title: TRL 1215-T50-3

source_name: 50 µM PFOA treated 38 weeks-3

value: 50 µM PFOA treated 38 weeks


title: TRL 1215-T50-2

status: Public on Aug 23 2023

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

hyb_protocol: Five and one-half micrograms (5.5 .g) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: 50 µM PFOA treated 38 weeks-2

label_protocol: One hundred nanograms (100 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: TRL 1215 cells were cultured and passaged once per week in William's E media containing 10% FBS

extract_protocol: Total RNA was isolated from cells by using AllPrep DNA/RNA/Protein Kit (Cat# 80004) from QIAGEN (Germantown, MD) according to the manufacturer's instructions

treatment_protocol: PFOA-treated cells were cultured in the same medium with addition of fresh PFOA each time at 10 µM (T10), 50 µM (T50) or 100 µM (T100) up to 38 weeks.

tag: tissue

value: liver

tag: cell line

tag: treatment


title: TetLowReg, low avidity GSW11-specific CD8+ TILs from regressing tumors [TetLow_6]

type: SRA

city: Oxford

first: Doreen

last: Lau

address: Old Road Campus Research Building, Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
The paired-end reads were aligned to the mouse reference genome GRCm39/mm39 with STAR 2.7.6a and the mapped reads were assigned to genomic features using featureCounts.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include reads per gene for each sample

organism: Mus musculus

source_name: tumor

growth_protocol: T cells were tetramer-sorted from CT26.WT tumours.

extract_protocol:
RNA was harvested using Zymo Quick RNA Miniprep Kit (Zymo, USA) prior to cDNA synthesis. The purified RNA was quantified using Qubit 4 Fluorometer (Invitrogen) and the quality was determined using the Agilent 2100 Bioanalyzer with the Agilent RNA 6000 nano kit (Agilent Technologies). RNA was reverse transcribed using SuperScript II (Invitrogen) and cDNA pre-amplification was performed using KAPA HiFi HotStart ReadyMix (Roche Molecular Systems) for 22 cycles of amplification. The cDNA libraries were purified with Agencourt AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. The cDNA product was then analyzed using the Agilent 2100 Bioanalyzer with the Agilent High Sensitivity DNA kit (Agilent Technologies).
Tagmentation and library preparation was undertaken using the Illumina Nextera XT DNA Library Preparation Kit (Illumina) according to manufacturer's instructions.

treatment_protocol: The schedule adopted in this study involved three intraperitoneal administrations of anti-PD-1 on day 3, 6 and 9 following subcutaneous implantation of CT26 tumors, which resulted in a variable impact on tumor growth rate during early tumor development and a 20-30% curative response rate.

value: tumor

value: mouse-derived

tag: cell type

value: T lymphocytes

tag: genotype

value: wildtype

value: PD-1 antibodies (Clone RMP1-14)


title: 2D_CVS11_8h_1

city: Pathum Thani

first: Papon

last: Muangsanit

state: Pathum Thani

address: 113 Thailand Science Park Phahonyothin Road Khlong Nueng, Khlong Luang, BIOTEC building, Room 345

department: BIOTEC

country: Thailand

institute: NSTDA

hyb_protocol: Purified total RNA samples were analyzed using the NanoString nCounter XT gene expression assay following the manufacturer’s protocol. Briefly, 5 µl of 50 ng of total RNAs were mixed with 2 μl of the Capture Probe set and 8 µl of hybridization buffer containing the Reporter CodeSet and mixtures were allowed to hybridize by incubation at 65 °C in a thermal cycler for 16 hours.

scan_protocol: Post-hybridization processing and data collection were performed using the nCounter Analysis System.

data_processing: Raw data were pre-processed using the nSolverTM 4.0 software according to nCounter gene expression data analysis guidelines. Data pre-processing included sample quality control (QC), background and normalization. Probes against 14 external RNA control consortiums (ERCC) consisted of 6 synthetic DNA positive and 8 negative controls. The geometric mean of positive control counts in each sample was applied to QC to evaluate overall assay efficiency, assay linearity and limit of detection (LOD). A correlation value higher than 0.95 indicated high assay efficiency. Negative controls were used to estimate non-specific binding of probes within the samples being run and background correction. Reference housekeeping genes were used for data normalization according to the nSolverTM 4.0 software.

label: Reporter CodeSet

organism: Homo sapiens

source_name: 2D culture

label_protocol: One hundred nanograms of purified total RNA were analyzed using the nCounter Analysis System (NanoString Technologies, WA, USA), according to the manufacturer’s instructions. The assay is based on direct detection of targets using molecular barcodes, without the necessity of reverse transcription and mRNA amplification.

growth_protocol: 10-day pre-differentiated neurons from hiPSC were plated in 24-well plates at a density of 1×10^5 cells/well to generate 2D cultures, while 3D cultures were prepared at a density of 1×10^6 cells/ml of collagen-Matrigel hydrogel (400 µl/well of 24-well plates). The NB medium was changed every 2-3 days and cells remained in culture for 7 days before virus adsorption.

extract_protocol: Total RNA was isolated using TRIzol following the manufacturer's instructions. Rabies virus-infected 2D and 3D samples were collected at 0, 8 and 24 hours post-infection. In 24-well plates, 2D samples were homogenized in 500 µl of TRIzol and 3D samples were homogenized in 1,000 µl of TRIzol by pipetting up and down several times until the homogenates appeared consistent with no visible clumping. RNA from TRIzol-lysed samples was purified using the Direct-zol RNA Microprep kit, treated with DNase I, eluted in 35 µl RNase-free water, and stored at -80 °C until used. The quality of the purified RNA was measured using the Nanodrop 2000 spectrophotometer. Gel electrophoresis was run to confirm there was no cellular DNA contamination of the purified total RNA.

treatment_protocol: 2D and 3D neuronal cultures were adsorbed with TH or CVS-11 at a multiplicity of infection of 0.5 for 2 hours. Cells were washed twice with PBS before adding fresh media.

tag: virus strain

tag: time point

value: 8 hour

value: hiPSC-derived neurons


title: 2D_Mock_8h_1

value: Non-infected


title: TetLowProg, low avidity GSW11-specific CD8+ TILs from progressing tumors [TetLow_10]


title: TetHighProg, high avidity GSW11-specific CD8+ TILs from progressing tumors [TetHigh_5]


title: N1_replicat1

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

country: China

institute: Hainan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data (2×150 bp PE reads) were quality controlled using Trim-Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
The remaining high quality Illumina reads were aligned to our previously published N. oceanica IMET1 genome (Gong, Kang, Kim, Wang, Wei, Xin, Shen, Wang, You, Lim, Jeong, Park, Oh, Pan, Poliner, Yang, Li-Beisson, Li, Hu, Poetsch, Farre, Chang, Jeong, Jeong, Xu, 2020) with STAR (Dobin, Davis, Schlesinger, Drenkow, Zaleski, Jha, Batut, Chaisson, Gingeras, 2013) with duplication marked using Picard (https://broadinstitute.github.io/picard/).
The abundance of expression was quantified using featureCounts (Liao, Smyth, Shi, 2014) and StringTie (Kovaka, Zimin, Pertea, Razaghi, Salzberg, Pertea, 2019). For each of the mRNA-Seq datasets under each experimental condition, gene expression was measured as the numbers of aligned reads to annotated genes by featureCounts (Liao, Smyth, Shi, 2014) and normalized to CPM, FPKM (fragments per kilobase of exon model per million mapped fragments) and TPM values. Besides, raw counts from featureCounts (Liao, Smyth, Shi, 2014) were used for the differential gene expression analysis with edgeR (R package)
Assembly: Nannochloropsis oceanica IMET1
Supplementary files format and content: Excel files include FPKM values for each Sample

organism: Nannochloropsis oceanica

source_name: Cells

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, trace metal mix (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and vitamin mix (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl).The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm).

extract_protocol:
Total microalgal RNA was extracted using Trizol reagents (Invitrogen, USA). The concentration and purity of the RNA were determined spectrophotometrically (NanoDrop-1000, Thermo Scientific, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were first cultured in f/2 medium at 25°C with 80±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5cm). The seed cultures were bubbled with air-level CO2. At the logarithmic phase (OD750=2.5), cells were harvested by centrifugation, one was sampled for RNA extraction as control (C0) with three replicates and the other was washed with fresh medium (nitrogen-free) for three times before being used for the following experiments. Cell pellets were inoculated into Nitrogen-free (for sampling of mRNA-seq, ChIP-seq and HiC-seq) and Nitrogen-repletion f/2 medium (for physiological measurement). Cultures started with the same initial cell concentration of OD750 = 2.5 and were exposed to continuous illumination of 50±5 μmol m−2 s−1. Cell aliquots were collected  for sampling of mRNA-seq, ChIP-seq and HiC-seq after being transferred to the designated conditions for one and two days  as nitrogen-deprivation samples (N1 and N2) with three replicates

tag: strain

value: Nitrogen-deprivation


title: TRL 1215-T50-1

source_name: 50 µM PFOA treated 38 weeks-1


title: C0_replicat2

value: Nitrogen-repletion


title: TetHighProg, high avidity GSW11-specific CD8+ TILs from progressing tumors [TetHigh_2]


title: TRL 1215-T10-3

source_name: 10 µM PFOA treated 38 weeks-3

value: 10 µM PFOA treated 38 weeks


title: 3D_Mock_0h_2

source_name: 3D culture

value: 0 hour


title: TetHighProg, high avidity GSW11-specific CD8+ TILs from progressing tumors [TetHigh_1]


title: 2D_Mock_8h_2


title: 2D_Mock_0h_2


title: N1_replicat2


title: C0_replicat1


title: 3D_Mock_0h_1


title: TRL 1215-T10-1

source_name: 10 µM PFOA treated 38 weeks-1


title: TRL 1215-control-3

source_name: passage-matched control-3

value: passage-matched controls


title: TRL 1215-T10-2

source_name: 10 µM PFOA treated 38 weeks-2


title: 2D_Mock_0h_1


title: Streptococcusmutans_Mono_Saliva_Rep1

status: Public on Aug 22 2023

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Assembly: NC_004350.2 for S. mutans UA159; CP079724.1 for S. oralis
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Streptococcus mutans

source_name: whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TY medium, with or without 50% human saliva, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.4)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: whole cell lysate

