title: 6110-KO-60

city: Jeollabuk-do

first: Hoang chan

last: Yu

state: Jeollabuk-do

address: 전북 덕진구 건지로 2, 전북대학교 의과대학 생화학교실 생명과학관 305호, jbnu

department: biochemistry

institute: jbnu

description: LysM-Cre; Sirt6 flox/flox, 60

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
reads were aligned to the reference genome sequence of Mus musculus (mm10) using HISAT2 v2.1.0 and StringTie v2.1.3b.
To facilitate log2 transformation, 1 was added to each FPKM value of filtered genes. Filtered data were log2 transformed and subjected to quantile normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BMMC

extract_protocol:
Bone marrow cells were obtained by flushing bone marrow from the femurs and tibias of mice. Cells were cultured in BMMC media and stored in RNA later solution. Total RNA was extracted using Trizol.
Total RNA (1 μg) was used for mRNA-Seq library preparation using the TruSeq RNA Sample Prep kit (Illumina, San Diego, Calif)

value: BMMC

value: Myeloid Sirt6 KO

value: LPS


title: 6110-KO-20

status: Public on Dec 20 2022

type: SRA

country: South Korea

description: LysM-Cre; Sirt6 flox/flox, 20

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype

tag: treatment


title: minE_Fe_starve__1

city: La Jolla

first: Cameron

last: Lamoureux

state: CA

address: 9500 Gilman Drive

department: Bioengineering

country: USA

institute: University of California San Diego

description:
minicoli_log_tpm.csv
minicoli_counts.csv

data_processing:
Raw read trimming was performed with Trim Galore using the default options, followed by FastQC on the trimmed reads.
Reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using bowtie with the following optional arguments: -X 1000, -3 3, -n 2
Read direction was inferred with RSEQC.
Read counts were generated with featureCounts with the following optional arguments: -p -B -C -P --fracOverlap 0.5
Quality control metrics were assembled with MultiQC and the final expression was reported in units of log2-transformed transcripts per million for each gene.
Assembly: NC_000913.3
Supplementary files format and content: minicoli_log_tpm.csv contains log2[TPM] values for all samples and genes.
Supplementary files format and content: minicoli_counts.csv contains raw read counts as computed by featureCounts for all samples and genes.

organism: Escherichia coli

source_name: bacterial cell

extract_protocol:
3 ml of cell broth (at an A600 ≈ 0.6) was immediately added to two volumes of Qiagen RNA-protect Bacteria Reagent (6 ml), vortexed for 5 s, incubated at room temperature for 5 min and immediately centrifuged for 10 min at 17,500 r.p.m. The supernatant was decanted, and the cell pellet was stored at −80 °C. Cell pellets were thawed and incubated with Ready-Lyse Lysozyme, SuperaseIn, protease K and 20% SDS for 20 min at 37 °C. Total RNA was isolated and purified using the Qiagen RNeasy Mini Kit columns and following vendor procedures. An on-column DNase treatment was performed for 30 min at room temperature. RNA was quantified using a Nano drop and quality assessed by running an RNA nano chip on a bioanalyser. The ribosomal RNA was removed using an Illumina Ribo-Zero rRNA removal kit for Gram-negative bacteria.
A KAPA Stranded RNA-Seq Kit (Kapa Biosystems KK8401) was used following the manufacturer’s protocol to create sequencing libraries with an average insert length of around 300 bp

tag: strain

value: bacterial cell

value: reduced strain - iron starvation

tag: Stage

value: mid-log phase culture


title: minE_glyc__2

value: reduced strain - glycerol


title: Omicron_104_1st

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: Blood samples were collected from the COVID-19 patients infected by Omicron varient.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

value: Female

tag: age

tag: group (by covid-19 vaccination, prior infection)

value: No vaccination, Prior infection

tag: omicron sublineage

tag: days after positive pcr results

value: day 0

tag: disease state

tag: geographical location

value: Austria

value: PBMC


title: Omicron_105_1st

value: No vaccination, No prior infection

value: day 3


title: Omicron_103_1st

value: day 2


title: SCN_ZT14_TRF_2_1

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description: Library name: A20SCN4

data_processing:
Basecalls were generated using CASAVA v1.8.
Data quality was assessed using FastQC v0.11.8.
Sequenced reads were aligned to the mm10 genome assembly using STAR v2.5.3a.
Reads were annotated to genes using Homer v4.10.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: raw.csv: Comma-separated text file includes the raw counts for each library (the sample resequencings are collapsed).

source_name: SCN

growth_protocol: 10-week-old C57BL/6J mice were purchased from the Jackson laboratory (#000664) and housed in 12 hr light:12 dark conditions for 2 weeks with normal chow diet.

extract_protocol:
RNA were extracted following the protocol from Allprep DNA/RNA Mini Kit (Qiagen) or using Trizol reagent, and RNA integrity number were measured through Agilent 2200 TapeStation system.
Libraries generated using Illumina TruSeq Stranded mRNA Sample Prep Kit, pooled and sequenced using an Illumina HiSeq 2500 or Novaseq 6000.

treatment_protocol: Mice were subjected to Ad-libitum feeding (ALF) or time-restricted feeding (TRF) of Western diet (45% fat, 17% sucrose, Research diets Inc. #12451) for 9 hr from ZT13-ZT22 for 7 weeks.

tag: tissue

value: suprachiasmatic nucleus

tag: feeding intervention

value: 9 hr time-restricted feeding

tag: time-point

value: wild type


title: minE_glyc__1


title: SCN_ZT14_TRF_1_2

description: Library name: A20SCN3


title: SCN_ZT14_ALF_2_2

description: Library name: A20SCN2

value: ad-libitum feeding


title: 6110-WT-20

description: Sirt6 flox/flox, 20

value: BMMC

value: WT

value: LPS


title: 6110-WT-0

description: Sirt6 flox/flox, 0


title: SCN_ZT14_TRF_1_1

description: Library name: A20SCN3


title: minE_glc__2

value: bacterial cell

value: reduced strain - glucose

value: mid-log phase culture


title: Omicron_100_1st

value: Male


title: Omicron_13_2nd

value: No vaccination, Prior infection


title: Omicron_101_1st

value: Female

value: Austria


title: SCN_ZT14_ALF_2_1

description: Library name: A20SCN2


title: Omicron_99_1st

value: No vaccination, No prior infection

value: PBMC


title: SCN_ZT14_TRF_2_2

description: Library name: A20SCN4


title: minE_fruc__2

value: reduced strain - fructose


title: minE_glc__1


title: 414-KO-20

description: LysM-Cre; Sirt6 flox/flox, 20

value: Myeloid Sirt6 KO


title: SCN_ZT14_ALF_1_2

description: Library name: A20SCN1

value: suprachiasmatic nucleus


title: Omicron_96_1st

value: day 0


title: 6110-KO-0

description: LysM-Cre; Sirt6 flox/flox, 0


title: 6110-WT-60

description: Sirt6 flox/flox, 60


title: 414-KO-0

description: LysM-Cre; Sirt6 flox/flox, 0


title: SCN_ZT14_ALF_1_1

description: Library name: A20SCN1

value: ad-libitum feeding

value: wild type


title: Omicron_94_1st

value: day 3


title: 414-WT-20

description: Sirt6 flox/flox, 20

value: BMMC

value: WT

value: LPS


title: minE_cyt__1

value: bacterial cell

value: reduced strain - cytidine

value: mid-log phase culture


title: SCN_ZT12_TRF_2_1

description: Library name: A19SCN4

value: 9 hr time-restricted feeding


title: Omicron_92_1st

value: Female

value: No vaccination, Prior infection

value: day 4

value: Austria


title: SCN_ZT12_TRF_1_2

description: Library name: A19SCN3


title: Omicron_90_1st

value: Male

value: Vaccination, No prior infection

value: day 1

value: PBMC


title: mg1655_glc__2

value: MG1655 glucose


title: SCN_ZT12_TRF_1_1

description: Library name: A19SCN3

value: suprachiasmatic nucleus

value: wild type


title: 414-WT-0

description: Sirt6 flox/flox, 0

value: BMMC

value: WT


title: 414-KO-60

description: LysM-Cre; Sirt6 flox/flox, 60

value: Myeloid Sirt6 KO

value: LPS


title: 4120-KO-60

description: LysM-Cre; Sirt6 flox/flox, 60


title: Omicron_89_1st

value: No vaccination, No prior infection


title: aldA_minE__1

value: bacterial cell

value: reduced strain - aldA complementation

value: mid-log phase culture


title: SCN_ZT12_ALF_2_2

description: Library name: A19SCN2

value: ad-libitum feeding


title: Omicron_88_1st

value: Female

value: Vaccination, Prior infection

value: day 3

value: Austria


title: 4120-KO-20

description: LysM-Cre; Sirt6 flox/flox, 20


title: minE_fruc__1

value: reduced strain - fructose


title: SCN_ZT12_ALF_2_1

description: Library name: A19SCN2


title: 4120-KO-0

description: LysM-Cre; Sirt6 flox/flox, 0


title: aldA_f1c2__1


title: aldA_AC_rna__5


title: Omicron_86_1st

value: day 4

value: PBMC


title: minE_cyt__2

value: reduced strain - cytidine


title: SCN_ZT12_ALF_1_2

description: Library name: A19SCN1

value: suprachiasmatic nucleus

value: wild type


title: SCN_ZT12_TRF_2_2

description: Library name: A19SCN4

value: 9 hr time-restricted feeding


title: 414-WT-60

description: Sirt6 flox/flox, 60

value: BMMC

value: WT

value: LPS


title: Omicron_85_1st

value: Male

value: No vaccination, No prior infection


title: 4120-WT-60

description: Sirt6 flox/flox, 60


title: Omicron_91_1st

value: day 0


title: SCN_ZT12_ALF_1_1

description: Library name: A19SCN1

value: ad-libitum feeding


title: mg1655_glc__1

value: bacterial cell

value: MG1655 glucose

value: mid-log phase culture


title: aldA_AC_rna__4

value: reduced strain - aldA complementation


title: aldA_AC_rna__3


title: 4120-WT-0

description: Sirt6 flox/flox, 0


title: iMPC_B3 rep3

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences were filtered out by tool Trimmomatic (version 0.38)
Reads were aligned to human reference hg38 by STAR aligner (version 2.7.5a)
Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.7.5a)
Genome_build: hg38
Supplementary_files_format_and_content: Gene count quantification by STAR aligner (option: --quantMode GeneCounts) (version 2.7.5a)

source_name: Human bone marrow

growth_protocol: MSCs were maintained in growth medium (h-DMEM  with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic .  Fibroblast growth factor 2 (1.5 ng/mL) ;iMPCs were maintained in growth medium (DMEM/F12  with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic .  Fibroblast growth factor 2 (1.5 ng/mL)

extract_protocol:
Human mesenchymal stromal cells (hMSCs) were isolated from the femoral heads ; iMPCs were differentiated from iPSCs
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both MSCs and iMPCs were culture with chondrogenic medium (CM: high-glucose DMEM supplemented with 1% antibiotic-antimycotic, 0.1 μM dexamethasone (Sigma-Aldrich), 40 μg/mL L-proline (Sigma-Aldrich), 10 μg/mL ITS+ (ThermoFisher, Waltham, MA), 50 μg/mL ascorbate 2-phosphate (Sigma-Aldrich), 10ng/mL transforming growth factor β3 (TGFβ3) for 21 days

