title: LID_112597_PID_10502

description:
Library name: LID_112597_PID_10502
dog_id:19159335 precision cohort year 1. dog age at collection:1.45206099323142


title: LID_112491_PID_10502

status: Public on Apr 15 2026

type: SRA

city: Tempe

first: Noah

last: Snyder-Mackler

state: AZ

address: 427 East Tyler Mall

country: USA

institute: Arizona State University

description:
Library name: LID_112491_PID_10502
dog_id:14161258 precision cohort year 1. dog age at collection:3.42386303140923

library_source: genomic

data_processing:
bcl2fastq
Supplementary files format and content: sumamrized to species level

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: feces metagenome

extract_protocol:
For each fecal sample, a lysate was prepared using the following procedure: The fecal collection tube was thawed and vortexed to homogenize the fecal sample in the storage solution. A small aliquot (∼200 µL) of the fecal slurry was removed using a fresh 1 mL serological pipette and transferred to a 2 mL tube pre-filled with garnet shards and a 6 mm zirconium bead (Benchmark Scientific, D1033-30G). To this tube, 365 µL of PowerBead solution (Qiagen, #12955-4-bs) and 20 µL of 20% sodium dodecyl sulfate (SDS) were added. The tubes were subjected to bead-beating using a TissueLyzer instrument for 45 seconds at 30 cycles per second. The resulting fecal homogenate was treated twice with Protein Precipitation Solution (MP Biomedical, product no. 116560203) to remove proteins.
metagenomic library prep doi: dx.doi.org/10.17504/protocols.io.rm7vzbob4vx1/v1

tag: tissue

value: feces metagenome

tag: batch


title: LID_112483_PID_10502

description:
Library name: LID_112483_PID_10502
dog_id:14402029 precision cohort year 1. dog age at collection:4.04483230663929


title: NT008B

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

description: Library name: Sample 6

library_source: transcriptomic

data_processing:
Adapter-trimmed reads in the FASTQ format wereused as inputs, wherein demultiplexing was performed using BaseSpace default settings
The trimmed FASTQ were aligned using STAR to the mouse genome (mm10)
Reads were quantified in TPM format using Salmon
Read count matrices generated above were processed for differential expression using DESeq
Read count matrices were subjected to further downstream analysis using iGEAK
Assembly: mm10
Supplementary files format and content: tab delimited raw counts with genes in rows and samples in columns

molecule: total RNA

organism: Mus musculus

source_name: Cortical tumor

growth_protocol: Primary murine cell lines were grown in NeuroCult basal medium containing 10% NeuroCult Proliferation Supplement (Stemcell Technologies, #05702) and supplemented with 2µg/mL heparin (Stemcell Technologies #07980) plus growth factors (Shenandoah Biotech #PB-500-20) including 20ng/mL Epidermal Growth Factor (EGF; #200-53), 20ng/mL Fibroblast Growth Factor-basic (FGF; #200-12), 10ng/mL PDGF-AA (#200-54) and 10ng/mL PDGF-BB (#200-58). Cultures were grown as neurosphere suspensions in ultra-low attachment PrimeSurface cell culture plates (SBio # #MS-90900).

extract_protocol:
RNA was isolated using the Quick-DNA/RNA Miniprep Plus Kit (Zymo Research, #D7003)
RNA libraries were prepared for bulk sequencing using standard Illumina protocols

value: Cortical tumor

tag: genotype

value: IDH1R132H+PIK3CAE545K+sgRNA Cic, Fubp1, Trp53


title: LID_112484_PID_10502

description:
Library name: LID_112484_PID_10502
dog_id:14331178 precision cohort year 1. dog age at collection:6.11516084873374


title: NT009

description: Library name: Sample 7


title: NT004

description: Library name: Sample 2


title: LID_112470_PID_10502

description:
Library name: LID_112470_PID_10502
dog_id:13899904 precision cohort year 1. dog age at collection:7.28989847136664


title: LID_112576_PID_10502

description:
Library name: LID_112576_PID_10502
dog_id:19047983 precision cohort year 1. dog age at collection:1.75127386113012


title: LID_112600_PID_10502

description:
Library name: LID_112600_PID_10502
dog_id:19130676 precision cohort year 1. dog age at collection:8.3603125712982


title: Follicular B cells, 18hr CpG, Rfx7 KO 3

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine (IRB)

description: Library name: Sample 11

data_processing:
We used FastQC v0.11.9 to assess the quality of the reads.
Adapters sequences were removed using cutadapt v2.8
Reads were subsequently mapped to the mouse genome using HISAT2 v2.1.0
Assembly: GENCODE vM30 (GRCm39)
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: Spleen

growth_protocol: Sorted FO B cells were seeded at 100’000 cells per well in 96-flat bottom well plate in complete medium (RPMI, 10% FBS, 1% Penicillin-Streptomycin, 1% MEM NEAA, 1% GlutaMAX, 1% Sodium pyruvate, 0.1% 2-mercaptoethanol, all from Gibco).

extract_protocol:
Total RNA was extracted from sorted cells with Monarch® Total RNA Miniprep Kit (New England Biolabs) according to the manufacturer’s instruction. Quality controls were performed on Bioanalyzer 2100 using RNA Integrity Number (RIN) > 8 (Agilent Technologies, Santa Clara, CA, USA) and Qubit V4 (Invitrogen Thermo Fisher Scientific, Waltham, MA, USA).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) was employed with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext® Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The sequencing of the pre-pools was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100cycles; Illumina). Samples were processed starting from stranded, single-ended 120bp-long sequencing reads.

treatment_protocol: For stimulation cells were activated with CpG (2 μg/ml) for 18h in vitro.

value: Spleen

tag: cell type

value: Follicular B cells

value: Rfx7 knock out

tag: treatment

value: 18hr CpG


title: NT005

description: Library name: Sample 3


title: NT003

description: Library name: Sample 1


title: Follicular B cells, 18hr CpG, Rfx7 KO 2

description: Library name: Sample 10


title: Follicular B cells, 18hr CpG, WT 4

description: Library name: Sample 8

value: Wild-type


title: LID_112475_PID_10502

description:
Library name: LID_112475_PID_10502
dog_id:14395294 precision cohort year 1. dog age at collection:10.3804852080006


title: LID_112418_PID_10501

description:
Library name: LID_112418_PID_10501
dog_id:18822302 precision cohort year 1. dog age at collection:0.795317134382843


title: LID_112356_PID_10501

description:
Library name: LID_112356_PID_10501
dog_id:17719904 precision cohort year 1. dog age at collection:4.3077800593201


title: Follicular B cells, 18hr CpG, WT 1

description: Library name: Sample 5


title: Follicular B cells, 18hr CpG, Rfx7 KO 1

description: Library name: Sample 9


title: LID_112530_PID_10502

description:
Library name: LID_112530_PID_10502
dog_id:15518392 precision cohort year 1. dog age at collection:10.2469769564225


title: Follicular B cells, 18hr CpG, WT 3

description: Library name: Sample 7


title: LID_112320_PID_10501

description:
Library name: LID_112320_PID_10501
dog_id:17908940 precision cohort year 1. dog age at collection:4.10818313179709


title: LID_112531_PID_10502

description:
Library name: LID_112531_PID_10502
dog_id:15594457 precision cohort year 1. dog age at collection:5.18124001825234


title: Follicular B cells, untreated, Rfx7 KO 2

description: Library name: Sample 4

value: Naive/Untreated


title: LID_112439_PID_10501

description:
Library name: LID_112439_PID_10501
dog_id:18709064 precision cohort year 1. dog age at collection:4.35791695185946


title: LID_112374_PID_10501

description:
Library name: LID_112374_PID_10501
dog_id:18671468 precision cohort year 1. dog age at collection:4.50576089436459


title: Follicular B cells, untreated, Rfx7 KO 1

description: Library name: Sample 3


title: Follicular B cells, untreated, WT 1

description: Library name: Sample 1


title: LID_112480_PID_10502

description:
Library name: LID_112480_PID_10502
dog_id:14436622 precision cohort year 1. dog age at collection:10.7996235455168


title: Follicular B cells, 18hr CpG, WT 2

description: Library name: Sample 6


title: Follicular B cells, untreated, WT 2

description: Library name: Sample 2


title: LID_112378_PID_10501

description:
Library name: LID_112378_PID_10501
dog_id:18708971 precision cohort year 1. dog age at collection:4.85557837097878


title: Pten;Trp53-knockout, Plgrktdelta139-147, Tumor4

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
38467_T2_PPPlgrktdelta139-147
tpm_values_ORF_samples.txt

data_processing:
Real-time base call (.bcl) files were converted to FASTQ files using Illumina bcl2fastq conversion software. Following Nextera adaptor trimming, sequencing reads were pseudoaligned and quantified using kallisto quant with the house mouse genome (mm10) used as a transcriptome index.
Assembly: mm10
Supplementary files format and content: tab-delimited text file provides TPM counts for each CRISPR sample.
Supplementary files format and content: tab-delimited text file provides TPM counts for each ORF sample.

source_name: mammary tumor

growth_protocol: Animal husbandry, ethical handling of mice, and all approved animal work was carried out according to guidelines approved by the Canadian Council on Animal Care and under protocols approved by the Centre for Phenogenomics Animal Care Committee (26-0272H).

extract_protocol:
RNA was extracted from approximately 3 x 105 freshly isolated, viable, nucleated FACS-purified tumor cells using the Quick-RNA Microprep Kit (R1050, Zymoresearch Inc.) according to manufacturer’s instructions. RNA was then treated with the kit-provided DNase I (R1050, Zymoresearch Inc.).
RNA quality was assessed using an Agilent 2100 Bioanalyzer. All RNA samples passed the quality control threshold of an RNA integrity number (RIN) score of >8.0. Full length cDNA libraries were generated from high quality total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634890, TaKaRa) according to manufacturer’s instructions. The quantity and quality of the purified full-length cDNA were measured by Qubit dsDNA High Sensitivity Assay kit (Q32851, ThermoFisher Scientific) and Agilent 2100 Bioanalyzer, respectively. The final barcoded sequencing libraries were prepared from full length cDNA using Nextera XT Library Prep Kit (FC-131-1024, Illumina) according to manufacturer’s instructions. The barcoded cDNA library quality was checking using an Agilent 2100 Bioanalyzer for fragment size and quantified by qRT-PCR on a BioRad CFX96 Touch Real-Time PCR Detection System (BioRad). Quality checked libraries were then loaded onto an Illumina NovaSeq 6000 running PE150 cycles.

treatment_protocol: To deliver lentivirus directly into the mammary gland, a noninvasive injection method was used that selectively transduces the mammary epithelium of female mice. The third and fourth inguinal mammary glands of female mice were injected between eight and twenty weeks of age, with age at time of injection matched between groups across all experiments. Lentiviruses were diluted to 1 x 107 pfu/mL in PBS and 10% (v/v) of Fast-Green dye for a total injection volume of 10 µL per mammary gland and injected using a pulled glass micropipette.

