title: D12-1

description: chemically induced neural crest cells D12

source_name: MEFs

value: embryo


title: D12-2

status: Public on Jun 09 2021

type: SRA

city: Wenzhou

first: ShaoHui

last: Pan

state: Zhejiang

address: Xueyuan road #270

country: China

institute: Wenzhou Medical University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Mus musculus

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Trizol

tag: strain

tag: tissue


title: LOAL_126

city: Nathan

first: Ido

last: Bar

state: QLD

address: 170 Kessels Road

department: School of Environment and Science

country: Australia

institute: Griffith University

description:
Len orientalis is used as the male parent and Lens culinaris is used as the female (egg) parent.
hari_filtered_V1.recode.vcf

data_processing:
Read trimming performed using custom perl script and Cutadapt v1.4.1 software. Reads were filtered by removing adaptor sequences along with reads and bases of low quality. Reads which had three consecutive N's and >3 consecutive nucleotides with Phred scores ≤ 20 were trimmed. Finally, any reads that were shorter than 50 bp were removed from the final set.
Parental read alignment to reference performed using BWA-MEM. SAM files were converted into binary format (BAM) files, sorted and indexed using SAMtools (version 1.9) sort and view options.
Variant calling performed through SAMtools mpileup and bcftools (version 1.9), and filtered using vcftools (v0.1.16).
RILs read alignment to reference performed using BWA-MEM. SAM files were converted into binary format (BAM) files, sorted and indexed using SAMtools (version 1.9) sort and view options.
Variant calling in RILs performed using SAMtools mpileup and bcftools (version 1.9), and filtered using vcftools (v0.1.16) with the SNP list identified from the parents.
Genome_build: Cassab reference transcriptome (Sudheesh et al., 2016).
Supplementary_files_format_and_content: vcf files include SNPs.

organism: Lens culinaris x Lens orientalis

source_name: leaf

extract_protocol:
Total RNA was extracted from selected young leaves of 14-day-old seedlings of parents and 140 RILs using the RNeasy® 96 kit (Qiagen Inc., Hilden, Germany) following the manufacturer’s instructions.
cDNA libraries were prepared for sequencing using standard Illumina protocols.

tag: line

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue

tag: age

value: 14 days


title: Meimi Tween40 Rep-2

city: West Lafayette

first: Teeratas

last: Kijpornyongpan

state: IN

address: 915 W State St

department: Botany and Plant Pathology

country: USA

institute: Purdue University

description:
MCA3882_T-R3
processed data file: Meimi_RawReadCount.txt
processed data file: Meimi_NormReadCount.csv

data_processing:
Adapter and low base-quality bases trimming by Cutadapt version 1.13 and Trimmomatics version 0.36 using default parameters.
Clean reads were mapped to the reference genomic sequence of each species (T. washingtonensis MCA 4186 v 1.0 and M. miltonrushii MCA 3882 v 1.0) through TopHat version 2.1.1 using default parameters.
BAM alignments were transformed into raw gene counts using htseq version 0.7.0 with default parameters and using proteinId as a feature.
Genome_build: JGI MycoCosm genome portal
Supplementary_files_format_and_content: *_RawReadCount.txt: Raw gene count in tab-delimited txt file.
Supplementary_files_format_and_content: *_NormReadCount.csv: Normalized gene count, using DESeq2 version 1.20.0, in comma-separated txt file.

organism: Meira miltonrushii

source_name: fungal biomass

growth_protocol: Fungal cultures were grown in Potato Dextrose Broth (PDB) for 7 days. After that, fungal biomasses were centrifuged and resuspended in sterile water.

extract_protocol:
The fungal biomasses were centrifuged, rinsed in sterile water three times and ground-frozen in liquid nitrogen. Total RNA of each sample was extracted using the Omega BioTek E.Z.N.A.® Fungal RNA Mini Kit (R6840-01).
Poly A+ libraries were prepared using Illumina’s TruSeq mRNA Library Prep Kit followed by manufacturer's protocol.

treatment_protocol: About 5 x 10^6 cells were inoculated into each experimental unit. We used Holliday's minimal media with 1% glucose or 1% Tween40 as a carbon source. The cultures were incubated at room temperature (25 C) for three days before RNA harvest.

tag: phenotype

value: Filamentous growth

value: Fungal biomass


title: LOAL_125


title: LOAL_127


title: TIGK PgSg Infected Sample 1

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

data_processing:
Fastq files were downloaded from sequencing center for analysis.
The GRCh38.p12 Homo sapiens genome was used for read alignment with STAR to generate bam format alignment files.
Samtools was used to merge the bam files for each sample and the pre- and post-alignment quaility was assesed for each sample using Picard tools.
Raw gene counts were generated and annotated with genome features using featureCounts.
DESeq2 was used to perform differential gene expression analysis using the recommened guidelines.
Performed a regularized log transformation on raw count data as outlined in Love et al. 2014 (DOI: 10.1186/s13059-014-0550-8) for principal component analysis.
Genome_build: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

organism: Homo sapiens

growth_protocol: TIGK cells were grown at 37℃ with 5% carbon dioxide. Porphyromonas gingivalis ATCC 33277 and Streptococcus gordonii DL1 were cultured anaerobically at 37℃.

extract_protocol:
RNA was extracted using RNAqueous-Micro Total RNA Isolation Kit (ThermoFisher).
Library construction was performed using the TruSeq Stranded Total RNA with RiboZero Plus Kit (Illumina) from 1 µg of total RNA.

treatment_protocol: TIGK cells were grown to ~80% confluence and challenged with bacteria at an MOI of 100 for 1 hr, followed by 23 hr in fresh medium.

tag: cell line

value: TIGK

tag: cell type


title: LOAL_128


title: Senescent cell, dep

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Total RNA was extracted and analyzed

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: biliary epithelial cell

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Biliary epithelial cells are cultured in DMEM/F-12 with 10%Nu-serum, EGF, insulin, forskolin and antibiotics

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Qiagen).

treatment_protocol: Cellular senescence was induced in BECs cultured in vitro incubation in serum depleted media or treatment with media containing 200 μM GCDC for 4-7 days

value: biliary epithelial cell

tag: treatment

value: serum depletion


title: Meimi Tween40 Rep-1

description:
MCA3882_T-R2
processed data file: Meimi_RawReadCount.txt
processed data file: Meimi_NormReadCount.csv


title: LOAL_124


title: Meimi Glucose Rep-3

description:
MCA3882_G-R5
processed data file: Meimi_RawReadCount.txt
processed data file: Meimi_NormReadCount.csv

value: Yeast growth


title: D7-2

description: chemically induced neural crest cells D7


title: TIGK Sg-only Infected Sample 4


title: LOAL_123


title: Meimi Glucose Rep-2

description:
MCA3882_G-R3
processed data file: Meimi_RawReadCount.txt
processed data file: Meimi_NormReadCount.csv


title: D7-1


title: Meimi Glucose Rep-1

description:
MCA3882_G-R1
processed data file: Meimi_RawReadCount.txt
processed data file: Meimi_NormReadCount.csv


title: TIGK Sg-only Infected Sample 3


title: TIGK Sg-only Infected Sample 5


title: LOAL_122


title: D0-3

description: MEFs


title: EW24_input_DNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Ewing sarcoma cell line EW-24 ChIP-Seq with ChIP antibody none

library_source: genomic

data_processing:
Raw sequencing data were aligned to human reference genome hg19 with bowtie2
Duplicates were eliminated with samtools
Peaks were called with MACS2, broad peak option for histone marks and narrow peak for transcription factors, and giving the respective input, mode FE
MACS2 output was converted intro bigwig with the UCSC bedGraphToBigWig tool
bigwig files were normalized cross cell-lines with the CHIPIN R tool
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format; files were generated via MACS2, UCSC bedGraphToBigWig and CHIPIN; indexed binary format indicating quantitatively ChIP signal in hg19 genome build

molecule: genomic DNA

source_name: Ewing sarcoma cell line

growth_protocol: Cell lines were cultured in RPMI 1640 medium with stable glutamine with 10% FCS and 100 units/ml penicillin and 100µg/ml streptomycin in a fully humidified environment at 37°C and 5% CO2. Cells were subcultured every 2-4 days.

extract_protocol:
Cells were fixed with 1% formalin for 10 min, glycine at final 200 mM was added for 5 min, cell surface was washed with ice-cold PBS three thimes, cells were lysed with the lysis buffers of the Diagenode iDeal ChIP-seq kit for transcription factors, DNA was sheared with Bioruptor Plus sonication device, cell debris was separated by centrifugation, genomic sheared DNA was added to ChIP antibodies coupled to magnetic beads. The next day, beads were washed with four washing buffers of the Diagenode iDeal ChIP-seq kit, DNA was eluted with the respective buffer and cleaned up with beads.
Libraries were constructed with the Illumina TruSeq ChIP library preparation kit following the manufacturer’s protocol

tag: chip antibody


title: TIGK Sg-only Infected Sample 2


title: LOAL_121


title: D0-2

description: MEFs


title: LOAL_120


title: TIGK Sg-only Infected Sample 1


title: TIGK Pg-only Infected Sample 5


title: D0-1

description: MEFs


title: EW24_H3K27me3_ChIPSeq

description: Ewing sarcoma cell line EW-24 ChIP-Seq with ChIP antibody H3K27me3 (Diagenode, C15410069, 2.9 µg)


title: TIGK Pg-only Infected Sample 4


title: control

description: Total RNA was extracted and analyzed

value: control


title: LOAL_119


title: EW24_H3K4me3_ChIPSeq

description: Ewing sarcoma cell line EW-24 ChIP-Seq with ChIP antibody H3K4me3 (Diagenode, C15410003, 1.4 µg)


title: ciCEC-P8-2

description: chemically induced corneal endothelial cells P8


title: EW24_H3K27ac_ChIPSeq

description: Ewing sarcoma cell line EW-24 ChIP-Seq with ChIP antibody H3K27ac (Abcam, ab4729, 1 µg)

value: H3K27ac (Abcam, ab4729, 1 µg)


title: ciCEC-P8-1


title: EW24_FLI1_ChIPSeq

description: Ewing sarcoma cell line EW-24 ChIP-Seq with ChIP antibody FLI1 (Abcam, ab15289, 2 µg)

value: FLI1 (Abcam, ab15289, 2 µg)


title: LOAL_117


title: TIGK Pg-only Infected Sample 3


title: ciCEC-P1-2

description: chemically induced corneal endothelial cells P1


title: TIGK Pg-only Infected Sample 2


title: TIGK Pg-only Infected Sample 1


title: LOAL_116


title: LOAL_115


title: PDC_R848 16h

city: Shanghai

first: Haibo

last: Zhou

address: No.160, Pujian Road

department: Department of Rheumatology

institute: Renji Hospital

description:
scRNA-seq
3'-end gene expression

data_processing:
the 10x Genomics Cell Ranger Single Cell Software Suite 2.1.1 was used to perform sample demultiplexing and single cell UMI counting
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output files: barcodes.tsv, genes.tsv, matrix.mtx

molecule: polyA RNA

source_name: plasmacytoid dendritic cells were stimulated with R848 for 16 hours

growth_protocol: primary  pDC cells

extract_protocol:
RNA were extracted from cells using Single Cell 3’ Reagent Kits v2
10x 3'-end single cell RNA-seq

treatment_protocol: pDC cells were stimulated by R848 for 16h

tag: Sex

value: female

value: blood

value: primary  pDC cells


title: OA440_MOI0_1_24hpi-Rep2 [P891_012]

city: Berlin

first: Fabian

last: Pott

state: Berlin

address: Charitéplatz 1

department: Institute for Virology

institute: Charité - Universitaetsmedizin Berlin

description:
CG_FP_012_S19
processed data file: integrated_24hpi.RDS

data_processing:
https://github.com/GoffinetLab/CHIKV_scRNAseq-fibroblast
creation of CHIKV reference genome Uploaded with the data files
alignment using cellranger (Cellranger v5.0 (10X Genomics))
Creation of Seurat object, preprocessing Seurat v4.0
Genome_build: human: hg38 release 102, CHIKV: DQ443544.2
Supplementary_files_format_and_content: RDS file of integrated data from all sample of each timepoint, genome build of human and CHIKV genes

growth_protocol: Primary human fibroblasts were obtained from synovial biopsies from donors suffering from osteoarthritis or a non-arthritic background, purified, and cultured in standard cell culture flask in Dulbecco’s modified Eagle’s medium - high glucose (DMEM, Sigma-Aldrich) supplemented with 20 % heat-inactivated fetal bovine serum (FBS, Sigma-Aldrich), 2mM L-Glutamine (Gibco), and 100 units/ml penicillin-streptomycin (Gibco).

