title: KUH132_MOCK_11398


title: KUH132_MOCK_11296

status: Public on Jun 17 2022

type: SRA

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

library_source: genomic

data_processing:
FastaQC-v0.11.3(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and fastp-v0.19.6(https://github.com/OpenGene/fastp) with default options were used for data quality control and filtering with the default parameters
BWA-MEM-v0.7.17 with default options was used to map the assembled data to the designed oligos sequence to preliminarily distinguish the data of each TRAP site
Julia-1.7.1 was used to calculate the read counts and editing read numbers to calculate the editing efficiency, R-4.1.3 was used to filter the editing efficiency.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include editing efficiency for each off-target site

molecule: other

organism: Homo sapiens

extract_protocol:
The on-target and off-target sites were amplified by PCRs
Library cloning started by PCR amplification of the 170-nt oligonucleotide pool, Firstly, the CRISPR SURRO-seq oligos diluted to 1 ng/μl and then performed PCR amplifications using the primers: TRAP-oligo (BsmBI GGA)-F and TRAP-oligo (BsmBI GGA)-R. The PCR reaction was carried out using PrimeSTAR HS DNA Polymerase (Takara, Japan) following the manufacturer`s instruction. The PCR products of SURRO-seq oligos were then used for Golden Gate Assembly (GGA) to generate the plasmids library. 36 parallel GGA reactions were performed and the ligation products were pooled into one tube. Transformation was then carried out using chemically competent DH5αcells. For each reaction, 10μl GGA ligation product was transformed in to 50 μl competent cells and all the transformed cells were spread on one LB plate (15 cm dish in diameter) with Xgal, IPTG and Amp selection. High ligation efficiency was determined by the presence of very few blue colonies. To ensure that there is sufficient coverage of each TRAP in the 12K CRISPRTRAP-seq library, 42 parallel transformations were performed, and all the bacterial colonies were scraped off and pooled together for plasmids midi-prep (PureLinkTM HiPure Plasmid DNA Midiprep Kit). For NGS-based quality quantification of TRAP coverage, midi-prep plasmids were used as DNA templates for TRAP PCR amplifications, followed by gel purification and NGS sequencing

tag: cell line

tag: cell type

value: human skin-derived fibroblasts

tag: treatment

value: MOCK

tag: molecule type

value: synthetic construct


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 152

city: Hangzhou

first: Fang

last: Ye

state: Zhejiang

address: 866 Yuhangtang Rd

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
For single cell CH-RNA-seq. Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using SnapTools. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-10,19-28 (NEO3,NEO4,META1,META2); the bases 1-10,42-51(NEO1,NEO2). UMI barcode:In read1, the bases 11-18(NEO3,NEO4,META1,META2); the bases 34-41(NEO1,NEO2).The raw fastq-format sequencing data from a DNBSEQ-T7 were first split into i7 indexed sub-libraries using splitBarcode (https://github.com/MGI-tech-bioinformatics/splitBarcode). For each sub-library, the revised Drop-seq core computational tool was used for data preprocessing  (http://mccarrolllab.org/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf). We used STAR (version 2.5.2a) with default parameters for mapping 3T3 cells and 293T cells. Reads from 3T3 cells and 293T cells were aligned to a merged hg19-mm10 reference genome (provided by Drop-seq group, GSE63269). To save mapping time , reads from axolotls were aligned to the axolotl genome (V3.0.0, https://www.axolotl-omics.org/assemblies) using another mapper bowtie. GTF annotation files were used to tag aligned reads. Cellular barcodes and unique molecular identifiers (UMIs) were directly extracted from Read1. A list of two rounds of cell barcode oligo sequences was used to correct the extracted cellular barcode from read1. Finally, the HTseq package was used to generate digital expression matrices of axolotl. For cell quality control of axolotl data, we excluded cells in which less than 200 transcripts were expressed. In the mixed-species experiment of 3T3 cells and 293T cells, Cellbarcode:In read1, the bases 1-10,42-51;UMI:In read1, the bases 34-41. The percentage of uniquely mapping reads for genomes of each species with over 85% UMIs assigned to one species was regarded as species-specific cells, while the remaining cells were labeled collisions. Count matrices of bulk RNA-seq of axolotl specimens were generated by featureCounts with default parameters.
For bulk RNA-seq, reads in bam file were aligned to the  genome assembly using STAR version (2.5.2a)  with default configurations. Next, merge the STAR alignment tagged bam were treated using DEseq2 with default configurationsand the reads are annotated with exon tags. Final featurecounts text files were used for downstream analysis.
Assembly: AmexG_v3.0.0(Axolotl genome assembly v3.0.0)(https://genome.axolotl-omics.org/cgi-bin/hgTracks?db=ambMex3&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=AMEXG_0030000001%3A1000%2D2000&hgsid=43238_8SJNnizHOy6T42X4YaUpQyigV8RT)or(https://www.axolotl-omics.org/assemblies)
Supplementary files format and content: tab-delimited text files of digital expression matrix (dge)(single-cell RNA-seq)

molecule: polyA RNA

organism: Ambystoma mexicanum

extract_protocol:
Total RNA of each tissue was purified using standard TRIzol based protocols for bulk RNA-seq;For single-cell RNA-seq, frozen cells of each tissue were thawed at 37 °C and centrifuged at 500×g for 5 min first. Then, fresh fixed or thawed frozen cells were resuspended with 100 µl PBS, and 400 µl Triton X-100 in PBS (10 µl 10% Triton X-100 in 390 µl PBS) was added. The mixture was incubated on ice for 3 min for permeabilization. Next, the cells were pelleted and resuspended with 500 µl DEPC-treated water, and 3 ml 0.1 N HCl was added slowly. After 5 min of incubation on ice, 3.5 ml Triton X-100 in Tris-HCl (35 µl 10% Triton X-100 in 3.5 ml 1 M Tris-HCl, pH 8.0) was added to quench permeabilization. Cells were then washed once with 1 ml of PBS and filtered with a 40 μm strainer. Cell density was determined using a blood cell counting chamber.
For bulk RNA-seq, RNA extraction followed reverse transcription, second strand DNA synthesis, transposase tagmentation and standard Illumina Nextera library construction. For single-cell RNA-seq, cell numbers for each tissue were estimated, and the corresponding volume of cells in PBS was split into four 96-well plates. For each well, 6.5 µl cells (from 5000 to 20000) was mixed with 0.5 µl 10 mM dNTPs (Thermo Fisher Scientific) and 0.5 µl 100 μM RT barcode primer (see Table S1). The mixture was incubated at 65 °C for 5 min and immediately placed on ice. Two microliters of 5X RT buffer (31 mM Tris-HCl, pH 8.0, 37.5 mM NaCl, 3.1 mM MgCl2, 10 mM DTT), 0.5 µl Maxima H Minus RTase (Thermo Fisher Scientific) and 0.1 µl Murine RNase inhibitor were premixed, and 2.5 µl RT mixture was added to each well. Reverse transcription was carried out by incubating the plates at gradient temperature: 3 cycles (8℃ for 12 s, 15℃ for 45 s, 20℃ for 45 s, 30℃ for 30 s, 42℃ for 2 min, and 55℃ for 3 min) and 55℃ for 60 min. After reverse transcription, plates were placed on ice for 1 min to stop the reaction. All reagents were pooled together into a 15 ml centrifuge tube and then centrifuged at 500 g for 5 min. Pellet was washed with PBS twice and resuspended with hybridization buffer (50 mM Tris-HCl, 10 mM MgCl2, 10 mM DTT, 0.1% Triton X-100, 10% PEG8000 (Sigma-Aldrich), 1% Murine RNase inhibitor). Hybridization buffer within cells was split into eight 96-well plates (3 µl for each well) and 2 µl 25 μM pre-annealing hybridization primers (50 μM HY head oligo, 50μM barcoded HY primer oligo, mixed equally and incubated at 95℃ for 2 min, then slowly cooled to 25℃ with a temperature ramp of −0.1℃/s) were added to each well (see in Table S1). Plates were incubated at 37 °C for 90 min, and 0.5 µl of 100 μM block tail primer oligo was added to block any redundant hybridization primers. After blocking for 30 min at 37 °C, all reagents were pooled into a 15 ml centrifuge tube and then centrifuged at 500 g for 5 min. The pellet was washed with PBS twice and resuspended in 40 µl of PBS. Then, 60 µl PNK mix (10 µl 10X PNK buffer (NEB), 20 µl T4 polynucleotide kinase (NEB), 10 µl 10 mM ATP (NEB), and 20 µl DEPC-treated water) was added. The PNK reaction was carried out at 37℃ for 30 min. Then, 1 ml ice-cold PBS was added to stop the reaction. Cells were then filtered using a 40μm strainer. The reagent was centrifuged at 500 g for 5 min after discarding the supernatants. The pellet was again resuspended in PBS, and the density of cells was estimated. After splitting into one or more 96-well plates. There were 5000~8000 cells per well. The volume was adjusted to 8 µl. Second strand synthesis mix (1.33 µl 10X buffer, 0.66 µl second strand synthesis enzyme mix) was added into each well and the plates were incubated at 16℃ for 3 hours (stop point at 4℃). Then, 10 µl cell lysis buffer (20 mM Tris pH 8.0, 400 mM NaCl, 100 mM EDTA, 4.4% SDS (Sangon Biotech)) and 2 µl proteinase K (Sangon Biotech) were added to the wells. Cell lysis was performed at 55℃ for 60 min. Then, 1 µl PMSF (1 mM) was added to quench the lysis reaction. The plates were incubated at 37℃ for 10 min. For each well, the mixture was then purified using 1.5X VAHTS DNA Clean Beads (Vazyme Biotech). Then, 10 µl of product in DEPC-treated water was transferred into new 96-well plates. For each plate, we randomly chose 10 wells to quantify the dsDNA concentration using Equalbit3.0. Tn5 transposase from the TruePrep DNA Library Prep Kit V2 (Vazyme Biotech) was used for cDNA tagmentation. Then, 10 µl of product in DEPC-treated water was transferred into a new 96-well plate. For each well, 14 µl PCR mix (12 µl 2X KAPA HiFi HotStart ReadyMix (Kapa Biosystems), 1 µl 10 mM P5 primer, and 1 µl 10 mM indexed P7 primer, see Table S1) was added to the plates. The PCR program was as follows: 72 °C for 5 min; 98 °C for 30 s; 12 cycles of 98 °C for 10 s, 60 °C for 30 s, and 72 °C for 1 min; 72 °C for 5 min; and a 4 °C hold. After pooling PCR products, two rounds of size selection with VAHTS DNA clean beads (Vazyme Biotech) were used to purify the DNA library between 300 and 500 bp. The libraries were finally mixed, and the concentration of dsDNA was quantified.The purified linear DNA library was circularized into single strand DNA (ssDNA) library using VAHTS® Circularization Kit for MGI (Vazyme). Then ssDNA library was amplified using DNBSEQ DNB preparation kit (MGI). Amplified DNA nanoball (DNB) was sequenced with custom primers on MGI DNBSQ-T7 with dark reaction model ( Single-cell RNA-seq: 100 cycles of read1 with dark reaction from 11-33, 100 cycles of read2;For NEO1,NEO2: PE150, no dark  reaction). Human and mouse cell line libraries were sequenced with custom primers on Illumina Hiseq Xten with pair-end 150bp mode.