value: Saliva; growth to OD600 0.4


title: Streptococcusmutans_Mono_TYG_Rep1

value: TYG; growth to OD600 0.4


title: Streptococcusmutans_Mono_Saliva_Rep2


title: Streptococcusmutans_Mono_Saliva_Rep3


title: Streptococcusmutans_Mono_TYG_Rep2


title: Mutansoralis_Coculture_Saliva_Rep1

description: 16_Co_Saliva_So34 / 16_Co_So34_Saliva

organism:
Streptococcus oralis
Streptococcus mutans


title: Streptococcusmutans_Mono_TYG_Rep3


title: Mutansoralis_Coculture_TYG_Rep3

description: 15_SMU_CoSo34_3  / 15_Co_So34_TYG


title: Mutansoralis_Coculture_TYG_Rep2

description: 14_SMU_CoSo34_2 / 14_Co_So34_TYG


title: Mutansoralis_Coculture_Saliva_Rep2

description: 17_Co_Saliva_So34 / 17_Co_So34_Saliva


title: Mutansoralis_Coculture_TYG_Rep1

description: 13_SMU_CoSo34_1 / 13_Co_So34_TYG


title: TRL 1215-control-1

source_name: passage-matched control-1

value: liver


title: Mutansoralis_Coculture_Saliva_Rep3

description: 18_Co_Saliva_So34 / 18_Co_So34_Saliva


title: NCI-H1299 cells, DAC+SB939 2

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

data_processing:
Sample adapters were trimmed using cutadapt (v2.6) and demultiplexed with barcode_splitter from FASTX-toolkit (v0.0.6). Small fragments (x < 30 nt) were dropped. Unique molecular identifier (UMI) extraction was performed using umi_tools (v1.0.1). By BLAST-Like Alignment Tool, rRNA reads were filtered and discarded. The rRNA index for Rn5s, Rn18s, Rs5-8s1 was constructed from NCBI annotations. Remaining reads were aligned with Spliced Transcripts Alignment to a Reference (STAR) (v2.7.10) to GRCh37/hg19. Following, PCR duplicates were removed using umi_tools.
Assembly: hg19
Supplementary files format and content: Coverage data in bigwig format (stranded)
Library strategy: Ribo-seq

growth_protocol: NCI-H1299 cells were cultivated in RPMI -1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were lysed in ice cold lysis buffer (20 mM Tris-HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 μg ml−1 cycloheximide, 1× EDTA-free Complete protease inhibitors) and the lysate was clarified by centrifugation at 5000 rpm. The clarified lysate was treated with 2U/μl RNase I for 45 min at room temperature and loaded on a linear sucrose gradient (7% to 47%) and centrifuged using the SW-41Ti rotor at 36,000 rpm for 2 h. Fractions containing monosomes were pooled, treated with proteinase K. RNA fragements thus obtained were purifed using Trizol reagent as per manufacturer's recommendations. RNA thus obtained was loaded on a 10% polyacrylamide urea (7M) gel and the 30-33 nt long RNA fragments were excised and purified by ethanol precipitation.
The Ribosome protected RNA fragements were 3'-dephosphorylated by treating with T4 PNK for 6 h at 37C, and 3' adaptor ligated using T4 RNA ligase 1 for 2.5 h at 37C. 3' adaptor ligated fragements were 5'phosphorylated by treating with T4PNK for 30 min at 37C, 5' adaptor ligated using T4 RNA ligase 1 for 18 h at 22C.

treatment_protocol:
Cells were treated with DMSO for 96 h, 500 nM Decitabine (DAC) for 96 h, DMSO for 78 h and then 500 nM SB939 for 18 h, or 500 nM DAC for 78 h and then 500 nM SB939 for 18 h. DAC containing media was refreshed every 24 h.
Following DMSO/DAC/SB939 treatments, cells were further treated with 100 µg/ml Cycloheximide alone, or in combination with 2 µg/ml Harringtonine and incubated at 37C for 10 min

value: Non-small cell lung cancer

value: WT

value: 500nM Decitabine + 500nM SB939


title: NCI-H1299 cells, DAC+SB939 1


title: ArcPMX6

city: Irvine

first: Andrea

last: Tenner

state: CA

address: 2419 McGaugh Hall

department: Molecular Biology and Biochemistry

institute: UCI

library_source: transcriptomic single cell

data_processing:
Illumina Split-seq: Reads were demultiplexed into 7 sublibraries using bcl2fastq and the provided adapter sequences.
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_1 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_1_S1_R1.fastq.gz --fq2 ArcPMX_splitseq_1_S1_R2.fastq.gz --output_dir analysis_1 --sample <replace with SAMPLE.txt>
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_2 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_2_S2_R1.fastq.gz --fq2 ArcPMX_splitseq_2_S2_R2.fastq.gz --output_dir analysis_2 --sample <replace with SAMPLE.txt>
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_3 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_3_S3_R1.fastq.gz --fq2 ArcPMX_splitseq_3_S3_R2.fastq.gz --output_dir analysis_3 --sample <replace with SAMPLE.txt>
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_4 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_4_S4_R1.fastq.gz --fq2 ArcPMX_splitseq_4_S4_R2.fastq.gz --output_dir analysis_4 --sample <replace with SAMPLE.txt>
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_5 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_5_S5_R1.fastq.gz --fq2 ArcPMX_splitseq_5_S5_R2.fastq.gz --output_dir analysis_5 --sample <replace with SAMPLE.txt>
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_6 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_6_S6_R1.fastq.gz --fq2 ArcPMX_splitseq_6_S6_R2.fastq.gz --output_dir analysis_6 --sample <replace with SAMPLE.txt>
Illumina Split-seq: Parse Biosciences' analysis software was run on the ArcPMX_splitseq_7 sublibrary: split-pipe --mode all --kit WT --chemistry v1 --genome_dir genomes/mm10 --fq1 ArcPMX_splitseq_7_S7_R1.fastq.gz --fq2 ArcPMX_splitseq_7_S7_R2.fastq.gz --output_dir analysis_7 --sample <replace with SAMPLE.txt>
Assembly: mm10
Supplementary files format and content: For Illumina Split-seq, Parse Biosciences analysis software (split-pipe) outputs are sparse cell-by-gene expression matrices in counts with corresponding cell metadata and a list of expressed genes (columns of expression matrix).

molecule: polyA RNA

source_name: hippocampus

extract_protocol:
Mouse microglial single-cell in hippocampi and hippocampi nuclei were collected for Split-seq and dispersed into 48 wells of a 96 well plate containing unique barcodes per well (24 wells of microglial cells, 24 wells of hippocampi nuclei).
Half hippocampi from 2-3 mice of the same sex, genotype and treatment were pooled for microglia isolation and processing (HBSS with Actinomycin D (5 μg/ml), Triptolide (10 μM) and Anisomycin (27.1 μg/ml)) (3 samples per sex/genotype/treatment) .  Following dissociation with gentle MACS Octo Dissociator and Adult Brain Dissociation Kit, cells were filtered (70 µm), debris removed, and myelin was cleared with Myelin removal beads II.  Microglia were isolated using Anti-CD11b MicroBeads. Cells were counted and resuspended in 0.05% BSA in DPBS, to reach a minimum of 1,000 cells/µL up to around 7,000 cells/µL. For sn-RNA-Seq, perfused half hippocampi (3 per sex/genotype/treatment) were placed into Nuclei Extraction Buffer (Miltenyi) with 0.2 U/µL RNase inhibitor), processed in gentleMACSTM Octo Dissociator, filtered (70 µm), centrifuged and resuspended in PBS with 0.1% BSA and 0.2 U/µL RNase inhibitor, passed through a 30 µm filter, and counted). 4 million nuclei were collected from the stock of each cell preparation, and processed per Parse Biosciences. RNA was reverse transcribed in situ and barcoded cDNA was extracted following Parse Biosciences’ Single Cell Whole Transcriptome Kit (also called Split-seq).
Illumina Split-seq: Parse Biosciences’ Single Cell Whole Transcriptome Kit (also called Split-seq).
Library preparation was performed following manufacturer’s instructions for the Single Cell Whole Transcriptome Kit, where the cells are mixed for the next 2 sets of barcoding reactions followed by sublibrary generation.

treatment_protocol: Wildtype and Arctic mice were treated or not for 12 weeks with PMX205, a cyclic hexipetide antagonist of the C5a receptor, C5aR1 (20ug/ml)  in drinking water.  Animals were separately housed during treatment until perfusion in  HBSS with Actimomycin D and Triptolide at 10 mo of age.

value: hippocampus


title: ArcPMX4


title: ArcPMX5


title: NCI-H1299 cells, DMSO 2

value: DMSO


title: ArcPMX3


title: NCI-H1299 cells, DMSO 1

tag: time


title: ArcPMX1


title: ArcPMX2


title: ArcPMX7


title: SW480 cells, DAC+SB939, biol rep 2

data_processing:
For the analysis of the known reference transcriptome assembly, RNA-seq data of the NCI-H1299 cell line were processed with the nf-core RNA-seq pipeline v1.2 with default parameters, unless mentioned otherwise. In short, raw sequences were aligned to the human reference genome hg19 by the aligner HISAT2 v2.1.0 with the -reverseStranded option in --pairedEnds mode. Transcripts were assembled using StringTie v1.3.4d utilizing the GENECODE annotation v29lift37. Gene counts were generated with the prepDE.py script, accompanying the StringTie v1.3.4d software. Coverage tracks were generated from bam files utilizing the deepTools’ (v3.3.1) function bamCoverage with the option –normalizeUsing RPKM. Replicates of the different NCI-H1299 treatments were merged using the software kenUtils (www.github.com/Arunken/kenutils) v377. For the de novo assembly of the NCI-H1299, NCI-H2122, NCI-H1395, OCI-AML3, HL60, HCT116, SE480, A172 and T98G cells’ transcriptomes, sorted bam files from the hg19 alignment were assembled using StringTie v2.1.1, evoking -m 200 -f 0.05 -c 1.5 -p 10 parameters. Individual assemblies of the NCI-H1299 data and the entire cell line panel were merged with stringtie --merge and default parameters. De novo assembled transcripts were compared and annotated with the GENECODE annotation v29lift37 utilizing GFF Utilities v0.11.2 function gffcompare with -R and -r parameters. Transcripts were classified according to their relationship with the closest reference transcript (class_code). The class_code was further simplified by merging transcripts classified as “s” (intron match on the opposite strand), “x” (exonic overlap on the opposite strand), “i” (fully contained within a reference intron), “y” (contains a reference within its intron(s)), “p” (possible polymerase run-on (no actual overlap)), or “u” (unknown, intergenic) as non-chimeric (novel) transcripts, transcripts classified as “m”,(retained intron(s), not all introns matched/covered), “j” (multi-exon with at least one junction match), “e” (single exon transfrag partially covering an intron, possible pre-mRNA fragment), or “o” (other same strand overlap with reference exons) as chimeric (novel) transcripts and transcripts classified as “=” (complete, exact match of intron chain) as known transcripts. Furthermore, the TSS of transcripts were annotated to the closest or overlapping TEs using the function distanceToNearest of the R package GenomicRanges v1.38.0. Quantification of the NCI-H1299, NCI-H2122, NCI-H1395, OCI-AML3, HL60, HCT116, SE480, A172 and T98G cells’ RNA-seq data with the individual de novo transcriptome assemblies was performed with the nf-core RNA-seq pipeline v1.2, as described earlier. Transcripts were assembled using StringTie v1.3.4d and the de novo transcriptome assemblies. Transcript counts were generated with the prepDE.py script, accompanying the StringTie v1.3.4d software.
Assembly: hg19
Supplementary files format and content: Coverage data in bigwig format (merged for all three biological replicates)

growth_protocol: NCI-H1299, NCI-H2122, NCI-H1395, OCI-AML3, HL60, HCT116, and SW480 cells were cultivated in RPMI -1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. A172 and T98G cells were cultivated in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.5-1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Kit following manufacturer's protocols.

