (lid at 30ºC). After ligation, the reaction mix was diluted to 100 μL and was purified using AMPure XP beads (Beckman Coulter, A63881) with 0.8X volume ratio and eluted into 40 μL nuclease-free water. Indexing PCR was carried out by mixing purified DNA with 25 μL of 2x NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0543L) and 2.5 μL of 20μM P7 binding primer, 48 sets of 2.5μL of 20μM indexing primer that houses an 8bp library index and water to 50μL. PCR cycling program: 98 °C, 2 min; 3 cycles of 98 °C, 20 s; 55 °C, 30 s; 72 °C, 20 s and 9 cycles 98 °C, 20 s; 65 °C, 30 s; 72 °C, 20 s; with a 1 min final extension at 72 °C, and 4 °C, hold at the end. Following final library indexing, DNA was double-side purified using 0.6x-0.8x SPRIselect (Beckman Coulter, B23318) magnetic beads and eluted into 15μL.

value: Blood cell line

value: Lymphoblast


title: inC-RNA-seq of K562 single-cell derived colonies cultured in the presence of epigenetic drugs (CAGE_Colonies)

type: SRA

city: Boston

state: MA

country: USA

description: Library name: K562_Clone_seq

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: 0.05 μM Dec, 0.7μM Aza, 0.4μM Vor (MedChemExpress) or no drugs (3 repeats)


title: 4hpa

status: Public on Sep 15 2025

city: Vienna

first: Juan

middle: Daniel

last: Montenegro

state: Vienna

address: Djerassiplatz 1

department: Department of neurobiology and developmental biology

country: Austria

institute: University of Vienna

description: Library name: 16_NvAgg4hr

library_source: transcriptomic single cell

data_processing:
Sequencing reads were mapped to the Nematostella vectensis genome (Zimmermann et al. 2023) using standard parameters of Cellranger v7.1.0 (Zheng et al. 2017). Filtered matrices were then used to proceed with analysis using Seurat v5 (Butler et al. 2018; Stuart et al. 2019). The libraries were filtered for cells with low read and feature counts and analyzed using our scripts (complete details at https://github.com/technau/Gast ruloids ).
Assembly: Nvec200 (https://simrbase.stowers.org/starletseaanemone)
Supplementary files format and content: Seurat object
Supplementary files format and content: RData: GO enrichment analysis of gene modules obtained from the original single cell object and using the package hdWGCNA.

organism: Nematostella vectensis

source_name: aggregates

extract_protocol:
Samples were washed with ice cold Calcium Magnesium Free (CMF) seawater briefly and the samples were allowed to settle. The CMF was then removed and they were resuspended in ACME (ACetic-MEthanol) prepared as described previously (Garcia-Castro et al. 2021) and tubes were left on the rocker for 20 min. The samples were then dissociated using a cut pipette tip every 5 min during the 20 min window and their dissociation status was checked until sufficient. Tubes were then spun at 400 rcf for 4 min at 4℃ and the supernatant was carefully removed without disturbing the loose cell pellet. The pellet was then resuspended with 1xPBS + 0.5% BSA + RNaseOUT (40U/ml) and DMSO was added to be 10% of the final volume. This cell mix was then stored at -80℃ until the day of  library preparation. On library preperation day, the tubes were left to thaw at RT and then spun again at 400 rcf for 4 min at 4℃ after which the cell pellet was resuspended in 1xPBS + 0.5% BSA + RNaseOUT (40U/ml) and the viability and concentration were then quantified using ViaStain™AOPI staining solution (Nexcelom) and the Cellometer X2.
Libraries for sequencing were prepared using the standard 10X pipeline for scRNAsequencing

value: aggregates

value: wt


title: 24hpf

description: Library name: gast5.ACME

source_name: gastrula

value: gastrula


title: Purified HEK293T (ISBM-083) NTVE from co-culture with Neuro2a (ISBM-095) via FLAG-pull-down_spike-in_2

status: Public on Sep 01 2025

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description:
Library name: 24L010911
FLAG Purified sample of co-cultivation of two stable NTVE lines

data_processing:
Deduplication via czid-dedup (paired-end mode)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

value: immortalized cell line

tag: genotype

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:FLAG; CAG-TetON3g (ISBM-083)

tag: rna origin

value: Supernatant

tag: spike-in

value: doxycycline 500ng/ul

tag: batch


title: NTVE lysate-1_ISBM-083_noDOX_spike-in

description:
Library name: 24L012560
Stable NTVE line, no induction of export system

value: Lysate


title: NTVE lysate-2_ISBM-083_noDOX_spike-in

description:
Library name: 24L012561
Stable NTVE line, no induction of export system


title: NTVE lysate-2_ISBM-083_spike-in

description:
Library name: 24L012564
Stable NTVE line


title: NTVE -3_ISBM-083_spike-in

description:
Library name: 24L011710
Stable NTVE line

molecule: total RNA


title: NTVE lysate-3_ISBM-083_noDOX_spike-in

description:
Library name: 24L012562
Stable NTVE line, no induction of export system


title: Purified HEK293T (ISBM-083) NTVE from co-culture with Neuro2a (ISBM-095) via FLAG-pull-down_spike-in_1

description:
Library name: 24L010910
FLAG Purified sample of co-cultivation of two stable NTVE lines


title: NTVE -2_ISBM-083_spike-in

description:
Library name: 24L011709
Stable NTVE line


title: NTVE lysate-3_ISBM-083_spike-in

description:
Library name: 24L012565
Stable NTVE line


title: NTVE -1_ISBM-064_spike-in

description:
Library name: 24L006497
Stable NTVE line, same SN sample as 24L006479

value: NTVE Gag:PABP(ZF:Hibit); Pgk-TetON3g (ISBM-064)


title: NTVE IFN-gamma-2_ISBM-064

description:
Library name: 24L006489
Stable NTVE line, 50 ng/ml IFN-gamma

value: 50 ng/ml interferone gamma + doxycycline 500ng/ul


title: NTVE -6_ISBM-064

description:
Library name: 24L006484
Stable NTVE line


title: NTVE IFN-gamma-3_ISBM-064

description:
Library name: 24L006490
Stable NTVE line, 50 ng/ml IFN-gamma


title: NTVE -2_ISBM-064_spike-in

description:
Library name: 24L006498
Stable NTVE line, same SN sample as 24L006480


title: NTVE -1_ISBM-083_spike-in

description:
Library name: 24L011708
Stable NTVE line


title: NTVE lysate-1_ISBM-083_spike-in

description:
Library name: 24L012563
Stable NTVE line


title: Supernatant Gag-1_ISBM-038_spike-in

description:
Library name: 24L011711
Stable exporter line without poly-A binding protein in the export system

value: Gag (ZF); Pgk-TetON3g (ISBM-038)


title: NTVE -3_ISBM-064

description:
Library name: 24L006481
Stable NTVE line


title: NTVE -5_ISBM-064

description:
Library name: 24L006483
Stable NTVE line


title: NTVE IFN-gamma-1_ISBM-064

description:
Library name: 24L006488
Stable NTVE line, 50 ng/ml IFN-gamma


title: Supernatant Gag-2_ISBM-038_spike-in

description:
Library name: 24L011712
Stable exporter line without poly-A binding protein in the export system


title: Supernatant Gag-3_ISBM-038_spike-in

description:
Library name: 24L011713
Stable exporter line without poly-A binding protein in the export system


title: NTVE -4_ISBM-064

description:
Library name: 24L006482
Stable NTVE line


title: Purified HEK293T (ISBM-083) NTVE from co-culture with Neuro2a (ISBM-095) via FLAG-pull-down_spike-in_3

description:
Library name: 24L010912
FLAG Purified sample of co-cultivation of two stable NTVE lines


title: NTVE -1_ISBM-064

description:
Library name: 24L006479
Stable NTVE line, same SN sample as 24L006497


title: NTVE lysate IFN-gamma-3_ISBM-064

description:
Library name: 24L006471
Stable NTVE line, 50 ng/ml IFN-gamma


title: NTVE lysate IFN-gamma-2_ISBM-064

description:
Library name: 24L006470
Stable NTVE line, 50 ng/ml IFN-gamma


title: NTVE lysate-6_ISBM-064

description:
Library name: 24L006465
Stable NTVE line


title: NTVE lysate-5_ISBM-064

description:
Library name: 24L006464
Stable NTVE line


title: NTVE lysate IFN-gamma-1_ISBM-064

description:
Library name: 24L006469
Stable NTVE line, 50 ng/ml IFN-gamma


title: NTVE lysate-2_ISBM-064

description:
Library name: 24L006461
Stable NTVE line


title: Gag PABP(ZF) lysate_ISBM-014

description:
Library name: 23L010009
Stable NTVE line

value: NTVE Gag:PABP(ZF); Pgk-TetON3g (ISBM-014)


title: NTVE lysate-1_ISBM-064

description:
Library name: 24L006460
Stable NTVE line


title: Gag PABPΔZF cytosolic fraction_ISBM-036

description:
Library name: 23L010014
Stable exporter line without zinc finger domains in the export system, cytosolic fraction from subcellular fractionation

value: NTVE Gag:PABP; Pgk-TetON3g (ISBM-036)

value: Cell Lysate (fractionated)


title: Gag(ZF) lysate_ISBM-038

description:
Library name: 23L010008
Stable exporter line without poly-A binding protein in the export system


title: NTVE (ASCL1 transactivated)-3_ISBM-015

description:
Library name: SN-ASCL1-3
Stable NTVE line, ASCL1 transactivation

value: NTVE Gag:PABP(ZF); Pgk-TetON3g + transactivation (ISBM-015)


title: Gag PABP lysate_ISBM-036

description:
Library name: 23L010011
Stable exporter line without zinc finger domains in the export system


title: NTVE -2_ISBM-064

description:
Library name: 24L006480
Stable NTVE line, same SN sample as 24L006498