value: mammary tumor


title: Pten;Trp53-knockout, Plgrktdelta139-147, Tumor3

description:
38468_T1_PPPlgrktdelta139-147
tpm_values_ORF_samples.txt


title: LID_112500_PID_10502

description:
Library name: LID_112500_PID_10502
dog_id:14692627 precision cohort year 1. dog age at collection:6.04149555099247


title: LID_112510_PID_10502

description:
Library name: LID_112510_PID_10502
dog_id:14571418 precision cohort year 1. dog age at collection:7.58504449007529


title: Pten;Trp53-knockout, Plgrktdelta139-147, Tumor1

description:
5851_T1_PPPlgrktdelta139-147
tpm_values_ORF_samples.txt


title: Pten;Trp53-knockout, Plgrktdelta139-147, Tumor2

description:
38467_T1_PPPlgrktdelta139-147
tpm_values_ORF_samples.txt


title: LID_112593_PID_10502

description:
Library name: LID_112593_PID_10502
dog_id:19173471 precision cohort year 1. dog age at collection:2.02991672370522


title: Pten;Trp53-knockout, PlgrktK147R, Tumor3

description:
38471_T2_PPPlgrktK147R
tpm_values_ORF_samples.txt


title: Pten;Trp53-knockout, PlgrktK147R, Tumor2

description:
38471_T1_PPPlgrktK147R
tpm_values_ORF_samples.txt


title: LID_112493_PID_10502

description:
Library name: LID_112493_PID_10502
dog_id:14312002 precision cohort year 1. dog age at collection:10.8594569929272


title: LID_112563_PID_10502

description:
Library name: LID_112563_PID_10502
dog_id:19049735 precision cohort year 1. dog age at collection:2.60573047380029


title: LID_112482_PID_10502

description:
Library name: LID_112482_PID_10502
dog_id:14413945 precision cohort year 1. dog age at collection:15.3003650467716


title: Pten;Trp53-knockout, HA, Tumor3

description:
43535_T1_PPHA
tpm_values_ORF_samples.txt

value: HA


title: Pten;Trp53-knockout, HA, Tumor1

description:
43533_T1_PPHA
tpm_values_ORF_samples.txt


title: LID_112523_PID_10502

description:
Library name: LID_112523_PID_10502
dog_id:15527242 precision cohort year 1. dog age at collection:6.99934405658225


title: Pten;Trp53-knockout, HA, Tumor2

description:
43534_T1_PPHA
tpm_values_ORF_samples.txt


title: LID_112496_PID_10502

description:
Library name: LID_112496_PID_10502
dog_id:14470762 precision cohort year 1. dog age at collection:13.6442790326261


title: LID_112536_PID_10502

description:
Library name: LID_112536_PID_10502
dog_id:16501495 precision cohort year 1. dog age at collection:11.7492584987452


title: LID_112492_PID_10502

description:
Library name: LID_112492_PID_10502
dog_id:14174761 precision cohort year 1. dog age at collection:2.17502281542323


title: LID_112521_PID_10502

description:
Library name: LID_112521_PID_10502
dog_id:15530194 precision cohort year 1. dog age at collection:6.41934747889573


title: Pten;Trp53-knockout, dgPlgrkt, Tumor4

description:
24879_T3_PPdgPlgrkt
tpm_values_CRISPR_samples.txt

value: dgPlgrkt


title: Pten;Trp53-knockout, PlgrktK147R, Tumor1

description:
38470_T1_PPPlgrktK147R
tpm_values_ORF_samples.txt


title: LID_112552_PID_10502

description:
Library name: LID_112552_PID_10502
dog_id:19049555 precision cohort year 1. dog age at collection:3.25088409765001


title: LID_112594_PID_10502

description:
Library name: LID_112594_PID_10502
dog_id:19148133 precision cohort year 1. dog age at collection:2.69780971937029


title: Pten;Trp53-knockout, dgPlgrkt, Tumor3

description:
24879_T1_PPdgPlgrkt
tpm_values_CRISPR_samples.txt


title: Pten;Trp53-knockout, dgPlgrkt, Tumor2

description:
24877_T2_PPdgPlgrkt
tpm_values_CRISPR_samples.txt


title: Pten;Trp53-knockout, dgPlgrkt, Tumor1

description:
24876_T1_PPdgPlgrkt
tpm_values_CRISPR_samples.txt


title: LID_112504_PID_10502

description:
Library name: LID_112504_PID_10502
dog_id:14624794 precision cohort year 1. dog age at collection:5.26873716632443


title: Pten;Trp53-knockout, dgTigre, Tumor2

description:
24564_T4_PPdgTigre
tpm_values_CRISPR_samples.txt

value: dgSHL


title: LID_112466_PID_10502

description:
Library name: LID_112466_PID_10502
dog_id:14111662 precision cohort year 1. dog age at collection:3.24304129591604


title: LID_112519_PID_10502

description:
Library name: LID_112519_PID_10502
dog_id:15554641 precision cohort year 1. dog age at collection:5.41980378736026


title: LID_112445_PID_10501

description:
Library name: LID_112445_PID_10501
dog_id:18957176 precision cohort year 1. dog age at collection:6.86289451669329


title: LID_112318_PID_10501

description:
Library name: LID_112318_PID_10501
dog_id:17967104 precision cohort year 1. dog age at collection:5.03641911932466


title: Pten;Trp53-knockout, dgHipp11, Tumor2

description:
24300_T1_PPdgHipp11
tpm_values_CRISPR_samples.txt


title: Pten;Trp53-knockout, dgTigre, Tumor1

description:
24564_T1_PPdgTigre
tpm_values_CRISPR_samples.txt


title: LID_112344_PID_10501

description:
Library name: LID_112344_PID_10501
dog_id:17790545 precision cohort year 1. dog age at collection:4.99768993839836


title: LID_112449_PID_10501

description:
Library name: LID_112449_PID_10501
dog_id:18925421 precision cohort year 1. dog age at collection:6.23032169746749


title: LID_112443_PID_10501

description:
Library name: LID_112443_PID_10501
dog_id:18760502 precision cohort year 1. dog age at collection:4.2916096281086


title: Gm20 single mutant V5 Rep1

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

description: Library name: Sample 11

data_processing:
Illumina software used for basecalling.
Sequenced reads were mapped to the  whole genome using bowtie HISAT2
Reads counts for each gene with  htseq-count
Assembly: Glycine max [L.] Merr Wm82.a2.v1
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

organism: Glycine max

source_name: seed

growth_protocol: Field trials were conducted at the Eastern Nebraska Research, Extension and Education Center (ENREEC; 41°08'41.3"N 96°26'14.0"W), Mead, NE, USA, in crop seasons. Each plot consisted of four 3m-rows (75 cm row to row). Data were collected from the plants in the inner two rows. After sowing for two weeks, a total number of plants were counted, and germination rates were calculated based on the initial number of seeds sown. Observations were performed for phenology according to a soybean guideline (Pedersen et al., 2004). At harvest, total seed weight per plot and one hundred seed weights were recorded. For 100-seed weight, only pink seeds were used for measurement of for the transgenic events.

extract_protocol:
Seeds from 3-5 plants were collected at indicated stages. RNA was isolated using QIAGEN RNA easy kit (QIAGEN) and treated with DNase (Turbo DNA free kit, Invitrogen), and the initial quality was verified by running the RNA on agarose gel.
standard Illumina RNA library protocol

value: seed

value: Gm20 single mutant


title: Gm20/Gm10 double mutant V5 Rep2

description: Library name: Sample 10

value: Gm20/Gm10 double mutant


title: Gm20 single mutant V5 Rep2

description: Library name: Sample 12


title: Pten;Trp53-knockout, dgHipp11, Tumor1

description:
24299_T1_PPdgHipp11
tpm_values_CRISPR_samples.txt


title: LID_112472_PID_10502

description:
Library name: LID_112472_PID_10502
dog_id:14028172 precision cohort year 1. dog age at collection:3.03171343828428


title: LID_112498_PID_10502

description:
Library name: LID_112498_PID_10502
dog_id:14519662 precision cohort year 1. dog age at collection:6.82949463837554


title: LID_112485_PID_10502

description:
Library name: LID_112485_PID_10502
dog_id:14311909 precision cohort year 1. dog age at collection:10.9810631987223


title: LID_112553_PID_10502

description:
Library name: LID_112553_PID_10502
dog_id:19002518 precision cohort year 1. dog age at collection:6.16133356148757


title: LID_112489_PID_10502

description:
Library name: LID_112489_PID_10502
dog_id:14161351 precision cohort year 1. dog age at collection:8.8361852612366


title: Gm20/Gm10 double mutant V5 Rep1

description: Library name: Sample 9


title: Gm20 single mutant R5 Rep1

description: Library name: Sample 5


title: Gm20/Gm10 double mutant R5 Rep2

description: Library name: Sample 4


title: Thorne V5 Rep1

description: Library name: Sample 7

value: WT Thorne


title: Gm20 single mutant R5 Rep2

description: Library name: Sample 6


title: LID_112585_PID_10502

description:
Library name: LID_112585_PID_10502
dog_id:19040231 precision cohort year 1. dog age at collection:5.90942276979238

value: feces metagenome


title: LID_112495_PID_10502

description:
Library name: LID_112495_PID_10502
dog_id:14471428 precision cohort year 1. dog age at collection:7.80469997718458


title: LID_112505_PID_10502

description:
Library name: LID_112505_PID_10502
dog_id:14492518 precision cohort year 1. dog age at collection:4.73508441706594


title: LID_112502_PID_10502

description:
Library name: LID_112502_PID_10502
dog_id:14471554 precision cohort year 1. dog age at collection:7.23203285420945


title: Thorne R5 Rep2

description: Library name: Sample 2


title: Gm20/Gm10 double mutant R5 Rep1

description: Library name: Sample 3


title: Thorne R5 Rep1

description: Library name: Sample 1


title: Thorne  V5 Rep2

description: Library name: Sample 8


title: LID_112554_PID_10502

description:
Library name: LID_112554_PID_10502
dog_id:19037108 precision cohort year 1. dog age at collection:6.24937257586128


title: Sensitive clinical isolate-WF001, bio rep 3

city: Birmingham

first: Keonte

middle: Jamel

last: Graves

state: AL

address: 1900 University Blvd, THT 230

department: Medicine-Infectious Diseases

institute: The University of Alabama at Birmingham

description: Library name: WF001-3

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Trichomonas_vaginalis reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed.
Assembly: txid5722
Supplementary files format and content: Tab-delimited text files include raw read counts for each sample

organism: Trichomonas vaginalis

source_name: trichomonad

growth_protocol: All T. vaginalis isolates were grown under anaerobic conditions using Diamond’s Trypticase-Yeast-Maltose (TYM) media.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA), according to the manufacturer’s instructions.
Pre-made library -- no library preparation performed

value: trichomonad

tag: phenotype

value: Sensitive

tag: group

value: clinical isolate


title: LID_112359_PID_10501

description:
Library name: LID_112359_PID_10501
dog_id:17717399 precision cohort year 1. dog age at collection:6.39408890409917


title: LID_112525_PID_10502

description:
Library name: LID_112525_PID_10502
dog_id:15524074 precision cohort year 1. dog age at collection:3.49731918777093


title: Sensitive clinical isolate-WF001, bio rep 1

description: Library name: WF001-1


title: LID_112481_PID_10502

description:
Library name: LID_112481_PID_10502
dog_id:14436940 precision cohort year 1. dog age at collection:5.8855806525211


title: Resistant clinical isolate-VC010, bio rep 1

description: Library name: VC010-1

value: Resistant


title: LID_112319_PID_10501

description:
Library name: LID_112319_PID_10501
dog_id:17962670 precision cohort year 1. dog age at collection:10.2871321013005


title: LID_112365_PID_10501

description:
Library name: LID_112365_PID_10501
dog_id:17707094 precision cohort year 1. dog age at collection:6.64388926914594


title: Resistant clinical isolate-VC006, bio rep 3

description: Library name: VC006-3


title: LID_112382_PID_10501

description:
Library name: LID_112382_PID_10501
dog_id:18703775 precision cohort year 1. dog age at collection:3.18794204882501


title: Sensitive clinical isolate-WF001, bio rep 2

description: Library name: WF001-2


title: Resistant clinical isolate-VC006, bio rep 2

description: Library name: VC006-2


title: Resistant clinical isolate-VC006, bio rep 1

description: Library name: VC006-1


title: LID_112349_PID_10501

description:
Library name: LID_112349_PID_10501
dog_id:17730260 precision cohort year 1. dog age at collection:2.89881359799224


title: LID_112506_PID_10502

description:
Library name: LID_112506_PID_10502
dog_id:14496121 precision cohort year 1. dog age at collection:14.5667351129363


title: LID_112327_PID_10501

description:
Library name: LID_112327_PID_10501
dog_id:17886881 precision cohort year 1. dog age at collection:4.60084417065937


title: LID_112467_PID_10502

description:
Library name: LID_112467_PID_10502
dog_id:14074693 precision cohort year 1. dog age at collection:5.2353981291353


