title: Cell line Exon18a, Day3, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: ADT: Adipose Tissue Biopsy, P5963_CW3

status: Public on Aug 30 2023

type: SRA

city: Nashville

first: Samuel

last: Bailin

address: 1161 21st Avenue South, MCN A-2200

country: USA

institute: Vanderbilt Universit Medical Center

library_source: transcriptomic

data_processing:
Indiviudal samples were input into Cellranger v6.0.0 with default parameters
Reads were mapped to hg38 and UMI count matrices were computed by Cellranger with default parameters
Assembly: hg38
Supplementary files format and content: Cellranger output with all samples aggregated together after quality control and doublet removal

molecule: total RNA

organism: Homo sapiens

source_name: subcutaneous adipose tissue

extract_protocol:
Custom adipose tissue dissociation.
10X 5' Gene Expression (GEX) and Antibody Expression (ADT) Library Construction

tag: disease state

value: HIV- diabetic

tag: tissue

value: subcutaneous adipose tissue

tag: number of donors


title: Null_Root_50DAS_LP_1

city: Riverside

first: Julia

last: Bailey-Serres

state: California

address: 900 University Ave

department: Department of Botany and Plant Sciences

institute: UC Riverside

data_processing:
Quality reports of raw reads were generated with the FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter sequences were trimmed using Cutadapt (Martin et al. 2011).
Sequences were aligned to the  IWGSC v1.1 reference genome using hisat2 (Kim et al. 2015). The OsPSTOL1 K-allele CDS was added as a separate chromosome.
Read count data in terms of RPKM (reads per kilobase per million) were calculated for exons on gene ( Genomic features exonsby). For samples with both single end and paired end reads, single end and paired end reads were aligned and counted seperately as described above. The counts were then added from the two alignments
Genome_build: IWGSC v1.1
Supplementary_files_format_and_content: Normalized RPKM for each sample. P-values for comparisons are given only for genes with 5 counts per million in at least three samples.

molecule: polyA RNA

organism: Triticum aestivum

source_name: 50 days after sowing roots

growth_protocol: For evaluation of growth under low P conditions, seeds of transgenic and null segregant plants were germinated as described above, except seeds were sterilized prior to being imbibed by incubating seeds in 50% (v/v) ethanol for 15 minutes, followed by incubating in 2% (w/v) sodium perchlorate for 10 minutes, and washing 5 times with sterile ddH2O. Seeds were pre-germinated on wet filter paper on sealed petri dishes in a growth chamber at 22°C, with 16 h light (115 µE info and dark cycle for 3 days. Five to six germinated seedlings of average size and similar developmental stage were transplanted into each pot containing a mix of 70% (v/v) #20 silica sand (Gillibrand) and 30% (v/v) Green Grades Profile™. Profile™ contains 10% (v/v) aluminum oxide which acts as a solid-state buffer for phosphate77. Prior to transplanting, the growth medium of each pot was pre-washed 16 times with 0.75 L Industrial H2O, with at least 4 hours between each wash to reduce the starting phosphate content to 25 μM. For the first 14 days after sowing (DAS), plants were sub-irrigated (from pot base) with unfertilized industrial water containing negligible amounts of phosphate and nitrogen. At 14 DAS, pots were sub-irrigated with 3 L of industrial water supplemented with the following nutrients: 2.3 mM NH4NO3, 2 mM KNO3, 0.00007 mM (NH4)Mo7O24, 0.01148 mM H3BO3, 0.002 mM CuSO4, 0.0094 mM Iron-EDTA, 0.003 mM MnSO4, and 0.0035 mM ZnSO4. For high phosphate (HP), the solution contained 436 µM KH2PO4, and for low phosphate (LP) this was substituted with 440 µM KCl. The industrial water used contains 1625 µM Ca2+, 375 µM Mg2+, and 656 µM SO42-.

extract_protocol:
Total RNA was extracted using TRizol reagent (Invitrogen) according to the manufacturer’s instructions. Following quantitation with a NanoDrop (Wilmington, DE), 15 µg of total-RNA was used to isolate mRNA using Dynabeads™ Oligo(dT)25 (Invitrogen) following the manufacture’s instructions.
mRNA-seq Libraries were produced using the non-strand specific Brad’s Rapid Ravi-seq procedure (Kumar et al. 2012).

tag: line

value: Null Segregant

tag: age

value: 50 DAS

tag: organ

value: Roots

tag: treatment

value: Low Phosphate

tag: cultivar

value: Fielder


title: Cell line Exon13.23, DMSO, Replicate 1

city: Frederick

first: Shyam

last: Sharan

state: MD

address: Building 560, Room 32-33

institute: Mouse Cancer Genetics Program

description: Sahu et al_Suppl file 2.xlsx

library_source: genomic

data_processing:
The reads were demultiplexed using bcl2fastq (Illumina) and fastq files were generated. The paired end reads were merged using FLASH and reads were aligned to the reference amplicon with a global sequence alignment algorithm using Needleman-Wunsch Alignment.
The total number of aligned reads were quantified using CRISPResso2 http://crispresso.pinellolab.org/submission  (63) and individual unique alignments were annotated with a custom-made variant caller modified from ANNOVAR (64) (release 2019-10-21) and the R/Bioconductor Biostrings package in R version 4.1.2 https://bioconductor.org/packages/Biostrings. Merged reads containing “N” bases were removed from the analysis.
Abundances of SNVs were quantified when the reads contained the synonymous PAM modification (HDR marker) and no other substitution or indels were present. The variants generated at a low frequency (less than 1 in 105 reads in any one of the replicates) were excluded from further analysis to prevent erroneous variant categorization. A pseudo count of 1 was added to all reads and for every sample and at all the conditions. Read counts for each SNVs were then normalized to the total read coverage of the sequencing library.
Dropout or enrichment scores were calculated by taking the ratio of frequency of the variants at day 14 in DMSO or cisplatin or olaparib over day 3. The scores were expressed in Log2 scale, which we define as function scores of SNVs in DMSO, cisplatin and olaparib.
The FSs, averaged over two independent replicates, were fit using a probit regression model for statistical modelling to calculate the probabilities of impact on function
Assembly: GRCh38
Supplementary files format and content: xlsx: Excel files include PIF, function scores, and additional annotations for all variants.
Library strategy: Amplicon sequencing

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Genomic DNA was extracted from the cell pellets using Zymo Genomic DNA Extraction kit
DNA libraries were prepared using TruSeq Nano DNA Library Prep kit

tag: cell line

tag: cell type

value: Embryonic stem cell


title: ADT: Adipose Tissue Biopsy, P5903_CW3


title: Null_Root_50DAS_LP_2

treatment_protocol: For high phosphate (HP), the solution contained 436 µM KH2PO4, and for low phosphate (LP) this was substituted with 440 µM KCl.


title: Cell line Exon13.23, Cisplatin, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: RNA: Adipose Tissue Biopsy, P5903_CW3


title: ADT: Adipose Tissue Biopsy, P5903_CW2

value: HIV+ diabetic


title: Null_Root_50DAS_HP_3

value: High Phosphate


title: Cell line Exon13.23, Olaparib, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: P/O replicate 5

type: RNA

city: London

first: Timothy

middle: RH

last: Regnault

state: Ontario

address: Medical Sciences Building, Room 216

department: Physiology and Pharmacology

country: Canada

institute: Western University

description: Gene expression data from BeWo cytotrophoblasts treated with 50 µM each Plmitate and Oleate for 72 hours

hyb_protocol: 3.5 µg DNA was targeted to be hybridized on GeneChip®  Clariom™ S human (Thermo Fisher Scientific) and incubated at 45°C in the Genechip® Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips® Fluidics Station 450 (ThermoFisher) using GeneChip Hybridization Wash and Stain kit according to the manufacturer’s instructions (ThermoFisher)

scan_protocol: The microarrays were finally scanned on a GeneChip® scanner 3000 (ThermoFisher)

data_processing: Data were processed using Transcriptome Analysis Console (TAC v4.0) and were normalized using the Robust Multiple-Array Averaging (RMA) method. Samples from each independent collection were paired for analysis (e.g. BSA control replicate 1 paired with PA replicate 1). Differential gene expression in each fatty acid treatment condition was compared to the BSA control samples in binary

label: biotin

source_name: BeWo Cytotrophoblast lysate

label_protocol: Sense-strand cDNA was synthesized from 100 ng of total RNA, and fragmentation and labeling were performed to produce ss DNA with the GeneChip® WT Terminal Labeling Kit according to manufacturer’s instructions (Thermo Fisher Scientific)

growth_protocol: BeWo trophoblasts were plated at 3.5x10^5 in 60 mm plates and allowed to attach to plates overnight in basal F12K media. Treatment was initiated the next day at time: 0 hours and cells were collected after 72 hours of treatment

extract_protocol: Samples were lysed in 900 uL TRIzol Reagent and automated RNA extraction was completed via Qiacube connect as per manufacturer's specifications. RNA extraction and subsequent microarray processing was performed at The Genome Quebec Innovation Facility

treatment_protocol: Cells were treated for 72H with dietary non-esterified fatty acids: 100 µM PA, 100 µM OA, 50 µM each PA and OA, BSA-alone control (0.3%)

value: BeWo Cytotrophoblasts

value: BeWo Cytotrophoblasts treated with Palmitate and Oleate (50 uM each)  for 72 Hours


title: Null_Root_50DAS_HP_1


title: Null_Root_50DAS_HP_2


title: P/O replicate 4


title: Cell line Exon13.2, Day3, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: P/O replicate 3


title: P/O replicate 1


title: P/O replicate 2


title: RNA: Adipose Tissue Biopsy, P5903_CW2


title: RNA: Adipose Tissue Biopsy, P5963_CW1

value: HIV+ non-diabetic and HIV+ prediabetic


title: PSTOL2_Crown_36DAS_LP_3

source_name: 36 days after sowing crowns

value: 36 DAS

value: Crowns


title: Cell line Exon13.23, DMSO, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: OA replicate 5

description: Gene expression data from BeWo cytotrophoblasts treated with 100 µM Oleate for 72 hours

value: BeWo Cytotrophoblasts treated with Oleate (100 uM)  for 72 Hours


title: Cell line Exon13.2, Olaparib, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: ADT: Adipose Tissue Biopsy, P5903_CW1


title: RNA: Adipose Tissue Biopsy, P5903_CW1


title: OA replicate 4


title: PSTOL2_Crown_36DAS_LP_2


title: Cell line Exon13.23, Cisplatin, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon13.2, Olaparib, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Crown_36DAS_LP_1


title: ADT: Adipose Tissue Biopsy, P5877_CW3


title: PSTOL2_Crown_36DAS_HP_3


title: Cell line Exon13.2, DMSO, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: OA replicate 3


title: RNA: Adipose Tissue Biopsy, P5877_CW3


title: Cell line Exon13.2, DMSO, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: Cell line Exon13.2, Day3, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Crown_36DAS_HP_1


title: RNA: Adipose Tissue Biopsy, P5877_CW2


title: ADT: Adipose Tissue Biopsy, P5877_CW2


title: Cell line Exon13.2, Cisplatin, Replicate 2

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL2_Crown_36DAS_HP_2


title: ADT: Adipose Tissue Biopsy, P5877_CW1


title: Cell line Exon13.2, Cisplatin, Replicate 1

description: Sahu et al_Suppl file 2.xlsx


title: PSTOL1_Crown_36DAS_LP_3


title: PSTOL1_Crown_36DAS_LP_2


title: OA replicate 1


title: PA replicate 4

description: Gene expression data from BeWo cytotrophoblasts treated with 100 µM Palmitate for 72 hours

value: BeWo Cytotrophoblasts treated with Palmitate (100 uM)  for 72 Hours


title: PA replicate 3


title: OA replicate 2


title: PSTOL1_Crown_36DAS_LP_1


title: PA replicate 2


title: PSTOL1_Crown_36DAS_HP_3


title: Monocyte p15 methylated 4 [M_p15_68l1]

first: Gabriella

last: Ficz

state: Rest of the World

address: Centre for Haemato-Oncology

country: United Kingdom

institute: Barts Cancer Institute, Queen Mary University of London

data_processing:
Reads were trimmed using Trimgalore v0.6.5 and mapped using hisat2.2.1 to the hg38/GRCh38 genome assembly. Gene counts were generated using featurecounts v2.0.3. DESeq2 Bioconductor package v1.40.0 was used on the RNA-Seq data to conduct differential expression analyses. Pvalues were adjusted using the Benjamini-Hochberg procedure. Genes with an adjusted pvalue smaller than 0.05 and an absolute log2fold change higher than 1 were assigned as differentially expressed. For the enrichment analysis, hallmark gene sets were used in a gene set enrichment analysis (GSEA) using clusterProfiler R package v4.8.0.
IMPORTANT: Raw fastq "[name].fq.gz" files were run on different lanes. Therefore, some samples will have more than two files for paired-end reads. Files need to be combined, the attached are raw files as obtained from Novogene.
Assembly: hg38
Supplementary files format and content: raw_counts.csv

