title: E74 human hand phalanges, digit 2, rep 6, MiSeq

description: Library name: HP2_late_rep6_miseq

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E74 human hand phalanges, digit 1, rep 6, MiSeq

status: Public on Aug 20 2025

type: SRA

city: Cambridge

first: Terence

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

country: USA

institute: Harvard University

description: Library name: HP1_late_rep6_miseq

library_source: transcriptomic

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3 -e 30
ribosomal read filtering with RiboDetector v0.2.7 -e rrna --chunk_size 512
Alignment to hg38 with STAR v2.7.1
Read counts generated with RSEM v1.3.3 --forward-prob 0
Differential expression calculated with DESeq2 v1.36.0
Assembly: hg38
Supplementary files format and content: RSEM output tab-delimited file with gene expression data, TPM, and FPKM

molecule: total RNA

organism: Homo sapiens

source_name: Hand phalanges, digit I

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

extract_protocol:
Embryos were microdissected under a light microscope in 10% fetal bovine serum (FBS) 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.. Each element was stripped of soft tissue and collected in a 2-ml tube containing 200 ul of TRIzol  and one 5-mm stainless steel bead. Each sample was then homogenized at 50 Hz for 2 min, followed by 1 min on ice, and a second homogenization at 50 Hz for 2 min. Samples were stored at -80˚C until RNA extraction was performed.  For each RNA extraction, samples were incubated at room temperature for 5 min and then centrifuged at 4˚C for 5 minutes at 12,000 x g. The supernatant was collected and transferred to a clean tube, to which 200 ul of chloroform was added per 1 ml of TRIzol. Each sample was then vortexed briefly and incubated at room temperature for 2 minutes before being transferred to a MaXtract tube  and centrifuged at 4˚C for 5 minutes at 12,000 x g. Following centrifugation, the aqueous phase was removed and transferred to a new microcentrifuge Eppendorf tube and an equal volume of 100% ethanol was added. After completion of this phenol-chloroform step, the RNA extraction continued using the Direct-zol RNA MicroPrep kit  following the manufacturer’s protocols and eluted in 15 ul of nuclease-free water. Samples were stored at -80˚C until library preparation. Aliquots of the samples were nanodropped to quantify the extracted RNA and to determine 260/230 and 260/280 values and then run on a HS RNA Tapestation tape to their determined their RNA integrity number (RIN) value. Only samples with RIN scores higher than 6 were used for subsequent steps so long as the average RIN for all tissues from that sample was greater than 7. Samples were then sent out for 7 rounds of sequencing on an Illumina MiSeq/NovaSeq 6000 at the Harvard Bauer Core in order to obtain ~30 million reads per sample.
Kapa mRNA HyperPrep Kit with 25 ng input volume

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.

tag: tissue

value: Hand phalanges, digit I

tag: cell type

value: chondrocytes

tag: Sex

value: Male


title: E72 human metatarsal, digit 4, rep 5, MiSeq

description: Library name: FM4_late_rep5_miseq

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E72 human metatarsal, digit 5, rep 5, MiSeq

description: Library name: FM5_late_rep5_miseq

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E72 human metatarsal, digit 3, rep 5, MiSeq

description: Library name: FM3_late_rep5_miseq

source_name: Metatarsal, digit III

value: Metatarsal, digit III


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

description: Library name: FP5_late_rep5_miseq

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E72 human metatarsal, digit 1, rep 5, MiSeq

description: Library name: FM1_late_rep5_miseq

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E72 human foot phalanges, digit 3, rep 5, MiSeq

description: Library name: FP3_late_rep5_miseq

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E72 human foot phalanges, digit 4, rep 5, MiSeq

description: Library name: FP4_late_rep5_miseq

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E72 human metacarpal, digit 4, rep 5, MiSeq

description: Library name: HM4_late_rep5_miseq

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


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

description: Library name: FP1_late_rep5_miseq

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E72 human metacarpal, digit 2, rep 5, MiSeq

description: Library name: HM2_late_rep5_miseq

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E72 human metacarpal, digit 5, rep 5, MiSeq

description: Library name: HM5_late_rep5_miseq

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E72 human metacarpal, digit 1, rep 5, MiSeq

description: Library name: HM1_late_rep5_miseq

source_name: Metacarpal, digit I

value: Metacarpal, digit I


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

description: Library name: HP5_late_rep5_miseq

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E72 human metacarpal, digit 3, rep 5, MiSeq

description: Library name: HM3_late_rep5_miseq

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E72 human hand phalanges, digit 3, rep 5, MiSeq

description: Library name: HP3_late_rep5_miseq

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


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

description: Library name: HP2_late_rep5_miseq

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II

value: chondrocytes


title: E72 human metatarsal, digit 5, rep 4, MiSeq

description: Library name: FM5_late_rep4_miseq

value: Male


title: E72 human hand phalanges, digit 4, rep 5, MiSeq

description: Library name: HP4_late_rep5_miseq

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: E72 human metatarsal, digit 3, rep 4, MiSeq

description: Library name: FM3_late_rep4_miseq

value: Metatarsal, digit III


title: E72 human metatarsal, digit 2, rep 4, MiSeq

description: Library name: FM2_late_rep4_miseq

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E72 human metatarsal, digit 4, rep 4, MiSeq

description: Library name: FM4_late_rep4_miseq

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E72 human foot phalanges, digit 5, rep 4, MiSeq

description: Library name: FP5_late_rep4_miseq

value: Foot phalanges, digit V


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

description: Library name: FP4_late_rep4_miseq

value: Footphalanges, digit IV


title: E72 human metatarsal, digit 1, rep 4, MiSeq

description: Library name: FM1_late_rep4_miseq

value: Metatarsal, digit I


title: E72 human foot phalanges, digit 3, rep 4, MiSeq

description: Library name: FP3_late_rep4_miseq

value: Foot phalanges, digit III


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

description: Library name: FP1_late_rep4_miseq

value: Foot phalanges, digit I


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

description: Library name: FP2_late_rep4_miseq

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E72 human metacarpal, digit 5, rep 4, MiSeq

description: Library name: HM5_late_rep4_miseq

value: Metacarpal, digit V


title: E72 human metacarpal, digit 4, rep 4, MiSeq

description: Library name: HM4_late_rep4_miseq

value: Metacarpal, digit IV


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

description: Library name: FP2_late_rep5_miseq


title: E72 human metacarpal, digit 3, rep 4, MiSeq

description: Library name: HM3_late_rep4_miseq

value: Metacarpal, digit II


title: E72 human metatarsal, digit 2, rep 5, MiSeq

description: Library name: FM2_late_rep5_miseq


title: E72 human metacarpal, digit 2, rep 4, MiSeq

description: Library name: HM2_late_rep4_miseq


title: E72 human metacarpal, digit 1, rep 4, MiSeq

description: Library name: HM1_late_rep4_miseq

value: Metacarpal, digit I


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

description: Library name: HP4_late_rep4_miseq


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

description: Library name: HP1_late_rep4_miseq

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E72 human hand phalanges, digit 5, rep 4, MiSeq

description: Library name: HP5_late_rep4_miseq

value: Hand phalanges, digit V

value: chondrocytes


title: E72 human hand phalanges, digit 3, rep 4, MiSeq

description: Library name: HP3_late_rep4_miseq

value: Hand phalanges, digit III

value: Male


title: E72 human metatarsal, digit 4, rep 3, MiSeq

description: Library name: FM4_late_rep3_miseq


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

description: Library name: HP2_late_rep4_miseq

value: Hand phalanges, digit II


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

description: Library name: HP1_late_rep5_miseq


title: E72 human metatarsal, digit 2, rep 3, MiSeq

description: Library name: FM2_late_rep3_miseq

value: Metatarsal, digit II


title: E72 human metatarsal, digit 5, rep 3, MiSeq

description: Library name: FM5_late_rep3_miseq

source_name: Metatarsal, digit V

value: Metatarsal, digit V


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

description: Library name: FP3_late_rep3_miseq

source_name: Foot phalanges, digit III


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

description: Library name: FP2_late_rep3_miseq


title: E72 human metatarsal, digit 1, rep 3, MiSeq

description: Library name: FM1_late_rep3_miseq

source_name: Metatarsal, digit I


title: E72 human foot phalanges, digit 4, rep 3, MiSeq

description: Library name: FP4_late_rep3_miseq

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E72 human metacarpal, digit 3, rep 3, MiSeq

description: Library name: HM3_late_rep3_miseq

value: Metacarpal, digit III


title: E72 human metacarpal, digit 4, rep 3, MiSeq

description: Library name: HM4_late_rep3_miseq

source_name: Metacarpal, digit IV


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

description: Library name: FP1_late_rep3_miseq

source_name: Foot phalanges, digit I


title: E72 human foot phalanges, digit 5, rep 3, MiSeq

description: Library name: FP5_late_rep3_miseq

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


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

description: Library name: HP3_late_rep3_miseq


title: E72 human hand phalanges, digit 4, rep 3, MiSeq

description: Library name: HP4_late_rep3_miseq

value: Hand phalanges, digit IV


title: E72 human hand phalanges, digit 5, rep 3, MiSeq

description: Library name: HP5_late_rep3_miseq


title: E72 human metacarpal, digit 1, rep 3, MiSeq

description: Library name: HM1_late_rep3_miseq

source_name: Metacarpal, digit I


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

description: Library name: HP1_late_rep3_miseq


title: E67 human metatarsal, digit 4, rep 2, MiSeq

description: Library name: FM4_late_rep2_miseq

value: Metatarsal, digit IV


title: E72 human metacarpal, digit 2, rep 3, MiSeq

description: Library name: HM2_late_rep3_miseq

source_name: Metacarpal, digit II


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

description: Library name: HP2_late_rep3_miseq


title: E67 human metatarsal, digit 3, rep 2, MiSeq

description: Library name: FM3_late_rep2_miseq

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E72 human metatarsal, digit 3, rep 3, MiSeq

description: Library name: FM3_late_rep3_miseq


title: E67 human metatarsal, digit 1, rep 2, MiSeq

description: Library name: FM1_late_rep2_miseq

value: Metatarsal, digit I


title: E67 human foot phalanges, digit 4, rep 2, MiSeq

description: Library name: FP4_late_rep2_miseq


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

description: Library name: FP3_late_rep2_miseq

value: Foot phalanges, digit III


title: E67 human foot phalanges, digit 5, rep 2, MiSeq

description: Library name: FP5_late_rep2_miseq


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

description: Library name: FP2_late_rep2_miseq

value: Foot phalanges, digit II


title: E67 human metacarpal, digit 5, rep 2, MiSeq

description: Library name: HM5_late_rep2_miseq

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E67 human foot phalanges, digit 1, rep 2, MiSeq

description: Library name: FP1_late_rep2_miseq

value: Foot phalanges, digit I


title: E72 human metacarpal, digit 5, rep 3, MiSeq

description: Library name: HM5_late_rep3_miseq

value: chondrocytes


title: E67 human metacarpal, digit 4, rep 2, MiSeq

description: Library name: HM4_late_rep2_miseq

value: Metacarpal, digit IV


title: E67 human metacarpal, digit 2, rep 2, MiSeq

description: Library name: HM2_late_rep2_miseq

value: Metacarpal, digit II

value: Male


title: E67 human hand phalanges, digit 4, rep 2, MiSeq

description: Library name: HP4_late_rep2_miseq


title: E67 human hand phalanges, digit 5, rep 2, MiSeq

description: Library name: HP5_late_rep2_miseq

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


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

description: Library name: HP2_late_rep2_miseq

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E67 human metatarsal, digit 5, rep 2, MiSeq

