title: HCMV 4w Rep 1

description: S8_HCMV-4wk Length, S8_HCMV-4wk Effective Length, S8_HCMV-4wk Expected Count, S8_HCMV-4wk TPM, S8_HCMV-4wk FPKM

value: HCMV

value: 4 wpi


title: Mock 4w Rep 1

status: Public on Jun 18 2022

type: SRA

city: Shreveport

first: Bailey

last: Mosher

state: LA

address: 1501 Kings Highway

department: Microbiology & Immunology

country: USA

institute: Louisiana State University Health - Shreveport

description: S7_Mock-4wk Length, S7_Mock-4wk Effective Length, S7_Mock-4wk Expected Count, S7_Mock-4wk TPM, S7_Mock-4wk FPKM

library_source: transcriptomic

data_processing:
Reads were aligned to a concatenated human and HCMV genome (chRHCMV_Lisa_KF2973391_ChrGRCh38p12_1-4-19).
Transcripts were quantified with RSEM 1.3.0.
Sequence reads were mapped to chRHCMV_Lisa_KF2973391_ChrGRCh38p12_1-4-19  using STAR 2.5.31.
Assembly: chRHCMV_Lisa_KF2973391_ChrGRCh38p12_1-4-19
Supplementary files format and content: tab-delimited text files include raw counts, TPM, FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Monocytes were cultered ex-vivo on fibronectin-treated cell culture plates in 10% human serum/RPMI, with fresh media replaced every other day to maintain cell viability

extract_protocol:
RNA was harvested using the RNA STAT-60 protocol. Total RNA was used for construction of sequencing libaries.
RNA libraries for RNAseq were prepared with the NEBNextUltra directional library kit and the TruSeq stranded mRNA kit (Illumina). A 1.8pM library was spiked with 1% PhiX as an internal control and pair end sequenced with 101 x 51 cycles.

tag: tissue

value: Peripheral blood

tag: cell line

value: Primary

tag: cell type

value: Monocyte

tag: genotype

value: WT

tag: treatment

tag: time


title: DAS_2_F

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
Sequencing data were processed with illumina2bam-tools v. 1.12
BAM files were converted to fastq format using SamToFastq.jar (picard-tools v1.100) with the INCLUDE_NON_PF_READS parameter set to FALSE (implemented in RefFreeDMA)
All reads were trimmed for adapter sequences and low-quality sequences using trimgalore v0.3.3 with the following command: trim_galore -q 20 --phred33 -a "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" --stringency 1 -e 0.1 --length 16 --output_dir $output_dir $input_fastq.
Reference-free processing (creation of the deduced genomes and processing) was performed using the RefFreeDMA software/pipeline (http://RefFreeDMA.computational-epigenetics.org)
Bisulfite alignment of the RRBS reads to the deduced genomes and to the reference genomes was performed using BSMAP v2.74 with the following command line: bsmap -a $input_fastq -d $ref_genome_fasta -o $output_bam -D C-CGG -w 100 -v 0.08 -r 1 -p 4 -n 0 -S 1 -f 5 –u (implemented in RefFreeDMA).
DNA methylation calling was performed using the biseqMethCalling.py software (Bock, 2010)(implemented in RefFreeDMA).
Genome_build: processed files list contains consensus genomes for each of 580 species
Supplementary_files_format_and_content: Tab-delimited text files include CpG methylation calls for each sample. The columns in the file correspond to thr chromosome, start and end of a CpG region, rationof methylated/non metylated, mean methylation in ‰ and the strand.

molecule: genomic DNA

organism: Leptoclinus maculatus

source_name: Fin

extract_protocol:
Reduced representation bisulfite sequencing (RRBS) was performed as described in Klughammer et al., Cell Reports 2015, using 100 ng of genomic DNA for most samples, while occasionally going down to 1 ng for samples with low DNA amounts (Supplementary Table 1). To assess the bisulfite conversion efficiency independent of CpG context, methylated and unmethylated spike-in controls were added at a concentration of 0.1%. For most samples, DNA was digested using the restriction enzymes MspI and TaqI in combination (as opposed to only MspI in the original protocol) in order to increase genome-wide coverage. For certain older samples, only MspI was used
Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. Fi-nally, the libraries were size selected by performing a 0.75× cleanup with AMPure XP beads (Beckman Coulter, A63881) retaining fragments of about 100 bp to 1000 bp length. The amount of effective li-brary was determined by qPCR, and samples were multiplexed in pools of 10 with similar qPCR Ct values. The pools were then subjected to bisulfite conversion, followed by library enrichment with PCR. Enrichment cycles were determined using qPCR and ranged from 6 to 18 (median: 11). After con-firming adequate fragment size distributions on Bioanalyzer High Sensitivity DNA chips (Agilent),

value: Fin

tag: Sex

tag: individual

tag: age

tag: sample type

value: converted


title: DAS_2_G

source_name: Gills

value: Gills


title: FTF_1_G

organism: Sufflamen chrysopterum

value: adult


title: BC_1_H

organism: Camelus ferus

source_name: Heart

value: Heart

value: f


title: DAS_2_M

source_name: Muscle

value: Muscle


title: Mock 2w Rep 1

description: S5_Mock-2wk Length, S5_Mock-2wk Effective Length, S5_Mock-2wk Expected Count, S5_Mock-2wk TPM, S5_Mock-2wk FPKM

value: 2 wpi


title: ATH_3_M

organism: Clupea harengus


title: CHK_3_D

organism: Gallus gallus

source_name: Duodenum

value: Duodenum


title: ATH_3_SB

source_name: Swimbladder

value: Swimbladder


title: CHK_3_M


title: GBG_2_G

organism: Ostorhinchus rueppellii


title: ATH_3_L

source_name: Liver

value: Liver


title: ISS_1_AR

organism: Fromia indica

source_name: Arm

value: Arm


title: ATH_3_K

source_name: Kidney

value: Kidney


title: BC_3_Gran

source_name: Granulocytes

value: Granulocytes


title: CHK_3_S

source_name: Spleen

value: Spleen


title: HCMV 24h Rep 1

description: S4_HCMV-24h Length, S4_HCMV-24h Effective Length, S4_HCMV-24h Expected Count, S4_HCMV-24h TPM, S4_HCMV-24h FPKM

value: Peripheral blood

value: Primary

value: Monocyte

value: HCMV

value: 24 hpi


title: CHK_3_LU

source_name: Lung

value: Lung

value: adult

value: converted


title: ATH_3_H

value: Heart


title: CHK_3_L_uc

value: f

value: unconverted


title: ISS_2_AR


title: ATH_2_M

value: Muscle


title: ATH_3_S


title: FTF_2_G

value: Gills


title: CFL_1_G

organism: Cheilopogon californicus


title: HCMV 4h Rep 1

description: S2_HCMV-4h Length, S2_HCMV-4h Effective Length, S2_HCMV-4h Expected Count, S2_HCMV-4h TPM, S2_HCMV-4h FPKM

value: WT

value: 4 hpi


title: CHK_3_L

value: Liver


title: ATH_2_K

value: Kidney


title: CHK_3_H


title: MCF7-D538G mutant  cells + OTX015 [D538G_OTX_1]

city: Dallas

first: SM

middle: N

last: Udden

state: TX

address: 2201 Inwood Road

department: Radiation Oncology

institute: UT Southwestern Medical Center

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore (v0.4.1). Quality-filtered reads were then aligned to the mouse reference genome GRCh38 (hg38) using the HISAT (v 2.0.1) aligner(41) using default settings and marked duplicates using Sambamba (v0.6.6)(42). Aligned reads were quantified using ‘featurecount’ (v1.4.6)(43) per gene ID against GENCODE v25.
Assembly: Quality-filtered reads were then aligned to the mouse reference genome GRCh38 (hg38) using the HISAT (v 2.0.1) aligner(41) using default settings and marked duplicates using Sambamba (v0.6.6)(42). Aligned reads were quantified using ‘featurecount’ (v1.4.6)(43) per gene ID against GENCODE v25.
Supplementary files format and content: Aligned reads were quantified using ‘featurecount’ (v1.4.6)(43) per gene ID against GENCODE v25.

source_name: Breast

growth_protocol: MCF7 or MCF7-Y637S/D538G mutant cells were cultured in phenol red-free medium, IMEM supplemented with 5% charcoal-dextran-treated calf serum and 2% penicillin-streptomycin in hormone-depleted conditions in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
The cells were then harvested and total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions. RNA quantity and purity was measured by a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and integrity was analyzed by an Agilent Bioanalyzer 2100 (Agilent Technologies).
RNA-seq libraries were prepared using Illumina TruSeq Standard mRNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100. RNA-seq libraries were sequenced on a SE75 (single end 75 base pair) NextSeq500 flow cell.

treatment_protocol: Hormone depletion was carried over 3 days by washing the cells with phenol red-free IMEM without serum (5 washings daily, 1 hour apart). At completion of washings each day, cells were re-cultured in phenol red-free IMEM supplemented with 5% charcoal-dextran-treated calf serum. On day 4, the cells were trypsinized and 1 x 106 cells were seeded on 10-cm culture dish. After overnight culture, the cells were treated with DMSO, 10 pM β-estradiol, or 1μM OTX015 for 24 hours.