tag: model

value: iMPCs-derived cartilage tissue-chondrogenic medium-3weeks


title: aldA_AC_rna__2


title: SCN_ZT10_TRF_1_2

description: Library name: A18SCN4


title: SCN_ZT10_TRF_1_1

description: Library name: A18SCN4


title: iMPCs

description: iMPCs

data_processing:
Data was processed by cellranger count function with default parameter setting (version 3.1.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered_feature_bc_matrix generated by cellranger (version 3.1.0)

source_name: iMPCs

extract_protocol:
Human mesenchymal stromal cells (hMSCs) were isolated from the femoral heads ; iMPCs were differentiated from iPSCs
10X single-cell RNA-Seq: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: iMPCs

value: MSCs-derived cartilage tissue-chondrogenic medium-3weeks


title: iMPC_B3 rep2


title: ChIP-seq_SCA7_KI_input DNA

city: Illkirch

first: Anna

last: Niewiadomska-Cimicka

address: 1 rue Laurent Fries

country: France

institute: IGBMC

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

molecule: genomic DNA

source_name: SCA7 retina

extract_protocol:
Batch of a chromatin was prepared from 6 retinas. Following cross-linking in 1 % paraformaldehyde (PFA), glycine was added to a final concentration of 0.46 M. Samples were washed in cold PBS/PIC and homogenized in lysis buffer. Chromatin was sonicated for 7 min using a Covaris ultrasonicator and centrifuged at 13 000 rpm for 5 min. Each 100 μl of chromatin sample was diluted 10 times and stored at -80°C until use. The supernatant was used for subsequent ChIP using antibodies against RNAPII (RPB1), H3K4me1, H3K9ac, H3K27ac, H3K36me3 (RPB1-7G5 in-house; ab8895, Abcam; ab4441, Abcam; ab4729 Abcam; ab9050 Abcam, respectively). Before immunoprecipitation the chromatin was precleared with Prot A or Prot G beads for 1 hour at 4 °C, and followed by o/n incubation with 3ug of the antibody at 4°C. Next Prot A or Prot G beads were added for a 3h incubation at 4°C. Subsequently the beads were washed and DNA-protein complexes were eluted from the beads, decrosslinked, and treated with proteinase K for 2 h at 43°C. DNA fragments were purified using phenol-chloroform, precipitated, and used for sequencing.
ChIP-seq libraries were prepared from 0.5-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5’ ends were ligated to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. In the final step, the 3’ ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 to 10 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents. The libraries were sequenced on Hiseq 4000 as single end 50 base reads following Illumina’s instructions.

value: retina

value: 12.5 weeks

tag: chip antibody


title: aldA_AC_rna__1

tag: cell type


title: SCN_ZT10_ALF_1_2

description: Library name: A18SCN2

value: suprachiasmatic nucleus

tag: genotype

value: wild type


title: iMPC_B3 rep1


title: ChIP-seq_WT_input DNA

source_name: WT retina

value: WT


title: MSC_B3 rep3


title: SCN_ZT10_ALF_1_1

description: Library name: A18SCN2


title: ChIP-seq_SCA7_KI_RNAPII_retina

value: RNAPII (in-house, RPB1-7G5)


title: MSC_B3 rep2


title: SCN_ZT8_TRF_2_2

description: Library name: A17SCN4

value: 9 hr time-restricted feeding


title: SCN_ZT8_TRF_2_1

description: Library name: A17SCN4


title: 4120-WT-20

description: Sirt6 flox/flox, 20

value: BMMC

tag: treatment

value: LPS


title: ChIP-seq_SCA7_KI_H3K4me1_retina

tag: strain

value: H3K4me1 (Abcam, ab8895)


title: ChIP-seq_SCA7_KI_H3K36me3_retina

value: H3K36me3 (Abcam, ab9050)


title: MSC_B3 rep1


title: SCN_ZT8_TRF_1_2

description: Library name: A17SCN3


title: ChIP-seq_SCA7_KI_H3K27ac_retina

value: H3K27ac (Abcam, ab4729)


title: ChIP-seq_SCA7_KI_H3K9ac_retina

value: H3K9ac (Abcam, ab4441)


title: SCN_ZT8_ALF_2_1

description: Library name: A17SCN2

value: ad-libitum feeding


title: ChIP-seq_WT_RNAPII_retina


title: Melanoma6474_21031_Visium (Melanoma samples from patients 6474 and  21031)

city: Brisbane

first: Quan

last: Nguyen

state: Queensland

address: 22 Burns Street, Indooroopilly

country: Australia

institute: Institute for Molecular Bioscience

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For scRNAseq: The BCL sequencing output file was converted to a FASTQ file using bcl2fastq/2.17. Read mapping was performed using CellRanger/3.0.2 against the Homo sapiens GRCh38p10 reference genome. After read mapping, cells were removed if they expressed <200 or >3000 genes, or if their read count consisted of >20% mitochondrial reads. The 51,147 cells in the sample P30 were randomly subsampled to 10,000 cells due to its much larger depth compared to other samples. The 13 mitochondrial and 101 ribosomal genes were removed. A total of 56,638 cells and 23,672 genes were retained after filtering. Data were processed and analysed using SCTransform from Seurat version 4.0 81. For comparison, batch correction was tested using Harmony with 3000 variable genes 82, LIGER with 3000 variable genes 95, and Seurat canonical correlation analysis (CCA) data integration with 5000 variable genes 81; CCA integration was found to be most suitable for our data (data not shown) and was thus used for downstream analysis. Data were re-scaled, regressed, and PCA transformed. UMAP plots were generated based on the first 20 PCs.For Visium, Reads were trimmed by cutadapt/1.8.3 to remove sequences from poly-A tails and template-switching-oligos. SpaceRanger V1.0 was used to map FASTQ reads to the human reference genome (version GRCh38-3.0.0). After read mapping, spots were removed if they expressed mitochondrial genes more than 20 percent. Thirteen mitochondrial and 103 ribosomal genes were removed from the samples that were originally fresh-frozen; these genes were not captured using the probe-based FFPE library preparation protocol. In total, we captured 14,990 transcriptional capture spots and 36,485 unique genes across all samples. Replicate samples from each of the three cancer types were integrated using Seurat CCI 81 with 3000] variable genes, and further processed using SCTransform 81. Uniform Manifold Approximation and Projection (UMAP) plots were generated based on the first 20 PCs of SCC and BCC, and the first 30 PCs for melanoma. Clustering was performed on each integrated cancer dataset separately, using resolutions of 0.5 for SCC, 0.3 for BCC and melanoma.
Assembly: GRCh38p10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
All samples were approved for research use under ethics approval numbers 2018000165 and 2017000318 by the University of Queensland’s Human Research Ethics Committees and 11QPAH477 by the Metro South Human Research Ethics Committee. All formalin-fixed, paraffin-embedded (FFPE) blocks were previously prepared following a standard fixation procedure in 10% formalin, processed in ethanol and xylene and embedded in paraffin wax. The four melanoma samples (patients 6747-085P, 21031-08TB, 48974-2B, 66487-1A) were collected during 2008-2018 and all blocks were stored at room temperature. Full patient IDs are abbreviated as 6747, 21031, 48974 and 66487 throughout this manuscript.For BCC and SCC samples from eight patients (B18, E15, F21, P30, P13, P04, R01, D12), all fresh-shaved biopsies were obtained in accordance with the approved ethics protocol (11QPAH477). The patients presented to the Princess Alexandra Hospital Dermatology Department between October 2018 and February 2020. Among these patients, three patients (B18, E15, F21) were diagnosed with both SCC and BCC and biopsies of both cancer types were collected. Five patients (B18, P30, P13, P04, R01) kindly consented to participate in the collection of 4 mm punch biopsy samples of non-sun exposed healthy skin for paired scRNA sequencing experiments. Lesion identity was confirmed by pathological inspection. Portions of each sample from these patients were also preserved with 10% formalin as described for FFPE samples above. To process fresh samples for scRNA sequencing, briefly, fresh-shaved biopsies were collected in DMEM for immediate tissue dissociation. Tissue was incubated in 10 mg/mL Dispase II (cat. No. 04942078001, Roche, Darmstadt, Germany) for 45 min at 37°C, snipped into small pieces with scissors, and incubated in 0.25% Trypsin for 2 min. The cells were disrupted gently with a pipette and filtered through 70 µm and 40 µm cell strainers, taken up in culture medium and spun down at 350 rcf. Resuspended cells were collected in PBS containing Foetal Calf Serum for single-cell sequencing.     For single cell RNA sequencing, the RNA extraction followed the 10x Genomics Chromium single-cell library preparation and sequencing. For the spatial transcriptomics, with fresh frozen samples, the RNA was drawn from the tissue sections to the glass slide by permeabilization and gavity. The polyA-tail mRNA were captured by poly-T. For formalin fixed paraffin embedded samples, the probes hybridized to the targeted RNAs inside the tissue, and successfully ligated probes were extracted and captured on the glass slide.
10x Genomics Chromium single-cell library preparation and sequencing was performed according to the manufacturer’s instructions, using the Single Cell 3' Library, Gel Bead and Multiplex Kit (version 2, PN-120233; 10x Genomics). Cell numbers were optimised to capture approximately 3,000 cells per reaction.For spatial transcriptomics, for fresh-frozen samples, tissue optimisation was performed as per the Visium Spatial Tissue Optimization User Guide (CG000238 Rev A, 10x Genomics), and a tissue permeabilisation time of 18-25 min was selected. For data generation, tissue was cryosectioned at 10 µm thickness and transferred to chilled Visium Spatial Gene Expression Slides (2000233, 10x Genomics, USA), and allowed to adhere by warming the back of the slide. Tissue sections were dried for 1 min at 37°C, fixed in chilled 100% methanol for 30 min, and stained with hematoxylin for 5 min and then eosin for 2 minutes, as per the Visium Spatial Gene Expression User Guide (CG000239 Rev A, 10x Genomics). Brightfield histology images were captured using a 10x objective on an Axio Z1 slide scanner (Zeiss). Brightfield images were exported as high-resolution tiff files using Zen software. This H&E staining and imaging protocol was used to stain all skin sections for histopathological annotation in this study. Libraries were sequenced on a NextSeq500 (Illumina) machine using a High Output 150 cycle kit (Illumina) at the University of Queensland Sequencing Facility, with the read structure as: Read1 - 28bp, Index1 - 10bp, Index2 - 10bp, Read2 - 120bp. The sequencing data was converted to FASTQ format as described above for scRNASeq data and the data was processed as described below. For FFPE samples, the FFPE blocks were sectioned at 5μm by rotary microtome and the sections were processed for spatial sequencing library prepration following the Visium Spatial Gene Expression for FFPE User Guide (CG000407, CG000408, CG000409 - 10x Genomics). The imaging and sequencing were similar to the protocol for the fresh-frozen samples as described above.
Single-cell transcriptome libraries were sequenced on an Illumina NextSeq500 machine, using a 150-cycle High Output reagent kit (NextSeq500/550 version 2, FC-404-2002; Illumina) with the following reads and indices: read 2 (98 bp), i7 index (8 bp), read 1 (cell barcodes and UMI; 26 bp).