description: Library name: FM5_late_rep2_miseq

value: Metatarsal, digit V


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

description: Library name: HP3_late_rep2_miseq

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


title: E67 human hand phalanges, digit 1, rep 2, MiSeq

description: Library name: HP1_late_rep2_miseq

value: Hand phalanges, digit I


title: E67 human metatarsal, digit 2, rep 1, MiSeq

description: Library name: FM2_late_rep1_miseq

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E67 human metatarsal, digit 5, rep 1, MiSeq

description: Library name: FM5_late_rep1_miseq


title: E67 human metatarsal, digit 1, rep 1, MiSeq

description: Library name: FM1_late_rep1_miseq


title: E67 human foot phalanges, digit 5, rep 1, MiSeq

description: Library name: FP5_late_rep1_miseq

value: Foot phalanges, digit V


title: E67 human metatarsal, digit 3, rep 1, MiSeq

description: Library name: FM3_late_rep1_miseq

value: Metatarsal, digit III


title: E67 human foot phalanges, digit 4, rep 1, MiSeq

description: Library name: FP4_late_rep1_miseq

value: Footphalanges, digit IV


title: E67 human metatarsal, digit 2, rep 2, MiSeq

description: Library name: FM2_late_rep2_miseq


title: E67 human metacarpal, digit 5, rep 1, MiSeq

description: Library name: HM5_late_rep1_miseq


title: E67 human metacarpal, digit 4, rep 1, MiSeq

description: Library name: HM4_late_rep1_miseq


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

description: Library name: FP1_late_rep1_miseq


title: E67 human metatarsal, digit 4, rep 1, MiSeq

description: Library name: FM4_late_rep1_miseq

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


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

description: Library name: FP3_late_rep1_miseq

value: Foot phalanges, digit III


title: E67 human foot phalanges, digit 2, rep 1, MiSeq

description: Library name: FP2_late_rep1_miseq

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E67 human metacarpal, digit 3, rep 2, MiSeq

description: Library name: HM3_late_rep2_miseq

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E67 human metacarpal, digit 3, rep 1, MiSeq

description: Library name: HM3_late_rep1_miseq

value: chondrocytes


title: E67 human metacarpal, digit 2, rep 1, MiSeq

description: Library name: HM2_late_rep1_miseq


title: E67 human metacarpal, digit 1, rep 2, MiSeq

description: Library name: HM1_late_rep2_miseq

value: Metacarpal, digit I


title: E67 human hand phalanges, digit 2, rep 1, MiSeq

description: Library name: HP2_late_rep1_miseq


title: E67 human hand phalanges, digit 4, rep 1, MiSeq

description: Library name: HP4_late_rep1_miseq

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: E59 human metatarsal, digit 5, rep 6

description: Library name: FM5_early_rep6

source_name: Metatarsal, digit V

value: Female


title: E59 human metatarsal, digit 4, rep 6

description: Library name: FM4_early_rep6


title: E59 human metatarsal, digit 2, rep 6

description: Library name: FM2_early_rep6


title: E59 human metatarsal, digit 3, rep 6

description: Library name: FM3_early_rep6


title: E59 human metatarsal, digit 1, rep 6

description: Library name: FM1_early_rep6

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E59 human foot phalanges, digit 4, rep 6

description: Library name: FP4_early_rep6

source_name: Footphalanges, digit IV


title: E59 human foot phalanges, digit 5, rep 6

description: Library name: FP5_early_rep6


title: E59 human foot phalanges, digit 2, rep 6

description: Library name: FP2_early_rep6


title: E59 human foot phalanges, digit 3, rep 6

description: Library name: FP3_early_rep6

source_name: Foot phalanges, digit III


title: E59 human foot phalanges, digit 1, rep 6

description: Library name: FP1_early_rep6

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E59 human metacarpal, digit 4, rep 6

description: Library name: HM4_early_rep6

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E59 human metacarpal, digit 5, rep 6

description: Library name: HM5_early_rep6

value: Metacarpal, digit V


title: E59 human metacarpal, digit 2, rep 6

description: Library name: HM2_early_rep6

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E59 human metacarpal, digit 3, rep 6

description: Library name: HM3_early_rep6


title: E59 human metacarpal, digit 1, rep 6

description: Library name: HM1_early_rep6

source_name: Metacarpal, digit I


title: E59 human hand phalanges, digit 5, rep 6

description: Library name: HP5_early_rep6

value: Hand phalanges, digit V


title: E59 human hand phalanges, digit 3, rep 6

description: Library name: HP3_early_rep6

value: Hand phalanges, digit III


title: E59 human hand phalanges, digit 2, rep 6

description: Library name: HP2_early_rep6

value: Hand phalanges, digit II


title: E67 human hand phalanges, digit 5, rep 1, MiSeq

description: Library name: HP5_late_rep1_miseq

value: Male


title: E59 human hand phalanges, digit 4, rep 6

description: Library name: HP4_early_rep6


title: E59 human hand phalanges, digit 1, rep 6

description: Library name: HP1_early_rep6

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E67 human metacarpal, digit 1, rep 1, MiSeq

description: Library name: HM1_late_rep1_miseq


title: E57 human metatarsal, digit 2, rep 5

description: Library name: FM2_early_rep5

value: Metatarsal, digit II


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

description: Library name: HP3_late_rep1_miseq


title: E57 human metatarsal, digit 3, rep 5

description: Library name: FM3_early_rep5

source_name: Metatarsal, digit III

value: Metatarsal, digit III


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

description: Library name: HP1_late_rep1_miseq


title: E57 human metatarsal, digit 5, rep 5

description: Library name: FM5_early_rep5

value: Metatarsal, digit V


title: E57 human metatarsal, digit 1, rep 5

description: Library name: FM1_early_rep5

value: chondrocytes


title: E57 human foot phalanges, digit 4, rep 5

description: Library name: FP4_early_rep5

value: Footphalanges, digit IV


title: E57 human foot phalanges, digit 5, rep 5

description: Library name: FP5_early_rep5

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E57 human foot phalanges, digit 3, rep 5

description: Library name: FP3_early_rep5

value: Foot phalanges, digit III


title: E57 human foot phalanges, digit 1, rep 5

description: Library name: FP1_early_rep5


title: E57 human foot phalanges, digit 2, rep 5

description: Library name: FP2_early_rep5

value: Foot phalanges, digit II


title: E57 human metacarpal, digit 5, rep 5

description: Library name: HM5_early_rep5

source_name: Metacarpal, digit V


title: E57 human metacarpal, digit 4, rep 5

description: Library name: HM4_early_rep5


title: E57 human metacarpal, digit 3, rep 5

description: Library name: HM3_early_rep5

value: Metacarpal, digit III


title: E57 human metacarpal, digit 1, rep 5

description: Library name: HM1_early_rep5

value: Metacarpal, digit I


title: E57 human metacarpal, digit 2, rep 5

description: Library name: HM2_early_rep5


title: E57 human hand phalanges, digit 4, rep 5

description: Library name: HP4_early_rep5

value: Hand phalanges, digit IV


title: E57 human hand phalanges, digit 3, rep 5

description: Library name: HP3_early_rep5

source_name: Hand phalanges, digit III


title: E54 human metatarsal, digit 5, rep 4

description: Library name: FM5_early_rep4


title: E57 human metatarsal, digit 4, rep 5

description: Library name: FM4_early_rep5

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E57 human hand phalanges, digit 2, rep 5

description: Library name: HP2_early_rep5

source_name: Hand phalanges, digit II


title: E57 human hand phalanges, digit 1, rep 5

description: Library name: HP1_early_rep5


title: E54 human metatarsal, digit 3, rep 4

description: Library name: FM3_early_rep4


title: E54 human metatarsal, digit 2, rep 4

description: Library name: FM2_early_rep4

source_name: Metatarsal, digit II


title: E54 human metatarsal, digit 4, rep 4

description: Library name: FM4_early_rep4


title: E54 human foot phalanges, digit 5, rep 4

description: Library name: FP5_early_rep4


title: E54 human foot phalanges, digit 4, rep 4

description: Library name: FP4_early_rep4


title: E54 human foot phalanges, digit 3, rep 4

description: Library name: FP3_early_rep4


title: E54 human metacarpal, digit 3, rep 4

description: Library name: HM3_early_rep4

value: Metacarpal, digit II


title: E54 human metatarsal, digit 1, rep 4

description: Library name: FM1_early_rep4

value: Metatarsal, digit I


title: E54 human foot phalanges, digit 2, rep 4

description: Library name: FP2_early_rep4

source_name: Foot phalanges, digit II


title: E54 human metacarpal, digit 4, rep 4

description: Library name: HM4_early_rep4

value: Metacarpal, digit IV


title: E54 human metacarpal, digit 5, rep 4

description: Library name: HM5_early_rep4

value: Metacarpal, digit V

value: Male


title: E54 human foot phalanges, digit 1, rep 4

description: Library name: FP1_early_rep4

value: Foot phalanges, digit I


title: E54 human metacarpal, digit 2, rep 4

description: Library name: HM2_early_rep4


title: E54 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: E54 human metacarpal, digit 1, rep 4

description: Library name: HM1_early_rep4


title: E54 human hand phalanges, digit 4, rep 4

description: Library name: HP4_early_rep4

source_name: Hand phalanges, digit IV


title: E54 human hand phalanges, digit 2, rep 4

description: Library name: HP2_early_rep4

value: Hand phalanges, digit II


title: E54 human hand phalanges, digit 1, rep 4

description: Library name: HP1_early_rep4

value: Hand phalanges, digit I

value: chondrocytes


title: E54 human hand phalanges, digit 3, rep 4

description: Library name: HP3_early_rep4

value: Hand phalanges, digit III


title: E54 human metatarsal, digit 4, rep 3

description: Library name: FM4_early_rep3


title: E54 human metatarsal, digit 2, rep 3

description: Library name: FM2_early_rep3

value: Metatarsal, digit II


title: E57 human hand phalanges, digit 5, rep 5

description: Library name: HP5_early_rep5


title: E54 human metatarsal, digit 1, rep 3

description: Library name: FM1_early_rep3

source_name: Metatarsal, digit I


title: E54 human metatarsal, digit 3, rep 3

description: Library name: FM3_early_rep3

value: Metatarsal, digit III


title: E54 human foot phalanges, digit 5, rep 3

description: Library name: FP5_early_rep3

value: Foot phalanges, digit V


title: E54 human foot phalanges, digit 2, rep 3

description: Library name: FP2_early_rep3

value: Foot phalanges, digit II


title: E54 human foot phalanges, digit 3, rep 3

description: Library name: FP3_early_rep3

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E54 human metacarpal, digit 4, rep 3

description: Library name: HM4_early_rep3


title: E54 human metacarpal, digit 1, rep 3

description: Library name: HM1_early_rep3

value: Metacarpal, digit I


title: E54 human metacarpal, digit 3, rep 3

description: Library name: HM3_early_rep3

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E54 human foot phalanges, digit 1, rep 3

description: Library name: FP1_early_rep3

source_name: Foot phalanges, digit I


title: E54 human metacarpal, digit 5, rep 3

description: Library name: HM5_early_rep3


title: E54 human hand phalanges, digit 1, rep 3

description: Library name: HP1_early_rep3


title: E54 human metacarpal, digit 2, rep 3

description: Library name: HM2_early_rep3

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E54 human hand phalanges, digit 5, rep 3