treatment_protocol: Cells were treated with DMSO for 96 h, 500 nM Decitabine (DAC) for 96 h, DMSO for 78 h and then 500 nM SB939 for 18 h, or 500 nM DAC for 78 h and then 500 nM SB939 for 18 h. DAC containing media was refreshed every 24 h.

value: Colorectal adenocarcinoma

value: 78 hours + 18 hours


title: SW480 cells, DMSO, biol rep 3

value: 96 hours


title: SW480 cells, DAC+SB939, biol rep 3


title: SW480 cells, DMSO, biol rep 2


title: SW480 cells, DAC+SB939, biol rep 1


title: SW480 cells, DMSO, biol rep 1


title: HCT116 cells, DAC+SB939, biol rep 1

value: Colorectal carcinoma


title: HCT116 cells, DMSO, biol rep 3


title: HCT116 cells, DMSO, biol rep 1


title: HCT116 cells, DMSO, biol rep 2


title: T98G cells, DAC+SB939, biol rep 3

value: Glioblastoma


title: T98G cells, DMSO, biol rep 2


title: T98G cells, DMSO, biol rep 3


title: A172 cells, DAC+SB939, biol rep 3


title: HCT116 cells, DAC+SB939, biol rep 3


title: A172 cells, DMSO, biol rep 3


title: T98G cells, DAC+SB939, biol rep 1


title: T98G cells, DMSO, biol rep 1


title: HCT116 cells, DAC+SB939, biol rep 2


title: A172 cells, DMSO, biol rep 2


title: NCI-H1395 cells, DAC+SB939, biol rep 1

value: Lung adenocarcinoma


title: NCI-H1395 cells, DAC+SB939, biol rep 3


title: NCI-H1395 cells, DAC+SB939, biol rep 2


title: A172 cells, DAC+SB939, biol rep 2


title: NCI-H2122 cells, DMSO, biol rep 3


title: NCI-H1395 cells, DMSO, biol rep 3


title: A172 cells, DMSO, biol rep 1


title: NCI-H1395 cells, DMSO, biol rep 2


title: A172 cells, DAC+SB939, biol rep 1


title: NCI-H2122 cells, DMSO, biol rep 2


title: NCI-H2122 cells, DAC+SB939, biol rep 2


title: NCI-H2122 cells, DAC+SB939, biol rep 3


title: NCI-H1395 cells, DMSO, biol rep 1


title: T98G cells, DAC+SB939, biol rep 2


title: NCI-H2122 cells, DAC+SB939, biol rep 1


title: NCI-H2122 cells, DMSO, biol rep 1


title: HL60 cells, DAC+SB939, biol rep 2

value: Acute promyelocytic leukemia


title: HL60 cells, DAC+SB939, biol rep 3


title: HL60 cells, DAC+SB939, biol rep 1


title: HL60 cells, DMSO, biol rep 1


title: OCI-AML3 cells, DAC+SB939, biol rep 1

value: Acute myeloid leukemia


title: OCI-AML3 cells, DAC+SB939, biol rep 3


title: OCI-AML3 cells, DAC+SB939, biol rep 2


title: OCI-AML3 cells, DMSO, biol rep 3


title: Kupffer cells, wild type, cdcdcd, repl 6

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

department: LIMES

country: Germany

institute: University of Bonn

description:
15
6027

data_processing:
The Agilent high-sensitivity D5000 assay was used to measure the size distribution of cDNA libraries on a Tapestation 4200 system (Agilent).
The cDNA libraries were quantified using a high-sensitivity dsDNA assay (Qubit).
To quantify the abundances of transcripts from the bulk RNA-seq data, Kallisto pseudo alignment was applied
Kallisto read counts were used fortheDESeq2 pipeline
Assembly: GRCm38.p5 (M16)
Supplementary files format and content: txt raw count matrix with transcripts as rows and samples as columns, done with kallisto and import to DESeq2 (see manuscript for more information)

source_name: liver

growth_protocol: in vivo

extract_protocol:
Adult mice were anesthetized and perfused with ice-cold PBS. For livers, 300 mg were collected, cut into small pieces, and incubated with 1 ml of double-concentrated digestion mix (PBS containing 1 mg/ mlcollagenase D (Roche), 100 U/mlDNase I (Sigma-Aldrich), 2.4 mg/ mlof dispase (Invitrogen) and 3% fetal calf serum (FCS) (Invitrogen) for 30 min at room temeprature before the mechanical disruption 100-μm filter.  The cell suspension was diluted in 3ml of FACS buffer (0,5% BSA, 2mmol EDTA in PBS).  Cells were stained by antibody mixes and sorted using FACS ARIATM III cell sorter (BD Biosciences) directly into 500ul QIAzol lysis buffer (Qiagen).
SmartSeq2 protocol

treatment_protocol: smaples taken from mice experiencing different types of diets (Maternal Obesity Model)

value: Kupffer cells

value: wild type

tag: age

value: Adult

tag: maternal diet

value: cdcd

tag: offspring diet

value: cd

tag: condition

value: cdcdcd

tag: biologicalreplicate

tag: merged


title: NCI-H1299 cells, DAC+SB939, biol rep 3

value: Non-small cell lung cancer

value: WT

value: 500nM Decitabine + 500nM SB939


title: OCI-AML3 cells, DMSO, biol rep 1

value: DMSO


title: NCI-H1299 cells, DAC, biol rep 3

value: 500nM Decitabine


title: NCI-H1299 cells, DMSO, biol rep 3

value: 96 hours


title: Kupffer cells, wild type, cdcdhfd, repl 6

description:
12
6024

value: liver

value: hfd

value: cdcdhfd


title: Kupffer cells, wild type, hfdhfdhfd, repl 4

description:
29
5980

value: hfdhfd

value: hfdhfdhfd


title: Kupffer cells, wild type, cdcdcd, repl 5

description:
14
6026

value: Kupffer cells


title: Kupffer cells, wild type, hfdhfdcd, repl 5

description:
31
5982

value: wild type

value: hfdhfdcd


title: Kupffer cells, wild type, hfdhfdhfd, repl 3

description:
28
5979

value: Adult


title: NCI-H1299 cells, DAC+SB939, biol rep 2

value: 78 hours + 18 hours


title: NCI-H1299 cells, SB939, biol rep 2

value: 18 hours


title: Kupffer cells, wild type, cdcdhfd, repl 7

description:
13
6025

value: cdcd


title: TRL 1215-control-2

source_name: passage-matched control-2

value: passage-matched controls


title: Kupffer cells, wild type, hfdcdcd, repl 4

description:
24
5954

value: hfdcd

value: cd

value: hfdcdcd


title: HL60 cells, DMSO, biol rep 3

value: Acute promyelocytic leukemia

value: WT

value: DMSO

value: 96 hours


title: HL60 cells, DMSO, biol rep 2


title: NCI-H1299 cells, DAC, biol rep 2

value: Non-small cell lung cancer

value: 500nM Decitabine


title: OCI-AML3 cells, DMSO, biol rep 2

value: Acute myeloid leukemia


title: Kupffer cells, wild type, hfdhfdcd, repl 3

description:
22
5952

value: liver

value: Kupffer cells

value: wild type

value: hfdhfd


title: Kupffer cells, wild type, hfdcdcd, repl 3

description:
23
5953

value: Adult


title: NCI-H1299 cells, DMSO, biol rep 2


title: NCI-H1299 cells, DAC+SB939, biol rep 1

value: 500nM Decitabine + 500nM SB939

value: 78 hours + 18 hours


title: Kupffer cells, wild type, hfdhfdcd, repl 2

description:
21
5951

value: hfdhfdcd


title: Kupffer cells, wild type, hfdcdhfd, repl 4

description:
9
5950

value: hfdcd

value: hfd

value: hfdcdhfd


title: NCI-H1299 cells, SB939, biol rep 1

value: WT

value: 18 hours


title: Kupffer cells, wild type, hfdcdcd, repl 2

description:
19
5949

value: cd

value: hfdcdcd


title: NCI-H1299 cells, DAC, biol rep 1

value: Non-small cell lung cancer

value: 500nM Decitabine

value: 96 hours


title: Kupffer cells, wild type, hfdhfdcd, repl 4

description:
30
5981

value: liver

value: Kupffer cells


title: Kupffer cells, wild type, hfdcdcd, repl 1

description:
18
5948

value: wild type


title: NCI-H1299 cells, SB939, biol rep 3


title: NCI-H1299 cells, DMSO, biol rep 1

value: DMSO


title: Kupffer cells, wild type, hfdhfdcd, repl 1

description:
17
5947

value: Adult

value: hfdhfd


title: KMM KO SERBP1, SERBP1-K68R, RIP, rep3

city: Nanjing

first: jing

last: zhou

address: longmian Street No.101

institute: Nanjing Medical University

description:
KR_3_IP
all_reads_counts.txt
KR3_peaks.txt

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then clean reads were aligned to the reference genome of Rattus norvegicus from https://www.ncbi.nlm.nih.gov/genome/ using STAR version 2.5.3a with default parameters
RBP binding genes were identificated by edgeR (version 3.12.1).
The exomePeak(Version 3.8) software was used for peak calling.
Peaks were annotated using bedtools（Version 2.25.0）.
The deepTools（version 2.4.1）was used for peak distribution analysis.
Assembly: Rattus norvegicus RGSC Rnor_6.0
Supplementary files format and content: peak text files
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: KMM

growth_protocol: Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and 150 μg/ml hygromycin B. Cells were cultured at 37℃ with 5% CO2

extract_protocol:
Cells were collected and dissolved in lysis buffer. Anti-myc antibody was incubated with magnetic beads and then cell lysates were added to immunoprecipitate RNA binds to SERBP1
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina®

treatment_protocol: The hygromycin B selection was removed one week prior to experiments

value: KMM

value: primary rat embryonic metanephric mesenchymal precursor

tag: overexpressing

tag: rip antibody

value: anti-myc (MBL,#M192-3)