value: Breast

value: Epithelial cells

value: D538G ESR1 mutation

tag: treatment and_time


title: Mock 24h Rep 1

description: S3_Mock-24h Length, S3_Mock-24h Effective Length, S3_Mock-24h Expected Count, S3_Mock-24h TPM, S3_Mock-24h FPKM

value: Peripheral blood

value: Primary

value: Monocyte


title: CHK_3_B

source_name: Brain

value: Brain

value: adult


title: Mock 4h Rep 1

description: S1_Mock-4h Length, S1_Mock-4h Effective Length, S1_Mock-4h Expected Count, S1_Mock-4h TPM, S1_Mock-4h FPKM


title: MAF_2_F

organism: Pterocaesio marri

value: Fin

value: converted


title: MCF7-D538G mutant  cells + E2 [D538G_E2_1]


title: MCF7-D538G mutant  cells + OTX015 [D538G_OTX_2]


title: ISS_1_AR_uc

value: Arm

value: unconverted


title: CFL_1_G_uc

value: Gills


title: MCF7-D538G mutant  cells + E2 [D538G_E2_2]


title: CHK_2_LU

value: Lung

value: f


title: MCF7-D538G mutant  cells, DMSO Control [D538G_Contl_2]

value: DMSO, 24h


title: MCF7-D538G mutant cells, DMSO Control [D538G_Contl_1]


title: ATH_2_SB

value: Swimbladder


title: BC_3_Leuc

source_name: Leucocytes

value: Leucocytes


title: CHK_2_M

value: Muscle


title: ATH_2_H

value: Heart


title: MCF7-Y537S mutant  cells + OTX015 [Y537S_OTX_2]

value: Breast

value: Epithelial cells

value: Y537S ESR1 mutation


title: ATH_1_SB


title: MCF7-Y537S mutant  cells + OTX015 [Y537S_OTX_1]


title: MAF_1_F_uc


title: CHK_2_L

value: Liver


title: MAF_1_F


title: ATH_2_L


title: ATH_1_L


title: MAF_3_F


title: ATH_1_H


title: ATH_1_K

value: Kidney


title: MCF7-Y537S mutant  cells + E2 [Y537S_E2_1]


title: CHK_2_D

value: Duodenum

value: adult


title: SPR_2_M

organism: Sebastes ovalis

value: converted


title: CHK_2_B

value: Brain


title: SPR_2_BL

source_name: Blood

value: Blood


title: MCF7-Y537S mutant  cells + E2 [Y537S_E2_2]


title: CHK_2_S

value: Spleen


title: ATH_1_G_uc

value: Gills

value: unconverted


title: ATH_1_G


title: CHK_2_H

value: f


title: SPR_2_G


title: CHK_1_L


title: ATH_1_M


title: SPR_1_G


title: MCF7 cells + E2 + OTX015 [WT_E2_OTX_1]

value: WT


title: SPR_1_M

value: Muscle


title: SPR_1_BL


title: MCF7-Y537S mutant  cells, DMSO Control [Y537S_Contl_2]

value: DMSO, 24h


title: MCF7 cells + E2   (E2 = b-estradiol) [WT_E2_1]

value: Breast


title: SRA_1_F

organism: Hemitripterus americanus

value: Fin


title: CHK_1_H

value: Heart


title: MCF7 cells +E2 + OTX015 [WT_E2_OTX_2]

value: Epithelial cells


title: MCF7 cells, DMSO Control [WT_Contl_2]


title: CHK_1_S


title: CHK_1_B


title: SCU_1_G

organism: Stenotomus chrysops


title: SBE_1_G

organism: Pristigenys alta


title: CHK_1_M


title: YFT_1_M_uc

organism: Thunnus albacares


title: YFT_1_M


title: MCF7 cells + E2   (E2 = b-estradiol) [WT_E2_2]


title: SWF_1_M

organism: Xiphias gladius


title: SBE_1_BL_uc


title: CHK_1_LU

value: Lung


title: SCU_1_F


title: SCU_1_F_uc


title: CHK_1_D

value: Duodenum


title: CHK_5_L

value: Liver

value: adult


title: SRA_1_L

value: converted


title: SRA_1_KF

value: Kidney


title: CHK_4_L

value: juvenil


title: MCF7-Y537S mutant cells, DMSO Control [Y537S_Contl_1]

value: Y537S ESR1 mutation


title: CHK_4_H


title: LUF_1_M

organism: Cyclopterus lumpus


title: SWF_1_M_uc

value: unconverted


title: SBE_1_BL

value: Blood


title: SRA_1_G

value: Gills


title: MCF7 cells, DMSO Control [WT_Contl_1]

organism: Homo sapiens

value: WT


title: 4E grown in the presence of homoserine S2

type: RNA

city: Toulouse

first: JEAN MARIE

last: FRANCOIS

address: 135 avenue de Rangueil

country: France

institute: Toulouse Biotechnology Institute

hyb_protocol: The labeled cDNA was hybridized on E. coli Gene Expression Microarrays (8 × 15K, Agilent) following the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol

scan_protocol: The slides were scanned on a Tecan scanner MS200 and analyzed by Feature Extraction V.11.5.1.1

data_processing:
Signals of each probe set were filtered according to the coefficient of variations with a cut-off value of 50 %. Significant changed expression was acquired by moderated t-test with a p-value of < 0.05 and a fold-change cut-off value of 2.0. Benjamini-Hochberg correction was performed (Hochberg and Benjamini, 1990).
Normalized signal intensity and log2 transformed in supplementary file.

organism: Escherichia coli

source_name: 4E grown in the presence of homoserine

label_protocol: The RNA were converted to cDNA using the Low Input Quick Amp labeling kit (Agilent) with dCTP(CY3) labelling

growth_protocol: An overnight pre-culture of the different E.coli strains in M9 medium/1 % glucose was inoculated in 0.3 L shake ﬂasks containing 50 ml of the same medium (initial OD600 of ∼0.2) in the absence or presence of 10 mM L-homoserine. Cultures were carried at 37 °C at 200 rpm until OD600 reached ~1.0 to 1.5. At this time, one ml of culture taken 3 to 5 times was collected in microcentrifuge tubes and centrifuged at 10,000g for 2 min. The cell pellets were quickly washed once with 1 ml cold water, resuspended and quickly centrifuged at as above. After draining remaining water on a towel, the tubes were thrown in liquid nitrogen and stored at -80°C until use. This procedure was repeated with three biological independent cultures and for each strain. RNA were extracted frozen cell pellets using the QIAGEN RNeasy Mini Kit RNA, quantified by NanoDrop (Thermo) and its quality control was validated on Bioanalyzer (Agilent Technologies). Only RNA samples with a RIN (RNA Integrity Number) higher than or equal to 9.00 were chosen for microarray analysis.

treatment_protocol: the treatment was the cultivation of the E. coli strains in the absence or in the presence of 10 mM homoserine

value: Homoserine adapted 4E strain

tag: strain

value: E coli K12 -MG1655

value: presence of homoserine


title: 4E grown in the absence of homoserine S2

source_name: 4E grown in the absence of homoserine

extract_protocol: RNA were extracted frozen cell pellets using the QIAGEN RNeasy Mini Kit RNA, quantified by NanoDrop (Thermo) and its quality control was validated on Bioanalyzer (Agilent Technologies). Only RNA samples with a RIN (RNA Integrity Number) higher than or equal to 9.00 were chosen for microarray analysis.

value: absence of homoserine


title: 4E grown in the presence of homoserine S1


title: SRA_1_M

value: Muscle


title: 4E grown in the absence of homoserine S1


title: SDF_2_B

organism: Squalus acanthias

value: Brain

value: juvenile


title: CHK_5_H

value: Heart

value: f


title: 4E grown in the absence of homoserine S3


title: SRA_1_K

value: adult

value: converted


title: 4E grown in the presence of homoserine S3


title: SRA_1_KF_uc

value: Kidney


title: FR_2_L

organism: Rattus norvegicus

value: Liver


title: LUF_1_M_uc

value: unconverted


title: SPR_1_BL_uc

value: Blood


title: thrL mutant grown in the presence of homoserine S3

value: {delta}thrL mutant


title: BCW_1_F_uc

organism: Labroides bicolor

source_name: Fin

value: Fin


title: FR_1_L


title: FR_2_H

source_name: Heart


title: BCW_1_M

source_name: Muscle


title: BCW_1_F


title: thrL mutant grown in the presence of homoserine S1


title: thrL mutant grown in the presence of homoserine S2


title: ACO_1_M

organism: Gadus morhua

value: juvenil


title: SDF_1_BL


title: YAN_1_M

organism: Centropyge heraldi


title: LFA_1_F_uc

organism: Compsanthias ventralis

value: m


title: YAN_1_M_uc


title: ACO_1_G

source_name: Gills

value: Gills


title: thrL mutant grown in the absence of homoserine S3

value: E coli K12 -MG1655

value: absence of homoserine


title: FR_1_H


title: LFA_1_F


title: GE_1_L

organism: Gekkonidae


title: 1231A3 iPSC, NCC differentiation, day 10

city: Fujisawa

first: Daisuke

last: Kamiya

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: CiRA

country: Japan

institute: Kyoto University

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent S5 XL sequencer (Torrent suite v5.16.1).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent S5 XL sequencer (Torrent suite v5.16.1).
RPM were calculated using plug-in software provided with the Ion Torrent S5 XL sequencer (ampliSeqRNA v5.6.0.3)
Assembly: hg19
Supplementary files format and content: Tab-delimited text file include gene symbol and gene expression in RPM for each sample

growth_protocol: 1231A3 human iPSC were cultured on an iMatrix-511 (Nippi, Tokyo, Japan)-coated cell culture plate or dish in StemFit AK03N (Ajinomoto, Tokyo, Japan). The medium was changed every 2 days

extract_protocol:
Total RNA was purified using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA)
10 ng of total RNA were reverse transcribed  to obtain single-stranded cDNA using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). cDNA libraries were  synthesised using the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel (Thermo Fisher Scientific) and the Ion Ampliseq Library Kit Plus (Thermo Fisher Scientific), according to the manufacturer’s protocol. Barcode-labeled cDNA libraries were analyzed using the Ion S5 XL System (Thermo Fisher Scientific) and the Ion 540 Chip Kit (Thermo Fisher Scientific).