title: NTVE (ASCL1 transactivated)-2_ISBM-015

description:
Library name: SN-ASCL1-2
Stable NTVE line, ASCL1 transactivation


title: NTVE -5_ISBM-014

description:
Library name: SN5
Stable NTVE line


title: NTVE -6_ISBM-014

description:
Library name: SN6
Stable NTVE line


title: NTVE (ASCL1 transactivated) lysate-2_ISBM-015

description:
Library name: L-ASCL1-2
Stable NTVE line, ASCL1 transactivation


title: NTVE -1_ISBM-014

description:
Library name: SN1
Stable NTVE line


title: NTVE -4_ISBM-014

description:
Library name: SN4
Stable NTVE line


title: NTVE (ASCL1 transactivated) lysate-3_ISBM-015

description:
Library name: L-ASCL1-3
Stable NTVE line, ASCL1 transactivation


title: NTVE -2_ISBM-014

description:
Library name: SN2
Stable NTVE line


title: NTVE (ASCL1 transactivated) lysate-1_ISBM-015

description:
Library name: L-ASCL1-1
Stable NTVE line, ASCL1 transactivation


title: NTVE lysate-6_ISBM-014

description:
Library name: L6
Stable NTVE line


title: NTVE lysate-3_ISBM-064

description:
Library name: 24L006462
Stable NTVE line


title: NTVE lysate-5_ISBM-014

description:
Library name: L5
Stable NTVE line


title: NTVE lysate-4_ISBM-064

description:
Library name: 24L006463
Stable NTVE line


title: NTVE lysate-4_ISBM-014

description:
Library name: L4
Stable NTVE line


title: NTVE (ASCL1 transactivated)-1_ISBM-015

description:
Library name: SN-ASCL1-1
Stable NTVE line, ASCL1 transactivation


title: NTVE -3_ISBM-014

description:
Library name: SN3
Stable NTVE line


title: NTVE lysate-2_ISBM-014

description:
Library name: L2
Stable NTVE line


title: NTVE lysate-1_ISBM-014

description:
Library name: L1
Stable NTVE line


title: NTVE-3_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010906
Stable NTVE line

organism: Mus musculus


title: Lysate of transient transfection of Gag:PABP

description:
Library name: DJJT01_s1-cellular
Transient expression of NTVE

value: WT

value: transfection with NTVE construct


title: NTVE lysate-3_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010903
Stable NTVE line


title: NTVE-1_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010904
Stable NTVE line


title: NTVE lysate-1_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010901
Stable NTVE line


title: NTVE-2_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010905
Stable NTVE line


title: E53 human metatarsal, digit 5, rep 4

status: Public on Aug 20 2025

city: Cambridge

first: Terence

last: Capellini

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard University

description: Library name: FM5_early_rep4

library_source: genomic

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3
Alignment to hg38 with Bowtie2 v2.3.4.1
duplicate removal with picard v2.9.0
mitochondrial read filtering with removeChrom.py
peak calling with MACS2 v2.1.1.2 -f bampe --nolambda –bdg --verbose
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Assembly: hg38
Supplementary files format and content: bed format; contains the coordinates of the peaks called
Supplementary files format and content: bigWig format

molecule: genomic DNA

source_name: Metatarsal, digit V

growth_protocol: in vivo collected human autopod chondrocytes from E53-E74

extract_protocol:
Embryonic tissue was microdissected under a light microscope in 5% fetal bovine serum in Dulbecco’s Modified Eagle Medium (DMEM) on ice. The pooled phalanges (proximal and distal for digit I; proximal, intermediate, and distal for digits II-V) and metapodials were collected separately for all digits in both the fore- and hind limbs. The right and left sides of each element were pooled together. ATAC-seq protocol was performed as described in Young et al., 2022. After ATAC-seq, samples were then sent out for 1-2 rounds of sequencing on an Illumina NovaSeq 6000 at the Harvard Bauer Core in order to obtain at least 40 million reads per sample.
ATAC-seq protocol was performed as described in Young et al., 2022.

treatment_protocol: Human products of conception were collected from late first-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

value: Metatarsal, digit V

value: chondrocytes

tag: Sex

value: Male


title: NTVE lysate-2_ISBM-061_NIH/3T3_spike-in

description:
Library name: 24L010902
Stable NTVE line

value: immortalized cell line


title: Purified Neuro2a (ISBM-095) NTVE from co-culture with HEK293T (ISBM-083) via HA-pull-down_spike-in_1

description:
Library name: 24L010907
HA Purified sample of co-cultivation of two stable NTVE lines

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:HA; CAG-TetON3g (ISBM-095)


title: E53 human metatarsal, digit 3, rep 4

description: Library name: FM3_early_rep4

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E53 human foot phalanges, digit 4, rep 4

description: Library name: FP4_early_rep4

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: Purified Neuro2a (ISBM-095) NTVE from co-culture with HEK293T (ISBM-083) via HA-pull-down_spike-in_2

description:
Library name: 24L010908
HA Purified sample of co-cultivation of two stable NTVE lines

value: Supernatant

value: doxycycline 500ng/ul


title: NTVE lysate-3_ISBM-014

description:
Library name: L3
Stable NTVE line

value: Lysate


title: E53 human metatarsal, digit 2, rep 4

description: Library name: FM2_early_rep4

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E53 human foot phalanges, digit 2, rep 4

description: Library name: FP2_early_rep4

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E53 human foot phalanges, digit 1, rep 4

description: Library name: FP1_early_rep4

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E53 human foot phalanges, digit 5, rep 4

description: Library name: FP5_early_rep4

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E53 human foot phalanges, digit 3, rep 4

description: Library name: FP3_early_rep4

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E53 human metacarpal, digit 4, rep 4

description: Library name: HM4_early_rep4

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: Supernatant of transient transfection of Gag:PABP

description:
Library name: DJJT01_s2-gag
Transient expression of NTVE

value: WT

value: transfection with NTVE construct


title: Purified Neuro2a (ISBM-095) NTVE from co-culture with HEK293T (ISBM-083) via HA-pull-down_spike-in_3

description:
Library name: 24L010909
HA Purified sample of co-cultivation of two stable NTVE lines


title: E53 human metatarsal, digit 1, rep 4

description: Library name: FM1_early_rep4

source_name: Metatarsal, digit I

value: Metatarsal, digit I

value: chondrocytes


title: E53 human metacarpal, digit 2, rep 4

description: Library name: HM2_early_rep4

source_name: Metacarpal, digit II

value: Metacarpal, digit II

value: Male


title: E53 human metacarpal, digit 3, rep 4

description: Library name: HM3_early_rep4

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E53 human hand phalanges, digit 4, rep 4

description: Library name: HP4_early_rep4

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: E53 human metacarpal, digit 5, rep 4

description: Library name: HM5_early_rep4

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E53 human metacarpal, digit 1, rep 4

description: Library name: HM1_early_rep4

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E53 human hand phalanges, digit 5, rep 4

description: Library name: HP5_early_rep4

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E53 human hand phalanges, digit 1, rep 4

description: Library name: HP1_early_rep4

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E53 human hand phalanges, digit 2, rep 4

description: Library name: HP2_early_rep4

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E59 human metatarsal, digit 5, rep 3

description: Library name: FM5_early_rep3

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E59 human metatarsal, digit 4, rep 3

description: Library name: FM4_early_rep3

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E59 human metatarsal, digit 3, rep 3

description: Library name: FM3_early_rep3

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E59 human metatarsal, digit 2, rep 3

description: Library name: FM2_early_rep3

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E59 human metatarsal, digit 1, rep 3

description: Library name: FM1_early_rep3


title: E53 human hand phalanges, digit 3, rep 4

description: Library name: HP3_early_rep4

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: E59 human foot phalanges, digit 3, rep 3

description: Library name: FP3_early_rep3

value: Foot phalanges, digit III


title: E59 human foot phalanges, digit 1, rep 3

description: Library name: FP1_early_rep3

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E59 human metacarpal, digit 1, rep 3

description: Library name: HM1_early_rep3

value: chondrocytes


title: E59 human metacarpal, digit 4, rep 3

description: Library name: HM4_early_rep3

value: Metacarpal, digit IV


title: E59 human hand phalanges, digit 1, rep 3

description: Library name: HP1_early_rep3

value: Male


title: E59 human hand phalanges, digit 5, rep 3

description: Library name: HP5_early_rep3


title: E59 human metacarpal, digit 5, rep 3

description: Library name: HM5_early_rep3


title: E59 human metacarpal, digit 2, rep 3

description: Library name: HM2_early_rep3

value: Metacarpal, digit II


title: E59 human hand phalanges, digit 3, rep 3

description: Library name: HP3_early_rep3


title: E59 human metacarpal, digit 3, rep 3

description: Library name: HM3_early_rep3

value: Metacarpal, digit III


title: E58 human metatarsal, digit 2, rep 2

description: Library name: FM2_early_rep2


title: E59 human hand phalanges, digit 2, rep 3

description: Library name: HP2_early_rep3


title: E59 human hand phalanges, digit 4, rep 3

description: Library name: HP4_early_rep3

value: Hand phalanges, digit IV


title: E59 human foot phalanges, digit 5, rep 3

description: Library name: FP5_early_rep3

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E58 human metatarsal, digit 1, rep 2

description: Library name: FM1_early_rep2

value: Metatarsal, digit I


title: E58 human metatarsal, digit 3, rep 2

description: Library name: FM3_early_rep2


title: E58 human foot phalanges, digit 5, rep 2

description: Library name: FP5_early_rep2


title: E58 human foot phalanges, digit 2, rep 2

description: Library name: FP2_early_rep2

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E58 human foot phalanges, digit 4, rep 2

description: Library name: FP4_early_rep2

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E58 human foot phalanges, digit 3, rep 2