tag: strain

value: d/d

tag: age

value: Adult (1year)

tag: tissue

value: brain, bladder, cloaca, eye, fore limb, hind limb, gill, gonad, pancreas, prostate, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail


title: KUH132_MOCK_11291


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 153


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 150


title: KUH132_MOCK_9506


title: KUH132_MOCK_11290


title: KUH132_MOCK_9490


title: KUH132_MOCK_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 149


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 148


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 157


title: KUH132_MOCK_6832


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 147


title: KUH132_MOCK_5679


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 146


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 143


title: KUH132_MOCK_5600


title: KUH132_MOCK_5675


title: KUH132_MOCK_5595


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 145


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 144


title: KUH132_MOCK_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 142


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 141


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 151


title: KUH132_MOCK_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 139


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 140


title: KUH132_MOCK_4729


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 138


title: KUH132_MOCK_5029


title: KUH132_HiFispCas9_VEGFAT2


title: KUH132_MOCK_6791


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 137


title: KUH132_MOCK_4708


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 136


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 134


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 135


title: KUH132_HiFispCas9_RGN11237


title: KUH132_HiFispCas9_RGN11189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 133


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 132


title: KUH132_HiFispCas9_RGN11208


title: KUH132_HiFispCas9_RGN11179


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 129


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 131


title: KUH132_HiFispCas9_11458


title: KUH132_HiFispCas9_HEK293TT4


title: KUH132_HiFispCas9_RGN11184


title: KUH132_HiFispCas9_11437


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 130


title: KUH132_HiFispCas9_11414


title: KUH132_HiFispCas9_11510


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 128


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 127


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 125


title: KUH132_HiFispCas9_9506


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 121


title: KUH132_HiFispCas9_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 126


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 123


title: KUH132_HiFispCas9_6791


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 119


title: KUH132_HiFispCas9_11291


title: KUH132_HiFispCas9_11398


title: KUH132_HiFispCas9_5675


title: KUH132_HiFispCas9_11397


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 124


title: KUH132_HiFispCas9_11296


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 122


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 114


title: KUH132_HiFispCas9_11290


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 120


title: KUH132_HiFispCas9_5595


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 112


title: KUH132_HiFispCas9_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 118


title: KUH132_HiFispCas9_9490


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 117


title: KUH132_HiFispCas9_6832


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 110


title: KUH132_HiFispCas9_5600


title: KUH132_HiFispCas9_5029


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 116


title: KUH132_HiFispCas9_4729


title: KUH132_HiFispCas9_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 109


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 113


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 115


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 108


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 104


title: HEK293T_spCas9_RGN11208

value: human embryonic kidney cells


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 111


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 103


title: KUH132_HiFispCas9_5679


title: KUH132_HiFispCas9_4708


title: HEK293T_spCas9_VEGFAT2


title: HEK293T_spCas9_RGN11237


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 99


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 107


title: HEK293T_spCas9_RGN11189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 105


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 95


title: HEK293T_spCas9_11414


title: HEK293T_spCas9_RGN11184


title: HEK293T_spCas9_11437


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 102


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 106


title: HEK293T_spCas9_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 93


title: HEK293T_spCas9_RGN11179


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 97


title: HEK293T_spCas9_11291


title: HEK293T_spCas9_11510


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 92


title: HEK293T_spCas9_11458


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 101


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 96


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 100


title: HEK293T_spCas9_11398


title: HEK293T_spCas9_9490


title: HEK293T_spCas9_11296


title: HEK293T_spCas9_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 89


title: HEK293T_spCas9_11290


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 88


title: HEK293T_spCas9_9506


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 91


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 98


title: HEK293T_spCas9_11397


title: HEK293T_spCas9_6832


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 94


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 85


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 90


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 87


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 83


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 84


title: HEK293T_spCas9_5679


title: HEK293T_spCas9_5600


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 86


title: HEK293T_spCas9_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 82


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 81


title: HEK293T_spCas9_6791


title: HEK293T_spCas9_5029


title: HEK293T_spCas9_4708


title: HEK293T_spCas9_4729


title: HEK293T_MOCK_VEGFAT2


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 80


title: HEK293T_spCas9_5675


title: HEK293T_MOCK_RGN11208


title: HEK293T_MOCK_RGN11237


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 76


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 75


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 77


title: HEK293T_MOCK_RGN11189


title: HEK293T_spCas9_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 78


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 74


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 73


title: HEK293T_spCas9_5595


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 72


title: HEK293T_MOCK_RGN11184


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 79


title: HEK293T_MOCK_RGN11179


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 70


title: HEK293T_MOCK_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 69


title: HEK293T_MOCK_11437


title: HEK293T_MOCK_11510


title: HEK293T_MOCK_11414


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 67


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 66


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 65


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 64


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 62


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 61


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 63


title: HEK293T_MOCK_11296


title: HEK293T_MOCK_9506


title: HEK293T_MOCK_11458


title: HEK293T_MOCK_11290


title: HEK293T_MOCK_9490


title: HEK293T_MOCK_11397


title: HEK293T_MOCK_11291


title: HEK293T_MOCK_6832


title: HEK293T_MOCK_11398


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 71


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 57


title: HEK293T_MOCK_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 59


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 60


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 58


title: HEK293T_MOCK_6791


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 56


title: HEK293T_MOCK_5679


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 68


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 54


title: HEK293T_MOCK_5675


title: HEK293T_MOCK_5600


title: HEK293T_MOCK_5595


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 53


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 52


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 51


title: HEK293T_MOCK_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 50


title: HEK293T_MOCK_5029


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 49


title: HEK293T_MOCK_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 48


title: HEK293T_MOCK_4729


title: HEK293T_HiFispCas9_RGN11237


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 47


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 46


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 45


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 55


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 43


title: HEK293T_HiFispCas9_RGN11208


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 44


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 42


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 41


title: HEK293T_HiFispCas9_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 40


title: HEK293T_HiFispCas9_11510


title: HEK293T_HiFispCas9_RGN11179


title: HEK293T_HiFispCas9_VEGFAT2


title: HEK293T_HiFispCas9_11458


title: HEK293T_HiFispCas9_11437


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 38


title: HEK293T_MOCK_4708


title: HEK293T_HiFispCas9_RGN11189


title: HEK293T_HiFispCas9_11414


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 37


title: HEK293T_HiFispCas9_RGN11184


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 36


title: HEK293T_HiFispCas9_11296


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 34


title: HEK293T_HiFispCas9_11291


title: HEK293T_HiFispCas9_11398


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 33


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 35


title: HEK293T_HiFispCas9_11397


title: HEK293T_HiFispCas9_9506


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 31


title: HEK293T_HiFispCas9_11290


title: HEK293T_HiFispCas9_9490


title: HEK293T_HiFispCas9_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 39