treatment_protocol: For NCC induction, iPS cells were cultured in StemFit Basic03 (equivalent to AK03N without bFGF, Ajinomoto, Tokyo, Japan) with 10 μM SB431542 (FUJIFILM Wako) and 1 μM CHIR99021 (Axon Medchem, Reston, VA, USA) for 10 days. Cells were collected every 2 days.

value: iPSCs derived from PBMC

value: WT

value: NCC differentiation


title: 1231A3 iPSC, NCC differentiation, day 10, CD271 high

value: day10 CD271 high


title: SDF_2_G

value: juvenile


title: ACO_1_G_uc


title: thrL* grown in the presence of homoserine S2

value: thrL* strain

value: presence of homoserine


title: thrL mutant grown in the absence of homoserine S2


title: 1231A3 iPSC, NCC differentiation, day 10, CD271 low

value: day10 CD271 low


title: SDF_1_BL_uc

value: unconverted


title: FR_1_H_uc

value: Heart

value: f

value: adult


title: thrL mutant grown in the absence of homoserine S1

value: {delta}thrL mutant


title: ALO_1_W

organism: Homarus americanus

value: juvenil

value: converted


title: 1231A3 iPSC, NCC differentiation, day 8


title: GE_1_L_uc

value: Liver


title: YSP_1_G

organism: Parapercis xanthozona

value: Gills


title: thrL* grown in the presence of homoserine S3

value: E coli K12 -MG1655


title: thrL* grown in the presence of homoserine S1


title: 1231A3 iPSC, NCC differentiation, day 6

value: iPSCs derived from PBMC

value: WT


title: ALO_1_W_uc


title: 1231A3 iPSC, NCC differentiation, day 4

value: NCC differentiation


title: RRH_1_L

organism: Potamochoerus porcus


title: YSP_1_G_uc


title: 1231A3 iPSC, NCC differentiation, day 2


title: thrL* grown in the absence of homoserine S3

value: absence of homoserine


title: thrL* grown in the absence of homoserine S1

value: thrL* strain


title: thrL* grown in the absence of homoserine S2


title: RRH_1_H


title: GE_1_LU

value: Lung


title: 1231A3 iPSC, NCC differentiation, day 0

value: day0 (iPSC)


title: SWC_1_F_uc

organism: Ariopsis felis

value: Fin

value: unconverted


title: BF_1_LU

organism: Polypedates otilophus

value: m


title: WT strain grown in the presence of homoserine S3

value: presence of homoserine


title: BF_1_L_uc

value: adult


title: PAT_2_G_uc

organism: Clavelina picta


title: BF_1_L


title: Recover 96h-samples 1

city: WuXi

first: Tao

last: Zheng

address: No.69, Xuejiali, Nanquan Town, Binhu District, Wuxi City, Jiangsu Province, China

country: China

institute: Wuxi Fisheries College, Nanjing Agricultural University

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Assembly: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary files format and content: xls include FPKM values for each Sample

organism: Tachysurus fulvidraco x Tachysurus vachelli

source_name: Intestine

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestine

value: Recover 96h after transport 16h


title: Recover 96h-samples 3


title: WT strain grown in the presence of homoserine S2


title: WT strain grown in the presence of homoserine S1


title: Transport 16h- samples 3

value: transport 16h


title: CHS_2_H

organism: Rupicapra rupicapra

value: Heart

value: f

value: converted


title: BSC_1_G

organism: Chromis punctipinnis

value: Gills


title: WT strain grown in the absence of homoserine S3

organism: Escherichia coli

value: WT

value: E coli K12 -MG1655


title: CHS_2_L

source_name: Liver

value: Liver


title: SAA_1_BL_uc

organism: Osteoglossum bicirrhosum

value: Blood


title: Transport 16h- samples 2


title: BSC_1_G_uc


title: WT strain grown in the absence of homoserine S2

value: absence of homoserine


title: RRH_1_H_uc


title: SWC_1_F

value: Fin


title: CHS_1_L_uc

value: unconverted


title: LSK_1_G_uc

organism: Leucoraja erinaceus


title: CHS_1_L

value: m


title: WT strain grown in the absence of homoserine S1


title: Transport 16h- samples 1


title: PAT_2_G


title: control sample 1

value: untreated


title: CHS_1_H

value: adult


title: control sample 2

value: Intestine


title: Recover 96h-samples 2

value: Recover 96h after transport 16h


title: SAA_1_BL


title: GB_1_VM

organism: Lepas anatifera


title: control sample 3


title: GB_1_VM_uc


title: LIL_1_H

organism: Agapornis lilianae


title: ASC_1_T

organism: Holothuria cinerascens

source_name: Tentacle

value: Tentacle


title: NE_1_L_uc

organism: Neurergus


title: NBD_2_F

organism: Pomacentrus coelestis


title: BMO_1_H

organism: Mungos mungo

value: Heart


title: NE_1_L

value: f


title: BMO_1_L

value: converted


title: ASC_2_T


title: BMO_1_L_uc


title: RLF_1_W

organism: Loweina rara

value: juvenil


title: BMO_2_L


title: BMO_2_H


title: MOLM13 cells, CC-90009 (CC-663), biol replicate 2

city: Boston

first: Adam

middle: S

last: Sperling

state: MA

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital

data_processing:
RNA sequencing (RNA-seq) data were aligned to hg19 using STAR
Expression quantification was done using Cufflinks to generate gene expression values in fragments per kilobase of transcript per million mapped reads (FPKM) units.
Assembly: HG19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

growth_protocol: MOLM13 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Library constuction performed by a commercial vendor (Novogene)

treatment_protocol: Cells were treated for 24 hours with vehicle (DMSO), 0.1uM CC-885 or 1uM CC-90009 (CC-663)

value: WT


title: LIL_1_L


title: SG_1_LU

organism: Petaurus breviceps

value: Lung


title: MOLM13 cells, CC-90009 (CC-663), biol replicate 1


title: MOLM13 cells, CC-885, biol replicate 2


title: LSK_1_G

value: Gills


title: SG_1_L_uc

value: Liver


title: MOLM13 cells, CC-885, biol replicate 1


title: ASC_1_T_uc


title: SG_1_L


title: RLF_1_W_uc


title: MOLM13 cells, DMSO, biol replicate 1

value: DMSO


title: MOLM13 cells, DMSO, biol replicate 2


title: HIPK4_T47D_5

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

country: United Kingdom

institute: University of York

description:
Knockdown of HIPK4 in T47D cells
T47D.txt

data_processing:
Align with hisat2
Establish count matrix with Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containg matrix of read counts for individual genes. Genes are stored by Entrez Gene ID.

source_name: breast

growth_protocol: Cells were grown in DMEM +10%FBS

extract_protocol:
RNA was extracted by  RNeasy mini kit
TruSeq RNA Library Prep Kit

treatment_protocol: Cells were treateded with SMARTpool siRNA targeting the gene of interest as per the manufactures protocol.

tag: sirna

tag: replicate


title: LIO_1_L

organism: Panthera leo


title: LIO_1_H


title: L3961_B2D_FF

city: Houston

first: Peter

last: Masschelin

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequences were mapped to the mm10 UCSC reference genome using STAR.
RPKM values were calcualted using FeatureCounts
DESeq2 was used to calculate differentially expressed genes with p values adjusted using the Benjamini and Hochberg's method for controlling false discovery rate (FDR)
Genes with significant differential expression were determined by p<0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files including FPKM for Ctrl vs. B2-Deficient (Ctrl_B2D_fpkm.txt)
Supplementary files format and content: tab-delimited text files including FPKM for Ctrl + Fenofibrate vs. B2-Deficient + Fenofibrate (CtrlFF_B2DFF_fpkm.txt)

organism: Mus musculus

source_name: C57BL/6J mice, B2-Deficient Diet, 9 weeks, FF weeks 7-9

extract_protocol:
Total Liver RNA was extracted using the Qiagen RNeasy Plus Mini Kit and sample quality confirmed by Bioanalyzer
mRNA libraries constructed with NEBNext Ultra RNA Library Prep Kit for Illumina. Size selection was perfomed using the AMPure XP system followed by analysis of library purity.

treatment_protocol: Mice were fasted overnight before harvest. Mice fed FF (Ctrl_FF and B2D_FF) were fasted overnight and administered FF 2 hours before harvest

value: B2-Deficient Diet, Fenofibrate


title: GRB2_T47D_6

description:
Knockdown of GRB2 in T47D cells
T47D.txt


title: L3962_B2D_FF


title: RUF_1_H

organism: Philomachus


title: NEK9_T47D_6

description:
Knockdown of NEK9 in T47D cells
T47D.txt


title: L3960_B2D_FF


title: LIL_1_H_uc

value: unconverted


title: GRB2_T47D_4


title: L3959_B2D_FF


title: PDL1_r2_donor_2_S9, Protein portion of REAPSeq

city: Cambridge

first: Cory

middle: Haley

last: White

address: 320 Bent St

department: DAGS

institute: Merck

library_source: other

data_processing:
Base Calling Software:  Cell Ranger v6.0
Commands:  mkfastq, count
Base-making parameters: RNA - "Y26n*,I10n*,I10n*,Y90n*", Protein - "Y26n*,I10n*,I10n*,Y25n*"
Expected cells parameter:  5000
Feature barcode reference:  Provided as file feature_reference.csv
Assembly: grch38 v3.0.0
Supplementary files format and content: Format: .rds data file, Content:  Seurat object in an R data file.
Format: .csv file, Content:  Feature reference file
Library strategy: REAP-seq

molecule: protein

source_name: Human PBMCs and Raji PD-L1 cells

growth_protocol: Human PBMCs were cultured in T cell expansion medium supplemented with 10 ng/mL IL-2 and CD3/CD28/CD2 T cell activator for 7 days, with replacement of culture media supplemented with 10 ng/mL IL-2 at days 3 and 5.  Raji PD-L1 cells were cultured in RPMI media supplemented with 10% FBS, 2 mM L-glutamine and 0.25 ug/mL puromycin for no more than 20 passages.