description: Library name: HP5_early_rep3


title: E54 human metatarsal, digit 5, rep 3

description: Library name: FM5_early_rep3

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E54 human hand phalanges, digit 3, rep 3

description: Library name: HP3_early_rep3


title: E53 human metatarsal, digit 4, rep 2

description: Library name: FM4_early_rep2

value: Metatarsal, digit IV


title: E53 human metatarsal, digit 3, rep 2

description: Library name: FM3_early_rep2

value: Male


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

description: Library name: FP4_early_rep2

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E53 human metatarsal, digit 1, rep 2

description: Library name: FM1_early_rep2

value: Metatarsal, digit I


title: E53 human metatarsal, digit 2, rep 2

description: Library name: FM2_early_rep2


title: E53 human foot phalanges, digit 3, rep 2

description: Library name: FP3_early_rep2


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

description: Library name: FP1_early_rep2

value: Foot phalanges, digit I


title: E53 human metacarpal, digit 4, rep 2

description: Library name: HM4_early_rep2

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E53 human metacarpal, digit 2, rep 2

description: Library name: HM2_early_rep2

value: chondrocytes


title: E53 human metacarpal, digit 1, rep 2

description: Library name: HM1_early_rep2

source_name: Metacarpal, digit I


title: E53 human hand phalanges, digit 5, rep 2

description: Library name: HP5_early_rep2

value: Hand phalanges, digit V


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

description: Library name: HP4_early_rep2

value: Hand phalanges, digit IV


title: E53 human hand phalanges, digit 3, rep 2

description: Library name: HP3_early_rep2

value: Hand phalanges, digit III


title: E53 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: E57 human metatarsal, digit 4, rep 1

description: Library name: FM4_early_rep1

value: Female


title: E54 human foot phalanges, digit 4, rep 3

description: Library name: FP4_early_rep3


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

description: Library name: HP2_early_rep2

value: Hand phalanges, digit II


title: E57 human metatarsal, digit 5, rep 1

description: Library name: FM5_early_rep1


title: E57 human metatarsal, digit 2, rep 1

description: Library name: FM2_early_rep1

value: Metatarsal, digit II


title: E57 human metatarsal, digit 3, rep 1

description: Library name: FM3_early_rep1

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E57 human metatarsal, digit 1, rep 1

description: Library name: FM1_early_rep1


title: E53 human foot phalanges, digit 5, rep 2

description: Library name: FP5_early_rep2

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E57 human foot phalanges, digit 4, rep 1

description: Library name: FP4_early_rep1


title: E57 human foot phalanges, digit 5, rep 1

description: Library name: FP5_early_rep1


title: E57 human foot phalanges, digit 2, rep 1

description: Library name: FP2_early_rep1

value: Foot phalanges, digit II


title: E54 human hand phalanges, digit 2, rep 3

description: Library name: HP2_early_rep3

source_name: Hand phalanges, digit II


title: E57 human metacarpal, digit 5, rep 1

description: Library name: HM5_early_rep1

source_name: Metacarpal, digit V

value: Metacarpal, digit V


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

description: Library name: FP2_early_rep2

source_name: Foot phalanges, digit II

value: Male


title: E57 human metacarpal, digit 3, rep 1

description: Library name: HM3_early_rep1

value: Metacarpal, digit II


title: E54 human hand phalanges, digit 4, rep 3

description: Library name: HP4_early_rep3


title: E53 human metatarsal, digit 5, rep 2

description: Library name: FM5_early_rep2

value: Metatarsal, digit V


title: E53 human metacarpal, digit 5, rep 2

description: Library name: HM5_early_rep2


title: E53 human metacarpal, digit 3, rep 2

description: Library name: HM3_early_rep2

value: Metacarpal, digit III


title: E57 human metacarpal, digit 1, rep 1

description: Library name: HM1_early_rep1

value: Metacarpal, digit I


title: E57 human metacarpal, digit 4, rep 1

description: Library name: HM4_early_rep1

value: Metacarpal, digit IV

value: chondrocytes


title: E57 human foot phalanges, digit 3, rep 1

description: Library name: FP3_early_rep1

value: Foot phalanges, digit III


title: E57 human hand phalanges, digit 5, rep 1

description: Library name: HP5_early_rep1

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E57 human hand phalanges, digit 4, rep 1

description: Library name: HP4_early_rep1

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: E57 human hand phalanges, digit 3, rep 1

description: Library name: HP3_early_rep1

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III

value: Female


title: E57 human hand phalanges, digit 2, rep 1

description: Library name: HP2_early_rep1

value: Hand phalanges, digit II


title: E74 human metatarsal, digit 5, rep 6

description: Library name: FM5_late_rep6


title: E74 human metatarsal, digit 3, rep 6

description: Library name: FM3_late_rep6

value: Metatarsal, digit III


title: E74 human metatarsal, digit 4, rep 6

description: Library name: FM4_late_rep6

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E74 human foot phalanges, digit 5, rep 6

description: Library name: FP5_late_rep6

value: Foot phalanges, digit V


title: E74 human metatarsal, digit 1, rep 6

description: Library name: FM1_late_rep6

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E57 human foot phalanges, digit 1, rep 1

description: Library name: FP1_early_rep1

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E74 human foot phalanges, digit 2, rep 6

description: Library name: FP2_late_rep6

value: Foot phalanges, digit II

value: Male


title: E74 human foot phalanges, digit 4, rep 6

description: Library name: FP4_late_rep6

value: Footphalanges, digit IV


title: E74 human foot phalanges, digit 3, rep 6

description: Library name: FP3_late_rep6

source_name: Foot phalanges, digit III


title: E57 human metacarpal, digit 2, rep 1

description: Library name: HM2_early_rep1

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E74 human metacarpal, digit 4, rep 6

description: Library name: HM4_late_rep6

value: Metacarpal, digit IV


title: E74 human foot phalanges, digit 1, rep 6

description: Library name: FP1_late_rep6

value: chondrocytes


title: E74 human metacarpal, digit 3, rep 6

description: Library name: HM3_late_rep6

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E74 human metacarpal, digit 5, rep 6

description: Library name: HM5_late_rep6

value: Metacarpal, digit V


title: E74 human hand phalanges, digit 1, rep 6

description: Library name: HP1_late_rep6

value: Hand phalanges, digit I


title: E72 human metatarsal, digit 5, rep 5

description: Library name: FM5_late_rep5

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E72 human metatarsal, digit 3, rep 5

description: Library name: FM3_late_rep5


title: E74 human metacarpal, digit 1, rep 6

description: Library name: HM1_late_rep6

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E72 human metatarsal, digit 4, rep 5

description: Library name: FM4_late_rep5


title: E74 human hand phalanges, digit 5, rep 6

description: Library name: HP5_late_rep6

value: Hand phalanges, digit V


title: E74 human hand phalanges, digit 3, rep 6

description: Library name: HP3_late_rep6

value: Hand phalanges, digit III


title: E74 human hand phalanges, digit 2, rep 6

description: Library name: HP2_late_rep6

value: Hand phalanges, digit II


title: E74 human hand phalanges, digit 4, rep 6

description: Library name: HP4_late_rep6

value: Hand phalanges, digit IV


title: E72 human metatarsal, digit 1, rep 5

description: Library name: FM1_late_rep5

value: Metatarsal, digit I


title: E72 human metatarsal, digit 2, rep 5

description: Library name: FM2_late_rep5

source_name: Metatarsal, digit II

value: Metatarsal, digit II


title: E57 human hand phalanges, digit 1, rep 1

description: Library name: HP1_early_rep1

source_name: Hand phalanges, digit I

value: Female


title: E74 human metatarsal, digit 2, rep 6

description: Library name: FM2_late_rep6

value: Male


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

description: Library name: FP5_late_rep5

source_name: Foot phalanges, digit V

value: Foot phalanges, digit V


title: E72 human foot phalanges, digit 4, rep 5

description: Library name: FP4_late_rep5

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


title: E72 human foot phalanges, digit 3, rep 5

description: Library name: FP3_late_rep5

value: Foot phalanges, digit III


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

description: Library name: FP2_late_rep5

value: Foot phalanges, digit II

value: chondrocytes


title: E74 human metacarpal, digit 2, rep 6

description: Library name: HM2_late_rep6

value: Metacarpal, digit II


title: E72 human metacarpal, digit 5, rep 5

description: Library name: HM5_late_rep5

source_name: Metacarpal, digit V

value: Metacarpal, digit V


title: E72 human metacarpal, digit 4, rep 5

description: Library name: HM4_late_rep5

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E72 human metacarpal, digit 2, rep 5

description: Library name: HM2_late_rep5


title: E72 human metacarpal, digit 3, rep 5

description: Library name: HM3_late_rep5

value: Metacarpal, digit III


title: E72 human metacarpal, digit 1, rep 5

description: Library name: HM1_late_rep5

value: Metacarpal, digit I


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

description: Library name: HP5_late_rep5

source_name: Hand phalanges, digit V

value: Hand phalanges, digit V


title: E72 human hand phalanges, digit 4, rep 5

description: Library name: HP4_late_rep5

source_name: Hand phalanges, digit IV


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

description: Library name: HP2_late_rep5

source_name: Hand phalanges, digit II

value: Hand phalanges, digit II


title: E72 human hand phalanges, digit 3, rep 5

description: Library name: HP3_late_rep5

source_name: Hand phalanges, digit III

value: Hand phalanges, digit III


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

description: Library name: HP1_late_rep5

value: Hand phalanges, digit I


title: E72 human metatarsal, digit 5, rep 4

description: Library name: FM5_late_rep4

value: Metatarsal, digit V


title: E72 human metatarsal, digit 4, rep 4

description: Library name: FM4_late_rep4

source_name: Metatarsal, digit IV

value: Metatarsal, digit IV


title: E72 human metatarsal, digit 3, rep 4

description: Library name: FM3_late_rep4

source_name: Metatarsal, digit III

value: Metatarsal, digit III

value: Male


title: E72 human metatarsal, digit 2, rep 4

description: Library name: FM2_late_rep4

value: Metatarsal, digit II


title: E72 human metatarsal, digit 1, rep 4

description: Library name: FM1_late_rep4

source_name: Metatarsal, digit I

value: Metatarsal, digit I


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

description: Library name: FP4_late_rep4

value: Footphalanges, digit IV


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

description: Library name: FP1_late_rep4

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I

value: chondrocytes


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

description: Library name: FP2_late_rep4

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E72 human foot phalanges, digit 3, rep 4

description: Library name: FP3_late_rep4

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E72 human metacarpal, digit 5, rep 4

description: Library name: HM5_late_rep4

value: Metacarpal, digit V


title: E72 human foot phalanges, digit 5, rep 4

description: Library name: FP5_late_rep4

value: Foot phalanges, digit V


title: E72 human metacarpal, digit 2, rep 4

description: Library name: HM2_late_rep4

source_name: Metacarpal, digit II

value: Metacarpal, digit II


title: E72 human metacarpal, digit 3, rep 4

description: Library name: HM3_late_rep4


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

description: Library name: FP1_late_rep5


title: E72 human hand phalanges, digit 5, rep 4

description: Library name: HP5_late_rep4

value: Hand phalanges, digit V


title: E72 human metacarpal, digit 1, rep 4

description: Library name: HM1_late_rep4

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E72 human hand phalanges, digit 3, rep 4