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 28


title: HEK293T_HiFispCas9_6832


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 32


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 26


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 30


title: HEK293T_HiFispCas9_5675


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 25


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 24


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 27


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 23


title: HEK293T_HiFispCas9_5600


title: HEK293T_HiFispCas9_5595


title: HEK293T_HiFispCas9_5035


title: HEK293T_HiFispCas9_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 29


title: HEK293T_HiFispCas9_5029


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 22


title: LibC(gRNA10613)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 21


title: HEK293T_HiFispCas9_4729


title: HEK293T_HiFispCas9_6791


title: HEK293T_HiFispCas9_4708


title: LibC(gRNA10603)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 19


title: HEK293T_HiFispCas9_5679


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 16


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 17


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 15


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 18


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 14


title: LibC(gRNA10593)_spCas9


title: LibC(gRNA10583)_spCas9


title: LibC(gRNA10573)_spCas9


title: LibC(gRNA10613)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 20


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 13


title: LibC(gRNA10603)_MOCK


title: LibC(gRNA10593)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 12


title: LibC(gRNA10583)_MOCK


title: LibC(gRNA10573)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 11


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 7


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 10


title: LibB(gRNA11240)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 8


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 6


title: LibB(gRNA11239)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 4


title: LibB(gRNA11238)_MOCK


title: LibB(gRNA11247)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 2


title: LibB(gRNA11237)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 1


title: LibB(gRNA11245)_MOCK


title: LibB(gRNA11258)_MOCK


title: LibB(gRNA11248)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 196


title: LibB(gRNA11253)_MOCK


title: LibB(gRNA11252)_MOCK


title: LibB(gRNA11251)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 195


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 5


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 193


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 194


title: LibB(gRNA11250)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 192


title: LibB(gRNA11242)_MOCK


title: LibB(gRNA11236)_MOCK


title: LibB(gRNA11243)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 3


title: LibB(gRNA11255)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 191


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 187


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 188


title: LibB(gRNA11257)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 186


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 184


title: LibB(gRNA11256)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 185


title: LibB(gRNA11235)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 183


title: LibB(gRNA11254)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 197


title: LibB(gRNA11193)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 190


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 181


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 182


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 179


title: LibB(gRNA11154)_MOCK


title: LibB(gRNA11153)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 180


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 178


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 177


title: LibB(gRNA11151)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 176


title: LibB(gRNA11152)_MOCK


title: LibB(gRNA11150)_MOCK


title: LibB(gRNA11190)_MOCK


title: LibB(gRNA11194)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 175


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 174


title: LibB(gRNA11148)_MOCK


title: LibB(gRNA11155)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 173


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 172


title: LibB(gRNA11149)_MOCK


title: LibB(gRNA11146)_MOCK


title: LibB(gRNA11147)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 170


title: LibB(gRNA11181)_MOCK


title: LibB(gRNA11189)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 168


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 167


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 169


title: LibB(gRNA11179)_MOCK


title: LibB(gRNA11176)_MOCK


title: LibB(gRNA11178)_MOCK


title: LibB(gRNA11177)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 165


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 166


title: LibB(gRNA11244)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 164


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 163


title: LibB(gRNA11192)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 161


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 159


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 160


title: LibB(gRNA11231)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 162


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 171


title: LibB(gRNA11234)_MOCK


title: LibB(gRNA11232)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 158


title: LibB(gRNA11230)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 157


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 156


title: LibB(gRNA11233)_MOCK


title: LibB(gRNA11226)_MOCK


title: LibB(gRNA11228)_MOCK


title: LibB(gRNA11227)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 155


title: LibB(gRNA11225)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 154


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 153


title: LibB(gRNA11222)_MOCK


title: LibB(gRNA11223)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 151


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 152


title: LibB(gRNA11221)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 150


title: LibB(gRNA11229)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 149


title: LibB(gRNA11220)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 148


title: LibB(gRNA11216)_MOCK


title: LibB(gRNA11218)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 146


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 145


title: LibB(gRNA11217)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 147


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 143


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 144


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 142


title: LibB(gRNA11215)_MOCK


title: LibB(gRNA11212)_MOCK


title: LibB(gRNA11213)_MOCK


title: LibB(gRNA11211)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 139


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 141


title: LibB(gRNA11214)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 140


title: LibB(gRNA11224)_MOCK


title: LibB(gRNA11208)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 138


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 137


title: LibB(gRNA11209)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 136


title: LibB(gRNA11204)_MOCK


title: LibB(gRNA11207)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 135


title: LibB(gRNA11206)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 134


title: LibB(gRNA11205)_MOCK


title: LibB(gRNA11219)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 131


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 133


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 132


title: LibB(gRNA11210)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 126


title: LibB(gRNA11198)_MOCK


title: LibB(gRNA11199)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 128


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 127


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 125


title: LibB(gRNA11195)_MOCK


title: LibB(gRNA11202)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 123


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 130


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 129


title: LibB(gRNA11160)_MOCK


title: LibB(gRNA11197)_MOCK


title: LibB(gRNA11203)_MOCK


title: LibB(gRNA11201)_MOCK


title: LibB(gRNA11196)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 121


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 124


title: LibB(gRNA11200)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 120


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 122


title: LibB(gRNA11159)_MOCK


title: LibB(gRNA11145)_MOCK


title: LibB(gRNA11158)_MOCK


title: LibB(gRNA11172)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 119


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 118


title: LibB(gRNA11174)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 117


title: LibB(gRNA11175)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 113


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 114


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 116


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 112


title: LibB(gRNA11171)_MOCK


title: LibB(gRNA11170)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 115


title: LibB(gRNA11169)_MOCK


title: LibB(gRNA11168)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 111


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 110


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 109


title: LibB(gRNA11164)_MOCK


title: LibB(gRNA11165)_MOCK


title: LibB(gRNA11163)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 108


title: LibB(gRNA11166)_MOCK


title: LibB(gRNA11173)_MOCK


title: LibB(gRNA11162)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 105


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 106


title: LibB(gRNA11161)_MOCK


title: LibB(gRNA11156)_MOCK


title: LibB(gRNA11167)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 104


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 101


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 103


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 99


title: LibB(gRNA11157)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 100


title: LibB(gRNA11187)_MOCK


title: LibB(gRNA11188)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 107


title: LibB(gRNA11186)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 98


title: LibB(gRNA11182)_MOCK


title: LibB(gRNA11184)_MOCK


title: LibB(gRNA11185)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 95


title: LibB(gRNA11183)_MOCK


title: LibB(gRNA11241)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 93


title: LibA(gRNA11284)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 102


title: LibA(gRNA11279)_MOCK


title: LibA(gRNA11297)_MOCK


title: LibA(gRNA11382)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 91


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 96


title: LibA(gRNA11390)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 90


title: LibA(gRNA11471)_MOCK


title: LibA(gRNA11259)_MOCK


title: LibA(gRNA11464)_MOCK


title: LibA(gRNA11376)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 89


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 85


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 88


title: LibB(gRNA11240)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 87


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 86


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 84


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 94


title: LibB(gRNA11239)_spCas9


title: LibB(gRNA11238)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 81


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 97


title: LibB(gRNA11237)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 79


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 80


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 78


title: LibB(gRNA11247)_spCas9


title: LibB(gRNA11258)_spCas9


title: LibB(gRNA11245)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 77


title: LibA(gRNA11386)_MOCK


title: LibA(gRNA11367)_MOCK


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 76


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 82


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 73


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 74


title: LibB(gRNA11252)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 72


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 70


title: LibB(gRNA11250)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 71


title: LibB(gRNA11251)_spCas9


title: LibB(gRNA11253)_spCas9


title: LibB(gRNA11243)_spCas9


title: LibB(gRNA11242)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 69


title: LibB(gRNA11236)_spCas9


title: LibB(gRNA11235)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 68