description: Library name: FP3_early_rep2

source_name: Foot phalanges, digit III


title: E58 human foot phalanges, digit 1, rep 2

description: Library name: FP1_early_rep2


title: E58 human metacarpal, digit 5, rep 2

description: Library name: HM5_early_rep2

value: Metacarpal, digit V


title: E58 human metacarpal, digit 4, rep 2

description: Library name: HM4_early_rep2

source_name: Metacarpal, digit IV


title: E58 human metacarpal, digit 3, rep 2

description: Library name: HM3_early_rep2

source_name: Metacarpal, digit III


title: E58 human metacarpal, digit 2, rep 2

description: Library name: HM2_early_rep2

source_name: Metacarpal, digit II


title: E59 human foot phalanges, digit 2, rep 3

description: Library name: FP2_early_rep3


title: E58 human metacarpal, digit 1, rep 2

description: Library name: HM1_early_rep2

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E58 human metatarsal, digit 5, rep 2

description: Library name: FM5_early_rep2

value: Metatarsal, digit V


title: E58 human hand phalanges, digit 5, rep 2

description: Library name: HP5_early_rep2

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E58 human hand phalanges, digit 3, rep 2

description: Library name: HP3_early_rep2

value: Hand phalanges, digit III


title: E58 human hand phalanges, digit 4, rep 2

description: Library name: HP4_early_rep2

source_name: Hand phalanges, digit IV


title: E53 human metatarsal, digit 4, rep 1

description: Library name: FM4_early_rep1

value: Metatarsal, digit IV


title: E58 human metatarsal, digit 4, rep 2

description: Library name: FM4_early_rep2


title: E58 human hand phalanges, digit 1, rep 2

description: Library name: HP1_early_rep2

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E53 human metatarsal, digit 3, rep 1

description: Library name: FM3_early_rep1

value: Metatarsal, digit III

value: chondrocytes


title: E53 human foot phalanges, digit 5, rep 1

description: Library name: FP5_early_rep1

value: Male


title: E53 human foot phalanges, digit 3, rep 1

description: Library name: FP3_early_rep1

value: Foot phalanges, digit III


title: E53 human metatarsal, digit 2, rep 1

description: Library name: FM2_early_rep1

value: Metatarsal, digit II


title: E53 human foot phalanges, digit 1, rep 1

description: Library name: FP1_early_rep1

value: Foot phalanges, digit I


title: E53 human metatarsal, digit 5, rep 1

description: Library name: FM5_early_rep1

source_name: Metatarsal, digit V


title: E58 human hand phalanges, digit 2, rep 2

description: Library name: HP2_early_rep2

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E53 human foot phalanges, digit 4, rep 1

description: Library name: FP4_early_rep1


title: E53 human metacarpal, digit 1, rep 1

description: Library name: HM1_early_rep1


title: E53 human metatarsal, digit 1, rep 1

description: Library name: FM1_early_rep1

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E53 human metacarpal, digit 3, rep 1

description: Library name: HM3_early_rep1

value: Metacarpal, digit III


title: E53 human foot phalanges, digit 2, rep 1

description: Library name: FP2_early_rep1

value: Foot phalanges, digit II


title: E53 human metacarpal, digit 4, rep 1

description: Library name: HM4_early_rep1

value: Metacarpal, digit IV


title: E53 human hand phalanges, digit 5, rep 1

description: Library name: HP5_early_rep1


title: E53 human metacarpal, digit 2, rep 1

description: Library name: HM2_early_rep1

value: Metacarpal, digit II


title: E53 human hand phalanges, digit 4, rep 1

description: Library name: HP4_early_rep1

value: Hand phalanges, digit IV


title: E53 human hand phalanges, digit 3, rep 1

description: Library name: HP3_early_rep1


title: E74 human metacarpal, digit 3, rep 4

description: Library name: HM3_late_rep4

value: Female


title: E67 human metatarsal, digit 5, rep 3

description: Library name: FM5_late_rep3

value: Metatarsal, digit V


title: E74 human hand phalanges, digit 3, rep 4

description: Library name: HP3_late_rep4

value: Hand phalanges, digit III


title: E53 human metacarpal, digit 5, rep 1

description: Library name: HM5_early_rep1

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E67 human metatarsal, digit 4, rep 3

description: Library name: FM4_late_rep3

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E67 human metatarsal, digit 2, rep 3

description: Library name: FM2_late_rep3

source_name: Metatarsal, digit II

value: chondrocytes


title: E67 human foot phalanges, digit 4, rep 3

description: Library name: FP4_late_rep3

value: Footphalanges, digit IV

value: Male


title: E67 human metatarsal, digit 3, rep 3

description: Library name: FM3_late_rep3

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E67 human foot phalanges, digit 3, rep 3

description: Library name: FP3_late_rep3

value: Foot phalanges, digit III


title: E67 human foot phalanges, digit 5, rep 3

description: Library name: FP5_late_rep3

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E67 human metacarpal, digit 5, rep 3

description: Library name: HM5_late_rep3


title: E67 human metacarpal, digit 4, rep 3

description: Library name: HM4_late_rep3


title: E67 human foot phalanges, digit 2, rep 3

description: Library name: FP2_late_rep3

source_name: Foot phalanges, digit II


title: E67 human metacarpal, digit 1, rep 3

description: Library name: HM1_late_rep3

value: Metacarpal, digit I


title: E67 human metatarsal, digit 1, rep 3

description: Library name: FM1_late_rep3

value: Metatarsal, digit I


title: E67 human metacarpal, digit 3, rep 3

description: Library name: HM3_late_rep3

value: Metacarpal, digit III


title: E67 human metacarpal, digit 2, rep 3

description: Library name: HM2_late_rep3


title: E67 human hand phalanges, digit 4, rep 3

description: Library name: HP4_late_rep3


title: E67 human hand phalanges, digit 3, rep 3

description: Library name: HP3_late_rep3

source_name: Hand phalanges, digit III


title: E67 human foot phalanges, digit 1, rep 3

description: Library name: FP1_late_rep3

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E67 human hand phalanges, digit 2, rep 3

description: Library name: HP2_late_rep3

value: Hand phalanges, digit II


title: E67 human hand phalanges, digit 5, rep 3

description: Library name: HP5_late_rep3

value: Hand phalanges, digit V


title: E72 human metatarsal, digit 4, rep 2

description: Library name: FM4_late_rep2


title: E72 human metatarsal, digit 3, rep 2

description: Library name: FM3_late_rep2


title: E53 human hand phalanges, digit 1, rep 1

description: Library name: HP1_early_rep1

value: Hand phalanges, digit I


title: E72 human metatarsal, digit 1, rep 2

description: Library name: FM1_late_rep2


title: E72 human foot phalanges, digit 5, rep 2

description: Library name: FP5_late_rep2


title: E72 human metatarsal, digit 2, rep 2

description: Library name: FM2_late_rep2

value: Metatarsal, digit II


title: E72 human foot phalanges, digit 4, rep 2

description: Library name: FP4_late_rep2

source_name: Footphalanges, digit IV


title: E67 human hand phalanges, digit 1, rep 3

description: Library name: HP1_late_rep3


title: E72 human foot phalanges, digit 2, rep 2

description: Library name: FP2_late_rep2

value: Foot phalanges, digit II


title: E72 human foot phalanges, digit 3, rep 2

description: Library name: FP3_late_rep2

source_name: Foot phalanges, digit III


title: E72 human foot phalanges, digit 1, rep 2

description: Library name: FP1_late_rep2


title: E72 human metacarpal, digit 2, rep 2

description: Library name: HM2_late_rep2

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E59 human foot phalanges, digit 4, rep 3

description: Library name: FP4_early_rep3


title: E72 human metacarpal, digit 4, rep 2

description: Library name: HM4_late_rep2

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E72 human metacarpal, digit 5, rep 2

description: Library name: HM5_late_rep2

value: Metacarpal, digit V

value: chondrocytes


title: E72 human metacarpal, digit 3, rep 2

description: Library name: HM3_late_rep2

source_name: Metacarpal, digit III

value: Male


title: E72 human hand phalanges, digit 2, rep 2

description: Library name: HP2_late_rep2


title: E72 human hand phalanges, digit 5, rep 2

description: Library name: HP5_late_rep2

source_name: Hand phalanges, digit V


title: E72 human metacarpal, digit 1, rep 2

description: Library name: HM1_late_rep2

source_name: Metacarpal, digit I


title: E72 human hand phalanges, digit 1, rep 2

description: Library name: HP1_late_rep2

source_name: Hand phalanges, digit I


title: E72 human metatarsal, digit 5, rep 2

description: Library name: FM5_late_rep2

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E72 human hand phalanges, digit 3, rep 2

description: Library name: HP3_late_rep2

value: Hand phalanges, digit III


title: E72 human metatarsal, digit 5, rep 1

description: Library name: FM5_late_rep1


title: E72 human metatarsal, digit 3, rep 1

description: Library name: FM3_late_rep1

value: Metatarsal, digit III


title: E72 human foot phalanges, digit 5, rep 1

description: Library name: FP5_late_rep1

value: Foot phalanges, digit V


title: E72 human metatarsal, digit 4, rep 1

description: Library name: FM4_late_rep1

value: Metatarsal, digit IV


title: E72 human metatarsal, digit 2, rep 1

description: Library name: FM2_late_rep1


title: E72 human foot phalanges, digit 4, rep 1

description: Library name: FP4_late_rep1

value: Footphalanges, digit IV


title: E72 human metacarpal, digit 5, rep 1

description: Library name: HM5_late_rep1

source_name: Metacarpal, digit V


title: E72 human foot phalanges, digit 2, rep 1

description: Library name: FP2_late_rep1


title: E72 human metatarsal, digit 1, rep 1

description: Library name: FM1_late_rep1

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E72 human foot phalanges, digit 3, rep 1

description: Library name: FP3_late_rep1

value: Foot phalanges, digit III


title: E72 human hand phalanges, digit 4, rep 2

description: Library name: HP4_late_rep2

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: E72 human hand phalanges, digit 5, rep 1