value: multiple cell types

value: skin

value: Above 18 years old


title: BCCB18_Viisum (BCC sample from patient B18)

description: 10x Genomics


title: scRNAseq_Data (SCC and BCC and non-cancer Samples of scRNAseq data)

description: 10x Genomics


title: Melanoma66487_48974_Visium (Melanoma samples from patients 66487 and  48974)

description: 10x Genomics


title: E15SCC_B18SCC_Visium (SCC samples from patients E15, B18)

description: 10x Genomics


title: BCCE15_BCCF21_Visium (BCC samples from patients E15 and F21)

description: 10x Genomics


title: F21SCC_Visium (SCC samples from patients F21)

description: 10x Genomics


title: SCN_ZT8_ALF_1_1

description: Library name: A17SCN1


title: SCN_ZT8_TRF_1_1

description: Library name: A17SCN3


title: ChIP-seq_WT_H3K36me3_retina

value: retina


title: ChIP-seq_WT_H3K4me1_retina

value: 12.5 weeks


title: larvae, cold dissociated, rep 3

city: Berlin

first: Anika

last: Neuschulz

address: Hannoversche Strasse 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
Demultiplexing (bcl2fastq v2.19), CELseq barcodes demultiplexed using custom code (https://github.com/anikaneuschulz/CELseq3-demultiplex)
mapping using STAR v2.7.3a
aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code (https://github.com/anikaneuschulz/MTglob_pipeline)
genome build/assembly: dr11.95
processed data files format and content: Tab-delimited mutation rates per gene

organism: Danio rerio

source_name: whole larvae, 48hpf

extract_protocol:
10  anesthetized larvae were washed twice in ice cold HBSS (Life Technologies GmbH #14175095) and resuspended in 200µl psychrophilic protease mix (1x Native Bacillus licheniformis Protease (Creative Enzymes #NATE-0633) in HBSS, 10 mM 4sU) and incubated on ice for 30 min. Dissociation was aided by pipetting up and down with a 200 µl tip ~25 times every 5 minutes. Enzymes were inactivated by adding 15 µl 10% BSA  (Sigma-Aldrich; #A4503) before spinning down and resuspending the cells in TRIzol
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: whole larvae, 48hpf

value: 30 min 4sU during dissociation

tag: time


title: SCN_ZT6_TRF_1_2

description: Library name: A16SCN4

value: suprachiasmatic nucleus

value: wild type


title: P30SCC_P13SCC_Visium (SCC samples from patients P30, P13)

description: 10x Genomics


title: SCN_ZT6_TRF_1_1

description: Library name: A16SCN4

value: 9 hr time-restricted feeding


title: ChIP-seq_WT_H3K27ac_retina

value: WT


title: larvae, cold dissociated, rep 2


title: SCN_ZT6_ALF_2_2

description: Library name: A16SCN2


title: ChIP-seq_WT_H3K9ac_retina


title: larvae, cold dissociated, rep 1


title: RNA-seq_635_SCA7_KI_homo_Rep3

data_processing:
Base calling : Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using Tophat v2.0.14 with bowtie v2.1.0.
Quantification : Gene expression was quantified using HTSeq v0.6.1 and Ensembl release 90 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

source_name: SCA7 KI retina

extract_protocol:
Retinas were flash frozen in liquid nitrogen and stored at -800C. The total RNA was obtained using RNeasy Micro Kit (Qiagen).
Total RNA-Seq libraries were generated from 1 µg of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the remaining RNA was fragmented into small pieces using divalent cations at 94°C for 2 minutes. RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Surplus PCR primers were removed using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were quality controlled and quantified using capillary electrophoresis.

value: SCA7 KI


title: larvae, homogenized

extract_protocol:
10 larvae were anesthesized on ice and homogenized in TRIzol
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: homogenized


title: SCN_ZT6_ALF_2_1

description: Library name: A16SCN2


title: SCN_ZT6_ALF_1_1

description: Library name: A16SCN1


title: RNA-seq_611_SCA7_KI_homo_Rep2


title: SCN_ZT4_TRF_2_2

description: Library name: A15SCN4


title: RNA-seq_604_SCA7_KI_homo_Rep1


title: larvae, injected

extract_protocol:
10 larvae injected with 5nl 4sU (100mM in 10 mM Tris•HCl pH 7.4, Carl Roth with Dextran fluorescein Thermo Fisher Scientific #7136)) were incubated at 28°C for 30 minutes, anesthesized on ice and homogenized in TRIzol
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: 30 min 4sU injected


title: RNA-seq_12_WT_Rep4


title: SCN_ZT4_TRF_2_1

description: Library name: A15SCN4


title: adult cardiomyocytes, 30 min 4sU, rep5

data_processing:
Demultiplexing (bcl2fastq v2.19), CELseq barcodes demultiplexed using custom code (https://github.com/anikaneuschulz/CELseq3-demultiplex)
mapping using STAR v2.7.3a
aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code (https://github.com/anikaneuschulz/MTglob_pipeline)
genome build/assembly: mm38 (Ensembl 100)
processed data files format and content: Tab-delimited mutation rates per gene

source_name: Adult cardiomyocytes

extract_protocol:
Hearts were excised and digested via retrograde perfusion with Liberase as described in Rudolph et. al. 2019 (https://doi.org/10.1073/pnas.1904385116). After perfusion, the left ventricle was cut, minced and dissociated py pipetting. Cardiomyocyted were sedimented by gravity any the pellett resuspended in TRIzol. 10mM 4sU was added to the buffers from mincing to sedimentation. Dissociation was performed at 42°C instead of 37°C
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: Adult cardiomyocytes

value: 10 weeks


title: RNA-seq_610_WT_Rep2


title: RNA-seq_636_WT_Rep3


title: SCN_ZT4_TRF_1_2

description: Library name: A15SCN3


title: mESC, 24h, 0uM

data_processing:
Demultiplexing (bcl2fastq v2.19), CELseq barcodes demultiplexed using custom code (https://github.com/anikaneuschulz/CELseq3-demultiplex)
mapping using STAR v2.7.3a
aggregation of mutation information and calculation of labeling rates per gene / in bulk using custom code (https://github.com/anikaneuschulz/MTglob_pipeline)
genome build/assembly: mm38 (Ensembl 100)
processed data files format and content: File 1 : total count of each mutation, file 2 : total count of each nucleotide

source_name: G4 ES cells

growth_protocol: G4 ES cells were grown on top of CD1 feeder cells in gelatinized dishes as described in George et. al., 2007 (https://doi.org/10.1073/pnas.0609277104) using ESCM medium (Knockout Dulbecco’s Modified Eagle’s Medium (DMEM), 4500 mg/ml glucose, with sodium pyruvate (Gibco, #10829-018), 15 % fetal calf serum (FCS) (Superior, Biochrom, #S0615), 1× glutamine (100x, Lonza, #BE17-605E), 200 mM, 1× penicillin/streptomycin  (100x, Lonza, #DE17-603), 1× nonessential amino acids (Gibco, #11140-35), 1× fresh 10 mM β-mercaptoethanol (Sigma #M-7522; 2-ME) , 1× nucleosides (Chemicon #ES-008D)) supplemented with 0.01 % LIF Murine Leukemia Inhibitory Factor ESGROTM (107 U/ml, Chemicon, #ESG1107). One day after seeding mESCs the medium was changed and supplemented with 4sU. Cells were incubated for varying timespans and trypsinized after. Feeder cells were depleted by letting them attach to fresh gelatinized plates for 1h (in the presence of 4sU) and only removing the supernatant containing mECSs. Harvested mESCs were then spun down and resuspended in TRIzol.

extract_protocol: RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

tag: cell line

value: G4 ES cells

value: mouse embryonic stem cells

value: No 4sU


title: SCN_ZT4_TRF_1_1

description: Library name: A15SCN3


title: larvae, dissociated

extract_protocol:
10  anaesthetized larvae were washed twice in ice cold HBSS (Life Technologies GmbH #14175095) and resuspended in 500 l TryplE Mix (1xTrypleE (Life Technologies GmbH #A1217701) in HBSS , 1mM EDTA pH 8 (Molekula #900493) 10 mM 4sU (Merck Chemicals GmbH #T4509) for labelled sample) and incubated at 37°C for 30 min. Enzymes were inactivated by adding 15 µl 10% BSA  (Sigma-Aldrich; #A4503) before spinning down and resuspending the cells in TRIzol
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

tag: age


title: Met5A_palbo_1

city: Bruxelles

first: Sabine

last: Paternot

address: 808 Route de Lennik

department: IRIBHM

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases using "Trimmomatic v.0.36".
Clean paired sequences were aligned to the human reference genome GRCh38 using “STAR” software v.2.5.3.
The number of reads per gene were obtained using "HTSeq" v.0.9.1.
Raw counts were normalized to obtain counts per 20 millions of reads (CP20M) that were used for differential expression analysis with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file containing matrix of counts normalized to 20 millions of reads for all genes in all samples.

source_name: Met5A Palbociclib

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS,  sodium pyruvate (1mM) and antibiotics. They were maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated using  the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quality was checked using a Fragment Analyzer 5200.
cDNA libraries were prepared from 100 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Englands Biolabs) following manufacturer's recommendations. Paired-end sequencing was performed with a NovaSeq 6000 (Illumina).

treatment_protocol: 300 000 to 1 000 000 cells were plated in 9 cm Petri-dishes and treated the day after with 0,1 % DMSO or 1 µM palbociclib for 9-10 days. Cells were trypsinized when necessary and medium was changed every 3-4 days. For drug washout experiments, cells were washed twice with PBS before incubation in complete medium for 48 hours.

value: Normal mesothelial cells immortalized by SV40

value: 1 uM palbociclib for 9 days


title: Met5A_ctrl_1

source_name: Met5A DMSO

value: 0,1 % DMSO for 9 days


title: MPP89_palbo_2

source_name: MPP89 Palbociclib

value: Malignant pleural mesothelioma cells


title: MPP89_palbo_1


title: SCN_ZT4_ALF_2_2

description: Library name: A15SCN2

value: ad-libitum feeding


title: adult cardiomyocytes, 30 min 4sU, rep4

value: 30 min 4sU during dissociation


title: MPP89_ctrl_2

source_name: MPP89 DMSO


title: RNA-seq_602_WT_Rep1

value: retina

value: 12.5 weeks


title: adult cardiomyocytes, 30 min 4sU, rep3

extract_protocol:
Hearts were excised and digested via retrograde perfusion with Liberase as described in Rudolph et. al. 2019 (https://doi.org/10.1073/pnas.1904385116). After perfusion, the left ventricle was cut, minced and dissociated py pipetting. Cardiomyocyted were sedimented by gravity any the pellett resuspended in TRIzol. 10mM 4sU was added to the buffers from mincing to sedimentation.
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: WT


title: SCN_ZT4_ALF_1_1

description: Library name: A15SCN1

value: suprachiasmatic nucleus

value: wild type


title: WT_TIAL_iCLIP_pro_B

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

institute: INSERM

data_processing:
See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Raw sequence reads were trimmed to remove both barcodes and adapters. AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
Remaining sequences were mapped to the mouse mm10 genome (Ensembl59 genome annotation) using Bowtie (Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).).
Deduplication and identification of unique cDNA counts was performed based on the  random bases present in the 5' barcode.
Position -1 of uniquely annotated reads to the genome was annotated as the crosslink site.
Peak enrichment analysis of Tial1 binding sites was performed. Unique Tia1 crosslink sites were identified as previously described (See Konig et al. for all details (Nature Structural & Molecular Biology 17, 909–915 (2010)). Briefly, 15 nucleotide windows flanking the crosslink site were generated, 100 permutations were allowed and multiple test correction of p-values (Benjamini-Hochberg) was performed to calculate FDR.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph file contain the annotation of unique individual Tial1-nucleotide crosslinks

source_name: pro B cells

growth_protocol: BM cells isolated from C57BL/6 mice were cultured in the presence of 10 ng/ml IL-7 as indicated above. At day 8, cells were washed with ice-cold PBS and irradiated with UV light (600 mJ/cm2, Stratalinker 2400).