description: Library name: HP3_late_rep4

value: Hand phalanges, digit III


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

description: Library name: HP2_late_rep4

value: Hand phalanges, digit II


title: E72 human metatarsal, digit 5, rep 3

description: Library name: FM5_late_rep3

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E72 human metatarsal, digit 3, rep 3

description: Library name: FM3_late_rep3

value: Metatarsal, digit III


title: E72 human metatarsal, digit 2, rep 3

description: Library name: FM2_late_rep3

source_name: Metatarsal, digit II

value: Male


title: E72 human metatarsal, digit 4, rep 3

description: Library name: FM4_late_rep3

value: Metatarsal, digit IV


title: E72 human metatarsal, digit 1, rep 3

description: Library name: FM1_late_rep3

value: Metatarsal, digit I


title: E72 human foot phalanges, digit 5, rep 3

description: Library name: FP5_late_rep3

source_name: Foot phalanges, digit V


title: E72 human foot phalanges, digit 4, rep 3

description: Library name: FP4_late_rep3

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV


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

description: Library name: FP3_late_rep3


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

description: Library name: FP2_late_rep3


title: E72 human metacarpal, digit 5, rep 3

description: Library name: HM5_late_rep3

source_name: Metacarpal, digit V


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

description: Library name: FP1_late_rep3

value: Foot phalanges, digit I


title: E72 human metacarpal, digit 2, rep 3

description: Library name: HM2_late_rep3

value: chondrocytes


title: E72 human metacarpal, digit 1, rep 3

description: Library name: HM1_late_rep3


title: E72 human metacarpal, digit 3, rep 3

description: Library name: HM3_late_rep3

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E72 human metacarpal, digit 4, rep 3

description: Library name: HM4_late_rep3

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E72 human metacarpal, digit 4, rep 4

description: Library name: HM4_late_rep4


title: E72 human hand phalanges, digit 5, rep 3

description: Library name: HP5_late_rep3

source_name: Hand phalanges, digit V


title: E72 human hand phalanges, digit 4, rep 3

description: Library name: HP4_late_rep3

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


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

description: Library name: HP3_late_rep3

source_name: Hand phalanges, digit III


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

description: Library name: HP2_late_rep3

source_name: Hand phalanges, digit II


title: E67 human metatarsal, digit 4, rep 2

description: Library name: FM4_late_rep2

source_name: Metatarsal, digit IV


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

description: Library name: HP4_late_rep4


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

description: Library name: HP1_late_rep3

source_name: Hand phalanges, digit I

value: Hand phalanges, digit I


title: E67 human metatarsal, digit 2, rep 2

description: Library name: FM2_late_rep2

value: Metatarsal, digit II


title: E67 human metatarsal, digit 3, rep 2

description: Library name: FM3_late_rep2

source_name: Metatarsal, digit III


title: E67 human metatarsal, digit 1, rep 2

description: Library name: FM1_late_rep2

source_name: Metatarsal, digit I


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

description: Library name: HP1_late_rep4


title: E67 human foot phalanges, digit 5, rep 2

description: Library name: FP5_late_rep2

value: Foot phalanges, digit V


title: E67 human foot phalanges, digit 4, rep 2

description: Library name: FP4_late_rep2


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

description: Library name: FP2_late_rep2

source_name: Foot phalanges, digit II

value: Foot phalanges, digit II


title: E67 human foot phalanges, digit 1, rep 2

description: Library name: FP1_late_rep2

source_name: Foot phalanges, digit I


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

description: Library name: FP3_late_rep2

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E67 human metacarpal, digit 5, rep 2

description: Library name: HM5_late_rep2

value: Metacarpal, digit V


title: E67 human metatarsal, digit 5, rep 2

description: Library name: FM5_late_rep2

source_name: Metatarsal, digit V

value: Metatarsal, digit V


title: E67 human metacarpal, digit 4, rep 2

description: Library name: HM4_late_rep2


title: E67 human metacarpal, digit 3, rep 2

description: Library name: HM3_late_rep2


title: E67 human metacarpal, digit 1, rep 2

description: Library name: HM1_late_rep2

source_name: Metacarpal, digit I

value: Metacarpal, digit I


title: E67 human hand phalanges, digit 5, rep 2

description: Library name: HP5_late_rep2

value: Hand phalanges, digit V

value: Male


title: E67 human hand phalanges, digit 4, rep 2

description: Library name: HP4_late_rep2


title: E67 human metacarpal, digit 2, rep 2

description: Library name: HM2_late_rep2

source_name: Metacarpal, digit II

value: Metacarpal, digit II


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

description: Library name: HP2_late_rep2

value: Hand phalanges, digit II


title: E67 human metatarsal, digit 5, rep 1

description: Library name: FM5_late_rep1


title: E67 human hand phalanges, digit 1, rep 2

description: Library name: HP1_late_rep2


title: E67 human metatarsal, digit 4, rep 1

description: Library name: FM4_late_rep1

value: Metatarsal, digit IV


title: E67 human metatarsal, digit 3, rep 1

description: Library name: FM3_late_rep1

value: Metatarsal, digit III

value: chondrocytes


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

description: Library name: HP3_late_rep2

value: Hand phalanges, digit III


title: E67 human metatarsal, digit 2, rep 1

description: Library name: FM2_late_rep1

source_name: Metatarsal, digit II


title: E67 human foot phalanges, digit 5, rep 1

description: Library name: FP5_late_rep1

source_name: Foot phalanges, digit V


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

description: Library name: FP3_late_rep1


title: E67 human foot phalanges, digit 2, rep 1

description: Library name: FP2_late_rep1


title: E67 human metatarsal, digit 1, rep 1

description: Library name: FM1_late_rep1

value: Metatarsal, digit I


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

description: Library name: FP1_late_rep1

value: Foot phalanges, digit I


title: E67 human metacarpal, digit 5, rep 1

description: Library name: HM5_late_rep1

source_name: Metacarpal, digit V


title: E67 human metacarpal, digit 3, rep 1

description: Library name: HM3_late_rep1


title: E67 human metacarpal, digit 2, rep 1

description: Library name: HM2_late_rep1


title: E67 human metacarpal, digit 4, rep 1

description: Library name: HM4_late_rep1

source_name: Metacarpal, digit IV

value: Metacarpal, digit IV


title: E67 human metacarpal, digit 1, rep 1

description: Library name: HM1_late_rep1


title: E67 human hand phalanges, digit 5, rep 1

description: Library name: HP5_late_rep1

source_name: Hand phalanges, digit V


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

description: Library name: HP3_late_rep1

source_name: Hand phalanges, digit III


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

description: Library name: HP1_late_rep1

value: Hand phalanges, digit I


title: E67 human hand phalanges, digit 4, rep 1

description: Library name: HP4_late_rep1

source_name: Hand phalanges, digit IV

value: Hand phalanges, digit IV


title: E15.5 mouse foot phalanges, digit 3, rep 2, MiSeq, KAPA (RNAseq)

description:
Library name: FP3_MiSeq_D_KAPA
Kapa mRNA HyperPrep kit for comparison with human samples

data_processing:
concatenate reads
adapter trimming with NGmerge v0.3 -e 30
ribosomal read filtering with RiboDetector v0.2.7  -e rrna  --chunk_size 512
Alignment to mm10 with STAR v2.7.1
Read counts generated with RSEM v1.3.3 --forward-prob 0.5
Differential expression calculated with DESeq2 v1.36.0
Assembly: mm10
Supplementary files format and content: RSEM output tab-delimited file with gene expression data, TPM, and FPKM

organism: Mus musculus

growth_protocol: in vivo collected E15.5 mouse autopod chondrocytes

extract_protocol:
Embryos were microdissected under a light microscope in 10% fetal bovine serum (FBS) in Dulbecco’s Modified Eagle Medium (DMEM) on ice and anatomically sexed. 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 fore- and hind limbs. The right and left sides of each element were pooled together. Each element was stripped of soft tissue and collected in a 2-ml tube containing 200 ul of TRIzol  and one 5-mm stainless steel bead. Each sample was then homogenized at 50 Hz for 2 min, followed by 1 min on ice, and a second homogenization at 50 Hz for 2 min. Samples were stored at -80˚C until RNA extraction was performed.  For each RNA extraction, samples were incubated at room temperature for 5 min and then centrifuged at 4˚C for 5 minutes at 12,000 x g. The supernatant was collected and transferred to a clean tube, to which 200 ul of chloroform was added per 1 ml of TRIzol. Each sample was then vortexed briefly and incubated at room temperature for 2 minutes before being transferred to a MaXtract tube  and centrifuged at 4˚C for 5 minutes at 12,000 x g. Following centrifugation, the aqueous phase was removed and transferred to a new microcentrifuge Eppendorf tube and an equal volume of 100% ethanol was added. After completion of this phenol-chloroform step, the RNA extraction continued using the Direct-zol RNA MicroPrep kit  following the manufacturer’s protocols and eluted in 15 ul of nuclease-free water. Samples were stored at -80˚C until library preparation. Aliquots of the samples were nanodropped to quantify the extracted RNA and to determine 260/230 and 260/280 values and then run on a HS RNA Tapestation tape to their determined their RNA integrity number (RIN) value. Only samples with RIN scores higher than 6 were used for subsequent steps so long as the average RIN for all tissues from that sample was greater than 7. Samples were then sent out for 3 rounds of sequencing on an Illumina MiSeq/NovaSeq 6000 at the Harvard Bauer Core in order to obtain ~40 million reads per sample.
Takara SMART-Seq v4 Ultra Low Input RNA Kit Library Preparation (2 samples also prepared using Kapa mRNA HyperPrep kit for comparison with human samples)

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

value: Foot phalanges, digit III

tag: strain

value: FVB/NJ


title: E15.5 mouse metatarsal, digit 5, rep 6, MiSeq (RNAseq)

description: Library name: FM5_MiSeq_I

value: Metatarsal, digit V

value: Female


title: E15.5 mouse metatarsal, digit 3, rep 6, MiSeq (RNAseq)

description: Library name: FM3_MiSeq_I


title: E15.5 mouse metatarsal, digit 1, rep 6, MiSeq (RNAseq)

description: Library name: FM1_MiSeq_I


title: E15.5 mouse foot phalanges, digit 5, rep 6, MiSeq (RNAseq)

description: Library name: FP5_MiSeq_I

value: Foot phalanges, digit V


title: E67 human foot phalanges, digit 4, rep 1

description: Library name: FP4_late_rep1

source_name: Footphalanges, digit IV

value: Footphalanges, digit IV

value: Male


title: E15.5 mouse foot phalanges, digit 3, rep 6, MiSeq (RNAseq)

description: Library name: FP3_MiSeq_I


title: E15.5 mouse metacarpal, digit 5, rep 6, MiSeq (RNAseq)

description: Library name: HM5_MiSeq_I

value: Metacarpal, digit V


title: E15.5 mouse hand phalanges, digit 3, rep 2, MiSeq, KAPA (RNAseq)

description:
Library name: HP3_MiSeq_D_KAPA
Kapa mRNA HyperPrep kit for comparison with human samples


title: E15.5 mouse metacarpal, digit 1, rep 6, MiSeq (RNAseq)

description: Library name: HM1_MiSeq_I

value: Metacarpal, digit I


title: E15.5 mouse hand phalanges, digit 5, rep 6, MiSeq (RNAseq)