title: KMM KO SERBP1, SERBP1-K68R, input, rep3

description:
KR_3_Input
all_reads_counts.txt
KR3_peaks.txt


title: Kupffer cells, wild type, hfdcdhfd, repl 2

description:
8
5861

tag: tissue

value: hfdcd

value: hfd

value: hfdcdhfd


title: Kupffer cells, wild type, hfdcdhfd, repl 3

description:
16
5946


title: KMM KO SERBP1, SERBP1-WT, input, rep3

description:
WT_3_Input
all_reads_counts.txt
WT3_peaks.txt

tag: cell line


title: KMM KO SERBP1, SERBP1-WT, RIP, rep3

description:
WT_3_IP
all_reads_counts.txt
WT3_peaks.txt


title: Kupffer cells, wild type, hfdcdhfd, repl 1

description:
7
5860


title: KMM KO SERBP1, SERBP1-K68R, input, rep2

description:
KR_2_Input
all_reads_counts.txt
KR2_peaks.txt


title: KMM KO SERBP1, SERBP1-K68R, RIP, rep2

description:
KR_2_IP
all_reads_counts.txt
KR2_peaks.txt


title: Kupffer cells, wild type, cdcdhfd, repl 5

description:
6
5859

value: cdcd

value: cdcdhfd


title: KMM KO SERBP1, SERBP1-WT, RIP, rep2

description:
WT_2_IP
all_reads_counts.txt
WT2_peaks.txt


title: KMM KO SERBP1, SERBP1-WT, input, rep2

description:
WT_2_Input
all_reads_counts.txt
WT2_peaks.txt


title: Kupffer cells, wild type, cdcdhfd, repl 2

description:
47
5826


title: Kupffer cells, wild type, cdcdhfd, repl 4

description:
49
5828


title: Kupffer cells, wild type, cdcdhfd, repl 3

description:
48
5827


title: KMM KO SERBP1, SERBP1-K68R, RIP, rep1

description:
KR_1_IP
all_reads_counts.txt
KR1_peaks.txt


title: Kupffer cells, wild type, cdcdcd, repl 4

description:
46
5825

value: cd

value: cdcdcd


title: KMM KO SERBP1, SERBP1-K68R, input, rep1

description:
KR_1_Input
all_reads_counts.txt
KR1_peaks.txt


title: whole exome sequencing of W1542

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

library_source: genomic

data_processing:
Library strategy: exome-seq
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters, and got the clean reads. Then the bwa software was used to map the reads to the IWGSC RefSeq V1.0.
The gatk software was used to call variation, and the variation information was saved as gVCF file.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: gVCF files were generated using gatk software, represents the variation information.

molecule: genomic DNA

organism: Triticum dicoccoides

source_name: W1542 leaf

extract_protocol: genomic DNA

value: leaf

tag: cultivar


title: Kupffer cells, wild type, hfdhfdhfd, repl 1

description:
43
5822

value: liver

tag: cell type

value: hfdhfdhfd


title: KMM KO SERBP1, SERBP1-WT, RIP, rep1

description:
WT_1_IP
all_reads_counts.txt
WT1_peaks.txt


title: whole exome sequencing of W1539

source_name: W1539 leaf


title: Kupffer cells, wild type, cdcdcd, repl 3

description:
45
5824

value: Kupffer cells

tag: genotype

value: wild type


title: whole exome sequencing of W1538

source_name: W1538 leaf


title: Kupffer cells, wild type, hfdhfdhfd, repl 2

description:
2
5823

value: Adult


title: KMM KO SERBP1, SERBP1-WT, input, rep1

description:
WT_1_Input
all_reads_counts.txt
WT1_peaks.txt


title: Kupffer cells, wild type, cdcdcd, repl 2

description:
41
5820


title: Kupffer cells, wild type, cdcdhfd, repl 1

description:
42
5821


title: whole exome sequencing of W1536

source_name: W1536 leaf


title: whole exome sequencing of W1532

source_name: W1532 leaf


title: whole exome sequencing of W1544

source_name: W1544 leaf


title: SUB280 WT+peroxide_rep1 [SM062M]

city: Bethesda

first: Nicholas

middle: R

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description: total RNA

data_processing:
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence by Cutadapt. These files are the raw data files uploaded on the GEO database.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
A custom python script is used to remove PCR duplicates by comparing the 7-nucleotide unique molecular identifiers (UMIs) in the libraries.
After trimming UMIs by Cutadapt, reads were aligned to human transcriptome by bowtie1 and mapped reads were processed by using custom python scripts.
Assembly: R64-1-1
Supplementary files format and content: Wiggle files for ribosome occupancy

organism: Saccharomyces cerevisiae

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3]

growth_protocol: SUB280 strain derivatives were grown in synthetic defined (SD) medium composed of D-Glucose (BD Difco, #215510), yeast nitrogen base (BD Difco, #291940) and drop-out amino acid medium without Leu and Trp (Sigma, #Y0750). SUB280 rad6Δ RAD6 and SUB280 rad6Δ RAD6(C88A) cells were grown in SD media supplemented with drop-out amino acid supplements without Leu, Trp and Ura (Sigma, #Y1771). S288C strain derivatives were grown in SD complete media by using drop-out amino acid supplements without Leu and Trp (Sigma, #Y0750) and supplementing it back with L-leucine (Sigma, #L800) and Tryptophan (Sigma, #T8941). Starter cultures were grown at 30°C overnight and then diluted to an OD600 of 0.001 (rad6Δ cells) or 0.0001 (WT cells) and were grown to a final OD600 between 0.5 and 0.6 for ~16 hours.

extract_protocol:
Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells. Ribosome profiling lysates were clarified, treated with RNase I, and run over sucrose gradients to extract either the monosome or the disome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Unless noted otherwise, the cultures were treated with freshly diluted H2O2 (peroxide) (Sigma, #216763), achieving a final concentration of 0.6 mM, for 30 minutes.

value: MATa lys2-801 leu2-3,112 ura3-52 his3- {delta}200 trp1-1[am] ubi1-{delta}1::TRP1 ubi2-{delta}2::ura3 ubi3-{delta}ub-2 ubi4-{delta}2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3]

tag: treatment

value: 0.6 mM hydrogen peroxide,30 min


title: Kupffer cells, wild type, cdcdcd, repl 1

description:
40
5819


title: whole exome sequencing of W1525

source_name: W1525 leaf


title: SUB280 rad6Δ+peroxide_rep2 [SM076M]

description: total RNA

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] rad6:kanMX4

value: MATa lys2-801 leu2-3,112 ura3-52 his3- {delta}200 trp1-1[am] ubi1-{delta}1::TRP1 ubi2-{delta}2::ura3 ubi3-{delta}ub-2 ubi4-{delta}2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] rad6:kanMX4


title: SUB280 rad6Δ_rep2 [SM075M]

description: total RNA

value: untreated


title: SUB280 WT_rep1 [SM061M]

description: total RNA


title: SUB280 rad6Δ+peroxide [SM066Fd]

description: disome footprints

data_processing:
Base calling and demultiplexing was performed at the NHLBI DNA Sequencing and Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and then trimmed to the start of the linker sequence by Cutadapt. These files are the raw data files uploaded on the GEO database.
Reads were aligned to a library of non coding RNA genes and those not matching were retained.
A custom python script is used to remove PCR duplicates by comparing the 7-nucleotide unique molecular identifiers (UMIs) in the libraries.
After trimming UMIs by Cutadapt, reads were aligned to human transcriptome by bowtie1 and mapped reads were processed by using custom python scripts.
Assembly: R64-1-1
Supplementary files format and content: Wiggle files for ribosome occupancy
Library strategy: Ribo-seq


title: SUB280 rad6Δ_rep1 [SM065M]

description: total RNA


title: whole exome sequencing of PI560126

organism: Amblyopyrum muticum

source_name: PI560126 leaf


title: whole exome sequencing of W1533

source_name: W1533 leaf


title: SUB280 WT+peroxide_rep2 [SM072M]

description: total RNA


title: SUB280 rad6Δ [SM065Fd]

description: disome footprints


title: whole exome sequencing of W1516

source_name: W1516 leaf


title: whole exome sequencing of PI560122

source_name: PI560122 leaf


title: whole exome sequencing of PI560127

source_name: PI560127 leaf


title: SUB280 WT_rep2 [SM071M]

description: total RNA


title: SUB280 WT+peroxide_rep2 [SM072Fd]

description: disome footprints


title: SUB280 WT+peroxide_rep1 [SM062Fd]

description: disome footprints


title: whole exome sequencing of Y437

organism: Aegilops sharonensis

source_name: Y437 leaf


title: whole exome sequencing of PI636562

source_name: PI636562 leaf


title: SUB280 rad6Δ+peroxide_rep1 [SM066M]

description: total RNA


title: whole exome sequencing of W1530

source_name: W1530 leaf


title: whole exome sequencing of TA1995

source_name: TA1995 leaf


title: SUB280 rad6Δ+peroxide_rep1 [SM066F]

description: monosome footprints


title: whole exome sequencing of PI560125

source_name: PI560125 leaf


title: whole exome sequencing of Y610

source_name: Y610 leaf


title: SUB280 WT_rep2 [SM071Fd]

description: disome footprints


title: NIL-qIGL1NIP rep3

city: nanjing

first: la

middle: yu

last: mei

address: xuanwu

institute: njau

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Oryza sativa from https://rapdb.dna.affrc.go.jp/ using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Assembly: tigr7
Supplementary files format and content: Matrix table with rpkm for all sample

organism: Oryza sativa

source_name: 8-10 cm young panicle

extract_protocol:
Total RNA was isolated from young panicles (8---10 10-cm long) with Plant Total RNA Isolation Kit (Vazyme, China) according to the manufacturer's instructions.2 μg total RNAs were used for stranded RNA sequencing library.
RNA sequencing library prepared by using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with PE150 model.

value: 8-10 cm young panicle

tag: line


title: whole exome sequencing of Y609

source_name: Y609 leaf


title: NIL-qIGL1NIP rep2


title: NIL-qigl1HD385 rep3


title: SUB280 rad6Δ+peroxide_rep2 [SM076F]

description: monosome footprints


title: SUB280 rad6Δ_rep1 [SM065F]

description: monosome footprints


title: whole exome sequencing of PI584374

source_name: PI584374 leaf


title: NIL-qigl1HD385 rep1


title: whole exome sequencing of PI599149

organism: Aegilops searsii

source_name: PI599149 leaf


title: whole exome sequencing of Y436

source_name: Y436 leaf


title: SUB280 WT_rep1 [SM061Fd]

description: disome footprints

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3]


title: SUB280 WT+peroxide_rep2 [SM072F]

description: monosome footprints


title: NIL-qIGL1NIP rep1


title: SUB280 rad6Δ_rep2 [SM075F]

description: monosome footprints

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3] rad6:kanMX4


title: whole exome sequencing of Y776_Y2132


title: whole exome sequencing of Y778_Y2134


title: SUB280 WT+peroxide_rep1 [SM062F]

description: monosome footprints


title: SUB280 WT_rep2 [SM071F]

description: monosome footprints


title: whole exome sequencing of Y445

source_name: Y445 leaf


title: NIL-qigl1HD385 rep2


title: whole exome sequencing of Y444

source_name: Y444 leaf


title: Ectopic donor - Lys+ recombinant #10

type: genomic

city: Fort Collins

first: Ruth

last: Watson

state: CO

address: 1385 Center Ave

department: ERHS

institute: Colorado State University

description: 550-10 was hybridized with APY89 reference strain instead of its parent strain APY85.

hyb_protocol: Labeled DNA was hybridized to the agilent arrays using the Agilent Oligo aCGH/ChIP-on-Chip hybridization kit (cat # 5188-5220), following the standard protocol. Custom arrays were used with 8 blocks per array and 15k probes per block.