extract_protocol: Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

treatment_protocol: CHIKV particles produced by electroporation of in-vitro transcribed full-length genomic RNA into BHK-21 cells were used to infect Fibroblasts at an MOI of 0.01, 0.1, 1, or 10 or mock-infected and harvested at 6 and 24 hpi for single-cell RNA-sequencing.

value: human primary synovial fibroblasts, knee

tag: tag

value: infected

tag: time point

value: 24 hours post infected


title: TIGK Non-infected Sample 5


title: Ehmt1∆/+; Ehmt1 iTg-neuron #2

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

description: Ehmt1∆/+; Ehmt1 iTg-neuron #2

data_processing:
ChIP-seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore v0.3.7, then aligned to the mm10 genome assembly using bowtie v0.12.7
Duplicated reads were removed by samtools v0.1.18
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using MACS v1.4.1

source_name: NeuN+ cells from cortex

extract_protocol:
0.6-1 million NeuN+ cells were sorted from mouse cortical region. After MNase treatment, dimethylated HistoneH3 Lysine9 was IP out using H3K9me2 antibody (clone#6D11).
N-ChIP libraries were prepared for sequencing using KAPA HyperPrep kit (Cat. #KK8500)

treatment_protocol: Tamoxifen treatment at 3 weeks old (2 times)

value: brain, cortex

value: 12 weeks old

tag: genotype

value: Ehmt1[delta]/+; Ehmt1 iTg; CamKII-CreER

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old

tag: antibody

value: H3K9me2 antibody (clone#6D11)


title: D7-3

value: embryo


title: LOAL_118

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue

value: 14 days


title: LOAL_113


title: TIGK Non-infected Sample 4

value: TIGK


title: ciCEC-P1-1


title: LOAL_114


title: OA440_MOI0_01_24hpi-Rep2 [P891_011]

description:
CG_FP_011_S18
processed data file: integrated_24hpi.RDS


title: TIGK Non-infected Sample 3


title: Ehmt1∆/+ #2

description: Ehmt1∆/+ #2


title: OA440_Mock_24hpi-Rep2 [P891_010]

description:
CG_FP_010_S17
processed data file: integrated_24hpi.RDS

value: mock


title: OA440_MOI0_1_6hpi-Rep2 [P891_009]

description:
CG_FP_009_S16
processed data file: integrated_6hpi.RDS

value: 6hours post infected


title: TIGK Non-infected Sample 2


title: Ehmt1∆/+; Ehmt1 iTg-neuron #1

description: Ehmt1∆/+; Ehmt1 iTg-neuron #1


title: LOAL_112

description:
Len orientalis is used as the male parent and Lens culinaris is used as the female (egg) parent.
hari_filtered_V1.recode.vcf


title: LOAL_111


title: OA440_MOI0_01_6hpi-Rep2 [P891_008]

description:
CG_FP_008_S15
processed data file: integrated_6hpi.RDS


title: WT #2

description: WT #2

value: wild type


title: TIGK Non-infected Sample 1


title: Ehmt1 iTg-neuron #1

description: Ehmt1 iTg-neuron #1

value: Ehmt1 iTg; CamKII-CreER


title: LOAL_110


title: OA440_Mock_6hpi-Rep2 [P891_007]

description:
CG_FP_007_S14
processed data file: integrated_6hpi.RDS

value: human primary synovial fibroblasts, knee


title: LOAL_109


title: TIGK Pg-infected sample treated with siOLFM4 3

data_processing:
Fastq files were downloaded from Illumina's BaseSpace for analysis.
Quality control was perfomed using FastQC (version 0.10.1). After examining the results of QC it was determined that no sequence trimming was required due to the sequences having a sufficiently high enough quality.
Reads were aligned to the Homo sapiens reference genome assembly (GRCm38.p6) using STAR (version 2.6) to generate alignment files in bam format.
HTSeq was used with the stranded option set to reverse to generate raw gene counts for every sample from aligned bam files produced from STAR.
DESeq2 was used to perform differential gene expression analysis using the recommened guidelines.
Performed a regularized log transformation on raw count data as outlined in Love et al. 2014 (DOI: 10.1186/s13059-014-0550-8) for principal component analysis.
Genome_build: Homo sapiens reference genome assembly GRCm38.p6
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

growth_protocol: TIGK cells were grown at 37℃ with 5% carbon dioxide. Porphyromonas gingivalis ATCC 33277 was cultured anaerobically at 37℃.

treatment_protocol: TIGK cells were grown to ~50-60% confluence and transfected with siRNA for 48 hr, followed by 24 hr in fresh medium. TIGK cells were then challenged with bacteria at an MOI of 100 for 1 hr, followed by 23 hr in fresh medium.


title: Ehmt1∆/+ #1

description: Ehmt1∆/+ #1


title: LOAL_108


title: HA1Q+APO1S_gRNAs_1

first: F. Nina

last: Papavasiliou

department: Tumor Immunology Unit

data_processing:
RNA-seq raw data from different lanes that belong to the same sample were pulled together. After adapter trimming with Trim Galore (v. 0.6.4; http://www.bioinformatics.babraham.ac.uk/projects/  trim_galore/ ), the trimmed reads were aligned using STAR (v. 2.7.3a) to a genome index inferred by the human reference genome (hg19) sequence, along with the RefSeq annotation, both publicly available at the genome browser at UCSC. For the alignments we considered reads that were uniquely mapped (STAR option: --outFilterMultimapNmax  1) to avoid multimapping between highly similar regions.
Aligned data (bam files) were deduplicated, sorted and indexed with SAMtools (v. 1.9; http://samtools.sourceforge.net).
SNVs in our samples were called with REDItools (v2; https://github.com/tflati/reditools2.0), considering the developers’ recommendations for data preparation prior to this step. Sticking to our previously published approach, we considered only high-quality sites (min. MeanQ > 30 in REDItools2), and we called editing in well-covered sites (min. 50 reads in aggregate of the two replicates per sample) that showed ≥ 10% for A-to-I and ≥ 5% for C-to-U editing frequency when compared to the control.
Fisher’s exact tests were performed for all the sites that fulfilled the aforementioned criteria and significantly differentially edited sites were considered those that showed adjusted p-value < 0.01.
Sites that were reported in the first 6 sites of a read, or in homopolymeric regions, or reported in the dbSNP (v. 142; excluding cDNA-based reported SNPs: http://www.ncbi.nlm.nih.gov/SNP/), were excluded throughout our output lists.
All genomic coordinates were annotated with Oncotator (v1.9.9.0) and Repeat Mask for Alu-SINE elements of UCSC Genome Browser both for hg19.
Genome_build: hg19
Supplementary_files_format_and_content: ReadcountsRaw_HA1QmA1S.csv: contains raw read-counts for the 293 Flp-In T-REx HALO-ADAR1Q + mAPOBEC1-SNAP-HIV-NES cell line replicates empty and transfected with gRNA
Supplementary_files_format_and_content: AGsignal_empty_vs_gRNA_HA1Q_APO1S.oncoOut.txt: tab-delimited txt file with all A-to-G editing sites with annotated coordinates after variant calling from comparison between the sample 1 and sample 2 (empty samples / reference level) vs sample 3 and sample 4 (gRNA samples).
Supplementary_files_format_and_content: CTsignal_empty_vs_gRNA_HA1Q_APO1S.oncoOut.txt: tab-delimited txt file with all C-to-U editing sites with annotated coordinates after variant calling from comparison between the sample 1 and sample 2 (empty samples / reference level) vs sample 3 and sample 4 (gRNA samples).

growth_protocol: 293 Flp-In T-REx HALO-ADAR1Q + mAPOBEC1-SNAP-HIV-NES cells were cultivated in Dulbecco’s Modified Eagle Medium (Life Technologies) supplemented with 10 % fetal bovine serum (Life Technologies), 15 µg/ml blasticidin and 100 µg/ml hygromycin (DMEM/FBS/B/H) at 37 °C with 5 % CO2 in a water saturated steam atmosphere.

extract_protocol:
RNA isolation was performed with the RNeasy MinElute Cleanup Kit from Qiagen, followed by DNase I digestion, which was again purified via RNeasy MinElute Cleanup Kit from Qiagen.
The library was prepared with the library preparation kit TruSeq Stranded mRNA by Illumina starting from 100 ng RNA. Samples were then sequenced on a NovaSeq 6000 by ILLUMINA with 50 million reads and 2 × 100 bp paired end.

treatment_protocol: 2⋅106 293 Flp-In T-REx HALO-ADAR1Q + mAPOBEC1-SNAP-HIV-NES cells were seeded in 2.5 ml DMEM/FBS/B/H supplemented with 10 ng/ml doxycycline in a 6 well plate. After 24 h, 8⋅104 cells per well were reverse transfected in 5 wells of a 96 well plate per sample. For the duplicate of the empty transfection, the cells were treated with an empty reverse transfection with 0.5 µl Lipofectamine 2000 only. For the duplicate of the guideRNA transfection, cells were reverse transfected with 2.5 pmol (snap)2-ACC and 2.5 pmol (halo)2-UAU with 0.5 µl Lipofectamine 2000. Doxycycline concentration was kept at 10 ng/ml and after further 48 h cells were harvested.

value: 293 Flp-In T-REx

value: HALO-ADAR1Q + mAPOBEC1-SNAP-HIV-NES

value: transfection of two guideRNAs (2.5 pmol (snap)2-ACC + 2.5 pmol (halo)2-UAU) with Lipofectamine 2000


title: TIGK Pg-infected sample treated with siOLFM4 1


title: Ehmt1 iTg-neuron #2

description: Ehmt1 iTg-neuron #2

value: brain, cortex

value: 12 weeks old


title: TIGK Pg-infected sample treated with siOLFM4 2


title: HA1Q+APO1S_empty_2

source_name: 293 Flp-In T-REx HALO-ADAR1Q + mAPOBEC1-SNAP-HIV-NES

value: empty transfection with Lipofectamine 2000


title: LOAL_107


title: total RNA from PT2016-176-CORE

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

data_processing:
Alignment to GrCh38 using GENCODE v27 transcripts.
Data normalization and analysis performed using default parameters in DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: text file containing matrix of raw transcript-level counts

source_name: normal lung sample

extract_protocol:
total RNA was extracted from lung tissue sections using the Qiagen AllPrep kit.
500 ng total RNA was used to prepare libraries with the TruSeq stranded mRNA library prep kit. rRNA-depleted libraries were prepared from 1 ug total RNA with the Epidemiology Ribo-Zero Gold rRNA Removal Kit. Libraries were sequenced at 80M reads on the Illumina NovaSeq 6000.