description: Library name: HP5_late_rep1

value: Hand phalanges, digit V


title: E72 human metacarpal, digit 2, rep 1

description: Library name: HM2_late_rep1


title: E72 human foot phalanges, digit 1, rep 1

description: Library name: FP1_late_rep1

value: Foot phalanges, digit I


title: E72 human hand phalanges, digit 4, rep 1

description: Library name: HP4_late_rep1


title: E72 human metacarpal, digit 4, rep 1

description: Library name: HM4_late_rep1


title: E72 human hand phalanges, digit 1, rep 1

description: Library name: HP1_late_rep1

value: Hand phalanges, digit I


title: E15.5 mouse metatarsal, digit 1, rep 3

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3
Alignment to mm10 with Bowtie2 v2.3.4.1
duplicate removal with picard v2.9.0
mitochondrial read filtering with removeChrom.py
peak calling with MACS3 v3.0.3.1.1.2 -f bampe --nolambda –bdg --verbose
IDR https://github.com/nboley/idr
idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
Assembly: mm10
Supplementary files format and content: bed format; contains the coordinates of the peaks called
Supplementary files format and content: bigWig format

growth_protocol: in vivo collected E15.5 mouse autopod chondrocytes

extract_protocol:
The fore- and hind limbs of three to five embryos were microdissected under a light microscope in 5% FBS/DMEM on ice. The pooled phalanges (proximal and distal for digit I, proximal, intermediate, and distal for digits III and V) and metapodials were collected separately for digits I, III, and V for both the forelimb and the hind limb. The right and left sides of each element were pooled together, resulting in a total pool of elements from 6 to 10 individual limbs. All embryos in each biological replicate were from the same litter. Samples were then sent out for 1-2 rounds of sequencing on an Illumina NovaSeq 6000 at the Harvard Bauer Core in order to obtain at least 40 million reads per sample.
ATAC-seq protocol was performed as described in Young et al., 2022.

treatment_protocol: E15.5 mouse embryos were collected from pregnant FVB/NJ females.

value: FVB/NJ


title: E72 human hand phalanges, digit 2, rep 1

description: Library name: HP2_late_rep1

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E15.5 mouse foot phalanges, digit 5, rep 3

source_name: Foot phalanges, digit V


title: E15.5 mouse metatarsal, digit 3, rep 3

source_name: Metatarsal, digit III


title: E15.5 mouse metatarsal, digit 5, rep 3


title: E15.5 mouse foot phalanges, digit 1, rep 3


title: E15.5 mouse hand phalanges, digit 3, rep 3

source_name: Hand phalanges, digit III


title: E15.5 mouse metacarpal, digit 5, rep 3

value: Metacarpal, digit V


title: E15.5 mouse metacarpal, digit 3, rep 3

value: Metacarpal, digit III

value: chondrocytes


title: E15.5 mouse hand phalanges, digit 5, rep 3


title: E15.5 mouse hand phalanges, digit 1, rep 3


title: E15.5 mouse metacarpal, digit 1, rep 3

value: Metacarpal, digit I


title: E15.5 mouse metatarsal, digit 5, rep 2

value: Metatarsal, digit V


title: E15.5 mouse foot phalanges, digit 3, rep 3


title: E15.5 mouse metatarsal, digit 3, rep 2

value: Metatarsal, digit III


title: E15.5 mouse foot phalanges, digit 3, rep 2


title: E15.5 mouse metacarpal, digit 3, rep 2


title: E15.5 mouse foot phalanges, digit 5, rep 2

value: Foot phalanges, digit V


title: E72 human metacarpal, digit 1, rep 1

description: Library name: HM1_late_rep1

value: Male


title: E15.5 mouse metatarsal, digit 1, rep 2


title: E15.5 mouse metacarpal, digit 1, rep 2


title: E15.5 mouse hand phalanges, digit 5, rep 2


title: E72 human hand phalanges, digit 3, rep 1

description: Library name: HP3_late_rep1

value: Hand phalanges, digit III


title: E15.5 mouse hand phalanges, digit 1, rep 2


title: E15.5 mouse hand phalanges, digit 3, rep 2


title: E15.5 mouse foot phalanges, digit 1, rep 2

source_name: Foot phalanges, digit I


title: E15.5 mouse metacarpal, digit 5, rep 2


title: E15.5 mouse metatarsal, digit 3, rep 1


title: E15.5 mouse metatarsal, digit 5, rep 1


title: E15.5 mouse metacarpal, digit 3, rep 1


title: E15.5 mouse foot phalanges, digit 3, rep 1


title: E15.5 mouse metatarsal, digit 1, rep 1

value: Metatarsal, digit I


title: E15.5 mouse metacarpal, digit 5, rep 1


title: E15.5 mouse hand phalanges, digit 1, rep 1


title: E15.5 mouse foot phalanges, digit 5, rep 1


title: snATAC-Seq - 620_2_rep2

status: Public on Jul 30 2025

city: Piscataway

first: Jiekun

last: Yang

state: NJ

address: 145 Bevier Rd

institute: Rutgers University

description:
Library name: D21-194107
10x Genomics

library_source: genomic single cell

data_processing:
We received the sequences, mapped the reads against the GRCh38 human reference genome, and quantified the read counts using cellranger-atac-2.0.0 pipeline (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Metastatic melanoma

extract_protocol:
We enzymatically digested and dissociated fresh tumor samples according to tissue dissociation kit protocols using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS and immediately processed for the generation of snATAC-seq libraries.
We performed snATAC-seq using the Chromium single cell ATAC v1 chemistry from 10x Genomics with the target of 5000 nuclei per sample. Then the libraries were profiled using the Novaseq S2 (Illumina) technology.

value: Metastatic melanoma

value: conventional dendritic cell


title: snATAC-Seq - 620_2_rep1

description:
Library name: D21-194106
10x Genomics


title: snATAC-Seq - 509_1

description:
Library name: D19-11973
10x Genomics


title: E15.5 mouse foot phalanges, digit 1, rep 1


title: E15.5 mouse hand phalanges, digit 3, rep 1


title: E15.5 mouse metacarpal, digit 1, rep 1


title: snATAC-Seq - 1098_1

description:
Library name: D21-194103
10x Genomics


title: E15.5 mouse hand phalanges, digit 5, rep 1

value: Hand phalanges, digit V


title: snATAC-Seq - 452_2

description:
Library name: D19-11974
10x Genomics


title: snATAC-Seq - 1009_1

description:
Library name: D19-11979
10x Genomics


title: snATAC-Seq - 509_2

description:
Library name: D19-11988
10x Genomics


title: snATAC-Seq - 776-1

description:
Library name: D19-11972
10x Genomics


title: snATAC-Seq - 1224_3_rep1

description:
Library name: D19-11983
10x Genomics


title: snATAC-Seq - 1098_4

description:
Library name: D19-11975
10x Genomics


title: Pooled_snRNA-seq_Human2_2

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

description:
Library name: Human heart tissue - Pooled 2
10x Genomics

data_processing:
The sequencing reads of the human dataset were aligned to the GRCh38 reference genome and processed with 10x Genomics Cell Ranger 7.0.0
Species-mixed (human and sheep) data were separately mapped to both the human genome (GRCh38) and the sheep genome (ARS-UI_Ramb_v2.0), whereas 4-sample-multiplexed human data were mapped to the human genome (GRCh38) only.
Assembly: GRCh38, ARS-UI_Ramb_v2.0
Supplementary files format and content: tab-delimited value files and matrix files

molecule: nuclear RNA

source_name: heart ventricle

extract_protocol:
Nuclei were isolated from heart tissue by mechanical disruption, followed by centrifugation through sucrose and purification from debris by FACS. In brief, frozen heart tissue (~100 mg) was suspended in 5 ml of lysis buffer and thawed on wet ice. When samples were pooled for 10x RNA-Seq (multiple human samples, or sheep and human), samples were either combined after (human real-world dataset) or prior to homogenization (human application dataset and sheep-human species-mixed dataset), where equivalent weights of each tissue sample were pooled. Next, samples were homogenized using a gentleMACS dissociator (Miltenyi) with gentleMACS M tubes and the Protein_01_01 protocol. 5 ml of lysis buffer containing NP-40 was added to the homogenate and incubated on wet ice for 15 min. Then, the suspension was filtered through a 30 μM cell strainer (Miltenyi). Residual nuclei were recovered by washing the M tube and filter with 2 ml of lysis buffer containing NP-40, which was then combined with the remainder of the homogenate. The homogenate was centrifuged in a swinging-bucket centrifuge (Eppendorf, 5920R) at 1000 g for 5 min (4 ℃, ramp speed 4/4). The supernatant was carefully removed and the pellet containing nuclei was resuspended in 2 ml of sucrose buffer, which was then layered on top of 2 ml of sucrose buffer. The sample was then centrifuged at 500 g for 5 min (Eppendorf, 5920R; 4 ℃, ramp speed of 4/4) to recover nuclei. The supernatant was removed and the pellet was resuspended in 500 μl of wash buffer and centrifuged at 500 g for 5 min (Eppendorf, 5920R; 4 ℃, ramp speed of 4/4). The supernatant was carefully removed and stained with 1 ml of staining buffer containing DAPI (1:1000; 7406). DAPI-positive nuclei were separated from cell debris by flow sorting using a SONY sorter instrument (SONY MA900) and collected into 50 μl of collection buffer. Sorted nuclei were then collected by centrifugation at 1000 g for 5 min (Eppendorf, 5920R; 4°C, ramp speed of 4/4), and the concentration was adjusted to 1,000 nuclei/µl targeted for predicted capture 10,000.
Nuclear suspensions were loaded on a 10x Chromium Controller (10x Genomics) and processed with 10x Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to the manufacturer’s protocol. Cell-RT mix was prepared, targeting 10,000 cells per sample. Library quantification and quality assessment were performed using the Bioanalyzer Agilent 2100 with a High Sensitivity DNA chip (Agilent Genomics). Indexed libraries were pooled equimolarly and sequenced on an Illumina NovaSeq 6000 by GenomeScan using paired-end 26x98-bp reads as the sequencing mode. Libraries were sequenced on the NovaSeq 6000 (Illumina) at 30,000 reads per nuclei resolution.