scan_protocol: Arrays were scanned using the Perkin Elmer scan array express. Scanner had two lasers, Green at 532 nm and Red at 635 nm.

data_processing: Gene Pix Pro sotware was used to analyze each block of the array and to quantify images. GPR files from Gene Pix Pro were loaded into Biodiscovery Nexus Copy Number software for visualization and CNV analysis.

source_name: 550-10 - Lys+ recombinant yeast cells

label_protocol: Labeled DNA using the BioPrime array CGH genomic labeling module (cat # 18095012) following their standard protocol. Reference DNA was labeled with Cy3-dUTP from (GE Healthcare Life Sciences cat # PA53022) and Experimental DNA was labeled with Cy5-dUTP (GE Healthcare Life Sciences cat # PA55022).

growth_protocol: Cells grown overnight in 7mL YPD at 30C on rotating drum.

extract_protocol: Genomic DNA extracted using the potassium acetate protocol. Genomic DNA was sonicated with a Bioruptor UCD200 on high (320W) in 30 second intervals (30 seconds on, 30 seconds off) for a total of 30 minutes. DNA was purified and concentrated using the ThermoScientific GeneJet gel extraction kit (cat # K0692) and eluted from columns with 35uL EB.

treatment_protocol: no treatments done on samples

tag: strain

source_name: APY89 - parent yeast cells


title: Ectopic donor - Lys+ recombinant #21

source_name: 550-21 - Lys+ recombinant yeast cells

source_name: APY85 - parent yeast cells


title: Ectopic donor - Lys+ recombinant #23

source_name: 550-23 - Lys+ recombinant yeast cells


title: whole exome sequencing of TA2355

source_name: TA2355 leaf


title: APY85_translocant_24

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-24

data_processing:
Bedgraph files were generated from sorted bam files with tinycov (https://github.com/cmdoret/tinycov)
Assembly: Saccharomyces cerevisiae R64-2-1
Supplementary files format and content: bedgraph files contain the coverage by 200 bp bins smoothed by 100 bp of Illumina paired-end reads
Supplementary files format and content: clc files contain the aligned SV-supporting Nanopore reads

growth_protocol: Growth in YP-lactate, addition of 2% galactose for 2 hours, and plating in SD-LYS media

extract_protocol:
Regular spheroplasting followed by Phenol:chloroform:IA extraction
Details on the library preparation for each data type in SRA raw file

treatment_protocol: Induction of a heterozygous HO-induced DSB on chr. V at the ura3 locus

value: Lys+ recombinant

value: Following DSB formation on chr. V and selection on SD-LYS media


title: Ectopic donor - Lys+ recombinant #11

source_name: 550-11 - Lys+ recombinant yeast cells


title: Allelic donor - Lys+ recombinant #10

source_name: AP10 - Lys+ recombinant yeast cells


title: APY85_translocant_22

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-22


title: APY85_translocant_19

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-19


title: Bronchoalveolar lavage cells, influenza, rep. 3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q18 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38.p5) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1.
Assembly: mm10
Supplementary files format and content: raw count matrix

source_name: Lung

extract_protocol: 100ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

value: Lung

value: Bronchoalveolar lavage cells

value: WT

value: Influenza virus


title: LNCaP-AI, shscramble, replicate 3

city: Tianjin

first: Mingpeng

last: zhang

state: tianjin

address: pingjiang road

institute: the Second Hospital of Tianjin Medical University

data_processing:
The RNA concentration of each sample was measured using a NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA). The OD260/OD280 values were used as an indicator of RNA purity. If the OD260/OD280 values were in the range of 1.8 ~ 2.1, the RNA purity was qualified, and the QC Results were marked as "Pass".
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified.
Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts for each sample
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Prostate

extract_protocol:
LNCaP-AI cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Prostate

value: LNCaP-AI

value: castration-resistant prostate cancer

value: Control

value: Androgen Deprivation Therapy


title: Bronchoalveolar lavage cells, influenza, rep. 2


title: Allelic donor - Lys+ recombinant #6

source_name: AP6 - Lys+ recombinant yeast cells


title: Allelic donor - Lys+ recombinant #4

source_name: AP4 - Lys+ recombinant yeast cells


title: Allelic donor - Lys+ recombinant #5

source_name: AP5 - Lys+ recombinant yeast cells


title: Ectopic donor - Lys+ recombinant #18

source_name: 550-18 - Lys+ recombinant yeast cells


title: Allelic donor - Lys+ recombinant #1

source_name: AP1 - Lys+ recombinant yeast cells


title: Bronchoalveolar lavage cells, influenza, rep. 1


title: APY85_translocant_17

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-17


title: LNCaP-AI, shscramble, replicate 1


title: LNCaP-AI, shMETTL1, replicate 2

value: METTL1 knockdown


title: Bronchoalveolar lavage cells, mock, rep. 3

value: PBS (mock control)


title: APY85_translocant_12

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-12


title: LNCaP-AI, shMETTL1, replicate 1


title: Allelic donor - Lys+ recombinant # 11

source_name: AP11 - Lys+ recombinant yeast cells


title: APY85_translocant_4

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-4


title: APY85_translocant_20

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-20


title: SUB280 WT_rep1 [SM061F]

description: monosome footprints

source_name: MATa lys2-801 leu2-3,112 ura3-52 his3- Δ200 trp1-1[am] ubi1-Δ1::TRP1 ubi2-Δ2::ura3 ubi3-Δub-2 ubi4-Δ2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3]

value: MATa lys2-801 leu2-3,112 ura3-52 his3- {delta}200 trp1-1[am] ubi1-{delta}1::TRP1 ubi2-{delta}2::ura3 ubi3-{delta}ub-2 ubi4-{delta}2::LEU2 [pUB39 Ub, LYS2][pUB100 Ubi1 tail, HIS3]


title: Allelic donor - Lys+ recombinant #3

source_name: AP3 - Lys+ recombinant yeast cells


title: APY85_translocant_1

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-1


title: Bronchoalveolar lavage cells, mock, rep. 1


title: APY85_parent

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP14

value: Lys- parent

value: Prior to DSB formation (Lys-)


title: APY89_parent

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP13


title: APY89_translocant_12

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP12


title: APY85_translocant_13

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-13


title: LNCaP-AI, shscramble, replicate 2


title: APY89_translocant_11

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP11


title: APY89_translocant_10

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP10


title: Alveolar epithelial cells, influenza, rep. 3

value: Alveolar epithelial


title: APY85_translocant_9

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
550-9

value: Lys+ recombinant


title: Alveolar epithelial cells, influenza, rep. 2


title: Bronchoalveolar lavage cells, mock, rep. 2


title: APY89_translocant_9

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP9

value: Following DSB formation on chr. V and selection on SD-LYS media


title: LNCaP-AI, shscramble, replicate3,input

data_processing:
poly(A)- enriched mRNA fraction was subjected to alkaline hydrolysis for fragmentation. RNA fragments were dephosphorylated with antarctic phosphatase (New England Biolabs, Inc., Massachusetts, USA), and then incubated in 1M aniline for cleavage.
RNA libraries were constructed with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Inc., Massachusetts, USA) by following the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).
Raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina HiSeq4000 sequencer.
Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated. Then these clean reads were aligned to human reference genome  (UCSC hg19) using bowtie2 software (v2.2.4) with end-to-end mode.
Raw m7G counts and coverage counts were calculated by bedtools (v2.24) software and in-house scripts, then m7G-ratio (define as: count/coverage) and m7G-fc (defined as: mG-ratio/Input-m7G-ratio) were also calculated. Differentially m7G sites were calculated based on m7G-fc. m7G sites weree annotated with gene information by bedtools software. GO and KEGG Pathway analysis were performed based on the differentially m7G sites-associated genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count, coverage, m7G-ratio, and m7G-fc for each sample

extract_protocol:
LNCaP-AI cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
m7G AlkAniline-Seq

value: Control input


title: LNCaP-AI, shMETTL1, replicate3, input

value: METTL1 knockdown input


title: LNCaP-AI, shMETTL1, replicate 3


title: LNCaP-AI, shscramble, replicate1,input


title: LNCaP-AI, shMETTL1, replicate2, input


title: APY89_translocant_6

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP6


title: Alveolar epithelial cells, influenza, rep. 1

value: Lung

value: WT


title: Alveolar epithelial cells, mock, rep.3


title: LNCaP-AI, shMETTL1, replicate1, input

value: Prostate


title: APY89_translocant_8

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP8


title: Alveolar epithelial cells, mock, rep.2


title: APY89_translocant_5

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP5


title: APY89_translocant_7

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP7


title: LNCaP-AI, shscramble, replicate2,input

value: LNCaP-AI


title: LNCaP-AI, shscramble, replicate3

value: castration-resistant prostate cancer


title: APY89_translocant_4

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP4


title: APY89_translocant_3

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1, and aCGH values
AP3


title: APY89_translocant_2

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP2


title: APY89_translocant_1

description:
Bedgraph coverage file of aligned reads on the S288c reference genome R64-2-1
AP1


title: LNCaP-AI, shscramble, replicate2

value: Control


title: Min6 cells, Snd1 KO3

city: Indianapolis

first: Jason

last: Spaeth

state: IN

address: 1210 Waterway Blvd

department: Pediatrics

institute: Indiana University

data_processing:
The generated FASTQ files were processed and interpreted using the Genialis visual informatics platform (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), and Trimmomatic was used to trim adapters and filter out poor quality reads. Trimmed reads were then mapped to the mm10UCSC reference genome using the HISAT2 aligner. Gene expression levels were quantified with HTSeq-count, and differential gene expression analyses performed with DESeq2. Poorly expressed genes, which have expression count summed over all samples below 10, were filtered out from the differential expression analysis input matrix.
Assembly: mm10
Supplementary files format and content: the .tab files are the Transcripts Per Million (TPM) reads for each designated gene in the mRNA-seq dataset

extract_protocol:
RNA extraction from Snd1 KO MIN6 cells was carried out following the manufacturer's instructions (Zymo Research, D7001)
One hundred nanograms of RNA from Control and Snd1 KO cell lines with RNA integrity numbers ≥ 7.0 was used for library following cDNA preparation (Takara) with the Nextera XT DNA Library Prep Kit (Illumina, Inc.). Each library was quantified, and quality accessed by Qubit and Agilent Bioanalyzer with average size of the library insert ~300-400 basepairs.

value: Mouse insulinoma cell line

value: Snd1 KO

value: CRISPR/Cas9 targeting exon 2


title: Alveolar epithelial cells, mock, rep.1

value: PBS (mock control)


title: Min6 cells, Snd1 KO1


title: Colon, DSS, Tnfr2ko, rep4

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

description:
DSS-R2FLVC-M20900-7
abundances_DSS_principal.csv

data_processing:
Reads within FASTQ files were pseudoaligned and quantified using kallisto, and differentially expressed transcripts between wildtype and knockout conditions were identified using sleuth.
Downstream analysis of data was performed with custom-written scripts in R.
Assembly: mm10
Supplementary files format and content: csv file with statistics from significance testing and tpm values for each detected transcript in each sample

source_name: colonic epithelium

extract_protocol:
Sorted cell suspensions were washed with saline. RNA was extracted using a standard TRIzol protocol.
Stranded polyA-enriched Illumina 1x75 bp libraries were prepared by SeqMatic, LLC for sequencing on an Illumina NextSeq (high output run). Approximately 10 million reads were recovered per sample.