extract_protocol: L3-ATT-App DNA Linker (/5rApp/WN ATT AGA TCG GAA GAG CGG TTC AG/3Bio/) linker primer and irCLIP_ddRT_43 primer (/5Phos/WWW TAACT NNNN AGA TCG GAA GAG CGT CGT GAT/iSp18/GGA TCC/iSp18/TAC TGA ACC GC) were used for library preparation as previously described for iCLIP

treatment_protocol: RIPA buffer and sonication (10s, x3) was used for cell lysate and clarification.  Protein:RNA complexes were immunoprecipitated for RNA extraction and small RNA library preparation

value: pro B cells

tag: index

value: NNNNAGTTANNN


title: MPP89_ctrl_1


title: day20_fos_yap1_oe

city: Saint Louis

first: Samantha

last: Morris

state: Missouri

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
Single-cell barcoded bam files were generated using CellRanger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
lineage barcodes were processed using our in house pipeline (https://github.com/morris-lab/newCloneCalling)
Assembly: mm10
Supplementary files format and content: H5 files for single-cell gene expression matrices

source_name: reprogrammed MEFs

extract_protocol:
FACS sorting
10x Genomics scRNA-seq library prep, with modifications to capture CellTags, as needed

value: reprogrammed MEFs


title: MSTO_washout

description: same experiment than MSTO_palbo_3

source_name: MSTO Palbociclib washout

value: 1 uM palbociclib for 10 days followed by drug washout for 48 hours


title: day20_yap1_oe

description: 10x Genomics


title: SCN_ZT2_TRF_2_2

description: Library name: A14SCN4

source_name: SCN

value: 9 hr time-restricted feeding


title: MSTO_palbo_3

source_name: MSTO Palbociclib

value: 1 uM palbociclib for 10 days


title: day20_fos_oe

description: 10x Genomics


title: day20_gfp_control_oe

description: 10x Genomics


title: day28_celltagged

description: 10x Genomics


title: KO_pro_B_4_IC24

description:
Polyadenylated RNA
mRNA-seq

data_processing:
Sample demultiplexing (all samples were loaded in 2 different lanes for sequencing). Data from each sample was then merged.
Raw sequence reads were trimmed to remove both barcodes and adapters using Trim Galore (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) (v0.4.4). Example: command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC lane2_L1_CGATGT_L002_R1.fastq.gz
Remaining paired-end reads were aligned to the mouse genome (GRCm38-release 102) and quantified with STAR-2.7.5a (with options --runMode alignReads --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic, with option --sjdbOverhang 100).
Alignment files were indexed using SamTools (v.1.9).
Differential expression analyses were performed with DESeq2 (v.1.28.1).
Differential alternative splicing (AS) was analysed with rMATS-4.0.2 and Python-2.7.2 (with options -t paired --readLength 100 --libType fr-firstrand).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Comma-separated files. DESeq2 results, DESeq2 normalized gene counts.

extract_protocol:
Total RNA from FACs-sorted pro-B cells was isolated using the RNeasy Microkit from Qiagen.
Libraries were generated using 10 ng of total RNA and the SMART-Seq Stranded mRNA kit following the instruction of the manufacturer (TakaraBio).

value: Pro B cells

value: Tia1 Tial1 double conditional knock out

tag: illumina index p5

value: AGGCTATA

tag: illumina index p7

value: TAATGCGC


title: SCN_ZT2_TRF_2_1

description: Library name: A14SCN4

extract_protocol:
RNA were extracted following the protocol from Allprep DNA/RNA Mini Kit (Qiagen) or using Trizol reagent, and RNA integrity number were measured through Agilent 2200 TapeStation system.
Libraries generated using Illumina TruSeq Stranded mRNA Sample Prep Kit, pooled and sequenced using an Illumina HiSeq 2500 or Novaseq 6000.


title: SCN_ZT2_TRF_1_2

description: Library name: A14SCN3


title: MSTO_palbo_2

value: Malignant pleural mesothelioma cells

value: 1 uM palbociclib for 9 days


title: SCN_ZT2_TRF_1_1

description: Library name: A14SCN3


title: day10_celltagged

description: 10x Genomics


title: MSTO_ctrl_3

source_name: MSTO DMSO

value: 0,1 % DMSO for 10 days


title: day4_celltagged

description: 10x Genomics


title: KO_pro_B_2_IC22

description:
Polyadenylated RNA
mRNA-seq

value: GAATTCGT


title: SCN_ZT2_ALF_2_1

description: Library name: A14SCN2

value: ad-libitum feeding


title: KO_pro_B_3_IC23

description:
Polyadenylated RNA
mRNA-seq

value: CTGAAGCT


title: SCN_ZT4_ALF_2_1

description: Library name: A15SCN2

value: suprachiasmatic nucleus

value: wild type


title: SCN_ZT2_ALF_2_2

description: Library name: A14SCN2


title: MSTO_ctrl_2

value: 0,1 % DMSO for 9 days


title: MSTO_ctrl_1


title: SCN_ZT2_ALF_1_2

description: Library name: A14SCN1


title: RNA-Seq mESCs KAT6A KO repl2

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
RNA-Seq data were aligned to mouse transcriptome GenCode.vM25 using RNA Star. Counts per gene were determined using FeatureCounts. Differentially expressed genes and normalized reads were determined using DeSeq2.
Assembly: mm38
Supplementary files format and content: tabular

growth_protocol: E14 mouse ES cells (E14TG2a) were cultured in DMEM, 15% FCS, 1 x L-Glutamine, 1 x Non-essential amino acids, 1 x Sodium pyruvate, 1 x Penicillin/Streptomycin , 0.15% β-mercaptoethanol and 100 Units/ml of LIF on gelatin-coated plates.

extract_protocol:
Total RNA was extracted by using the RNeasy Mini system (Qiagen) including an on-column DNaseI digestion.
RNA-Seq libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: KAT6A KO mESCs were obtaiend using CRISPR/Cas9 mediated genome editing.

value: mouse ES cells

value: KAT6A KO


title: KO_pro_B_1_IC21

description:
Polyadenylated RNA
mRNA-seq

value: ATTCAGAA


title: Brain from Nav1.8CreROSA26DTA mouse injected with PBS

type: RNA

city: Tsukuba

first: Yutaro

last: Kumagai

state: Ibaraki

address: Central 5-41, Higashi 1-1-1

department: BRD

country: Japan

institute: AIST

hyb_protocol: Hybridization was done by using Gene Expression Hybridization Kit (Agilent) according to the manufacturer's instruction.

scan_protocol: Scanning was performed by Agilent Microarray Scanner with 3 micro meter Scan Resolution and 20 bit TIFF dynamic range.

data_processing: Spot intensities were measured by using Agilent Feature Extraction 11.0.1.1.

label_protocol: Laballing was performed by using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instruction.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted by using TRIzol reagent (Invitrogen).

treatment_protocol: Wild-type or Nav1.8CreROSA26DTA mice were injected with 20 mg/kg BW of LPS i.p. and whole brains were harvested at 12 hours after injection.

value: brain

tag: agent

value: PBS


title: H28_washout

description: same experiment than H28_palbo_3

source_name: H28 Palbociclib washout

value: 1 uM palbociclib for 10 days followed by drug washout for 48 hours


title: RNA-Seq mESCs KAT6A KO repl1


title: WT_pro_B_4_IC20

description:
Polyadenylated RNA
mRNA-seq

value: Pro B cells

value: WT

value: AGGCTATA

value: GAGATTCC


title: Brain from wild-type mouse injected with LPS

value: wild-type

value: LPS


title: MSTO_palbo_1

value: Malignant pleural mesothelioma cells

value: 1 uM palbociclib for 9 days


title: Brain from wild-type mouse injected with PBS


title: H28_palbo_3

source_name: H28 Palbociclib

value: 1 uM palbociclib for 10 days


title: Brain from Nav1.8CreROSA26DTA mouse injected with LPS


title: H28_palbo_2


title: RNA-Seq mESCs Control repl2

value: Control


title: RNA-Seq mESCs Control repl1


title: WT_pro_B_3_IC19

description:
Polyadenylated RNA
mRNA-seq

value: CGCTCATT


title: WT_pro_B_2_IC18

description:
Polyadenylated RNA
mRNA-seq

value: TCCGGAGA


title: mESC, 24h, 10mM

value: G4 ES cells

value: mouse embryonic stem cells

value: 24h 10mM 4sU


title: H28_palbo_1


title: SCN_ZT0_TRF_1_2

description: Library name: A13SCN3

value: suprachiasmatic nucleus

value: 9 hr time-restricted feeding

value: wild type


title: SCN_ZT0_TRF_1_1

description: Library name: A13SCN3


title: H28_ctrl_2

source_name: H28 DMSO

value: 0,1 % DMSO for 9 days


title: B.bigemina tick3

city: Pullman

first: Massaro

middle: Wilson

last: Ueti

state: Washington

address: 3003 ADBF Washington State Univ, 3003 ADBF, Grimes Way

institute: USDA ARS Animal Disease Research Unit

data_processing:
HiSeq control software HCS 2.2.58 RTA 1.18.64
TopHat v2.0.12 alignment
HTC v 0.6.1 counts
edgeR 3.12.1. DE analysis
Assembly: BOND RefSeq GCF_000981445.1
Supplementary files format and content: Excel with read counts raw and normalized, log CPM, fold change, FDR, significance

organism: Babesia bigemina

source_name: Mexico

extract_protocol:
TriZol extraction
Illumina TruSeq mRNA, poly A selected

value: Mexico

value: Rhipicephalus microplus hemocytes

value: kinete stage parasites


title: H28_ctrl_3

value: 0,1 % DMSO for 10 days


title: mESC, 2h, 10mM

value: WT

value: 2h 10mM 4sU


title: SCN_ZT2_ALF_1_1

description: Library name: A14SCN1

value: ad-libitum feeding


title: WT_pro_B_1_IC17

description:
Polyadenylated RNA
mRNA-seq

value: Pro B cells

value: AGGCTATA

value: ATTACTCG


title: SCN_ZT0_ALF_2_2

description: Library name: A13SCN2


title: B.bigemina tick2


title: B.bigemina tick1


title: H28_ctrl_1

value: Malignant pleural mesothelioma cells


title: mESC, 24h, 1mM

value: G4 ES cells

value: mouse embryonic stem cells

value: 24h 1mM 4sU


title: SCN_ZT0_TRF_2_2

description: Library name: A13SCN4

value: suprachiasmatic nucleus

value: 9 hr time-restricted feeding


title: SCN_ZT0_ALF_1_2

description: Library name: A13SCN1

value: wild type


title: SCN_ZT0_TRF_2_1

description: Library name: A13SCN4


title: mESC, 6h, 1mM

value: 6h 1mM 4sU


title: SCN_ZT0_ALF_2_1

description: Library name: A13SCN2


title: mESC, 2h, 1mM

value: 2h 1mM 4sU


title: mESC, 6h, 10mM

value: 6h 10mM 4sU


title: SCN_ZT0_ALF_1_1

description: Library name: A13SCN1


title: B.bigemina blood2

value: Mexico

value: bovine erythrocytes

value: blood stage parasites


title: H2452_palbo_2

source_name: H2452 Palbociclib

value: 1 uM palbociclib for 9 days


title: B.bigemina blood1


title: B.bigemina blood3


title: REST_KO_SC_2

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
Spinal cord tissue of resting Lhx1os KO mice
REST_KO_1872_SC_S28