title: Resistant clinical isolate-VC005, bio rep 2

description: Library name: VC005-2


title: Resistant clinical isolate-VC005, bio rep 3

description: Library name: VC005-3


title: Resistant clinical isolate-VC010, bio rep 2

description: Library name: VC010-2


title: LID_112357_PID_10501

description:
Library name: LID_112357_PID_10501
dog_id:17719811 precision cohort year 1. dog age at collection:3.39345197353411


title: Resistant clinical isolate-VC004, bio rep 2

description: Library name: VC004-2


title: Resistant clinical isolate-VC010, bio rep 3

description: Library name: VC010-3


title: Resistant clinical isolate-VC005, bio rep 1

description: Library name: VC005-1


title: Resistant clinical isolate-VC004, bio rep 3

description: Library name: VC004-3


title: Resistant clinical isolate-VC004, bio rep 1

description: Library name: VC004-1


title: LID_112569_PID_10502

description:
Library name: LID_112569_PID_10502
dog_id:19112856 precision cohort year 1. dog age at collection:9.852270134611


title: LID_112488_PID_10502

description:
Library name: LID_112488_PID_10502
dog_id:14211766 precision cohort year 1. dog age at collection:8.92143889269146


title: Sensitive clinical isolate-VC003, bio rep 2

description: Library name: VC003-2


title: Sensitive clinical isolate-VC003, bio rep 3

description: Library name: VC003-3


title: Sensitive clinical isolate-VC001, bio rep 3

description: Library name: VC001-3


title: Sensitive clinical isolate-VC001, bio rep 2

description: Library name: VC001-2


title: LID_112559_PID_10502

description:
Library name: LID_112559_PID_10502
dog_id:19003091 precision cohort year 1. dog age at collection:7.65973648186174


title: LID_112541_PID_10502

description:
Library name: LID_112541_PID_10502
dog_id:16395610 precision cohort year 1. dog age at collection:3.39356605065024


title: LID_112513_PID_10502

description:
Library name: LID_112513_PID_10502
dog_id:14530819 precision cohort year 1. dog age at collection:4.247376226329


title: LID_112538_PID_10502

description:
Library name: LID_112538_PID_10502
dog_id:16457713 precision cohort year 1. dog age at collection:4.39550536162446


title: Sensitive clinical isolate-VC001, bio rep 1

description: Library name: VC001-1


title: LID_112469_PID_10502

description:
Library name: LID_112469_PID_10502
dog_id:13950556 precision cohort year 1. dog age at collection:11.2207962582706


title: Resistant clinical isolate-TV1062, bio rep 2

description: Library name: TV1062-2


title: Resistant clinical isolate-TV1062, bio rep 1

description: Library name: TV1062-1


title: LID_112518_PID_10502

description:
Library name: LID_112518_PID_10502
dog_id:15525343 precision cohort year 1. dog age at collection:3.24842193322686


title: LID_112499_PID_10502

description:
Library name: LID_112499_PID_10502
dog_id:14490886 precision cohort year 1. dog age at collection:6.07112708190737


title: Sensitive clinical isolate-TV1054, bio rep 3

description: Library name: TV1054-3


title: Sensitive clinical isolate-VC003, bio rep 1

description: Library name: VC003-1


title: Resistant clinical isolate-TV1062, bio rep 3

description: Library name: TV1062-3


title: LID_112533_PID_10502

description:
Library name: LID_112533_PID_10502
dog_id:15452104 precision cohort year 1. dog age at collection:7.5684462696783


title: LID_112503_PID_10502

description:
Library name: LID_112503_PID_10502
dog_id:14618509 precision cohort year 1. dog age at collection:4.43925393566051


title: LID_112478_PID_10502

description:
Library name: LID_112478_PID_10502
dog_id:14384332 precision cohort year 1. dog age at collection:10.2107764849038


title: LID_112375_PID_10501

description:
Library name: LID_112375_PID_10501
dog_id:18702848 precision cohort year 1. dog age at collection:1.35346794433037


title: LID_112330_PID_10501

description:
Library name: LID_112330_PID_10501
dog_id:17901434 precision cohort year 1. dog age at collection:6.40246406570842


title: Sensitive clinical isolate-TV1054, bio rep 1

description: Library name: TV1054-1


title: LID_112324_PID_10501

description:
Library name: LID_112324_PID_10501
dog_id:17913038 precision cohort year 1. dog age at collection:2.27341432808579


title: Sensitive clinical isolate-TV1054, bio rep 2

description: Library name: TV1054-2


title: LID_112598_PID_10502

description:
Library name: LID_112598_PID_10502
dog_id:19249062 precision cohort year 1. dog age at collection:6.63492470910335


title: Sensitive clinical isolate-TV1038, bio rep 3

description: Library name: TV1038-3


title: LID_112534_PID_10502

description:
Library name: LID_112534_PID_10502
dog_id:15443131 precision cohort year 1. dog age at collection:8.0618012776637


title: LID_112401_PID_10501

description:
Library name: LID_112401_PID_10501
dog_id:18777260 precision cohort year 1. dog age at collection:1.29343486196669


title: Sensitive clinical isolate-TV1038, bio rep 1

description: Library name: TV1038-1


title: LID_112325_PID_10501

description:
Library name: LID_112325_PID_10501
dog_id:17962766 precision cohort year 1. dog age at collection:11.4511749942961


title: LID_112560_PID_10502

description:
Library name: LID_112560_PID_10502
dog_id:18995408 precision cohort year 1. dog age at collection:4.1626739676021


title: Resistant clinical isolate-TV009, bio rep 2

description: Library name: TV009-2


title: LID_112511_PID_10502

description:
Library name: LID_112511_PID_10502
dog_id:14496214 precision cohort year 1. dog age at collection:2.81867442391056


title: LID_112583_PID_10502

description:
Library name: LID_112583_PID_10502
dog_id:19071288 precision cohort year 1. dog age at collection:6.09542550764317


title: Resistant clinical isolate-TV009, bio rep 1

description: Library name: TV009-1


title: LID_112516_PID_10502

description:
Library name: LID_112516_PID_10502
dog_id:15524170 precision cohort year 1. dog age at collection:5.41672370522473


title: Resistant clinical isolate-LUP009, bio rep 1

description: Library name: LUP009-1


title: Sensitive clinical isolate-LUP008, bio rep 3

description: Library name: LUP008-3


title: LID_112582_PID_10502

description:
Library name: LID_112582_PID_10502
dog_id:19078011 precision cohort year 1. dog age at collection:3.2646874287018


title: Resistant clinical isolate-LUP009, bio rep 2

description: Library name: LUP009-2


title: LID_112542_PID_10502

description:
Library name: LID_112542_PID_10502
dog_id:16502569 precision cohort year 1. dog age at collection:5.91264544832307


title: Sensitive clinical isolate-LUP008, bio rep 1

description: Library name: LUP008-1


title: Sensitive clinical isolate-LUP007, bio rep 3

description: Library name: LUP007-3


title: LID_112468_PID_10502

description:
Library name: LID_112468_PID_10502
dog_id:13993669 precision cohort year 1. dog age at collection:2.71991216062058


title: Resistant clinical isolate-TV009, bio rep 3

description: Library name: TV009-3


title: Sensitive clinical isolate-LUP008, bio rep 2

description: Library name: LUP008-2


title: Sensitive clinical isolate-LUP007, bio rep 2

description: Library name: LUP007-2


title: Sensitive clinical isolate-LUP007, bio rep 1

description: Library name: LUP007-1


title: LID_112580_PID_10502

description:
Library name: LID_112580_PID_10502
dog_id:19071381 precision cohort year 1. dog age at collection:5.43041295916039


title: LID_112515_PID_10502

description:
Library name: LID_112515_PID_10502
dog_id:15529813 precision cohort year 1. dog age at collection:5.49874515172256


title: LID_112487_PID_10502

description:
Library name: LID_112487_PID_10502
dog_id:14179258 precision cohort year 1. dog age at collection:2.42719028062971


title: Resistant clinical isolate-LUP009, bio rep 3

description: Library name: LUP009-3


title: LID_112509_PID_10502

description:
Library name: LID_112509_PID_10502
dog_id:14569921 precision cohort year 1. dog age at collection:9.1731690622861


title: LID_112328_PID_10501

description:
Library name: LID_112328_PID_10501
dog_id:17943947 precision cohort year 1. dog age at collection:3.1196668948209


title: Sensitive clinical isolate-LUP006, bio rep 1

description: Library name: LUP006-1


title: LID_112385_PID_10501

description:
Library name: LID_112385_PID_10501
dog_id:18687608 precision cohort year 1. dog age at collection:5.523309757396


title: LID_112352_PID_10501

description:
Library name: LID_112352_PID_10501
dog_id:17731715 precision cohort year 1. dog age at collection:3.31154460415241


title: LID_112546_PID_10502

description:
Library name: LID_112546_PID_10502
dog_id:19048082 precision cohort year 1. dog age at collection:4.00159707962583


title: Sensitive clinical isolate-LUP006, bio rep 3

description: Library name: LUP006-3


title: LID_112333_PID_10501

description:
Library name: LID_112333_PID_10501
dog_id:17882270 precision cohort year 1. dog age at collection:5.2688797627196


title: Sensitive clinical isolate-LUP006, bio rep 2

description: Library name: LUP006-2


title: Sensitive clinical isolate-LUP005, bio rep 2

description: Library name: LUP005-2


title: Sensitive clinical isolate-LUP004, bio rep 2

description: Library name: LUP004-2


title: Sensitive clinical isolate-LUP005, bio rep 1

description: Library name: LUP005-1


title: LID_112581_PID_10502

description:
Library name: LID_112581_PID_10502
dog_id:19082232 precision cohort year 1. dog age at collection:3.10021674652065


title: Sensitive clinical isolate-LUP004, bio rep 3

description: Library name: LUP004-3


title: LID_112540_PID_10502

description:
Library name: LID_112540_PID_10502
dog_id:16514947 precision cohort year 1. dog age at collection:2.75245265799681


title: LID_112397_PID_10501

description:
Library name: LID_112397_PID_10501
dog_id:18883634 precision cohort year 1. dog age at collection:2.31211498973306


title: LID_112388_PID_10501

description:
Library name: LID_112388_PID_10501
dog_id:18656021 precision cohort year 1. dog age at collection:2.17513689253936


title: LID_112517_PID_10502

description:
Library name: LID_112517_PID_10502
dog_id:15554548 precision cohort year 1. dog age at collection:5.25273785078713


title: LID_112360_PID_10501

description:
Library name: LID_112360_PID_10501
dog_id:17643632 precision cohort year 1. dog age at collection:7.1305042208533


title: Sensitive clinical isolate-LUP005, bio rep 3

description: Library name: LUP005-3


title: LID_112573_PID_10502

description:
Library name: LID_112573_PID_10502
dog_id:19130508 precision cohort year 1. dog age at collection:10.4406608867594


title: Sensitive clinical isolate-LUP003, bio rep 1

description: Library name: LUP003-1


title: Sensitive clinical isolate-LUP003, bio rep 3

description: Library name: LUP003-3


title: LID_112486_PID_10502

description:
Library name: LID_112486_PID_10502
dog_id:14381299 precision cohort year 1. dog age at collection:4.20938854665754


title: Sensitive clinical isolate-LUP002, bio rep 3

description: Library name: LUP002-3


title: LID_1066407_PID_10500

description:
Library name: LID_1066407_PID_10500
dog_id:18618983 precision cohort year 1. dog age at collection:3.33898015058179


title: Sensitive clinical isolate-LUP004, bio rep 1

description: Library name: LUP004-1


title: LID_1066405_PID_10500

description:
Library name: LID_1066405_PID_10500
dog_id:18527510 precision cohort year 1. dog age at collection:2.26865160848734


title: Sensitive clinical isolate-LUP002, bio rep 2

description: Library name: LUP002-2


title: Sensitive clinical isolate-LUP002, bio rep 1

description: Library name: LUP002-1


title: Sensitive clinical isolate-LUP003, bio rep 2

description: Library name: LUP003-2


title: Sensitive clinical isolate-LUP001, bio rep 3

description: Library name: LUP001-3


title: LID_1066399_PID_10500

description:
Library name: LID_1066399_PID_10500
dog_id:18602315 precision cohort year 1. dog age at collection:1.33709787816564