tag: race

value: white

value: female

tag: ethnicity

value: non-hispanic

tag: diagnosis

value: normal

tag: smoking

value: Never

tag: tissue type

value: control


title: LOAL_106

tag: line

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

tag: tissue

value: Leaf tissue

value: 14 days


title: LOAL_105

tag: age


title: TIGK Non-infected sample treated with siOLFM4 2

tag: cell line

value: TIGK


title: HA1Q+APO1S_empty_1

tag: cell type


title: yck2 Low-glucose rep01 [YCK2_L1]

city: Chapel Hill

first: Henrik

last: Dohlman

state: NC

address: 120 Mason Farm Rd, 4th Floor

department: Pharmacology

institute: University of North Carolina at Chapel Hill

data_processing:
75bp, HS4000 paired end run, with 1 mismatch used in demultiplexing with bcl2fastq ver 2.20.0.
STAR (2.7.3a) genome indices was generated by using Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa as --genomeFastaFiles and Saccharomyces_cerevisiae.R64-1-1.99.gtf as --sjdbGTFfile. All fa and gtf files are downloaded from Ensembl.org
STAR (2.7.3a) and the previously generated genome indices were used for alignment with parameter --outSAMunmapped Within --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
generate transcriptome FA file by using gffread in SALMON (1.2.1) with -g Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa Saccharomyces_cerevisiae.R64-1-1.99.gtf
quantification was performed with SALMON (1.2.1) quant mode, with parameters -l ISR
Genome_build: R64-1-1 (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database), INSDC Assembly GCA_000146045.2, Sep 2011
Supplementary_files_format_and_content: sf files are TSV format file listing the name (Name) of each transcript, its length (Length), effective length (EffectiveLength) (more details on this in the documentation), and its abundance in terms of Transcripts Per Million (TPM) and estimated number of reads (NumReads) originating from this transcript
Supplementary_files_format_and_content: csv files are comma delminated matrix with genes on the rows and samples on the columns. the numbers are DESeq2 normalized counts with batch effect taken into control. For allmuts_wtH (design = ~batch+genotype); for allmuts_gxt (design = ~batch+genotype+treatment+genotype:treatment).

organism: Saccharomyces cerevisiae

source_name: log phase cell

growth_protocol: All strains were cultivated in the same way and maintained at 30 oC unless otherwise indicated. Cells were inoculated into Synthetic Complete (SC) (2% glucose) overnight and grown to saturation, then back diluted and kept in log phase overnight. The next morning, the culture was harvested when OD reached 1.0. For each genotype, 90 ml of culture (OD=1.0) was split into 2 tubes (45 ml each) for later high or low glucose treatment. For each tube, cells were centrifuged and resuspended twice with SC (0.05% glucose). Cells were then resuspended into 10 ml SC (0.05% glucose) and cultivated for 1 h.

extract_protocol:
500 μL of cell culture was aliquoted into a 1.7 mL microfuge tube and centrifuged at 1000 x g for 1 min at 4 °C. After discarding supernatant, the cell pellet was flash frozen by liquid nitrogen and stored at -80 °C. Cell pellets were resuspended with 600 μL buffer RLT 1% (v/v) 2-mercaptoethanol from the QIAGEN RNeasy Mini Kit (Cat No.: 74106) and then added into 2 mL OMNI prefilled ceramic bead tubes (SKU: 19-632). Tubes were loaded onto an OMNI Bead Mill Homogenizer (SKU:19-040E) for 3 beating cycles. For each cycle, samples were agitated at 5 m/s for 1 min at 4 °C and then cooled on ice for 3 min between each cycle. The resulting lysate was clarified by centrifugation at 11,000 xg and then used for total RNA extraction with QIAGEN RNeasy Mini Kit (Cat No.: 74106) with on-column DNase digestion according to manufacturer’s instructions. Extracted total RNA for each sample was checked for purity and quantified with Invitrogen Qubit 2.0 Fluorometer (Cat No.: Q32866) and Qubit RNA HS Assay kit (Cat No.: Q32855) according to manufacturer’s instructions.
KAPA Stranded mRNA Seq Kit (96 RXN) (Cat#07962207001) was used with 3 ug of total RNA for the construction of sequencing libraries. KAPA standard protocol was followed. Customized unique dual indexed barcodes from Perkin Elmer were used.

treatment_protocol: For high glucose treatment, 245 μL 65.5% glucose was added to 10 mL cell culture and for low glucose treatment, 245 μL 0.05% glucose was added to 10 mL cell culture, each for exactly 10 min.

tag: treatment

value: 0.05% glucose

tag: biological replicate


title: TIGK Non-infected sample treated with siOLFM4 1


title: total RNA from PT2016-172-CORE

tag: Sex

value: male


title: LOAL_104


title: TIGK Non-infected sample treated with siOLFM4 3


title: LOAL_103


title: TIGK Pg-infected sample treated with siC 3


title: total RNA from PT2016-168-CORE

value: Ever


title: TIGK Pg-infected sample treated with siC 2


title: total RNA from PT2016-167-CORE


title: yck2 High-glucose rep01 [YCK2_H1]

value: 2% glucose


title: WT #1

description: WT #1

tag: strain

value: brain, cortex

value: wild type

value: tamoxifen treatment (100 mg/kg, 2 times) at 3 weeks old

value: H3K9me2 antibody (clone#6D11)


title: yck1 Low-glucose rep02 [YCK1_L2]


title: LOAL_101


title: yck1 Low-glucose rep01 [YCK1_L1]


title: HA1Q+APO1S_gRNAs_2

value: 293 Flp-In T-REx

value: HALO-ADAR1Q + mAPOBEC1-SNAP-HIV-NES

value: transfection of two guideRNAs (2.5 pmol (snap)2-ACC + 2.5 pmol (halo)2-UAU) with Lipofectamine 2000


title: LOAL_100


title: total RNA from PT2016-155-CORE

value: white

value: non-hispanic

value: normal


title: TIGK Pg-infected sample treated with siC 1


title: yck2 Low-glucose rep02 [YCK2_L2]


title: TIGK Non-infected sample treated with siC 3


title: yck1 High-glucose rep02 [YCK1_H2]


title: yck2 High-glucose rep02 [YCK2_H2]


title: total RNA from PT2016-151-CORE

value: control


title: total RNA from PT2016-144-CORE


title: LOAL_99

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue

value: 14 days


title: LOAL_98


title: total RNA from PT2016-131-CORE

value: female


title: TIGK Non-infected sample treated with siC 1

value: TIGK


title: yck1 High-glucose rep01 [YCK1_H1]

value: 2% glucose


title: LOAL_97


title: TIGK Non-infected sample treated with siC 2


title: snf3rgt2 Low-glucose rep02 [SNF3RGT2_L2]

value: 0.05% glucose


title: snf3rgt2 High-glucose rep02 [SNF3RGT2_H2]


title: snf3rgt2 High-glucose rep01 [SNF3RGT2_H1]


title: total RNA from PT2016-072-CORE

value: Never


title: snf3rgt2 Low-glucose rep01 [SNF3RGT2_L1]


title: rgt2 Low-glucose rep02 [RGT2_L2]


title: LOAL_94


title: LOAL_93


title: total RNA from PT2016-065-CORE

value: male

value: Ever


title: total RNA from PT2016-050-CORE


title: total RNA from PT2016-070-CORE


title: rgt2 Low-glucose rep01 [RGT2_L1]


title: LOAL_95


title: total RNA from PT2016-045-CORE


title: LOAL_92


title: total RNA from PT2016-098-CORE


title: rgt2 High-glucose rep02 [RGT2_H2]


title: LOAL_96


title: total RNA from LTRC_XX293881

source_name: IPF lung sample

value: ipf

value: explant


title: LOAL_90


title: total RNA from LTRC_XX274606

value: biopsy


title: snf3 Low-glucose rep02 [SNF3_L2]


title: snf3 Low-glucose rep01 [SNF3_L1]


title: LOAL_89


title: total RNA from LTRC_XX266525

value: white


title: Blood-POD-rep4

city: Beijing

first: Jinghua

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at The Agilent Feature Extraction Software (version 11.0.1.1) was used to analyze and extract array images. Quantile normalization and subsequent data processing were conducted in GeneSpring GX v12.1 software package (Agilent Technologies). Threshold defined as fold-change > 2.0 (Student’s t test, P < 0.05) was used as a volcano plot filtering for DE lncRNAs and mRNAs.

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Blood total RNA was extracted and purified using TRIzol Reagent (Invitrogen) and RNasey Mini Kit (Qiagen) from POD group (n=4) and Ctrl group (n=4). The quantity and purity of total RNA samples were measured by NanoDrop ND-1000 (ThermoFisher) .

value: blood


title: Blood-POD-rep2


title: Blood-POD-rep3


title: Blood-POD-rep1


title: Blood-Ctrl-rep3


title: snf3 High-glucose rep02 [SNF3_H2]


title: Blood-Ctrl-rep2


title: LOAL_87


title: total RNA from LTRC_XX264609

value: non-hispanic


title: LOAL_91


title: LOAL_85


title: snf3 High-glucose rep01 [SNF3_H1]


title: Blood-Ctrl-rep1


title: total RNA from LTRC_XX223383


title: TPK3 Low-glucose rep02 [TPK3_L2]


title: TPK3 Low-glucose rep01 [TPK3_L1]


title: oxidized Casein MR diet C_MR_3425

city: Baton Rouge

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

description: oxidized Casein MR diet

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: counts

source_name: liver

extract_protocol: none provided by the submitter

value: Male

value: 4 months


title: oxidized Casein MR diet C_MR_3438

description: oxidized Casein MR diet


title: oxidized Casein MR diet C_MR_3431

description: oxidized Casein MR diet


title: LOAL_88

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue


title: oxidized Casein MR diet C_MR_3433

description: oxidized Casein MR diet


title: oxidized Casein MR diet C_MR_3419

description: oxidized Casein MR diet


title: total RNA from LTRC_XX220877


title: total RNA from LTRC_XX204089

value: female


title: Casein Control diet C_C_3437

description: Casein Control diet


title: oxidized Casein MR diet C_MR_3412

description: oxidized Casein MR diet


title: LOAL_82

value: 14 days


title: total RNA from LTRC_XX233433


title: total RNA from LTRC_XX195360


title: Casein Control diet C_C_3436

description: Casein Control diet


title: LOAL_84


title: LOAL_81


title: total RNA from LTRC_XX189243


title: LOAL_80


title: TPK2 Low-glucose rep01 [TPK2_L1]


title: total RNA from LTRC_XX123969


title: LOAL_83


title: TPK3 High-glucose rep02 [TPK3_H2]

value: 2% glucose


title: Casein Control diet C_C_3429

description: Casein Control diet


title: TPK3 High-glucose rep01 [TPK3_H1]


title: LOAL_79


title: Casein Control diet C_C_3421

description: Casein Control diet


title: total RNA from LTRC_XX123624


title: LOAL_78


title: TPK2 Low-glucose rep02 [TPK2_L2]

value: 0.05% glucose


title: TPK2 High-glucose rep02 [TPK2_H2]


title: total RNA from LTRC_XX118079

value: Never


title: TPK2 High-glucose rep01 [TPK2_H1]


title: Casein Control diet C_C_3413

description: Casein Control diet


title: rgt2 High-glucose rep01 [RGT2_H1]


title: Casein Control diet C_C_3407

description: Casein Control diet


title: TPK1 Low-glucose rep01 [TPK1_L1]


title: total RNA from LTRC_XX112291

value: male


title: LOAL_76


title: elemental amino acids MR diet E_MR_3424

description: elemental amino acids MR diet


title: LOAL_74


title: total RNA from LTRC_XX096521

value: Ever


title: LOAL_75


title: LOAL_77


title: TPK1 High-glucose rep02 [TPK1_H2]


title: LOAL_73


title: total RNA from LTRC_XX105331

value: ipf


title: total RNA from LTRC_XX064909

value: explant


title: TPK1 High-glucose rep01 [TPK1_H1]