data_processing:
Basecalling performed by NovaSeq 6000 software RTA3
Illumina adapter remotion and quality trimming was performed with a combination of Cutadapt and Trimmomatic softwares (see methods for further details).
Preprocessed reads were aligned to reference genome (GRCm38) using STAR (2.5.2b) aligner software (39) with specific parameters: --outSAMstrandField intronMotif --outSAMattrIHstart 0 --outSAMtype BAM SortedByCoordinate  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04  --outFilterIntronMotifs RemoveNoncanonical
After alignment Gene loci fragment quantification were performed on Ensemble (release 99) mouse gene annotation gtf using htseq-count software (40) with these parameters: “-s reverse” and “-m intersection-strict”
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv file with gene fragment quantifications

source_name: Spinal Cord

extract_protocol:
Mice were weighed and then sacrificed by cervical dislocation. Relevant tissues were snap frozen in liquid nitrogen and stored at -80°C. Prior to protein or RNA extraction, tissues were ground to a powder using a pestle and mortar pre-chilled with liquid nitrogen. For protein extraction, tissue powders were homogenized using TissueRuptor II (QIAGEN) in RIPA buffer. The homogenates were centrifuged at 13,000xg for 10 minutes at 4°C and the supernatant was collected and quantified with the Bradford colorimetric reaction (Biorad). Total RNA was isolated from tissue powder using QIAzol Lysis Reagent (Qiagen)/chloroform extraction followed by spin-column purification (RNeasy Mini Kit; Qiagen). 15’ minute on-column DNase treatment was performed, according to manufacturer’s instructions.
Illumina "Truseq Stranded mRNA" kit was used to prepare cDNA libraries for Lhx1os +/+ and Lhx1os -/- mice spinal cord samples

treatment_protocol: Lhx1os knockout mice were generated in EMBL Monterotondo at the Gene Editing and Embryology Facility (GEEF) in the C57BL/6J background using a CRISPR genome-editing system. A single guide RNA, targeting the second exon of Lhx1os, was designed using the https://chopchop.cbu.uib.no/ resource and delivered in fertilized eggs together with an in vitro transcribed Cas9 mRNA and a synthetic poly(A) site in the form of a 200nt-long single-stranded donor oligonucleotide (ssODN). ssODN was composed of 100 nt of homology arms and 100 nt of a minimal synthetic poly-A signal, followed by two repetition of the polymerase destabilizing MAZ sequences.

value: Spinal Cord

tag: Sex

value: male

value: 3 months

value: Lhx1os -/-


title: H2452_palbo_1

value: Malignant pleural mesothelioma cells


title: REST_KO_SC_1

description:
Spinal cord tissue of resting Lhx1os KO mice
REST_KO_1870_SC_S27

tag: tissue


title: H2452_ctrl_3

source_name: H2452 DMSO

value: 0,1 % DMSO for 10 days


title: REST_WT_SC_3

description:
Spinal cord tissue of resting WT mice
REST_WT_1875_SC_S26

value: WT


title: H2452_ctrl_2

value: 0,1 % DMSO for 9 days


title: mESC, 2h, 100uM

source_name: G4 ES cells

value: G4 ES cells

value: mouse embryonic stem cells

value: 2h 100uM 4sU


title: mESC, 6h, 100uM

value: 6h 100uM 4sU


title: prenatal cardiomyocytes, 30min 4sU, rep3

source_name: Prenatal cardiomyocytes

extract_protocol:
Embryonic hearts were microdissected away from the embryo, minced with a scalpel in PBS w/ 10mM 4sU and transferred into pre‑warmed 0.25% trypsin‑EDTA (Thermo Fisher Scientific #25200056) and 10 mM 4sU. The hearts were digested for 15 min at 37°C with several rounds of vigorous pipetting and then spun down. The cell pellet was washed twice in 20% FCS in PBS solution, centrifuged and resuspended in 1 ml PBS. The remaining cell suspension was incubated for 30 min in the dark with 1 µl reconstituted fluorescent reactive dye (Thermo Fisher Scientific #L34955) to determine cell viability. After another wash in PBS, cells were resuspended in 0.5 ml 5% FCS in PBS solution. The cell suspensions were then incubated with 1 µg/ml Alexa Fluor 647 Rat Anti-Mouse VCAM-1 (BD Biosciences #561612) for 15 min in the dark. The cells were centrifuged at 450 g for 5 min, resuspended in PBS and filtered using a 70 µm strainer into a polypropylene tube. Live, VCAM-1+ cardiomyocytes were sorted using a BD FACSAria II (BD Biosciences), transferred to 1.5 ml tubes and centrifuged at 450 g for 5 min. The cell pellets were resuspended in 1 ml TRIzol
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: Prenatal cardiomyocytes

value: 30 min 4sU during dissociation

value: E17.5 embryos


title: H2452_washout

description: same experiment than H2452_palbo_3

source_name: H2452 Palbociclib washout

value: 1 uM palbociclib for 10 days followed by drug washout for 48 hours


title: T cells, 15min, PBS, 2

type: protein

city: Freiburg

first: Natalie

last: Koehler

address: Breisacher Str. 115

institute: University Medical Center Freiburg

description: Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody

hyb_protocol: 5 μg of protein per well was loaded onto the PamChip and the assay was run on a PamStation96 (PamGene International).

scan_protocol: The degree of phosphorylation was measured in real time via the kinetic image capture program, Evolve (PamGene International), which captures FITC-labeled anti-phosphotyrosine antibody binding to each phosphorylated peptide substrate.   Following 60 min incubation, the signal intensities for each peptide were analyzed using BioNavigator Software (PamGene International).

data_processing: Only peptides that showed kinetics (increase of signal in time) on at least 25 % of the arrays were included in the analysis. Nominal coefficient of variation (CV) was calculated per peptide using a 2-component error fit model using overall mean as input and was used as a filter to remove low-intensity spots. Only peptides that showed nominal CV <0.5 were included in the analysis. For kinase interpretation, a ranked list of putative kinases responsible for differences in the peptide phosphorylation was generated by upstream kinase analysis (UKA, PamGene International).

label: PY20 FITC

molecule: protein

source_name: T cells, PBS, 15 min stim

label_protocol: We used the PTK PamGene Array according to the manufacturer's instructions

growth_protocol: Spleens were isolated from 2 wildtype (WT) C57BL/6 mice and meshed through a 100 µM cell strainer into a PBS filled dish. T cells were isolated using the Pan T cell isolation kit (Miltenyi). 1Mio CD4/CD8 T cells were cultured in 6-well format in 1mlµL RPMI+10%FCS per well.

extract_protocol: PamGene lysates were prepared according to manufacturers instructions with M-PER Mammalian Protein Extraction Reagent (ThermoFisher) containing Halt phosphatase and Halt protease inhibitor cocktails (ThermoFisher). Total protein was quantified using the Pierce BCA Protein Assay Kit (ThermoFisher).

treatment_protocol: PBS or hBD-2 (60µL/mL) were added for 20 min before T cells were stimulated with anti-CD3/anti-CD28 microbeads in a 1:1 bead-to-cell ratio for 15 min.

value: splenic CD4/CD8 T cells

value: spleen

value: wildtype

tag: gender

value: female

value: PBS

tag: pamchip number


title: T cells, 15min, hBD2, 2

source_name: T cells, hBD-2, 15 min stim


title: H2452_ctrl_1

value: Malignant pleural mesothelioma cells


title: H2452_palbo_3

value: 1 uM palbociclib for 10 days


title: prenatal cardiomyocytes, 30min 4sU, rep2

value: WT


title: REST_WT_SC_1

description:
Spinal cord tissue of resting WT mice
REST_WT_1869_SC_S24

value: Spinal Cord

value: male

value: 3 months


title: T cells, 15min, hBD2, 1


title: H2052_washout

description: same experiment than H2052_palbo_2

source_name: H2052 Palbociclib washout


title: prenatal cardiomyocytes, 30min 4sU, rep1


title: H2052_palbo_2

source_name: H2052 Palbociclib


title: T cells, 15min, PBS, 1


title: mESC, 24h, 100uM

value: G4 ES cells

value: mouse embryonic stem cells


title: adult cardiomyocytes, no 4sU, rep2

source_name: Adult cardiomyocytes

extract_protocol:
Hearts were excised and digested via retrograde perfusion with Liberase as described in Rudolph et. al. 2019 (https://doi.org/10.1073/pnas.1904385116). In labeled samples 10mM 4sU was addedised, minced and dissociated py pipetting. Cardiomyocyted were sedimented by gravity any the pellett resuspended in TRIzol. In labeled samples 10mM 4sU was added to the buffers from mincing to sedimentation.
RNA was extracted using TRIzol-Chloroform-Isopropanol according to the manufacturer’s instructions. Iodiacetamide Treatment was carried out on extracted RNA in 50% DMSO as described in Herzog et. Al 2017 (https://doi.org/10.1038/nmeth.4435). libraries for RNA-seq were prepared following a CELseq protocol as published in Holler & Junker 2019 (https://doi.org/10.1007/978-1-4939-9009-2_9). Sequencing adapters were switched – Insert is in read 1!

value: Adult cardiomyocytes

value: no 4sU

value: 10 weeks


title: adult cardiomyocytes, 30 min 4sU, rep2

value: 30 min 4sU during dissociation


title: H2052_ctrl_1

source_name: H2052 DMSO

value: 0,1 % DMSO for 9 days


title: H2052_ctrl_2

value: 0,1 % DMSO for 10 days


title: adult cardiomyocytes, no 4sU, rep1


title: REST_WT_SC_2

description:
Spinal cord tissue of resting WT mice
REST_WT_1871_SC_S25


title: adult cardiomyocytes, 30 min 4sU, rep1


title: ICH+rhCDNF_S3

status: Public on Dec 19 2022

city: Helsinki

first: Vassilis

last: Stratoulias

state: <None>

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software (v2.20.0.422) was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (v0.36). Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to Rnor_6.0  genome using STAR aligner (2.5.3a) with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software (Subread package v1.6.4). Parameters used: -s 2 -T 20 -t exon -g gene_id -a Rattus_norvegicus.Rnor_6.0.98.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance), filtering of results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Assembly: Rnor_6.0 (GCA_000001895.4) from Ensembl Release 98.
Supplementary files format and content: Raw gene count matrix of sequenced reads (featureCounts meta-feature level) as .xlsx

organism: Rattus norvegicus

source_name: CD11b+positive cells

extract_protocol:
Nucleospin Tissue kit (Qiagen)
NEBNext Ultra Directional RNA Library Prep+rRNA depletion (NEB)

value: SD

value: brain (hemorrhagic striatum)

value: Male


title: ICH+rhCDNF_S2


title: ICH+rhCDNF_S1


title: Met5A

source_name: Met5A untreated

value: Normal mesothelial cells immortalized by SV40

value: Untreated


title: ICH+rhCDNF_S4


title: ICH+Saline_S1


title: ICH+Saline_S5


title: ICH+Saline_S4


title: H2052_palbo_1

value: Malignant pleural mesothelioma cells

value: 1 uM palbociclib for 9 days


title: ICH+Saline_S3


title: ICH+Saline_S2


title: synovial tissue Pre from case2

city: Kyoto

first: Shigeo

last: Yoshida

state: Kyoto

address: 54, Kawahara-cho, Shogoin, Sakyo-ku

department: Orthopaedics

institute: Kyoto University

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45 ̊C on Clariom S Array, Human. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: synovial tissue of knee before high tibial osteotomy