title: LID_1066403_PID_10500

description:
Library name: LID_1066403_PID_10500
dog_id:18539450 precision cohort year 1. dog age at collection:3.32221081451061


title: LID_1066391_PID_10500

description:
Library name: LID_1066391_PID_10500
dog_id:18458003 precision cohort year 1. dog age at collection:3.13569472963723


title: Sensitive clinical isolate-LUP001, bio rep 2

description: Library name: LUP001-2


title: Sensitive clinical isolate-LUP001, bio rep 1

description: Library name: LUP001-1


title: Sensitive clinical isolate-ECU001, bio rep 2

description: Library name: ECU001-2


title: Sensitive clinical isolate-ECU001, bio rep 1

description: Library name: ECU001-1


title: LID_1066385_PID_10500

description:
Library name: LID_1066385_PID_10500
dog_id:18488006 precision cohort year 1. dog age at collection:6.8899441022131


title: LID_1066388_PID_10500

description:
Library name: LID_1066388_PID_10500
dog_id:18468596 precision cohort year 1. dog age at collection:2.13655030800821


title: Resistant CDC isolate-6505, bio rep 3

description: Library name: CDC6505-3

value: CDC isolate


title: LID_1066386_PID_10500

description:
Library name: LID_1066386_PID_10500
dog_id:18508343 precision cohort year 1. dog age at collection:4.69966347250741


title: Sensitive clinical isolate-ECU001, bio rep 3

description: Library name: ECU001-3


title: LID_1066383_PID_10499

description:
Library name: LID_1066383_PID_10499
dog_id:18508145 precision cohort year 1. dog age at collection:4.2344094607955


title: LID_1066384_PID_10499

description:
Library name: LID_1066384_PID_10499
dog_id:18508241 precision cohort year 1. dog age at collection:2.23283139402236


title: Resistant CDC isolate-6505, bio rep 1

description: Library name: CDC6505-1


title: Resistant CDC isolate-6505, bio rep 2

description: Library name: CDC6505-2


title: Resistant CDC isolate-5601, bio rep 2

description: Library name: CDC5601-2


title: LID_1066380_PID_10499

description:
Library name: LID_1066380_PID_10499
dog_id:18449753 precision cohort year 1. dog age at collection:1.04959502623774


title: Resistant CDC isolate-5601, bio rep 3

description: Library name: CDC5601-3


title: LID_1066379_PID_10499

description:
Library name: LID_1066379_PID_10499
dog_id:18498320 precision cohort year 1. dog age at collection:5.40014449768043


title: LID_1066381_PID_10499

description:
Library name: LID_1066381_PID_10499
dog_id:18503276 precision cohort year 1. dog age at collection:10.399441022131


title: Resistant CDC isolate-1650, bio rep 3

description: Library name: CDC1650-3


title: Resistant CDC isolate-5601, bio rep 1

description: Library name: CDC5601-1


title: LID_1066378_PID_10499

description:
Library name: LID_1066378_PID_10499
dog_id:18316244 precision cohort year 1. dog age at collection:2.46269678302533


title: LID_1066390_PID_10500

description:
Library name: LID_1066390_PID_10500
dog_id:18461120 precision cohort year 1. dog age at collection:6.30105521332421


title: LID_1066372_PID_10499

description:
Library name: LID_1066372_PID_10499
dog_id:18322091 precision cohort year 1. dog age at collection:5.77549623545517


title: LID_1066373_PID_10499

description:
Library name: LID_1066373_PID_10499
dog_id:18322154 precision cohort year 1. dog age at collection:2.36116814966918


title: Resistant CDC isolate-1650, bio rep 2

description: Library name: CDC1650-2


title: Resistant CDC isolate-1650, bio rep 1

description: Library name: CDC1650-1


title: Resistant CDC isolate-1631, bio rep 3

description: Library name: CDC1631-3


title: LID_1066369_PID_10499

description:
Library name: LID_1066369_PID_10499
dog_id:18343646 precision cohort year 1. dog age at collection:2.09822039698836


title: LID_1066371_PID_10499

description:
Library name: LID_1066371_PID_10499
dog_id:18380630 precision cohort year 1. dog age at collection:4.37063655030801


title: Resistant CDC isolate-1631, bio rep 2

description: Library name: CDC1631-2


title: LID_1066368_PID_10499

description:
Library name: LID_1066368_PID_10499
dog_id:18371069 precision cohort year 1. dog age at collection:9.28296828656172


title: Resistant CDC isolate-1631, bio rep 1

description: Library name: CDC1631-1


title: LID_1066367_PID_10499

description:
Library name: LID_1066367_PID_10499
dog_id:18362078 precision cohort year 1. dog age at collection:4.20117499429614


title: Resistant CDC isolate-1629, bio rep 1

description: Library name: CDC1629-1


title: Resistant CDC isolate-1629, bio rep 2

description: Library name: CDC1629-2


title: LID_1066364_PID_10499

description:
Library name: LID_1066364_PID_10499
dog_id:18444488 precision cohort year 1. dog age at collection:2.38061829796943


title: Resistant CDC isolate-1629, bio rep 3

description: Library name: CDC1629-3


title: Resistant CDC isolate-1582, bio rep 3

description: Library name: CDC1582-3


title: LID_1066366_PID_10499

description:
Library name: LID_1066366_PID_10499
dog_id:18367568 precision cohort year 1. dog age at collection:4.36824093086927


title: LID_1066362_PID_10499

description:
Library name: LID_1066362_PID_10499
dog_id:18396275 precision cohort year 1. dog age at collection:8.28629553578219


title: Resistant CDC isolate-1582, bio rep 2

description: Library name: CDC1582-2


title: LID_1066360_PID_10499

description:
Library name: LID_1066360_PID_10499
dog_id:18376688 precision cohort year 1. dog age at collection:3.6176895581413


title: Resistant CDC isolate-1550, bio rep 3

description: Library name: CDC1550-3


title: Resistant CDC isolate-1582, bio rep 1

description: Library name: CDC1582-1


title: LID_1066358_PID_10499

description:
Library name: LID_1066358_PID_10499
dog_id:14734216 precision cohort year 1. dog age at collection:10.3918548939083


title: Resistant CDC isolate-1550, bio rep 2

description: Library name: CDC1550-2


title: LID_1066363_PID_10499

description:
Library name: LID_1066363_PID_10499
dog_id:18340928 precision cohort year 1. dog age at collection:12.1130732375086


title: LID_1066352_PID_10499

description:
Library name: LID_1066352_PID_10499
dog_id:15021227 precision cohort year 1. dog age at collection:6.95248688113165


title: Resistant CDC isolate-0685, bio rep 3

description: Library name: CDC0685-3


title: Resistant CDC isolate-0685, bio rep 2

description: Library name: CDC0685-2


title: LID_1066355_PID_10499

description:
Library name: LID_1066355_PID_10499
dog_id:14808215 precision cohort year 1. dog age at collection:3.82366529774127


title: Sensitive CDC isolate-520, bio rep 3

description: Library name: CDC520-3


title: Resistant CDC isolate-1550, bio rep 1

description: Library name: CDC1550-1


title: Resistant CDC isolate-0685, bio rep 1

description: Library name: CDC0685-1


title: LID_1066348_PID_10498

description:
Library name: LID_1066348_PID_10498
dog_id:14992124 precision cohort year 1. dog age at collection:10.2851737774736


title: LID_1066357_PID_10499

description:
Library name: LID_1066357_PID_10499
dog_id:14743846 precision cohort year 1. dog age at collection:3.80692448094912


title: LID_1066345_PID_10498

description:
Library name: LID_1066345_PID_10498
dog_id:14746114 precision cohort year 1. dog age at collection:8.80044109818237


title: LID_1066347_PID_10498

description:
Library name: LID_1066347_PID_10498
dog_id:14770297 precision cohort year 1. dog age at collection:5.95377024868811


title: Sensitive CDC isolate-520, bio rep 1

description: Library name: CDC520-1


title: LID_1066351_PID_10499

description:
Library name: LID_1066351_PID_10499
dog_id:14921573 precision cohort year 1. dog age at collection:9.34852840520192


title: LID_1066343_PID_10498

description:
Library name: LID_1066343_PID_10498
dog_id:14906750 precision cohort year 1. dog age at collection:6.0160848733744


title: LID_1066349_PID_10500

description:
Library name: LID_1066349_PID_10500
dog_id:14733400 precision cohort year 1. dog age at collection:8.83915126625599


title: LID_1066344_PID_10498

description:
Library name: LID_1066344_PID_10498
dog_id:14830730 precision cohort year 1. dog age at collection:6.97969427332877


title: LID_1066341_PID_10498

description:
Library name: LID_1066341_PID_10498
dog_id:14990015 precision cohort year 1. dog age at collection:2.19986310746064


title: LID_1066340_PID_10498

description:
Library name: LID_1066340_PID_10498
dog_id:15254227 precision cohort year 1. dog age at collection:7.75456308464522


title: LID_1066339_PID_10498

description:
Library name: LID_1066339_PID_10498
dog_id:15297196 precision cohort year 1. dog age at collection:8.26389839531523


title: LID_1066342_PID_10498

description:
Library name: LID_1066342_PID_10498
dog_id:14763676 precision cohort year 1. dog age at collection:9.39259639516313


title: Sensitive CDC isolate-520, bio rep 2

description: Library name: CDC520-2


title: HPV6_GLHC_C

city: Boston

first: Elizabeth

middle: A

last: White

state: MA

address: 150 Harrison Ave, Jaharis 909

department: Developmental, Molecular, and Chemical Biology

institute: Tufts University School of Medicine

description: Library name: Sample 15

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house (Novogene) perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts[3] v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0).
Assembly: hg38
Supplementary files format and content: gene expression quantification table, calculated all genes' FPKM

molecule: polyA RNA

organism: Homo sapiens

source_name: Primary human forekin keratinocytes

growth_protocol: Primary human keratinocytes stably harboring retroviral expression vectors were grown to 30% confluence in keratinocyte serum-free medium with 0.5 ug/ml puromycin

extract_protocol:
RNA was isolated with Qiagen RNeasy mini kit in White Laboratory and polyA RNA was isolated using oligo dT beads at Novogene Corporation
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation

value: Primary human forekin keratinocytes

value: Tranduced with HPV6 E7 expressing retrovirus (MSCV-P 6E7 ∆GLHC-Untagged)


title: HPV6_GLHC_B

description: Library name: Sample 14


title: Ketogenic amino acids mixture 96h late phase C

type: RNA

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

country: Germany

institute: Saarland University

description: AA lateC8

hyb_protocol: Agilent hybridisation kit

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing: Feature extraction and statistical analysis were performed using the limma R package (moderated t-test, p adj < 0.05, Benjamini–Hochberg correction, ≥1-fold change)

organism: Yarrowia lipolytica

source_name: cell biomass

label_protocol: Agilent labeling kit (one color)

growth_protocol: baffled 500 mL shake flask, 50 mL yeast nitrogen base (YNB) minimal medium with different nutrient concentrations (20 g L-1 glycerol, 5 g L-1 ammonium sulfate, MES buffer pH = 6.8), 28°C, 230 rpm, initial OD600 = 0.1

extract_protocol: mRNA extracted from harvested cell pellets using RiboPure Yeast RNA extraction kit

treatment_protocol: Cells (2 mL) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

value: The Hyb6 strain at 96 h in the late stationary phase after 15 mM ketogenic amino acids mixture addition

tag: strain

tag: growth phase

value: late stationary phase


title: Ketogenic amino acids mixture 48h early phase C

description: AA earlyC7

value: The Hyb6 strain at 48 h in the early stationary phase after 15 mM ketogenic amino acids mixture addition

value: early stationary phase


title: LID_1066336_PID_10498

description:
Library name: LID_1066336_PID_10498
dog_id:15175222 precision cohort year 1. dog age at collection:5.06930184804928


title: HPV6E7_wt_C

description: Library name: Sample 12

value: Tranduced with HPV6 E7 expressing retrovirus (MSCV-P 6E7-Untagged)


title: mdsc12_high BMI

city: Bangkok

first: Rangsima

last: Reantragoon

address: 1873 Rama 4 Road

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

hyb_protocol: Approximately 10 mg of the amplified products were subjected to gene expression analysis using the nCounter Myeloid Innate Immunity Gene Expression Panel (NanoString Technologies). The amplified products were hybridized with a reporter and capture probes for 770 genes at 65℃ for 18 hours before loading and immobilizing on the cartridge in a Prep Station of the nCounter MAX/FLEX Analysis System. Gene transcripts were read using a Digital Analyzer.