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 67


title: LibB(gRNA11254)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 66


title: LibB(gRNA11248)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 65


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 75


title: LibB(gRNA11257)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 64


title: LibB(gRNA11256)_spCas9


title: LibB(gRNA11194)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 63


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 62


title: LibB(gRNA11154)_spCas9


title: LibB(gRNA11155)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 59


title: LibB(gRNA11151)_spCas9


title: LibB(gRNA11190)_spCas9


title: LibB(gRNA11152)_spCas9


title: LibB(gRNA11193)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 61


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 57


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 58


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 54


title: LibB(gRNA11149)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 55


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 52


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 56


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 51


title: LibB(gRNA11147)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 50


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 60


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 53


title: LibB(gRNA11189)_spCas9


title: LibB(gRNA11148)_spCas9


title: LibB(gRNA11146)_spCas9


title: LibB(gRNA11192)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 48


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 49


title: LibB(gRNA11153)_spCas9


title: LibB(gRNA11181)_spCas9


title: LibB(gRNA11179)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 44


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 45


title: LibB(gRNA11255)_spCas9


title: LibB(gRNA11176)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 41


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 92


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 40


title: LibB(gRNA11150)_spCas9


title: LibB(gRNA11234)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 47


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 46


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 43


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 39


title: LibB(gRNA11244)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 42


title: LibB(gRNA11232)_spCas9


title: LibB(gRNA11231)_spCas9


title: LibB(gRNA11230)_spCas9


title: LibB(gRNA11178)_spCas9


title: LibB(gRNA11229)_spCas9


title: LibB(gRNA11228)_spCas9


title: LibB(gRNA11233)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 38


title: LibB(gRNA11177)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 35


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 37


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 33


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 32


title: LibB(gRNA11222)_spCas9


title: LibB(gRNA11223)_spCas9


title: LibB(gRNA11224)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 31


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 29


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 34


title: LibB(gRNA11221)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 36


title: LibB(gRNA11220)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 30


title: LibB(gRNA11219)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 28


title: LibB(gRNA11226)_spCas9


title: LibB(gRNA11218)_spCas9


title: LibB(gRNA11217)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 26


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 25


title: LibB(gRNA11227)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 24


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 27


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 23


title: LibB(gRNA11216)_spCas9


title: LibB(gRNA11215)_spCas9


title: LibB(gRNA11214)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 22


title: LibB(gRNA11213)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 21


title: LibB(gRNA11212)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 17


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 19


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 20


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 18


title: LibB(gRNA11209)_spCas9


title: LibB(gRNA11207)_spCas9


title: LibB(gRNA11208)_spCas9


title: LibB(gRNA11206)_spCas9


title: LibB(gRNA11205)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 15


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 16


title: LibB(gRNA11203)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 12


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 11


title: LibB(gRNA11204)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 10


title: LibB(gRNA11202)_spCas9


title: LibB(gRNA11201)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 14


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 8


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 83


title: LibB(gRNA11200)_spCas9


title: LibB(gRNA11210)_spCas9


title: LibB(gRNA11199)_spCas9


title: LibB(gRNA11198)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 7


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 6


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 13


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 5


title: LibB(gRNA11196)_spCas9


title: LibB(gRNA11195)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 3


title: LibB(gRNA11172)_spCas9


title: LibB(gRNA11160)_spCas9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 2


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch1), NEO1, sublibrary 1


title: LibB(gRNA11159)_spCas9


title: LibB(gRNA11158)_spCas9


title: LibB(gRNA11173)_spCas9


title: LibB(gRNA11175)_spCas9


title: LibB(gRNA11145)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl stomach (Batch2)

data_processing:
For single cell CH-ATAC-seq. Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using SnapTools. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-20.
For bulk RNA-seq, reads in bam file were aligned to the  genome assembly using STAR version (2.5.2a)  with default configurations. Next, merge the STAR alignment tagged bam were treated using DEseq2 with default configurationsand the reads are annotated with exon tags. Final featurecounts text files were used for downstream analysis.
Genome_build: AmexG_v3.0.0 (Axolotl genome assembly v3.0.0) (https://genome.axolotl-omics.org/cgi-bin/hgTracks?db=ambMex3&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=AMEXG_0030000001%3A1000%2D2000&hgsid=43238_8SJNnizHOy6T42X4YaUpQyigV8RT) or (https://www.axolotl-omics.org/assemblies)
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) (Bulk RNA-seq); Snap files of mapped fragments and peaks in single cells (scATAC-seq); scATAC-seq_SampleCellBarcode.xlsx was used to divide different samples in raw data and processed data; Rdata (extracted fromSnap files) of processed single cells fragment matrix and clustering (scATAC-seq):  digest.RDS (Stomach_Intestine_Cloaca_Bladder), kidney.RDS (Kidney_Liver_Spleen), lung.RDS (Lung_Skin_Gill), neuron.RDS (Brain_Eye_Heart), locomotor.RDS (Hindlimb_Forelimb_Tail).

extract_protocol:
Total RNA of each tissue was purified using standard TRIzol based protocols for bulk RNA-seq; For single-nucleus lysate of single cell ATAC-seq, tissues were simply rinsed with 0.8X PBS, and dried tissues were snap-frozen in a clean mortar with liquid-nitrogen, fragile tissues were then grounded into powder and transferred into 1ml of ice-cold lysis buffer (0.1% IGEPAL CA-630 (Sigma-ALDRICH), 0.01% digitonin (Stemcell), 0.1% Tween-20 (Diamond), 1%BSA,10mM Tris-HCL pH7.5 (Thermo Fisher Scientific), 10mM NaCl (Sangon Biotech), 3mM MgCl2 (Thermo Fisher Scientific) in DEPC Treated Water (Sangon Biotech)). The lysis was performed on ice for 3min, and 5ml of RSBT (0.1% Tween-20, 1%BSA, 10mM Tris-HCL pH7.5, 10mM NaCl, 3mM MgCl2 in DEPC Treated Water) was added, the medium was then filtered through a 40μm strainer to remove the debris and clumps for each sample. Nuclei were washed with RSBT for 1 time and pellet was resuspended with 5ml 1X PBS, after which 140ul of 37% formaldehyde solution (HUSHI) was added to a final concentration at 1%. Nuclei were incubated at room temperature for 10min, then 250ul 2.5M Glycine (Diamond) was added to quench the reaction at the same condition for 5min, and finally the mixture was placed on ice for 15min to stop cross-linking completely. After washing with 1ml RSBT for 1 time, nucleus pellet could be resuspended with freezing buffer (50mM Tris-HCL pH8.0 (Thermo Fisher Scientific), 25% Glycerol (Sangon Biotech), 5mM Mg (OAc)2, (Sangon Biotech), 0.1mM EDTA (Thermo Fisher Scientific) in DEPC Treated Water).
For bulk RNA-seq, RNA extraction followed reverse transcription, second strand DNA synthesis, transposase tagmentation and standard Illumina Nextera library construction. For single-cell ATAC-seq, library preparations were performed with the combinatorial hybridization seq protocls, 96-384 uniquely indexed Tn5 transposase were assembled prior to tagmentation. For each well, the Tn5 primers (25pM Tn5 primer A oligo, 50pM Tn5 ME oligo, as well as 25pM the barcoded Tn5 primer B oligo) were mixed, then the plate was incubated at 95℃ for 2min and slowly cooled to 10℃ with a temperature ramp of −0.1℃/s. Tn5 transposase (Vazyme Biotech) was diluted and mixed with annealed Tn5 primers, and the mixture was then incubated at 30℃ for 60min,which leads to a final indexed Tn5concentration of 40ng/ul. Frozen nuclei in freezing buffer were thawed at 37℃ and centrifuged at 500g for 5min. Thawed frozen nuclei or fresh fixed nuclei were resuspended with 1ml RSBT and filtered with a 40um cell strainer to remove any clumps during cryopreserving. Nuclei was centrifuged at 500g for 5min and resuspended in tagmentation buffer (10mM Tris-HCl pH7.5, 5mM MgCl2, 10% DMF (Sigma-ALDRICH), 1%BSA, 0.1% Tween-20, 0.01% digitonin and 0.4X PBS). For each tissue, nuclei density was determined using a blood cell counting chamber. Nuclei were then split into 96-well plates. For each well, 23.5ul nuclei (10000-15000 nuclei) was mixed with 1.5ul indexed Tn5. Then the tagmentation was carried out at 55℃ for 30min, and 25ul 2X stop buffer (40mM EDTA,1mM Spermidine) was separately added into 96 wells. The plate was incubated at 37℃ for 15min to completely stop tagmentation. All the reagent was pooled together into a 15ml centrifuge tube and then centrifuged at 500g for 5min. The pellet was washed twice with RSBT before split into new 96-well plates. Hybridization buffer within cells were split into eight 96-well plates (3ul for each well) and 2ul 25μM pre-annealing hybridization primers (50μM HY head oligo,50μM barcoded HY primer oligo, mixed equally and incubated at 95℃ for 2min, then slowly cooled to 25℃ with a temperature ramp of −0.1℃ /s) were added to each well. Plates were incubated at 37℃ for 90 min and 0.5ul 100μM block tail primer oligo was added to block any redundant hybridization primers. After blocking for 30min at 37℃, all reagents were pooled into a 15ml centrifuge tube and then centrifuged at 500g for 5min. Pellet was washed with inPBS twice and resuspended with 40ul inPBS. Then 60ul PNK mix (10ul 10X PNK buffer (NEB), 20ul T4 Polynucleotide Kinase (NEB), 10ul 10mM ATP (NEB), 20ul DEPC treated water) was added. The PNK reaction was carried out at 37℃ for 30min. After PNK reaction, 1ml ice-cold RSBT was added in pooled reagent were then filtered using a 40μm cell strainer. The medium was centrifuged at 500g for 5min. After discarding the supernatants, the pellet was again resuspended with RSBT. The density of nuclei was estimated and nuclei were split into new 96-well plates (5000-8000 nuclei per well). The volume of each well was adjusted to 8ul. Then 2ul gap-fill mix (1ul 10X Ampligase DNA ligase buffer, 0.3ul Ampligase DNA ligase (Lucigen), 0.5ul 10mM dNTP, 0.2ul T4 DNA polymerse (NEB)) was then added into each well. The plates were incubated at 37℃ for 60 min. Then 2ul nuclei lysis buffer (1ul 10mM Tris-HCl pH8.0,0.5ul proteinase K,0.5ul 1%SDS) was added to release the fragments in nuclei by incubating at 55℃ for 60 min. For each well, the mixture was then purified using 1.5X VAHTS DNA Clean Beads. Then 10ul product in DEPC treated water was then transferred into a new 96-well plate. For each well, 14ul PCR mix (12ul 2X KAPA HiFi HotStart ReadyMix (Kapa Biosystems), 1ul 10mM P5 primer,1ul 10mM indexed P7 primer) were added to the plates. The PCR program was as follows: 72°C for 5 min; 98°C for 3 min; 12 cycles of 98°C 10 s, 65°C 15 s, and 72°C 1 min; 72°C 5 min and 4°C hold. After pooling PCR products, 1.0X VAHTS DNA Clean Beads were used to purify the DNA library, the concentration of dsDNA was quantified. The purified linear DNA library was circularized into single strand DNA (ssDNA) library using VAHTS® Circularization Kit for MGI (Vazyme). Then ssDNA library was amplified using DNBSEQ DNB preparation kit (MGI). Amplified DNA nanoball (DNB) was sequenced with custom primers on MGI DNBSQ-T7 with dark reaction model ( CH-ATAC-seq: 100 cycles of read1 with dark reaction from 11-33,44-62, 100 cycles of read2).