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit(Thermo Fisher Scientific) following the manufacturer's instructions.

extract_protocol: Total RNA was extracted using a TRIzol reagent and purified using RNeasy Mini Kits.

value: synovial tissue

tag: case

tag: status

value: pre


title: synovial tissue Post from case2

source_name: synovial tissue of knee after high tibial osteotomy

value: post


title: synovial tissue Post from case1


title: synovial tissue Pre from case3


title: adult_mouse_hippocampus

description: 10x Genomics

data_processing:
Reads were demultiplexed using bcl2fastq v2.19.
Data was mapped using cellranger v6.1.1
MD tags were added using samtools v1.14
mutation calling and quality filtering (illumina Q20) using custom code (see https://github.com/anikaneuschulz/MTglob_pipeline)
removal of reads with at least 1,2,3,4 labelling events and re-generation of count matrices
Assembly: mm38 (Ensmbl 98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Animals were perfused with PBS before the brain extraction. Cells were isolated using the Adult Brain Dissociation Kit (ABDK, Miltenyi Biotec). In brief, mice were anaesthetised (Narcorene, 100mg/kg, i.p., Merial GmbH, Germany) and perfused transcardially with 10 ml of 0.9 % saline solution containing 1 U/ml of heparin (Heparin-Natrium-250 000-ratiopharm, Ratiopharm, Ulm, Germany) followed by 50 ml of 0.1M PBS (pH 7.4). Next, the brains were gently extracted from the skull (Papouin 2018) and immediately placed in ice cold HBSS. For the hippocampus isolation, brains where put on an ice cold metal platform and the hippocampus was dissected out of the whole brain as described by Spijker. Hippocampi were then placed in the ABDK enzyme mix and dissociated for 30 min at 37°C according to the manufacturer's instructions in the presence of 10mM 4sU. Afterwards the cell suspension underwent myelin removal with 35% SIP (Solution Isotonic Percoll) for 25min at 4°C. Live cells were sorted next with all steps being performed on ice and/or with pre-chilled buffers and equipment at 4°C. Cells were stained with BD Pharmingen™ Calcein AM dye for live/dead cell staining at 10 μM final concentration for 30-40min on ice. Afterwards the cell suspension was spun down for 5 min at 300g, before being resuspended in 500 μl of FACS buffer. Next, cells were sorted using an ARIA II sorter with 70 µl nozzle at the speed of 10k cells/sec.
Cells were spun down and resuspended in HBSS, before cold methanol was added drop-wise while gently agitating on a vortexer. Afterwards the cells were fixed at -20°C for at least 30 minutes. For IAA treatment the samples were brought back to RT and IAA dissolved in 20% HBSS / 80% MeOH (Th. Geyer #1437.2511) was added to a final concentration of 10 mM IAA. After converting for 13 hours, the cells were spun down at 1000 g and 4°C for 10 min, the supernatant was removed and quencing buffer added (3x SSC (Carl Roth GmbH #1054.1), 0.1% BSA,  1 U/µl SuperRNase IN (Life Technologies GmbH #AM2694), 100 mM DTT. We incubated the sample at RT for 5 min on order to quench the remaining IAA. Afterwards the cells were spun down again and resuspended in a small amount of resuspension buffer (1.5x SSC,  0.5 U/µl SuperRNase IN,  0.01% BSA) and loaded onto the chromium controller using a Chromium Single Cell 3’ v3.1 kit (10x Genomics #1000121). Importantly, the volume of SSC buffer introduced into reverse transcription needs to be as low as possible to avoid inhibiting the reaction.After successful encapsulation we proceeded with library preparation according to the manufacturer's instructions.

tag: cell type

value: hippocampus cells

value: hippocampus

value: 10-14 weeks old


title: ICH+rhCDNF_S5


title: synovial tissue Post from case3


title: 86-12-PanCK-

city: Tucson

first: Bonnie

last: LaFleur

state: AZ

address: 4151 W Speedway Blvd

institute: University of Arizona

description: UACC June 2022 086 | 012 | PanCK-

data_processing:
Data from the Nanostring DSP instrument were Q3 normalized. Data from expirement 1 (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_1.txt) and expirement 2 (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_2.txt) were combined after log2 transformation using Combat (linear empirical Bayes) to remove the batch effect from samples 88/99 versus 7, 15, 80, and 86 that were run in two batches points in time. The Q3 log2 batch corrected data can be found in UACC_SKin_Transcriptomics_log2_Q3_BatchCorrected.txt
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Q3 normalized reads (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_2.txt) and the combined experiment 1 and experiment 2 log2 batch corrected Q3 reads ( UACC_SKin_Transcriptomics_log2_Q3_BatchCorrected.txt).

source_name: Skin

extract_protocol:
All human tissue was sourced from the Skin Cancer Prevention Program Biorepository at the University of Arizona Cancer Center. The protocol has been approved by the Institutional Review Board at the University of Arizona (Protocol Title: Biomarker development for early phase melanoma prevention trials; Protocol Number: 2012277005). A set of matched sun protected and actinic keratosis from two individuals were used for in this study. Tissue blocks were sectioned with a 5 µm thickness and mounted in the center of the slide (Superfrost Plus Micro slides, VWR) within an area of 35.3 mm long by 14.1 mm wide to allow detection by the NanoString GeoMx DSP instrument.
Sample preparation was performed following Leica Biosystems Bond RX FFPE RNA Slide Preparation Protocol in the GeoMx NGS Slide Preparation User Manual (NanoString, MAN-10115-03 for software version v2.1). This assay relies upon photocleavable RNA probes coupled to oligonucleotide tags that allow the selection of tissue compartments of interest for RNA analysis. Slides were baked at 60°C for 60 minutes. Samples were loaded into Leica Bond Rx for deparaffinization and antigen retrieval with the following settings; Bake and Dewax preparation program, 150µl buffer dispense volume, HIER 20 minutes with ER2 at 100°C, 1µ/mL proteinase K for 15 minutes. Slides were briefly stored in 1x PBS. Excess PBS was removed from slides before the addition of 200µL Whole Transcriptome Assay (WTA) probe sets diluted 1:10 in Buffer R (NanoString), covered with Hybrislips (Grace Biolabs, 714022) and incubated at 37°C overnight in a hybridization chamber lined with Kimwipes moistened with 2x SSC. Unbound probes were removed by washing twice at 37°C for 25 minutes in 50% Formamide (ThermoFisher, AM9324)/2x SSC followed by two washes at room temperature in 2x SSC for 2 minutes. Slides were blocked with 200µL Buffer W (NanoString) for 30 minutes followed by 1 hour incubation at room temperature in a humidity chamber with morphology marker solution comprised of 1µL PMEL17 (Novus Biologicals, NBP2-34638AF647), 2µL CD45 (Cell Signaling Technology, 13917BF), 0.66µL Pan-cytokeratin (Novus Biologicals, NBP2-33200AF488), 10µL Syto83 (ThermoFisher, S11364) in Buffer W (NanoString) to 200µL per slide. Slides were subsequently washed twice with 2x SSC before loading onto NanoString GeoMx DSP instrument.
Slides were loaded and scanned on GeoMx instrument according to GeoMx DSP Instrument User Manual (NanoString, MAN-10116-03 for software version v2.1) with the following scan exposure times; 200ms FITC/525nm, 60ms Cy3/568nm, 250ms Texas Red/615nm, 300ms Cy5/666nm. 12 polygonal regions of interest (ROI) were selected per slide with segmentation masks applied to each ROI selecting Pan-cytokeratin positive and Pan-cytokeratin negative areas within each ROI. Channel thresholds were adjusted to maximize inclusion of signal areas and minimize inclusion of non-signal areas with default settings for erode, N-dilate, hole size and particle size

value: Skin

tag: aoi

value: PanCK-

tag: region

value: Sun Protected

tag: region label

tag: sample

value: 78 years


title: 86-6-PanCK-

description: UACC June 2022 086 | 006 | PanCK-

value: AK Edge


title: 86-11-PanCK+

description: UACC June 2022 086 | 011 | PanCK+

value: PanCK+


title: 86-4-PanCK+

description: UACC June 2022 086 | 004 | PanCK+

value: AK Center

value: Male


title: 86-5-PanCK-

description: UACC June 2022 086 | 005 | PanCK-


title: 86-12-PanCK+

description: UACC June 2022 086 | 012 | PanCK+


title: 86-8-PanCK+

description: UACC June 2022 086 | 008 | PanCK+


title: 86-7-PanCK+

description: UACC June 2022 086 | 007 | PanCK+


title: 86-11-PanCK-

description: UACC June 2022 086 | 011 | PanCK-


title: 86-5-PanCK+

description: UACC June 2022 086 | 005 | PanCK+


title: 86-10-PanCK-

description: UACC June 2022 086 | 010 | PanCK-


title: 86-8-PanCK-

description: UACC June 2022 086 | 008 | PanCK-


title: 86-7-PanCK-

description: UACC June 2022 086 | 007 | PanCK-


title: NCI-H460_siTILR

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: Whole Human Genome oligo DNA microarray with 41000 distinct probes was scanned using an Agilent DNA microarray scanner (G2505B, Agilent Technologies). Images were quantified using Agilent Feature Extraction Software.