data_processing:
Raw data from the digital analyzer were evaluated for the quality and normalized to internal positive and negative controls and geometric mean of 38 housekeeping genes. Expression values of genes were calculated as log2 fold-change from the mean of internal negative control and were considered as upregulated and downregulated when the log2 fold-change expression value was greater than 0.5 and lower than -0.5, respectively.
nSolver software computed normalize signal intensity

source_name: Infrapatellar fat pad

extract_protocol: Total RNA extracted from MDSC using the RNeasy Mini Kit (QIAGEN) was converted to cDNA and amplified with multiplex primers that were specific myeloid innate immunity-related genes using nCounter Low RNA Input Kit according to the manufacturer's instruction (NanoString Technologies).

tag: tissue source

value: Infrapatellar fat pad

value: MDSC

tag: bmi

value: High BMI (> 35 kg/m2)


title: mdsc10_high BMI


title: HPV6_GLHC_A

description: Library name: Sample 13


title: Reference 96h late phase A

description: Ref lateA3

value: The Hyb6 strain at 96 h in the late stationary phase under nonsupplemented condition


title: Reference 96h late phase B

description: Ref lateB3


title: HPV6E7_wt_B

description: Library name: Sample 11


title: mdsc11_high BMI


title: HPV6E7_wt_A

description: Library name: Sample 10


title: Ketogenic amino acids mixture 48h early phase A

description: AA earlyA7


title: mdsc8_moderate BMI

value: Moderate BMI (25-35 kg/m2)


title: mdsc9_high BMI


title: Reference 48h early phase A

description: Ref earlyA2

value: The Hyb6 strain at 48 h in the early stationary phase under nonsupplemented condition


title: Reference 48h early phase C

description: Ref earlyC2


title: Lysine 48h early phase C

description: Lys earlyC5

value: The Hyb6 strain at 48 h in the early stationary phase after 15 mM lysine addition


title: Reference 10h exp phase B

description: Ref expB1

value: The Hyb6 strain at 10 h in the exponential phase under nonsupplemented condition

value: exponential growth


title: S. agalactiae (COH1) in KSFM only Bio Rep 3

city: Aurora

first: Kelly

middle: S.

last: Doran

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
Library name: COH1_KSFM_3
Column name in processed data file: COH1_KSFM_3
COH1KSFMUniqueReads.txt

data_processing:
BCL convert v4.2.4 for demultiplexing, quality control, and adapter trimming
CLC Genomics Workbench (Qiagen; v21.0.5)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Reads were aligned to GBS rRNA, A. muciniphila rRNA, and human rRNA for rRNA removal and unmapped reads used for RNA-seq
Unmapped sequence reads were then mapped to NZ_HG939456.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NZ_HG939456.1 with sRNAs (S. agalactiae)
Supplementary files format and content: COH1KSFMUniqueReads.txt is a tab-delimited text file of counts for S. agalactiae genes for each sample containing S. agalactiae only.
Supplementary files format and content: COH1hVECUniqueReads.txt is a tab-delimited text file of counts for S. agalactiae genes for each sample containing S. agalactiae on hVECs.
Supplementary files format and content: COH1AMhVECUniqueReads.txt is a tab-delimited text file of counts for S. agalactiae genes for each sample containing S. agalactiae and A. muciniphila on hVECs.

organism: Streptococcus agalactiae

source_name: Bacterial

growth_protocol: Human vaginal epithelial (VK2/E6E7; ATCC Cat# CRL-2616) cell line were maintained in keratinocyte serum-free medium (KSFM; Gibco) supplemented with 0.5 ng/ml human recombinant epidermal growth factor and 0.05 mg/ml bovine pituitary extract at 37°C in 5% CO2.

extract_protocol:
Total RNA was prepared using a RNeasy kit (Qiagen) and DNA was removed using a Turbo DNA-free™ kit (Invitrogen). RNA concentrations were ≥50ng/µl in 25 µl.
Libraries were prepared with the Illumina Stranded Total RNA Prep ligation with Ribo-Zero Plus rRNA depletion kit.

treatment_protocol: GBS was grown in biological triplicate overnight and subcultured (1:10) in fresh media to mid-logarithmic phase and standardized to an OD600 of 0.4 (CFU~1x10^9). A. muciniphila was grown in biological triplicate overnight and standardized to an OD600 of 0.4 (CFU ~4x10^8). hVECs monolayers were infected at a multiplicity of infection (MOI) of ~100 in a 12-well plate and incubated for 4 hours at 37°C in 5% CO2. Co-infection was performed at a 1:1 ratio (Total bacterial MOI = 200).  Appropriate controls were run alongside.

value: Bacterial

value: WT

value: S. agalactiae grown in KSFM media


title: HPV16_DLYC_C

description: Library name: Sample 9

value: Primary human forekin keratinocytes

value: Tranduced with HPV16 E7 expressing retrovirus (MSCV-P 16E7 ∆DLYC-Untagged)


title: S. agalactiae (COH1) in KSFM only Bio Rep 2

description:
Library name: COH1_KSFM_2
Column name in processed data file: COH1_KSFM_2
COH1KSFMUniqueReads.txt


title: S. agalactiae (COH1) in KSFM only Bio Rep 1

description:
Library name: COH1_KSFM_1
Column name in processed data file: COH1_KSFM_1
COH1KSFMUniqueReads.txt


title: Reference 10h exp phase A

description: Ref expA1


title: Ketogenic amino acids mixture 96h late phase A

description: AA lateA8

value: The Hyb6 strain at 96 h in the late stationary phase after 15 mM ketogenic amino acids mixture addition

value: late stationary phase


title: Reference 10h exp phase C

description: Ref expC1


title: mdsc6_moderate BMI


title: Ketogenic amino acids mixture 96h late phase B

description: AA lateB8


title: mdsc7_moderate BMI


title: Reference 96h late phase C

description: Ref lateC3


title: HPV16_DLYC_A

description: Library name: Sample 7


title: Retina, Epac1 KO, OIR, P17

city: Galveston

first: Wenbo

state: TX

address: 301 University Blvd.

department: Ophthalmology

institute: University of Texas Medical Branch

description: Library name: Epac1_OIR

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were de-multiplexed and converted to FASTQ files using the bcl2fastq conversion software (Illumina). The Cell Ranger software suite (10x Genomics) was utilized for subsequent data processing.
Sequencing reads were aligned to the GRCm38 mouse reference genome using the STAR aligner (integrated within Cell Ranger). High-quality cells were identified based on the distribution of Unique Molecular Identifier (UMI) counts and gene expression signatures, with empty droplets and low-quality cells filtered out using default Cell Ranger parameters.
Transcript abundance was measured by counting the number of UMIs associated with each gene in each cell. The pipeline generated filtered feature-barcode gene expression matrices in HDF5 (.h5) format for each sample.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Filtered feature-barcode count matrices in HDF5 (.h5) format

source_name: retina

extract_protocol:
Retinas from WT and Epac1−/− mice under both OIR and RA conditions were dissected in cold PBS, followed by enzymatic digestion with papain solution (LK003150, Worthington Biochemical Corporation, Lakewood, NJ) for 20 min at 37 °C. The resulting single-cell suspension was filtered through a 40 µm cell strainer to remove undigested tissue and centrifuged at 300 g for 5 min to obtain cell pellets. These pellets were resuspended in PBS containing 0.5 % BSA and filtered again using tip strainers (H13680-0040, ThermoFisher Scientific, Waltham, MA). Approximately 10,000 cells per group were loaded onto the chip.
Single-cell libraries were constructed using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits (v3.1) according to the manufacturer’s instructions.

treatment_protocol: For the Oxygen-Induced Retinopathy (OIR) model, pups were exposed to 70% oxygen in a specialized chamber from postnatal day 7 (P7) to P12, then returned to room air until postnatal day 17 (P17).

value: retina

value: Epac1 knockout

value: Oxygen-Induced Retinopathy

tag: age

tag: Sex

value: mixed


title: HPV16_DLYC_B

description: Library name: Sample 8


title: Retina, WT, OIR, P17

description: Library name: WT_OIR

value: Wild Type


title: mdsc5_moderate BMI

value: Infrapatellar fat pad

value: MDSC

value: Moderate BMI (25-35 kg/m2)


title: Lysine 10h exp phase A

description: Lys expA4

value: The Hyb6 strain at 10 h in the exponential phase before 15 mM lysine addition


title: Reference 48h early phase B

description: Ref earlyB2

value: The Hyb6 strain at 48 h in the early stationary phase under nonsupplemented condition

value: early stationary phase


title: Retina, Epac1 KO, Room Air, P17

description: Library name: Epac1_RA

value: Room Air


title: Ketogenic amino acids mixture 48h early phase B

description: AA earlyB7

value: The Hyb6 strain at 48 h in the early stationary phase after 15 mM ketogenic amino acids mixture addition


title: HPV16E7_wt_C

description: Library name: Sample 6

value: Primary human forekin keratinocytes

value: Tranduced with HPV16 E7 expressing retrovirus (MSCV-P 16E7-Untagged)


title: T cells, melanoma, knocked out with the 57-gene panel [HTO]

city: Cambridge

first: Jiaqi

address: 75 Ames St

institute: MIT; Broad Institute

description:
Library name: Screen 2, HTO
10x Genomics

data_processing:
Screens 1 and 2 were processed and normalized separately using the same pipeline. Readouts from the in vivo CRISPR screens were processed with Cell Ranger to generate raw count matrices. After merging all sequencing lanes within each screen, we obtained 71,393 cells for Screen 1 and 75,227 cells for Screen 2. Quality control was performed to remove low-quality cells that either (i) received no perturbation or multiple perturbations, or (ii) have elevated mitochondrial read fractions, indicative of stressed or dying cells. To reduce technical noise, relatively stringent thresholds were applied. For Screen 1, cells were removed if they met any of the following criteria: fewer than 5 sgRNA UMIs; a ratio of the second-most abundant sgRNA to the most abundant sgRNA greater than 40%; a ratio of the most abundant sgRNA less than 60%; or a number of detected features (as called by Cell Ranger 63) not equal to one. Cells with more than 5% mitochondrial counts were removed. After filtering, 31,009 cells remained. For Screen 2, additional antibody hashtagging was performed on individual mice prior to pooling. The same thresholds as in Screen 1 were applied for perturbation assignment, and cells with zero or more than one antibody hashtag were additionally removed. Cells with more than 10% mitochondrial counts were initially filtered; however, this threshold resulted in a distinct Leiden cluster with high mitochondrial content, which was subsequently removed. After quality control, 25,738 cells remained.
Assembly: Mouse mm10
Supplementary files format and content: Filtered count matrix
Supplementary files format and content: AnnData file containing merged lanes after data processing