description: Library name: HP5_MiSeq_I

value: Hand phalanges, digit V


title: E15.5 mouse foot phalanges, digit 1, rep 6, MiSeq (RNAseq)

description: Library name: FP1_MiSeq_I

value: chondrocytes


title: E15.5 mouse metacarpal, digit 3, rep 6, MiSeq (RNAseq)

description: Library name: HM3_MiSeq_I

source_name: Metacarpal, digit III

value: Metacarpal, digit III


title: E15.5 mouse hand phalanges, digit 3, rep 6, MiSeq (RNAseq)

description: Library name: HP3_MiSeq_I

value: Hand phalanges, digit III


title: E15.5 mouse hand phalanges, digit 1, rep 6, MiSeq (RNAseq)

description: Library name: HP1_MiSeq_I

source_name: Hand phalanges, digit I


title: E15.5 mouse metatarsal, digit 5, rep 5, MiSeq (RNAseq)

description: Library name: FM5_MiSeq_H


title: E15.5 mouse metatarsal, digit 3, rep 5, MiSeq (RNAseq)

description: Library name: FM3_MiSeq_H

source_name: Metatarsal, digit III

value: Metatarsal, digit III


title: E15.5 mouse foot phalanges, digit 5, rep 5, MiSeq (RNAseq)

description: Library name: FP5_MiSeq_H


title: E15.5 mouse metatarsal, digit 1, rep 5, MiSeq (RNAseq)

description: Library name: FM1_MiSeq_H

source_name: Metatarsal, digit I

value: Metatarsal, digit I


title: E15.5 mouse metacarpal, digit 5, rep 5, MiSeq (RNAseq)

description: Library name: HM5_MiSeq_H


title: E15.5 mouse hand phalanges, digit 5, rep 5, MiSeq (RNAseq)

description: Library name: HP5_MiSeq_H


title: E15.5 mouse foot phalanges, digit 1, rep 5, MiSeq (RNAseq)

description: Library name: FP1_MiSeq_H

source_name: Foot phalanges, digit I

value: Foot phalanges, digit I


title: E15.5 mouse metacarpal, digit 1, rep 5, MiSeq (RNAseq)

description: Library name: HM1_MiSeq_H


title: E15.5 mouse metacarpal, digit 3, rep 5, MiSeq (RNAseq)

description: Library name: HM3_MiSeq_H


title: E67 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 metatarsal, digit 3, rep 4, MiSeq (RNAseq)

description: Library name: FM3_MiSeq_G


title: E15.5 mouse hand phalanges, digit 3, rep 5, MiSeq (RNAseq)

description: Library name: HP3_MiSeq_H


title: E15.5 mouse hand phalanges, digit 1, rep 5, MiSeq (RNAseq)

description: Library name: HP1_MiSeq_H

value: Hand phalanges, digit I


title: E15.5 mouse metatarsal, digit 5, rep 4, MiSeq (RNAseq)

description: Library name: FM5_MiSeq_G

source_name: Metatarsal, digit V

value: FVB/NJ


title: E15.5 mouse metatarsal, digit 1, rep 4, MiSeq (RNAseq)

description: Library name: FM1_MiSeq_G


title: E15.5 mouse foot phalanges, digit 5, rep 4, MiSeq (RNAseq)

description: Library name: FP5_MiSeq_G


title: E15.5 mouse metacarpal, digit 5, rep 4, MiSeq (RNAseq)

description: Library name: HM5_MiSeq_G


title: E15.5 mouse foot phalanges, digit 1, rep 4, MiSeq (RNAseq)

description: Library name: FP1_MiSeq_G


title: E15.5 mouse hand phalanges, digit 1, rep 4, MiSeq (RNAseq)

description: Library name: HP1_MiSeq_G


title: E15.5 mouse metacarpal, digit 3, rep 4, MiSeq (RNAseq)

description: Library name: HM3_MiSeq_G


title: E15.5 mouse hand phalanges, digit 3, rep 4, MiSeq (RNAseq)

description: Library name: HP3_MiSeq_G


title: E15.5 mouse metatarsal, digit 5, rep 3, MiSeq (RNAseq)

description: Library name: FM5_MiSeq_F

value: Metatarsal, digit V


title: E15.5 mouse metacarpal, digit 1, rep 4, MiSeq (RNAseq)

description: Library name: HM1_MiSeq_G

source_name: Metacarpal, digit I


title: E15.5 mouse hand phalanges, digit 5, rep 4, MiSeq (RNAseq)

description: Library name: HP5_MiSeq_G


title: E15.5 mouse foot phalanges, digit 3, rep 5, MiSeq (RNAseq)

description: Library name: FP3_MiSeq_H

source_name: Foot phalanges, digit III

value: Foot phalanges, digit III


title: E15.5 mouse foot phalanges, digit 5, rep 3, MiSeq (RNAseq)

description: Library name: FP5_MiSeq_F

value: Foot phalanges, digit V

value: Female


title: E15.5 mouse metacarpal, digit 5, rep 3, MiSeq (RNAseq)

description: Library name: HM5_MiSeq_F


title: E15.5 mouse foot phalanges, digit 3, rep 3, MiSeq (RNAseq)

description: Library name: FP3_MiSeq_F


title: E15.5 mouse metatarsal, digit 3, rep 3, MiSeq (RNAseq)

description: Library name: FM3_MiSeq_F


title: E15.5 mouse foot phalanges, digit 1, rep 3, MiSeq (RNAseq)

description: Library name: FP1_MiSeq_F


title: E15.5 mouse metacarpal, digit 1, rep 3, MiSeq (RNAseq)

description: Library name: HM1_MiSeq_F


title: E15.5 mouse metacarpal, digit 3, rep 3, MiSeq (RNAseq)

description: Library name: HM3_MiSeq_F


title: E15.5 mouse hand phalanges, digit 1, rep 3, MiSeq (RNAseq)

description: Library name: HP1_MiSeq_F


title: E15.5 mouse metatarsal, digit 3, rep 2, MiSeq (RNAseq)

description: Library name: FM3_MiSeq_D

value: Male


title: E15.5 mouse metatarsal, digit 5, rep 2, MiSeq (RNAseq)

description: Library name: FM5_MiSeq_D


title: E15.5 mouse metatarsal, digit 1, rep 2, MiSeq (RNAseq)

description: Library name: FM1_MiSeq_D


title: E15.5 mouse foot phalanges, digit 1, rep 2, MiSeq (RNAseq)

description: Library name: FP1_MiSeq_D


title: E15.5 mouse foot phalanges, digit 3, rep 2, MiSeq (RNAseq)

description: Library name: FP3_MiSeq_D


title: E15.5 mouse foot phalanges, digit 5, rep 2, MiSeq (RNAseq)

description: Library name: FP5_MiSeq_D


title: E15.5 mouse foot phalanges, digit 3, rep 4, MiSeq (RNAseq)

description: Library name: FP3_MiSeq_G


title: E15.5 mouse metacarpal, digit 5, rep 2, MiSeq (RNAseq)

description: Library name: HM5_MiSeq_D

value: Metacarpal, digit V


title: E15.5 mouse metacarpal, digit 1, rep 2, MiSeq (RNAseq)

description: Library name: HM1_MiSeq_D

value: Metacarpal, digit I


title: E15.5 mouse metacarpal, digit 3, rep 2, MiSeq (RNAseq)

description: Library name: HM3_MiSeq_D


title: E15.5 mouse metatarsal, digit 1, rep 3, MiSeq (RNAseq)

description: Library name: FM1_MiSeq_F


title: E15.5 mouse hand phalanges, digit 3, rep 2, MiSeq (RNAseq)

description: Library name: HP3_MiSeq_D


title: E15.5 mouse hand phalanges, digit 5, rep 2, MiSeq (RNAseq)

description: Library name: HP5_MiSeq_D

value: Hand phalanges, digit V


title: E15.5 mouse hand phalanges, digit 1, rep 2, MiSeq (RNAseq)

description: Library name: HP1_MiSeq_D

value: chondrocytes


title: E15.5 mouse metatarsal, digit 3, rep 1, MiSeq (RNAseq)

description: Library name: FM3_MiSeq_A


title: E15.5 mouse metatarsal, digit 5, rep 1, MiSeq (RNAseq)

description: Library name: FM5_MiSeq_A


title: E15.5 mouse foot phalanges, digit 5, rep 1, MiSeq (RNAseq)

description: Library name: FP5_MiSeq_A


title: E15.5 mouse metatarsal, digit 1, rep 1, MiSeq (RNAseq)

description: Library name: FM1_MiSeq_A


title: E15.5 mouse foot phalanges, digit 3, rep 1, MiSeq (RNAseq)

description: Library name: FP3_MiSeq_A


title: E15.5 mouse hand phalanges, digit 5, rep 3, MiSeq (RNAseq)

description: Library name: HP5_MiSeq_F


title: E15.5 mouse metacarpal, digit 1, rep 1, Mi Seq (RNAseq)

description: Library name: HM1_MiSeq_A


title: E15.5 mouse metacarpal, digit 5, rep 1,MiSeq (RNAseq)

description: Library name: HM5_MiSeq_A


title: E15.5 mouse hand phalanges, digit 5, rep 1, MiSeq (RNAseq)

description: Library name: HP5_MiSeq_A


title: E15.5 mouse foot phalanges, digit 1, rep 1, MiSeq (RNAseq)

description: Library name: FP1_MiSeq_A


title: E15.5 mouse hand phalanges, digit 3, rep 1, MiSeq (RNAseq)

description: Library name: HP3_MiSeq_A


title: E15.5 mouse metacarpal, digit 3, rep 1, MiSeq (RNAseq)

description: Library name: HM3_MiSeq_A

value: Metacarpal, digit III


title: E15.5 mouse hand phalanges, digit 3, rep 3, MiSeq (RNAseq)

description: Library name: HP3_MiSeq_F

value: Hand phalanges, digit III


title: E15.5 mouse hand phalanges, digit 1, rep 1, MiSeq (RNAseq)

description: Library name: HP1_MiSeq_A


title: E15.5 mouse foot phalanges, digit 3, rep 2, KAPA (RNAseq)

description:
Library name: FP3_D_KAPA
Kapa mRNA HyperPrep kit for comparison with human samples


title: E15.5 mouse hand phalanges, digit 3, rep 2, KAPA (RNAseq)

description:
Library name: HP3_D_KAPA
Kapa mRNA HyperPrep kit for comparison with human samples


title: E15.5 mouse metatarsal, digit 1, rep 6 (RNAseq)

description: Library name: FM1_I


title: E15.5 mouse metatarsal, digit 3, rep 6 (RNAseq)

description: Library name: FM3_I

value: Metatarsal, digit III


title: E15.5 mouse foot phalanges, digit 1, rep 6 (RNAseq)

description: Library name: FP1_I


title: E15.5 mouse metatarsal, digit 5, rep 6 (RNAseq)

description: Library name: FM5_I


title: E15.5 mouse metacarpal, digit 5, rep 6 (RNAseq)

description: Library name: HM5_I


title: E15.5 mouse foot phalanges, digit 3, rep 6 (RNAseq)

description: Library name: FP3_I


title: E15.5 mouse metacarpal, digit 3, rep 6 (RNAseq)

description: Library name: HM3_I


title: E15.5 mouse hand phalanges, digit 3, rep 6 (RNAseq)

description: Library name: HP3_I


title: E15.5 mouse metatarsal, digit 5, rep 5 (RNAseq)

description: Library name: FM5_H


title: E15.5 mouse metacarpal, digit 1, rep 6 (RNAseq)