source_name: humanised murine bone marrow

extract_protocol:
RNA was purified using RNAeasy microkit (Qiagen) from Monocytes and Granulocytes isolated from humanised murine bone marrow
SMART-Seq V4 Ultra Low Input RNA kit for Sequencing 480 Rxns (Cat No. 634893, Takara) - amplification performed by Novogene UK
Novogene NGS RNA Library Prep Set (PT042)  - proprietary kit

value: humanised murine bone marrow

value: Monocyte

tag: genotype

value: p15 methylated

value: p15 guide RNA


title: PA replicate 5


title: Monocyte p15 methylated 5 [M_p15_68r1]


title: RNA: Adipose Tissue Biopsy, P5836_CW3

value: HIV- diabetic

value: subcutaneous adipose tissue


title: Monocyte p15 methylated 3 [M_p15_31r1]


title: PSTOL1_Crown_36DAS_HP_1

value: Fielder


title: BSA control recplicate 5

description: Gene expression data from BeWo cytotrophoblasts treated with 0.3% fatty acid-free BSA for 72 hours

value: BeWo Cytotrophoblasts treated with BSA contol (0.3%) for 72 Hours


title: PSTOL1_Crown_36DAS_HP_2


title: ADT: Adipose Tissue Biopsy, P5836_CW2

value: HIV+ diabetic


title: PA replicate 1


title: Monocyte p15 methylated 1 [M_p15_31l1]


title: RNA: Adipose Tissue Biopsy, P5877_CW1


title: Null_Crown_36DAS_LP_3

value: Null Segregant

value: Low Phosphate


title: ADT: Adipose Tissue Biopsy, P5836_CW3


title: Monocyte Control 5 [M_WT_67r1l1]

value: Control

value: non-targeting guide RNA


title: ADT: Adipose Tissue Biopsy, P5836_CW1

value: HIV+ non-diabetic and HIV+ prediabetic


title: C40.Z.M

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

description:
R40
Zebrafinch_RNAseq.xlsx

data_processing:
Quality of sequenced CAGE reads was checked by using FastQC v0.11.5 and then trimmed with fastx_trimmer -Q33 -l 75 (FASTX Toolkit 0.0.14). Moirai removeN script was applied to remove reads with “N” nucleotides. CAGE reads matching to adapters or rRNA (Moirai defined rRNA for galGal3) were removed with Trimmomatic-0.38 and RNAdust 1.06, respectively.
Trimmed CAGE reads were aligned with BWA 0.7.10-r789 and unmapped reads realigned with Hisat2 v2.1.0
Alignments were processed into CTSS (CAGE transcription start sites) and CAGE peaks with PromoterPipeline (https://github.com/Population-Transcriptomics/C1-CAGE-preview) with default threshold of at least 10 TPM (tags per million) in one of the samples.
CAGE peaks were associated with nearby transcripts located on the same strand by using ChIPseeker v1.32.0 package for R.
Quality of sequenced RNAseq reads was checked by using FastQC v0.11.5 and then trimmed with Trimmomatic-0.38
Trimmed RNAseq reads were aligned to reference genome assemblies by using Hisat2 v2.1.0, counted with HTSeq v2.0.1, and normalized by library size and exon length in edgeR v3.42.2.
Assembly: galGal6 (GCF_000002315.6)
Assembly: Coturnix_japonica_2.1 (GCF_001577835.2)
Assembly: MGAL_WU_HG_1.0 (GCA_905368555.1)
Assembly: GT_SO_6221 (http://gigadb.org/dataset/100559)
Assembly: ZJU1.0 (GCF_015476345.1)
Assembly: bTaeGut2.pat.W.v2 (GCF_008822105.2)
Assembly: ZJU1.0 (GCA_016128335.1)
Supplementary files format and content: xlsx files with CAGE peaks coordinates, TSS position, associated genes, tag per million normalized counts
Supplementary files format and content: xlsx files with RNAseq raw and FPKM counts

organism: Taeniopygia guttata

source_name: embryonic fibroblasts P5

growth_protocol: Embryonic fibroblast cells were isolated from eggs incubated for ~10 days at 38.5 °C to reach stage HH36. Embryos were then treated by resection of head and neck, limb, skin and fat deposit, and internal developing organs. The remained trunk portion was trypsinized at 37°C, followed by neutralization and centrifugation to obtain digested cell pellet. Cell pellet was resuspended with DMEM/10%FBS and seeded in DMEM/10%FBS or DMEM/F12/10%FBS for expansion.

extract_protocol:
Total RNA was prepared using commercial reagents (TRIzol, Invitrogen) from each sample of avian embryonic fibroblast cells at the fifth passage (P5).
5ug of RNA from each fibroblast sample was used for nAnTi-CAGE and polyA RNAseq libraries preparation and subsequent sequencing using the Illumina HiSeq2500 platform (K. K. DNAForm, Yokohama, Japan)

value: embryonic fibroblasts P5

tag: Sex

value: male

tag: medium

value: DMEM/10percent FBS


title: Monocyte Control 4 [M_WT_67r1]

value: humanised murine bone marrow


title: ADT: Adipose Tissue Biopsy, P5657_CW3


title: Monocyte Control 3 [M_WT_67nm]

value: Monocyte


title: C39.Z.F

description:
R39
Zebrafinch_RNAseq.xlsx

value: female


title: RNA: Adipose Tissue Biopsy, P5836_CW1


title: Monocyte p15 methylated 2 [M_p15_31nm]

value: p15 methylated

value: p15 guide RNA


title: Null_Crown_36DAS_LP_2

value: 36 DAS

value: Crowns


title: Null_Crown_36DAS_HP_3

value: High Phosphate

value: Fielder


title: RNA: Adipose Tissue Biopsy, P5836_CW2

value: HIV+ diabetic

value: subcutaneous adipose tissue


title: Null_Crown_36DAS_LP_1

value: Null Segregant

value: Low Phosphate


title: RNA: Adipose Tissue Biopsy, P5657_CW3

value: HIV- diabetic


title: Monocyte Control 2 [M_WT_67l1]

value: Control

value: non-targeting guide RNA


title: zFinch-EF [C42]

description:
C42
ZebraFinch_CAGE.xlsx

value: embryonic fibroblasts P5

value: DMEM/10percent FBS


title: zFinch-EF [C41]

description:
C41
ZebraFinch_CAGE.xlsx


title: ADT: Adipose Tissue Biopsy, P5657_CW1

value: HIV+ non-diabetic and HIV+ prediabetic


title: PSTOL2_Root_50DAS_LP_2

value: 50 DAS

value: Roots


title: Null_Crown_36DAS_HP_2


title: Monocyte Control 1 [M_WT_30nm]

value: humanised murine bone marrow

value: Monocyte


title: zFinch-EF [C40]

description:
C40
ZebraFinch_CAGE.xlsx

value: female


title: RNA: Adipose Tissue Biopsy, P5657_CW1


title: Granulocyte p15 methylated 5 [G_p15_68r1]

value: Granulocyte

value: p15 methylated

value: p15 guide RNA


title: Null_Crown_36DAS_HP_1

value: 36 DAS

value: Crowns

value: High Phosphate

value: Fielder


title: PSTOL2_Root_36DAS_LP_3

source_name: 36 days after sowing roots

value: Low Phosphate


title: ADT: Adipose Tissue Biopsy, P5573_CW3

value: HIV- diabetic

value: subcutaneous adipose tissue


title: zFinch-EF [C39]

description:
C39
ZebraFinch_CAGE.xlsx

value: embryonic fibroblasts P5

value: male

value: DMEM/10percent FBS


title: C23.E.M

description:
R23
Emu_RNAseq.xlsx

organism: Dromaius novaehollandiae

value: DMEM/F12/10percent FBS


title: Granulocyte p15 methylated 4 [G_p15_68l1]

value: humanised murine bone marrow


title: RNA: Adipose Tissue Biopsy, P5573_CW3


title: Granulocyte p15 methylated 3 [G_p15_31r1]


title: C20.E.F

description:
R20
Emu_RNAseq.xlsx


title: PSTOL2_Root_36DAS_LP_1

value: Roots


title: ADT: Adipose Tissue Biopsy, P5573_CW2

value: HIV+ diabetic


title: PSTOL2_Root_36DAS_LP_2


title: PSTOL2_Root_36DAS_HP_3


title: Granulocyte p15 methylated 2 [G_p15_31nm]

value: Granulocyte


title: Duck-EF 2020-01 F12 P5 [C31]

description:
C31
Duck_CAGE.xlsx

organism: Anas platyrhynchos

value: female


title: RNA: Adipose Tissue Biopsy, P5573_CW2


title: Granulocyte p15 methylated 1 [G_p15_31l1]

value: p15 methylated

value: p15 guide RNA


title: Emu-EF 2020-03 High P5 (2nd) [C24]

description:
C24
Emu_CAGE.xlsx


title: Emu-EF 2020-03 F12 P5 [C23]

description:
C23
Emu_CAGE.xlsx


title: ADT: Adipose Tissue Biopsy, P5573_CW1

value: HIV+ non-diabetic and HIV+ prediabetic


title: Emu-EF 2020-02 High P5 [C22]

description:
C22
Emu_CAGE.xlsx


title: RNA: Adipose Tissue Biopsy, P5573_CW1


title: Granulocyte Control 4 [G_WT_67r1l1]

value: Control

value: non-targeting guide RNA


title: Granulocyte Control 3 [G_WT_67nm]


title: Emu-EF 2020-02 F12 P5 [C21]

description:
C21
Emu_CAGE.xlsx


title: ADT: Adipose Tissue Biopsy, P5544_CW3


title: Emu-EF 2020-01 High P5 [C20]

description:
C20
Emu_CAGE.xlsx


title: RNA: Adipose Tissue Biopsy, P5544_CW3


title: PSTOL1_Root_36DAS_LP_3

value: 36 DAS

value: Low Phosphate

value: Fielder


title: PSTOL2_Root_36DAS_HP_2

value: High Phosphate


title: Granulocyte Control 2 [G_WT_67l1]


title: PSTOL2_Root_36DAS_HP_1


title: Granulocyte Control 1 [G_WT_30nm]


title: BSA control recplicate 3

value: BeWo Cytotrophoblasts

value: BeWo Cytotrophoblasts treated with BSA contol (0.3%) for 72 Hours


title: Emu-EF 2020-01 F12 P5 [C19]

description:
C19
Emu_CAGE.xlsx

value: embryonic fibroblasts P5

value: DMEM/F12/10percent FBS


title: PSTOL1_Root_36DAS_LP_1

value: Roots


title: PSTOL1_Root_36DAS_LP_2


title: PSTOL1_Root_36DAS_HP_3


title: OE_3

city: Guangzhou

first: Min

last: Luo

state: Guangdong

address: No.651,Dongdeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Featurecounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And the expected number of Fragments of Per Kilobase of transcript sequence Per millions base paires (PFKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.

source_name: HCT116 cells

extract_protocol:
RNA was harvested with Fast Tissue RNA Purification Kit (EZB-RN5). And 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

value: HCT116 cells


title: ADT: Adipose Tissue Biopsy, P5344_CW2 2

value: HIV+ diabetic

value: subcutaneous adipose tissue


title: RNA: Adipose Tissue Biopsy, P5344_CW2 2


title: OE_2


title: PSTOL1_Root_36DAS_HP_2


title: BSA control recplicate 4


title: Graphene-coated copper, replicate 3

city: RAPID CITY

first: Venkataramana

last: Gadhamshetty

state: SD

address: 501 E St Joseph St, South Dakota Mines

department: Civil and Environmental Engineering

institute: South Dakota Mines

description: 3 Graphene Cu VS No copper control_FC

data_processing:
The bioinformatics pipelines and data analysis were performed using a web-based scientific assessment platform called Galaxy.
The raw RNA-seq reads were subjected to QC analysis using the FASTQC tool in GALAXY.
The quality-checked reads were then trimmed for adapters and linkers using the Trimmomatic tool (Galaxy version 2.11).
Assembly: The QC reads were mapped against the corresponding reference genomes (OA-G20 - NCBI Reference sequence: NC_007519.1) using the HISAT2 (Galaxy Version 2.2.1+galaxy1) alignment tool.
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including fold changes for each sample

organism: Oleidesulfovibrio alaskensis

source_name: Bacterial culture

growth_protocol: Oleidesulfovibrio alaskensis was grown in lactate C media in serum bottle under anaerobic condition purged with N2. The cultures were incubated at 34 °C under shaking conditions at 120 rpm for 7 days.