value: heart ventricle


title: snATAC-Seq - 1227_1

description:
Library name: D19-11985
10x Genomics


title: snATAC-Seq - 1224_3_rep2

description:
Library name: D19-11984
10x Genomics


title: Pooled_snRNA-seq_Human4_3

description:
Library name: Human heart tissue - Pooled 3
10x Genomics

source_name: heart atria

value: heart atria


title: Pooled_snRNA-seq_Human2_1

description:
Library name: Human heart tissue - Pooled 1
10x Genomics


title: Pooled_snRNA-seq_Mixed2_4

description:
Library name: Human sheep heart tissue - Pooled 4
10x Genomics

organism:
Homo sapiens
Ovis aries

source_name: heart ventricle and atria

value: heart ventricle and atria


title: snATAC-Seq - 856_1

description:
Library name: D19-11980
10x Genomics


title: Individual_snRNA-seq_Donor_6

description:
Library name: Human heart tissue - Donor 6
10x Genomics


title: Individual_snRNA-seq_Donor_3

description:
Library name: Human heart tissue - Donor 3
10x Genomics


title: snATAC-Seq - 1098_3

description:
Library name: D19-9146
10x Genomics


title: Individual_snRNA-seq_Donor_4

description:
Library name: Human heart tissue - Donor 4
10x Genomics


title: Individual_snRNA-seq_Donor_1

description:
Library name: Human heart tissue - Donor 1
10x Genomics


title: Heart_bulkRNA-seq_Donor_4

description: Library name: Human heart tissue - Donor4

data_processing:
Sequencing reads from bulk RNA-seq were trimmed by Trim Galore! and aligned with STAR to the same reference genome used for the single-nucleus RNA-seq.
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the homo sapiens transcriptome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited value files

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) from homogenised frozen left ventricular human cardiac according to the manufacturer’s protocol.
From 1 μg of RNA, RNA-seq libraries were prepared with the TruSeq RNA Sample Preparation Kit following the manufacturer's manual. Sequencing was performed on Illumina NovaSeq 6000 (2x150 bp paired-end reads).


title: Individual_snRNA-seq_Donor_2

description:
Library name: Human heart tissue - Donor 2
10x Genomics


title: Heart_bulkRNA-seq_Donor_3

description: Library name: Human heart tissue - Donor3


title: Heart_bulkRNA-seq_Donor_6

description: Library name: Human heart tissue - Donor6


title: Heart_bulkRNA-seq_Donor_2

description: Library name: Human heart tissue - Donor2


title: Individual_snRNA-seq_Donor_5

description:
Library name: Human heart tissue - Donor 5
10x Genomics


title: Heart_bulkRNA-seq_Donor_1

description: Library name: Human heart tissue - Donor1


title: A4476_011625

city: New York

first: Samuel

last: Sternberg

address: 701 W. 168th Street, HHSC 726

institute: Columbia University

description: Library name: A4476_011625

data_processing:
ChIP-seq paired-end reads were trimmed and mapped to a custom E. coli MG1655 reference genome (based on GenBank accession NC_000913.3) using fastp (Chen et al., 2018) and Bowtie2 (Langmead et al., 2012) with default parameters, respectively. The custom E. coli MG1655 strain has genomically encoded GFP and RFP genes, in between which custom TnpB target sites were inserted. A genomic lacZ/lacI region and flanking regions, which are partially identical to plasmid-encoded sequences, were masked in all alignments (genomic coordinates 366,386-367,588).
Mapped reads were sorted and indexed using the SAMtools software package (Li et al., 2009) (samtools sort and samtools index commands, respectively). For all data sets, the command samtools view was used to eliminate multi-mapping reads with a MAPQ-score <10 (-bq 10 option).
Alignments were normalised by CPM (Counts Per Million) and converted to 1 bp-bin bigwig files using the deepTools2 (Ramirez et al., 2016) command bamCoverage (--normalizeUsing CPM -bs 1 parameters).
After normalization, genome-mapping reads were visualised in IGV (Robinson et al., 2011). The Bedtools software package (bedtools makewindows -w 1000 and bedtools map -o max) (Quinlan et al., 2010) and IGV were used to generate all genome-wide views. Maximum read coverage values were plotted in 1-kb bins across the genome, as described previously (Cooper et al., 2018).
Peaks were called on pre-normalised alignments using MACS3 (Zhang et al., 2008), with the parameters -g 4500000 --nomodel --extsize 400 -q 0.05 -B, with respect to a non-immunoprecipitated control sample of Eco_dTnpB (-n option). The peak summit coordinates in the MACS3 output summits.bed file were extended to encompass a 200-bp window using the following Bedtools command: bedtools slop -l 100 -r 99. Sequence motifs were identified using MEME ChIP (Bailey et al., 2009) with default parameters.
Assembly: NC_000913.3
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.
RIP-seq data processing was performed as described in Tang et al. 2024. RIP-seq and corresponding input datasets were processed using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp.
Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3) and relevant plasmid sequences using bwa-mem2 (v2.2.1) with default parameters.
SAMtools (v1.17) was used to sort and index alignments.
Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, with combined top and bottom strand alignments, or separation of top and bottom strand alignments, and scaling of coverage according to sequencing depth (based on the total number of reads passing initial trimming and length filtering).
Coverage tracks were visualized in IGV.
For transcriptome-wide analyses of RNAs enriched by RIP-seq, aligned reads were assigned to annotated transcriptome features using featureCounts (v2.0.2) with -s 1 for strandedness.
The resulting counts matrices were passed to DESeq2 to calculate fold-change and FDR (using the Benjamini-Hochberg procedure) between input and IP for each annotated transcript.
Comparisons were visualized using ggplot2, plotting the “baseMean” (mean normalized counts across all conditions) against log2(fold change).
Assembly: NC_000913.3
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.
RNA-seq datasets were processed as described in Tang et al. 2024, using cutadapt (v4.2) to remove Illumina adapter sequences, trim low-quality ends from reads, and filter out reads shorter than 15 bp.
Reads were mapped to combined reference files containing the MG1655 genome (NC_000913.3) and relevant plasmid sequence using bwa-mem2 (v2.2.1) with default parameters.
SAMtools (v1.17) was used to sort and index alignments.
Coverage tracks were generated using bamCoverage (v3.5.1) with a bin size of 1, separation of top and bottom strand alignments, and scaling of coverage according to sequencing depth (based on the total number of reads passing initial trimming and length filtering).
Coverage tracks were visualized in IGV.
For transcriptome-wide analyses of RNAs, aligned reads were assigned to annotated transcriptome features using featureCounts (v2.0.2) with -s 1 for strandedness.
The resulting counts matrices were passed to DESeq2 to calculate fold-change and FDR (using the Benjamini-Hochberg procedure) between input and IP for each annotated transcript.
Comparisons were visualized using ggplot2, plotting the “baseMean” (mean normalized counts across all conditions) against log2(fold change).
Assembly: CP001509.1 and native F. taeanensis genome (MCCC strain 1K06699)
Supplementary files format and content: bigWig (.bw) files represent CPM-normalized files, generated using deepTools2 bamCoverage.
Supplementary files format and content: .xlsx file contains meta information on individual sequencing files.

organism: Escherichia coli

growth_protocol:
For ChIP-seq, E. coli transformations were performed using a single plasmid encoding dCas12f, σE and HTH proteins as well as two non-coding regions downstream of the native dCas12f-encoding gene and in between the σE and HTH-encoding genes. Either dCas12f, σE or HTH were 3xFLAG-tagged. Protein and gRNA components were expressed using separate constitutive promoters. The E. coli growth protocol generally followed the ChIP-seq protocols that were previously described (Hoffmann, Kim, Beh et al. 2022; Meers et al. 2023; Wiegand et al. 2024) with exception for cells grown in liquid media instead of solid media. In brief, colonies were inoculated into 25 ml liquid LB media. After 16 h incubation at 37 °C in liquid LB media with antibiotics, cells were harvested.
For RIP-seq, E. coli cells were grown as for ChIP-sample generation.
For RNA-seq, E. coli transformations were performed using two plasmids encoding a) dCas12f, σE and HTH proteins as well as two non-coding regions encoding a gRNA and a potential ncRNA (protein and gRNA components were expressed using separate constitutive promoters) and b) a plasmid encoding the native F. taeanesis RNA polymerase subunit genes rpoA, rpoB, rpoC and rpoZ driven by two T7 promoters and required induction by 0.01 mM IPTG. Colonies were inoculated into liquid LB media. After around 24 h incubation at 28 °C in liquid LB media with antibiotics, cells were harvested. Native F. taeanensis (MCCC strain 1K06699) cells were grown in Marine Broth 2216 (Difco) for 3 days at 28°C before harvesting.