treatment_protocol: Vil1::Cre;Tnfr2-f/f mice and control Tnfr2-f/f mice were treated with water or 3% dextran sulfate sodium (DSS) for 6 days. Mice were dissected 12 days after the beginning of treatment. The distal colonic mucosa was digested with Liberase and DNAse I, and the resulting single-cell suspension was stained with an antibody against EpCAM. EpCAM+ cells were sorted by FACS.

value: colonic epithelium

tag: cage

value: d

tag: Sex

value: F

value: DSS


title: LNCaP-AI, shscramble, replicate1

value: Androgen Deprivation Therapy


title: Min6 cells, Snd1 KO2


title: Colon, Water, Tnfr2ko, rep5

description:
water-R2FLVC-M20834-9
abundances_water_principal.csv

value: b

value: Water


title: LNCaP-AI, shMETTL1, replicate3

value: METTL1 knockdown


title: LNCaP-AI, shMETTL1, replicate1


title: Colon, DSS, Tnfr2ko, rep3

description:
DSS-R2FLVC-M20830-6
abundances_DSS_principal.csv


title: Min6 cells, CN2

value: control

value: CRISPR/Cas9 targeting Intron 2


title: Min6 cells, CN3


title: GSC_KD_3

city: Toronto

first: Sunit

last: Das

state: Ontario

address: 30 Bond St

department: Division of Neurosurgery

country: Canada

institute: St. Michael's Hospital

description: library type: rRNA-depleted stranded (HMR)

data_processing:
We filtered out reads with poor quality using FastQC.
We used RNAstar to map the reads to the genome (hg38), and annotated genes using SAMtools.
We used DESeq2 to analyze differential expression.  For the purpose of differential expression analysis, genes with <1 RPKM were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: processed data files represent raw counts and differential gene analysis in the CASCADES knockdown vs. scrambled control glioma neural stem cells and fetal neural stem cells, respectively

source_name: glioma stem cells - knockdown 3

growth_protocol: GliNS1 and HFNS were cultured and expanded on plates coated with 0.01% poly-L-ornithine (Sigma, Cat # P4957) followed by 1% laminin (Sigma, Cat # L2020) in phosphate buffered saline (PBS) solution.  Briefly, the cells were thawed at room temperature, and combined with 10mL of Dulbecco’s Modified Eagle Medium with F12 (DMEM/F12) (Wisent, Cat #219-095-XK) in a 15mL conical tube. By centrifuging at 800rpm for 3mins, the cells were pelleted; the supernatant was aspirated, and the cell pellet was resuspended in 10mL of neural stem cell (NSC) culture media, and plated onto laminin-coated plates. The NSC media was composed of Neurocult NS-A basal medium human (Stem Cell Technologies, Cat #05750) along with L-glutamine (Sigma, Cat #G7513), antibiotic/antimycotic (Sigma, Cat #A5955), bovine serum albumin, epidermal growth factor, basic fibroblast growth factor, B27 supplement, N7 supplement, and heparin.  The media was changed every 3-4 days, and the cells were passaged upon reaching ~80% confluence.

extract_protocol:
The RNA was extracted using Qiagen RNeasy kit following the manufacturer's protocol.  The RNA concentration and quality was validated using Bioanalyzer.
RNA was extracted using RNeasy kit (Qiagen).  For ribosomal depletion, 1–2 mg of total RNA was used for Ribo-Zero rRNA Removal kit (Illumina) according to the manufacturer’s protocol. Ribosomal-depleted library was processed for TruSeq Stranded Total RNA sequencing according to the manufacturer’s protocol (Illumina). The quality and quantity of total RNA and final libraries were assessed using Agilent Technologies 2100 Bioanalyzer.  RIN (RNA Integrity Number) of >9 was used for the sequencing experiments.  Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer’s protocols.

treatment_protocol: The cells were cultured in 6-well plates, using normal NSC culture medium.  Twenty-four hours before siRNA knockdown was performed, the cells were incubated with NSC culture medium without antibiotic/antimycotic.  The siRNAs were designed using Custom RNAi Design Tool by Integrated DNA Technologies (IDT) (Coralville, Iowa), and were resuspended in Tris-EDTA (TE) buffer to a final concentration of 20μM.  For each well, 2μL of siRNA was combined with 138μL of Opti-Mem Reduced Serum Medium with GlutaMax Supplement (Life Technologies, Cat #51985-034) and incubated at room temperature for 5 minutes.  Meanwhile, 16.5μL of Oligofectamine Transfection Reagent (Life Technologies, Cat #12252-011) was combined with 43.5μL of Opti-Mem.  The diluted siRNA + Opti-Mem was then combined with Oligofectamine + Opti-Mem, and incubated at room temperature for 15 minutes to allow complexes to form.  The GliNS1 cells were washed once with Opti-Mem, and 1.3mL of Opti-Mem was added to each well, followed by addition of 200μL of siRNA+Oligofectamine complex.  The cells were then incubated at 37°C for 4 hours, and the media was replaced by NSC culture medium without antibiotics/antimycotics.  The RNA was extracted 72 hours later.

value: glioma stem cells

value: knockdown of CASCADES


title: Colon, Water, Tnfr2ko, rep4

description:
water-R2FLVC-M20829-8
abundances_water_principal.csv


title: GSC_KD_2

source_name: glioma stem cells - knockdown 2


title: Colon, DSS, Tnfr2ko, rep2

description:
DSS-R2FLVC-M20828-5
abundances_DSS_principal.csv


title: Min6 cells, CN1


title: Colon, Water, Tnfr2ko, rep3

description:
water-R2FLVC-M20824-7
abundances_water_principal.csv


title: Colon, DSS, Control, rep3

description:
DSS-R2F-M20827-4
abundances_DSS_principal.csv

value: c


title: DRN-20661, WT

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

data_processing:
Sequencing adapters were trimmed from the raw reads with skewer (version 0.2.2)
Reads were aligned to the mouse genome version GRCm38_p6. A STAR index (version 2.7.1a) and built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the --sjdbGTFfile argument. Alignments were obtained with the following parameters: --readFilesCommand zcat --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.6 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantMode GeneCounts --outSAMunmapped Within --outSAMattributes NH HI AS nM MD XS --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outBAMcompression 6. Gene level counts were obtained using featureCounts from the subread package (version 1.6.2). Gene symbols and biotype information were extracted from the Gencode GTF file.
Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen). Post-alignment quality control reports were generated using MultiQC (version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 4.2). Gene symbols and biotype information were extracted from the Gencode GTF file.
To calculate normalized counts per million (CPM) TMM normalization was applied across all genes annotated as protein_coding with the edgeR R package (version 3.40.2).
Assembly: GRCm38
Supplementary files format and content: Excel (XLSX) file with three worksheets: sample annotations, raw count matrix, normalized count matrix (CPM)

source_name: brain

extract_protocol:
Total RNA was extracted from mouse brain tissue using the Qiagen RNeasy plus kit (Qiagen 74034).
Libraries were generated using the QuantSeq 3' mRNA-seq Library Prep Kit FWD for Illumina (Lexogen A01173) with the UMI second strand synthesis module to identify and remove PCR duplicates, following the protocol defined by the manufacturer. Briefly, total RNA was used as input for oligo dT priming during reverse transcription, followed by RNA removal. Unique Molecular Identifiers were introduced during second strand synthesis and cDNA was purified using magnetic beads followed by 14 cycles of PCR with dual indexes and PCR purification. Library quantity and quality were assessed with Qubit 1X dsDNA HS Assay Kits (Invitrogen Q33231) and Bioanalyzer High Sense DNA chip (Agilent 5067-4626). Libraries were pooled in equimolar ratios and sequencing reads were generated on an Illumina NovaSeq 6000 instrument (100 bp single end) by SeqMatic (Fremont, CA, USA)

value: female

tag: age

value: 90 days

tag: batch

value: brain

tag: region

value: anterior right hemisphere

value: wildtype


title: DRN-20646, Mutant

value: male

value: 101 days


title: DRN-20651, Mutant

value: 93 days


title: DRN-20648, Mutant

value: 104 days


title: DRN-20653, WT

value: 92 days


title: DRN-20662, Mutant


title: DRN-20655, WT


title: DRN-20634, WT

value: 105 days


title: DRN-20657, Mutant


title: DRN-20645, WT

value: 91 days


title: GSC_KD_1

source_name: glioma stem cells - knockdown 1


title: DRN-20630, WT


title: GSC_SC_3

source_name: glioma stem cells - scrambled control 3

value: scrambled control


title: DRN-20642, WT

value: 113 days


title: DRN-20635, WT

value: 111 days


title: LNCaP-AI, shMETTL1, replicate2

value: Prostate

value: LNCaP-AI

value: castration-resistant prostate cancer

value: METTL1 knockdown

value: Androgen Deprivation Therapy


title: Colon, Water, Control, rep4

description:
water-R2F-M20818-6
abundances_water_principal.csv

value: colonic epithelium

value: b

value: F

value: Water


title: GSC_SC_2

source_name: glioma stem cells - scrambled control 2

value: glioma stem cells


title: DRN-20632, Mutant

value: male

value: 108 days

value: brain

value: anterior right hemisphere


title: Colon, DSS, Control, rep2

description:
DSS-R2F-M20819-2
abundances_DSS_principal.csv

value: d

value: DSS


title: Colon, Water, Control, rep3

description:
water-R2F-M20791-5
abundances_water_principal.csv

value: a

value: M


city: Bronx

first: Wei

state: NEW YORK

address: 1300 Morris Park Avenue, Ullmann 117

institute: Albert Einstein College of Medicine

data_processing:
Fastq sequences were mapped to the human genome (GRCh38-3.0.0) using CellRanger (3.1.0).
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix Format

source_name: CONCEPT telencephalon-eye organoids

growth_protocol: CONCEPT telencephalon-eye organoids at day 24 were generated as follows. A humidified incubator at 37°C with 5% CO2 was used for culture. H1 hESCs that were passaged using ReLeSR two days before experiments were detached using Dispase (GIBCO 17105041) and then harvested by centrifugation. After that, the cell pellets were suspended in ice-cold Matrigel. After gelling at 37 °C for 15-20 minutes, the hESC/Matrigel clump was gently dispersed in a N2B27 Medium (DMEM/F12+GlutaMAX (GIBCO):Neurobasal medium (GIBCO) = 1:1, 0.5 x B27 supplement (GIBCO), 0.5 x N2 supplement (GIBCO), 0.1 mM β-mercaptoethanol, and 0.2 mM L-GlutaMax) for floating culture. With the starting day of cell differentiation designated as day 0, cysts with a single lumen formed on day 1. On day 4 or 5, individual cysts were passaged to Matrigel-coated 24-well plates at a density of 2-6 cysts per well. Cysts spontaneously attached to the culture surface and grew. On day 12, attached cell colonies were grown in a KSR medium (GMEM medium supplemented with 10% knockout serum replacement, 1 mM sodium pyruvate, 0.1 mM non-essential amino acids, 2 mM l-glutamine, and 55 μM 2-mercaptoethanol; all the culture reagents were from Life Technologies). Culture mediums were changed every two or three days.