extract_protocol:
T cells were isolated using CD3 microbeads, resuspended at a concentration 1-2x10^7/mL in staining buffer plus 10% FBS. 50 uL of cells were incubated with 10 uL TruStain FcX Fc for 10 min at 4C. A lyophilized cocktail of 204 TotalSeqC antibodies were reconstituted in 50ul staining buffer. The antibody cocktail and 1 uL Total SeqC Streptavidin-PE were added to the samples and incubated for 30min at 4C, and washed 3x with 10 mL of cold staining buffer.  The cell pellets were resuspended at 1x10^6/mL in staining buffer prior to processing for sequencing.
10X Single Cell 5'V2_VDJ_Cell Surface Protein dual index protocol
use poly-dT to capture 5’ ends of the polyadenylated transcript in the final library

treatment_protocol: Raji PD-L1 cells were incubated with Isotype or PD-L1 VHH-Fc-RFT for 1 hour.  PBMCs were incubated with 5 uM LFA-1 inhibitor for 30 min.

value: Human PBMCs and Raji PD-L1 cells

value: donor 2


title: LIO_1_H_uc

value: adult


title: PDL1_donor_3_S12, Protein portion of REAPSeq

value: donor 3


title: PDL1_r2_donor_1_S4, Protein portion of REAPSeq

value: donor 1


title: PDL1_donor_2_S7, Protein portion of REAPSeq


title: PDL1_r2_donor_3_S14, Protein portion of REAPSeq


title: RUF_1_L

value: m


title: IP_2_L_uc

organism: Python molurus


title: KSR1_T47D_6

description:
Knockdown of KSR1 in T47D cells
T47D.txt


title: CAMK2D_T47D_1

description:
Knockdown of CAMK2D in T47D cells
T47D.txt


title: L3957_Ctrl_FF

source_name: C57BL/6J mice, Ctrl Diet, 9 weeks, FF weeks 7-9

value: Control Diet, Fenofibrate


title: L3956_Ctrl_FF


title: ESR1_T47D_6

description:
Knockdown of ESR1 in T47D cells
T47D.txt


title: IP_2_S

source_name: Spleen

value: Spleen


title: IP_2_L

value: converted


title: RUF_1_H_uc

value: Heart


title: PDL1_antiPD1mAb_r2_donor_3_S15, Protein portion of REAPSeq

value: LFA-1 inhibitor


title: CSNK1A1_T47D_3

description:
Knockdown of CSNK1A1 in T47D cells
T47D.txt


title: PDL1_antiPD1mAb_r2_donor_2_S10, Protein portion of REAPSeq


title: L3955_Ctrl_FF

value: WT


title: LIMK1_T47D_4

description:
Knockdown of LIMK1 in T47D cells
T47D.txt


title: L3954_Ctrl_FF


title: CDK8_T47D_5

description:
Knockdown of CDK8 in T47D cells
T47D.txt


title: L3210_B2D

source_name: C57BL/6J mice, B2-Deficient Diet, 1 Month

value: B2-Deficient Diet


title: IP_2_LU

source_name: Lung

value: Lung


title: IP_2_H


title: PDL1_antiPD1mAb_donor_3_S13, Protein portion of REAPSeq


title: PDL1_donor_1_S2, Protein portion of REAPSeq


title: HIPK4_T47D_1


title: PDL1_antiPD1mAb_r2_donor_1_S5, Protein portion of REAPSeq


title: IP_1_LU

value: f


title: L3208_B2D

value: Liver


title: L3209_B2D


title: MKNK2_T47D_6

description:
Knockdown of MKNK2 in T47D cells
T47D.txt


title: IP_1_H


title: CSNK1A1_T47D_4


title: KSR1_T47D_4


title: IP_1_S


title: L3207_B2D


title: PDL1_antiPD1mAb_donor_2_S8, Protein portion of REAPSeq


title: L3206_B2D


title: isotype_donor_3_S11, Protein portion of REAPSeq

value: Isotype


title: L3205_Ctrl

source_name: C57BL/6J mice, Ctrl Diet, 1 Month

value: Control Diet


title: PDL1_antiPD1mAb_donor_1_S3, Protein portion of REAPSeq

value: Human PBMCs and Raji PD-L1 cells


title: LIMK1_T47D_5


title: isotype_donor_2_S6, Protein portion of REAPSeq

value: donor 2


title: WM_1_L

organism: Apodemus sylvaticus

value: adult


title: IP_1_L


title: CDK8_T47D_2


title: CTRL_T47D_3

description:
Control in T47D
T47D.txt

value: CTRL


title: L3204_Ctrl


title: WC_1_L

organism: Cacatua alba

value: juvenil


title: WM_1_H


title: PDL1_r2_donor_3_S14, Transcript portion of REAPSeq

value: donor 3


title: L3202_Ctrl


title: CAMK2D_T47D_4


title: PDL1_r2_donor_1_S4, Transcript portion of REAPSeq

value: donor 1


title: MKNK2_T47D_2


title: PDL1_donor_3_S12, Transcript portion of REAPSeq


title: L3203_Ctrl


title: NEK9_T47D_3


title: L3201_Ctrl


title: isotype_donor_1_S1, Protein portion of REAPSeq


title: WC_1_H_uc

value: unconverted


title: PDL1_donor_2_S7, Transcript portion of REAPSeq


title: ESR1_T47D_1


title: Srebf2 transfection, TF3, bulk-RNAseq

city: St. Louis

first: Barak

last: Cohen

state: Missouri

address: 4515 McKinley Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

data_processing:
Counts for each gene were obtained using Kallisto version 0.43.0 using the parameters -t 4 -b 200
Assembly: mm10
Supplementary files format and content: Tab-separated values files for abundances of each gene in each sample.

extract_protocol:
NIH3T3-CG cells were released from 6-well plates using Trypsin and we extracted total RNA using Qiagen RNEasy.
Library construction and sequencing was performed at Novogene corporation
bulk mRNA sequencing