extract_protocol:
RNA was extracted using TRIzol Max Bacterial RNA Isolation Kit (Ambion, Life Technologies) and purified using RNA clean and concentrator kit (Zymo Research).
Swift Rapid RNA Library Kit (Swift Biosciences)

treatment_protocol: The cultures were exposed to pristine copper and graphene-coated copper. Here no copper (no treatment) served as the control.

value: Bacterial culture

value: G20 WT

value: Graphene copper


title: OE_1


title: ADT: Adipose Tissue Biopsy, P5544_CW1

value: HIV+ non-diabetic and HIV+ prediabetic


title: BSA control recplicate 2


title: Graphene-coated copper, replicate 2

description: 3 Graphene Cu VS No copper control_FC


title: Graphene-coated copper, replicate 1

description: 3 Graphene Cu VS No copper control_FC


title: PSTOL1_Root_36DAS_HP_1

value: 36 DAS


title: WT_3


title: BSA control recplicate 1


title: RNA: Adipose Tissue Biopsy, P5544_CW1


title: Null_Root_36DAS_LP_3

value: Null Segregant

value: Low Phosphate


title: ADT: Adipose Tissue Biopsy, P5344_CW3

value: HIV- diabetic


title: Pristine copper, replicate 2

description: 2 Pristine Cu VS Graphene Cu_FC

value: Pristine copper


title: Pristine copper, replicate 1

description: 2 Pristine Cu VS Graphene Cu_FC


title: Null_Root_36DAS_LP_2

value: Fielder


title: Null_Root_36DAS_LP_1


title: WT_1


title: RNA: Adipose Tissue Biopsy, P5344_CW3


title: Null_Root_36DAS_HP_3

value: High Phosphate


title: ADT: Adipose Tissue Biopsy, P5344_CW2 1


title: KO_2


title: KO_3


title: No treatment (Control), replicate 2

description: 1 No copper conrol VS Pristine Cu_FC

value: No treatment (Control)


title: No treatment (Control), replicate 3

description: 1 No copper conrol VS Pristine Cu_FC


title: Null_Root_36DAS_HP_2

value: Roots


title: ADT: Adipose Tissue Biopsy, P5344_CW1


title: RNA: Adipose Tissue Biopsy, P5344_CW1


title: Null_Root_36DAS_HP_1


title: Pristine copper, replicate 3

description: 2 Pristine Cu VS Graphene Cu_FC


title: KO_1

value: colon


title: WT_2

value: HCT116 cells


title: RNA: Adipose Tissue Biopsy, P5344_CW2 1

value: HIV+ diabetic


title: TFΔ Δume6 a/α GlcNAc CO₂ [SAMPLE 83]

status: Public on Aug 29 2023

city: San Francisco

first: Matthew

last: Lohse

state: CA

address: 44 Vicksburg Street

institute: BioSynesis, Inc.

description: RNA quantity was normalized to a concentration of 20 ng/µL in a volume of at least 20 µL. Samples were processed on a nCounter Sprint Profiler using a custom CodeSet with probes designed against 68 genes and 4 UTRs from Candida albicans

hyb_protocol: Default nCounter Sprint Profiler protocol

scan_protocol: Samples were processed on a nCounter Sprint Profiler (NanoString Technologies) at the LCA-Genome Core Facility at the University of California, San Francisco.

data_processing: Read count data was processed using the nSolver analysis software (NanoString Technologies). Raw counts were exported from nSolver (version 4.0.70) and then normalized with R (version 4.0.2) (R Core Team 2019) using the tidyverse package (version 1.3.0) (Wickham 2017). All data was normalized based on five housekeeping genes (PGA59, TBP1, HTA1, PAT1 (C4_04870C), DYN1). The geometric mean of these five housekeeping genes for each sample was calculated, and the difference between the geometric mean of these housekeeping genes across all samples and the geometric mean of these five housekeeping genes in each individual sample was determined. This difference was then subtracted from all reads in that individual sample to normalize the data and these normalized read counts were used for all further comparisons and analyses.

organism: Candida albicans

source_name: TFΔ Δume6 a/α GlcNAc CO₂

growth_protocol: Cultures of strains being profiled were most commonly grown in SCGlcNAc+aa+Uri with 5% CO2; when needed cultures were grown in SCD+aa+Uri and/or ambient air. Cultures were 2 mL in 24-well deep well format plates sealed with Breathe-Easy® sealing membranes (Diversified Biotech, BEM-1). Ambient air cultures were agitated at 200rpm at 25°C in a Excella E25 Incubator (New Brunswick Scientific), CO2 cultures were agitated at 600rpm at 25°C in an Incu-Mixer MP shaker (Benchmark) placed in an anerobic chamber (COY Lab Products) set to 21% O2 and 5% CO2 at room temperature (approximately 22°C). Overnight cultures were diluted back between 10- and 50-fold into fresh media and allowed to grow for approximately five hours. At this point, 1.5 mL of each strain was centrifuged, decanted, and flash frozen before storing at -80°C.

extract_protocol: Total RNA was extracted using a MasterPure™ Yeast RNA Purification Kit (Lucigen MPY03100), RNA concentration was then determined using a Qubit® RNA BR Kit and Qubit® Fluorometer (Molecular Probes / Life Tchnologies), and RNA quantity was normalized to a concentration of 20 ng/µL in a volume of at least 20 µL.

treatment_protocol: No treatament other than different growth conditions (e.g. glucose or GlcNAc as carbon source, ambient air or 5% carbon dioxide atmoshpere)

tag: strain

value: SC5314 a/α Δ/Δume6

tag: carbon source

value: GlcNAc

tag: atmosphere

value: 5% Carbon dioxide


title: No treatment (Control), replicate 1

description: 1 No copper conrol VS Pristine Cu_FC

value: Bacterial culture

value: G20 WT


title: TFΔ Δsfl2 a/α GlcNAc CO₂ [SAMPLE 77]

source_name: TFΔ Δsfl2 a/α GlcNAc CO₂

value: SC5314 a/α Δ/Δsfl2


title: TFΔ Δsfl2 a/α GlcNAc CO₂ [SAMPLE 78]


title: P75010 α/Δ GlcNAc CO₂ [SAMPLE 71]

source_name: P75010 α/Δ GlcNAc CO₂


title: TFΔ CONTROL a/α GlcNAc CO₂ [SAMPLE 76]

source_name: TFΔ CONTROL a/α GlcNAc CO₂

value: SC5314 a/α TFKO control


title: TFΔ Δrfx2 a/α GlcNAc CO₂ [SAMPLE 82]

source_name: TFΔ Δrfx2 a/α GlcNAc CO₂

value: SC5314 a/α Δ/Δrfx2


title: TFΔ Δbrg1 a/α GlcNAc CO₂ [SAMPLE 79]

source_name: TFΔ Δbrg1 a/α GlcNAc CO₂

value: SC5314 a/α Δ/Δbrg1


title: CEM133 Glucose air [SAMPLE 61]

source_name: CEM133 Glucose air

value: glucose

value: ambient air


title: CEM134 GlcNAc CO₂ [SAMPLE 59]

source_name: CEM134 GlcNAc CO₂


title: CEM134 GlcNAc CO₂ [SAMPLE 60]


title: CEM133 GlcNAc CO₂ [SAMPLE 58]

source_name: CEM133 GlcNAc CO₂


title: CEM133 Glucose air [SAMPLE 62]


title: CEM134 Glucose air [SAMPLE 63]

source_name: CEM134 Glucose air


title: CEM133 GlcNAc CO₂ [SAMPLE 57]


title: CI32 Glucose air [SAMPLE 54]

source_name: CI32 Glucose air

value: CI32 a/α


title: CI21 Glucose air [SAMPLE 51]

source_name: CI21 Glucose air

value: CI21 a/α


title: TFΔ Δume6 a/α GlcNAc CO₂ [SAMPLE 84]


title: TFΔ SC5314 a/α GlcNAc CO₂ [SAMPLE 73]

source_name: TFΔ SC5314 a/α GlcNAc CO₂


title: SC5314 a/α Glucose CO₂ [SAMPLE 50]

source_name: SC5314 a/α Glucose CO₂


title: TFΔ Δrfx2 a/α GlcNAc CO₂ [SAMPLE 81]


title: SC5314 a/α Glucose CO₂ [SAMPLE 49]


title: SC5314 a/α Glucose air [SAMPLE 42]

source_name: SC5314 a/α Glucose air


title: SC5314 a/α GlcNAc air [SAMPLE 44]

source_name: SC5314 a/α GlcNAc air


title: CEM134 Glucose air [SAMPLE 64]


title: CI21 GlcNAc CO₂ [SAMPLE 39]

source_name: CI21 GlcNAc CO₂


title: CI21 GlcNAc CO₂ [SAMPLE 40]


title: CI23 GlcNAc CO₂ [SAMPLE 38]

source_name: CI23 GlcNAc CO₂

value: CI23 a/α


title: TFΔ CONTROL a/α GlcNAc CO₂ [SAMPLE 75]


title: CI32 GlcNAc CO₂ [SAMPLE 33]

source_name: CI32 GlcNAc CO₂


title: CI32 a/Δ GlcNAc CO₂ [SAMPLE 67]

source_name: CI32 a/Δ GlcNAc CO₂

value: CI32 a/Δ


title: TFΔ Δbrg1 a/α GlcNAc CO₂ [SAMPLE 80]


title: P75010 α/Δ GlcNAc CO₂ [SAMPLE 72]

source_name: P75010 α/Δ GlcNAc CO₂


title: SC5314 a/α GlcNAc CO₂ [SAMPLE 36]

source_name: SC5314 a/α GlcNAc CO₂


title: CI32 a/Δ GlcNAc CO₂ [SAMPLE 68]


title: CI32 Glucose air [SAMPLE 53]


title: CI34 Glucose air [SAMPLE 48]

source_name: CI34 Glucose air

value: CI34 a/α


title: CI06 GlcNAc CO₂ [SAMPLE 30]

source_name: CI06 GlcNAc CO₂

value: CI06 a/α


title: CI17 Glucose air [SAMPLE 46]

source_name: CI17 Glucose air

value: CI17 a/α


title: SC5314 a/α GlcNAc air [SAMPLE 43]

value: GlcNAc


title: CI34 Glucose air [SAMPLE 47]


title: CI21 Glucose air [SAMPLE 52]


title: CI17 Glucose air [SAMPLE 45]


title: CI02 GlcNAc CO₂ [SAMPLE 27]

source_name: CI02 GlcNAc CO₂

value: CI02 a/α

value: 5% Carbon dioxide


title: CI32 GlcNAc CO₂ [SAMPLE 34]


title: CI06 GlcNAc CO₂ [SAMPLE 29]


title: SC5314 a/α GlcNAc CO₂ [SAMPLE 35]


title: CI23 GlcNAc CO₂ [SAMPLE 37]


title: CI18 GlcNAc CO₂ [SAMPLE 32]

source_name: CI18 GlcNAc CO₂

value: CI18 a/α


title: CI36 GlcNAc CO₂ [SAMPLE 26]

source_name: CI36 GlcNAc CO₂

value: CI36 a/α


title: SC5314 a/α Glucose air [SAMPLE 41]


title: TFΔ SC5314 a/α GlcNAc CO₂ [SAMPLE 74]


title: CI18 GlcNAc CO₂ [SAMPLE 31]


title: CI02 GlcNAc CO₂ [SAMPLE 28]


title: sunflower stem, ZT32, West side, rep3

city: Davis

first: Stacey

last: Harmer

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

data_processing:
Reads were filtered for quality using fastx toolkit so that at least 95 percent of bases must have a score of 20
Read counts were generated using salmon-1.4.0 against a transcriptome biult using cufflinks v2.2.1 gffread using the Ha412HOv2.0 genome and the Eugene annotation (HAN412_Eugene_curated_v1)
Counts were then normalized using edgeR TMM method and counts-per-million were extracted
Assembly: Ha412HOv2.0 genome and the Eugene annotation (HAN412_Eugene_curated_v1)  from the sunflower genome database
Supplementary files format and content: phototropism_counts.csv, contains the raw Salmon generated counts of the phototropism data
Supplementary files format and content: phototropism_cpm.csv, contains the edgeR normalized counts-per-million of the phototropism data
Supplementary files format and content: Heliotropism_counts.csv, contains the raw Salmon generated counts of the heliotropism data
Supplementary files format and content: Heliotropism_cpm.csv, contains the edgeR normalized counts-per-million of the heliotropism data

organism: Helianthus annuus

source_name: stem

growth_protocol: Sunflower seeds (HA412-HO) were obtained from USDA North Central Regional Plant Introduction Station (USDA Germplasm Resources Information Network ID: PI 603993). Seeds were germinated in flats (filled with SunGro® Sunshine® mix #1) covered with a lid for two days. Lids were then removed and plants were grown in controlled environment chambers in 16 light:8 dark with 180 µmol m–2  s–1 fluorescent light at constant 25 °C.