value: stomach


title: Bulk-RNA-seq dataset of Metamorphosed axolotl tail (Batch1)

value: tail


title: Bulk-RNA-seq dataset of Metamorphosed axolotl tail (Batch2)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl stomach (Batch1)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl spleen (Batch2)

value: spleen


title: LibB(gRNA11174)_spCas9


title: LibB(gRNA11171)_spCas9


title: LibB(gRNA11197)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl skin (Batch2)

value: skin


title: LibB(gRNA11170)_spCas9


title: LibB(gRNA11169)_spCas9


title: LibB(gRNA11168)_spCas9


title: LibB(gRNA11167)_spCas9


title: LibB(gRNA11166)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl lung (Batch2)

value: lung


title: Bulk-RNA-seq dataset of Metamorphosed axolotl lung (Batch1)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl liver (Batch2)

value: liver


title: Bulk-RNA-seq dataset of Metamorphosed axolotl liver (Batch1)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl kidney (Batch2)

value: kidney


title: Bulk-RNA-seq dataset of Metamorphosed axolotl spleen (Batch1)


title: LibB(gRNA11165)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl kidney (Batch1)


title: LibB(gRNA11225)_spCas9


title: LibB(gRNA11164)_spCas9


title: LibB(gRNA11163)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl intestine (Batch2)

value: intestine


title: LibB(gRNA11162)_spCas9


title: LibB(gRNA11157)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl forelimb (Batch1)

value: Forelimb


title: Bulk-RNA-seq dataset of Metamorphosed axolotl heart (Batch1)

value: Heart


title: LibB(gRNA11187)_spCas9


title: LibB(gRNA11156)_spCas9


title: LibB(gRNA11161)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl skin (Batch1)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl eye (Batch2)

value: Eye


title: Bulk-RNA-seq dataset of Metamorphosed axolotl eye (Batch1)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl Cloacalchamber (Batch2)

value: Cloacalchamber


title: Bulk-RNA-seq dataset of Metamorphosed axolotl intestine (Batch1)


title: LibB(gRNA11188)_spCas9

value: synthetic construct


title: LibB(gRNA11183)_spCas9


title: LibB(gRNA11184)_spCas9


title: LibB(gRNA11186)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl brain (Batch1)

value: d/d

value: Brain


title: Bulk-RNA-seq dataset of Metamorphosed axolotl bladder (Batch2)

value: Adult (1year)

value: Bladder


title: LibB(gRNA11182)_spCas9

value: human embryonic kidney cells


title: Bulk-RNA-seq dataset of Metamorphosed axolotl bladder (Batch1)


title: Bulk-RNA-seq dataset of Metamorphosed axolotl hindlimb (Batch1)

value: hindlimb


title: Bulk-RNA-seq dataset of Metamorphosed axolotl Cloacalchamber (Batch1)


title: LibA(gRNA11284)_spCas9


title: LibB(gRNA11185)_spCas9


title: LibA(gRNA11297)_spCas9


title: LibA(gRNA11382)_spCas9


title: LibA(gRNA11390)_spCas9


title: Bulk-RNA-seq dataset of neotenic axolotl tail (Batch1)

value: tail


title: Bulk-RNA-seq dataset of neotenic axolotl stomach (Batch1)

value: stomach


title: Bulk-RNA-seq dataset of neotenic axolotl tail (Batch2)


title: LibB(gRNA11241)_spCas9


title: Bulk-RNA-seq dataset of neotenic axolotl skin (Batch2)

value: skin


title: LibA(gRNA11464)_spCas9


title: Bulk-RNA-seq dataset of Metamorphosed axolotl hindlimb (Batch2)


title: Bulk-RNA-seq dataset of neotenic axolotl spleen (Batch2)

value: spleen


title: LibA(gRNA11386)_spCas9


title: LibA(gRNA11471)_spCas9


title: LibA(gRNA11279)_spCas9


title: Bulk-RNA-seq dataset of neotenic axolotl lung (Batch1)

value: lung


title: Bulk-RNA-seq dataset of neotenic axolotl spleen (Batch1)


title: Bulk-RNA-seq dataset of neotenic axolotl liver (Batch2)

value: liver


title: Bulk-RNA-seq dataset of neotenic axolotl liver (Batch1)


title: LibA(gRNA11367)_spCas9


title: Bulk-RNA-seq dataset of neotenic axolotl kidney (Batch2)

value: kidney


title: Fly, Female, 3 day, 1000 mg/kg/day, rep3

city: San Diego

first: Goran

last: Bozinovic

state: CA

address: 3030 Bunker Hill St

country: USA

institute: Boz Life Science Research and Teaching Institute

description: 100 pooled brains

data_processing:
Base call was performed via NextSeq 1000/2000 Control Software Suite v1.4.1
Raw data from shallow RNA sequencing were demultiplexed by Scripps Research Genomics Core using BBTools (version 37.62) (Bushnell et al., 2017).
Unique Molecular Identifiers (UMI) were extracted from the sequencing results using UMI-tools (version 1.1.2) (Smith et al., 2017). Sequencing data quality was assessed in R via FastQCR (version 0.1.2) (Kassambara, 2019). SortMeRNA (version 4.3.4) was used to filter out rRNA . Trimmomatic (version 0.39) was used to remove the first 16 bases of each read, trim reads with a sliding-window of 4 bases and a minimum Phred score of 30, and remove resulting reads shorter than 18 bases (Bolger et al., 2014). The trimmed reads were aligned to D. melanogaster genome (FlyBase 6.32) via STAR (version 2.7.10a) (Dobin et al., 2013). PCR duplicates were removed using extracted UMI via UMI-tools. Gene counts based on reads mapping were generated through HTSeq (version 2.0.1) (Putri et al., 2022).
Identified genes with non-zero counts were selected from the raw output, and gene expression was normalized via trimmed mean of M-values (TMM) (Robinson & Oshlack, 2010). Average log counts per million (CPM) values were calculated via the aveLogCPM function of edgeR (version 3.36.0) (Robinson et al., 2010) and visualized via ggplot2 (version 3.3.5) (Wickham, 2016). Low count threshold was determined to be 6 counts per million, and low count filtering was performed via the filtered.data function of NOISeq (version 2.38.0) (Tarazona et al., 2015). Because RNA isolation was performed sequentially for the replicates (batches) of the 24 experimental conditions, potential batch effects were removed via the ARSyNseq function of NOISeq.
Relative to the control condition, pairwise comparison to determine differentially expressed genes for each HFPO-DA exposure concentration was performed through NOISeq, with the probability of differential expression threshold, q, set to 0.90.
Assembly: FlyBase 6.32
Supplementary files format and content: genx_fly_normalized.csv; contains the final normalized (as described in the data processing steps) gene counts that entered NOISeq analysis; column titles (Row 1) match the library names, and row titles (Column 1) are gene IDs

organism: Drosophila melanogaster

source_name: brain

growth_protocol: Oregon wild-type Drosophila melanogaster (Carolina Biological Supply Company) were reared on standard cornmeal agar medium, 12-hour light/dark cycle at 25°C. Female and male virgin flies less than 4 hours post-eclosion were separately collected under CO2. Flies were aged to 3, 7, or 14 days post-eclosion and snap frozen at -80°C. Subsequently, brains were dissected in phosphate buffered saline.