extract_protocol:
For ChIP-seq, liquid LB overnight E. coli cultures were made up to 40 ml of volume using LB media. Crosslinking and immunoprecipitation generally followed our previous ChIP-seq protocols (Hoffmann, Kim, Beh et al., 2022; Meers et al., 2023), based on previously established protocols (Bonocora and Wade, 2015; Davis et al. 2011). 1 ml of 37% formaldehyde (Fisher Scientific) was added to the tubes containing 40 ml of overnight culture (~1% final concentration), and the solution was mixed immediately by inverting and vortexing. Crosslinking was performed by gently shaking at room temperature for 20 min. To stop crosslinking, 4.6 ml of 2.5 M glycine (~0.25 M final concentration) were added, followed by 10 min incubation with gentle shaking. Cells were pelleted at 4 °C by spinning at 4,000 x g for 8 min. The following steps were performed on ice, using buffers that had been sterile-filtered through a 0.22 µm filter. The supernatant was discarded and pellets were fully resuspended in 40 ml TBS buffer (20 mM Tris-HCl pH 7.5, 0.15 M NaCl) by vortexing. After another spin at 4,000 x g for 8 min at 4°C, the supernatant was removed and the pellet again resuspended in 40 ml TBS buffer. Next, the OD at 600 nm was measured for a 1:1 mixture of the cell suspension and fresh TBS buffer, and a standardised volume equivalent to 40 ml of OD600 = 0.6 was aliquoted into new 50 ml conical tubes. A final 8 min spin at 4,000 x g and 4 °C was performed, cells were pelleted, and the supernatant was discarded. Residual liquid was removed by briefly inverting the tube, and cell pellets were flash frozen using liquid nitrogen and stored at -80 °C or kept on ice for the subsequent steps. Bovine serum albumin (GoldBio) was dissolved in 1X PBS buffer (Gibco) and sterile-filtered to generate a 5 mg/ml BSA solution. For each sample, 25 µl of Dynabeads Protein G (Thermo Fisher) slurry (hereafter referred to as ‘beads’ or ‘magnetic beads’) were prepared for immunoprecipitation. Beads from up to 250 µl of the initial slurry were processed together in a single tube, and washes were performed at room temperature, as follows: The slurry was transferred to a 1.5 ml tube and placed onto a magnetic rack until the beads had fully settled. The supernatant was removed carefully, 1 ml BSA solution was added, and beads were fully resuspended by vortexing, followed by rotating for 30 seconds. This was repeated for three more washes. Finally, beads were resuspended in 25 µl (× n samples) of BSA solution, followed by addition of 4 µl (× n samples) of monoclonal ANTI-FLAG M2 antibody produced in mouse (Sigma-Aldrich). The suspension was moved to 4 °C and rotated for >3 h to conjugate antibodies to magnetic beads. While conjugation was proceeding, crosslinked cell pellets were thawed on ice, resuspended in FA Lysis Buffer 150 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 150 mM NaCl) with protease inhibitor cocktail (Sigma-Aldrich) and transferred to a 1 ml milliTUBE AFA Fiber (Covaris). Samples were sonicated on a M220 Focused-ultrasonicator (Covaris) with the following SonoLab 7.2 settings: min. temp. 4°C, set point 6 °C, max. temp. 8°C, peak power 75.0, duty factor 10, cycles/bursts 200, 17.5 min sonication time. After sonication, samples were cleared of cell debris by centrifugation at 20,000 x g and 4 °C for 20 min. The pellet was discarded, and the supernatant (~1 ml) was transferred into a fresh tube and kept on ice for immunoprecipitation. For non-inmunoprecipitated input control samples, 10 µl (~1%) of the sheared cleared lysate were transferred into a separate 1.5 ml tube, flash-frozen in liquid nitrogen, and stored at -80 °C. After >3 h, the conjugation mixture of magnetic beads and antibody was washed four times as described above, but at 4 °C. Next, the beads were resuspended in 30 µl (× n samples) FA Lysis Buffer 150 with protease inhibitor, and 31 µl of resuspended antibody-conjugated beads were mixed with each sample of sheared cell lysate. Samples were rotated overnight for 12–16 h at 4 °C for immunoprecipitation of FLAG-tagged proteins. The next day, tubes containing beads were placed on a magnetic rack and the supernatant was discarded. Then, six bead washes were performed at room temperature as follows, using 1 ml of each buffer followed by sample rotation for 1.5 min: (1) Two washes with FA Lysis Buffer 150 (without protease inhibitor); (2) one wash with FA Lysis Buffer 500 (50 mM HEPES-KOH pH 7.5, 0.1% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); (3) one wash with ChIP Wash Buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (w/v) sodium deoxycholate, 0.1% (w/v) SDS, 1 mM EDTA, 1% (v/v) Triton X-100, 500 mM NaCl); and (4) two washes with TE Buffer 10/1 (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were then placed on a magnetic rack, the supernatant was removed, and beads were resuspended in 200 µl of ChIP Elution Buffer (1% (w/v) SDS, 0.1 M NaHCO3), freshly made on the day of the washes. To release protein-DNA complexes from beads, the suspensions were incubated at 65 °C for 1.25 h with gentle vortexing every 15 min to resuspend settled beads. During this incubation, the non-immunoprecipitated input samples were thawed, and 190 µl of ChIP Elution Buffer was added, followed by the addition of 10 µl of 5 M NaCl. After the 1.25 h incubation of the immunoprecipitated samples was complete, tubes were placed back onto a magnetic rack, and the supernatant containing eluted protein-DNA complexes was transferred to a new tube. 9.75 µl of 5 M NaCl were added to ~195 µl of eluate, and samples (both immunoprecipitated and non-immunoprecipitated controls) were incubated at 65°C overnight (without shaking) to reverse-crosslink proteins and DNA. The next day, samples were mixed with 1 µl of 10 mg/ml RNase A (Thermo Fisher) and incubated for 1 h at 37 °C, followed by addition of 2.8 µl of 20 mg/ml Proteinase K (Fisher Scientific) and 1 h incubation at 55 °C. After the addition of 1 ml of buffer PB (QIAGEN recipe), samples were purified using QIAquick spin columns (QIAGEN) and eluted in 40 ul TE Buffer 10/0.1 (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).
For ChIP-seq, Illumina libraries were generated for immunoprecipitated and input samples using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Sample concentrations for ChIP-seq were determined using the DeNovix dsDNA Ultra High Sensitivity Kit. Starting DNA amounts were standardised such that an approximately equal mass of all input and immunoprecipitated DNA was used for library preparation. After adapter ligation, a single PCR amplification was performed to add Illumina barcodes, and ~450 bp-sized DNA fragments were selected using a two-sided AMPure XP bead (Beckman Coulter) size selection, as follows: The volume of barcoded immunoprecipitated and input DNA was brought up to 50 µl with TE Buffer 10/0.1; in the first size selection step, 0.55X AMPure beads (27.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the supernatant was discarded and the AMPure beads were kept; in the second size selection step, 0.35X AMPure beads (17.5 µl) were added to the DNA, the sample was placed on a magnetic rack, and the AMPure beads were discarded and the supernatant was kept. The concentration of DNA was determined for pooling using the DeNovix dsDNA High Sensitivity Kit. Illumina libraries were sequenced in paired-end mode on the Illumina NextSeq 500 and Element Biosciences Aviti Cloudbreak Freestyle platform.
The extraction protocol was performed as described in Tang et al. 2024. After overnight growth, cells equivalent to 20 ml of OD600=0.5 were aliquoted. Cells were harvested by centrifugation at 4000 × g for 10 min at 4°C, and the supernatant was removed. The pellet was washed with cold TBS (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM NaCl) and spun down again as before. The supernatant was removed, and the pellet was flash-frozen in liquid nitrogen and stored at -80°C. Antibodies for immunoprecipitation were conjugated to magnetic beads as follows: for each sample, 60 μl Dynabeads Protein G (Thermo Fisher Scientific) were washed 3× in 1 ml IP lysis buffer (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM KCl, 1 mM MgCl2, 0.2% Triton X-100), resuspended in 1 ml IP lysis buffer, combined with 20 μl anti-FLAG M2 antibody (Sigma-Aldrich, F1804), and rotated for >3 hours at 4°C. Antibody-bead complexes were washed 2× to remove unconjugated antibodies and resuspended in 60 μl of IP lysis buffer per sample. Flash-frozen pellets were thawed on ice and resuspended in 1.2 ml IP lysis buffer supplemented with 1× cOmplete Protease Inhibitor Cocktail (Roche) and 0.1 U μl−1 SUPERase•In RNase Inhibitor (Thermo Fisher Scientific). To lyse cells, samples were sonicated using a 1/8″ sonicator probe for 1.5 min total (2 s ON, 5 s OFF) at 20% amplitude. To clear cell debris and insoluble material, lysates were centrifuged at 21,000 × g for 15 min at 4 °C, and 1 ml supernatant was transferred to a new tube. At this point, two small volumes of each sample (10 μl for RIP-seq and 10 μl for cDIP-seq) were set aside as “input” starting material and stored at -80°C. For immunoprecipitation, each sample was combined with 60 μl antibody-bead complex and rotated overnight at 4°C. The next day, each sample was washed 3× with 1 ml ice-cold IP wash buffer (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM KCl, 1 mM MgCl2), using a magnetic rack to immobilize the beads in between each wash. During the final wash, each sample was separated into two separate 500 μl volumes for downstream RIP or cDIP processing. For RIP elution, the supernatant was removed, and beads were resuspended in 1000 μl TRIzol (Thermo Fisher Scientific). After 5 min incubation at RT, the supernatant containing eluted RNA was transferred to a new tube and combined with 200 μl chloroform. Samples were mixed vigorously by inversion, incubated at RT for 3 min, and centrifuged at 12,000 × g for 15 min at 4°C. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator-5 kit (Zymo Research) and eluted in 15 μl RNase-free water. RNA from input samples was isolated in the same manner using TRIzol and column purification. Purified RNA was stored at -80°C before proceeding to library preparation.
For RIP-seq library preparation (input and RIP eluates), RNA was fragmented by random hydrolysis by combining 7 μl RNA, 6 μl water, and 2 μl NEBuffer 2, and heating to 92°C for 2 min. To remove DNA and prepare RNA ends for adapter ligation, samples were treated with 2 μl TURBO DNase (Thermo Fisher Scientific) and 2 μl RppH (NEB) in the presence of 1 μl SUPERase•In RNase Inhibitor for 30 min at 37°C. This was followed by treatment with 1 μl T4 PNK (NEB) in 1× T4 DNA ligase buffer (NEB) for 30 min at 37°C. Reactions were column-purified using the Zymo RNA Clean and Concentrator-5 kit and eluted in 10.5 μl RNase-free water. RNA concentrations were quantified using the DeNovix RNA Assay. Illumina sequencing libraries were prepared using the NEBNext Small RNA Library Prep kit. Illumna ibraries were sequenced in paired-end mode on the Illumina NextSeq 500 and Element Biosciences Aviti Cloudbreak Freestyle platform.
For RNA-seq, overnight cultures were generally processed as described in Tang et al. 2024. Cells equivalent to 20 ml of OD600 = 0.5 were aliquoted and harvested by centrifugation at 4000 × g for 10 min at 4°C, and the supernatant was removed. The pellet was washed with cold TBS (20 mM Tris-HCl, pH 7.5 at 25°C, 150 mM NaCl) and spun down again as before. The supernatant was removed, and the pellet was flash-frozen in liquid nitrogen and stored at -80°C. Cell pellets were resuspended in 1,000 μl TRIzol (Thermo Fisher Scientific). After 5 min incubation at RT, the supernatant containing eluted RNA was transferred to a new tube and combined with 200 μl chloroform. Samples were mixed vigorously by inversion, incubated at RT for 3 min, and centrifuged at 12,000 × g for 15 min at 4°C. RNA was isolated from the upper aqueous phase using the RNA Clean & Concentrator kit (Zymo Research) and eluted in 15 μl RNase-free water. Purified RNA was stored at -80°C before proceeding to library preparation.
For RNA-seq library preparation, RNA was fragmented by random hydrolysis by combining 7 μl RNA, 6 μl water, and 2 μl NEBuffer 2, and heating to 92°C for 2 min. To remove DNA and prepare RNA ends for adapter ligation, samples were treated with 2 μl TURBO DNase (Thermo Fisher Scientific) and 2 μl RppH (NEB) in the presence of 1 μl SUPERase•In RNase Inhibitor for 30 min at 37°C. This was followed by treatment with 1 μl T4 PNK (NEB) in 1× T4 DNA ligase buffer (NEB) for 30 min at 37°C. Reactions were column-purified using the Zymo RNA Clean and Concentrator-5 kit and eluted in 10.5 μl RNase-free water. RNA concentrations were quantified using the DeNovix RNA Assay. Illumina sequencing libraries were prepared using the NEBNext Small RNA Library Prep kit, and libraries were sequenced on an Illumina NextSeq 500 or Element Biosciences Aviti instrument in paired-end mode with 75 or 150 cycles per end.