description: Library name: HM1_I


title: E15.5 mouse foot phalanges, digit 5, rep 5 (RNAseq)

description: Library name: FP5_H


title: E15.5 mouse hand phalanges, digit 5, rep 6 (RNAseq)

description: Library name: HP5_I


title: E15.5 mouse metatarsal, digit 3, rep 5 (RNAseq)

description: Library name: FM3_H


title: E15.5 mouse metacarpal, digit 3, rep 5 (RNAseq)

description: Library name: HM3_H


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

description: Library name: FP1_H


title: E15.5 mouse hand phalanges, digit 5, rep 5 (RNAseq)

description: Library name: HP5_H


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

description: Library name: HP3_H


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

description: Library name: HP1_H


title: E15.5 mouse metatarsal, digit 5, rep 4 (RNAseq)

description: Library name: FM5_G


title: E15.5 mouse metatarsal, digit 3, rep 4 (RNAseq)

description: Library name: FM3_G


title: E15.5 mouse foot phalanges, digit 5, rep 4 (RNAseq)

description: Library name: FP5_G


title: E15.5 mouse metatarsal, digit 1, rep 4 (RNAseq)

description: Library name: FM1_G

value: Metatarsal, digit I


title: E15.5 mouse foot phalanges, digit 5, rep 6 (RNAseq)

description: Library name: FP5_I


title: E15.5 mouse metacarpal, digit 5, rep 4 (RNAseq)

description: Library name: HM5_G


title: E15.5 mouse foot phalanges, digit 3, rep 4 (RNAseq)

description: Library name: FP3_G


title: E15.5 mouse metacarpal, digit 1, rep 4 (RNAseq)

description: Library name: HM1_G


title: E15.5 mouse metacarpal, digit 3, rep 4 (RNAseq)

description: Library name: HM3_G


title: E15.5 mouse hand phalanges, digit 5, rep 4 (RNAseq)

description: Library name: HP5_G


title: E15.5 mouse hand phalanges, digit 3, rep 4 (RNAseq)

description: Library name: HP3_G


title: E15.5 mouse metatarsal, digit 5, rep 3 (RNAseq)

description: Library name: FM5_F


title: E15.5 mouse hand phalanges, digit 1, rep 4 (RNAseq)

description: Library name: HP1_G


title: E15.5 mouse hand phalanges, digit 1, rep 6 (RNAseq)

description: Library name: HP1_I


title: E15.5 mouse metatarsal, digit 1, rep 5 (RNAseq)

description: Library name: FM1_H


title: E15.5 mouse metatarsal, digit 3, rep 3 (RNAseq)

description: Library name: FM3_F


title: E15.5 mouse metacarpal, digit 5, rep 5 (RNAseq)

description: Library name: HM5_H


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

description: Library name: FM1_F


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

description: Library name: FP5_F


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

description: Library name: FP3_H


title: E15.5 mouse metacarpal, digit 1, rep 5 (RNAseq)

description: Library name: HM1_H


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

description: Library name: FP1_F

value: Foot phalanges, digit I


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

description: Library name: FP3_F


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

description: Library name: HM1_F


title: E15.5 mouse metacarpal, digit 3, rep 3 (RNAseq)

description: Library name: HM3_F


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

description: Library name: HP5_F


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

description: Library name: HP1_F


title: E15.5 mouse foot phalanges, digit 1, rep 4 (RNAseq)

description: Library name: FP1_G


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

description: Library name: FM3_D


title: E15.5 mouse metatarsal, digit 5, rep 2 (RNAseq)

description: Library name: FM5_D


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

description: Library name: FP5_D


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

description: Library name: HP3_F


title: E15.5 mouse metacarpal, digit 5, rep 2 (RNAseq)

description: Library name: HM5_D


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

description: Library name: FP1_D


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

description: Library name: FM1_D


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

description: Library name: FP3_D


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

description: Library name: HP3_D


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

description: Library name: HM3_D


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

description: Library name: HM1_D


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

description: Library name: HP5_D


title: E15.5 mouse metatarsal, digit 5, rep 1 (RNAseq)

description: Library name: FM5_A


title: E15.5 mouse metatarsal, digit 1, rep 1 (RNAseq)

description: Library name: FM1_A


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

description: Library name: FM3_A


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

description: Library name: HP1_D


title: E15.5 mouse metacarpal, digit 5, rep 3 (RNAseq)

description: Library name: HM5_F


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

description: Library name: FP3_A


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

description: Library name: FP5_A


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

description: Library name: FP1_A


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

description: Library name: HM3_A


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

description: Library name: HP5_A


title: E15.5 mouse metacarpal, digit 1, rep 1 (RNAseq)

description: Library name: HM1_A


title: E15.5 mouse metacarpal, digit 5, rep 1 (RNAseq)

description: Library name: HM5_A


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

description: Library name: HP3_A


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

description: Library name: HP1_A


title: MP_167_B

status: Public on Aug 12 2025

city: Brisbane

first: Yufan

last: Feng

state: QLD

address: Building 71/918 RBWH Herston

department: UQ Centre for Clinical Research

country: Australia

institute: The University of Queensland

description: Library name: VLP67_D

data_processing:
Sequencing data were demultiplexed using bcl2fastq software (v2.20.0.422, Illumina). The SpaceRanger Software v2.0.0 (10X Genomics) and the GRCh38-2020-A reference genome were used to process fastq files and map the reads to H&E images.
Assembly: GRCh38-2020-A
Supplementary files format and content: H5 file, TIFF file, six processed spatial data files for spatial transcriptomics analysis, one annotation file used for specific analyses in the associated paper, one features.tsv file containing the feature (gene) information corresponding to the expression matrix.
Library strategy: Spatial Transcriptomics

source_name: MpBC

extract_protocol:
The FFPE tissue blocks were processed as per manufacturer’s instructions. In brief, 5 µm tissue sections were placed on a Visium Spatial Slide (10X Genomics). Hematoxylin and eosin (H&E) staining of the tissue sections were imaged using Aperio XT Brightfield Automated Slide Scanner (Leica, DE; 20x). Sections were destained and de-crosslinked prior to hybridisation with human transcriptome probes which underwent probe extension and library construction.
The libraries were sequenced at the UQ Institute for Molecular Bioscience, using Illumina NovaSeq 6000 (Illumina) with paired-end dual-indexing (28 cycles for Read 1, 10 cycles for i7, 10 cycles for i5, 50 cycles for Read 2) at a depth of ~25000 reads per section. Mitochondrial and ribosomal genes were removed before normalization. Low-quality genes (expressed in less than 3 spots/barcodes) and low-quality spots (expressing less than 10 genes) were also excluded from further analysis.

value: MpBC


title: MP_10_C

description: Library name: VLP68_D


title: MP_14_B

description: Library name: VLP67_B


title: MP_167_A

description: Library name: VLP67_C


title: new-onset cancer patient 7

status: Public on Aug 08 2025

city: Rockwall

first: Wei

last: Zhang

state: TX

address: 2500 Summer Lee Dr

institute: Neo7 Bioscience

description:
Library name: cancer_Patient7
blood RNA-seq of new-onset cancer patient 7

data_processing:
The raw sequencing data, in the form of paired-end Fastq files, were first organized by sample and read type (R1 and R2). These Fastq files were stored in a dedicated directory, and the cat command was used to group them based on their sample identifiers. The R1 and R2 files for each sample were then merged into a single file for each read type, resulting in forward and reverse merged files that were ready for downstream analysis. Quality control checks were performed before the alignment step to ensure the integrity of the data. The sequencing reads were aligned to the human reference genome (hg38) using STAR, a widely used aligner for RNA sequencing data. STAR efficiently handles read alignment in a multi-threaded environment, optimizing processing time. The aligned reads were then outputted as BAM files, sorted by coordinate, which is standard practice for subsequent analysis steps.
To investigate transcriptomic alterations associated with mRNA vaccine–related outcomes, we performed two distinct differential expression analyses, each comparing one patient group to a common pool of healthy controls (n = 803). The first comparison included individuals from group 1, who developed nonmalignant new-onset symptoms following mRNA vaccination (n = 3), while the second comprised individuals from group 2, diagnosed with cancer as a new-onset condition shortly after vaccination (n = 7). For both analyses, raw gene counts generated from Salmon were input into DESeq2, which applied internal normalization and modeled dispersion using the negative binomial distribution. Shrinkage of log₂ fold changes was performed using the “apeglm” method to improve effect size estimation, particularly for genes with low read counts.
To visualize the global patterns of gene expression, volcano plots were generated for each comparison. In these plots, the x-axis represents the log₂ fold change, and the y-axis represents the negative log₁₀ of the adjusted p-value. Genes with log₂ fold change greater than +1 and an adjusted p-value (padj) below 0.05 were considered significantly upregulated and were colored red, while those with log₂ fold change less than -1 and padj < 0.05 were considered significantly downregulated and were colored blue. All remaining genes that did not meet these criteria were displayed in gray.
Assembly: hg38
Supplementary files format and content: csv file contains TPM for all samples

source_name: Blood

extract_protocol:
Total RNA was extracted using the Quick-DNA/RNA Viral Kit (Zymo Research), following the manufacturer’s protocol for whole blood RNA extraction. All procedures were conducted in a biosafety level 2 (BSL-2) cabinet (Esco Labculture A2). Briefly, lysis buffer was added to blood samples to inactivate pathogens, followed by ethanol precipitation and column-based RNA purification. Eluted RNA was quantified and stored at −80°C until library preparation.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit, incorporating ribosomal RNA depletion and strand-specific cDNA synthesis. RNA was fragmented enzymatically, reverse-transcribed to first-strand cDNA, and converted to double-stranded cDNA. Following end repair and adenylation, Illumina-specific adapters were ligated, and libraries were amplified by PCR. Quality and fragment size distribution were assessed using the High Sensitivity DNA kits on the TapeStation 4200 (Agilent Technologies). Libraries were stored at −20°C prior to sequencing. Normalized and pooled libraries were sequenced on the Illumina NextSeq 550 platform using the NextSeq 500/550 High Output Kit v2.5 (300 cycles), targeting a coverage depth of 200× per sample. PhiX was added at 1% as an internal control. Paired-end sequencing reads were collected, and sequencing quality metrics (e.g., Q30 scores, cluster density) were monitored in real-time using Illumina’s Sequencing Analysis Viewer.