value: Embryonic fibroblasts

value: Srebf2 TF


title: HU_1_H_uc

organism: Capromyidae

value: Heart


title: Srebf2 transfection, TF2, bulk-RNAseq


title: Srebf2 transfection, TF1, bulk-RNAseq


title: HU_1_H

value: converted


title: PDL1_r2_donor_2_S9, Transcript portion of REAPSeq


title: ESR1_T47D_5


title: HU_1_L


title: PDL1_antiPD1mAb_r2_donor_3_S15, Transcript portion of REAPSeq

value: LFA-1 inhibitor


title: Srebf2 transfection, control3, bulk-RNAseq

value: control


title: WM_1_H_uc

value: f


title: Srebf2 transfection, control2, bulk-RNAseq


title: WC_1_H


title: PDL1_antiPD1mAb_r2_donor_2_S10, Transcript portion of REAPSeq


title: Srebf2 transfection, control1, bulk-RNAseq


title: CAMK2D_T47D_6


title: CSNK1A1_T47D_1


title: GRB2_T47D_5


title: CAMK2D_T47D_2


title: PDL1_donor_1_S2, Transcript portion of REAPSeq


title: PDL1_antiPD1mAb_donor_3_S13, Transcript portion of REAPSeq


title: IE_1_H_uc

organism: Aquila heliaca


title: Jun transfection, TF2, bulk-RNAseq

value: Jun TF


title: PDL1_antiPD1mAb_r2_donor_1_S5, Transcript portion of REAPSeq


title: IE_1_L

value: Liver


title: PDL1_antiPD1mAb_donor_2_S8, Transcript portion of REAPSeq

value: Human PBMCs and Raji PD-L1 cells


title: NEK9_T47D_4


title: Jun transfection, TF1, bulk-RNAseq


title: IE_1_H


title: CTRL_T47D_2

description:
Control in T47D
T47D.txt


title: PDL1_antiPD1mAb_donor_1_S3, Transcript portion of REAPSeq


title: IE_2_L


title: Jun transfection, TF3, bulk-RNAseq


title: isotype_donor_3_S11, Transcript portion of REAPSeq

value: Isotype


title: Jun_Egr1 transfection, control3, bulk-RNAseq


title: WS_1_L

organism: Ciconia ciconia

value: m

value: adult


title: HIPK4_T47D_4


title: IE_2_H


title: CDK8_T47D_4


title: isotype_donor_2_S6, Transcript portion of REAPSeq

value: donor 2


title: Jun_Egr1 transfection, control2, bulk-RNAseq


title: WS_1_H_uc


title: isotype_donor_1_S1, Transcript portion of REAPSeq


title: LIMK1_T47D_3


title: Jun_Egr1 transfection, control1, bulk-RNAseq


title: DO_1_L

organism: Equus asinus asinus

value: old


title: Egr1 transfection, TF3, bulk-RNAseq

value: Egr1 TF


title: WS_1_H


title: KSR1_T47D_3


title: Egr1 transfection, TF2, bulk-RNAseq


title: DO_1_H_uc

value: unconverted


title: CTRL_T47D_1

description:
Control in T47D
T47D.txt

value: CTRL


title: DO_1_H


title: Egr1 transfection, TF1, bulk-RNAseq

value: Embryonic fibroblasts


title: MKNK2_T47D_3


title: JA_1_LU

organism: Panthera onca

value: Lung


title: CSNK1A1_MCF7_2

description:
Knockdown of CSNK1A1 in MCF7 cells
MCF7.txt


title: Snai1 transfection, TF2, bulk-RNAseq

value: Snai1 TF


title: JA_1_H_uc

value: Heart


title: LIMK1_MCF7_3

description:
Knockdown of LIMK1 in MCF7 cells
MCF7.txt


title: Snai1 transfection, TF3, bulk-RNAseq


title: MKNK2_MCF7_1

description:
Knockdown of MKNK2 in MCF7 cells
MCF7.txt


title: JA_1_H

value: converted


title: Prrx1_Snai1 transfection, control3, bulk-RNAseq

value: control


title: Snai1 transfection, TF1, bulk-RNAseq


title: HIPK4_T47D_2


title: HIPK4_MCF7_2

description:
Knockdown of HIPK4 in MCF7 cells
MCF7.txt


title: ESR1_MCF7_1

description:
Knockdown of ESR1 in MCF7 cells
MCF7.txt


title: Prrx1_Snai1 transfection, control2, bulk-RNAseq


title: JA_2_L

value: f


title: BI_1_H

organism: Euplectes


title: Prrx1_Snai1 transfection, control1, bulk-RNAseq


title: BI_1_B

source_name: Brain

value: Brain


title: JA_2_H


title: Prrx1 transfection, TF3, bulk-RNAseq

value: Prrx1 TF


title: CDK8_MCF7_5

description:
Knockdown of CDK8 in MCF7 cells
MCF7.txt


title: NEK9_MCF7_3

description:
Knockdown of NEK9 in MCF7 cells
MCF7.txt


title: CTRL_MCF7_3

description:
Control in MCF7
MCF7.txt


title: BI_1_S

value: Spleen


title: Prrx1 transfection, TF1, bulk-RNAseq


title: BI_1_LU


title: Prrx1 transfection, TF2, bulk-RNAseq


title: CAMK2D_MCF7_3

description:
Knockdown of CAMK2D in MCF7 cells
MCF7.txt


title: BI_2_LU


title: BI_1_L

value: Liver


title: K562 CUT&Tag anti-PARP1 Replicate B

city: Ithaca

first: Charles

middle: Grahe

last: Danko

state: NY

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

institute: Cornell University

description: CUT&Tag

data_processing:
fastq files were trimmed from Nextera adaptor-associated sequences using cutadapt
trimmed fastq files were  mapped to hg38 human genome assembly using bowtie2
We then used bedtools genomecov to generate bedgraph files and calculated background-normalized PARP1 binding using macs2 bdgcmp command
Supplementary files format and content: bigwig files - containing either raw counts or baseline-normalized fold-enrichment scores
Library strategy: CUT&Tag

growth_protocol: K562 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1X penicillin streptomycin antibiotic.

extract_protocol:
24h prior to the experiment, cells were split at a final concentration of 0.5 million cells/mL in fresh RPMI + 10% FBS + Antibiotic-antimycotic. PARP1 CUT&Tag was done in two replicates with 250,000 K562 cells each for baseline control and anti-PARP1 CUT&Tag. Experiments were done according to the bench top CUT&Tag V.3 protocol developed by the Henikoff lab (Kaya-Okur et al. protocols.io, 2020). using CUTANA™ Concanavalin A Conjugated Paramagnetic Beads (EpiCypher, SKU: 21-1401) and pAG-Tn5 for CUT&Tag (EpiCypher, SKU: 15-1017), with the following exceptions: (A) cells were not cross-linked and (B) NE1 buffer was used to extract and permeabilize nuclei. For anti-PARP1 CUT&Tag, we used an antibody against the N-terminal of PARP1 (Active Motif, AB_2793257). An anti-IgG antibody (Cell signaling, Normal Rabbit IgG #2729) was used as baseline control.
Library construction protocol was as described at the bench top CUT&Tag V.3 protocol developed by the Henikoff lab (Kaya-Okur et al. protocols.io, 2020).

tag: chip antibody

value: anti-N-terminal of PARP1 (Active Motif, AB_2793257)


title: K562 CUT&Tag anti-PARP1 Replicate A

description: CUT&Tag


title: CAMK2D_MCF7_1


title: CSNK1A1_MCF7_1


title: NEK9_MCF7_6


title: CDK8_MCF7_1


title: BI_2_L

value: adult


title: NEK9_MCF7_1


title: BI_2_H


title: K562 CUT&Tag IgG control Replicate B

description: CUT&Tag

value: anti-IgG antibody (Cell signaling, Normal Rabbit IgG #2729)


title: K562 CUT&Tag IgG control Replicate A

description: CUT&Tag


title: MAG_2_H

organism: Colobus guereza


title: BI_2_B


title: MAG_2_L


title: KSR1_MCF7_2

description:
Knockdown of KSR1 in MCF7 cells
MCF7.txt


title: BI_1_LU_uc


title: MAG_1_L


title: GRB2_MCF7_1

description:
Knockdown of GRB2 in MCF7 cells
MCF7.txt


title: HIPK4_MCF7_6


title: MAG_1_H


title: CAMK2D_MCF7_2


title: ESR1_MCF7_5


title: MAG_2_L_uc


title: TAM_2_L

organism: Saguinus

value: m


title: MKNK2_MCF7_3


title: LIMK1_MCF7_4


title: CTRL_MCF7_2

description:
Control in MCF7
MCF7.txt


title: M1_(RTA-1_0), biological rep1

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from Sprague-Dawley (SD) rats with injured tendons

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on  [RTA-1_0] Affymetrix Rat Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing: The data were analyzed with Expression Console™, Version 1.3.1.

label: biotin

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: All rats were kept at least 1 wk at 22°C and 55% relative humidity in a 12-h day/night lighting environment with free access to food and water.

extract_protocol: For microarray profiling, the rats tendons total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, Canada) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using UV-Vis Spectrophotometer (Thermo, NanoDrop 2000, USA) at the absorbance of 260 nm. The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix GeneChip, Santa Clara CA, USA), which contains 65957 gene-level probe sets.

treatment_protocol: All rats were randomly undertaken control surgery or injured tendons.Tendons were harvested 1 weeks following injured tendons and performed to further analysis.

value: Sprague-Dawley

value: tendon


title: ZF_11_Ery

organism: Danio rerio

source_name: Erythrocytes

value: Erythrocytes


title: CSNK1A1_MCF7_3

organism: Homo sapiens


title: TAM_2_H


title: CON3_(RTA-1_0), biological rep3

description: Gene expression data from Sprague-Dawley (SD) rats with control surgery


title: ZF_10_Ery_uc

value: unconverted


title: TAM_1_LU_uc

value: Lung


title: M2_(RTA-1_0), biological rep2

source_name: Sprague-Dawley (SD) rats with injured tendons


title: ZF_11_LymphoP

source_name: Lymphocytes+

value: Lymphocytes+


title: TAM_1_LU

value: converted


title: M3_(RTA-1_0), biological rep3


title: CON2_(RTA-1_0), biological rep2

source_name: Sprague-Dawley (SD) rats with control surgery


title: HIPK4_MCF7_3


title: DEH_1_H_uc

organism: Tockus deckeni

source_name: Heart

value: Heart


title: TAM_1_H


title: CTRL_MCF7_5

description:
Control in MCF7
MCF7.txt

value: CTRL


title: CSNK1A1_MCF7_5


title: ZF_10_LymphoP

value: f


title: ZF_10_Ery


title: ZF_6_MacroP

source_name: Macrophages+

value: Macrophages+


title: DEH_1_L

source_name: Liver


title: CON1_(RTA-1_0), biological rep1


title: NAS_1_L

organism: Nasua


title: ESR1_MCF7_3


title: GRB2_MCF7_4


title: GRB2_MCF7_5


title: ZF_9_Ery


title: DEH_1_H


title: NAS_1_H_uc


title: LIMK1_MCF7_2


title: ZF_9_GranP

source_name: Granulocytes+

value: Granulocytes+


title: T3: Roscovitine

city: Nanjing

first: Yuncheng

last: Bei

state: Jiangsu

address: Zhongshan Road No.321

department: Oncology

institute: Nanjing Drum Tower Hospital

data_processing:
Quality control - Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome - Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level - FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

organism: Mus musculus

source_name: 4T1 cells

growth_protocol: 106 4T1 cells were seeded in 6-well culture plate, and maintained in RPMI 1640 media supplemented with 1% penicillin-streptomycin and 10% fetal bovine serum. All cells were cultured at 37 oC with 5% CO2.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All cells were treated with Roscovitine (10 mM) or DMSO as control for 24 h.

value: 4T1 cells

tag: subtype

value: Triple Negative Breast Cancer (TNBC)

value: Roscovitine


title: ZF_8_Ery

value: adult


title: NAS_2_L

value: Liver


title: KSR1_MCF7_4

source_name: breast


title: CDK8_MCF7_3


title: NAS_1_H


title: ZF_8_GranP


title: NAS_2_LU


title: NEK9_MCF7_5


title: T2: Roscovitine


title: ZF_7_LymphoN

source_name: Lymphocytes-

value: Lymphocytes-


title: C3: vehicle

value: vehicle


title: KSR1_MCF7_5


title: WBU_1_H_uc

organism: Bubalus

value: m


title: ZF_7_LymphoP


title: WBU_1_H


title: C1: vehicle


title: T1: Roscovitine


title: C2: vehicle


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, T-lymphocyte, 007, rep2

status: Public on Jun 17 2022

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

description: Gene expression of healthy keratinocytes in passage 3 co-cultured with T-lymphocyte from human tissue-engineered skin substitutes