source_name: CD8+ T cells

extract_protocol:
Naïve CD8 T cells were isolated from spleens of H11-Cas9 × OT-I mice (6–16 weeks old, male and female) using magnetic bead–based enrichment for naïve CD8 T cells. Purified naïve CD8 T cells were transduced with pooled lentivirus on retronectin-coated plates in complete T cell medium supplemented with IL-7 and IL-15 at 10 ng/mL. Viral input was titrated on T cells to achieve 20–40% Thy1.1 positivity, consistent with predominantly single-perturbation transduction in pooled screens. Cells were maintained in IL-7/IL-15–supplemented medium for 5 days post-transduction without TCR activation. On day 5 post-transduction, Thy1.1+ cells were enriched by magnetic selection to generate a transduced donor population. Enriched Thy1.1+ OT-I Cas9+ CD8+ T cells were adoptively transferred into congenic recipient mice by tail vein injection (5 × 105 cells per mouse). Congenic markers varied by experiment; donor and recipient combinations (CD45.1/CD45.2) together with Thy1.1 expression were used to enable identification of transferred T cells by flow cytometry. T cells were transferred one day prior to tumor implantation. Recipient mice were implanted subcutaneously with B16-OVA melanoma cells (5 × 105 cells per injection) in 200 µL PBS into bilateral flanks. Tumor growth and general health were monitored in accordance with animal welfare guidelines. Tumors were excised, minced, and dissociated using Miltenyi tumor dissociation kits to recover tumor-infiltrating lymphocytes. Dissociated material was filtered to remove debris, and lymphocytes were enriched by density gradient separation with LympholyteM (Cedarlane). CD8 T cells were subsequently purified from tumor infiltrates using Miltenyi magnetic bead–based CD8 enrichment. Only tumor-derived T cells were used for downstream single-cell profiling.
To enable multiplexing of samples from individual mice in the second validation screen (Screen 2), purified tumor-infiltrating T cells from each mouse were stained with BioLegend mouse TotalSeq-C hashtag antibodies according to the manufacturer’s protocol, including stringent washing steps to minimize ambient oligonucleotide background. Hashtag-labeled samples were pooled and processed using the 10x Genomics Chromium 5′ single-cell gene expression workflow with Feature Barcode chemistry for cell-surface antibody–derived tags and direct CRISPR guide capture. Libraries were prepared following the manufacturer’s instructions to generate: (i) 5′ gene expression libraries, (ii) feature barcode libraries for hashtags and cell-surface proteins when appropriate, and (iii) guide capture libraries reporting sgRNA identity. Final libraries were sequenced on an Illumina NextSeq platform using 10x Genomics–recommended read configurations and target sequencing depths for 5′ gene expression, feature barcode, and direct guide capture libraries.

value: CD8+ T cells


title: mdsc4_low BMI

value: Low BMI (<25 kg/m2)


title: Retina, WT, Room Air, P17

description: Library name: WT_RA

value: retina


title: SC5314 wor3△/△bcr1△/△, bio rep3

city: Athens

first: Katharina

last: Goerlich

state: GA

address: 120E Green St

department: Microbiology

institute: University of Georgia

description: Library name: KG90_3

data_processing:
Original data file from high-throughput sequencing platform (Illumina) is transformed to sequenced reads by CASAVA base recognition.
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Removed reads with adapter contamination. Removed reads when uncertain nucleotides constitute more than 10% of either read. Removed reads when low quality nucleotides constitute more than 50% of the read.
Assembly: HISAT2 was used to align reads to provided reference genome (assembly 22)
Supplementary files format and content: FPKM values for each sample based on condition

organism: Candida albicans

source_name: Yeast and hyphae

growth_protocol: C. albicans cells were grown in RPMI for 4hrs at 37C shaking.

extract_protocol:
RNA extraction was performed by disrupting cells with Zirconia beads and isolating RNA using 25:24:1 phenol:chloroform:isoamylalcohol in combination with a Qiagen Rneasy Mini Kit
Sequencing libraries were generated by purifying messenger RNA from total RNA using poly-T oligo–attached magnetic beads. The first cDNA was synthesized using random hexamer primers, followed by sequencing of both ends of cDNA fragments using the Illumina platform

value: Yeast and hyphae

value: RPMI, 4hrs


title: mdsc3_low BMI


title: T cells, melanoma, knocked out with the 57-gene panel [GEX]

description:
Library name: Screen 2, GEX
10x Genomics


title: HPV16E7_wt_B

description: Library name: Sample 5


title: SC5314 wor3△/△bcr1△/△, bio rep2

description: Library name: KG90_2


title: HPV16E7_wt_A

description: Library name: Sample 4


title: mdsc2_low BMI


title: SC5314 wor3△/△bcr1△/△, bio rep1

description: Library name: KG90_1


title: GFP_A

description: Library name: Sample 1

value: Tranduced with control retrovirus (MSCV-P GFP-Un)


title: GFP_B

description: Library name: Sample 2


title: CRC5_T

city: Beijing

first: Qiangfeng

middle: Cliff

address: No. 1 Qinghuayuan Street

country: China

institute: Tsinghua University

description: Library name: CRC5_T

data_processing:
Step 1 (RNA Alignment): CellRanger (v.7.1.0) was used to process fastq files, align reads to the reference genome, and generate gene-by-cell matrices.
Step 2 (Cell-ID Processing): Combinatorial index reads were deduplicated using seqkit (v. 2.5.1) , extracted using umi_tools (v1.1.4) , and adapter-trimmed using cutadapt (v.4.4).
Step 3 (Data Filtering): Single-cell RNA data was filtered using scanpy (v.1.9.1) to retain cells with >200 genes and <20% mitochondrial reads, and genes detected in >=3 cells.
Step 4 (Interaction Assignment): Cell-IDs were filtered based on valid droplet abundance, and cells assigned to clumps with <=20 cells were retained for downstream cell-cell interaction analysis.
Assembly: (Kidney, Intestine): mm10; (CRC): hg38
Supplementary files format and content: Text files (.txt) containing the processed combinatorial indices (Cell-IDs) assigned to each cell barcode, which are used to reconstruct cell clumps and infer cell-cell interactions.

source_name: colorectum

extract_protocol:
Kidneys were minced and digested with dissociation solution (Dispase II, Collagenase IV, DNase I, CaCl2) at 37 °C for 20 minutes. The tissue was filtered through a 70 μm cell strainer, and red blood cells were lysed to collect cell clumps. Intestines were cut into fragments and incubated in 10 mM EDTA-PBS on ice. Fragments were shaken to release crypt fractions, which were then strained through a 70-μm filter to isolate cell clumps. Tumor and normal tissues were minced and filtered through a 70 μm cell strainer. Following red blood cell lysis, cell clumps were collected for subsequent experiments.
Cell clumps were labeled with an 'anchor' cholesterol-modified oligonucleotide (CMO) to tag plasma membranes. Clumps then underwent three rounds of split-pool barcode ligation to generate a unique combinatorial index per clump. After labeling, clumps were dissociated into single cells using TrypLE Express Enzyme. Single cells were processed using the 10x Genomics 3' V3.1 Kit. Both mRNA libraries and Cell-ID libraries were prepared according to the 10x Genomics protocol

value: tumor

tag: disease state

value: colorectal cancer (CRC)


title: GFP_C

description: Library name: Sample 3


title: SC5314 wor3△/△, bio rep3

description: Library name: MC501_3


title: CRC5_N

description: Library name: CRC5_N

value: adjacent normal


title: RFP_TT-seq_rep1

city: Amsterdam

first: Elzo

last: de Wit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: RFP_rep1

data_processing:
*library strategy: TT-seq
Reads were mapped to the mm10 genome using the STAR aligner (v2.7.9) and filtered for paired and uniquely mapped reads using samtools (v1.19.2).
Reads were assigned to 129 or CAST allele by mapping to assembled 129 and CAST genomes and assigning each reads to the allele with a better alignment score (AS bam tag).
Active transcription units were called by fitting a two-state HMM model using the R/Bioconductor package GenoSTAN and read counts in transcription units were generated using the “summarizeOverlaps” function from the R/Bioconductor package GenomicAlignments.
Assembly: mm10
Supplementary files format and content: bigwig files contain normalized coverage tracks for allele-resolved and ambiguous reads.

source_name: Embryo

growth_protocol: Mouse embryonic stem cell lines were cultured as described previously (Liu et al., 2021, 2025; van Schaik et al., 2022). Briefly, the 129/Castaneus F1 hybrid methylation reporter cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10-4 M, Sigma-Aldrich). The cell lines were passaged every 2  days in daily culture.

extract_protocol:
TTchem-seq on sorted methylation reporter populations was performed following an established protocol (Gregersen et al., 2020). Briefly, cells were labelled for 10 min using 2 mM 4SU, total RNA was isolated and fragmented and streptavidin coated MicroBeads were used to enrich the 4SU‐biotin labeled RNA
KAPA RNA HyperPrep kit (Roche) with dual indexing adapters was used to prepare the libraries which were sequenced on a NextSeq 550.

value: Embryo

tag: cell line

value: 129/CAST F1 hybrid SCR methylation reporter mESC

value: Embryonic stem cells

tag: sample group

value: RFP


title: SC5314 wor3△/△, bio rep1

description: Library name: MC501_1


title: HUCCT1_IgG

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Library name: AK253_3

data_processing:
trimmed with ktrim version 1.6.0 Parameters: -s 26 -t 6
Reads were mapped with bowtie2 version 2.5.4 Parameters:  --very-sensitive -X 1000
Peak Calling was performed with genrich version 0.6.1
Assembly: GRCh38.p14
Supplementary files format and content: The narrowPeak files in bed-format were created with genrich peak calling software

extract_protocol:
Chromatin preparation and DNA prurification were performed with the SimpleChIP® Enzymatic Chromatin IP Kit (Magnetic Beads, Cell Signaling #9003)
ChIP-Seq Library Protocol from BGI

value: CCA cell line

tag: chip antibody

value: IgG


title: T cells, melanoma, knocked out with the 57-gene panel

description:
Library name: Screen 2
10x Genomics


title: RFP_TT-seq_rep2

description: Library name: RFP_rep2

tag: tissue


title: mdsc1_low BMI

value: Infrapatellar fat pad

value: MDSC


title: CRC4_N

description: Library name: CRC4_N


title: HUCCT1_TAF4

description: Library name: AK253_2


title: SC5314 wor2△/△bcr1△/△, bio rep3

description: Library name: KG439_3


title: CRC4_T

description: Library name: CRC4_T


title: SC5314 wor2△/△bcr1△/△, bio rep2

description: Library name: KG439_2


title: GFP_TT-seq_rep1

description: Library name: GFP_rep1

value: GFP


title: HUCCT1_SBNO1

description: Library name: AK253_1


title: GFP_TT-seq_rep2

description: Library name: GFP_rep2


title: T cells, melanoma, knocked out with the 73-gene panel

description:
Library name: Screen 1
10x Genomics

value: CD8+ T cells


title: DP_TT-seq_rep2

description: Library name: DP_rep2

value: DP


title: SC5314 wor2△/△bcr1△/△, bio rep1

description: Library name: KG439_1

value: Yeast and hyphae


title: CRC3_T

description: Library name: CRC3_T


title: Dimemorfan_3

city: Kodaira

first: Lili

last: Quan

state: Tokyo

address: 4-1-1 Ogawa-Higashi

department: National Institute of Neuroscience

country: Japan

institute: National Center of Neurology and Psychiatry

description:
Library name: Dimemorfan_3
Dimemorfan_raw_count.tsv

data_processing:
The generated reads were mapped to the rat reference genome (Rn6) or human reference genome (hg19) using TopHat (version 2.1.1) after adapter trimming by Trimmomatic.
Assembly: Rn6, hg19
Supplementary files format and content: Etching_raw_count.tsv
Supplementary files format and content: Dimemorfan_raw_count.tsv

source_name: iPSC

extract_protocol:
Total RNA was isolated from rat primary oligodendrocytes or iPSC-derived oligodendrocytes using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Full-length cDNA was synthesized from total RNA using a SMART-Seq stranded (TaKaRa) according to manufacturer instructions. An Illumina library was prepared using a Nextera XT DNA Library Prep Kit (Illumina) according to SMART-seq kit instructions. Sequencing was performed using an Illumina NovaSeq 6000 sequencer (Illumina) in the 101-base single end mode for rat samples and DNBSEQ-G400 sequencer (MGI) in a single-end mode (150 bp) for human samples.