title: total RNA from LTRC_XX048508


title: elemental amino acids MR diet E_MR_3420

description: elemental amino acids MR diet


title: LOAL_69


title: elemental amino acids MR diet E_MR_3405

description: elemental amino acids MR diet


title: TPK1 Low-glucose rep02 [TPK1_L2]


title: LOAL_68


title: elemental amino acids MR diet E_MR_3403

description: elemental amino acids MR diet


title: LOAL_70


title: pde2 Low-glucose rep01 [PDE2_L1]


title: total RNA from LTRC_XX038185


title: total RNA from LTRC_XX022285


title: elemental amino acids Control diet E_C_3430

description: elemental amino acids Control diet


title: pde2 High-glucose rep01 [PDE2_H1]


title: pde1 Low-glucose rep02 [PDE1_L2]


title: pde2 High-glucose rep02 [PDE2_H2]


title: elemental amino acids MR diet E_MR_3423

description: elemental amino acids MR diet


title: Blood-Ctrl-rep4


title: LOAL_67


title: pde2 Low-glucose rep02 [PDE2_L2]


title: elemental amino acids Control diet E_C_3428

description: elemental amino acids Control diet


title: total RNA from LTRC_XX021054


title: total RNA from LTRC_XX066548


title: elemental amino acids MR diet E_MR_3416

description: elemental amino acids MR diet


title: elemental amino acids Control diet E_C_3427

description: elemental amino acids Control diet


title: LOAL_65


title: total RNA from LTRC_XX005390


title: elemental amino acids Control diet E_C_3418

description: elemental amino acids Control diet


title: elemental amino acids Control diet E_C_3401

description: elemental amino acids Control diet


title: HCC2

first: qiudong

last: zhao

address: 225 Changhai Road

department: Tumor Immunology and Gene Therapy Center

institute: Shanghai Eastern Hepatobiliary Surgery Hospital

description: one sample from human liver cancer

data_processing:
Sequencing depth of tumor samples was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Cells defined as endothelia, fibroblast and macrophage were used as reference to identify somatic copy number variations with the R package inferCNV (v0.8.2).
We constructed single-cell trajectory of each tumor by using reversed graph embedding method implemented in R Monocle package (version 2.6.3)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: liver cancer

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 30 v3 Reagent Kit user guide.

value: liver


title: pde1 High-glucose rep01 [PDE1_H1]


title: HCC1

description: one sample from human liver cancer


title: LOAL_63


title: pde1 High-glucose rep02 [PDE1_H2]


title: oxidized Casein MR diet 3433 OX CAS MR

description: oxidized Casein MR diet

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.4.3, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.18.1 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Mouse – GRCm38.84  mm10
Supplementary_files_format_and_content: tab-delimited text containing DESeq2 normalized counts

source_name: IWAT

growth_protocol: Mice were obtained from JAX at 4 weeks of age, began the experimental diets at 5 weeks of age and remained on these diets for 12 weeks total. There were 8 mice in each group. Procedures performed during lifetime: Body weights, food and water intake were taken daily for the first two weeks, and every other day thereafter. NMR was performed weekly. Energy expenditure was measured using Oxymax on almost all mice in two separate cohorts in weeks 9 and 10. IPGTTs were performed in weeks 10 and 11. ITTs were performed in week 11. Animals were sacrificed after a 4h fast using CO2 inhalation and decapitation.

extract_protocol:
Flash frozen IWAT was dissected and a small piece was placed in Trizol. After homogenization, BCP was added, samples were vortexed vigorously, and then spun. The aqueous phase was combined with an equal volume of ethanol and the sample was processed through a Qiagen RNeasy column according to the manufacturer's instructions. mRNA was stored at -80°C and samples were diluted to 130ng/µl for RNAseq.
Quant-Seq  3' mRNA-Seq Library Prep Kit
indexed and pooled samples, 50bp forward read

treatment_protocol: The diets used consisted of standard diet containing elemental amino acids with a methionine concentration of either 0.86% methionine (control, E_C) or 0.17% methionine (MR, E-MR; Dyets).  Dyets also produced pellets with casein as protein source – a casein control (pelleted diet with casein protein, C_C), and oxidized casein MR (C_MR). Casein oxidation resulted in loss of methionine, which was added back at the same concentration as present in the elemental methionine restricted diet.

tag: dietary protein source

value: casein

tag: dietary methionine restriction

value: yes


title: LOAL_62


title: ras2 Low-glucose rep02 [RAS2_L2]

tag: genotype


title: ras2 Low-glucose rep01 [RAS2_L1]


title: LOAL_61


title: LOAL_66


title: elemental amino acids Control diet E_C_3417

description: elemental amino acids Control diet


title: Control2

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Gene abundance estimates were obtained for each sample using kallisto 0.44.0, with the Ensembl v96 transcriptome as the reference.
The abundance levels were normalized using the DESeq between-sample normalization approach.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: DND41_MB1_vs_Control_DESeqNormalizedCounts.csv: Comma-separated values file includes the DESeq normalized counts for all samples.

growth_protocol: DND41 cells were plated in triplicates in RPMI supplemented with 10% FBS.

extract_protocol:
RNA was extracted using QIAGEN QIAshredder (#79656) and RNeasy Mini (#74106) kits.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: DND41 cells were treated with control (DMSO) or MB1-47 (4mM) in RPMI supplemented with 10% FBS for 24h.

value: T-ALL cell line

value: DMSO (Control)


title: Control3

description: DND41_MB1_vs_Control_DESeqNormalizedCounts.csv


title: pde1 Low-glucose rep01 [PDE1_L1]


title: ras2 High-glucose rep02 [RAS2_H2]


title: oxidized Casein MR diet 3419 OX CAS MR

description: oxidized Casein MR diet

value: Male

value: 4 months


title: Control1


title: ras2 High-glucose rep01 [RAS2_H1]


title: oxidized Casein MR diet 3438 OX CAS MR

description: oxidized Casein MR diet


title: MB1_3


title: ras1 Low-glucose rep02 [RAS1_L2]


title: LOAL_59

data_processing:
Read trimming performed using custom perl script and Cutadapt v1.4.1 software. Reads were filtered by removing adaptor sequences along with reads and bases of low quality. Reads which had three consecutive N's and >3 consecutive nucleotides with Phred scores ≤ 20 were trimmed. Finally, any reads that were shorter than 50 bp were removed from the final set.
Parental read alignment to reference performed using BWA-MEM. SAM files were converted into binary format (BAM) files, sorted and indexed using SAMtools (version 1.9) sort and view options.
Variant calling performed through SAMtools mpileup and bcftools (version 1.9), and filtered using vcftools (v0.1.16).
RILs read alignment to reference performed using BWA-MEM. SAM files were converted into binary format (BAM) files, sorted and indexed using SAMtools (version 1.9) sort and view options.
Variant calling in RILs performed using SAMtools mpileup and bcftools (version 1.9), and filtered using vcftools (v0.1.16) with the SNP list identified from the parents.
Genome_build: Cassab reference transcriptome (Sudheesh et al., 2016).
Supplementary_files_format_and_content: vcf files include SNPs.

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue


title: LOAL_60

value: 14 days


title: oxidized Casein MR diet 3425 OX CAS MR

description: oxidized Casein MR diet


title: LOAL_58


title: LOAL_64


title: oxidized Casein MR diet 3431 OX CAS MR

description: oxidized Casein MR diet


title: ras1 Low-glucose rep01 [RAS1_L1]


title: LOAL_57


title: oxidized Casein MR diet 3412 OX CAS MR

description: oxidized Casein MR diet


title: CLL9_3

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 10X chemistry: Single Cell 5' PE

data_processing:
demultiplexing of illumina BCL files with cellranger mkfastq version 3.1
alignment of sequencing reads to hg38 reference genome using cellranger count version 3.1
calling of single cells using the default parameters in cellranger
Genome_build: hg38
Supplementary_files_format_and_content: filtered feature matrix

source_name: Richter's patient 9 timepoint 2 - Bone marrow

extract_protocol:
Ficoll density centrifugation
droplet-based scRNA-seq (3' scRNA-seq and 5' scRNA-seq) using the chromium platform (10x Genomics)

value: Bone marrow

tag: disease state

value: CLL Richter's transformation

tag: wbc

tag: cd19+ cd5+ (percentage)

tag: time

value: Bone marrow Richter's phase


title: ras1 High-glucose rep01 [RAS1_H1]

value: 2% glucose


title: CLL9_2

description: 10X chemistry: Single Cell 5' PE

source_name: Richter's patient 9 timepoint 2 - Peripheral blood

value: Peripheral blood

value: Peripheral blood Richter's phase


title: LOAL_54

extract_protocol:
Total RNA was extracted from selected young leaves of 14-day-old seedlings of parents and 140 RILs using the RNeasy® 96 kit (Qiagen Inc., Hilden, Germany) following the manufacturer’s instructions.
cDNA libraries were prepared for sequencing using standard Illumina protocols.


title: ras1 High-glucose rep02 [RAS1_H2]


title: CLL9_1

description: 10X chemistry: Single Cell 5' PE

source_name: Richter's patient 9 timepoint 1

value: CLL active disease

value: Peripheral blood CLL phase


title: LOAL_52


title: Casein Control diet 3421 CAS CON

description: Casein Control diet

value: casein

value: no


title: rgs2 Low-glucose rep02 [RGS2_L2]

value: 0.05% glucose


title: Casein Control diet 3436 CAS CON

description: Casein Control diet


title: Casein Control diet 3407 CAS CON

description: Casein Control diet


title: LOAL_51


title: Casein Control diet 3413 CAS CON

description: Casein Control diet


title: rgs2 High-glucose rep02 [RGS2_H2]


title: Casein Control diet 3429 CAS CON

description: Casein Control diet


title: rgs2 High-glucose rep01 [RGS2_H1]


title: LOAL_53


title: CLL8_2

description: 10X chemistry: Single Cell 5' R2-only

source_name: Ibrutinib patient 8 timepoint 2

value: Ibrutinib 7 months


title: MB1_2

value: T-ALL cell line


title: rgs2 Low-glucose rep01 [RGS2_L1]


title: CLL8_3

description: 10X chemistry: Single Cell 5' PE

source_name: Ibrutinib patient 8 timepoint 3

value: Ibrutinib 14 months


title: LOAL_55

source_name: leaf

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: CLL7_3

description: 10X chemistry: Single Cell 5' PE

source_name: Ibrutinib patient 7 timepoint 3

value: Ibrutinib 16 months


title: LOAL_50

value: Leaf tissue

value: 14 days


title: MB1_1


title: CLL8_1

description: 10X chemistry: Single Cell 5' R2-only

source_name: Ibrutinib patient 8 timepoint 1

value: Pretreatment Ibrutinib


title: LOAL_49


title: gpa2 Low-glucose rep02 [GPA2_L2]


title: gpa2 Low-glucose rep01 [GPA2_L1]


title: Casein Control diet 3437 CAS CON

description: Casein Control diet

value: Male

value: 4 months


title: elemental amino acids MR diet 3424 ELE MR

description: elemental amino acids MR diet

value: elemental amino acids

value: yes


title: elemental amino acids MR diet 3405 ELE MR

description: elemental amino acids MR diet


title: gpa2 High-glucose rep02 [GPA2_H2]

value: 2% glucose


title: CLL7_1

description: 10X chemistry: Single Cell 5' R2-only

source_name: Ibrutinib patient 7 timepoint 1

value: Peripheral blood

value: CLL active disease


title: LOAL_47


title: CLL7_2

description: 10X chemistry: Single Cell 5' R2-only

source_name: Ibrutinib patient 7 timepoint 2

value: Ibrutinib 6 months


title: CLL6_4

description: 10X chemistry: Single Cell 5' PE

source_name: RIC/Ibrutinib relapse patient 6 timepoint 4

value: Ibrutinib 21 months


title: gpa2 High-glucose rep01 [GPA2_H1]