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
gPixNormIQR : The normalized Inter-quartile range of all of the inlier pixels per feature. The range is computed independently in each channel.

source_name: Primary human keratinocytes

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol:
Skin biopsies were washed in antibiotics-containing PBS, cut into 3 mm × 100 to 150 mm strips, and incubated overnight at 4°C in a 500 μg/mL thermolysin-HEPES solution. The epithelium was subsequently peeled from the dermis with sterile tweezers. Epidermal strips were then incubated for 30 minutes in a trypsin-ethylenediaminetretraacetic acid (EDTA) solution (0.05% w/v of porcine trypsin 1-250, 0.01% w/v of EDTA, 2.8 mM of D-glucose, 100 IU/mL of penicillin G, 25 μg/mL of gentamicin, and phenol red) in PBS at 37°C on a stirring plate. A DME-HAM was used to neutralize trypsin activity. DME-HAM was used to wash and resuspend the cell pellets. Keratinocytes were seeded at 1.4 × 104 cells/cm2 on iHFL (lethally irradiated (6000 rad) human fibroblasts feeder layer) in DME-Ham (Dulbecco–Vogt modification of Eagle's medium with Ham's F12 in a 3:1 ratio supplemented with 5% Fetal Clone II serum, 5 μg/ml of insulin, 0.4 μg/ml of hydrocortisone, 10 ng/ml of epidermal growth factor, 0.212 mg/ml of isoproterenol hydrochloride, 100 IU/ml of penicillin and 25 μg/ml of gentamycin.). Cells were kept in incubators at 37°C, 8% CO2, and 95 ± 5% humidity. Medium was changed three times per week. When cells attained 75-95% confluence, they were passaged.
T cells were isolated directly from anticoagulated peripheral blood obtained from healthy donors by negative immunomagnetic selection. For this step, the EasySep™ Direct Human T Cell Isolation Kit was used according to the manufacturer’s instructions under sterile conditions and at room temperature. T cells were then cultured for 7 days at 37°C in an 8% CO2 atmosphere with various cytokines to induce their polarization in Th1 and Th17 cells. During the first 3 days, T cells were seeded in 12-wells plates at 2 x 106/ml with their respective cytokine mixture. Th1 polarization was achieved by adding IL-12 (20 ng/ml) and anti-IL-4 (5 µg/ml) while anti-IFNγ (10 µg/ml), anti-IL-4 (5 µg/ml), IL-1β (20 ng/ml) and IL-6 (40 ng/ml) were added in the medium for Th17 polarization. After these 3 days, Th1 and Th17 were separately exposed to 25 ng/ml of phorbol 12-myristate 13-acetate and to 1 µg/ml of ionomycin for 4 hours at 37°C. Following this stimulation, T cells were reseeded (2 x 106/ml) in 12-wells plates for an additional 4 days at 37°C under 8% CO2 with IL-2 (30U/ml) for Th1 cells and with IL-2 (10 U/ml) and IL-23 (20 ng/ml) for Th17 cells.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: The two-layers hTECs were produced following the self-assembly approach. Briefly, dermal fibroblasts were cultured in the presence of ascorbic acid (50 μg/ml) for 35 days to promote the production of their own extracellular matrix (ECM). Two fibroblasts sheets were then superimposed to form a reconstructed stroma, on which keratinocyte were seeded. Reconstructed tissues were cultured for 7 days under submerged conditions in complete DME-HAM supplemented with ascorbate and then transferred to the air-liquid interface for 7 days in EGF-free DME-HAM to induce epithelial differentiation. At day 35, the previously polarized Th1 and Th17 cells were seeded to a total of 0.5 x 106 T cells per sheet on half of the dermal fibroblast sheets, with a ratio of 1:1. At the same time, keratinocytes were seeded on the other dermal fibroblast sheets. Keratinocytes and T cells were maintained in submerged culture in their respective medium for one additional week. Once T cells were added to the 3D skin model, the culture medium was supplemented with IL-2 (10 U/ml) and IL-23 (20 ng/ml) until the end of the culture period. At day 35, a fibroblast sheet with keratinocytes was superimposed on a T cell-containing fibroblast sheet, thus forming a skin substitute comprising a T-cell-enriched dermis and an epidermis. These newly formed skin substitutes were then raised at the air-liquid interface and kept in culture for a final 3 weeks in the keratinocytes culture medium depleted of EGF to allow complete differentiation of the epidermis.

tag: individual id

value: Primary human keratinocytes

tag: pathology

value: Healthy

tag: co-culture

value: T-lymphocyte

value: female


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, 006, rep1

description: Gene expression of healthy keratinocytes in passage 3 from human tissue-engineered skin substitutes

tag: cell type

value: no cell


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, 003, rep1

description: Gene expression of psoriatic non-lesional keratinocytes in passage 3 from human tissue-engineered skin substitutes

value: Psoriatic non-lesional

value: male


title: MPTP mouse SNpc, 24 h treatment, treated [SO_5062_Set2_24M3_SNC]

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).

tag: tissue

value: Substantia nigra pars compacta

value: MPTP


title: MPTP mouse SNpc, 24 h treatment, treated [SO_5062_Set2_24M2_SNC]

tag: treatment


title: MPTP mouse SNpc, 24 h treatment, treated [SO_5406_Set5_24M15NcNov]

tag: time


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, T-lymphocyte, 004, rep1

description: Gene expression of psoriatic non-lesional keratinocytes in passage 3 co-cultured with T-lymphocyte from human tissue-engineered skin substitutes

tag: Sex


title: MPTP mouse SNpc, 24 h treatment, treated [SO_5406_Repl_Set5_24M4_SNc_Nov]


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, T-lymphocyte, 004, rep1

description: Gene expression of psoriatic lesional keratinocytes in passage 3 co-cultured with T-lymphocyte from human tissue-engineered skin substitutes

value: Psoriatic lesional


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, T-lymphocyte, 006, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, 001, rep1

description: Gene expression of psoriatic lesional keratinocytes in passage 3 from human tissue-engineered skin substitutes


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, T-lymphocyte, 002, rep2


title: ZF_5_MacroP

value: Macrophages+

value: f

tag: individual

value: converted


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, T-lymphocyte, 002, rep1

tag: age


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, T-lymphocyte, 002, rep2


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, T-lymphocyte, 006, rep2


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, T-lymphocyte, 007, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, 004, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, T-lymphocyte, 002, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, T-lymphocyte, 005, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, 005, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, T-lymphocyte, 003, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, 002, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, non-lesional, T-lymphocyte, 003, rep1


title: MPTP mouse SNpc, 24 h treatment, treated [SO_5062_Set2_24M1_SNC]


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, 004, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, 002, rep1


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, 003, rep1


title: MPTP mouse SNpc, 14 days treatment, control [SO-4248-C3]

value: control (saline)

value: 14 days


title: MPTP mouse SNpc, 24 h treatment, control [SO_5062_Set2_24C1_SNC]


title: MPTP mouse SNpc, 14 days treatment, treated [SO-4248-T3]


title: MPTP mouse SNpc, 24 h treatment, control [SO_5406_Set5_24C2SNcNov]


title: MPTP mouse SNpc, 24 h treatment, control [SO_5406_Set5_24C3SNcNov]


title: MPTP mouse SNpc, 14 days treatment, control [SO-4248-C2]


title: MPTP mouse SNpc, 14 days treatment, treated [SO-4248-T2]


title: MPTP mouse SNpc, 14 days treatment, treated [SO-4248-T1]


title: MPTP mouse SNpc, 14 days treatment, control [SO-4248-C1]


title: Cell Bank cultured skin substitute, human keratinocytes, psoriatic, lesional, T-lymphocyte, 001, rep1


title: IP EIF4E4 rep1

city: Recife

first: MARIA

middle: JOSE RIBEIRO

last: BEZERRA

state: PE

department: Microbiologia

country: Brazil

institute: Fiocruz-PE

description:
Sample 13
mRNAs co-immunprecipitated with EIF4E4 IP reaction using wild type cells, replicate 1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using Trimmomatic version 0.36 with default parameters
The reads were then mapped to T. brucei 927 whole genome using STAR software, version  2.7.0a with --quantMode GeneCounts option to obtain the raw counts files
Assembly: TbruceiTREU927, version 2019-07-13
Supplementary files format and content: raw counts text files for every gene and every sample

molecule: polyA RNA

organism: Trypanosoma brucei

source_name: T. brucei cytoplasmic extract

growth_protocol: Exponentially growth T.brucei procyclics on mid log phase culture were harvested to a concentration of 1 to 2x109 cells/ml. The cells were lysis using nitrogen cavitation method.