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using GeneSpring software.

source_name: NCI-H460 cells were transfected with siTILR

label_protocol: cRNA was generated and labeled with Cy3 or Cy5 (CyDye, Amersham Pharmacia Biotech, Piscataway, NJ) using the Low RNA Fluorescen

growth_protocol: A549, SK-LC-5, SK-LC-7 and NCI-H460 cells were cultured with 10% (v/v) FBS-containing RPMI 1640 at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: The cells were transfected with miRNA mimics or siRNAs.

tag: cell line

value: mixture of 20 cell lines


title: 86-9-PanCK+

description: UACC June 2022 086 | 009 | PanCK+

tag: age


title: synovial tissue Pre from case1


title: SK-LC-7_miR-20a

source_name: SK-LC-7 cells were transfected with miR-20a


title: SK-LC-5_miR-20a

source_name: SK-LC-5 cells were transfected with miR-20a


title: SK-LC-5_NC

source_name: SK-LC-5 cells were transfected with Negative Control


title: NCI-H460_siControl

source_name: NCI-H460 cells were transfected with siControl


title: A549_miR-20a

source_name: A549 cells were transfected with miR-20a


title: 86-6-PanCK+

description: UACC June 2022 086 | 006 | PanCK+


title: A549_NC

source_name: A549 cells were transfected with Negative Control


title: SK-LC-7_NC

source_name: SK-LC-7 cells were transfected with Negative Control


title: 86-10-PanCK+

description: UACC June 2022 086 | 010 | PanCK+


title: 86-4-PanCK-

description: UACC June 2022 086 | 004 | PanCK-


title: 86-2-PanCK-

description: UACC June 2022 086 | 002 | PanCK-


title: 86-2-PanCK+

description: UACC June 2022 086 | 002 | PanCK+


title: 86-3-PanCK-

description: UACC June 2022 086 | 003 | PanCK-


title: 86-3-PanCK+

description: UACC June 2022 086 | 003 | PanCK+


title: 80-9-PanCK+

description: UACC June 2022 080 | 009 | PanCK+

value: Female

value: 61 years


title: 80-10-PanCK+

description: UACC June 2022 080 | 010 | PanCK+


title: 80-9-PanCK-

description: UACC June 2022 080 | 009 | PanCK-


title: 80-10-PanCK-

description: UACC June 2022 080 | 010 | PanCK-


title: 80-11-PanCK+

description: UACC June 2022 080 | 011 | PanCK+


title: 80-12-PanCK+

description: UACC June 2022 080 | 012 | PanCK+


title: 80-12-PanCK-

description: UACC June 2022 080 | 012 | PanCK-


title: 86-1-PanCK-

description: UACC June 2022 086 | 001 | PanCK-


title: 86-1-PanCK+

description: UACC June 2022 086 | 001 | PanCK+


title: 80-11-PanCK-

description: UACC June 2022 080 | 011 | PanCK-


title: 3_4_0pq__2

city: La Jolla

first: Kevin

last: Rychel

address: 9500 Gilman Dr

institute: University of California San Diego

description: See http://aledb.org/stats/?ale_experiment_id=1540 for mutations.

data_processing:
All processing of files was done using code from https://github.com/avsastry/modulome-workflow
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM)).
iModulon analysis was performed and can be viewed at https://imodulondb.org/dataset.html?organism=e_coli&dataset=precise1k
Assembly: NC_000913.3
Supplementary files format and content: CSV file with log(transcripts per million) for each gene in the NC_000913.3 genome.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cultures

growth_protocol: Strains were grown overnight in M9 minimal media with 0.4% w/v glucose as a carbon source. Fresh media was inoculated with the overnight culture at an initial 600 nm optical density (OD) of 0.025. Cultures were aerated with a stir bar at 1100 rpm in a water bath maintained at 37°C until OD reached 0.5. 50 mM PQ was added to reach the desired concentration in stressed flasks. After 20 minutes, samples were harvested for transcriptomics.

extract_protocol:
3 mL of induced culture was added to 6 mL of RNAProtect Bacteria Reagent (Qiagen) and vortexed, then left at room temperature to incubate for 5 minutes. Cells were pelleted, resuspended in 400 μL elution buffer, and then split into two tubes with one kept as a spare. One pellet was then lysed enzymatically with addition of lysozyme, proteinase-K, and 20% SDS. SUPERase-In was added to maintain the integrity of the RNA. RNA isolation was then performed according to  the RNeasy Mini Kit (Qiagen) protocol.
 rRNA was depleted using the Ribo-Zero rRNA Removal Kit for gram negative bacteria according to the protocol. Libraries were constructed for paired-end sequencing using a KAPA RNAseq Library Preparation kit.

value: cultures

tag: genotype

tag: treatment

value: 0 uM paraquat


title: 80-8-PanCK-

description: UACC June 2022 080 | 008 | PanCK-


title: 3_4_750pq__1

value: 750 uM paraquat


title: 80-8-PanCK+

description: UACC June 2022 080 | 008 | PanCK+


title: 3_4_250pq__1

value: 250 uM paraquat


title: 3_4_250pq__2


title: 3_4_750pq__2


title: 80-7-PanCK+

description: UACC June 2022 080 | 007 | PanCK+


title: 80-6-PanCK+

description: UACC June 2022 080 | 006 | PanCK+


title: 3_3_750pq__2


title: 3_3_250pq__2


title: 3_3_750pq__1


title: 80-6-PanCK-

description: UACC June 2022 080 | 006 | PanCK-


title: 3_4_0pq__1


title: 3_3_250pq__1


title: 80-5-PanCK+

description: UACC June 2022 080 | 005 | PanCK+


title: 3_3_0pq__3


title: 80-5-PanCK-

description: UACC June 2022 080 | 005 | PanCK-


title: 80-4-PanCK+

description: UACC June 2022 080 | 004 | PanCK+


title: 3_3_0pq__4


title: 3_3_0pq__2


title: 80-4-PanCK-

description: UACC June 2022 080 | 004 | PanCK-


title: 3_3_0pq__1


title: 80-3-PanCK+

description: UACC June 2022 080 | 003 | PanCK+


title: 3_2_750pq__2


title: 3_2_750pq__1


title: 3_2_250pq__2


title: 80-2-PanCK+

description: UACC June 2022 080 | 002 | PanCK+


title: 3_2_250pq__1


title: 3_2_0pq__4


title: 3_2_0pq__3


title: 80-2-PanCK-

description: UACC June 2022 080 | 002 | PanCK-


title: 80-1-PanCK+

description: UACC June 2022 080 | 001 | PanCK+


title: 3_2_0pq__2


title: 3_2_0pq__1


title: 15-11-PanCK-

description: UACC June 2022 015 | 011 | PanCk-

value: 75 years


title: 15-10-PanCK+

description: UACC June 2022 015 | 010 | PanCK+


title: 80-1-PanCK-

description: UACC June 2022 080 | 001 | PanCK-


title: 15-10-PanCK-

description: UACC June 2022 015 | 010 | PanCk-


title: 15-9-PanCK+

description: UACC June 2022 015 | 009 | PanCK+


title: 3_1_250pq__2


title: 3_1_750pq__1


title: 3_1_750pq__2


title: 15-9-PanCK-

description: UACC June 2022 015 | 009 | PanCk-


title: 3_1_250pq__1


title: 15-8-PanCK-

description: UACC June 2022 015 | 008 | PanCk-


title: 15-8-PanCK+

description: UACC June 2022 015 | 008 | PanCK+


title: 80-3-PanCK-

description: UACC June 2022 080 | 003 | PanCK-


title: 15-7-PanCK+

description: UACC June 2022 015 | 007 | PanCK+


title: 3_1_0pq__1


title: 3_0_750pq__2


title: 3_0_750pq__1


title: 15-11-PanCK+

description: UACC June 2022 015 | 011 | PanCK+


title: 15-6-PanCK-

description: UACC June 2022 015 | 006 | PanCk-


title: 3_0_250pq__2


title: 3_0_250pq__1


title: 3_0_0pq__2


title: 15-5-PanCK+

description: UACC June 2022 015 | 005 | PanCK+


title: 3_0_0pq__1


title: 15-5-PanCK-

description: UACC June 2022 015 | 005 | PanCk-


title: 15-4-PanCK+

description: UACC June 2022 015 | 004 | PanCK+


title: 2_3_750pq__2


title: 15-4-PanCK-

description: UACC June 2022 015 | 004 | PanCk-


title: 15-3-PanCK+

description: UACC June 2022 015 | 003 | PanCK+


title: 2_3_750pq__1


title: 15-3-PanCK-

description: UACC June 2022 015 | 003 | PanCk-


title: 2_3_250pq__1


title: 15-2-PanCK+

description: UACC June 2022 015 | 002 | PanCK+


title: 2_3_250pq__2


title: 2_3_0pq__2


title: 3_1_0pq__2


title: 15-7-PanCK-

description: UACC June 2022 015 | 007 | PanCk-


title: 2_3_0pq__1


title: 15-1-PanCK+

description: UACC June 2022 015 | 001 | PanCK+


title: 15-2-PanCK-

description: UACC June 2022 015 | 002 | PanCk-


title: 2_2_750pq__2


title: 2_2_750pq__1


title: 15-6-PanCK+

description: UACC June 2022 015 | 006 | PanCK+


title: 15-1-PanCK-

description: UACC June 2022 015 | 001 | PanCk-


title: 7-10-PanCK+

description: UACC June 2022 007 | 010 | PanCK+


title: 2_2_250pq__2


title: 2_2_250pq__1


title: 7-9-PanCK+

description: UACC June 2022 007 | 009 | PanCK+


title: 2_2_0pq__2


title: 7-9-PanCK-

description: UACC June 2022 007 | 009 | PanCK-


title: 7-8-PanCK-

description: UACC June 2022 007 | 008 | PanCK-


title: 7-7-PanCK+

description: UACC June 2022 007 | 007 | PanCK+


title: 7-8-PanCK+

description: UACC June 2022 007 | 008 | PanCK+


title: 7-7-PanCK-

description: UACC June 2022 007 | 007 | PanCK-


title: 2_1_250pq__2


title: 2_1_750pq__2


title: 2_1_750pq__1


title: 7-6-PanCK-

description: UACC June 2022 007 | 006 | PanCK-


title: 2_1_0pq__2


title: 2_1_0pq__1


title: 7-6-PanCK+

description: UACC June 2022 007 | 006 | PanCK+


title: 2_0_750pq__2


title: 2_0_750pq__1


title: 7-10-PanCK-

description: UACC June 2022 007 | 010 | PanCK-


title: 7-5-PanCK-

description: UACC June 2022 007 | 005 | PanCK-


title: 7-4-PanCK-

description: UACC June 2022 007 | 004 | PanCK-


title: 7-3-PanCK+

description: UACC June 2022 007 | 003 | PanCK+


title: 1_4_750pq__3


title: 1_4_750pq__2


title: 7-3-PanCK-

description: UACC June 2022 007 | 003 | PanCK-


title: 7-2-PanCK+

description: UACC June 2022 007 | 002 | PanCK+


title: 7-2-PanCK-

description: UACC June 2022 007 | 002 | PanCK-


title: 2_2_0pq__1


title: 1_4_250pq__2


title: 1_4_250pq__1


title: 7-1-PanCK-

description: UACC June 2022 007 | 001 | PanCK-


title: 1_4_0pq__2


title: 2_1_250pq__1


title: 1_4_0pq__1


title: 7-5-PanCK+

description: UACC June 2022 007 | 005 | PanCK+


title: 1_3_750pq__2


title: 99-12-PanCK+

description: SAZT20099-1.SAZT20099-3.|.012.|.panckPos

data_processing:
Data from the Nanostring DSP instrument were Q3 normalized. Data from expirement 1 (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_1.txt) and expirement 2 (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_2.txt) were combined after log2 transformation using Combat (linear empirical Bayes) to remove the batch effect from samples 88/99 versus 7, 15, 80, and 86 that were run in two batches points in time. The Q3 log2 batch corrected data can be found in UACC_SKin_Transcriptomics_log2_Q3_BatchCorrected.txt
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Q3 normalized reads (UACC_dermal_transcriptional_change_from_sunProtected_to_actinic_kertosis_expirement_1.txt) and the combined experiment 1 and experiment 2 log2 batch corrected Q3 reads ( UACC_SKin_Transcriptomics_log2_Q3_BatchCorrected.txt).