value: Blood

tag: treatment

value: Vaccinated


title: new-onset cancer patient 6

description:
Library name: cancer_Patient6
blood RNA-seq of new-onset cancer patient 6


title: MP_14_A

description: Library name: VLP67_A


title: new-onset cancer patient 2

description:
Library name: cancer_Patient2
blood RNA-seq of new-onset cancer patient 2


title: new-onset cancer patient 5

description:
Library name: cancer_Patient5
blood RNA-seq of new-onset cancer patient 5


title: new-onset cancer patient 1

description:
Library name: cancer_Patient1
blood RNA-seq of new-onset cancer patient 1


description:
Library name: spike_Patient2
blood RNA-seq of new-onset post-vaccination symptoms patient 2


description:
Library name: spike_Patient1
blood RNA-seq of new-onset post-vaccination symptoms patient 1


title: new-onset cancer patient 3

description:
Library name: cancer_Patient3
blood RNA-seq of new-onset cancer patient 3


title: AML3_UNT_rep2

status: Public on Jul 22 2025

city: Beirut

first: Hiba

last: El Hajj

address: Bliss street

department: Department of Experimental Pathology, Immunology and Microbiology

country: Lebanon

institute: American University of Beirut

description: Library name: AML3_UNT_n2

data_processing:
Quality check for raw sequencing reads was performed using FastQC v0.12.1
RNA-seq reads were aligned to hg38 genome assembly using hisat2 v2.2.1
RNA-seq count matrix was generated using FeatureCounts v2.0.6 from SubRead package
Assembly: hg38
Supplementary files format and content: processed data files include featureCounts file

molecule: polyA RNA

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FBS and 1% pen/strep

extract_protocol:
Whole-cell RNA from one million cells of OCI-AML3 cells with or without RA treatment were purified using RNeasy Mini Kit (QIAGEN Cat#74134)
Non strand specific library  Messenger RNA was purified from total RNA using poly-T oligo-attached  magnetic beads. After fragmentation, the first strand cDNA was  synthesized using random hexamer primers followed by the second  strand cDNA synthesis. The library was ready after end repair, A-tailing,  adapter ligation, size selection, amplification, and purification. The  library was checked with Qubit and real-time PCR for quantification and  bioanalyzer for size distribution detection.

treatment_protocol: Retinoic acid was added to the cell culture medium at a final concentration of 1uM

tag: cell line

value: acute myeloid leukemia

tag: genotype

value: human hyperdiploid karyotype - 48(45-50)<2n>X/XY, +1, +5, +8, der(1)t(1;18)(p11;q11), i(5p), del(13)(q13q21), dup(17)(q21q25) - sideline with r(Y)x1-2 - hemizygous for RB1

value: Retinoic acid

tag: batch

value: ACC 582


title: AML3_RA4H_rep1

description: Library name: AML3_RA4H_n1

value: Untreated


title: MP_170

description: Library name: VLP68_A


title: AML3_RA2H_rep2

description: Library name: AML3_RA2H_n2


title: AML3_UNT_rep1

description: Library name: AML3_UNT_n1


title: AML3_RA2H_rep1

description: Library name: AML3_RA2H_n1


title: MP_10_B

description: Library name: VLP68_C


title: Young and aged mouse brain, oligodendrocyte-enriched

status: Public on Jul 30 2025

city: New York

first: Junyue

last: Cao

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: Library name: Young_Aged_brain

library_source: transcriptomic single cell

data_processing:
Low quality cells were removed using UMI cutoffs of >500 for mouse brain and >1000 for cell lines. Doublets were removed using custom pipelines, Scrublet, and manual inspection. Initial mouse brain cell type annotations were generated using the Allen Institute MapMyCells tool and validated by checking marker expression. Further oligodendrocyte subtypes were manually annotated using specific marker expression.
Assembly: mm39, hg38
Supplementary files format and content: gene count matrix, cell metadata, exon count matrix, gene metadata, exon metadata

molecule: nuclear RNA

source_name: brain

extract_protocol:
hypotonic lysis buffer for nuclei extraction from cell lines and mouse brains
after HCR RNA FISH labeling of target cell type and FACS isolation, combinatorial indexing-based single-nucleus RNA-seq was performed.

value: brain


title: AML3_UNT_rep3

description: Library name: AML3_UNT_n3


title: AML3_RA4H_rep2

description: Library name: AML3_RA4H_n2


title: MP_10_A

description: Library name: VLP68_B


title: new-onset cancer patient 4

description:
Library name: cancer_Patient4
blood RNA-seq of new-onset cancer patient 4


title: HepG2, Library_MI, 24h, rep2

status: Public on Jul 01 2025

city: Amsterdam

first: Noud

last: Klaassen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Insitute

description: Library name: Motif_Insertion_Library_HepG2_Replicate2

data_processing:
See methods
Assembly: hg19
Supplementary files format and content: count tables and normalized (log2RPM) data

growth_protocol: cells were cultured according to manufacters protocol

extract_protocol:
Standard RNA extraction protocols see methods paper
Various different protocols

treatment_protocol: cells were transfected by either nucleofection or lipofection

value: Hepatocellular carcinoma


title: HepG2, Library_MI, 24h, rep1

description: Library name: Motif_Insertion_Library_HepG2_Replicate1


title: Lung of tumor-bearing (KP) mice replicate 1 (scATAC-seq)

status: Public on Jul 07 2025

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description: 10x Genomics

library_source: genomic single cell

data_processing:
scRNA-seq: Fastq reads from scRNA-seq samples were aligned to the mm10 reference transcriptome followed by count matrix generation using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses.
scATAC-seq: Fastq reads from scATAC-seq samples were aligned to mouse genome reference mm10 using cellranger-atac v2.0.0. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 5000). FRIP scores were also used for filtering data prior to downstream analyses.
multiome (RNA + ATAC): Fastq files from human scATAC-seq and 10x Genomics multiome samples were aligned to human genome reference hg38 using cellranger-atac v2.0.0 or cellranger-arc v2.0.0 respectively. Fragment files were parsed with ArchR v1.0.2 and initial quality control was applied based on sequencing depth and transposition quality (minTSS = 8, minFrags = 3000). FRIP scores were also used for filtering data prior to downstream analyses.
Assembly: Mouse:mm10; Human: hg38
Supplementary files format and content: scRNA-seq, scATAC-seq and 10x Multiome (RNA + ATAC): cellranger processed outputs (barcode, peak/feature matrix).

molecule: genomic DNA

source_name: Lung tumor

extract_protocol:
Mouse: myeloid cells were sorted from respective tissues (Lung/BM/blood) based on markers described in Methods section. For scRNA-seq, cells were encapsulated following 10x Genomics Chromium Next GEM Single Cell 3ʹ v3.1 protocol. For scATAC-seq, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC v1.1 protocol. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei or cells were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Human: CD45positive cells after sorting or bead-based enrichment were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell ATAC Kit v1.1 or Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol. In case of low-input samples (with <100,000 cells), we utilized 0.2 ml PCR tubes and centrifuged at 4C using swinging rotor buckets to maximize nuclear recovery. For human NSCLC sample multiome assays, cells were subjected to nuclei isolation following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol in the presence of RNAse inhibitor (Sigma) and DTT (Sigma) to prevent RNA degradation. Nuclei quality was verified by brightfield microscopy prior to loading. A target recovery number of 8000~10000 nuclei were loaded onto each lane of a 10X Chromium chip according to manufacturer’s instructions.
Mouse: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. scRNA-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell pooled on the Illumina NovaSeq 6000 S2 100 cycle kit. scATAC-seq libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.
Human: Libraries were prepared according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer. Libraries were sequenced at a targeted depth of minimum 25,000 read pairs per cell using the Illumina NovaSeq 6000 S2 100 cycle kit.

treatment_protocol:
Mouse: myeloid cells excluding mature neutrophils were sorted from processed tissues (Lung/BM/blood) of naïve or KP Tumor-bearing mice in PBS+0.04% BSA, based on surface markers described in Methods section.
Human: CD45 positive cells were bead-enriched from processed tissues (Lung Tumor/Lung adjacent normal/PBMC) of patients with NSCLC. In one patient, viable CD45 positive cells were sorted from respective tissues (Lung Tumor/Lung adjacent normal/PBMC), based on surface markers described in Methods section.

value: Lung tumor

value: immune

value: Tumor-bearing

tag: time

value: late


title: K562, Library_MI, 24h, rep2

description: Library name: Motif_Insertion_Library_K562_Replicate2

value: Myelogenous leukemia


title: K562, Library_MI, 24h, rep3

description: Library name: Motif_Insertion_Library_K562_Replicate3


description:
Library name: spike_Patient3
blood RNA-seq of new-onset post-vaccination symptoms patient 3


title: K562, Library_MI, 24h, rep1

description: Library name: Motif_Insertion_Library_K562_Replicate1


title: Library_MI_pDNA_counts

description: Library name: Motif_Insertion_Library_plasmid

library_source: other

molecule: other

source_name: plasmid

value: plasmid


title: HepG2, Library_SynProm_Large, 24h, rep2

description: Library name: Synthetic_Promoter_Library_large_232bp_HepG2_Replicate2


title: HepG2, Library_SynProm_Large, 24h, rep1

description: Library name: Synthetic_Promoter_Library_large_232bp_HepG2_Replicate1


title: K562, Library_SynProm_Large, 24h, rep2

description: Library name: Synthetic_Promoter_Library_large_232bp_K562_Replicate2


title: K562, Library_SynProm_Large, 24h, rep1

description: Library name: Synthetic_Promoter_Library_large_232bp_K562_Replicate1


title: Library_SynProm_Large_pDNA

description: Library name: Synthetic_Promoter_Library_large_232bp_plasmid


title: Library_SynProm_Small_pDNA

description: Library name: Synthetic_Promoter_Library_small_70bp_plasmid


title: HEK293, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_HEK293_Replicate2

value: Embryonic kidney


title: K562, Library_SynProm_Small, 24h, rep2

description: Library name: Synthetic_Promoter_Library_small_70bp_K562_Replicate2


title: HepG2, Library_SynProm_Small, 24h, rep1

description: Library name: Synthetic_Promoter_Library_small_70bp_HepG2_Replicate1


title: HEK293, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_HEK293_Replicate1


title: K562, Library_SynProm_Small, 24h, rep1

description: Library name: Synthetic_Promoter_Library_small_70bp_K562_Replicate1


title: HepG2, Library_SynProm_Small, 24h, rep2

description: Library name: Synthetic_Promoter_Library_small_70bp_HepG2_Replicate2


title: U2OS, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_U2OS_Replicate1

value: Osteosarcoma


title: HCT116, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_HCT116_Replicate1

value: Colorectal carcinoma


title: HCT116, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_HCT116_Replicate2


title: LNCaP, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_LNCaP_Replicate1

source_name: LNCaP

value: LNCaP

value: Prostate carcinoma


title: HepG2, Library_SM, 24h, rep3

description: Library name: Saturated_Mutagenesis_Library_HepG2_Replicate3


title: MCF7, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_MCF7_Replicate1

value: Breast adenocarcinoma


title: LNCaP, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_LNCaP_Replicate2


title: HepG2, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_HepG2_Replicate2


title: K562, Library_SM, 24h, rep3

description: Library name: Saturated_Mutagenesis_Library_K562_Replicate3


title: HepG2, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_HepG2_Replicate1


title: AML3_RA4H_rep3

description: Library name: AML3_RA4H_n3

value: Blood

value: acute myeloid leukemia

value: human hyperdiploid karyotype - 48(45-50)<2n>X/XY, +1, +5, +8, der(1)t(1;18)(p11;q11), i(5p), del(13)(q13q21), dup(17)(q21q25) - sideline with r(Y)x1-2 - hemizygous for RB1

value: Retinoic acid


title: U2OS, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_U2OS_Replicate2


title: Batch2_TC2

status: Public on Jul 16 2025

type: genomic

first: Yelena

last: Nemirovskaya

address: 1230 York Avenue

institute: Rockefeller University

hyb_protocol: Hybridization was conducted per Illumina's recommended protocol.

scan_protocol: Scanning was conducted per Illumina's recommended protocol.

data_processing: The IDAT files were imported into R for data processing. The preprocessQuantile method, implemented in the packag eminfi, was used for normalization. Detection P values for all probed genomic positions were computed to exclude failed probes. Probes in X and Y chromosomes were also excluded. Probes in the EPIC V2 array were renamed according to the corresponding loci targeted in the EPIC V1 array. PCA was performed using batch-corrected beta values. Differential methylation analysis was performed using M values and a standard limma workflow.