extract_protocol:
Imunoprecipitation triplicates were carried out with cytoplasmic extracts derived from wild-type T.brucei and transfected cells expressing EIF4E3-RNAi and EIF4E4-RNAi were extracted according with the QIAGEN RNAeasy Mini Kit protocol.
RNA Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: untreated

value: T. brucei Lister 427

tag: genotype

value: Wild-type

value: wild type

tag: ip antibody

value: Dynabeads Protein A for Immunoprecipitation (Thermo Scientific, 10001D) coupled with in-house produced rabbit polyclonal-antibodies anti-EIF3E4


title: IP EIF4E3 with RNAi of EIF4E4 rep2

description:
Sample 8
mRNAs co-immunprecipitated with EIF4E3 IP reaction using EIF4E4 RNAi induced cells, replicate 2

tag: strain

value: EIF4E4 RNAi

value: Dynabeads Protein A for Immunoprecipitation (Thermo Scientific, 10001D) coupled with in-house produced rabbit polyclonal-antibodies anti-EIF3E3


title: Control 2 rep2

description:
Sample 11
Negative control for samples 13-18, replicate 2 co-immunprecipitated with EIF4E4 IP

value: Negative control


title: IP EIF4E3 with RNAi of EIF4E4 rep1

description:
Sample 7
mRNAs co-immunprecipitated with EIF4E3 IP reaction using EIF4E4 RNAi induced cells, replicate 1


title: Control 2 rep3

description:
Sample 12
Negative control for samples 13-18, replicate 3 co-immunprecipitated with EIF4E4 IP


title: IP EIF4E4 rep2

description:
Sample 14
mRNAs co-immunprecipitated with EIF4E4 IP reaction using wild type cells, replicate 2


title: MPTP mouse SNpc, 24 h treatment, control [SO_5062_Set2_24C3_SNC]


title: IP EIF4E4 with RNAi of EIF4E3 rep3

description:
Sample 18
mRNAs co-immunprecipitated with EIF4E4 IP reaction using EIF4E3 RNAi induced cells, replicate 3

value: EIF4E3 RNAi


title: Cell Bank cultured skin substitute, human keratinocytes, healthy, 007, rep1

value: Primary human keratinocytes

value: Healthy

value: no cell

value: female


title: IP EIF4E3 rep3

description:
Sample 6
mRNAs co-immunprecipitated with EIF4E3 IP reaction using wild type cells, replicate 3


title: IP EIF4E3 with RNAi of EIF4E4 rep3

description:
Sample 9
mRNAs co-immunprecipitated with EIF4E3 IP reaction using EIF4E4 RNAi induced cells, replicate 3


title: Control 2 rep1

description:
Sample 10
Negative control for samples 13-18, replicate 1 co-immunprecipitated with EIF4E4 IP


title: IP EIF4E3 rep1

description:
Sample 4
mRNAs co-immunprecipitated with EIF4E3 IP reaction using wild type cells, replicate 1


title: Control human umbilical vein endothelial cells

city: Foshan

first: gong

last: meiling

address: Foshan university

institute: College of Life Sciences and Engineering

description: Control ECV304 cells, untreated, harvested cultured cells on the 2nd, 4th and 6th day for experiment

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: The chip was scanned in Agilent 2565BA gene chip scanner, and the scanned data were analyzed and homogenized by Feature Extraction software.

source_name: human umbilical vein endothelial cells

label_protocol: 4 µg of total RNA were primed with 5 µl of  T7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 1 µl MMLV, and 10 µM  dNTP,0.1 M DTT, with 25 µM dCTP, 10 mM each Cy3-label and Cy5-label

growth_protocol: ECV304 cells were cultured in maintenance medium (MEM, Gibco, US) containing 10% fetal bovine serum, glutamine, sodium bicarbonate and penicillin

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Images were quantified using Agilent Feature Extraction Software

tag: cell line

value: Human umbilical vein endothelial like cell line

value: umbilical vein


title: Human umbilical vein endothelial like cells infected with HSV-2

description: Infected ECV304 cells were harvested and cultured on the 2nd, 4th and 6th day for experiment


title: IP EIF4E4 with RNAi of EIF4E3 rep2

description:
Sample 17
mRNAs co-immunprecipitated with EIF4E4 IP reaction using EIF4E3 RNAi induced cells, replicate 2


title: IP EIF4E3 rep2

description:
Sample 5
mRNAs co-immunprecipitated with EIF4E3 IP reaction using wild type cells, replicate 2


title: IP EIF4E4 rep3

description:
Sample 15
mRNAs co-immunprecipitated with EIF4E4 IP reaction using wild type cells, replicate 3


title: IP EIF4E4 with RNAi of EIF4E3 rep1

description:
Sample 16
mRNAs co-immunprecipitated with EIF4E4 IP reaction using EIF4E3 RNAi induced cells, replicate 1


title: MPTP mouse SNpc, 24 h treatment, control [SO_5062_Set2_24C2_SNC]

value: Substantia nigra pars compacta


title: Control rep3

description:
Sample 3
Negative control for samples 4-9, replicate 3  co-immunprecipitated with EIF4E3 IP


title: Control rep2

description:
Sample 2
Negative control for samples 4-9, replicate 2  co-immunprecipitated with EIF4E3 IP


title: Control rep1

description:
Sample 1
Negative control for samples 4-9, replicate 1  co-immunprecipitated with EIF4E3 IP