extract_protocol:
Pooled brains (100 brains/sample) were homogenized in TRIzol via a bead mill. Total RNA was isolated using the TRIzol reagent protocol (Invitrogen, Carlsbad, CA) and stored at -80°C.
cDNA library preparation and shallow RNA-Seq were performed at Scripps Research Genomics Core. Sample quality was assessed using a 2100 Bioanalyzer Instrument (part number: G2939BA, Agilent Technologies, Inc., Santa Clara, California, USA). Library preparation for RNA-Seq was performed via an early access kit, HTP RNA-Seq Library Prep, from iGenomX (now acquired by Twist Bioscience, South San Francisco, California, USA) with slight modifications. Briefly, PCR products 350–800 base pairs long were purified via 2% agarose gel electrophoresis, quantitated using Qubit dsDNA HS assay kit (catalog number: Q33231, Invitrogen™), and analyzed on a 4150 TapeStation System (part number: G2992AA, Agilent Technologies, Inc.).

treatment_protocol: Female and male virgin flies were separately collected for each experimental condition at less than 4 hours post-eclosion under light CO2 anesthesia and placed in either the control or treatment group. Female and male flies remained separated after collection. Control flies continued their diet on standard cornmeal agar medium while treated flies were fed cornmeal agar medium with HFPO-DA (CASRN: 13252-13-6; Catalog No. 2121-3-13; Synquest) incorporated at 10 mg/kg/day, 100 mg/kg/day, or 1000 mg/kg/day. Dosage calculations assume that flies typically eat 1.5 μL of food per day (Ja et al., 2007) and weigh about 10 μN (1 mg) (Dickinson and Götz, 1996).

tag: Sex

value: Female

value: brain

tag: time

value: 3 days post-eclosion

tag: genotype

value: Oregon wild-type

value: HFPO-DA

tag: dose

value: 1000 mg/kg/day


title: Bulk-RNA-seq dataset of neotenic axolotl lung (Batch2)

value: d/d

value: Adult (1year)


title: Bulk-RNA-seq dataset of neotenic axolotl kidney (Batch1)


title: Fly, Female, 3 day, 1000 mg/kg/day, rep1

description: 100 pooled brains


title: Bulk-RNA-seq dataset of neotenic axolotl skin (Batch1)


title: Bulk-RNA-seq dataset of neotenic axolotl intestine (Batch1)

value: intestine


title: Bulk-RNA-seq dataset of neotenic axolotl intestine (Batch2)


title: LibA(gRNA11259)_spCas9

value: human embryonic kidney cells

value: synthetic construct


title: Bulk-RNA-seq dataset of neotenic axolotl hindlimb (Batch1)

value: hindlimb


title: Bulk-RNA-seq dataset of neotenic axolotl stomach (Batch2)

value: stomach


title: Bulk-RNA-seq dataset of neotenic axolotl hindlimb (Batch2)


title: LibA(gRNA11376)_spCas9


title: Bulk-RNA-seq dataset of neotenic axolotl gonad (Batch1)

value: Gonad


title: Bulk-RNA-seq dataset of neotenic axolotl gonad (Batch2)


title: Bulk-RNA-seq dataset of neotenic axolotl gill (Batch2)

value: Gill


title: Fly, Female, 3 day, 100 mg/kg/day, rep3

description: 100 pooled brains

value: 100 mg/kg/day


title: Fly, Female, 7 day, 100 mg/kg/day, rep2

description: 100 pooled brains

value: 7 days post-eclosion


title: Fly, Male, 3 day, 1000 mg/kg/day, rep3

description: 100 pooled brains

value: Male


title: Fly, Male, 3 day, 1000 mg/kg/day, rep2

description: 100 pooled brains

value: brain


title: Fly, Female, 3 day, 100 mg/kg/day, rep2

description: 100 pooled brains

value: Female

value: 3 days post-eclosion


title: Fly, Male, 3 day, 1000 mg/kg/day, rep1

description: 100 pooled brains

value: Oregon wild-type

value: HFPO-DA


title: Fly, Female, 7 day, 100 mg/kg/day, rep1

description: 100 pooled brains


title: Fly, Female, 3 day, 1000 mg/kg/day, rep2

description: 100 pooled brains

value: 1000 mg/kg/day


title: Fly, Female, 7 day, 100 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Female, 3 day, 100 mg/kg/day, rep1

description: 100 pooled brains


title: Bulk-RNA-seq dataset of neotenic axolotl gill (Batch1)

value: d/d

value: Adult (1year)


title: Fly, Male, 14 day, 100 mg/kg/day, rep3

description: 100 pooled brains

value: 14 days post-eclosion


title: Fly, Male, 14 day, 100 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Male, 14 day, 100 mg/kg/day, rep1

description: 100 pooled brains


title: Bulk-RNA-seq dataset of neotenic axolotl forelimb (Batch2)

value: Forelimb


title: LibB(gRNA11211)_spCas9

value: human embryonic kidney cells

value: synthetic construct


title: Bulk-RNA-seq dataset of neotenic axolotl heart (Batch2)

value: Heart


title: Bulk-RNA-seq dataset of neotenic axolotl heart (Batch1)


title: Bulk-RNA-seq dataset of neotenic axolotl forelimb (Batch1)


title: Fly, Male, 3 day, 100 mg/kg/day, rep3

description: 100 pooled brains


title: Bulk-RNA-seq dataset of neotenic axolotl brain (Batch1)

value: Brain


title: Bulk-RNA-seq dataset of neotenic axolotl brain (Batch2)


title: Bulk-RNA-seq dataset of neotenic axolotl eye (Batch2)

value: Eye


title: Fly, Male, 7 day, 100 mg/kg/day, rep3

description: 100 pooled brains

value: 7 days post-eclosion

value: 100 mg/kg/day


title: Fly, Female, 14 day, 10 mg/kg/day, rep2

description: 100 pooled brains

value: brain

value: 10 mg/kg/day


title: Bulk-RNA-seq dataset of neotenic axolotl bladder (Batch2)

value: Bladder


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 30

value: bladder, brain, cloaca, eye, fore limb, hind limb, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail, gonad


title: Fly, Female, 7 day, 10 mg/kg/day, rep3

description: 100 pooled brains

value: Female

value: Oregon wild-type

value: HFPO-DA


title: Bulk-RNA-seq dataset of neotenic axolotl Cloacalchamber (Batch1)

value: d/d

value: Adult (1year)

value: Cloacalchamber


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 29


title: Bulk-RNA-seq dataset of neotenic axolotl eye (Batch1)


title: Fly, Male, 7 day, 100 mg/kg/day, rep1

description: 100 pooled brains

value: Male


title: Bulk-RNA-seq dataset of neotenic axolotl Cloacalchamber (Batch2)


title: Fly, Female, 3 day, 10 mg/kg/day, rep5

description: 100 pooled brains

value: 3 days post-eclosion


title: Fly, Male, 3 day, 100 mg/kg/day, rep2

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 25


title: Fly, Female, 14 day, 10 mg/kg/day, rep3

description: 100 pooled brains

value: 14 days post-eclosion


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 32


title: Bulk-RNA-seq dataset of neotenic axolotl bladder (Batch1)


title: Fly, Male, 3 day, 100 mg/kg/day, rep1

description: 100 pooled brains


title: Fly, Male, 14 day, 10 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Female, 7 day, 10 mg/kg/day, rep2

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 31


title: Fly, Male, 14 day, 10 mg/kg/day, rep1

description: 100 pooled brains


title: Fly, Male, 7 day, 100 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Female, 14 day, 10 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 21


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 20


title: Fly, Male, 3 day, 10 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Male, 7 day, 10 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Female, 3 day, 10 mg/kg/day, rep3

description: 100 pooled brains; outlier removed from analysis


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 18


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 28


title: Fly, Female, 7 day, 10 mg/kg/day, rep1

description: 100 pooled brains


title: Fly, Female, 3 day, 10 mg/kg/day, rep4

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 27


title: Fly, Male, 3 day, 10 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 26


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 16


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 15


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 12


title: Fly, Female, 14 day, 0 mg/kg/day, rep1

description: 100 pooled brains

value: untreated

value: 0 mg/kg/day


title: Fly, Female, 7 day, 0 mg/kg/day, rep2

description: 100 pooled brains

value: 7 days post-eclosion


title: Fly, Male, 14 day, 10 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Male, 7 day, 10 mg/kg/day, rep1

description: 100 pooled brains


title: Fly, Female, 7 day, 0 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 10


title: Fly, Female, 3 day, 0 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Male, 7 day, 10 mg/kg/day, rep3

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 22


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 9


title: Fly, Female, 3 day, 0 mg/kg/day, rep2

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 19


title: Fly, Female, 3 day, 0 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 24


title: Fly, Male, 3 day, 10 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Male, 14 day, 0 mg/kg/day, rep3