title: elemental amino acids MR diet 3416 ELE MR

description: elemental amino acids MR diet


title: LOAL_46


title: CLL6_3

description: 10X chemistry: Single Cell 5' PE

source_name: RIC/Ibrutinib relapse patient 6 timepoint 3

value: Ibrutinib 1 month


title: LOAL_44


title: elemental amino acids MR diet 3403 ELE MR

description: elemental amino acids MR diet


title: elemental amino acids MR diet 3420 ELE MR

description: elemental amino acids MR diet


title: LOAL_45


title: gpr1 Low-glucose rep01 [GPR1_L1]

source_name: log phase cell

value: 0.05% glucose


title: gpr1 Low-glucose rep02 [GPR1_L2]


title: CLL6_1

description: 10X chemistry: Single Cell 5' PE

source_name: RIC/Ibrutinib relapse patient 6 timepoint 1

value: Pretreatment FCR


title: LOAL_48

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: CLL5_2

description: 10X chemistry: Single Cell 5' PE

source_name: RIC relapse patient 5 timepoint 2

value: Relapse post-RIC


title: elemental amino acids MR diet 3423 ELE MR

description: elemental amino acids MR diet


title: asc1 Low-glucose rep02 [ASC1_L2]


title: gpr1 High-glucose rep02 [GPR1_H2]


title: LOAL_43

value: Leaf tissue


title: elemental amino acids Control diet 3418 ELE CON

description: elemental amino acids Control diet

value: no


title: CLL6_2

description: 10X chemistry: Single Cell 5' PE

source_name: RIC/Ibrutinib relapse patient 6 timepoint 2


title: gpr1 High-glucose rep01 [GPR1_H1]


title: asc1 Low-glucose rep01 [ASC1_L1]


title: elemental amino acids Control diet 3430 ELE CON

description: elemental amino acids Control diet

source_name: IWAT


title: LOAL_42

value: 14 days


title: asc1 High-glucose rep02 [ASC1_H2]


title: elemental amino acids Control diet 3401 ELE CON

description: elemental amino acids Control diet

value: Male


title: CLL4_1

description: 10X chemistry: Single Cell 5' PE

source_name: RIC relapse patient 4 timepoint 1


title: asc1 High-glucose rep01 [ASC1_H1]


title: LOAL_39


title: elemental amino acids Control diet 3428 ELE CON

description: elemental amino acids Control diet

value: 4 months


title: LOAL_41


title: elemental amino acids Control diet 3417 ELE CON

description: elemental amino acids Control diet

value: elemental amino acids


title: LOAL_38


title: LOAL_40


title: CLL3_2

description: 10X chemistry: Single Cell 5' PE

source_name: FCR relapse patient 3 timepoint 2

value: Relapse post-FCR


title: CLL3_1

description: 10X chemistry: Single Cell 5' PE

source_name: FCR relapse patient 3 timepoint 1


title: elemental amino acids Control diet 3427 ELE CON

description: elemental amino acids Control diet


title: LOAL_37


title: wt Low-glucose rep02 [WT_L2]

value: wildtype


title: CLL5_1

description: 10X chemistry: Single Cell 5' PE

source_name: RIC relapse patient 5 timepoint 1

value: Peripheral blood


title: wt Low-glucose rep01 [WT_L1]


title: siHmg20a, biological rep2

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

data_processing:
the libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NextSeq500 HIGH-Output and 2x75bp length parameters
The RNA-seq data were aligned using Subjunc function from Rsubread [1] v.1.28.1 bioconductor package, to map reads to the mm9 mouse reference genome, using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bam files with duplicates removed using the samtools [2] v.0.1.19 rmdup command. FeatureCounts() function from Rsubread v.1.28.1 bioconductor package was used to assign reads to UCSC mm9 genes using GTF.featureType="exon" and GTF.attrType="gene_id" parameters on duplicate removed bam files. Then differential gene expression analysis was performed using the voom/limma [6] v.3.34.9 and edgeR [7,8] v.3.20.9 bioconductor packages. Genes that were expressed at > 1 counts per million mapped reads in ≥2 replicates were analyzed. CalcNormFactors() function using TMM method was used to normalize samples.
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: Raw counts per UCSC knownGenes at exon level for all treatments.

source_name: Murine astrocytes

growth_protocol: Primary hypothalamic astrocytes were isolated and cultured as previously described {Fuente-Martin, 2016 #8734;Fuente-Martin, 2012 #8735}. Briefly, hypothalamus from 2 to 4-days-old C57BL/6J male mice were extracted under sterile conditions and triturated in Dulbecco’s modified Eagle’s Medium(DMEM) F-12 (Gibco, Thermo Fisher Scientific, MA, USA) containing 1% penicillin-streptomycin (Gibco). The suspension was centrifuged and the pellet resuspended in DMEM F-12 + 10% FBS + 1% antibiotics. Cells were grown in this culture media in T75 culture flasks at 37ºC and 5% CO2. The culture medium was refreshed every 2 days.At confluence, microglia and oligodendroglia were detached by shaking flasks at 220 rpm for 16 hours at 37°C. The remaining attached astrocytes were then used for experiments.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the NextSeq500 HIGH-Output and 2x75bp length parameters

treatment_protocol: Two independent cultures (replicates) were treated with each one of the following siRNA: siControl,siHmg20a

value: Cells transfected  with siHmg20A RNA

tag: tissue origin

value: astrocytes


title: LOAL_36

source_name: leaf

tag: line


title: CLL2_2

description: 10X chemistry: Single Cell 5' PE

source_name: FCR relapse patient 2 timepoint 2

tag: tissue

value: CLL active disease


title: wt High-glucose rep02 [WT_H2]

value: 2% glucose


title: LOAL_35

tag: age


title: CLL4_2

description: 10X chemistry: Single Cell 5' PE

source_name: RIC relapse patient 4 timepoint 2


title: CLL2_1

description: 10X chemistry: Single Cell 5' PE

source_name: FCR relapse patient 2 timepoint 1


title: siControl (siHmg20a control), biological rep2

value: Cells transfected  with siControl RNA


title: siHmg20a, biological rep1


title: wt High-glucose rep01 [WT_H1]


title: CLL1_5.2

description: 10X chemistry: Single Cell 3' v2

source_name: FCR relapse patient 1 timepoint 5


title: siControl (siHmg20a control), biological rep1

value: Cells transfected with siControl RNA


title: CLL1_5.1

description: 10X chemistry: Single Cell 3' v2


title: TEADi_C

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

description: ad_TEADi (Treatment)

data_processing:
Reads were trimmed using Cutadapt 1.18 for adapters and low-quality bases
alignment to the mouse reference genome, mm10, was performed using STAR 2.7.0f
Gene counts were calculated using Quantify to annotation model with Ensembl Transcripts release 96 (Partek E/M, PartekFlow 8.0.19.0819)
counts were filtered to exclude genes with maximum <= 5.0 counts with Partek Flow 8.0.19.0819
Counts were added +1 and gene expression was normalized to TMM using PartekFlow 8.0.19.0819
TMM values were used for differential analysis to identify genes that are differentially expressed using the GSA function in PartekFlow 8.0.19.0819 with q value calculation, by comparing the siYT samples to siCon samples and TEADi to GFP samples.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files includes TMM values and GSA analysis for all samples

source_name: BCC keratinocytes

growth_protocol: Cells were cultured using EpiLife medium with 60 µM calcium (GIBCO MEPI500CA), supplemented with defined growth supplement (EDGS, GIBCO S0125), mouse EGF (10ng/ml, R&D Systems 2028EG200), and Y-27632 compound (10 µM, Tocris Bioscience 12-541-0)

extract_protocol:
RNA was isolated and processed using TRIZOL according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq mRNA Prep Kit RS-122-2101

treatment_protocol: Cells were transduced one day after plating and harvested 48hs later. siRNAs were siGENOME SMARTpool from Dharmacon/Horizon, siYAP1 (M-046247-01-0010), siTAZ (M-041057-01-0010), and non-targeting control siRNA (D-001206-13). siRNA was transfected at a concentration of 8 pmol cm-2 using Lipofectamine RNAiMAX (Invitrogen) according to manufacturer’s instructions. For adenoviral transduction, cells were incubated with a multiplicity of infection (MOI) of 25 with adeno-GFP (control) or adeno-TEADi for the indicated times. TEADi adenoviruses were produced, purified and titered by Vector Biolabs in an adenoviral-Type 5 (dE1/E3) backbone with a CMV promoter. As a GFP control Ad-CMV-GFP (Vector Biolabs, catalog no. 1060) was used.

value: Skin

value: basal cell carcinoma

value: TEADi


title: LOAL_34

first: Ido

last: Bar

institute: Griffith University

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue


title: LOAL_31

value: 14 days


title: CLL1_3.2

description: 10X chemistry: Single Cell 3' v2

source_name: FCR relapse patient 1 timepoint 3

value: Pretreatment FCR


title: TEADi_B

description: ad_TEADi (Treatment)


title: LOAL_32


title: LOAL_30


title: CLL1_3.1

description: 10X chemistry: Single Cell 3' v2


title: CLL1_1.2

description: 10X chemistry: Single Cell 3' v2

source_name: FCR relapse patient 1 timepoint 1

value: Watchful waiting


title: TEADi_A

description: ad_TEADi (Treatment)


title: GFP_C

description: ad_GFP (control)

value: GFP


title: CLL1_1.1

description: 10X chemistry: Single Cell 3' v2


title: GFP_B

description: ad_GFP (control)


title: LOAL_28


title: LOAL_27


title: CLL9_4.CD19neg: Richter's patient 9 timepoint 2 - Lymph node CD19- cells

data_processing:
demultiplexing of illumina BCL files with cellranger-atac mkfastq version 1.2
alignment of sequencing reads to a modified hg38 reference using cellranger-atac count version 1.2
calling of single cells using the default parameters in cellranger-atac
Genome_build: hg38
Supplementary_files_format_and_content: processed fragment files from cellranger-atac count

source_name: Lymph node

extract_protocol:
Ficoll density centrifugation, if applicable selection of CD19+/- fractions using CD19 selection beads
droplet-based scATAC-seq optimized for capture of mitochondrial DNA (mtscATAC-seq) described in Lareau et al. (PMID 32788668)

value: lymph node

value: CLL Richter's transformation

value: Lymph node Richter's phase CD19- cells


title: GFP_A

description: ad_GFP (control)


title: IgG-CT

city: Xiamen

first: liu

last: kai

state: Fujian

address: Xiang'an Campus, Xiamen University, Xiang'an District

institute: Xiamen University

data_processing:
Library strategy: CUT&Tag
Illumina Casava1.8 software used for basecalling.
Adapter trimming was performed using trimmomatic version 0.39
reads were aligned to the mm10 genome using  Bowtie2 version 2.3.4.3
peaks were called using MACS2 version 2.2.7.1 with the following setting: -f BAMPE -q 0.05 -B --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools version 3.2.1
Supplementary_files_format_and_content: peak text files

source_name: Spleen

extract_protocol:
cells were tagged with concanavalin A-coated magnetic beads and then incubated with primary antibody (rabbit polyclonal anti-Histone H3 (acetyl K27) antibody (ab4729, Abcam), rabbit polyclonal anti- Histone H3 (trimethyl K27) antibody (07-449, Millipore), Rabbit IgG Isotype Control (3900, CST)). After incubated with secondary antibody (goat anti- rabbit IgG H&L (ab6702, abcam)), cells were incubated with Hyperactive pG-Tn5 Transposon and then resuspended in tagmentation buffer for tagmentation.
DNA was purified and amplified by 15-17 PCR cycles to generate the libraries. Libraries were sequenced on an Illumina Nova-PE150 following the manufacturer's protocols.
CUT-tag

treatment_protocol: On day 5 post-infection with LCMV Armstrong, transferred P14 cells were sorted from the spleen of donor mice.