value: iPSC

value: oligodendrocytes


title: CRC2_N

description: Library name: CRC2_N


title: Dimemorfan_2

description:
Library name: Dimemorfan_2
Dimemorfan_raw_count.tsv


title: SC5314 wor2△/△, bio rep3

description: Library name: KG233_3

value: RPMI, 4hrs


title: DP_TT-seq_rep1

description: Library name: DP_rep1


title: WaplCtcf_6H_4C-seq_rep2

description:
Library name: WaplCtcf_6H_rep2
raw_fragment_counts_depletions.rds

data_processing:
Restriction fragment maps for the DpnII and Csp6I digestion were created using the R/Bioconductor package Biostrings.
Viewpoints were demultiplexed by scanning raw reads for viewpoint-specific primer sequences.
For the allele-resolved 4C, the reads were further split into alleles based on the sequenced bases at the SNP positions located downstream from the reverse primers.
Reads were aligned to the mm10 genome using bwa-aln (v0.7.17-r1188) and filtered for paired and uniquely mapped reads using samtools (v1.19.2).
Fragment counts were generated by counting the reads with exact matches of start or end positions to fragment boundaries. The fragment counts were scaled to the total library counts per million and smoothed using a rolling mean with a window size of 21 fragments.
Assembly: mm10
Supplementary files format and content: rds files contain raw fragment counts as a RangedSummarizedExperiment object
Library strategy: 4C-Seq

growth_protocol: Mouse embryonic stem cell lines were cultured as described previously (Liu et al., 2021, 2025; van Schaik et al., 2022). Briefly, the degron-tagged cell lines and the 129/Castaneus F1 hybrid methylation reporter cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10-4 M, Sigma-Aldrich). The cell lines were passaged every 2  days in daily culture.

extract_protocol:
10 million cells were collected per sample. Cells were crosslinked, lysed, and chromatin was digested with the primary restriction enzyme DpnII. After ligation, crosslinks were reversed and DNA was purified according to established 4C-seq protocols (van de Werken et al., 2012; Haarhuis et al., 2017).
Purified 4C DNA was digested with the secondary restriction enzyme Csp6I and religated to generate small circular DNA fragments. These fragments were amplified by PCR using viewpoint-specific primers. Libraries were indexed using a two-step PCR method to enable multiplexed sequencing. For allele-resolved 4C-seq, a reverse primer specific to a single nucleotide variant was used. Final PCR products were purified and quantified prior to sequencing.

value: WAPL-AID/CTCF-AID mESC

value: auxin 6h


title: CRC2_T

description: Library name: CRC2_T1

value: tumor

value: colorectal cancer (CRC)


title: WaplCtcf_6H_4C-seq_rep1

description:
Library name: WaplCtcf_6H_rep1
raw_fragment_counts_depletions.rds

value: Embryo

value: Embryonic stem cells


title: CRC2_T2

description: Library name: CRC2_T2


title: Dimemorfan_1

description:
Library name: Dimemorfan_1
Dimemorfan_raw_count.tsv


title: CRC1_T

description: Library name: CRC1_T


title: SC5314 wor2△/△, bio rep1

description: Library name: KG233_1


title: SC5314 bcr1△/△, bio rep3

description: Library name: ED39_3


title: Control_3

description:
Library name: Control_3
Dimemorfan_raw_count.tsv


title: Control_2

description:
Library name: Control_2
Dimemorfan_raw_count.tsv


title: WaplCtcf_3H_4C-seq_rep1

description:
Library name: WaplCtcf_3H_rep1
raw_fragment_counts_depletions.rds

value: auxin 3h


title: WaplCtcf_3H_4C-seq_rep2

description:
Library name: WaplCtcf_3H_rep2
raw_fragment_counts_depletions.rds


title: SC5314 bcr1△/△, bio rep2

description: Library name: ED39_2


title: WaplCtcf_0H_4C-seq_rep2

description:
Library name: WaplCtcf_0H_rep2
raw_fragment_counts_depletions.rds

value: untreated


title: Control_1

description:
Library name: Control_1
Dimemorfan_raw_count.tsv


title: SC5314 wor2△/△, bio rep2

description: Library name: KG233_2


title: SC5314 bcr1△/△, bio rep1

description: Library name: ED39_1


title: WaplCtcf_0H_4C-seq_rep1

description:
Library name: WaplCtcf_0H_rep1
raw_fragment_counts_depletions.rds


title: S. agalactiae (COH1) + A. muciniphila hVECs in KSFM Bio Rep 3

description:
Library name: VK2_COH1_AM_3
Column name in processed data file: VK2_COH1_AM_3
COH1AMhVECUniqueReads.txt

organism:
Streptococcus agalactiae
Homo sapiens
Akkermansia muciniphila

value: Bacterial

value: Vaginal epithelial cells

value: WT

value: Human vaginal epithelial cells infected with S. agalactiae and A. muciniphila


title: Huh-7 cells, CENPF, biol rep 1

first: Saiping

last: Qi

address: 95 Yong-an Road, Xi-Cheng District

institute: Beijing Friendship Hospital, Capital Medical University

description: Library name: Sample_11

data_processing:
The image data of the sequenced fragments measured by high-throughput sequencers are converted into sequence data (reads) by CASAVA base recognition, and the files are in fastq format, which mainly contain the sequence information of the sequenced fragments as well as their corresponding sequencing quality information.
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: 1)  Trim Smart-seq2 public primer sequence from the Reads (If the length of trimmed Reads is lower than 30bp, reads should be discarded. If it is PE sequence, both of the reads must be removed ); 2)  Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads); 3)  Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% . If either one of the PE Reads defined as low quality, we will remove both ends of the reads);4)  Remove the reads whose N base more than 5% for total bases (If either one of the PE Reads had high Ns bases, we will remove both ends of the reads).
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
Assembly: GRCh38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Huh-7 cells

growth_protocol: HCCLM3 and Huh-7 cells were maintained in DMEM supplemented with 10% fetal bovineserum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using an Ultrapure RNA Kit (CW0581; CWBIO, China) following the manufacturer’s instructions.The Nanodrop2000 microspectrophotometer detects sample purity and concentration.The Labchip GX touch microfluidic capillary system detects the integrity of RNA samples.
(1) Total RNA samples were tested and then enriched for eukaryotic mRNA by Oligo(dT) magnetic beads; (2) Add Fragmentation Buffer for mRNA fragmentation; (3) One strand of cDNA was synthesised using a six-base random primer using mRNA as a template, followed by the synthesis of the second strand of cDNA using buffer, dNTPs, DNA polymerase I and RNase H, and cDNA purification; (4) Purified double-stranded cDNA was subjected to end repair, base A was added, sequencing junctions were added, and fragments were screened to recover cDNA around 350 bp; (5) PCR enrichment was performed to obtain cDNA libraries. (6) Using Qubit 3.0 to initially quantify concentrations, the Agilent 2100 system initially assessed library fragment size. After meeting expectations,the effective concentration of the library was accurately quantified using the Bio-RAD CFX 96 Fluorescent Quantitative PCR Instrument.

value: Huh-7 cells

value: hepatocellular carcinoma cells

value: CENPF overexpression


title: Huh-7 cells, Control, biol rep 2

description: Library name: Sample_10


title: SC5314 WT, bio rep3

description: Library name: MC22_3

value: Yeast and hyphae


title: Wapl_6H_4C-seq_rep2

description:
Library name: Wapl_6H_rep2
raw_fragment_counts_depletions.rds

value: WAPL-AID mESC


title: Huh-7 cells, Control, biol rep 1

description: Library name: Sample_9


title: S. agalactiae (COH1) + A. muciniphila hVECs in KSFM Bio Rep 2

description:
Library name: VK2_COH1_AM_2
Column name in processed data file: VK2_COH1_AM_2
COH1AMhVECUniqueReads.txt


title: S. agalactiae (COH1) + A. muciniphila hVECs in KSFM Bio Rep 1

description:
Library name: VK2_COH1_AM_1
Column name in processed data file: VK2_COH1_AM_1
COH1AMhVECUniqueReads.txt


title: SC5314 WT, bio rep2

description: Library name: MC22_2

value: RPMI, 4hrs


title: Huh-7 cells, CENPF, biol rep 2

description: Library name: Sample_12


title: SC5314 WT, bio rep1

description: Library name: MC22_1


title: Huh-7 cells, shCENPF, biol rep 2

description: Library name: Sample_8

value: CENPF knockdown


title: S. agalactiae (COH1)  + hVECs in KSFM Bio Rep 3

description:
Library name: VK2_COH1_3
Column name in processed data file: VK2_COH1_3
COH1hVECUniqueReads.txt

organism:
Streptococcus agalactiae
Homo sapiens

value: Human vaginal epithelial cells infected with S. agalactiae


title: Wapl_6H_4C-seq_rep1

description:
Library name: Wapl_6H_rep1
raw_fragment_counts_depletions.rds

value: auxin 6h


title: Huh-7 cells, shCENPF, biol rep 1

description: Library name: Sample_7


title: SC5314 wor3△△bcr1△△, bio rep 3

description: Library name: wor3bcr1_3

data_processing:
Original data file from high-throughput sequencing platform (Illumina) is transformed to sequenced reads by CASAVA base recognition.
Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Removed reads with adapter contamination. Removed reads when uncertain nucleotides constitute more than 10% of either read. Removed reads when low quality nucleotides constitute more than 50% of the read.
Assembly: HISAT2 was used to align reads to provided reference genome
Supplementary files format and content: xls files include FPKM values for each sample based on condition

growth_protocol: C. albicans cells were grown in RPMI+10% Serum for 4hrs at 37C shaking.

value: RPMI+10% FBS, 4hrs


title: Wapl_3H_4C-seq_rep2

description:
Library name: Wapl_3H_rep2
raw_fragment_counts_depletions.rds

value: Embryo

value: Embryonic stem cells


title: Huh-7 cells, shNC, biol rep 2

description: Library name: Sample_6


title: SC5314 wor3△△bcr1△△, bio rep 2

description: Library name: wor3bcr1_2


title: SC5314 wor3△/△, bio rep2

description: Library name: MC501_2


title: Wapl_3H_4C-seq_rep1

description:
Library name: Wapl_3H_rep1
raw_fragment_counts_depletions.rds

value: auxin 3h


title: S. agalactiae (COH1)  + hVECs in KSFM Bio Rep 2

description:
Library name: VK2_COH1_2
Column name in processed data file: VK2_COH1_2
COH1hVECUniqueReads.txt

value: Bacterial


title: S. agalactiae (COH1)  + hVECs in KSFM Bio Rep 1

description:
Library name: VK2_COH1_1
Column name in processed data file: VK2_COH1_1
COH1hVECUniqueReads.txt

value: Vaginal epithelial cells


title: Wapl_0H_4C-seq_rep2

description:
Library name: Wapl_0H_rep2
raw_fragment_counts_depletions.rds

value: untreated


title: HCCLM3 cells, CENPF, biol rep 2

description: Library name: Sample_4

source_name: HCCLM3 cells

value: HCCLM3 cells


title: Huh-7 cells, shNC, biol rep 1

description: Library name: Sample_5

value: Huh-7 cells

value: WT


title: Wapl_0H_4C-seq_rep1

description:
Library name: Wapl_0H_rep1
raw_fragment_counts_depletions.rds


title: SC5314 wor3△△bcr1△△, bio rep 1

description: Library name: wor3bcr1_1


title: SC5314 bcr1△△, bio rep 3

description: Library name: bcr1_3


title: SC5314 bcr1△△, bio rep 1

description: Library name: bcr1_1


title: SC5314 bcr1△△, bio rep 2

description: Library name: bcr1_2


title: RFP_SCR_only_4C-seq_rep1

description:
Library name: RFP_SCR_only_rep1
raw_fragment_counts_methyl_undepleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter mESC


title: LNCaP_Control

city: Davie

first: Appu

last: Rathinavelu

state: FL

department: Rumbaugh Goodwin Institute for Cancer Research

institute: Barry and Judy Silverman College of Pharmacy, Nova Southeastern University