treatment_protocol:
For ChIP-seq, dCas12f systems were heterologously expressed in E. coli MG1655 using constitutive promoters.
For RIP-seq, dCas12f systems were heterologously expressed in E. coli MG1655 using constitutive promoters.
For RNA-seq, dCas12f systems were heterologously expressed in E. coli BL21(DE3) using constitutive promoters and the native F. taeanensis RNA polymerase was induced from T7 promoters with 0.01 mM IPTG.

tag: strain

tag: culture type

value: Liquid cell culture

tag: induction parameters

value: constitutive expression, 0.01 mM IPTG for F. taeanensis RNAP, 24 h, 28°C


title: A4427_011625

description: Library name: A4427_011625


title: A4442_011625

description: Library name: A4442_011625


title: A4467_011625

description: Library name: A4467_011625


title: Heart_bulkRNA-seq_Donor_5

description: Library name: Human heart tissue - Donor5


title: A4425_011625

description: Library name: A4425_011625


title: A4473_092424

description: Library name: A4473_092424

organism: Flagellimonas taeanensis

source_name: MCCC strain 1K06699

value: MCCC strain 1K06699

value: native expression in F. taeanensis


title: A4420_011625

description: Library name: A4420_011625


title: A4414_011625

description: Library name: A4414_011625


title: A4500_112224

description: Library name: A4500_112224


title: A4490_112224

description: Library name: A4490_112224


title: A4485_112224

description: Library name: A4485_112224


title: A4470_112224

description: Library name: A4470_112224


title: A4488_112224

description: Library name: A4488_112224


title: A4455_011625

description: Library name: A4455_011625


title: A4422_011625

description: Library name: A4422_011625


title: A4473_111324

description: Library name: A4473_111324


title: A4481_011625

description: Library name: A4481_011625


title: A4464_112224

description: Library name: A4464_112224


title: A4461_112224

description: Library name: A4461_112224


title: A4443_112224

description: Library name: A4443_112224


title: A4446_112224

description: Library name: A4446_112224


title: A4457_112224

description: Library name: A4457_112224


title: A4440_112224

description: Library name: A4440_112224


title: A4439_112224

description: Library name: A4439_112224


title: A4438_112224

description: Library name: A4438_112224


title: A4449_112224

description: Library name: A4449_112224


title: A4412_112224

description: Library name: A4412_112224


title: A4434_112224

description: Library name: A4434_112224


title: A4501_092424

description: Library name: A4501_092424


title: A4416_112224

description: Library name: A4416_112224


title: A4413_112224

description: Library name: A4413_112224


title: A4459_112224

description: Library name: A4459_112224


title: c3 replicat 3

status: Public on Jul 15 2025

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

country: France

institute: Institut Pasteur

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: Leptospira interrogans serovar manilae, NZ_CP011931.1
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Leptospira interrogans

source_name: bacterial cells

extract_protocol:
Total RNA was extracted from biofilm or planktonic cells. Cells were collected by centrifugation for 15 min at 3000xg at 4°C and resuspended in 1mL TRIzol
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit following manufacturer's protocol

value: bacterial cells

value: Manilae strain L500

value: serovar Manilae strain L500


title: A4409_112224

description: Library name: A4409_112224


title: A4407_112224

description: Library name: A4407_112224


title: A4431_112224

description: Library name: A4431_112224


title: A4444_112224

description: Library name: A4444_112224


title: A4400_112224

description: Library name: A4400_112224


title: A4408_112224

description: Library name: A4408_112224


title: A4411_112224

description: Library name: A4411_112224


title: A4491_092424

description: Library name: A4491_092424


title: A4415_092424

description: Library name: A4415_092424


title: A4433_092424

description: Library name: A4433_092424


title: c3 replicat 2

value: Manilae strain L499

value: serovar Manilae strain L499


title: Thy, replicate 4, scRNA-seq

status: Public on Jul 21 2025

city: Seoul

first: Suyeong

last: Park

address: 1, Gwanak-ro, Gwanak-gu, Seoul, Republic of Korea

department: College of Pharmacy

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
FASTQ files were produced by converting BCL files with Illumina bcl2fastq.
The gene expression and TCR data from these FASTQ files were analyzed using Cell Ranger(v.6.1.2) for both gene expression and TCR data.
Assembly: GRCh38-2020-A
Supplementary files format and content: Barcodes.tsv.gv', 'features.tsv.gv' and 'matrix.mtx.gz' files are uploaded and prefixed with individual library name for gene expression analysis.
Supplementary files format and content: Specifically, for TCR analysis, the ‘filtered_contig_annotations.csv’ file was refined to include only high-confidence, complete, and productive contigs associated with either TCRα or TCRβ chains.

source_name: NKT, MAIT and γδ T cells

extract_protocol:
Human thymus samples were obtained from cardiac patients who underwent cardiac surgery. Thymocytes were isolated by density gradient centrifugation using Ficoll-Paque (GE Healthcare Life Science). Single cell suspensions of thymocytes were stained with BV421 conjugated Anti-Human TCRγ/δ or PE conjugated CD1d and APC conjugated MR1 tetramers and enriched with anti-PE and anti-APC microbeads (Miltenyi) according to the manufacturer’s instructions. CD3+CD19- cells were identified within the single-cell-resolved lymphocyte gating. CD3+tet+ cells were then sorted and collected in RPMI-1640 with 50% FBS. The sorting purity exceeded 96%. Subsequently, iNKT, MAIT and γδ T cells were combined and processed simultaneously.
Single-cell libraries was constructed according to the manufacturer’s instructions (10x Genomics). Samples were processed using 10X genomics's Single Cell 5' R2-only chemistry, as per the manufacturer’s recommendations.

value: thymus

value: NKT, MAIT and delta-gamma T cells


title: A4465_092424

description: Library name: A4465_092424


title: c3p16 replicat 3

value: Manilae strain L496

value: serovar Manilae strain L496


title: WT PQ 50 replicate 4

source_name: Manilae strain L495

value: Manilae strain L495

value: serovar Manilae strain L495


title: c3p16 replicat 2


title: c3 replicat 1

value: Manilae strain L498

value: serovar Manilae strain L498


title: c3p16 replicat 4

value: Manilae strain L497

value: serovar Manilae strain L497


title: E53 human metatarsal, digit 4, rep 4

description: Library name: FM4_early_rep4

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV

value: chondrocytes

value: Male


title: WT PQ 10 replicate 4

value: bacterial cells


title: WT untreated replicate 3


title: WT PQ 50 replicate 2


title: WT untreated replicate 2


title: WT PQ 10 replicate 2


title: WT PQ 50 replicate 1


title: WT PQ 10 replicate 1


title: HEK293_Input

status: Public on Jul 12 2025

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

description: Library name: HEK293_Input

data_processing:
After initial assessment of read quality, pThr4 single-end ChIP-Seq reads were mapped onto human reference genome, hg38, using BWA v.0.7.17. with default parameters.
Coverage tracks in .bigwig format were generated from filtered .bam files (mapq > 20). Normalization was performed using log2-ratio of read counts over Input.
TSS/TES profiling was done using plotProfile on matrices generated with 50-bp bins using the computeMatrix function from the deeptools v.2.2.3
Assembly: hg38
Supplementary files format and content: bw, bed

source_name: embryonic kidney

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Crosslinking was performed using 1% formaldehyde for 10 min. Crosslinking was quenched with 0.125 M glycine for 5 min. Cells were successively lysed in lysis buffer LB1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1× PI), LB2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1× PI) and LB3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1× PI). Chromatin was sonicated to an average size of ~200–500 bp using UCD-200 Biorupter (30s on and 30 s off for 30 min). A total of 5 μg of pThr4 antibody (Active Motif, cat: 61361) was pre-mixed in a 50μl volume of Dynabeads protein A or protein G (Invitrogen) and was added to each sonicated chromatin sample and incubated overnight at 4°C. The chromatin-bound beads were washed two times with low salt buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 150mM NaCl), once with high salt wash buffer (0.1% Na Deoxycholate, 1% Triton X-100, 1mM EDTA, 50mM HEPES pH 7.5, 500mM NaCl), once with LiCl wash buffer (250mM LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1mM EDTA, 10mM Tris-Cl pH 8.0) and twice in TE buffer. The chromatin was reverse crosslinked overnight at 65°C with shaking at 750rpm. After DNA extraction using phenol-chloroform, the DNA was resuspended in 10mM Tris-HCl pH 8.0.
The extracted DNA was used to construct the ChIP-seq library using the NEBNext Ultra II DNA Library Prep Kit followed by sequencing with an Illumina HiSeq 3000.