value: spleen

value: female

value: day 5 post-infection

value: 12 weeks

tag: chip antibody

value: Rabbit IgG Isotype Control (3900, CST)


title: WT-ATAC rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
Adapter trimming was performed using trimmomatic version 0.39
reads were aligned to the mm10 genome using  Bowtie2 version 2.3.4.3
peaks were called using MACS2 version 2.2.7.1 with the following setting: -f BAMPE -q 0.05 -B --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools version 3.2.1
Supplementary_files_format_and_content: peak text files

extract_protocol:
Cells were lysed using RIPA buffer. The unfixed nuclei of these cells were tagged using Tn5 transposase (TruePrep DNA Library Prep Kit V2 for Illumina).
Library fragments were generated by 10–12 PCR cycles, and finally sequenced on an Illumina Nova-PE150 following the manufacturer's protocols.

value: wild type


title: WT-ATAC rep2


title: C1qbp-KO-ATAC rep1

value: C1qpb KO


title: C1qbp-KO-H3K27Ac rep1

value: H3K27Ac (ab4729, Abcam)


title: C1qbp-KO-ATAC rep2


title: siYT_C

value: Skin

value: basal cell carcinoma

value: pooled siRNAs targeting YAP1 and TAZ


title: CLL9_4.CD19pos.5: Richter's patient 9 timepoint 2 - Lymph node CD19+ cells 5

value: Lymph node Richter's phase CD19+ cells


title: LOAL_25

city: Nathan

address: 170 Kessels Road

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue

value: 14 days


title: CLL9_4.CD19pos.4: Richter's patient 9 timepoint 2 - Lymph node CD19+ cells 4

value: lymph node

value: CLL Richter's transformation


title: WT-H3K27Ac rep1

value: spleen


title: C1qbp-KO-H3K27Ac rep2

value: female


title: WT-H3K27Ac rep2

value: day 5 post-infection


title: siYT_B


title: CLL9_4.CD19pos.3: Richter's patient 9 timepoint 2 - Lymph node CD19+ cells 3


title: LOAL_24


title: siYT_A


title: C1qbp-KO-H3K27me3 rep2

value: 12 weeks

value: H3K27me3  (07-449, Millipore)


title: LOAL_23


title: LOAL_26


title: siCON_C

description: siControl

value: non-targeting control siRNA


title: CLL9_4.CD19pos.2: Richter's patient 9 timepoint 2 - Lymph node CD19+ cells 2


title: CLL9_4.CD19pos.1: Richter's patient 9 timepoint 2 - Lymph node CD19+ cells 1


title: LOAL_22


title: CLL9_3: Richter's patient 9 timepoint 2 - Bone marrow

source_name: Bone marrow

value: bone marrow

value: Bone marrow Richter's phase


title: WT-H3K27me3 rep2

value: wild type


title: CLL9_2: Richter's patient 9 timepoint 2 - Peripheral blood

source_name: Peripheral blood

value: blood

value: Peripheral blood Richter's phase


title: WT-H3K27me3 rep1


title: LOAL_20


title: siCON_A

description: siControl

value: Skin

value: basal cell carcinoma


title: LOAL_19

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue


title: CLL9_1: Richter's patient 9 timepoint 1

value: CLL active disease

value: Peripheral blood CLL phase


title: LOAL_18

value: 14 days


title: Candida glabrata planktonic rep3 [re-analysis]

city: CHANDIGARH

first: KHEM

last: RAJ

state: Chandigarh

address: Deparment of Microbiology, BMS Block-I, PANJAB UNI, PANJAB UNIVERSITY, SECTOR -25

department: Microbiology

country: India

institute: PANJAB UNIVERSITY

description: This is duplicated sample record of GSM4626566 for the convenient retrieval of the complete raw data from SRA

data_processing:
Quality check for allr Fastq raw read RNA sequence files was performed by open source quality check software FastQC.
Based on the quality, we trimmed sequence reads usingTrimmommatic software (http://www.usadellab.org/cms/index.php?page=trimmomatic) and retained only high-quality sequence for further analysis
We imported the reconstructed and quantified full-length transcripts generated by the Tuxedo pipeline into to R environment using the IsoformSwitchAnalyzeR package (v1.5.4). IsoformSwitchAnalyzR is a R package that evaluates the statistical identification of isoform switching from RNA-Seq derived novel and annotated isoforms. R script for detection of isoform switching and usage is provided.
Genome_build: CBS138 genome and gene model downloaded from Ensembl database.   (ftp://ftp.ensemblgenomes.org/pub/fungi/release34/gtf/fungi_ascomycota1_collection/cadida_glabrata/ Candida_glabrata.ASM254v2.34.gtf.gz)
Supplementary_files_format_and_content: Matrix table with raw isofrm counts for  every sample;

organism: Nakaseomyces glabratus

source_name: Candida glabrata cells

growth_protocol: 100 μL of log phase culture was added to polystyrene 96-well microtiter plate in RPMI-1640 medium and only medium without the cells  used as control. The plate was incubated for 24h at 37°C. Next, the medium was carefully aspirated without disrupting the biofilm formed in the wells and washed with sterile PBS

extract_protocol:
RNA was extracted using Hi-PurA yeast RNA purification kit from biofilm and planktonic growth phase and sequenced by Illumina Hi-Seq 2500 platform with 250bp paired chemistry
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth phase

value: Planktonic


title: C1qbp-KO-H3K27me3 rep1

value: spleen

value: C1qpb KO

value: female

tag: treatment

value: day 5 post-infection


title: Candida glabrata planktonic rep1 [re-analysis]

description: This is duplicated sample record of GSM4626564 for the convenient retrieval of the complete raw data from SRA


title: Candida glabrata planktonic rep2 [re-analysis]

description: This is duplicated sample record of GSM4626565 for the convenient retrieval of the complete raw data from SRA


title: LOAL_17


title: CLL8_2: Ibrutinib patient 8 timepoint 2

value: Ibrutinib 7 months


title: CLL8_3: Ibrutinib patient 8 timepoint 3

value: Ibrutinib 14 months


title: Candida glabrata biofilm rep3 [re-analysis]

description: This is duplicated sample record of GSM4626563 for the convenient retrieval of the complete raw data from SRA

value: Biofilm


title: LOAL_16


title: TAC3

city: Guangzhou

first: Shan

last: Ye

state: Guangdong

address: 250 Changgang East Road

department: Department of Geriatrics

institute: the Second Affiliated Hospital of Guangzhou Medical University

data_processing:
The RNA of different samples was used for library construction by KAPA Stranded RNA-seq library Prep Kit.
The library was sequenced by Illumina NovaSeq 6000 Sequencing system.
Image analysis and base recognition were carried out by Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8).
R software was used to calculate  fragments per kb per million reads (FPKM) scores in each library
Genome_build: mm9
Supplementary_files_format_and_content: Include Fold_Change, p value and FPKM values for each Sample.

source_name: heart tissue

growth_protocol: The mice were fed a standard laboratory diet and housed under standard conditions.

extract_protocol:
The mice were sacrificed at 21 days after TAC and hearts were harvested. Total RNA was isolated from heart tissues using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TAC group received transverse aortic constriction to establish myocardial hypertrophy. The TAC+PUE group mice received puerarin (100 mg/kg per day) by intraperitoneal 3 days before TAC and continued for 21 days after TAC.In the sham group, mice received the surgical procedures but without the constriction.

value: heart

value: 10 weeks old

value: TAC


title: TAC+PUE2

value: TAC+PUE


title: TAC+PUE1


title: TAC2


title: CLL8_1: Ibrutinib patient 8 timepoint 1

value: blood

value: Pretreatment Ibrutinib


title: CLL7_3: Ibrutinib patient 7 timepoint 3

value: CLL active disease

value: Ibrutinib 16 months


title: Candida glabrata biofilm rep2 [re-analysis]

description: This is duplicated sample record of GSM4626562 for the convenient retrieval of the complete raw data from SRA


title: LOAL_21

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue

value: 14 days


title: TAC+PUE3


title: LOAL_15


title: siCON_B

description: siControl

value: Skin

value: basal cell carcinoma

value: non-targeting control siRNA


title: Candida glabrata biofilm rep1 [re-analysis]

description: This is duplicated sample record of GSM4626561 for the convenient retrieval of the complete raw data from SRA


title: LOAL_14


title: sham3

value: sham


title: Candida glabrata planktonic rep3

data_processing:
Quality check for allr Fastq raw read RNA sequence files was performed by open source quality check software FastQC.
Based on the quality, we trimmed sequence reads usingTrimmommatic software (http://www.usadellab.org/cms/index.php?page=trimmomatic) and retained only high-quality sequence for further analysis
Tuxedo pipeline was used for RNA Seq data analysis, which consists of integrated bioinformatics tools (Tophat2, Cufflink, Cuffmerge, Cuffdiff, and CummeRbund). RNA Seq data was processed with packages that are interconnected sequentially with each other. Output file from one step is used as an input file in subsequent steps. All pre-processed reads from both libraries were concatenated and aligned to the reference genome of C.glabarata, strain CBS138 by Tophat2 program (version2.1.1) with default parameters using Bowtie 2 aligner of Tophat2.
Genome_build: CBS138 genome and gene model downloaded from Ensembl database.   (ftp://ftp.ensemblgenomes.org/pub/fungi/release34/gtf/fungi_ascomycota1_collection/cadida_glabrata/ Candida_glabrata.ASM254v2.34.gtf.gz)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Candida glabrata planktonic

value: Planktonic growth phase


title: CLL7_2.CD19neg: Ibrutinib patient 7 timepoint 2 - CD19- cells

value: Ibrutinib 6 months CD19- cells


title: LOAL_13


title: sham2

value: heart


title: Candida glabrata planktonic rep2


title: CLL7_1.CD19pos: Ibrutinib patient 7 timepoint 1 - CD19+ cells

value: Pretreatment Ibrutinib CD19+ cells


title: sham1

value: 10 weeks old


title: LOAL_11


title: Candida glabrata planktonic rep1


title: Candida glabrata biofilm rep3

source_name: Candida glabrata biofilm

value: Biofilm growth phase


title: CLL7_1.CD19neg: Ibrutinib patient 7 timepoint 1 - CD19- cells

value: blood

value: Pretreatment Ibrutinib CD19- cells


title: LOAL_10


title: Sample-8: Whole bladder cells C57Bl/6 with MB49 tumor

city: Uppsala

first: Iliana

middle: Kyriaki

last: Kerzeli

state: Uppsala

address: Husargatan 3

country: Sweden

institute: Uppsala University

data_processing:
Illumina Basecalling, Novaseq 6000
Demultiplexed raw fastq files were proessed by 10X Genomics cellranger pipeline (v 3.0.1)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized and filtered gene counts for every gene and every sample

extract_protocol:
Bladders were dissociated with the mouse tumor dissociation kit (Miltenyi cat. 130-096-730) according to the manufacturer’s instructions to create single cell suspensions. Samples were submitted to downstream procedures if viability was 75% or higher. Samples were processed using Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics cat. 1000092) according to the manufacturer’s instructions.
Samples were processed using Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics cat. 1000092) according to the manufacturer’s instructions.