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturer's (Qiagen) instructions using their web-based Gene Globe software package
For the normalization, we used the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1, and RPLP0.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)
The normalization and all the data analysis were performed according to the manufacturer's (Qiagen) instructions using their web-based Gene Globe software package

label: SYBR Green

source_name: Human prostate adenocarcinoma cell line - ATCC - CRL-1740

label_protocol: PCR assays were performed using the PAHS-012Z RT² Profiler PCR Array Human Apoptosis (Qiagen, SABiosciences, Valencia, CA, USA)—following the manufacturer’s instructions. Reverse transcription (cDNA) was synthesized from 1000 ng of total RNA using the RT2 First Strand Kit (Qiagen, SABiosciences, Valencia, CA, USA). Quantitative reverse transcriptase PCR (qRT-PCR) was conducted using the ABI StepOnePlus Real-time PCR Instrument (Applied Biosystems, Foster City, CA, USA) with 40 cycles at 94°C for 15 seconds and 60°C for 60 seconds.

growth_protocol: LNCaP prostate cancer cells were cultured in RPMI-1640 complete medium supplemented with 10% FBS, 10,000 U/mL penicillin, 10,000 µg/mL streptomycin, 1% (+)-l-glutamine, and 1% amphotericin B (Atlanta Biologicals, Lawrenceville, GA, USA). The cells were grown at 37 °C under a humidified air/CO2 (19:1) atmosphere. All experiments were conducted using cells in the logarithmic phase of growth. The LNCaP cells were incubated with C-PC (500 µg/mL). All incubations were carried out for 24 h.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit according to the manufacturer’s instructions (Qiagen, Valencia, CA, USA)

treatment_protocol: LNCaP cells were treated with C-PC (500 µg/mL) for 24 hours.

value: Epithelial cells

tag: agent


title: HCCLM3 cells, Control, biol rep 2

description: Library name: Sample_2

value: hepatocellular carcinoma cells

tag: genotype


title: LNCaP_test

description: Test

tag: cell type

value: C-PC (500 µg/mL)


title: NSC, Sham, 5 day, biol 3

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: Library name: Sample_5_Sham_3

data_processing:
Reads were mapped using STAR v.2.7.10a
Assembly: Rnor_6.0
Supplementary files format and content: excel file with Log2 normalized read counts

organism: Rattus norvegicus

source_name: Adult hippocampal NSC

growth_protocol: cells were grown in NSC expansion media composed of 50:50 Dulbecco’s Modified Eagle Medium (DMEM)/F12 supplemented with 2% B-27, 20ng/mL FGF, and 1% antimycotic/antibiotic. For differentiation of mature neurons, NSC were seeded on laminin-coated 8-well chamber slides or 6-well plates for 24-hours in NSC expansion media to allow for attachment, then switched to neuronal differentiation media containing 50:50 DMEM/F12, 2% B-27 supplement, 1% antimycotic/antibiotic, 1μM retinoic acid, and 5μM Forskolin for five days, changing media every other day

extract_protocol:
RNA was isolated from triplicate sham- and NPLT-treated NSC 24-hours after treatment, or from mature neurons after a 5-day differentiation using the Direct-Zol RNA miniprep kit (Zymo research)
library preparation was using NEBNext Ultra II RNA library for illumina sequencing kit (Catalog# E7775) combined with NEBNext polyA mRNA magnetic module (Catalog# E7490)

treatment_protocol: NSC were dissociated using Accutase (Millipore-Sigma) for accurate counting, and 600,000 NSC were added to a single well of a 96-well plate. To simulate optoacoustic ultrasound generation that occurs by thermoelastic expansion of tissue during NPLT treatment (44), a photoabsorbent black membrane was adhered to the base of the well using ultrasound gel. The purpose of the membrane is to completely absorb light energy and reflect only optoacoustic ultrasound waves back into the well. Cells were placed beneath the 3mm diameter laser probe with approximately 14mm from the tip of the probe to the bottom of the well, resulting in a laser spot of 0.11cm2 and treated for approximately five minutes with 808nm NPLT (20Hz, ~5mJ/pulse, 10ns pulse width) for a total dose of ~30J at a fluence of 300J/cm2 (Fig 1). Sham-treated NSC were plated in the same density for the same duration but not exposed to the NPLT device

value: Adult hippocampal NSC

tag: treatment

value: Sham

tag: time

value: 5 days


title: HCCLM3 cells, Control, biol rep 1

description: Library name: Sample_1


title: SC5314 wor3△△, bio rep 2

description: Library name: wor3_2

value: Yeast and hyphae

value: RPMI+10% FBS, 4hrs


title: RFP_SCR_only_4C-seq_rep2

description:
Library name: RFP_SCR_only_rep2
raw_fragment_counts_methyl_undepleted.rds

value: Embryo

value: Embryonic stem cells


title: NSC, Sham, 5 day, biol 1

description: Library name: Sample_5_Sham_1


title: RFP_dTAG_3h_4C-seq_rep3

description:
Library name: RFP_dTAG_3h_rep3
raw_fragment_counts_methyl_depleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter/RAD21-FKBP mESC

value: dTAG-13 3h


title: RFP_dTAG_3h_4C-seq_rep2

description:
Library name: RFP_dTAG_3h_rep2
raw_fragment_counts_methyl_depleted.rds


title: HCCLM3 cells, CENPF, biol rep 1

description: Library name: Sample_3

value: CENPF overexpression


title: SC5314 wor3△△, bio rep 3

description: Library name: wor3_3


title: NSC, NPLT, 5 day, biol 2

description: Library name: Sample_5_NPLT_2

value: NPLT


title: SC5314 wor3△△, bio rep 1

description: Library name: wor3_1


title: OGD_U_2

city: Hefei

first: Jianhua

last: Qin

state: Anhui

address: No.96 JinZhai Road Baohe District

department: School of Biomedical engineering

institute: University of Science and Technology of China

description: Library name: OGD_U_2

data_processing:
STAR software (version 2.5.3a) with default parameters
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: GRCh38_release110
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted from iBMECs and brain cells separately using TRizol reagent (Invitrogen) . cDNA synthesis was performed using PrimeScript RT Master Mix kit (TaKaRa; Cat #: RR036A) .
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: Brain

value: human induced pluripotent stem cells

value: iPSC-derived pericytes and astrocytes

value: OGD 24h


title: NSC, NPLT, 5 day, biol 3

description: Library name: Sample_5_NPLT_3

value: WT


title: RFP_prom_only

description:
Library name: RFP_prom_only
raw_fragment_counts_methyl_undepleted.rds

value: 129/CAST F1 hybrid SCR methylation reporter mESC


title: OGD_U_3

description: Library name: OGD_U_3


title: RFP_dTAG_3h_4C-seq_rep1

description:
Library name: RFP_dTAG_3h_rep1
raw_fragment_counts_methyl_depleted.rds


title: SC5314 WT, bio rep 3

description: Library name: WT_3


title: NSC, Sham, 5 day, biol 2

description: Library name: Sample_5_Sham_2

value: Adult hippocampal NSC


title: OGD_U_1

description: Library name: OGD_U_1


title: RFP_DMSO_3h_4C-seq_rep3

description:
Library name: RFP_DMSO_3h_rep3
raw_fragment_counts_methyl_depleted.rds

value: DMSO 3h


title: OGD_D_3

description: Library name: OGD_D_3

value: iPSC-derived brain microvascular endothelial cells


title: NSC, NPLT, 5 day, biol 1

description: Library name: Sample_5_NPLT_1

value: 5 days


title: RFP_DMSO_3h_4C-seq_rep2

description:
Library name: RFP_DMSO_3h_rep2
raw_fragment_counts_methyl_depleted.rds


title: SC5314 WT, bio rep 2

description: Library name: WT_2

value: Yeast and hyphae

value: RPMI+10% FBS, 4hrs


title: NSC, Sham, 24 hour, biol 3

description: Library name: Sample_24_Sham_3

value: Sham

value: 24 hour


title: RFP_DMSO_3h_4C-seq_rep1

description:
Library name: RFP_DMSO_3h_rep1
raw_fragment_counts_methyl_depleted.rds

value: Embryo

value: 129/CAST F1 hybrid SCR methylation reporter/RAD21-FKBP mESC

value: Embryonic stem cells


title: SC5314 WT, bio rep 1

description: Library name: WT_1


title: OGD_D_2

description: Library name: OGD_D_2

value: Brain


title: NSC, Sham, 24 hour, biol 2

description: Library name: Sample_24_Sham_2


title: RFP_both_VP

description:
Library name: RFP_both_VP
raw_fragment_counts_methyl_undepleted.rds


title: Heated seeds rep2

city: Fukuoka

first: Yushi

last: Ishibashi

address: 744 Motooka

institute: Kyushu university

data_processing:
All read data were checked with FastQC (v0.11.7) and trimmed by Trimmomatic (v-0.38)
Trimmed reads were mapped to the transcript in the reference Os-Nipponbare-Reference-IRGSP-1.0 using Bowtie2 aligner within RSEM [R]. The abundance estimation of genes and isoforms with RSEM generated basic counts data (expected counts).
The raw read counts of all samples were processed through edgeR package (v3.26.3) of Bioconductor, and normalized CPM counts were generated.
Ditection of differentially expressed genes (DEGs)  were carried out with edgeR program. Normalized counts per million (CPM) values, log fold-changes (logFC) and p-values were obtained from the normalized CPM values.
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: incubate at 30 degreeC

extract_protocol:
Total RNA was harvested using Phenol/Chloroform and LiCl.
The sequencing libraries were prepared from 1 ug of total RNA with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer's instructions. Cluster amplification and 150 bp paired-end sequencing was performed according to the manufacturer’s protocol (Illumina) for NovaSeq (Illumina).

value: leaf

tag: cultivar

value: Nipponbare


title: Ctr_U_2

description: Library name: Ctr_U_2

value: human induced pluripotent stem cells

value: iPSC-derived pericytes and astrocytes

value: Control


title: NSC, NPLT, 24 hour, biol 2

description: Library name: Sample_24_NPLT_2

value: Adult hippocampal NSC

value: WT

value: NPLT


title: Ctr_U_3

description: Library name: Ctr_U_3


title: NSC, Sham, 24 hour, biol 1

description: Library name: Sample_24_Sham_1


title: Rad21_6H_4C-seq_rep1

description:
Library name: Rad21_6H_rep1
raw_fragment_counts_depletions.rds

value: RAD21-AID mESC

value: auxin 6h


title: Rad21_6H_4C-seq_rep2

description:
Library name: Rad21_6H_rep2
raw_fragment_counts_depletions.rds


title: NSC, NPLT, 24 hour, biol 3

description: Library name: Sample_24_NPLT_3


title: NSC, NPLT, 24 hour, biol 1

description: Library name: Sample_24_NPLT_1


title: Control seeds rep2

source_name: incubate at 25 degreeC


title: Ctr_D_3

description: Library name: Ctr_D_3

value: iPSC-derived brain microvascular endothelial cells


title: Rad21_3H_4C-seq_rep2

description:
Library name: Rad21_3H_rep2
raw_fragment_counts_depletions.rds

value: auxin 3h


title: Heated seeds rep1


title: SL IP rep2

city: Dallas

first: Zheng

last: Xing

address: 5323 Harry Hines Blvd.

institute: UT Southwestern

description: Library name: Sample 8

data_processing:
Reference genome Saccharomyces cerevisiae (R64-1-1) and gene model annotation files were downloaded from ensembl. Index of the reference genome was built, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Saccharomyces cerevisiae (R64-1-1)
Supplementary files format and content: Read count normalized by ERCC spike-in in excel format

organism: Saccharomyces cerevisiae

source_name: yeast

extract_protocol:
Total RBA was extracted using acidic phenol extraction and polyA RNA was putified with oligo dT dynabeads.
Library was constructed by Novogene using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input as intructed by the manufacturer.

value: yeast

value: MATa CEN.PK

value: SL 1h


title: Control seeds rep1


title: Rad21_3H_4C-seq_rep1

description:
Library name: Rad21_3H_rep1
raw_fragment_counts_depletions.rds

value: Embryo

value: Embryonic stem cells


title: OGD_D_1

description: Library name: OGD_D_1

value: Brain

value: OGD 24h