extract_protocol:
RNA was extracted according to the high-throughput method found in "A High-Throughput Method for Illumina RNA-seq Library Preparation" from Kumar et al. 2012.
RNA-seq libraries were prepared according to the high-throughput method found in "A High-Throughput Method for Illumina RNA-seq Library Preparation" from Kumar et al. 2012.

treatment_protocol: For heliotropism experiments, sunflowers were transplanted to the field 4-5 days after germination. At two weeks old stem tissue was collected from the east and west sides of these plants every 4 hours for 2 days starting at ZT0.

value: stem

value: WT

value: West side

tag: time

tag: experiment

value: heliotropism


title: sunflower stem, ZT32, West side, rep2

tag: tissue


title: sunflower stem, ZT32, East side, rep3

value: East side


title: sunflower stem, ZT32, East side, rep2


title: sunflower stem, ZT32, East side, rep1


title: CI16 GlcNAc CO₂ [SAMPLE 7]

source_name: CI16 GlcNAc CO₂

value: CI16 a/α


title: CI16 GlcNAc CO₂ [SAMPLE 8]


title: sunflower stem, ZT28, West side, rep3


title: CI19 GlcNAc CO₂ [SAMPLE 10]

source_name: CI19 GlcNAc CO₂

value: CI19 a/α


title: CI19 GlcNAc CO₂ [SAMPLE 9]


title: CI07 GlcNAc CO₂ [SAMPLE 17]

source_name: CI07 GlcNAc CO₂

value: CI07 a/α


title: CI27 GlcNAc CO₂ [SAMPLE 11]

source_name: CI27 GlcNAc CO₂

value: CI27 a/α


title: CI07 GlcNAc CO₂ [SAMPLE 18]


title: CI17 GlcNAc CO₂ [SAMPLE 19]

source_name: CI17 GlcNAc CO₂


title: CI27 GlcNAc CO₂ [SAMPLE 12]


title: CI34 GlcNAc CO₂ [SAMPLE 13]

source_name: CI34 GlcNAc CO₂

value: CI34 a/α


title: CI34 GlcNAc CO₂ [SAMPLE 14]


title: CI35 GlcNAc CO₂ [SAMPLE 16]

source_name: CI35 GlcNAc CO₂

value: CI35 a/α


title: CI35 GlcNAc CO₂ [SAMPLE 15]


title: sunflower stem, ZT32, West side, rep1


title: sunflower stem, ZT24, West side, rep3


title: sunflower stem, ZT28, West side, rep2


title: sunflower stem, ZT24, West side, rep2


title: sunflower stem, ZT28, East side, rep3


title: sunflower stem, ZT24, West side, rep1


title: sunflower stem, ZT28, East side, rep1


title: sunflower stem, ZT28, East side, rep2


title: CI17 GlcNAc CO₂ [SAMPLE 20]

value: CI17 a/α


title: SC5314 α GlcNAc CO₂ [SAMPLE 22]

source_name: SC5314 α GlcNAc CO₂

value: SC5314 white α/Δ

value: GlcNAc


title: CI36 GlcNAc CO₂ [SAMPLE 25]

value: 5% Carbon dioxide


title: sunflower stem, ZT28, West side, rep1


title: SC5314 α GlcNAc CO₂ [SAMPLE 21]


title: SC5314 a Opaque GlcNAc CO₂ [SAMPLE 6]

source_name: SC5314 a Opaque GlcNAc CO₂

value: SC5314 opaque a/Δ


title: sunflower stem, ZT20, West side, rep3


title: sunflower stem, ZT24, East side, rep3


title: sunflower stem, ZT24, East side, rep2


title: sunflower stem, ZT20, West side, rep2


title: sunflower stem, ZT20, East side, rep1


title: sunflower stem, ZT16, West side, rep2


title: sunflower stem, ZT16, West side, rep3


title: sunflower stem, ZT24, East side, rep1


title: sunflower stem, ZT20, East side, rep3


title: SC5314 a/α GlcNAc CO₂ [SAMPLE 2]

source_name: SC5314 a/α GlcNAc CO₂


title: SC5314 a/α GlcNAc CO₂ [SAMPLE 1]


title: sunflower stem, ZT16, West side, rep1


title: sunflower stem, ZT20, East side, rep2


title: sunflower stem, ZT20, West side, rep1


title: Stroke ME4-L

city: Bryan

first: Rajesh

last: Miranda

state: Texas

address: 8441 Riverside Pkwy

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University School of Medicine

data_processing:
Trimmomatic read trimmer was used to evaluate and trim all adapter sequences and low quality bases. Reads were scanned with a sliding window of 5, cutting when the average quality per base drops below 20, then trimming reads at the beginning and end if base quality drops below 25, and then if the read length is less than 35.
HISAT2 was used for read mapping
HTSeq generated transcript-wise counts
DESeq2 was used for normalizing counts, calculating fold change, and differential analysis.
Assembly: rn7
Supplementary files format and content: raw counts
Supplementary files format and content: normalized counts
Supplementary files format and content: result file

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Adult Sprague-Dawley rats were purchased from Envigo and breeding was done in house to produce fetuses for experiments.

extract_protocol:
Mesenteric adipose and liver were dissected from 5 month old animals that had either undergone Middle Cerebral Artery Occlussion 2 days prior or from littermates that were stroke-naive. Tissue flash frozen in liquid nitrogen and stored at -80 degrees Celcius. RNA was isolated using the Qiagen RNeasy Mini Kit.
RNA quantity was assessed using an Agilent TapeStation RNA assay.  Total RNA concentration was quantified via Qubit Fluorometric assay and subsequently all samples were normalized to an equivalent starting concentration. Sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Library Preparation kit (Illumina; San Diego, CA). Each sample was uniquely indexed (barcoded) to allow for pooling of all samples in a single sequencing run. Library size and quality were then assessed with an Agilent TapeStation D1000 DNA assay. Samples were normalized to ~4nM and pooled equally. Sequencing was performed on an Illumina NovaSeq S4 Flow Cell, XP running with a 150 cycle, paired‐end (2x150) sequencing run to generate approximately 50 million read pairs per sample.

treatment_protocol: Pregnant dams were distributed between treatment groups, vaporized ethanol or room air as control, and received treatment by vapor chamber for 12 days from gestationl day 8-20.

value: Sprague-Dawley

value: Liver

value: 5 month

value: Vaporized Ethanol

tag: stroke status

value: Stroke

value: Male


title: SC5314 a Opaque GlcNAc CO₂ [SAMPLE 5]


title: Stroke ME3-L


title: SC5314 a GlcNAc CO₂ [SAMPLE 4]

source_name: SC5314 a GlcNAc CO₂

value: SC5314 white a/Δ


title: SC5314 a GlcNAc CO₂ [SAMPLE 3]


title: sunflower stem, ZT12, East side, rep2

value: stem

value: WT

value: East side

value: heliotropism


title: sunflower stem, ZT12, West side, rep3

value: West side


title: sunflower stem, ZT12, East side, rep3


title: Stroke FE3-L

value: Female


title: Stroke ME1-L


title: Stroke FE2-L


title: Stroke ME2-L


title: sunflower stem, ZT12, West side, rep2


title: Stroke FE4-L


title: sunflower stem, ZT12, West side, rep1


title: sunflower stem, ZT16, East side, rep1


title: sunflower stem, ZT8, West side, rep3


title: sunflower stem, ZT12, East side, rep1


title: sunflower stem, ZT8, West side, rep1


title: Stroke FC4-L

value: Room air (control)


title: Stroke MC1-L


title: Stroke MC2-L


title: Stroke FE1-L


title: Stroke FC3-L


title: sunflower stem, ZT8, West side, rep2


title: sunflower stem, ZT16, East side, rep3


title: Stroke FC2-L


title: sunflower stem, ZT16, East side, rep2


title: Stroke ME4-A

source_name: Mesenteric Adipose

value: Mesenteric Adipose


title: sunflower stem, ZT4, West side, rep3


title: sunflower stem, ZT4, West side, rep2


title: Stroke FE4-A


title: Stroke ME1-A


title: sunflower stem, ZT4, East side, rep3


title: Stroke ME3-A


title: sunflower stem, ZT4, West side, rep1


title: sunflower stem, ZT4, East side, rep1


title: sunflower stem, ZT4, East side, rep2


title: Stroke FC1-L


title: Stroke ME2-A


title: Stroke FE3-A


title: sunflower stem, ZT8, East side, rep2


title: sunflower stem, ZT0, West side, rep3


title: Stroke MC3-L


title: sunflower stem, ZT8, East side, rep3


title: 03-T-KPT-LN-D

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

description: Relapse N

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 19.5h in an Eppendorf thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing: Data were analyzed with nSolver software version 4.0 and ROSALIND online software.

label: fluorescent probe

organism: Canis lupus familiaris

source_name: lymph node aspirate

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from frozen lymph node aspirates using Qiagen RNEasy kit per the manufacturer's instructions.

value: Relapse

tag: pfs

tag: ost

tag: treatment arm

tag: fail <90 days y vs n

value: N


title: 05-T-DOXRV-LN-D

description: Relapse Y

value: Y


title: Stroke FE2-A

value: Sprague-Dawley

tag: age

tag: treatment


title: sunflower stem, ZT8, East side, rep1


title: 07-T-KPT-LN-D

description: Relapse Y


title: 02-T-TAK-LN-D

description: Relapse Y


title: 02-T-DOXRV-LN-D

description: Relapse N


title: 07-T-TAK-LN-D

description: Relapse Y


title: sunflower stem, ZT0, West side, rep2


title: 06-T-DOXRV-LN-D

description: Relapse Y


title: Stroke FE1-A

value: 5 month


title: 05-T-KPT-LN-D

description: Relapse Y


title: sunflower stem, ZT0, West side, rep1


title: 03-T-TAK-LN-D

description: Relapse N


title: Stroke MC3-A


title: sunflower stem, ZT0, East side, rep3


title: Stroke MC2-A


title: sunflower stem, ZT0, East side, rep2


title: Stroke MC1-A


title: sunflower stem, ZT0, East side, rep1


title: 02-T-KPT-LN-D

description: Relapse N


title: sunflower stem, ZT44, West side, rep3


title: 01-T-TAK-LN-D

description: Relapse N


title: sunflower stem, ZT44, West side, rep2


title: Stroke FC4-A


title: 06-T-DOXRV-LN-A

description: Baseline Y


title: 05-T-TAK-LN-A

description: Baseline N


title: 01-T-KPT-LN-D

description: Relapse N


title: Stroke FC3-A


title: Stroke FC2-A


title: 05-T-DOXRV-LN-A

description: Baseline Y


title: 04-T-DOXRV-LN-A

description: Baseline N


title: 03-T-TAK-LN-A

description: Baseline N


title: 02-T-TAK-LN-A

description: Baseline Y


title: sunflower stem, ZT44, West side, rep1


title: sunflower stem, ZT44, East side, rep3


title: Stroke FC1-A


title: No stroke ME4-L

value: Liver

value: Vaporized Ethanol

value: No Stroke


title: sunflower stem, ZT44, East side, rep2


title: 01-T-TAK-LN-A

description: Baseline N


title: 07-T-KPT9274-LN-A

description: Baseline Y


title: sunflower stem, ZT44, East side, rep1


title: 06-T-KPTT9274-LN-D

description: Relapse N


title: 01-T-DOXRV-LN-A

description: Baseline N


title: sunflower stem, ZT40, West side, rep2


title: sunflower stem, ZT40, West side, rep3


title: 07-T-TAK-LN-A

description: Baseline Y


title: No stroke ME1-L

value: Male


title: No stroke ME2-L


title: sunflower stem, ZT40, West side, rep1

value: stem


title: No stroke FE3-L


title: No stroke FE4-L


title: 03-T-DOXRV1001-LN-D

description: Relapse N


title: 04-T-KPT9274-LN-A

description: Baseline Y


title: 03-T-KPT9274-LN-A

description: Baseline N


title: 04-T-DOXRV1001-LN-D

description: Relapse N


title: 06-T-KPT9274-LN-A

description: Baseline N


title: empty_well

city: New York

first: Meri

last: Rogava

state: New York

address: 650 W 168th St, New York, NY 10032

department: Hematology Oncology

institute: Columbia University

data_processing:
data processing steps were performed as described previously (Doench et al., 2016). CRISPR–Cas9 screens were analyzed using software packages MAGeCK and MAGeCKFlute. MAGeCK allows to analyze CRISPR/Cas9 screen data, and performs quality control, read count generation and normalization, calculated beta score to evaluate gene selection performance. MAGeCK’s robust rank aggregation (RRA) method was used to identify significantly enriched or depleted CRISPR-screen hits in cells and tumors. MAGeCKFlute R package was used for data analysis and visualization.
For RNAseq data analysis the tximeta R package (Love et al. 2020) was used to import transcript-level quantification data quantified with Salmon package (Patro et al. 2017). Reads were mapped to mouse reference - Mus_musculus.GRCm38.97 and DESeq2 package was applied to generate normalized data.
Genome_build: Mus_musculus.GRCm38.97

organism: blank sample

source_name: mouse melanoma cell line

growth_protocol: Mouse melanoma cell line HCmel12 (gift from Prof. Thomas Tueting, Magdeburg, Germany) were grown in ‘complete’ RPMI-1640 medium (Gibson Bioscience) supplemented with 10%FBS (Gibco™ 10437028), 10mM non-essential amino acids, 1mM HEPES (all from Life Technologies), 20 µM 2-mercaptoethanol (Sigma), 100 IU per ml penicillin and 100 µg/ml-1 streptomycin (Invitrogen). Cell lines were routinely tested for mycoplasma contamination using Lonza MycoAlert Kit (Cat. # LT07-318).