tag: race/ethnicity

value: White/non-Hispanic


title: 99-12-PanCK-

description: SAZT20099-1.SAZT20099-3.|.012.|.panckNeg

value: Skin


title: 7-1-PanCK+

description: UACC June 2022 007 | 001 | PanCK+


title: 99-11-PanCK+

description: SAZT20099-1.SAZT20099-3.|.011.|.panckPos


title: 99-11-PanCK-

description: SAZT20099-1.SAZT20099-3.|.011.|.panckNeg

value: PanCK-


title: 1_4_750pq__4


title: 7-4-PanCK+

description: UACC June 2022 007 | 004 | PanCK+


title: 1_3_250pq__2


title: 1_3_250pq__3


title: 1_3_250pq__1


title: 99-10-PanCK-

description: SAZT20099-1.SAZT20099-3.|.010.|.panckNeg

value: Sun Protected


title: 99-10-PanCK+

description: SAZT20099-1.SAZT20099-3.|.010.|.panckPos


title: 1_3_750pq__1


title: 1_4_750pq__1


title: 1_3_250pq__4


title: 1_3_0pq__2


title: 99-9-PanCK-

description: SAZT20099-1.SAZT20099-3.|.009.|.panckNeg


title: 99-9-PanCK+

description: SAZT20099-1.SAZT20099-3.|.009.|.panckPos


title: 1_3_0pq__1


title: 99-8-PanCK+

description: SAZT20099-1.SAZT20099-3.|.008.|.panckPos


title: 1_2_750pq__2


title: 99-8-PanCK-

description: SAZT20099-1.SAZT20099-3.|.008.|.panckNeg


title: 1_2_750pq__1


title: 99-7-PanCK+

description: SAZT20099-1.SAZT20099-3.|.007.|.panckPos


title: 1_2_250pq__2


title: 99-7-PanCK-

description: SAZT20099-1.SAZT20099-3.|.007.|.panckNeg


title: 99-6-PanCK+

description: SAZT20099-1.SAZT20099-3.|.006.|.panckPos


title: 1_2_250pq__1


title: 99-5-PanCK+

description: SAZT20099-1.SAZT20099-3.|.005.|.panckPos


title: Staphylococcus aureus, ArlRS-, glucose-, Replicate 3

city: Urbana

first: Thomas

middle: E

last: Kehl-Fie

state: Il

address: 601 South Goodwin Avenue, MC-110

department: Microbiology

institute: University of Illinois at Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.20 Conversion Software (Illumina).
Adapters were trimmed from the 3' end of reads using Trimmomatic. Sequences matching the first 33 nt of the adapters used in library preparation were trimmed.
Rockhopper v2.0.3, with kentUtils v353 and SAMtools v1.9, was used for aligning reads to the genome, generating transcript counts, and predicting operons.
TMM normalization of transcript counts was performed with edgeR v3.34.0.  Transcripts were filtered if they did not have at least 0.5 counts per million in all three samples of at least one experimental group.  TMM normalization was re-done after filtering.
Assembly: GCF_000010465.1_ASM1046v1
Supplementary files format and content: Log-counts-per-million values after filtering are provided in tab-delimited text. Transcript metadata is included, including transcript and gene name, strand, transcription and translation start and stop sites, locus tag identifiers from the previous genome version, and KEGG pathways.
Supplementary files format and content: Raw counts before filtering are provided in tab-delimited text. Transcript metadata is included, including transcript and gene name, strand, transcription and translation start and stop sites, locus tag identifiers from the previous genome version, and KEGG pathways.

organism: Staphylococcus aureus

source_name: bacterial liquid culture

extract_protocol:
RNA was isolates using LETS buffer.
Ribosomal RNA was removed with the Ribozero kit (Illumina). The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

tag: strain

value: Newman

value: bacterial liquid culture

value: ArlRS-

value: glucose-


title: Staphylococcus aureus, ArlRS-, glucose-, Replicate 2


title: 99-6-PanCK-

description: SAZT20099-1.SAZT20099-3.|.006.|.panckNeg

value: AK Center

tag: Sex

value: Male


title: 1_2_0pq__2

tag: tissue


title: Staphylococcus aureus, ArlRS-, glucose-, Replicate 1


title: 99-5-PanCK-

description: SAZT20099-1.SAZT20099-3.|.005.|.panckNeg

value: AK Edge


title: 1_2_0pq__1

description: See http://aledb.org/stats/?ale_experiment_id=1540 for mutations.


title: 99-4-PanCK-

description: SAZT20099-1.SAZT20099-3.|.004.|.panckNeg


title: Staphylococcus aureus, ArlRS-, glucose+, Replicate 3

value: glucose+


title: 99-4-PanCK+

description: SAZT20099-1.SAZT20099-3.|.004.|.panckPos

value: PanCK+


title: 99-3-PanCK+

description: SAZT20099-1.SAZT20099-3.|.003.|.panckPos


title: 1_1_750pq__1

value: cultures


title: Staphylococcus aureus, ArlRS-, glucose+, Replicate 2


title: 99-2-PanCK+

description: SAZT20099-1.SAZT20099-3.|.002.|.panckPos


title: 1_1_750pq__2

value: 750 uM paraquat


title: 99-3-PanCK-

description: SAZT20099-1.SAZT20099-3.|.003.|.panckNeg


title: 99-2-PanCK-

description: SAZT20099-1.SAZT20099-3.|.002.|.panckNeg


title: 1_1_250pq__2

value: 250 uM paraquat


title: 99-1-PanCK+

description: SAZT20099-1.SAZT20099-3.|.001.|.panckPos

value: 75 years


title: 99-1-PanCK-

description: SAZT20099-1.SAZT20099-3.|.001.|.panckNeg

value: White/non-Hispanic


title: 88-12-PanCK+

description: SAZT20088-1.SATZ20088-3.|.012.|.panckPos

value: Skin

value: 67 years


title: Staphylococcus aureus, ArlRS-, glucose+, Replicate 1


title: Staphylococcus aureus, ArlRS+, glucose-, Replicate 3

value: ArlRS+


title: 1_1_250pq__1


title: 88-12-PanCK-

description: SAZT20088-1.SATZ20088-3.|.012.|.panckNeg

value: PanCK-

value: Sun Protected


title: Staphylococcus aureus, ArlRS+, glucose-, Replicate 2

value: Newman

value: bacterial liquid culture


title: 1_1_0pq__2

value: 0 uM paraquat


title: 88-11-PanCK+

description: SAZT20088-1.SATZ20088-3.|.011.|.panckPos

value: Male


title: Staphylococcus aureus, ArlRS+, glucose-, Replicate 1

value: glucose-


title: 88-10-PanCK+

description: SAZT20088-1.SATZ20088-3.|.010.|.panckPos


title: 88-11-PanCK-

description: SAZT20088-1.SATZ20088-3.|.011.|.panckNeg


title: 1_1_0pq__1


title: 88-10-PanCK-

description: SAZT20088-1.SATZ20088-3.|.010.|.panckNeg


title: Staphylococcus aureus, ArlRS+, glucose+, Replicate 3

value: glucose+


title: 1_0_750pq__2


title: 88-9-PanCK+

description: SAZT20088-1.SATZ20088-3.|.009.|.panckPos

value: PanCK+


title: 88-8-PanCK+

description: SAZT20088-1.SATZ20088-3.|.008.|.panckPos


title: 1_0_750pq__1

description: See http://aledb.org/stats/?ale_experiment_id=1540 for mutations.

value: cultures


title: 88-9-PanCK-

description: SAZT20088-1.SATZ20088-3.|.009.|.panckNeg


title: Staphylococcus aureus, ArlRS+, glucose+, Replicate 2


title: 88-8-PanCK-

description: SAZT20088-1.SATZ20088-3.|.008.|.panckNeg


title: 88-7-PanCK+

description: SAZT20088-1.SATZ20088-3.|.007.|.panckPos


title: 88-7-PanCK-

description: SAZT20088-1.SATZ20088-3.|.007.|.panckNeg


title: 88-6-PanCK+

description: SAZT20088-1.SATZ20088-3.|.006.|.panckPos

value: AK Center


title: LZ_Double_3

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description: Germinal center B cells Isolated from Spleen Using Facs sorting

data_processing:
The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

source_name: Spleen

extract_protocol:
Spleens removed and prepared into single cell suspension using frosted slides. Lysed Spenocytes were stained negatively selected for B cells and stained with antibody for FACS Sorting of Germinal Center Dark zone and Germinal center Light zone. 1000 Cells were acquired for each sample and subjected to cDNA synthesis and amplification using SMART-Seq Ultra v4 Ultra kit.
 Sequencing libraries of the amplicons passing QC were constructed using the Nextera XT DNA Library Preparation Kit (Illumina, Inc.).

treatment_protocol: treated mice were given 6 doses each of 200ug and 250ug of CTLA4-IG and Anti-CD40L, respectively, over a 2 week period starting at 18 weeks of age.

value: 6 Doses of CTLA4-IG and 6 doses of Anti-CD40L

value: Spleen


title: 88-6-PanCK-

description: SAZT20088-1.SATZ20088-3.|.006.|.panckNeg

value: White/non-Hispanic


title: ESC, Zfp266-KO, rep3

city: Edinburgh

first: Keisuke

last: Kaji

state: Midlothian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

description:
condition_ESC_KO_vs_ESC_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
ESC_6

data_processing:
Quality control of reads using FastQC
Read trimming and adapter removal using Cutadapt
Quality control of trimmed reads using FastQC
Read mapping to GRCM38.p6 reference genome using STAR
Assign reads to genomic features using Rsubread
Differential expression analysis using DESeq2
Assembly: GRCm38.p6
Supplementary files format and content: CSV, RDS

source_name: mESC_Zfp266 KO_Clone3

growth_protocol: For MEFs, 1x10^5 cells were transduced with either a non-targeting control sgRNA or Zfp266 sgRNA. 96 hours after transduction, MEFs were harvested for RNA extraction. For reprogramming samples, cells were transduced with either a non-targeting control or Zfp266 sgRNA 24 hours prior to the beginning of reprogramming. OSKM expression was induced by adding reprogramming media to the transduced cells (ESC media + 300ng/ml doxycycline + 10ug/ml Vitamin C). Cells were harvested at D3, D5 and D7 of reprogramming and 1x10^5 cells were sorted per sample, per timepoint for RNA extraction. iPSCs were lifted at D15 of reprogramming and individual iPSCs were sorted into single wells. Clones were grow in ESC media without doxycycline and 1ug/ml Puromycin to select for stable iPSCs and Zfp266 KO was confirmed by genotyping. KO ESCs were generated by transfecting cells with a Zfp266 gRNA plasmid expressing BFP. Individual BFP+ ESCs were sorted into single wells and genotyped to confirm Zfp266 KO. 1x10^5 iPSCs or ESCs were use for RNA extraction.

extract_protocol:
Cells were homogenised with the Qiashredder kit (Qiagen) and total RNA was extracted with the RNeasy Plus Micro Kit (Qiagen).
RNA-Seq libraries were prepared using the NEB Ultra II stranded mRNA Library prep kit (NEB).
Bulk mRNA-Seq

treatment_protocol: Transduction with either a non-targeting control or Zfp266 sgRNA.

value: Zfp266 KO

value: Embryonic Stem Cells


title: ESC, Zfp266-KO, rep1

description:
condition_ESC_KO_vs_ESC_WT.rsubread.csv
counts.rsubread.csv
dds.rsubread.rds
logcounts.rsubread.csv
normcounts.rsubread.csv
ESC_4

source_name: mESC_Zfp266 KO_Clone1


title: 88-5-PanCK+

description: SAZT20088-1.SATZ20088-3.|.005.|.panckPos

value: Skin

value: AK Edge

value: 67 years


title: 88-5-PanCK-

description: SAZT20088-1.SATZ20088-3.|.005.|.panckNeg

value: PanCK-