treatment_protocol: To prepare pThr4_Mut samples for pThr4 ChIP, we treated HEK293 cell lysate with catalytically dead Ssu72 (Mutant) at 4°C for 30 minutes before binding to the 6D7 antibody. Every Mut sample corresponds to its paired Ssu72-treated sample (rep1, rep2).

value: embryonic kidney

value: normal

value: WT


title: WT untreated replicate 4


title: WT PQ 50 replicate 3


title: HEK293_Ssu72_rep1

description: Library name: HEK293_Ssu72_rep1_ChIP


title: HEK293_Ssu72_rep2

description: Library name: HEK293_Ssu72_rep2_ChIP


title: HEK293_Mut_rep2

description: Library name: HEK293_Mut_rep2_ChIP

value: Mutant-phosphatase


title: WT PQ 10 replicate 3


title: HCT116 cells, shNC2 rep2

status: Public on Jul 01 2025

city: Guangzhou

first: Ziyang

last: Wang

state: --- Select One ---

address: 58 Zhongshan 2nd Road

country: China

institute: Ziyang Wang, Doctor, The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: HCT116 cells were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HCT116 cells were infected with shNC, WDR43 knockdown lentiviruses for 48 h, and then screened by puromycin for 3 days.

value: colorectal carcinoma cells

value: Control

value: transfected with shNC


title: HCT116 cells, shWDR43, rep2

value: WDR43 knockdown

value: transfected with shWDR43


title: Crpaf1 rep 2

status: Public on Jun 25 2025

city: Beijing

first: Yan

last: Li

address: Haidian

institute: Capital Normal University

description: Library name: Crpaf1_2

data_processing:
Reads were mapped to the Chlamydomonas reinhardtii genome using bowtie2. Only the uniquely mapped reads were saved.
ChIP peaks were identified using HOMER
Assembly: Chlamydomonas reinhardtii CC-4532 v6.1
Supplementary files format and content: peaks.txt files were the output result from macs3 callpeak progress, containing the location and fold enrichment information of peaks.

organism: Chlamydomonas reinhardtii

source_name: single algal cells

extract_protocol:
Through systematic biochemical analyses, we identified a novel protein-protein interaction between PAF1 and SKIP in Chlamydomonas reinhardtii.  To investigate the functional significance of this interaction, we generated targeted mutants using CRISPR-Cas9 genome editing technology.  Phenotypic characterization revealed that both PAF1 and SKIP mutants exhibit coordinated regulation of the cell cycle progression.  To elucidate the molecular mechanism underlying PAF1-SKIP mediated cell cycle regulation, we employed an integrated multi-omics approach.  RNA sequencing (RNA-seq) analysis was performed to identify differentially expressed genes, while chromatin immunoprecipitation sequencing (ChIP-seq) was utilized to map the genomic loci directly bound by the PAF1-SKIP protein complex.  This comprehensive strategy enabled us to delineate the transcriptional network governed by the PAF1-SKIP regulatory module.
The ChIP product was treated with End Prep Enzyme Mix for end repairing, 5' Phosphorylation and dA-tailing in one reaction, followed by ligation to adaptors with a "T" base overhang. Adaptor ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer.

value: single algal cells


title: Crskip rep 1

description: Library name: Crskip_1

value: skip


title: Crskip rep 2

description: Library name: Crskip_2


title: HEK293_Mut_rep1

description: Library name: HEK293_Mut_rep1_ChIP


title: deltaHNSdeltaStpA_MicroC_biol_rep2

status: Public on Jun 24 2025

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

description: Library name: ag32

data_processing:
The raw reads were processed with distiller-nf pipeline using NC_000913.3 E.coli reference genome and BWA as an aligner.
Assembly: NC_000913.3
Supplementary files format and content: cooler (.cool, a contact matrix) file for each sample

growth_protocol: E. coli K-12 MG1655 strain was grown in Luria-Bertani broth at 37 °C and 200 rpm until reaching an OD600 of ~ 0.6.

extract_protocol: Cells were fixed with 3% formaldehyde and 2 mM DSG followed by treatment with lysozyme. DNA was digested with MNase. DNA ends were labeled with biotin and ligated followed by removal of biotin from non-ligated ends by Exonuclease III. The sample was de-crosslinked at 65 °C in the presence of Proteinase K followed by phenol-chloroform extraction and ethanol precipitation. RNA was removed by RNase A treatment and DNA was further purified with AMpure XP beads. Downstream steps included sonication, biotin pull down, end repair, A-tailing, ligation of Illumina Y adapters, and PCR amplification.

treatment_protocol: For heat shock treatment, cells were incubated in a water bath at 44 °C for 10 min. For transcription inhibition, cells were treated with 25 or 750 µg/mL rifampicin for 40 min at 37 °C and 200 rpm. To induce DNA damage, cells were exposed to 70 µg/mL bleomycin for 10 min at 37 °C and 200 rpm. For DNA gyrase inhibition, cells were treated with 0.025 or 0.25 µg/mL ciprofloxacin or 25 or 250 µg/mL novobiocin for 15 min at 37 °C and 200 rpm. For netropsin treatment, cells were grown to an OD600 ~ 0.4, followed by the addition of netropsin to a final concentration of 20 or 200 µg/mL and incubation for 30 min at 37 °C and 200 rpm.

value: bacteria

value: delta HNS delta StpA


title: Crpaf1 rep 1

description: Library name: Crpaf1_1


title: HCT116 cells, shWDR43, rep1


title: 1063_3

description:
Mucosal Sample 3
10x Genomics

data_processing:
We received the sequences, mapped the reads against the GRCh38 human reference genome, and quantified the read counts using Cell Ranger pipeline version 3.1.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
We enzymatically digested and dissociated fresh tumor samples according to tissue dissociation kit protocols using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS.
Briefly, 5000-6000 cells were profiled per sample using the Chromium Single Cell 3’ RNA reagent kit v3 according to the 10X Genomics protocol. The generated cDNA libraries were indexed, pooled, and sequenced in batches.

value: Metastatic melanoma


title: 620_2

description:
Sample 39
10x Genomics


title: HCT116 cells, shNC2 rep1


title: 406_2

description:
Sample 36
10x Genomics


title: WT untreated replicate 1

value: Manilae strain L495

value: serovar Manilae strain L495


title: deltaHNSdeltaStpA_MicroC_biol_rep1

description: Library name: ag31


title: 1224_1

description:
Sample 34
10x Genomics


title: 1063_2

description:
Mucosal Sample 2
10x Genomics


title: 880_1

description:
Sample 31
10x Genomics


title: 808_1

description:
Sample 32
10x Genomics


title: 1138_1

description:
Sample 28
10x Genomics


title: 1098_3

description:
Sample 29
10x Genomics


title: 964_1

description:
Sample 24
10x Genomics


title: 620_1

description:
Sample 27
10x Genomics


title: 1063_1

description:
Sample 26 (Mucosal Sample 1)
10x Genomics


title: 1098_1

description:
Sample 33
10x Genomics


title: 479_1

description:
Sample 20
10x Genomics


title: 98_1

description:
Sample 23
10x Genomics


title: 1224_2

description:
Sample 35
10x Genomics


title: 856_1

description:
Sample 16
10x Genomics


title: 406_4

description:
Sample 25
10x Genomics


title: 509_1

description:
Sample 14
10x Genomics


title: 1009_1

description:
Sample 17
10x Genomics


title: 978_1

description:
Sample 22
10x Genomics


title: 1171_1

description:
Sample 18
10x Genomics


title: 1098_2

description:
Sample 37
10x Genomics


title: 406_1

description:
Sample 19
10x Genomics


title: 1087_1

description:
Sample 10 (Mucosal Sample 5)
10x Genomics


title: 1098_4

description:
Sample 13
10x Genomics


title: 1227_1

description:
Sample 9
10x Genomics


title: 776_1

description:
Sample 15
10x Genomics


title: 509_2

description:
Sample 11
10x Genomics


title: 452_2

description:
Sample 12
10x Genomics


title: 1037_1

description:
Sample 7
10x Genomics


title: 854_1

description:
Sample 8
10x Genomics


title: 1122_1

description:
Sample 30
10x Genomics


title: 1232_1

description:
Sample 6 (Mucosal Sample 4)
10x Genomics


title: 1098_5

description:
Sample 5
10x Genomics


title: 1224_3

description:
Sample 4
10x Genomics


title: 406_3

description:
Sample 3
10x Genomics


title: Slide 1, Xenium In Situ Spatial Gene Expression

status: Public on May 30 2025

type: RNA

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: The Xenium samples underwent several rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Baysor (v0.6.2) was used to re-segment cells with prior being default segmentations (cell_boundaries.parquet). Scanpy (v1.10.1) workflows were used for normalization to the median the downstream analysis.
The processed anndata object (processed_data.h5ad) contains cells after re-segmentation and integration. .X contains log-normalized counts.

label: Xenium Human Probe Set

source_name: 5 µm kidney section

label_protocol: Xenium Human Probe Set

extract_protocol: 5 μm sections were taken for Xenium.

value: kidney


title: Slide 9, Xenium In Situ Spatial Gene Expression


title: Slide 5, Xenium In Situ Spatial Gene Expression


title: 926_1

description:
Sample 2
10x Genomics


title: Slide 7, Xenium In Situ Spatial Gene Expression


title: Slide 6, Xenium In Situ Spatial Gene Expression


title: Slide 3, Xenium In Situ Spatial Gene Expression


title: Slide 8, Xenium In Situ Spatial Gene Expression


title: Slide 4, Xenium In Situ Spatial Gene Expression