extract_protocol:
Genomic DNA from cells (edited for 10, 14, 21, 28, 35, 42, 49 and 52 days) and mouse tissue (primary tumor, lung, liver, lymph node), was extracted using Qiagen kit for DNeasy Blood & Tissue Kit (69506,Qiagen).
The procedure of amplifying pooled sgRNA library was based on the protocol described previously (Doench et al., 2016). Sequencing libraries were constructed as previously described (Doench et al., 2016) and sequenced on an Illumina HiSeq2500 Instrument.
sgRNA enrichment sequencing

treatment_protocol: HCmel12-Cas9 melanoma cells were transduced at a MOI < 0.1 with lentivirus produced from a kinome-wide lentiviral mouse CRISPR knockout guide library containing 2,852 sgRNAs (Brie, Addgene # 75316) with at least 1000-fold representation (cells per construct) in each infection replicate. Spin-infected ~30 million HCmel12_Cas9 cells with the kinome CRISPR lentivirus library at MOI =0.1 in multiple 6-well plates at Day 0, and transferred the cells into T75 flasks at Day 2. Blasticidin selection (10 µg/ml) started at Day 2, and cells were harvested at Day 7. Puromycin selection stated at day 2 and lasted the entire experiment. On day 14 tumor cells were harvested and used for in vivo screening experiment. In parallel to in vivo screening experiment, cells were kept in culture and continued to edit for 21, 28, 35, 42, 49 and 52 days, the entire duration in parallel to in vivo editing. In vitro edited cells were palleted and used for downstream gDNA extraction and library preparations. For in vivo screening, 3x106 of library-transduced HCmel12-Cas9 cells were injected into the right flank or lateral tail vein of the mice. Tumor growth and signs of sickness was monitored over time. Mice were euthanized after 4 weeks and tumors, lungs, lymph node and liver were evaluated for metastasis presence, lesions dissected for gDNA isolation, amplification of the sgRNA region, and sequencing.

tag: cell line

tag: pertubation/treatment

tag: sample origin

value: no sample


title: 05-T-KPT9274-LN-A

description: Baseline Y


title: sunflower stem, ZT40, East side, rep3

tag: genotype

value: WT

value: East side


title: 02-T-DOXRV-LN-A

description: Baseline N


title: 02-T-KPT9274-LN-A

description: Baseline N


title: No stroke FE2-L

tag: strain

tag: Sex


title: Ten worms population, biol rep 1

city: Warsaw

first: Michal

last: Turek

address: Pwinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Caenorhabditis elegans reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: WBcel235
Supplementary files format and content: comma-delimited csv file including raw counts for each sample
Supplementary files format and content: comma-delimited csv file include RPKM values for each Sample

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Worms were maintained on nematode growth medium (NGM) plates seeded with bacteria Escherichia coli OP50 at 20°C

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus mini kit following the manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB, Ipswich, MA, USA)

treatment_protocol: Worms were grown as solitary animals or in a ten worms population

value: whole organism

tag: developmental stage

value: adulthood day 2


title: Ten worms population, biol rep 2


title: Ten worms population, biol rep 3


title: Solitary worms, biol rep 3


title: sunflower stem, ZT40, East side, rep2

source_name: stem

tag: time

value: heliotropism


title: sunflower stem, ZT40, East side, rep1

tag: experiment


title: Solitary worms, biol rep 2

tag: tissue


title: 03-T-DOXRV-LN-A

description: Baseline N


title: Solitary worms, biol rep 1


title: sunflower stem, ZT36, West side, rep3

value: West side


title: BAT-WT4-IGG

city: Shanghai

first: Jiang-Feng

last: Ke

address: 600 Yishan Road

institute: Shanghai sixth people's hospital

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
The high quality reads were aligned to the human reference genome (UCSC mm10) with hisat2 software
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified
Assembly: mm10
Supplementary files format and content: mRNA_Expression profilling.xls，Contains mRNA Expression information

source_name: Brown adipose tissue

extract_protocol:
Total RNA was extracted using Trizol reagent
The RNA immunoprecipitation assay was carried out with GenSeq® RIP kit (GenSeq Inc., China) according to the manufacturer’s instructions. rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA). RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.

value: Brown adipose tissue

tag: fraction

value: IgG


title: BAT-WT4-IP

value: IP


title: WT-cold-BAT-IgG

tag: protocol

value: cold


title: sunflower stem, ZT36, West side, rep2


title: Splenic GC B cells, DZ_KO1

city: Toulouse

first: Manuel

middle: D

last: Diaz-Munoz

address: CHU Purpan, BP3028

country: France

institute: INSERM

data_processing:
Sample raw sequencing files were processed using nextflow nf-core/RNAseq pipeline (v3.8.1).
Reads from different sequencing lanes were concatenated using bash cat utility, trimmed with Cutadapt (v3.4) and Trimgalore (v.0.6.7). The quality of resulting reads was assessed with FASTQC-0.11.9 using default parameters.
paired-end reads were aligned to the mouse genome (GRCm39-v106) and quantified with Salmon v1.5.2. Alignment files were indexed using SamTools (v. 1.15.1).
R (v4.0.2) and DESeq2 (v1.28.1) was used for differential expression analysis using default parameters.
Assembly: mm10 (GRCm39-v106)
Supplementary files format and content: csv file =  DESeq2 normalized gene counts

source_name: Spleen

extract_protocol:
After cell FACs sorting, total RNA was isolated using the Rneasy Micro kit from Qiagen. Quantity and quality of RNA was measured in a BioAnalyser prior library generation.
NEBNext® cDNA synthesis, Amplification and library generation #E6420
150 bp PE sequencing

value: Spleen

tag: cell type

value: Primary B cells

tag: zone

value: DZ GC B cell

tag: mouse strain

value: Tia1 Tial1 KO

value: In vivo immunization with NP-KLH alum (100 ug, ip)

tag: neb index id (for illumina)

tag: neb index sequence

value: i5 TTGCTTGC i7 CTGATGAG


title: No stroke MC2-L

value: Sprague-Dawley

value: Liver

tag: age

value: 5 month

tag: treatment

value: Room air (control)

tag: stroke status

value: No Stroke

value: Male


title: No stroke MC3-L


title: Splenic GC B cells, DZ_KO2

tag: genotype

value: i5 TGTGGCAT i7 GCAGAAGA


title: No stroke FC4-L

tag: strain

value: Female


title: WT-cold-BAT-IP

value: Brown adipose tissue


title: No stroke MC1-L

tag: Sex


title: sunflower stem, ZT36, East side, rep3

value: stem

value: WT

value: East side

value: heliotropism


title: Splenic GC B cells, DZ_WT2

value: Spleen

value: Primary B cells

value: DZ GC B cell

value: Wild type

value: i5 ACTACGGA i7 GGATCTGA


title: No stroke FE1-L

value: Sprague-Dawley

value: Liver

value: Vaporized Ethanol


title: No stroke FC3-L

value: 5 month

value: Room air (control)

value: No Stroke


title: No stroke ME3-L

value: Male


title: Splenic GC B cells, DZ_WT3

value: In vivo immunization with NP-KLH alum (100 ug, ip)

value: i5 AAGCGGAA i7 AACCTACG


title: sunflower stem, ZT36, East side, rep1

value: stem

value: WT


title: Splenic GC B cells, DZ_WT4

value: i5 CGGAACAA i7 AAGCGACT


title: Splenic GC B cells, DZ_WT1

value: Spleen

value: i5 GAGAGGTT i7 GGATCTGA


title: Splenic GC B cells, LZ_KO3

value: Primary B cells

value: LZ GC B cell

value: Tia1 Tial1 KO

value: i5 ACTACGGA i7 GCAGAAGA


title: sunflower stem, ZT36, East side, rep2

value: East side

value: heliotropism


title: No stroke FC2-L

value: Sprague-Dawley

value: Liver

value: 5 month

value: Female


title: No stroke FC1-L

value: Room air (control)

value: No Stroke


title: sunflower stem, ZT21, lit side, rep6

treatment_protocol: For phototropism experiments, two-week old chamber-grown sunflowers were placed in front of unidirectional blue lights (Yescom 225 Blue LEDs Grow Light Ultrathin Panel, 280 µmol  m–2  s–1) in a growth chamber at constant 25 °C. Plants were placed in front of the lights and ZT3 and tissue was collected from the shaded and lit sides of stems at 9 different timepoints from ZT3 to ZT21

value: stem

value: Lit side

value: phototropism


title: Splenic GC B cells, LZ_KO1

value: Spleen

value: In vivo immunization with NP-KLH alum (100 ug, ip)

value: i5 ACTACGGA i7 AAGCGTTC


title: sunflower stem, ZT36, West side, rep1

value: WT

value: West side


title: sunflower stem, ZT21, lit side, rep5


title: Splenic GC B cells, LZ_WT3

value: Primary B cells

value: LZ GC B cell

value: Wild type

value: i5 AAGCGGAA i7 TGATCACG


title: Splenic GC B cells, LZ_WT2

value: i5 AAGCGGAA i7 GGATCTGA


title: No stroke ME3-A

value: Sprague-Dawley

value: Mesenteric Adipose

value: 5 month

value: Vaporized Ethanol

value: Male


title: No stroke ME4-A

value: No Stroke


title: No stroke ME2-A


title: sunflower stem, ZT21, lit side, rep4

value: stem

value: Lit side

value: phototropism


title: sunflower stem, ZT21, lit side, rep3


title: No stroke ME1-A


title: sunflower stem, ZT21, lit side, rep2


title: Splenic GC B cells, LZ_KO2

value: Spleen

value: Tia1 Tial1 KO

value: In vivo immunization with NP-KLH alum (100 ug, ip)

value: i5 GGTAAGCT i7 GCAGAAGA


title: 01-T-KPT9274-LN-A

description: Baseline N

tag: pfs

tag: ost

tag: treatment arm

tag: fail <90 days y vs n

value: N


title: No stroke FE4-A

tag: tissue

value: Female


title: No stroke FE3-A


title: RNAseq_mTOR WT HSCs_DMSO_2

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

description: RNAseq

data_processing:
Sequence reads were trimmed using Trim Galore! v0.4.2 and cutadapt v1.9.1.
The trimmed reads were aligned to the reference mouse genome version mm10 using STAR v2.6.1e.
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8.
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package.
Raw counts were normalized as Fragments Per Kilobase of transcript per Million mapped reads(FPKM).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: bone marrow

growth_protocol: HSC cells from poly(I:C)-treated mTOR WT mice were sorted by FACS and then cultured in StemSpan SFEM medium.

extract_protocol:
RNA were extracted using miRNeasy Micro Kit (Qiagen, 217084).
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: mTOR WT HSC cells were cultured in normal StemSpan SFEM medium or medium with 0.01% DMSO respectively and then followed by RNA-seq.