title: U2OS_spCas9_RGN11208

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

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

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

value: epithelial morphology

tag: molecule type

value: synthetic construct


title: U2OS_spCas9_RGN11237


title: U2OS_spCas9_VEGFAT2


title: U2OS_spCas9_RGN11179


title: U2OS_spCas9_RGN11189


title: U2OS_spCas9_RGN11184


title: U2OS_spCas9_HEK293TT4


title: U2OS_spCas9_11296


title: U2OS_spCas9_11458


title: U2OS_spCas9_11398


title: U2OS_spCas9_11290


title: U2OS_spCas9_11414


title: U2OS_spCas9_11437


title: U2OS_spCas9_11510


title: U2OS_spCas9_6832


title: U2OS_spCas9_9506


title: U2OS_spCas9_6873


title: U2OS_spCas9_9490


title: U2OS_spCas9_5679


title: U2OS_spCas9_5600


title: U2OS_spCas9_5595


title: U2OS_spCas9_5035


title: U2OS_spCas9_5032


title: U2OS_spCas9_4708


title: U2OS_spCas9_11397


title: U2OS_spCas9_4729


title: U2OS_MOCK_RGN11208

value: MOCK


title: U2OS_MOCK_RGN11237


title: U2OS_spCas9_11291


title: U2OS_MOCK_RGN11184


title: U2OS_MOCK_RGN11179


title: U2OS_MOCK_11510


title: U2OS_MOCK_HEK293TT4


title: U2OS_MOCK_11414


title: U2OS_spCas9_6791


title: U2OS_MOCK_RGN11189


title: U2OS_MOCK_11437


title: U2OS_MOCK_11397


title: U2OS_MOCK_11458


title: U2OS_MOCK_11291


title: U2OS_MOCK_11398


title: U2OS_spCas9_5675


title: U2OS_MOCK_11296


title: U2OS_MOCK_11290


title: U2OS_spCas9_5029


title: U2OS_MOCK_6832


title: U2OS_MOCK_6791


title: U2OS_MOCK_9490


title: U2OS_MOCK_5679


title: U2OS_MOCK_5600


title: U2OS_MOCK_VEGFAT2


title: U2OS_MOCK_5675


title: U2OS_MOCK_5035


title: U2OS_MOCK_5029


title: U2OS_MOCK_4729


title: U2OS_MOCK_5595


title: U2OS_HiFispCas9_VEGFAT2


title: U2OS_MOCK_5032


title: U2OS_MOCK_4708


title: U2OS_MOCK_6873


title: U2OS_HiFispCas9_RGN11208


title: U2OS_HiFispCas9_HEK293TT4


title: U2OS_HiFispCas9_11437


title: U2OS_HiFispCas9_11291


title: U2OS_HiFispCas9_RGN11184


title: U2OS_HiFispCas9_11458


title: U2OS_HiFispCas9_11510


title: U2OS_HiFispCas9_RGN11189


title: U2OS_HiFispCas9_RGN11179


title: U2OS_HiFispCas9_9506


title: U2OS_HiFispCas9_11398


title: U2OS_HiFispCas9_RGN11237


title: U2OS_HiFispCas9_11414


title: U2OS_HiFispCas9_11296


title: U2OS_HiFispCas9_11397


title: U2OS_HiFispCas9_5679


title: U2OS_MOCK_9506


title: U2OS_HiFispCas9_9490


title: U2OS_HiFispCas9_6832


title: U2OS_HiFispCas9_6873


title: U2OS_HiFispCas9_6791


title: U2OS_HiFispCas9_5595


title: U2OS_HiFispCas9_5675


title: U2OS_HiFispCas9_5032


title: U2OS_HiFispCas9_5035


title: U2OS_HiFispCas9_5029


title: U2OS_HiFispCas9_4729


title: SKOV3_spCas9_RGN11208


title: SKOV3_spCas9_RGN11189


title: SKOV3_spCas9_RGN11184


title: U2OS_HiFispCas9_4708


title: U2OS_HiFispCas9_11290


title: SKOV3_spCas9_11414


title: SKOV3_spCas9_11398


title: SKOV3_spCas9_RGN11237


title: SKOV3_spCas9_HEK293TT4


title: SKOV3_spCas9_VEGFAT2


title: SKOV3_spCas9_11397


title: SKOV3_spCas9_11510


title: SKOV3_spCas9_11437


title: SKOV3_spCas9_RGN11179


title: SKOV3_spCas9_6832


title: SKOV3_spCas9_11296


title: SKOV3_spCas9_11290


title: SKOV3_spCas9_9506


title: U2OS_HiFispCas9_5600


title: SKOV3_spCas9_6873


title: SKOV3_spCas9_6791


title: SKOV3_spCas9_5679


title: SKOV3_spCas9_5675


title: SKOV3_spCas9_5595


title: SKOV3_spCas9_5029


title: SKOV3_spCas9_4729


title: SKOV3_spCas9_5600


title: SKOV3_spCas9_11458


title: SKOV3_MOCK_RGN11208


title: SKOV3_spCas9_9490


title: SKOV3_MOCK_RGN11237


title: SKOV3_spCas9_5032


title: SKOV3_MOCK_11510


title: SKOV3_MOCK_HEK293TT4


title: SKOV3_spCas9_5035


title: SKOV3_MOCK_11414


title: SKOV3_spCas9_4708


title: SKOV3_MOCK_VEGFAT2


title: SKOV3_spCas9_11291


title: SKOV3_MOCK_11397


title: SKOV3_MOCK_11398


title: SKOV3_MOCK_11296


title: SKOV3_MOCK_RGN11179


title: SKOV3_MOCK_11437


title: SKOV3_MOCK_RGN11189


title: SKOV3_MOCK_9506


title: SKOV3_MOCK_11290


title: SKOV3_MOCK_11291


title: SKOV3_MOCK_9490


title: SKOV3_MOCK_6832


title: SKOV3_MOCK_RGN11184


title: SKOV3_MOCK_6791


title: SKOV3_MOCK_5595


title: SKOV3_MOCK_6873


title: SKOV3_MOCK_5679


title: SKOV3_MOCK_5029


title: SKOV3_HiFispCas9_VEGFAT2


title: SKOV3_MOCK_5675


title: SKOV3_MOCK_5032


title: SKOV3_MOCK_4729


title: SKOV3_HiFispCas9_RGN11189


title: SKOV3_MOCK_5035


title: SKOV3_MOCK_11458


title: SKOV3_HiFispCas9_RGN11179


title: SKOV3_MOCK_4708


title: SKOV3_HiFispCas9_RGN11208


title: SKOV3_HiFispCas9_RGN11184


title: SKOV3_MOCK_5600


title: SKOV3_HiFispCas9_11510


title: SKOV3_HiFispCas9_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 81

city: Hangzhou

first: Fang

last: Ye

state: Zhejiang

address: 866 Yuhangtang Rd

institute: Zhejiang University

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)

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.

value: d/d

value: Adult (1year)

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


title: SKOV3_HiFispCas9_11414


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 79


title: SKOV3_HiFispCas9_RGN11237


title: SKOV3_HiFispCas9_11398


title: SKOV3_HiFispCas9_11397


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 75


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 76


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 77


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 78


title: SKOV3_HiFispCas9_11437


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 80


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 74


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 72


title: SKOV3_HiFispCas9_11296


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 73


title: SKOV3_HiFispCas9_11291


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 71


title: SKOV3_HiFispCas9_11458


title: SKOV3_HiFispCas9_9490


title: SKOV3_HiFispCas9_11290


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 70


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 69


title: SKOV3_HiFispCas9_9506


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 67


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 68


title: SKOV3_HiFispCas9_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 66


title: SKOV3_HiFispCas9_5679


title: SKOV3_HiFispCas9_6791


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 65


title: SKOV3_HiFispCas9_5675


title: SKOV3_HiFispCas9_5595


title: SKOV3_HiFispCas9_5600


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 63


title: SKOV3_HiFispCas9_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 60


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 64


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 61


title: SKOV3_HiFispCas9_5029


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 62


title: SKOV3_HiFispCas9_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 59


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 58


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 57


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 56


title: SKOV3_HiFispCas9_6832


title: SKOV3_HiFispCas9_4708


title: PC9_spCas9_RGN11208

value: lung adenocarcinoma


title: PC9_spCas9_VEGFAT2


title: PC9_spCas9_RGN11237


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 54


title: PC9_spCas9_RGN11189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 53


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 52


title: PC9_spCas9_RGN11184


title: PC9_spCas9_RGN11179


title: SKOV3_HiFispCas9_4729


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 50


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 49


title: PC9_spCas9_HEK293TT4


title: PC9_spCas9_11510


title: PC9_spCas9_11458


title: PC9_spCas9_11437


title: PC9_spCas9_11414


title: PC9_spCas9_11398


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 47


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 48


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 46


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 44


title: PC9_spCas9_11397


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 45


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 55


title: PC9_spCas9_11296


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 43


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 42


title: PC9_spCas9_11291


title: PC9_spCas9_11290


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 41


title: PC9_spCas9_9490


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 51


title: PC9_spCas9_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 38


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 40


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 37


title: PC9_spCas9_6832


title: PC9_spCas9_9506


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 36


title: PC9_spCas9_5679


title: PC9_spCas9_6791


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 35


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 33


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 34


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 32


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 30


title: PC9_spCas9_5600


title: PC9_spCas9_5675


title: PC9_spCas9_5595


title: PC9_spCas9_5035


title: PC9_spCas9_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 29


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 39


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 27


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 31


title: PC9_spCas9_5029


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 26


title: PC9_spCas9_4729


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 28


title: PC9_MOCK_VEGFAT2


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 25


title: PC9_MOCK_RGN11208


title: PC9_MOCK_RGN11237


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 23


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 22


title: PC9_MOCK_RGN11189


title: PC9_MOCK_RGN11179


title: PC9_MOCK_RGN11184


title: PC9_spCas9_4708


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 21


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 20


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 18


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 19


title: PC9_MOCK_11414


title: PC9_MOCK_11510


title: PC9_MOCK_11458


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 24


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 16


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 15


title: PC9_MOCK_11437


title: PC9_MOCK_11397


title: PC9_MOCK_11296


title: PC9_MOCK_11398


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 14


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 13


title: PC9_MOCK_11290


title: PC9_MOCK_11291


title: PC9_MOCK_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 10


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 11


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 12


title: PC9_MOCK_6832


title: PC9_MOCK_9490


title: PC9_MOCK_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 8


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 7


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 17


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 6


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 5


title: PC9_MOCK_6791


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 4


title: PC9_MOCK_5675


title: PC9_MOCK_5600


title: PC9_MOCK_5035


title: PC9_MOCK_9506


title: PC9_MOCK_5595


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 48


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 2


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 1


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 9


title: PC9_MOCK_5679


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 46


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 47


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 45


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch4), NEO4, sublibrary 3


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 43


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 41


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 44


title: PC9_MOCK_4729


title: PC9_MOCK_4708


title: PC9_HiFispCas9_VEGFAT2


title: PC9_MOCK_5032


title: PC9_MOCK_5029


title: PC9_HiFispCas9_RGN11184


title: PC9_HiFispCas9_RGN11237


title: PC9_HiFispCas9_RGN11189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 39


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 42


title: PC9_HiFispCas9_RGN11179


title: PC9_HiFispCas9_RGN11208


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 38


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 37


title: PC9_HiFispCas9_11510


title: PC9_HiFispCas9_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 34


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 35


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 36


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 33


title: PC9_HiFispCas9_11414


title: PC9_HiFispCas9_11398


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 40


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 32


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 31


title: PC9_HiFispCas9_11296


title: PC9_HiFispCas9_11397


title: PC9_HiFispCas9_11290


title: PC9_HiFispCas9_9506


title: PC9_HiFispCas9_11458


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 30


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 26


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 28


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 23


title: PC9_HiFispCas9_6873


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 27


title: PC9_HiFispCas9_9490


title: PC9_HiFispCas9_6832


title: PC9_HiFispCas9_6791


title: PC9_HiFispCas9_11437


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 20


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 29


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 22


title: PC9_HiFispCas9_5679


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 24


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 21


title: PC9_HiFispCas9_5675


title: PC9_HiFispCas9_5600


title: PC9_HiFispCas9_5029


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 19


title: PC9_HiFispCas9_5032


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 25


title: PC9_HiFispCas9_11291


title: PC9_HiFispCas9_5595


title: PC9_HiFispCas9_4729


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 15


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 18


title: PC9_HiFispCas9_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 17


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 16


title: KUH132_spCas9_RGN11237

value: human skin-derived fibroblasts


title: KUH132_spCas9_VEGFAT2


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 13


title: KUH132_spCas9_RGN11208


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 14


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 11


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 10


title: KUH132_spCas9_RGN11179


title: KUH132_spCas9_RGN11184


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 8


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 7


title: KUH132_spCas9_11510


title: PC9_HiFispCas9_4708


title: KUH132_spCas9_HEK293TT4


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 9


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 5


title: KUH132_spCas9_11397


title: KUH132_spCas9_11398


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 4


title: KUH132_spCas9_11437


title: KUH132_spCas9_11414


title: KUH132_spCas9_11458


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 6


title: KUH132_spCas9_9506


title: KUH132_spCas9_11291


title: KUH132_spCas9_11296


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 12


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 180


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 1


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 3


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch3), NEO3, sublibrary 2


title: KUH132_spCas9_6873


title: KUH132_spCas9_9490


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 178


title: KUH132_spCas9_RGN11189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 183


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 182


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 181


title: KUH132_spCas9_5679


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 179


title: KUH132_spCas9_11290


title: KUH132_spCas9_6791


title: KUH132_spCas9_5675


title: KUH132_spCas9_5600


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 176


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 174


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 173


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 177


title: KUH132_spCas9_6832


title: KUH132_spCas9_5595


title: KUH132_spCas9_5029


title: KUH132_spCas9_5032


title: KUH132_spCas9_4708


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 172


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 167


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 166


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 171


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 175


title: KUH132_spCas9_5035


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 168


title: KUH132_MOCK_VEGFAT2


title: KUH132_spCas9_4729


title: KUH132_MOCK_RGN11208


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 164


title: KUH132_MOCK_RGN11237


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 165


title: KUH132_MOCK_RGN11189


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 170


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 163


title: KUH132_MOCK_RGN11184


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 161


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 162


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 160


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 159


title: KUH132_MOCK_RGN11179


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 158


title: KUH132_MOCK_11510


title: KUH132_MOCK_HEK293TT4


title: KUH132_MOCK_11414


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 156


title: KUH132_MOCK_11437


title: KUH132_MOCK_11458


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 169


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 154


title: Single-cell RNA-seq dataset of neotenic axolotl (Batch2), NEO2, sublibrary 155


title: KUH132_MOCK_11397