extract_protocol:
10,000 dissociated cells were captured using Chromium Controller (10x Genomics).
Manufacturer instructions of the 10x Genomics Single Cell 3’ version 3.1 kit was followed.

treatment_protocol: There is no other treatment.

value: Wild type

tag: Stage

value: Day 24


title: DRN-20628, Mutant

value: 105 days


title: DRN-20625, WT

value: female

value: 114 days

value: wildtype


title: DRN-20623, WT


title: Colon, DSS, Tnfr2ko, rep1

description:
DSS-R2FLVC-M20820-3
abundances_DSS_principal.csv

value: colonic epithelium

value: c

value: F


title: GSC_SC_1

source_name: glioma stem cells - scrambled control 1

value: glioma stem cells

value: scrambled control


title: DRN-20621, WT

value: brain


title: Colon, Water, Tnfr2ko, rep1

description:
water-R2FLVC-M20207-3
abundances_water_principal.csv

value: Water


title: DRN-20619, Mutant

value: anterior right hemisphere


title: HF_KD_2

source_name: human fetal neural stem cells - knockdown 2

value: fetal neural stem cells

value: knockdown of CASCADES


title: Colon, Water, Control, rep2

description:
water-R2F-M19240-2
abundances_water_principal.csv

value: b


title: HF_KD_1

source_name: human fetal neural stem cells - knockdown 1


title: HF_KD_3

source_name: human fetal neural stem cells - knockdown 3


title: Colon, DSS, Control, rep1

description:
DSS-R2F-M19243-1
abundances_DSS_principal.csv

value: d

value: DSS


title: DRN-20618, WT

value: 104 days


title: DRN-20616, Mutant

value: female

value: 113 days


title: HF_SC_3

source_name: human fetal neural stem cells - scrambled control 3


title: Colon, Water, Control, rep1

description:
water-R2F-M19080-1
abundances_water_principal.csv

value: a

value: M


title: Hepatocytes, wt, hfdhfdhfd, repl 6

description:
526
raw_counts_HC_Hif1a_ko.txt
12692

source_name: liver

value: liver

value: Hepatocytes

value: wt

value: Adult

tag: maternal diet

value: hfdhfd

tag: offspring diet

value: hfd

tag: condition

value: hfdhfdhfd

tag: biologicalreplicate

tag: merged


title: Hepatocytes, wt, hfdhfdhfd, repl 4

description:
524
raw_counts_HC_Hif1a_ko.txt
12690

tag: tissue


title: Hepatocytes, Hif1a ko, hfdhfdhfd, repl 2

description:
511
raw_counts_HC_Hif1a_ko.txt
12677

tag: cell type

value: Hif1a ko

value: hfdhfdhfd_Hif1a ko_Hepatocytes


title: Colon, Water, Tnfr2ko, rep2

description:
water-R2FLVC-M20210-4
abundances_water_principal.csv

value: colonic epithelium

tag: genotype

value: Water


title: Hepatocytes, wt, hfdcdcd, repl 1

description:
500
raw_counts_HC_Hif1a_ko.txt
12666

value: hfdcd

value: cd

value: hfdcdcd


title: Hepatocytes, wt, hfdhfdhfd, repl 3

description:
499
raw_counts_HC_Hif1a_ko.txt
12665


title: Hepatocytes, wt, hfdcdcd, repl 2

description:
501
raw_counts_HC_Hif1a_ko.txt
12667


title: PBS

city: Wenzhou

first: hao

last: yin

address: Chashan Higher Education Park, Wenzhou, Zhejiang Province, China

institute: Wenzhou Medical University

description:
10x Genomics
barcodes.tsv
features.tsv
matrix.mtx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
FACS analysis of tumour-infiltrating lymphocytes and tumour-infiltrating lymphocytes isolated in tumour models was performed after staining with a PE-conjugated anti- mouse CD45 antibody (clone 30-F11, Biolegend). CD45+ immune cells were then enriched using a BD FACS Aria III flow cytometer. Cell viability was monitored in real time during the preparation of single CD45+ immune cell suspensions. Ten thousand cells (~600 single cells per microlitre) from each experimental group were barcoded and pooled using a 10x Genomics device. Samples were prepared according to the manufacturer's protocol and sequenced on an Illumina NextSeq sequencer. The Cell Ranger Analysis Pipeline (v.3.0.2) was used for sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of sequencing runs. For quality control of the single-cell RNA-sequencing process, cells with fewer than 300 genes detected and cells with mitochondrial-encoding gene transcript counts exceeding 15% of total transcript counts were removed from subsequent analyses. Genes detected in less than three cells in the entire dataset were also excluded, resulting in a preliminary expression matrix of 15603 cells. After obtaining the digital gene expression data matrix, dimensionality reduction, clustering and differential gene expression analysis were performed using Seurat (v.3.0.0.9000)
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol:
LC-2: To construct the tumour model, 4T1 cells (1 × 10^6 cells/mouse) in 25 μl PBS were implanted into the right flanks of BALB/c female mice (6–8 weeks). Mice were intravenously injected with PBS on day 7, and each of the treatments was followed by NIR light (980 nm, 1.0 W cm-2, 5 min) on days 8, 9, and 10. Tumors were collected on day 13.
LC-5: To construct the tumour model, 4T1 cells (1 × 10^6 cells/mouse) in 25 μl PBS were implanted into the right flanks of BALB/c female mice (6–8 weeks). Mice were intravenously injected with PBS on day 7, and each of the treatments was followed by NIR light (980 nm, 1.0 W cm-2, 5 min) on days 8, 9, and 10. Tumors were collected on day 13.
LC-6: To construct the tumour model, 4T1 cells (1 × 10^6 cells/mouse) in 25 μl PBS were implanted into the right flanks of BALB/c female mice (6–8 weeks). Mice were intravenously injected with TIOs on day 7, and each of the treatments was followed by NIR light (980 nm, 1.0 W cm-2, 5 min) on days 8, 9, and 10. Tumors were collected on day 13.
PBS: To construct the tumour model, 4T1 cells (1 × 10^6 cells/mouse) in 25 μl PBS were implanted into the right flanks of BALB/c female mice (6–8 weeks). Mice were intravenously injected with TIOs on day 7, and each of the treatments was followed by NIR light (980 nm, 1.0 W cm-2, 5 min) on days 8, 9, and 10. Tumors were collected on day 13.

tag: cell line

value: tumor

value: Female

value: 6-8 weeks old


title: LC-6


title: Hepatocytes, Hif1a ko, hfdcdcd, repl 3

description:
527
raw_counts_HC_Hif1a_ko.txt
12693

data_processing:
The Agilent high-sensitivity D5000 assay was used to measure the size distribution of cDNA libraries on a Tapestation 4200 system (Agilent).
The cDNA libraries were quantified using a high-sensitivity dsDNA assay (Qubit).
To quantify the abundances of transcripts from the bulk RNA-seq data, Kallisto pseudo alignment was applied
Kallisto read counts were used fortheDESeq2 pipeline
Assembly: GRCm38.p5 (M16)
Supplementary files format and content: txt raw count matrix with transcripts as rows and samples as columns, done with kallisto and import to DESeq2 (see manuscript for more information)

value: liver

value: hfdcdcd_Hif1a ko_Hepatocytes


title: Hepatocytes, wt, hfdhfdhfd, repl 2

description:
489
raw_counts_HC_Hif1a_ko.txt
12655

value: Hepatocytes

value: wt


title: HF_SC_1

source_name: human fetal neural stem cells - scrambled control 1

value: fetal neural stem cells

value: scrambled control


title: HSF2KO IR Sample 2 RNA Seq

city: Augusta

first: Nahid

middle: F

last: Mivechi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description:
kol2
hsf2 VS B6 IR RNA seq original.csv

data_processing:
For Lin-cKit+ cells, the sequencing was performed on the Illumina HiSeq4000 platform and one lane of Hi Seq 50bp SR for the sequencing.   For K562 cells, RNA-seq analyses was performed on a Novaseq 6000 S1 v1.5.  with PolyA+ (mRNA) using 100M paired reads (200M total)
For K562 cell: RNA-seq reads were aligned to reference genome UCSC/hg38 using STAR program with default settings.
For K562 cell: rMATs software with default setting was used to identify and quantify alternative splicing events
For Lin-cKit+ cells: The RNAseq analysis was performed on biostatistics computing cluster. The quality control of the raw FASTQ files were perfomed using FastQC v. 0.11.8. The raw reads were mapped to mouse genome mm10 using STAR aligner with default settings. The read counts and normalization was performed using R package DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: MVG9mRNA_rawcountsM.csv (human samples),  hsf2 VS B6 IR RNA seq original.csv (mouse samples)

source_name: Bone Marrow Lin-cKit+ cells

extract_protocol: RNA was isolated using the Qiagen RNeasy plus micro-kit (for mouse bone marrow Lin-cKit+Sca1+ cells) or Qiagen RNeasy plus mini-kit (for tumor cell lines)

treatment_protocol: The mice were not treated or treated 250 Rad IR. The K562 cells lines were not treated.