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 17


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 23


title: Fly, Male, 14 day, 0 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Female, 14 day, 0 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Female, 14 day, 0 mg/kg/day, rep2

description: 100 pooled brains


title: Fly, Male, 14 day, 0 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 14


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 4


title: Fly, Male, 7 day, 0 mg/kg/day, rep3

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 13


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 56


title: Fly, Female, 7 day, 0 mg/kg/day, rep3

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 11


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 8


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 7


title: Fly, Male, 7 day, 0 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 6


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 53


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 52


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 3


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 50


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 1


title: Fly, Male, 7 day, 0 mg/kg/day, rep2

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 2


title: Fly, Male, 3 day, 0 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 55


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 48


title: Fly, Male, 3 day, 0 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Female, 3 day, 10 mg/kg/day, rep2

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 46


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch2), META2, sublibrary 5


title: female dnTGFB secretin 2

city: Indianapolis

first: Lindsey

last: Kennedy

state: IN

address: 702 Rotary Circle

institute: Indiana University School of Medicine

data_processing: data was generated and processed by GeneWiz (Azenta)

molecule: total RNA

organism: Mus musculus

source_name: intrahepatic cholangiocytes

growth_protocol: animal were bred and kept in normal housing conditions until 32 wks of age at which time WT mice were sacrificed and used, or secretin treated mice were treated for 8 wks and sacrified and used at 40 wks of age.

extract_protocol:
intrahepatic cholangiocytes were extracted with a proprietary antibody that binds to all intrahepatic cholangiocytes (generated by Dr. Faris Brown, Brown University) followed by magnetic bead binding and separation
RNA selected by poly(A) selection
RNA-seq generated from 500 ng total RNA per sample

treatment_protocol: at 32 wks of age mice were IP implanted with osmotic minipumps containing sectetin at a dosage of 4 ug/kg BW/day. After 1 month, mice were implanted with another minipump for the same dosage.

value: intrahepatic cholangiocytes

value: dominant-negative transforming growth factor beta receptor II

value: secretin 8 wks


title: female dnTGFB 3

value: wild-type


title: female dnTGFB 2


title: female dnTGFB secretin 1


title: Fly, Female, 14 day, 1000 mg/kg/day, rep3

description: 100 pooled brains

value: brain

value: 1000 mg/kg/day


title: female dnTGFB secretin 3


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 54

value: bladder, brain, cloaca, eye, fore limb, hind limb, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail, gonad


title: Fly, Male, 3 day, 0 mg/kg/day, rep2

description: 100 pooled brains

value: Oregon wild-type


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 51

value: d/d


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 43

value: Adult (1year)


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 40


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 41


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 42


title: female dnTGFB 1


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 49


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 39


title: female WT secretin 3


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 47


title: female WT secretin 2


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 44


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 37


title: Fly, Female, 14 day, 1000 mg/kg/day, rep2

description: 100 pooled brains

value: Female

value: HFPO-DA


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 45


title: female WT secretin 1


title: Fly, Female, 7 day, 1000 mg/kg/day, rep3

description: 100 pooled brains


title: Fly, Female, 7 day, 1000 mg/kg/day, rep2

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 36


title: Human SNpc, Parkinson's disease, patient [HsRNAPD5SNc_R1.AT.fastq.gz]

city: Bangalore

first: Vijayalakshmi

last: Ravindranath

address: C.V. Raman Avenue

country: India

institute: Centre for Brain Research

data_processing:
The raw sequencing data, in the form of FastQ files was checked for quality using FastQC, following which the low quality reads and adapter sequences were removed using Trimmomatic (v0.36).
Further, TopHat2 (v2.1.1) was used for alignment of reads to mouse or human genomes.
The resultant alignment files are in the bam (binary alignment/map) format, which were further sorted in the order of names of genes using Samtools, 0.1.19 and finally the numbers of counts for each read in each sample were generated using htseq-count.
DESeq2 version 1.22.2 was used for normalization of read counts. DESeq2 analysis was performed on R version 3.5.1.
Assembly: Ensembl genome GRCm38 (mouse) and GRCh37 (human).
Supplementary files format and content: *.txt: Tab-delimited text files include counts values for each Sample.

source_name: Substantia nigra pars compacta

extract_protocol:
All the reagents used for RNA isolation and cDNA synthesis were prepared in RNase free conditions using DEPC water. RNA from mouse brain tissue was isolated using TRIzol reagent (Invitrogen Cat# 15596018) and bromo-chlorophenol (BCP) (Molecular Research Centre, Inc. Cat# BP151). RNA was isolated from human autopsy brain tissue using the RNeasy Plus Universal Mini Kit (Qiagen Cat# 73404).
RNA libraries for RNA-seq for mouse RNA were prepared using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB #E7420G, 30061409) following manufacturer's protocols. RNA-seq library preparation for human tissue samples was performed using the TruSeq RNA Library Prep Kit v2 (Catalog IDs: RS-122-2001, RS-122-2002).

value: Substantia nigra pars compacta

tag: disease state

value: Parkinson's disease


title: Fly, Female, 14 day, 1000 mg/kg/day, rep1

value: 14 days post-eclosion


title: female WT 3


title: male dnTGFB secretin 2


title: female WT 1


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 38


title: Fly, Male, 14 day, 1000 mg/kg/day, rep3

description: 100 pooled brains

value: Male


title: Fly, Female, 7 day, 1000 mg/kg/day, rep1

description: 100 pooled brains

value: 7 days post-eclosion


title: male dnTGFB secretin 3

value: intrahepatic cholangiocytes


title: female WT 2


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 34


title: Human SNpc, Parkinson's disease, patient [HsRNAPD4SNc_R1.AT.fastq.gz]


title: male dnTGFB secretin 1

value: dominant-negative transforming growth factor beta receptor II


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 32


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 33


title: Fly, Male, 14 day, 1000 mg/kg/day, rep2

description: 100 pooled brains


title: Human SNpc, Parkinson's disease, patient [HsRNAPD2SNc_R1.AT.fastq.gz]


title: Human SNpc, Parkinson's disease, patient [HsRNAPD1SNc_R1.AT.fastq.gz]


title: male dnTGFB 3


title: male dnTGFB 2


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 31


title: Fly, Male, 14 day, 1000 mg/kg/day, rep1

description: 100 pooled brains


title: Fly, Male, 7 day, 1000 mg/kg/day, rep2

description: 100 pooled brains


title: Human SNpc, Parkinson's disease, control [HsRNAC4SNc_R1.AT.fastq.gz]

value: Control


title: Human SNpc, Parkinson's disease, control [HsRNAC2SNc_R1.AT.fastq.gz]


title: Fly, Male, 7 day, 1000 mg/kg/day, rep3

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 28


title: Fly, Male, 7 day, 1000 mg/kg/day, rep1

description: 100 pooled brains


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 35


title: Fly, Female, 14 day, 100 mg/kg/day, rep2

description: 100 pooled brains

value: 100 mg/kg/day


title: male dnTGFB 1

value: wild-type


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 26


title: male WT 3


title: male WT secretin 2

value: secretin 8 wks


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 30

value: bladder, brain, cloaca, eye, fore limb, hind limb, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail, gonad


title: male WT 2


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 29


title: 293T_Input_1

city: Changsha

first: Jiankang

last: Wang

state: Hunan

address: Lushan

institute: School of biology

data_processing:
Sequencing reads were aligned to human reference genome (hg38) using Bowtie version 1.2.2 with “-n2 -m1” parameters
Peak calling was performed using MACS2 version 2.2.6 with default settings
Assembly: hg38
Supplementary files format and content: bed files of ChIP-seq peak

molecule: genomic DNA

growth_protocol: Cells (JCRB Cell Bank) were cultured in DMEM containing 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Chromatin immunoprecipitation was performed as previously described (Komata, M., et al., Chromatin immunoprecipitation protocol for mammalian cells. Methods Mol Biol, 2014. 1164: p. 33-8.).
ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (New England BioLabs).

tag: antibody

value: Input

value: NT

tag: cell line/type


title: Human SNpc, Parkinson's disease, control [HsRNAC1SNc_R1.AT.fastq.gz]