value: bone marrow

value: hematopoietic stem cells (HSCs)

value: mTOR WT HSC cells cultured in medium with 0.01% DMSO


title: RNAseq_mTOR WT HSCs_DMSO_1

description: RNAseq


title: RNAseq_mTOR WT HSCs_3

description: RNAseq

value: mTOR WT HSC cells cultured in normal medium


title: RNAseq_mTOR WT HSCs_DMSO_3

description: RNAseq


title: RNAseq_mTOR WT HSCs_DMSO_4

description: RNAseq


title: RNAseq_mTOR WT HSCs_4

description: RNAseq


title: RNAseq_mTOR WT HSCs_2

description: RNAseq


title: sunflower stem, ZT21, lit side, rep1

value: WT

tag: time

tag: experiment


title: RNAseq_mTOR WT HSCs_1

description: RNAseq

tag: cell type


title: Splenic GC B cells, LZ_WT4

value: Primary B cells

tag: zone

value: LZ GC B cell

tag: mouse strain

value: Wild type

value: i5 CGGAACAA i7 AAGGCGTA


title: No stroke FE2-A

value: Sprague-Dawley

value: Mesenteric Adipose

value: 5 month

value: Vaporized Ethanol

value: No Stroke


title: sunflower stem, ZT21, shaded side, rep6

value: stem

value: Shaded side

value: phototropism


title: Splenic GC B cells, LZ_WT1

value: Spleen

value: In vivo immunization with NP-KLH alum (100 ug, ip)

tag: neb index id (for illumina)

tag: neb index sequence

value: i5 ACTACGGA i7 TTCCTCCT


title: sunflower stem, ZT21, shaded side, rep5

tag: treatment


title: MR13

library_source: transcriptomic single cell

data_processing:
Following single sample pre-processing and filtering, we merged all biological samples (n = 16 murine tumors) to yield a total of 98,126cells with a median library size of 2,065 transcripts per cell. Genes detected in fewer than 5 cells (n = 12,621) were excluded. Cell doublet scores computed in individual samples were subsequently assessed in the merged library. A doublet score threshold was computed based on where the first derivative of the distribution (smoothed using the Savitzky-Golay filter from SciPy (v1.6.3)) plateaued to zero was used to remove 2,520 (2.6%) putative doublet cells with doublet score greater than the threshold from the merged cell atlas.
In order to construct a count matrix from raw reads, we used CellRanger (v6.0.2) for sample demultiplexing, alignment to CellRanger’s refdata-gex-mm10-2020-Areference, barcode processing, and collapsing groups of reads with the same unique molecular identifier (UMI), cell barcode and gene annotation. The count matrix was then loaded into python using scanpy1 (v1.7.2) for subsequent pre-processing and downstream analyses. Redundant gene instances (n = 38) were collapsed by summing their cumulative molecule counts. We then followed several filtering steps within each sample to ensure high data quality.
Genome_build: Mus_musculus.GRCm38.97

source_name: mouse melanoma model_HCMel12

extract_protocol: For scRNAseq Cells were counted and ~15,000 cells were separated for droplet-based RNA capture and reverse transcription using 10x Genomics reagents and a Chromium controller.

tag: cell line

tag: pertubation/treatment

value: Liver

tag: sample origin

value: in vivo


title: MR12

value: Lung


title: No stroke FE1-A

tag: strain

tag: age

tag: stroke status

tag: Sex

value: Female


title: sunflower stem, ZT21, shaded side, rep3

tag: genotype

value: WT


title: No stroke MC3-A

tag: tissue

value: Room air (control)

value: Male


title: MR11


title: MR10


title: sunflower stem, ZT21, shaded side, rep2

tag: time


title: No stroke MC1-A

value: Sprague-Dawley

value: Mesenteric Adipose


title: MR07


title: No stroke FC4-A

value: 5 month


title: MR16


title: MR08


title: sunflower stem, ZT18, lit side, rep6

value: Lit side

tag: experiment


title: MR09


title: No stroke FC3-A

value: No Stroke


title: sunflower stem, ZT21, shaded side, rep1

value: stem

value: Shaded side


title: MR15


title: MR04


title: sunflower stem, ZT18, lit side, rep5

value: phototropism


title: MR05


title: MR02


title: No stroke FC2-A


title: MR14


title: sunflower stem, ZT18, lit side, rep4


title: MR06


title: No stroke MC2-A


title: mouse 4530, Ncoa5+/-Tip30+/- [m4530_CIA_T30]

city: East Lansing

first: Hua

last: Xiao

state: Michigan

address: 567 WILSON RD, RM 2201

department: Physiology

institute: Michigan State University

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4530_CIA_T30
DESeq2_normcounts.csv

data_processing:
Raw data was delivered by Novogene. Approximately 50 million reads were generated for each sample.
Raw data were trimmed to remove low quality and adapter reads using Trimmomatic 0.36 with the parameter: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36, and aligned to Ensembl GRCm38r92 fenmale genome using STAR 2.6.0c
Count normalization and gene expression analysis were conducted using DESeq2 1.28.1
Gene expression table was generated using DESeq2 normalized counts.
Assembly: Ensembl GRCm38
Supplementary files format and content: Bam files are output alignment files by STAR for each sample. Csv file contains DESeq2 normalized counts for all samples.

source_name: liver

growth_protocol: All mice were housed in Optimice cages at Michigan State University animal facility on a 12:12-h light-dark cycle and fed standard rodent diet ad libitum

extract_protocol:
A piece of liver was cut from samples collected from mice shortly after euthanasia and freshly frozen in liquid nitrogen. Livers were homogenized in TRIzol and total RNA was extracted using a combined TRIzol and RNeasy Mini Kit (Qiagen) method. RNA quality control was performed using the Nanodrop Spectrophotometer (Thermo Fisher) and Bioanalyzer (Agilent).
250~300bp insert cDNA library preparation was carried out by Novogene. Generally mRNA was enriched using oligo(dT) beads. mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. (Method provided by Novogene)

value: liver

tag: cell type

value: mainly hepatocyte


title: MR01

value: Liver


title: No stroke FC1-A


title: mouse 4383, Ncoa5+/- [m4383_CIA_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4383_CIA_WT
DESeq2_normcounts.csv


title: mouse 4382, wild-type [m4382_WT_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4382_WT_WT
DESeq2_normcounts.csv


title: mouse 4361, wild-type [m4361_WT_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4361_WT_WT
DESeq2_normcounts.csv


title: MR03

value: in vivo


title: mouse 4359, Ncoa5+/-Tip30+/- [m4359_CIA_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4359_CIA_T30
DESeq2_normcounts.csv


title: sunflower stem, ZT18, lit side, rep2


title: ac57

city: Houston

first: Michael

last: Green

state: TX

address: 1515 Holcombe Blvd

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

description: 10x Genomics

library_source: other

data_processing:
Transcript level counting with cell ranger v6.0.0
TCR contig annotations with cell ranger v6.0.0
Assembly: hg38
Supplementary files format and content: gene expression matrix
Supplementary files format and content: TCR contig annotations

molecule: other

source_name: Blood cell culture

extract_protocol:
After completion of CAR T cell infusion, the infusion bag was washed with PBS to obtain residual cells for scRNA-seq and scTCR-seq.
Libraries were generated using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 3′ V5.1 reagent kits (10x Genomics) according to manufacturer's protocol.
RNA-Seq and TCR-seq

value: Blood cell culture

tag: disease setting

value: rrLBCL

value: CART


title: mouse 4358, Ncoa5+/- [m4358_CIA_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4358_CIA_WT
DESeq2_normcounts.csv


title: ac59

description: 10x Genomics


title: ac58

description: 10x Genomics


title: sunflower stem, ZT18, lit side, rep1

value: WT


title: mouse 4254, Ncoa5+/- [m4254_CIA_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4254_CIA_WT
DESeq2_normcounts.csv


title: mouse 4357, Tip30+/- [m4357_WT_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4357_WT_T30
DESeq2_normcounts.csv


title: ac56

description: 10x Genomics


title: ac55

description: 10x Genomics


title: sunflower stem, ZT18, shaded side, rep5


title: sunflower stem, ZT18, shaded side, rep4


title: sunflower stem, ZT21, shaded side, rep4


title: mouse 4253, wild-type [m4253_WT_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4253_WT_WT
DESeq2_normcounts.csv


title: mouse 4238, Ncoa5+/-Tip30+/- [m4238_CIA_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4238_CIA_T30
DESeq2_normcounts.csv


title: mouse 4252, wild-type [m4252_WT_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4252_WT_WT
DESeq2_normcounts.csv


title: mouse 4237, Ncoa5+/-Tip30+/- [m4237_CIA_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4237_CIA_T30
DESeq2_normcounts.csv


title: mouse 4207, Tip30+/- [m4207_WT_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4207_WT_T30
DESeq2_normcounts.csv


title: sunflower stem, ZT18, lit side, rep3


title: mouse 4187, Tip30+/- [m4187_WT_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4187_WT_T30
DESeq2_normcounts.csv


title: mouse 4184, Tip30+/- [m4184_WT_T30]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4184_WT_T30
DESeq2_normcounts.csv


title: ac51

description: 10x Genomics


title: sunflower stem, ZT18, shaded side, rep1


title: Ear SmoM2 induced 6weeks keratinocytes

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

description: 10x Genomics

data_processing:
Quality control and downstream analysis were performed using the Seurat R package (v.4.1.0). For each sample, all of the cells passed the following criteria: showed expression of more than 2000 and less than 7000 unique genes and had less than 10% UMI counts belonging to mitochondrial sequences.
Read counts were normalized by NormalizeData function of Seurat, with parameter ‘normalization.method = LogNormalize and scale.factor=10000’.
A PCA for each sample was calculated using the scaled expression data of the most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes).
UMAP calculation and graph-based clustering were done for each sample using the appropriate functions from Seurat (default parameters) with the respective PCA results as input.
In addition, to verify proliferating stages, the  S-phase and GS/M-phase scores were regressed out by CellCycleScoring function, implemented in the Seurat.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: proceeded R objects

source_name: Ear

extract_protocol:
To isolate skin epidermal cells, ears were dissected, opened in two along the cartilage with forceps and incubated in DMEM (Dubelcco’s Modified Eagle’s Medium- Gibco, thermo Fisher Scientific) - 0,25% Trypsin (Gibco, Thermo Fisher Scientific) overnight at 4°C. The back skin was first shaved with electric clippers, dissected and the hypodermis was then removed by scratching it with a scalpel. The remaining tissue (epidermis-dermis) was finally incubated in DMEM-0,25% trypsin overnight at 4°C by placing the dermis in contact with the solution. The day after, the epidermis was carefully separated from the dermis by using a scalpel and then incubated on a rocking plate (100 rpm) at room temperature for 5 min. Trypsin was neutralized by adding DMEM supplemented with 5% of Chelex-treated Fetal Calf Serum (CFCS) and epidermal cells were mechanically dissociated by pipetting 10 times. Samples were filtrated on a 70µm filter then on a 40µm filter and washed in a PBS-2% CFCS. Single cells were incubated with a biotinylated anti-CD34 primary antibody (clone RAM34; BD Biosciences; dilution 1:50) diluted in PBS-2% CFSC, for one hour on ice on a rocking plate, and protected from light. Cells were washed with PBS-2% CFCS, incubated for 45 min on ice, on a rocking plate, with streptavidin-APC secondary antibody (BD Biosciences; 1:400), washed again and finally resuspended in a Hoechst (10mg/ml) solution diluted at 1:4000 in PBS-2% CFCS.  Cell sorting was performed on a BD FACS Aria II using the FACSDiva software at the ULB Flow Cytometry Platform: living epidermal cells were gated by forward scatter, side scatter, and negative for Hoechst. SmoM2 mutated cells were isolated based on the expression of the YFP fused to the oncogene. Smom2-YFP expressing cells from the hair follicle bulge were excluded by the CD34-APC staining.  For wild type tissues living IFE and infundibulum cells were sorted on the negative expression of the CD34 marker only.
10,000 single cells from the back skin and ear skin were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).