value: Bone Marrow Lin-cKit+ cells

tag: treatment

value: IR

tag: replicate

value: Replicate 2


title: HSF2KO IR Sample 1 RNA Seq

description:
kol1
hsf2 VS B6 IR RNA seq original.csv

value: Replicate 1


title: LC-5


title: Hepatocytes, wt, cdcdhfd, repl 5

description:
98
raw_counts_HC_Hif1a_ko.txt
12647

extract_protocol:
Adult mice were anesthetized and perfused with ice-cold PBS. For livers, 300 mg were collected, cut into small pieces, and incubated with 1 ml of double-concentrated digestion mix (PBS containing 1 mg/ mlcollagenase D (Roche), 100 U/mlDNase I (Sigma-Aldrich), 2.4 mg/ mlof dispase (Invitrogen) and 3% fetal calf serum (FCS) (Invitrogen) for 30 min at room temeprature before the mechanical disruption 100-μm filter.  The cell suspension was diluted in 3ml of FACS buffer (0,5% BSA, 2mmol EDTA in PBS).  Cells were stained by antibody mixes and sorted using FACS ARIATM III cell sorter (BD Biosciences) directly into 500ul QIAzol lysis buffer (Qiagen).
SmartSeq2 protocol

value: Adult

value: cdcd

value: hfd

value: cdcdhfd


title: Hepatocytes, Hif1a ko, hfdhfdhfd, repl 1

description:
488
raw_counts_HC_Hif1a_ko.txt
12654

value: Hif1a ko

value: hfdhfd

value: hfdhfdhfd

value: hfdhfdhfd_Hif1a ko_Hepatocytes


title: LC-2

value: tumor

value: Female

value: 6-8 weeks old


title: HSF2KO control Sample 2 RNA Seq

description:
ko2
hsf2 VS B6 IR RNA seq original.csv

value: control


title: Hepatocytes, Hif1a ko, cdcdhfd, repl 5

description:
95
raw_counts_HC_Hif1a_ko.txt
12645

value: liver

value: Hepatocytes

value: cdcdhfd_Hif1a ko_Hepatocytes


title: Hepatocytes, wt, cdcdhfd, repl 4

description:
96
raw_counts_HC_Hif1a_ko.txt
12646

value: wt


title: HSF2KO control Sample 1 RNA Seq

description:
ko1
hsf2 VS B6 IR RNA seq original.csv

value: Bone Marrow Lin-cKit+ cells

value: Replicate 1


title: HF_SC_2

source_name: human fetal neural stem cells - scrambled control 2

value: fetal neural stem cells

value: scrambled control


title: Hepatocytes, wt, hfdhfdhfd, repl 5

description:
525
raw_counts_HC_Hif1a_ko.txt
12691

value: Adult

value: hfd


title: Hepatocytes, Hif1a ko, cdcdhfd, repl 4

description:
94
raw_counts_HC_Hif1a_ko.txt
12644

value: Hif1a ko

value: cdcd

value: cdcdhfd


title: 86559-Hic5-KO

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt 1.2.1
Trimmed sequence reads were mapped to GrCM38/mm10 using Bowtie2
Read count quantification was performed using Partek E/M algirithm to Ensembl Transcripts release 86, and normalization performed using RPKM
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary CAFs

growth_protocol: CAFs were freshly isolated from Hic-5+/- (HET) and Hic-5-/- (KO) tumors of MMTV-PyMT mice as previously described (Goreczny et al., 2017). Tumors were minced and digested in digestion media (2mg/mL collagenase, 2mg/mL trypsin in 50:50 DMEM:F12, 5% FBS, 5μg/mL Insulin and 10 I.U. penicillin/10 μg/mL streptomycin) for 50 minutes at 37°C. Differential centrifugation was performed to separate the single CAFs from tumor organoids. CAFs were cultured in PyMT media (50:50 DMEM:F12 with 10% FBS, 2 mM L-glutamine and 10 I.U. penicillin/10 μg/mL streptomycin at 5% CO2 and 37°C.

extract_protocol:
RNA was harvested using Trizol. 1.0 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit RiboZero Gold (Illumina) following manufacturer protocol.

value: primary CAFs

value: cancer associated fibroblast

value: knockout


title: 86559-Hic5-Het

value: heterozygous


title: Senescent MAF replicate 3

city: Rochester

first: Sarah

middle: Katherine

last: Jachim

state: MN

address: 222 3rd Ave SW

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

data_processing:
Base-calling was performed using Illumina’s RTA version 3.4.4
Data was mapped to reference genome mm10 using MAPRseq v3.1.4
Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (RPKM – Reads Per Kilobase per Million mapped reads) reads
Assembly: mm10
Supplementary files format and content: .tsv file contains raw count data for all samples

source_name: Primary MAF

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 3% O2.

extract_protocol:
Cells were collected in TRIzol reagent (Invitrogen) and RNA was extracted according to manufacturer instructions.
cDNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions for the TruSeq Stranded mRNA Sample Prep Kit (Illumina)

treatment_protocol: Control cells were sham irradiated, and Senescent cells were exposed to 20gy x-ray irradiation using a RS2000 X-Ray Inducer (RAD Source Technologies). Cells were treated with 100nM dexamethasone (Sigma) for two hours, and collected 12 hours later.

value: Primary MAF

value: Mouse adult fibroblast

tag: cell subtype

value: Senescent MAF


title: Senescent MAF replicate 2


title: Hepatocytes, Hif1a ko, cdcdcd, repl 5

city: Bonn

first: Elvira

last: Mass

address: Carl-Troll-Str, 31

institute: University of Bonn

description:
81
raw_counts_HC_Hif1a_ko.txt
12631

value: liver

value: Hepatocytes

value: cd

value: cdcdcd

value: cdcdcd_Hif1a ko_Hepatocytes


title: WT IR sample 2 RNA seq

description:
wtl2
hsf2 VS B6 IR RNA seq original.csv

value: Bone Marrow Lin-cKit+ cells

value: WT

value: IR

value: Replicate 2


title: WT IR sample 1 RNA seq

description:
wtl1
hsf2 VS B6 IR RNA seq original.csv

value: Replicate 1


title: Senescent MAF replicate 1


title: Control MAF replicate 3

value: Control MAF


title: 75456-Hic5-Het

value: primary CAFs

value: cancer associated fibroblast


title: Control MAFreplicate 2

value: Control MAFreplicate 2


title: 75219-Hic5-Het

value: heterozygous


title: WT control sample 1 RNA seq

description:
wt1
hsf2 VS B6 IR RNA seq original.csv

value: Control


title: Hepatocytes, Hif1a ko, hfdcdcd, repl 2

description:
69
raw_counts_HC_Hif1a_ko.txt
12619

value: Hif1a ko

value: Adult

value: hfdcd

value: hfdcdcd

value: hfdcdcd_Hif1a ko_Hepatocytes


title: Hepatocytes, Hif1a ko, cdcdcd, repl 4

description:
80
raw_counts_HC_Hif1a_ko.txt
12630

value: liver

value: Hepatocytes

value: cdcd

value: cd

value: cdcdcd

value: cdcdcd_Hif1a ko_Hepatocytes


title: Control MAF replicate 1

value: Primary MAF

value: Mouse adult fibroblast

value: Control MAF


title: 74483-Hic5-KO

value: primary CAFs

value: cancer associated fibroblast

value: knockout


title: Hepatocytes, Hif1a ko, cdcdcd, repl 3

description:
79
raw_counts_HC_Hif1a_ko.txt
12629

value: Hif1a ko


title: Hepatocytes, wt, hfdhfdhfd, repl 1

description:
68
raw_counts_HC_Hif1a_ko.txt
12618

value: wt

value: Adult

value: hfdhfd

value: hfd

value: hfdhfdhfd


title: Lung, Ctrl, rep 3

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina HiSeq4000 sequencer with single 50 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the mm9 mouse reference genome by TopHat2 (Version2.0.11) .
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes read counts at gene level for each sample

source_name: Lung

growth_protocol: To generate the AEC2-specific FASN knockdown mice, FASN loxp/loxp homozygous mice were crossed with SftpcCreERT2+/+ mice to generate FASN loxp/loxp SftpcCreERT2+/- mice (FASNKO). FASN-/- SftpcCreERT2+/- littermates served as controls(Ctrl). All animals were housed in pathogen-free environment in humidity and temperature-controlled rooms on a 12-12-h light-dark cycle. Mice were given food and water freely.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) and was purified by the RNeasy Plus Mini Kit (Qiagen), together with DNA digestion with the RNA free DNase set (Qiagen).RNA quality was determined by 260:280 ratio and the RNA integrity number (RIN) determined by an Agilent Technologies 2100 Bioanalyzer. Only high quality RNA samples with a 260:280 ratio > 1.6 and a RIN > 7 were used for the library construction using the TruSeq Stranded mRNA Library Preparation kit (Illumina), according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen (T5648, Sigma-Aldrich) was prepared as a 20 mg/ml stock solution in sunflower seed oil (S5007, Sigma-Aldrich). Mice were injected once a day for 3 days (100 mg/kg), followed by a 3-day rest period, and then injected again for another 3 days at 5 weeks of age. Age and sex-matched mice were used for experiments after 8 weeks of age.

value: Lung

value: Alveolar type 2 cells

value: Ctrl


title: Lung, Ctrl, rep 2


title: Hepatocytes, wt, cdcdhfd, repl 3

description:
67
raw_counts_HC_Hif1a_ko.txt
12617

value: liver

value: Hepatocytes

value: cdcd

value: cdcdhfd


title: DNase-seq_Tcf7-KO_rep2

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: Tcf7fl/fl-RorcCre #2

data_processing:
Reads were aligned to mouse genome (mm10) with bowtie2 version 2.4.2 (PMID: 22388286)
Peak and FDR were calculated  from SICER  version 2.0 (PMID: 24743992) against mm10 genome
Genome_build: mm10
Supplementary_files_format_and_content: First colum: chrom; second column: start; three column: end; four column: peak_read_count; five column: control_read_count; six column: p_value; seven column: fold_change; eight column: FDR;

source_name: Peyer's patches

extract_protocol:
300 cells from each cell type were collected by fluorescence-activated cell sorting. Then, 40 ul lysis buffer contain 0.3 U DNase I was added to each samples and incubated at 37 °C for 5 minutes. Reactions were stopped by adding stop buffer,  containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 55 °C overnight, and DNA was purified by phenol–chloroform extraction followed by precipitation with ethanol in the presence of 20 μg glycogen.
the Dnase-seq libraries were prepared through as previously described (PMID: 31358996)

value: Peyer's patches

tag: strain


title: DPP-7-WT-2

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Statistical tests for differential expression were performed using sleuth.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual transcripts for each sample as well as statistical results for differential gene abundance between genotypes.

source_name: colonic organoid

growth_protocol: Colonic epithelial crypts were isolated from colons of wildtype or Tnfr2-/- mice, embedded within Matrigel, and grown with a layer of Intesticult media. The resulting organoids were passaged 5 times before filtration through a 70-µm nylon mesh filter and subsequent seeding for the experiment. Organoids of both wildtype and knockout genotypes were isolated at 1, 2, 3, 5, and 7 days post-passage.

extract_protocol:
Organoids were placed in Trizol and homogenized. The Direct-zol kit (Zymo) was used to isolate total RNA.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on a NextSeq High Output Run.

tag: days post passage

value: WT


title: Lung, Ctrl, rep 1


title: DNase-seq_Tcf7-KO_rep1

description: Tcf7fl/fl-RorcCre #1


title: Hepatocytes, Hif1a ko, cdcdhfd, repl 3

description:
66
raw_counts_HC_Hif1a_ko.txt
12616

tag: age

value: cdcdhfd_Hif1a ko_Hepatocytes


title: DPP-7-KO-2


title: DNase-seq_Ctrl_rep2

description: Tcf7+/+ #2


title: Lung, FASNKO, rep 3

value: AEC2-specific FASN knockdown


title: 75957-Hic5-KO

value: primary CAFs

value: cancer associated fibroblast

value: knockout


title: DPP-7-KO-1


title: Lung, FASNKO, rep 2


title: WT control sample 2 RNA seq

description:
wt2
hsf2 VS B6 IR RNA seq original.csv

value: Bone Marrow Lin-cKit+ cells

value: Control

value: Replicate 2


title: DNase-seq_Ctrl_rep1

description: Tcf7+/+ #1