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 25

value: d/d

value: Adult (1year)


title: male WT 1


title: Fly, Female, 14 day, 100 mg/kg/day, rep3

description: 100 pooled brains

value: Female

value: brain

value: Oregon wild-type

value: HFPO-DA


title: male WT secretin 1


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 27


title: Fly, Female, 3 day, 10 mg/kg/day, rep1

value: 3 days post-eclosion

value: 10 mg/kg/day


title: Bcell_Input_1

value: Bcell


title: male WT secretin 3

value: intrahepatic cholangiocytes

value: dominant-negative transforming growth factor beta receptor II


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 23


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 24


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 22


title: Bcell_CTCF_1

value: CTCF (07-729, Merck Millipore)


title: Fly, Female, 14 day, 100 mg/kg/day, rep1

description: 100 pooled brains

value: 14 days post-eclosion

value: 100 mg/kg/day


title: 293T_CTCF_1


title: Single-cell RNA-seq dataset of metamorphosed axolotl (Batch1), META1, sublibrary 21

value: bladder, brain, cloaca, eye, fore limb, hind limb, heart, intestine, kidney, liver, lung, skin, spleen, stomach, tail, gonad


title: RNA_GFP_Pos

city: New York

first: Peter

last: Smibert

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Fastqs were generated using CellRanger mkfastq 6.0.0
Sequencing reads were aligned usingCellRanger count to the mm10 reference genome
Assembly: mm10
Supplementary files format and content: Per-cell scRNA-seq gene expression counts (h5)

source_name: Immune cells

extract_protocol: Standard 10x Genomics protocol for 5' scRNA-seq

tag: magnetic depletion

value: TCRb, B220, Ter199, CD3

tag: sorting conditions

value: GFP+ and live

value: Adig


title: RNA_Ref

value: all live


title: iPSC neurons, GPNMB homozygous knockout, day 14 of differentiation, rep5

city: Philadelphia

first: Alice

middle: S

last: Chen-Plotkin

state: PA

address: 150 Johnson Pavilion

department: Neurology

institute: University of Pennsylvania

data_processing:
QC assessed using FastQC and summarized with MultiQC.
Adapters removal and reads filtering by conducted by Trimmomatic Version 0.39 with following parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:5:20 MINLEN:50 AVGQUAL:30 HEADCROP:10
Alignment with Bowtie 2 with the following parameters: bowtie2 -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 --nofw -p 32 -k 200 -x,
Read counts at the gene level were estimated by an expectation maximization algorithm built in RSEM.
Assembly: GRChg38
Supplementary files format and content: Matrix_of_raw_counts_per_gene_estimated_by_RSEM.txt: Matrix of raw read counts per gene estimated by RSEM. Each column is a sample and each row is a gene.

source_name: iPSC-N

growth_protocol: Human induced pluripotent stem cells (iPSC) with Neurog1 and Neurog2 in a bicistronic doxycycline-inducible expression cassette (provided by George Church lab) were used to generation of GPNMB wild-type (WT), heterozygote (Het), and knock-out (KO) iPSC and rapid induction of iPSC-derived neurons (iPSC-N). CRISPR knock out was achieved with sgRNA (Synthego) and recombinant Cas9 protein. iPSC cultures were maintained on Matrigel-coated 6cm tissue culture plates with mTeSR1 media and mechanically passaged every 4 days with StemMACS passaging solution XF. D0 iPSC-N were isolated 4 days after passaging, prior to neuronal induction. Neuronal induction was carried out by dissociating cells with Accutane, resuspending in N2 pre-differentiation media (KnockOut DMEM/F12 with 1x N-2 supplement, 1x MEM NEAA, 10ng/ml BDNF, 10ng/ml NT-3, 0.2ug/ml Laminin, and 2ug/ml doxycycline hyclate) with 10ug/ml Y-27632, and plating in matrigel-coated 6-well plates at 700k cells/well. Media was changed daily on days 1 and 2. On day 3, pre-differentiated iPSC-N were dissociated with accutase, resuspended in neuronal media (50% DMEM/F12, 50% Neurobasal-A media, 1x MEM NEAA, 0.5x N-2 supplement, 0.5x GlutaMAX supplement, 0.5x B27 supplement, 10ng/ml BDNF, 10ng/ml NT-3, 1ug/ml Laminin, and 2ug/ml doxycycline), and re-plated on PDL/matrigel coated glass coverslips at 200k cells/well in a 12-well plate format. Half-media changes were performed every 7 days and mature iPSC-N were harvested on D14 after induction.

extract_protocol:
RNA was extracted using QIAGEN RNeasy ® mini kit.
Library preparation was performed by the Penn Next Generation Sequencing (NGS) Core staff with the TruSeq Stranded mRNA Library Prep kit (Illumina cat #20020595) using 225ng total RNA and following manufacturer instructions.

value: iPSC-N

value: iPSC-derived neurons

value: GPNMB homozygous knock-out

value: Doxycycline induced differentiation

tag: time point

value: Day 14

tag: replicate


title: iPSC neurons, wild type, day 14 of differentiation, rep2

tag: cell line

tag: cell type

value: WT


title: iPSC neurons, wild type, day 14 of differentiation, rep3

tag: treatment


title: iPSC neurons, wild type, day 14 of differentiation, rep5


title: iPSC neurons, wild type, day 14 of differentiation, rep1


title: Cytosol non-infected RPF, replicate 3

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

description:
raw_counts_RPF.tsv
Cyt_12_RPF

data_processing:
Library strategy: Ribo-seq
Since mammalian transcripts usually feature several different splice isoforms that can feature different ORFs, we determined the most prominent mRNA isoform for each gene present in our RNA-seq samples to allow a gene-based analysis. To do so, we removed read-through and NMD transcripts from the Appris principal isoforms annotation (http://ubio.bioinfo.cnio.es/data/appris/) for hg38 (based on GENCODE v24) and quantified all remaining transcripts using kallisto (v0.43.0), selecting the protein coding isoform which on average was expressed highest after sleuth’s (v0.29.0) between-sample normalization of the kallisto TPM values. In case multiple transcripts showed equal expression, they were ranked according to the following criteria: 1. Appris classification scheme ('PRINCIPAL:1', 'PRINCIPAL:2', 'PRINCIPAL:3', 'PRINCIPAL:4', 'PRINCIPAL:5', 'ALTERNATIVE:1', 'ALTERNATIVE:2'), 2. lowest CCDS and 3. lowest ENST ID. Lastly, we created a custom bowtie transcriptome index for our HEK 293T cells for ribosome footprint mapping. Prior to mapping to the custom index, we removed sequencing adaptors and trimmed the ribosome profiling reads using cutadapt (v1.91, settings: -a CTGTAGGCACCATCAAT --quality-base 33 -q 28,28 -m 25 -M 35). All surviving Ribo-seq reads were next mapped to an index of known tRNA, rRNA, snRNA, snoRNA and miRNA genes based on GENCODE v24 via bowtie (v1.2.1) and only non-mapping reads were used for mapping to the custom transcriptome index (bowtie v1.2.1, default settings) and subsequent analyses. Read assignment to A- and P-site as well as footprint counting was performed using riboWaltz, selecting reads of 29-33 nt length and using 14-18 nt as corresponding P-site offsets across all samples.  RNA-sequencing reads were mapped against a combined human (hg38) and CHIKV (KT449801.1) genome using TopHat2 (v2.1.0, settings: --max-multihits 1 --b2-very-sensitive --no-coverage-search --library-type fr-firststrand) and supplying an additional transcriptome index based on GENCODE v24. Reads were subsequently quantified using featureCounts (v1.5.1, settings: -s 2 -Q 1 -p) using our custom HEK 293T transcriptome annotation. All genes with fewer than 5 RPF and 10 RNA-seq reads in either ER or cytosol were discarded before continuing our quantitative differential translation analysis. In addition, since RNA-seq reads mapping to the CHIKV SP region can originate from both the full-length CHIKV RNA (NSP ORF) as well as the subgenomic RNA (SP ORF), we calculated the average coverage across the NSP region to estimate how many reads mapping to the SP region should originate from the full-length (=NSP) isoform, assuming a uniform sequencing coverage. Using these estimates we then re-assigned a discrete number of reads from the SP to the NSP ORF for each sample prior to the differential expression analysis. Quantitative analysis of both RNA-seq and Ribo-seq counts were performed using limma-voom (v3.32.2), where changes in relative translational efficiency caused by CHIKV infection were independently modeled for ER and cytosol via an interaction term (~sequencing_type * infection_status).
Genome_build: hg38
Supplementary_files_format_and_content: The file raw_counts_mRNA.tsv contains raw mRNA read counts, whereas raw_counts_RPF.tsv contains raw ribosome footprint counts. Each column represents one sample in lexicographical order.

source_name: whole cell

growth_protocol: Hek293T cells were grown at 37C and 5% CO2 in DMEM + 10% FBS. When reaching 80% confluence cells were splitted.

extract_protocol:
Total RNA was extracted by a hot-phenol protocol and mRNA isolated using the TruSeq stranded mRNA library prep kit (Illumina). For ribosome profiling lysates were treated with RNAse I and subjected to polysome profiling. RNA was collected from the monosome peak and size-selected using a denaturing urea gel. Ribosomal RNA was removed using the Ribo-Zero Gold rRNA Removal kit (Epicenter).
RPF libraries were prepared using the protocol described in (Ingolia, 2009), (Nedialkova and Leidel, 2015) and (Jungfleisch et al. 2017). For RNA-seq libraries, the TruSeq stranded mRNA library prep kit (Illumina) was used.

treatment_protocol: 12 h mock or 12 h CHIKV infection

value: HEK 293T

value: 12 h mock infection

tag: cellular fraction

value: cytosol

tag: molecule

value: Ribosome footprints