value: Ear

value: SmoM2 Keratinocyte

tag: mutation

value: Tamoxifen (1mg/30g), 45 days before sacrifice


title: Ear Wildtype with CellPlex library

description: 10x Genomics

value: Keratinocyte


title: mouse 4251, Ncoa5+/- [m4251_CIA_WT]

description:
cDNA library synthesized by mRNA template enriched from total RNA
m4251_CIA_WT
DESeq2_normcounts.csv


title: Ear SmoM2 induced 3weeks keratinocytes

description: 10x Genomics

value: Tamoxifen (1mg/30g), 21 days before sacrifice


title: ac50

description: 10x Genomics


title: Ear Wildtype with GEX library

description: 10x Genomics


title: sunflower stem, ZT15, lit side, rep5

value: Lit side


title: BackSkin SmoM2 induced 3weeks keratinocytes

description: 10x Genomics

source_name: BackSkin

value: BackSkin


title: ac49

description: 10x Genomics


title: ac48

description: 10x Genomics


title: sunflower stem, ZT18, shaded side, rep3

value: stem

value: Shaded side


title: sunflower stem, ZT15, lit side, rep6

value: phototropism


title: sunflower stem, ZT15, lit side, rep4


title: 970, Ets1

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Data processing was performing using Chipseq ATACseq Pipelines 1.0.1 (https://github.com/russell-ryan-lab/ChIPseq_ATACseq_pipelines).
Paired-end reads were aligned to using BWA 0.7.17.
Read duplicates were removed using Picard 2.22.3 and multimapping reads were also removed.
Peak calling was performed using Homer 4.10 findPeaks (“style -factor” for human CDC73 amd "style -histone” for mouse H3K27ac). Peaks falling within ENCODE exclusion / problematic regions were removed (https://github.com/Boyle-Lab/Blacklist).
Coverage/signal files (bigWig) were produced using DeepTools 3.4.3 bamCoverage.
H2K120Ub1 was quantified over genes defined in the GENCODE M15 mouse annotation (basic GTF). Raw counts and RPKM-normalized counts were computed using Homer 4.10 analyzeRepeats.pl in a strand-insensitive manner using parameters: (-raw or -rpkm) -gid -count genes -strand both.
Assembly: mm10, hg19
Supplementary files format and content: H2K120Ub1 quantification files (read coverage over genes) are tab-delimited text files with headers and include gene annotations, raw counts (0.5 per read in paired-end data, as per Homer analyzeRepeats.pl), and RPKM.  Sample matrices fir counts and RPKM are also included for H2K120Ub1 data.

source_name: T-cell acute lymphoblastic leukemia

growth_protocol: T-ALL cell lines were grown in RPMI 1640 (Invitrogen) supplemented with 10% fetal bovine serum (Hyclone or Gibco), 2 mM L-glutamine, 2-mercaptoethanol (0.0005% (v/v), Sigma), penicillin and streptomycin.

extract_protocol:
Cells were crosslinked for most samples by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. For Ets1. For H3K27ac and H2K120ub1, cells were crosslinked with 1% formaldehyde at room temperature. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a QSonica Q800 bath sonicator in 0.3% SDS-containing lysis buffer. Samples were diluted 1:3.3 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples (vehicle-treated only), 1:8 diluted sonicated chromatin (whole cell extract) was added directly to the reverse crosslinking step without immunoprecipitation.
Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced on the Illumina NextSeq 550 (38 bp reads) or on the Illumina NovaSeq 6000 (151 bp reads) .

treatment_protocol: Murine T-ALL cells were treated with EtOH or OHT at 6nM for 30 hours prior to harvesting. THP-6 T-ALL cells were lentivirally transduced with pLKO.1-type shRNA for 2 days  and then selected with puromycin for 2 days prior to harvesting.

value: T-cell acute lymphoblastic leukemia

tag: chip-seq antibody

value: Ets1 (CST #D808A)

value: Rosa26CreERT2 Cdc73f/f


title: ac53

description: 10x Genomics

value: Blood cell culture


title: sunflower stem, ZT15, lit side, rep3


title: BackSkin Wildtype with CellPlex library

description: 10x Genomics


title: BackSkin SmoM2 induced 6weeks keratinocytes

description: 10x Genomics


title: 969, Ets1


title: ac54

description: 10x Genomics

value: rrLBCL


title: BackSkin Wildtype with GEX library

description: 10x Genomics


title: sunflower stem, ZT18, shaded side, rep6


title: sunflower stem, ZT18, shaded side, rep2


title: sunflower stem, ZT15, lit side, rep2


title: 970, input


title: ac46

description: 10x Genomics

value: CART


title: ac45

description: 10x Genomics


title: sunflower stem, ZT15, lit side, rep1

value: WT


title: 969, input


title: 970, H2K120ub1, OHT, 3

value: OHT


title: 970, H2K120ub1, OHT, 1


title: sunflower stem, ZT15, shaded side, rep6


title: 708, input

value: Rosa26CreERT2 Cdc73+/+


title: 970, H2K120ub1, OHT, 2


title: ac44

description: 10x Genomics


title: 970, H2K120ub1, EtOH, 3

value: EtOH


title: sunflower stem, ZT15, shaded side, rep5


title: 970, H2K120ub1, EtOH, 1


title: sunflower stem, ZT15, shaded side, rep4


title: ac52

description: 10x Genomics


title: sunflower stem, ZT15, shaded side, rep3


title: ac42

description: 10x Genomics


title: ac43

description: 10x Genomics


title: 970, H2K120ub1, EtOH, 2


title: ac40

description: 10x Genomics


title: 969, H2K120ub1, OHT, 2


title: 969, H2K120ub1, EtOH, 1


title: 708, H3K27ac, OHT, 3

value: H3K27Ac (Active Motif #39133)


title: ac41

description: 10x Genomics


title: 969, H2K120ub1, EtOH, 2


title: sunflower stem, ZT15, shaded side, rep1


title: 708, H3K27ac, OHT, 2


title: ac39

description: 10x Genomics


title: 969, H2K120ub1, OHT, 3


title: 708, H3K27ac, EtOH, 3


title: 708, H3K27ac, OHT, 1


title: 969, H2K120ub1, OHT, 1


title: 708, H3K27ac, EtOH, 2


title: sunflower stem, ZT12, lit side, rep6


title: sunflower stem, ZT12, lit side, rep4


title: 970, H3K27ac, OHT, 1


title: ac37

description: 10x Genomics


title: sunflower stem, ZT12, lit side, rep3


title: ac38

description: 10x Genomics


title: 970, H3K27ac, EtOH, 3


title: 970, H3K27ac, OHT, 3


title: 970, H3K27ac, EtOH, 2


title: ac35

description: 10x Genomics


title: ac36

description: 10x Genomics


title: 969, H2K120ub1, EtOH, 3


title: sunflower stem, ZT12, lit side, rep5


title: 970, H3K27ac, EtOH, 1


title: sunflower stem, ZT15, shaded side, rep2


title: 969, H3K27ac, OHT, 3


title: sunflower stem, ZT12, lit side, rep2


title: ac34

description: 10x Genomics


title: sunflower stem, ZT12, lit side, rep1


title: 969, H3K27ac, OHT, 2


title: 969, H3K27ac, OHT, 1


title: 970, H3K27ac, OHT, 2


title: ac33

description: 10x Genomics


title: sunflower stem, ZT12, shaded side, rep6


title: 969, H3K27ac, EtOH, 3


title: 969, H3K27ac, EtOH, 1


title: sunflower stem, ZT12, shaded side, rep5


title: 969, H3K27ac, EtOH, 2


title: ac31

description: 10x Genomics


title: ac29

description: 10x Genomics


title: sunflower stem, ZT12, shaded side, rep4


title: ac30

description: 10x Genomics


title: sunflower stem, ZT12, shaded side, rep3


title: 708, BruUV-seq, OHT, 1

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were trimmed using BBDuk (BB Tools 38.46). The bundled adapter sequences and following parameters were used for paired-end reads: ktrim=r, mink=11, hdist=1, k=31.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank BK000964.3) and the mitochondrial genomes (from the mm10 reference sequence) using Bowtie2 (2.3.3).
Reads that did not align to rRNA or the mitochondrial genome were subsequently mapped to the mouse genome build mm10/GRCm38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version M15.
Coverages were determined using BEDTools2 2.28.0 as (1 / read length) for each base in the genome. These base coverages were used to obtain pseudo-read counts in strand-specific regions of interest using bedtools intersect.
Bru-seq: Reads Per Kilobase per Megabase of library size (RPKM) were calculated for meta-transcripts ("genes") defined by merging exons and intervening intronic spaces from all isoforms of a gene in the GENCODE M15 "basic" annotation. Genes were quantified by summing pseudo-counts falling within the features (exons and intronic spaces) and normalized by the effective gene length (sum of feature lengths) and by the size of the library (uniquely mapped read count).
Bru-seq: differential gene expression was performed using DESeq2 1.18.1.  The apeglm method was used for log2 fold change shrinkage (Zhu, et al. 2018).
BruUV-seq: Uniquely aligned read pairs were separated by strand using sambamba 0.8.0 and the following filters: 1) plus strand filter: (not secondary_alignment and proper_pair) and ((first_of_pair and reverse_strand and template_length > -1000 and template_length < -150) or (second_of_pair and not reverse_strand and template_length < 1000 and template_length > 150)); 2) minus strand filter: (not secondary_alignment and proper_pair) and ((first_of_pair and not reverse_strand and template_length < 1000 and template_length > 150) or (second_of_pair and reverse_strand and template_length > -1000 and template_length < -150)).
BruUV-seq: Peaks were called per strand using MACS2 2.2.7.1 and the parameters: --BAMPE -g mm -p 0.01 --SPMR --keep-dup 1 --call-summits. Differential peak analysis was performed using DiffBind 3.6. and the parameter summits=FALSE was set for the dba.count function.
BruUV-seq: Coverage/signal was computed using DeepTools 3.5.1. Uniquely mapped reads (MAPQ >= 255) were RPKM normalized using the total number of uniquely mapped reads and the bin size was set to 1.
Assembly: mm10
Supplementary files format and content: Gene expression data for each Bru-seq sample (<sample>_genes.bed) is in a 9-column, tab-delimited text file with header (BED6-compatible) containing gene annotation, raw counts, and RPKM.
Supplementary files format and content: Cdc73_Bru-seq_counts.bed and Cdc73_Bru-seq_rpkm.bed are tab-delimited gene expression matrices for the experiment (with headers) containing BED6-compatible annotations in the first 6 columns.
Supplementary files format and content: Coverage/signal for both Bru-seq and BruUV-seq is in bigWig format.
Supplementary files format and content: BruUV-seq peaks are in narrowPeak format.
Supplementary files format and content: Differential gene expression (Bru-seq) results for the 708, 969, and 970 cell lines are in 3 CSV files with headers and one Excel file with 3 sheets.
Library strategy: BruUV-seq

extract_protocol:
Cells were lysed directly in TRIzol followed by isolation of total RNA. The isolated total RNA was further treated with DNAse (TURBO DNA-free Kit; Invitrogen) and a spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2014; Paulsen et al., 2013), but with the following modifications. Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first strand synthesis. A universal ligation adapter and dual-index, barcoded primers were used for PCR. Size selection for all libraries was via agarose gel excision.

treatment_protocol: Murine T-ALL cells were treated with EtOH or OHT at 6nM for 30 hours prior to harvesting.  At 29.5 h, cells were gently centrifuged and the media reserved, leaving behind a minimal volume to allow the cells to spread out.  For BruUV-seq, cells were irradiated with 200 J/m^2 UV-C light. Cells were then resuspended in reserved condition media containing 2mM bromouridine for the final 0.5 h of incubation.