tag: tumor stage

value: Orthotopic tumor MB49 day 5

tag: tumor induction

value: Orthotopic instillation of tumor cell line in the bladder

value: bladder


title: LOAL_9

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis

value: Leaf tissue


title: Candida glabrata biofilm rep1

tag: strain


title: Candida glabrata biofilm rep2


title: Sample-11: Whole bladder cells healthy Hgf-Cdk4R24C

value: Healthy animals


title: CLL7_2.CD19pos: Ibrutinib patient 7 timepoint 2 - CD19+ cells

value: CLL active disease

value: Ibrutinib 6 months CD19+ cells


title: LOAL_8

value: 14 days


title: Sample-6: Whole bladder cells female MIBC Hgf-Cdk4R24C

value: MIBC

value: Carcinogen exposure


title: CLL6_4: RIC/Ibrutinib relapse patient 6 timepoint 4

value: Ibrutinib 21 months


title: CLL6_3: RIC/Ibrutinib relapse patient 6 timepoint 3

value: Ibrutinib 1 month


title: Sample-7: Whole bladder cells C57Bl/6  healthy

source_name: Whole bladder cells C57Bl/6  healthy


title: CLL6_1: RIC/Ibrutinib relapse patient 6 timepoint 1

value: Pretreatment FCR


title: CLL6_2: RIC/Ibrutinib relapse patient 6 timepoint 2

value: Relapse post-RIC


title: Sample-5: Whole bladder cells male MIBC Hgf-Cdk4R24C


title: LOAL_12

source_name: leaf


title: LOAL_7


title: DHF2_C

city: Ratchathewi

first: Ponpan

last: Matangkasombut

state: Bangkok

address: 272 Thanon Rama VI

country: Thailand

institute: Mahidol University

data_processing:
Nextera adapter sequences were removed using Trimmomatic version 0.36
Trimmed reads were mapped and aligned using HISAT2  (2.1.0) with GRCh38 as the reference genome.
Normalized relative transcript abundances as Transcripts Per Kilobase Million (TPM) were obtained using StringTie (1.3.5)
Raw read counts were obtained with the HTseq-count version 0.6.1p1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited files of reads counts or TPM values for each sample

source_name: DHF_Convalescent phase

extract_protocol:
Helper ILCs were sorted into 96 well plate containing lysis buffer using FACS Aria III. Sorted cells were lysed, reverse transcribed, whole transcriptome amplified, and generateded library according to SMART-Seq2 protocol (Picelli, 2014)
Libraries were contructed using Nextera XT kit from pre-amplified cDNA

tag: subject status

value: DENV infected patient

tag: Sex

value: M

tag: severity

value: DHF

tag: timepoint

value: Convalescent phase

tag: cell type

value: innate lymphoid cells


title: LOAL_6

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: DHF1_C


title: DHF3_F

source_name: DHF_Febrile phase

value: F

value: Febrile phase


title: DHF3_C


title: TAC1

value: heart

value: 10 weeks old

value: TAC


title: Sample-3: Whole bladder cells male NMIBC Hgf-Cdk4R24C

value: NMIBC

value: bladder


title: LOAL_4

value: Leaf tissue

value: 14 days


title: invitro, 100cell, transcriptome

city: Philadelphia

first: Kamen

middle: P

last: Simeonov

state: PA

address: 3800 Spruce St

institute: University of Pennsylvania

data_processing:
Demultiplexed fastq files are obtained either by illumina basespace or 10x Cell Ranger v3
10x Cell Ranger v3 was used to align transcriptomes and a custom pipeline was used to align barcodes (https://github.com/mckennalab/SingleCellLineage/)
Sparse expression matrices for transcriptomes were produced using 10x Cell Ranger v3
Clonal and subclonal annotation was produced from barcode data using custom scripts (https://github.com/ksimeono/macsGESTALT)
Genome_build: mm10
Supplementary_files_format_and_content: .tsv files are tab seperated txt files and .mtx files are sparse expression matrices

source_name: cancer cells

growth_protocol: PDAC cells were cultured in complete media (DMEM, 10% FBS, 1% glutamine with penicillin and streptomycin).

extract_protocol:
Tissues were collected, single-cell dissociated, GFP+ cells were FACS isolated, samples were then loaded for 10x encapsulation (Chromium Single Cell 3’ Reagent Kits v3)
Single cell RNA-seq libraries were prepared as in the 10x Chromium Single Cell 3' v3 user guide (Rev A) until Step 2.3. After cDNA amplification, the 100 µL cDNA PCR was split 50:50 for separate barcode and transcriptome library preparation. Transcriptome library construction continued as in the 10x user guide instructions. Barcode libraries were prepared using a custom targeted PCR, followed by an indexing PCR, barcode libraries were then size-selected using SPRI beads.
scRNAseq; sc transcriptome libraries were sequenced on the Illumina NovaSeq 6000 System with 100-cycle S2 Reagent Kits with the following run parameters: Read 1 - 28 cycles, i7 index - 8 cycles, Read 2 - 91; sc barcode libraries were sequenced on the Illumina MiSeq with 600-cycle v3 Reagent Kits with the following run parameters: Read 1 - 28 cycles, i7 index - 8 cycles, Read 2 - 500.

treatment_protocol: macsGESTALT PDAC cells were thawed and expanded for 2-4 d prior to dissociation and orthotopic injection into 10 week old NOD/SCID male mice (Jackson Laboratory). Approximately 30,000 PDAC cells were injected into the surgically-exposed tail of the pancreas. Cells were allowed to engraft; then doxycycline was initiated 1 week post-injection and given continuously in the drinking water at 1 mg/mL. Mice were harvested at approximately 5 weeks post injection, once reaching morbidity.

tag: harvest-site

value: Cultured cells

tag: experiment

value: invitro

tag: info-type

value: transcriptome


title: LOAL_5

state: QLD

tag: line


title: CLL4_1: RIC relapse patient 4 timepoint 1

tag: tissue

value: blood

tag: disease state

value: CLL active disease

tag: wbc

value: Pretreatment FCR


title: DHF2_F

value: DENV infected patient

tag: age

value: M

value: DHF

value: innate lymphoid cells


title: LOAL_3

value: Recombinant inbred line derived from cross Lens culinaris x Lens orientalis


title: DHF1_F

value: Febrile phase


title: LOAL_2


title: LOAL_29


title: DF3_C

source_name: DF_Convalescent phase

value: F

value: DF

value: Convalescent phase


title: CLL3_2: FCR relapse patient 3 timepoint 2

tag: treatment

value: Relapse post-FCR


title: Mouse2, Lung, transcriptome

value: Lung


title: CLL5_2: RIC relapse patient 5 timepoint 2

value: Relapse post-RIC


title: Sample-4: Whole bladder cells female NMIBC Hgf-Cdk4R24C

tag: tumor stage

value: NMIBC

value: Carcinogen exposure

value: bladder


title: CLL3_1: FCR relapse patient 3 timepoint 1

value: blood

value: CLL active disease


title: LOAL_1

value: Leaf tissue

value: 14 days


title: Mouse2, Liver, transcriptome

value: Liver

value: transcriptome


title: CLL2_2: FCR relapse patient 2 timepoint 2


title: DF2_C

value: DENV infected patient

value: M

value: innate lymphoid cells


title: Mouse2, Peritoneal mets, transcriptome

value: Peritoneal mets


title: CLL5_1: RIC relapse patient 5 timepoint 1

value: Pretreatment FCR


title: CLL2_1: FCR relapse patient 2 timepoint 1


title: CLL4_2: RIC relapse patient 4 timepoint 2


title: Mouse2, Primary tumor, transcriptome

value: Primary tumor


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t5 + Rapamycin t4 WCE

city: Vienna

first: Franz

last: Klein

address: Dr. Bohr-Gasse 9

department: Chromosome Biology

country: Austria

institute: Max Perutz Labs, University of Vienna

data_processing:
library strategy: Protec-seq
Unaligned bam files were converted to fastq files with the help of SamToFastq.jar (picard-tools v1.119). Adapter sequences were trimmed by cutadapt (version 1.8.1) with a maximum error rate of 0.15 and minimum clipped read length of 15 nt (options -O 1 -e 0.15 -m 15 --max-n 3). Clipped read pairs were aligned with the help of NextGenMap (version 0.5.5) to both ASMv1 and the calibration genome ZP591 in order to obtain specific S. cer. and S. kud. alignments, as well as read counts for both the ChIP and the WCE samples. Reads aligning to both genomes, typically only 0.2% of the clipped reads, were discarded. In order to map the 5-prime ends accurately and sensitively, global (end-to-end) alignments, a maximum error rate of 4%, and a kmer-size of 9 were applied. In addition, a maximal insert size of 1000nt was set (upper limit of Illumina sequencing machines), and multiple hits were discarded.
Calibration factors (see supplementary file) were calculated by multiplication of the occupancy ratio (OR), IP.asmv1 x WCE.zp591 / IP.zp591 x WCE.asmv1, with the read count normalization factor (to 10M, RP10M), 10M/IP.asmv1. Conversion of alignment data to various data formats representing dDSB fragments or their 5-prime ends were performed with custom Java scripts. dDSB fragment lengths were determined by the distance between start and ends of read pairs (see fd files). Since these fragments include the 2 nt overhangs generated by the Spo11 staggered cuts at both ends, the cleavage axis distances are obtained by subtracting 2 nt from the respective original fragment lengths.
Wiggle files were created with the help of IGVTools v. 2.3.72.
Genome_build: ASM205788v1 (GenBank accession GCA_002057885.1; "ASMv1") for S. cer.; ZP591 (GenBank accession GCA_000167075.2) for S. kud.
Supplementary_files_format_and_content: For each Protec-Seq IP sample, wiggle files of dDSB fragment 5-prime ends are provided as gz-compressed file archives containing one file each for Watson and Crick (numbers preceding the .wig file extension correspond to the RGB color code). Likewise, fragment depth (fd) files containing chromosome, start, length and depth of each dDSB fragment are listed.

organism:
Saccharomyces cerevisiae
Saccharomyces kudriavzevii

source_name: meiotic yeast cells

growth_protocol: Diploid SK1 strains were induced to undergo meiosis synchronously and were sampled at desired time points in sporulation medium. Diploid SK1 yeast strains from a frozen stock were grown on YPD plates for 2 days at 30°C. Single colonies were inoculated in 5ml YPD and grown over night at 30°C. For synchronous sporulation, the saturated YPD cultures were inoculated in SPS pre-sporulation medium (0.5% Yeast extract, 1% Peptone, 0.17% Yeast nitrogen base (without amino acids and without ammonium sulfate), 1% potassium acetate, 1% ammonium sulfate, 0.05 M potassium biphtalate, pH 5.5) and grown, shaking vigorously, to an OD660 of 1.0 (4x10^7cells/ml). Cells were harvested by centrifugation, washed once and resuspended in sporulation medium (SPM, 2% potassium acetate, 0.1% polypropylene glycol). The meiotic progression of the cells was monitored by DAPI staining and/or western blot analysis.