label: Cy3 and Cy5

source_name: Peripheral blood

label_protocol: The DNA was deaminated with the EZ-96 DNA Methylation Kit (Zymo Resaerch).

growth_protocol: MACS-enriched CD4 T-cell blasts were cultured in STEMCELL ImmunoCult T-Cell Expansion Medium supplemented with 10ng/mL of human IL-2 for 2 weeks.

extract_protocol: Genomic DNA was extracted using PureLink Genomic DNA Mini Kit with Proteinase and RNase treatment.

value: Peripheral blood

value: MACS-enriched CD4+ T-cell blasts

value: CD4+ T cells


title: Library_SM_pDNA_counts

description: Library name: Saturated_Mutagenesis_Library_plasmid


title: Bone marrow of naive mice replicate 1 (scATAC-seq)

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow

value: immune

value: Naive


title: HepG2, Library_MH4, 24h; Nutlin3a, rep2

description: Library name: PARM_Training_Library_HepG2_Nutlin3A_Replicate2

value: Hepatocellular carcinoma


title: K562, Library_MH4, 24h; phorbol 12-myristate 13-acetate, rep1

description: Library name: PARM_Training_Library_K562_PMA_Replicate1

value: Myelogenous leukemia


title: K562, Library_MH4, 24h, DMSO, rep2

description: Library name: PARM_Training_Library_K562_DMSO_Control_Replicate2


title: K562, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_K562_Replicate2


title: K562, Library_SM, 24h, rep1

description: Library name: Saturated_Mutagenesis_Library_K562_Replicate1


title: HepG2, Library_MH4, 24h; Nutlin3a, rep1

description: Library name: PARM_Training_Library_HepG2_Nutlin3A_Replicate1


title: HepG2, Library_MH4, 24h, DMSO, rep2

description: Library name: PARM_Training_Library_HepG2_DMSO_Control_Replicate2


title: K562, Library_MH4, 24h; phorbol 12-myristate 13-acetate, rep2

description: Library name: PARM_Training_Library_K562_PMA_Replicate2


title: K562, Library_MH4, 24h, DMSO, rep1

description: Library name: PARM_Training_Library_K562_DMSO_Control_Replicate1


title: K562, Library_MH4, 24h, control, rep2

description: Library name: PARM_Training_Library_K562_HeatShock_Control_Replicate2


title: K562, Library_MH4, 24h, control, rep1

description: Library name: PARM_Training_Library_K562_HeatShock_Control_Replicate1


title: Batch1_MB11340.1

value: Tbet-/-


title: Batch1_MB18767

tag: subject status

value: LY9-deficient individual


title: Batch2_JL5383


title: HEK293, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_HEK293_Replicate2

value: Embryonic kidney


title: K562, Library_MH4, 24h; 3h heatshock (43C), rep2

description: Library name: PARM_Training_Library_K562_HeatShock_Replicate2


title: Batch1_MB1584

value: RORg-/-

value: RORgamma-deficient patient


title: AGS, Library_pHY3, 24h, rep2

description: Library name: PARM_Training_Library_AGS_Replicate2

source_name: AGS

value: AGS

value: Gastric adenocarcinoma


title: Batch1_CTL419

value: healthy control


title: Batch2_CTL354


title: Batch1_CTL441


title: Batch1_CTL446


title: HAP1, Library_pHY3, 24h, rep2

description: Library name: PARM_Training_Library_HAP1_Replicate2

value: Near-haploid chronic myelogenous leukemia


title: Batch1_MB11044

value: Peripheral blood


title: K562, Library_MH4, 24h; 3h heatshock (43C), rep1

description: Library name: PARM_Training_Library_K562_HeatShock_Replicate1


title: HAP1, Library_pHY3, 24h, rep1

description: Library name: PARM_Training_Library_HAP1_Replicate1


title: Batch1_MB30233

value: MACS-enriched CD4+ T-cell blasts


title: HepG2, Library_MH4, 24h, DMSO, rep1

description: Library name: PARM_Training_Library_HepG2_DMSO_Control_Replicate1


title: HEK293, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_HEK293_Replicate1


title: U2OS, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_U2OS_Replicate2

value: Osteosarcoma


title: Batch1_MB11340

value: CD4+ T cells


title: Batch2_CTL441


title: MCF7, Library_SM, 24h, rep2

description: Library name: Saturated_Mutagenesis_Library_MCF7_Replicate2

value: Breast adenocarcinoma


title: AGS, Library_pHY3, 24h, rep1

description: Library name: PARM_Training_Library_AGS_Replicate1


title: HCT116, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_HCT116_Replicate1

value: Colorectal carcinoma


title: HepG2, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_HepG2_Replicate1

value: Hepatocellular carcinoma


title: Batch1_MB35918


title: MCF7, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_MCF7_Replicate2


title: HepG2, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_HepG2_Replicate2


title: K562, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_K562_Replicate1

value: Myelogenous leukemia


title: Library_pHY3_pDNA_counts

description: Library name: PARM_Training_Library_v1_pHY3_plasmid

value: plasmid


title: K562, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_K562_Replicate2


title: Batch1_CTL447


title: HCT116, Library_MH4, 24h, rep2

description: Library name: PARM_Training_Library_HCT116_Replicate2


title: LNCaP, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_LNCaP_Replicate1

value: LNCaP

value: Prostate carcinoma


title: MCF7, Library_MH4, 24h, rep1

description: Library name: PARM_Training_Library_MCF7_Replicate1


title: Library_pHY3_iPCR_bc_fragment_mapping

description: Library name: PARM_Training_Library_v1_pHY3_barcode_fragment_mapping


title: Library_MH4_pDNA_counts

description: Library name: PARM_Training_Library_v2_MH4_plasmid


title: CN212 Control ATAC

status: Public on Jun 23 2025

city: Sevilla

first: Eloisa

last: Andujar

state: Sevilla

address: Avda Americo vespucio s/n

department: GENOMICS UNIT

country: Spain

institute: CABIMER-CSIC

description:
Former title: CN211 Control ATAC
10x genomics (scMultiome-SEQ)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger ARC software v7.0  (https://www.10xgenomics.com/support/software/cell-ranger-arc/latest)
CellRanger count and aggr functions to aggregate reads across sequencing lanes into a single set of  barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files (CellRanger ARC output files:  barcodes.tsv.gz, features.tsv.gz,matrix.mtx.gz)

extract_protocol:
Human peripheral blood mononuclear cells were isolated by Ficoll-Paque density gradient centrifugation and cryopreserved 2x10e6 cells per sample. Cell viability was 95% or greater for all samples. PBMCs were quickly thawed at 37°C in a water bath and washed with culture medium RPMI 1640 supplemented with 10% FBS. DNase treatment was done before the nuclei isolation. The nuclei isolation was conducted with an RNase inhibitor. Nuclei suspension was filtered with a 40μm cell strainer and counted in a Countess 3 FL Automated Cell Counter (Invitrogen); all samples had <5% live cells. High-quality nuclei were checked by 60x brightfield microscopy. The targeted number of nuclei was 5000 nuclei per sample. Finally, Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) was used to generate single-cell multiome data.
CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevF (Using a microfluidic chip, the nuclei of different patients are partitioned into nanoliterscale Gel Beads-in-emulsion (GEMs) with thousands of Barcodes to separately and uniquely index the transposed DNA and cDNA of each individual nucleus. ATAC and gene expression (GEX) libraries are generated from the same pool of pre-amplified transposed DNA/cDNA and sequenced)

value: Blood

value: PBMCs

tag: disease state

value: control


title: Batch2_TC1


title: d80 CF, proximal lung, sample 4

status: Public on Jun 18 2025

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description:
Library name: AXH120
10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.1.0
Assembly: Oar_v4.0/oviAri4 (Texel)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Ovis aries

source_name: Proximal lung

extract_protocol:
i. For single cell isolation from proximal or distal lung ~300 mg of tissue was cut into 2-3 mm pieces and subjected to two rounds of digestion.  First in 5ml of collagenase solution (200 U/ml collagenase, 40 IU/ml DNase I  (all from Worthington), 3 mM CaCl2, at 37°C, with continuous stirring for 30-40 min. Alternatively, Roche Liberase TL (Millipore Sigma) containing 100 µg/ml collagenase was used.  Tissue clumps were then disassociated by pipetting 10 times in a 5 ml serological pipette and left to settle for 3-4 min at which point the supernatant was collected and stored on ice as cell suspension 1. Second, 5 ml of fresh collagenase digestion solution as above was added to the settled tissue clumps remaining after the first digestion and again stirred at 37°C for 30-40 min, at which point very little tissue debris remained. The supernatant (cell suspension 2) was pooled with cell suspension 1 and together passed through a cell strainer (200 µm, pluriSelect) to remove any tissue debris. The strained cell suspension was then centrifuged at 300 x g for 5 min, washed once in HBSS (Sigma Aldrich) + 2% FBS and centrifuged again. 4 ml of 1× Red Blood Cell Lysis Solution (Miltenyi Biotec 130-094-183) was added to the cell pellet which was vortexed for 5 seconds and then incubated for 5 minutes at room temperature. After 10 ml of HBSS with 2% FBS was added, the mixture was centrifuged at 300 × g for 5 min and the supernatant was removed. The cell pellet was then digested with 3 ml of Accutase (Stem Cell Technologies, #AT104) for 15-25 min with frequent gentle pipetting with a wide-bore pipette after which time cells were visualized under a microscope. If any cell clumps persisted these were collected by centrifugation and further digested with 3 ml of Accutase for an additional 10-15 min. Accutase was removed by washing the cells with 5 ml HBSS + 2% FBS, followed by centrifugation to collect the cells. The supernatant was discarded, and the cell pellet was resuspended in 0.5-1.0 ml HBSS, passed through a 20-µm mini cell strainer (pluriSelect) and cells counted. ii) Single-cell RNA-sequencing and analysis ii) Approximately 3000- 5000 cells per tissue sample were used for scRNA-seq using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3, or v3.1.  After quality control of both cDNA and final libraries using Tapestation, the libraries were sequenced on a NovaSeq 6000 machine. Reads were aligned to the Oar_v4.0/oviAri4 (Texel) genome using Cell Ranger 3.1.0. Cells were filtered for quality using cuts for standard metrics: library size, number of detected genes and mitochondrial read percentage. Ribosomal protein genes were also filtered out. The resulting objects were normalized and batch-corrected using the Seurat R package, version 5.1.0, followed by clustering and UMAP (Uniform Manifold Approximation and Projection) dimensionality reduction. Seurat was also used to find cluster markers by performing differential gene expression analysis between clusters using the receiver operating characteristic (ROC) method.
Libraries generated from single cells according to the manufacturer's protocol for 10X Genomics Chromium Single Cell 3' Reagent Kits v3 or 3.1.

value: Proximal lung

value: male

value: CF


title: CN212 Control GEX

description:
Former title: CN211 Control GEX
10x genomics (scMultiome-SEQ)


title: d80 CF, proximal lung, sample 3

description:
Library name: AXH119
10x Genomics


title: d80 CF, proximal lung, sample 2

description:
Library name: AXH082
10x Genomics


title: d80 WT, proximal lung, sample 4

description:
Library name: AXH065
10x Genomics

value: WT


title: d80 CF, proximal lung, sample 1

description:
Library name: AXH058
10x Genomics