tag: labeling agent

value: bromouridine (Bru)

tag: bru labeling_time_(h)

tag: bru-rna ip_antibody

value: anti-BrdU

tag: uv-c irradiation_(j/m^2)


title: 708, BruUV-seq, EtOH, 1

tag: cell line

tag: treatment


title: 708,BruUV-seq, OHT, 2


title: sunflower stem, ZT12, shaded side, rep1

tag: strain


title: sunflower stem, ZT12, shaded side, rep2


title: 970, BruUV-seq, OHT, 1


title: 970, BruUV-seq, OHT, 3


title: 708, BruUV-seq, EtOH, 3


title: 970,BruUV-seq, OHT, 2


title: sunflower stem, ZT9, lit side, rep6

value: Lit side


title: ac27

description: 10x Genomics


title: 970, BruUV-seq, EtOH, 3


title: ac26

description: 10x Genomics


title: ac32

description: 10x Genomics


title: 708, BruUV-seq, OHT, 3


title: 970, BruUV-seq, EtOH, 1


title: 969, BruUV-seq, OHT, 3


title: ac25

description: 10x Genomics


title: sunflower stem, ZT9, lit side, rep5

value: stem


title: 708, BruUV-seq, EtOH, 2


title: ac24

description: 10x Genomics


title: sunflower stem, ZT9, lit side, rep4


title: 969, BruUV-seq, OHT, 2


title: ac28

description: 10x Genomics


title: 969, BruUV-seq, EtOH, 3


title: 969, BruUV-seq, OHT, 1


title: ac23

description: 10x Genomics


title: 969, BruUV-seq, EtOH, 2


title: ac22

description: 10x Genomics


title: 708, Bru-seq, OHT, 1

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were trimmed using BBDuk (BB Tools 38.46). The bundled adapter sequences and following parameters were used for paired-end reads: ktrim=r, mink=11, hdist=1, k=31.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank BK000964.3) and the mitochondrial genomes (from the mm10 reference sequence) using Bowtie2 (2.3.3).
Reads that did not align to rRNA or the mitochondrial genome were subsequently mapped to the mouse genome build mm10/GRCm38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version M15.
Coverages were determined using BEDTools2 2.28.0 as (1 / read length) for each base in the genome. These base coverages were used to obtain pseudo-read counts in strand-specific regions of interest using bedtools intersect.
Bru-seq: Reads Per Kilobase per Megabase of library size (RPKM) were calculated for meta-transcripts ("genes") defined by merging exons and intervening intronic spaces from all isoforms of a gene in the GENCODE M15 "basic" annotation. Genes were quantified by summing pseudo-counts falling within the features (exons and intronic spaces) and normalized by the effective gene length (sum of feature lengths) and by the size of the library (uniquely mapped read count).
Bru-seq: differential gene expression was performed using DESeq2 1.18.1.  The apeglm method was used for log2 fold change shrinkage (Zhu, et al. 2018).
BruUV-seq: Uniquely aligned read pairs were separated by strand using sambamba 0.8.0 and the following filters: 1) plus strand filter: (not secondary_alignment and proper_pair) and ((first_of_pair and reverse_strand and template_length > -1000 and template_length < -150) or (second_of_pair and not reverse_strand and template_length < 1000 and template_length > 150)); 2) minus strand filter: (not secondary_alignment and proper_pair) and ((first_of_pair and not reverse_strand and template_length < 1000 and template_length > 150) or (second_of_pair and reverse_strand and template_length > -1000 and template_length < -150)).
BruUV-seq: Peaks were called per strand using MACS2 2.2.7.1 and the parameters: --BAMPE -g mm -p 0.01 --SPMR --keep-dup 1 --call-summits. Differential peak analysis was performed using DiffBind 3.6. and the parameter summits=FALSE was set for the dba.count function.
BruUV-seq: Coverage/signal was computed using DeepTools 3.5.1. Uniquely mapped reads (MAPQ >= 255) were RPKM normalized using the total number of uniquely mapped reads and the bin size was set to 1.
Assembly: mm10
Supplementary files format and content: Gene expression data for each Bru-seq sample (<sample>_genes.bed) is in a 9-column, tab-delimited text file with header (BED6-compatible) containing gene annotation, raw counts, and RPKM.
Supplementary files format and content: Cdc73_Bru-seq_counts.bed and Cdc73_Bru-seq_rpkm.bed are tab-delimited gene expression matrices for the experiment (with headers) containing BED6-compatible annotations in the first 6 columns.
Supplementary files format and content: Coverage/signal for both Bru-seq and BruUV-seq is in bigWig format.
Supplementary files format and content: BruUV-seq peaks are in narrowPeak format.
Supplementary files format and content: Differential gene expression (Bru-seq) results for the 708, 969, and 970 cell lines are in 3 CSV files with headers and one Excel file with 3 sheets.
Library strategy: Bru-seq


title: 708, Bru-seq, OHT, 3


title: sunflower stem, ZT9, lit side, rep1


title: 969, BruUV-seq, EtOH, 1


title: 708,Bru-seq, OHT, 2


title: ac21

description: 10x Genomics


title: sunflower stem, ZT9, lit side, rep2


title: sunflower stem, ZT9, shaded side, rep6

value: Shaded side


title: 708, Bru-seq, EtOH, 3


title: 708, Bru-seq, EtOH, 2


title: ac20

description: 10x Genomics


title: 708, Bru-seq, EtOH, 1


title: sunflower stem, ZT9, shaded side, rep5

value: phototropism


title: ac19

description: 10x Genomics


title: sunflower stem, ZT9, lit side, rep3


title: ac47

description: 10x Genomics


title: 970,Bru-seq, OHT, 2

value: T-cell acute lymphoblastic leukemia


title: 970, Bru-seq, OHT, 1


title: ac18

description: 10x Genomics


title: 970, Bru-seq, EtOH, 2


title: 970, Bru-seq, EtOH, 3


title: sunflower stem, ZT9, shaded side, rep3


title: sunflower stem, ZT9, shaded side, rep4


title: sunflower stem, ZT9, shaded side, rep2


title: sunflower stem, ZT9, shaded side, rep1


title: ac15

description: 10x Genomics


title: ac16

description: 10x Genomics


title: 969, Bru-seq, OHT, 3


title: 969, Bru-seq, OHT, 2


title: sunflower stem, ZT7, lit side, rep6


title: 969, Bru-seq, EtOH, 2


title: 969, Bru-seq, OHT, 1


title: 970, Bru-seq, EtOH, 1


title: ac17

description: 10x Genomics


title: ac14

description: 10x Genomics


title: sunflower stem, ZT7, lit side, rep5


title: 969, Bru-seq, EtOH, 1


title: ac13

description: 10x Genomics


title: 969, Bru-seq, EtOH, 3


title: mESC_WT_FLAG

city: Shinjuku

first: Haruhiko

last: Siomi

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology

institute: Keio University School of Medicine

data_processing: Base calling was performed using bcl2fastq v2.20 to generate raw reads.  Quality control and adapter trimming was done using fastp (Chen et al., 2018) v0.23.2.  For RNA-seq, quality controlled reads were aligned to GRCm38.p6 reference genome using STAR (Dobin et al., 2013) v2.7.9a with default arguments. Reads were counted against GRCm38.p6 comprehensive gene annotation (Frankish et al., 2020) and mm10 repeats from UCSC RepeatMasker using FeatureCounts (Liao et al., 2014) v2.0.1 with multi mapping reads discard for non-TE features and count fractionally for TEs. For CUT&RUN-seq, quality controller reads were aligned to GRCm38.p6 reference genome using Bowtie2 (Langmead and Salzberg, 2012) v2.4.1 with default arguments.  For CUT&RUN, Peaks were called in each biological replicated using MACS3 (Zhang et al., 2008) v3.0.0a6 callpeak function (-f BAMPE). Quantitative histone modification analysis with replicated samples was performed using MAnorm2 (Tu et al., 2021) v1.2.0.  For visualization of CUT&RUN results, alignment tracks were generated using deepTools (Ramírez et al., 2016) v3.5.1 bamCoverage function (--binSize 10 --normalizeusing CPM --smoothLength 30). Visualization of genomic tracks was performed using trackplot (Pohl and Beato, 2014) v1.3.10.

source_name: culture cell

growth_protocol: Eight-weeks old female and male B6D2F1 (BDF1) mice were purchased from the Japan SLC, Inc. All animal experiments were reviewed and approved by the Institutional Animal Care and Use Committee (protocol no. 09105-(10) and 11045-(6)) at Keio University, where mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 14/10 hour light/dark cycle).

extract_protocol:
For RNA-seq of embryos, 30 middle-2C embryos were collected 20 hours after microinjection in each independent biological replicates. Zona pellucida was removed by treating the embryos with Acidic Tyrode’s solution. For RNA-seq of culture cells, total RNA was prepared using RNeasy Kit according to the manufacturer’s instruction. The RNA solution was subjected to TURBO DNase treatment according to the manufacturer’s instructions to remove genomic DNA carryover. For CUT&RUN, 1×105 culture cells freshly prepared by trypsin digestion were used to perform CUT&RUN assay with CUT&RUN Assay Kit (Cell Signaling Technology, 86652) according to the manufacturer’s instructions.
For RNA-seq of embryos, libraries were constructed with SMART-Seq Stranded Kit (TaKaRa, 634442) and indexed with SMARTer RNA Unique Dual Index Kit (TaKaRa, 634451) according to the manufacturer’s instructions. For RNA-seq of culture cells, libraries were constructed using 1µg total RNA with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) and indexed with NEBNext Multiplex Oligos for Illumina (NEB, E6440S) according to the manufacturer’s instructions. For CUT&RUN, enriched DNAs were subjected to library construction using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L) with the adapter ligation step performed at 50°C instead of 65°C to prevent denature of small DNA inserts. The libraries were indexed with NEBNext Multiplex Oligos for Illumina according to the manufacturer’s instructions.

treatment_protocol: 8-weeks-old BDF1 female mice were injected with 150µL CARD HyperOva (Kyudo Co., Ltd.). After 48 hours, the female mice were injected with 5IU hCG (ASKA Animal Health Co., Ltd.) and mated with BDF1 male mice. After 22 hours, PN3 zygotes were collected. Cumulus cells were removed by briefly culture the zygotes in KSOM medium (Merck, MR-101-D) supplemented with 0.3µg/µL hyaluronidase (Merck, H4272). Embryos were cultured in KSOM medium drops covered with liquid paraffin (Nacalai Tesque, 26137-85) under 5% CO2 at 37°C. After 4 hours, PBS containing either 40µM scramble ASO, 20µM anti-Dux ASO, 20µM anti-Obox4 ASO, 40µM equal molar anti-Dux/anti-Obox4 ASO mixture, or 40µM equal molar anti-Dux/anti-Obox4 ASO mixture with 100ng/μL codon-optimized Obox4 mRNA were microinjected into male pronuclei of zygotes using FemtoJet 4i microinjector (Eppendorf, 5252000013).

value: culture cell

value: ESC

tag: background strain


title: 970, Bru-seq, OHT, 3

value: Rosa26CreERT2 Cdc73f/f


title: mESC_TRE_3FLAG_Dux_FLAG


title: 970, BruUV-seq, EtOH, 2


title: sunflower stem, ZT7, lit side, rep4


title: ac12

description: 10x Genomics

value: Blood cell culture

value: rrLBCL


title: sunflower stem, ZT7, lit side, rep3

value: WT


title: RNAseq_ESC_WT_PlaB_rep2

value: pladienolide B


title: ac11

description: 10x Genomics

value: CART


title: RNAseq_ESC_WT_PlaB_rep3


title: RNAseq_ESC_WT_PlaB_rep1


title: ac10

description: 10x Genomics


title: sunflower stem, ZT7, lit side, rep2


title: sunflower stem, ZT7, lit side, rep1


title: ac08

description: 10x Genomics


title: sunflower stem, ZT7, shaded side, rep6


title: RNAseq_ESC_Obox4_KO_PlaB_rep2

value: Obox4 single KO


title: RNAseq_ESC_Dux_KO_PlaB_rep3

value: Dux single KO


title: RNAseq_ESC_Obox4_KO_PlaB_rep1


title: RNAseq_ESC_Dux_KO_PlaB_rep2


title: ac07

description: 10x Genomics


title: sunflower stem, ZT7, shaded side, rep5


title: RNAseq_ESC_double_KO_PlaB_rep3

value: Obox4/Dux double KO


title: ac06

description: 10x Genomics


title: RNAseq_ESC_Dux_KO_PlaB_rep1


title: RNAseq_ESC_double_KO_PlaB_rep2


title: RNAseq_ESC_double_KO_PlaB_rep1


title: sunflower stem, ZT7, shaded side, rep3


title: sunflower stem, ZT7, shaded side, rep4


title: RNAseq_morula_scramble_KD_rep2

source_name: emrbyo

value: emrbyo

value: morula

value: Scramble KD


title: RNAseq_morula_scramble_KD_rep1


title: RNAseq_ESC_Obox4_KO_PlaB_rep3


title: RNAseq_morula_double_KD_rep2

value: Dux/Obox4 double KD


title: ac04

description: 10x Genomics


title: sunflower stem, ZT7, shaded side, rep2

value: stem

value: Shaded side

value: phototropism


title: RNAseq_2C_scramble_KD_rep2

value: 2C embryo


title: sunflower stem, ZT7, shaded side, rep1


title: RNAseq_2C_scramble_KD_rep1


title: ac09

description: 10x Genomics


title: ac03

description: 10x Genomics


title: RNAseq_morula_double_KD_rep1


title: sunflower stem, ZT5, lit side, rep6

value: Lit side


title: RNAseq_2C_rescue_KD_rep1

value: Dux/Obox4 double KD rescued by Obox4 mRNA


title: RNAseq_2C_Obox4_KD_rep2

value: Obox4 KD


title: ac01

description: 10x Genomics

value: Blood cell culture

value: rrLBCL


title: ac02

description: 10x Genomics

value: CART


title: sunflower stem, ZT5, lit side, rep5

value: WT


title: RNAseq_2C_Obox4_KD_rep1


title: RNAseq_2C_Dux_KD_rep2

value: Dux KD


title: RNAseq_2C_Dux_KD_rep1


title: ac05

description: 10x Genomics


title: sunflower stem, ZT5, lit side, rep4


title: RNAseq_2C_doubke_KD_rep2


title: sunflower stem, ZT5, lit side, rep3