extract_protocol:
At the desired time points, cells were harvested from 100 ml meiotic cultures and collected by centrifugation (4 min, 2,000 rpm , 4°C), washed once with ice-cold 1xTBS, centrifuged again and pellets were frozen at -80°C. Cells pellets were lysed in 2.4 ml ice-cold lysis buffer (50 mM Hepes-KOH pH=7.5, 150 mM NaCl, 5 mM EDTA, 1% Trition X-100, 0.1% Na-deoxycholate, 1 protease inhibitor tablet (Roche, Complete Protease Inhibitor Cocktail)). For spike-in experiments, 20-30 % of S. kud. meiotic cells were added to S. cer. cells. All steps were carried out at 4°C unless stated. Cells were opened with glass beads 2 x 20 sec, 5.5 m/s in a FastPrep-24™ 5G Instrument (MP Biomedicals). The cell lysates were centrifuged at full speed for 10 min at 4°C and the supernatants were transferred into new Eppendorf tubes. A pre-clearing step was performed by incubating the soluble chromatin fractions with Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) for 1 hour at 4°C. After removing 40 µl of the lysate for the whole cell extract (WCE), chromatin immunoprecipitation was carried out by incubating the lysates with Dynabeads Pan Mouse IgG magnetic beads (Invitrogen) coupled to anti-myc antibody (9E11, mouse monoclonal AB) for 3 hours at 4°C. Thereafter, the beads were washed 2 times with 1 ml lysis buffer, 2 times with 1 ml lysis buffer high salt, 3 times with 1 ml washing buffer (10 mM Tris-HCL pH=8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 5 mM EDTA) and finally 2 times with 1 ml 10 mM Tris-HCl pH=8.0. Unprotected DNA or partially protected DNA was digested with 3 µl ExonucleaseV (NEB) in NebBuffer 4 (50 mM K-acetate, 20 mM Tris-acetate, 10 mM Mg-acetate and 1 mM DTT at pH=7.9 containing 1 mM ATP) for 30 min at 37°C. In parallel, RNA was removed by incubation with 10 µl RNase (Dnase-free, Roche). The reaction was stopped by the addition of 11 mM EDTA, the beads were washed 3 times with ice-cold 1xTE and incubated at 65°C for 30min in elution buffer (50 mM Tris-HCL pH=8.0, 10 mM EDTA, 1 % SDS). Spo11-protected DNA complexes were digested over night using 12 µl Proteinase K (Sigma) at 50°C. DNA was extracted once with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated with 0.5 μg/μl glycogen (Roche), 200 mM NaCl and 2.5 volumes of 96 % ethanol. The DNA was pelleted by centrifugation at 4°C for 1 hour, washed once with 1 ml of 70% ethanol and centrifuged again. After air-drying the pellet for 5 min, the DNA was resuspended in 60 µl 10 mM Tris-Cl pH=8.0. The WCE control was digested with RNase and proteinase K, followed by DNA extraction exactly as with the immunoprecipitated samples.
The immunoprecipitated DNA was digested with 3 µl hTdp2 (BPS Bioscience) in 1x hTdp2 Buffer (50 mM Tris-HCl pH7.4, 1 mM MgCl2, 50 mM KCl, 1 mM DTT, 0.1 mg/ml BSA) at 25°C for 30 min. The DNA was extracted with phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated as described above. The hTdp2 digested DNA was end-repaired, A-tailed and adapters were ligated to the DNA ends using the NEBNext Ultra II DNA Library Preparation Kit (NEB) according to the manufacturer´s instructions except that we aimed to select for fragments between 140 bp  - 1000 bp length using Agencourt AMPure XP beads (Beckman Coulter). This necessary step likely results in under-representation of the shortest inserts. For amplification, we used either the NEBNext multiplex oligos or the NEBNext dual indexes primer sets. Before library preparation of the WCE control, we fragmented the DNA using NEBNext dsDNA fragmentase (NEB) according to the manufacturer´s protocol. Briefly, we incubated 32µl of the WCE control in 1x fragmentase reaction buffer V2 (50 mM NaCl, 20 mM Tris-HCl, 0.1 mg/ml BSA, 0.15% Triton® X-100, 15 mM MgCl2, pH 7.5@25°C) with 4µl NEBNext dsDNA fragmentase at 37°C for 20 min. The reaction was stopped by the addition of 5 µl of 0.5 M EDTA and the DNA was extracted by phenol/chloroform/isoamyl alcohol (25:24:1) and precipitated as described above. The library preparation of the WCE control was performed the same way as for the immunoprecipitated samples. The concentration and the molarity of the library were determined by NanoDrop™ 3300 Fluorospectrometer and Agilent 2100 Bioanalyzer.

tag: antibody

tag: index 1

value: AAGCGTTC

tag: index 2

value: GGTAAGCT


title: invitro, 5cell, transcriptome

value: Cultured cells

value: invitro


title: DF3_F

source_name: DF_Febrile phase

tag: subject status

tag: Sex

value: F

value: DF

value: Febrile phase


title: CLL1_5: FCR relapse patient 1 timepoint 5

value: blood

value: CLL active disease

value: Relapse post-FCR


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t5 + Rapamycin t4 ChIP

description: Figure EDF5d

tag: strain

value: anti-myc (9E11, mouse monoclonal) antibody

value: TGATCACG


title: DF2_F

value: DENV infected patient

value: M

tag: severity

tag: timepoint

tag: cell type


title: Mouse1, CTCs, transcriptome

tag: harvest-site

value: Blood

tag: experiment

tag: info-type

value: transcriptome


title: CLL1_4: FCR relapse patient 1 timepoint 4

tag: tissue

tag: disease state

value: CLL remission

value: Remission


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t5 WCE

value: AAGCGACT

value: GGTAAGCT


title: DF1_F

tag: age

value: innate lymphoid cells


title: ILW_180

description:
Parent
Unimelb_parents_2.vcf

organism: Lens orientalis

tag: line

value: ILWL 180

value: Leaf tissue

value: 14 days


title: Mouse1, Liver, transcriptome

value: Liver


title: Mouse1, Lung, transcriptome

value: Lung


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t4.5 + Rapamycin t4 WCE

value: AAGCGTTC

value: CGGAACAA


title: CLL1_1: FCR relapse patient 1 timepoint 1

value: blood

value: CLL active disease

tag: wbc

tag: treatment

value: Watchful waiting


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t5 ChIP

description: Figure EDF5d

tag: antibody

value: anti-myc (9E11, mouse monoclonal) antibody

tag: index 1

value: GGATCTGA


title: DF1_C

tag: subject status

value: DENV infected patient

value: M

value: DF

value: Convalescent phase


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t4.5 + Rapamycin t4 ChIP

description: Figure EDF5d

value: TGATCACG

tag: index 2


title: CLL1_2: FCR relapse patient 1 timepoint 2


title: HUH7 siNPM1-rep2

first: Xuerui

address: Haidian District

department: School of Life Sciences

institute: Tsinghua University

data_processing:
clean RNA-seq reads were mapped to human genome(version hg19) via STAR with genecounts method
Genome_build: hg19

source_name: HUH7 cell line

growth_protocol: HUHU7 cells were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were treated with siRNA for 48h, then total RNA was isolated via Trizol reagent.
Firstly, a Ribozero Kit (Epicentre) was used to remove ribosomal RNA. Then RNA seq library was constructed using an NEB Next Ultra Directional RNA Library Prep Kit (NEB). RNA-seq was carried out with Illumina HiSeq X Ten.

treatment_protocol: HUHU7 cells were seeded into 6 hole plate(typically 2 × 105 cells into a hole) and transfected siRNA-LETN, siRNA-NPM1 and siRNA-NC with Lipofectamine RNAiMAX respectively.

value: HUH7 cell line

value: hepatocellular carcinoma cells


title: Mouse1, Peritoneal mets, transcriptome

value: Peritoneal mets

value: transcriptome


title: HUH7 siLETN-rep2


title: HUH7 siNPM1-rep1


title: HA1Q+SA2Q_gRNAs_2

city: Heidelberg

first: F. Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
RNA-seq raw data from different lanes that belong to the same sample were pulled together. After adapter trimming with Trim Galore (v. 0.6.4; http://www.bioinformatics.babraham.ac.uk/projects/  trim_galore/ ), the trimmed reads were aligned using STAR (v. 2.7.3a) to a genome index inferred by the human reference genome (hg19) sequence, along with the RefSeq annotation, both publicly available at the genome browser at UCSC. For the alignments we considered reads that were uniquely mapped (STAR option: --outFilterMultimapNmax  1) to avoid multimapping between highly similar regions.
Aligned data (bam files) were deduplicated, sorted and indexed with SAMtools (v. 1.9; http://samtools.sourceforge.net).
SNVs in our samples were called with REDItools (v2; https://github.com/tflati/reditools2.0), considering the developers’ recommendations for data preparation prior to this step. Sticking to our previously published approach, we considered only high-quality sites (min. MeanQ > 30 in REDItools2), and we called editing in well-covered sites (min. 50 reads in aggregate of the two replicates per sample) that showed ≥ 10% editing frequency when compared to the control.
Fisher’s exact tests were performed for all the sites that fulfilled the aforementioned criteria and significantly differentially edited sites were considered those that showed adjusted p-value < 0.01.
Sites that were reported in the first 6 sites of a read, or in homopolymeric regions, or reported in the dbSNP (v. 142; excluding cDNA-based reported SNPs: http://www.ncbi.nlm.nih.gov/SNP/), were excluded throughout our output lists.
All genomic coordinates were annotated with Oncotator (v1.9.9.0) and Repeat Mask for Alu-SINE elements of UCSC Genome Browser both for hg19.
Genome_build: hg19
Supplementary_files_format_and_content: allSamples_readcounts.txt: tab-delimited text file includes raw read-counts for all samples sample
Supplementary_files_format_and_content: AGsignal_empty_vs_gRNA.oncoOut.txt: tab-delimited txt file with all A-to-G editing sites with annotated coordinates after variant calling from comparison between the sample 1 and sample 2 (empty samples / reference level) vs sample 3 and sample 4 (gRNA samples).

growth_protocol: 293 Flp-In T-REx HALO-ADAR1Q + SNAP-ADAR2Q cells were cultivated in Dulbecco’s Modified Eagle Medium (Life Technologies) supplemented with 10 % fetal bovine serum (Life Technologies), 15 µg/ml blasticidin and 100 µg/ml hygromycin (DMEM/FBS/B/H) at 37 °C with 5 % CO2 in a water saturated steam atmosphere.

extract_protocol:
RNA isolation was performed with the RNeasy MinElute Cleanup Kit from Qiagen, followed by DNase I digestion, which was again purified via RNeasy MinElute Cleanup Kit from Qiagen.
The library was prepared with the library preparation kit TruSeq Stranded mRNA by Illumina starting from 100 ng RNA. Samples were then sequenced on a NovaSeq 6000 by ILLUMINA with 50 million reads and 2 × 100 bp paired end.

treatment_protocol: 2⋅106 293 Flp-In T-REx HALO-ADAR1Q + SNAP-ADAR2Q cells were seeded in 2.5 ml DMEM/FBS/B/H supplemented with 10 ng/ml doxycycline in a 6 well plate. After 24 h, 8⋅104 cells per well were reverse transfected in 5 wells of a 96 well plate per sample. For the duplicate of the empty transfection, the cells were treated with an empty reverse transfection with 0.5 µl Lipofectamine 2000 only. For the duplicate of the guideRNA transfection, cells were reverse transfected with 0.5 pmol (snap)2-CAG and 0.5 pmol (halo)2-CAU with 0.5 µl Lipofectamine 2000. Doxycycline concentration was kept at 10 ng/ml and after further 24 h cells were harvested.

value: 293 Flp-In T-REx

tag: genotype

value: HALO-ADAR1Q + SNAP-ADAR2Q

value: transfection of two guideRNAs (0.5 pmol (snap)2-CAG + 0.5 pmol (halo)2-CAU) with Lipofectamine 2000


title: Mouse1, Primary tumor, transcriptome

value: Primary tumor


title: HUH7 siLETN-rep1

last: Yang


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t4 WCE

tag: strain

value: AAGCGACT

value: AAGCGGAA


title: Mouse1, Surgical site, transcriptome

value: Surgical site


title: CLL1_3: FCR relapse patient 1 timepoint 3

value: blood

value: CLL active disease

value: Pretreatment FCR


title: HA1Q+SA2Q_gRNAs_1

source_name: 293 Flp-In T-REx HALO-ADAR1Q + SNAP-ADAR2Q


title: dDSB Spo11-myc18 Rec104-FRB-HA3 rad50S t4 ChIP

description: Figure EDF5d

value: anti-myc (9E11, mouse monoclonal) antibody

value: GGATCTGA