title: RNA_dcp2D_Replicate_1

extract_protocol: For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using Zymo RNA Clean and Concentrator kit. Five µg of total RNA was randomly fragmented by mixing with 2× alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ≈ 9.3). After incubation for 20 min at 95ºC, fragmentation reactions were mixed with ice-cold stop solution (300 mM NaOAc pH 5.5, 30 µg GlycoBlue (Invitrogen; AM9516)). RNA was precipitated by adding one part of isopropanol followed by the standard protocol of precipitation. Fragment size selection, library generation, and sequencing were carried out using the same protocol described above for RPF library preparation, except the Ribo-Zero Gold rRNA Removal Kit (Illumina; MRZ11124C) was employed to remove rRNA after linker-ligation.


title: RNA_dcp2D_Replicate_2

status: Public on Feb 07 2023

type: SRA

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

state: Maryland

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For ribosome profiling and parallel RNA-Sequencing, Raw_counts_Ribo (Ribo-sequencing) and Raw_counts_RNA (RNA-sequencing), each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Whole cells

tag: genotype


title: Stage E6.5 embryo 1 section 3 region P

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo

organism: Mus musculus

source_name: Mouse embryonic cells

growth_protocol: Embryos from pre-gastrulation to late-gastrulation mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

tag: developmental stage

value: Early-gastrulation embryo (E6.5)

tag: tag


title: HT1080_ctrl

type: genomic

city: Hall in Tirol

first: Charlotte

middle: Dafni

last: Vavourakis

state: Tirol

address: Milser Str. 10

department: Research Institute for Biomedical Aging Research

country: Austria

institute: University of Innsbruck

description: HT1080 control

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to  Illumina Human MethylationEPIC methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, ChAMP, impute

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: HT1080, control

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell pellets using the Allprep DNA/RNA/protein mini kit (Qiagen) and Genomic DNA Clean & Concentrator-10 kit (Zymo) according to standard instructions

tag: cell line

tag: growth medium

value: MEM (9.6 g/l) and Sodium Bicarbonate (1.5g/l) solved in A.d., with 10% FCS, 100 U/ml Penicillin, and 100 μg/ml Streptomycin

tag: treatment

value: DMSO


title: RNA_WT_Replicate_2


title: RNA_WT_Replicate_1

extract_protocol: For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using Zymo RNA Clean and Concentrator kit. Five µg of total RNA was randomly fragmented by mixing with 2× alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ≈ 9.3). After incubation for 20 min at 95ºC, fragmentation reactions were mixed with ice-cold stop solution (300 mM NaOAc pH 5.5, 30 µg GlycoBlue (Invitrogen; AM9516)). RNA was precipitated by adding one part of isopropanol followed by the standard protocol of precipitation. Fragment size selection, library generation, and sequencing were carried out using the same protocol described above for RPF library preparation, except the Ribo-Zero Gold rRNA Removal Kit (Illumina; MRZ11124C) was employed to remove rRNA after linker-ligation..


title: Stage E6.5 embryo 1 section 2 region P


title: Stage E6.5 embryo 1 section 2 region A


title: Cal51_apo_L

description: Cal51 late apoptosis

source_name: Cal51, BH3 mims, 20h

value: Nalm6 (CVCL_0092; DSMZ ACC 128)

value: DMEM with 10% FCS, 1% L-Glutamin,100 U/ml Penicillin, 100 μg/ml Streptomycin

value: BH3 mimetics S63845 and ABT-737


title: T_RNA_xrn1D_Replicate_1

extract_protocol: For RNA-seq, total RNA was extracted using hot-phenol method and the library was prepared by NHLBI Sequencing and Genomics Core at NIH (Bethesda, MD) using TruSeq Stranded mRNA Library Prep Kit (Illumina)


title: RNA_dcp2-EE_Replicate_2


title: Ribo_dcp2-EE_Replicate_2

data_processing:
As described earlier (Martin-Marcos et al. 2017), Illumina sequencing reads were trimmed to remove the constant adapter sequence, mixed sample sequences were separated by the sample barcodes followed by removal of PCR duplicates using a custom Python (3.7) script. The sequences aligned to yeast non-coding RNAs were removed using bowtie (Langmead et al., 2009) and non-rRNA reads (unaligned reads) were then mapped to the S. cerevisiae genome (R64-1-1 S288C Saccer3 Genome Assembly) using TopHat (Trapnell et al., 2009). Only uniquely mapped reads from the final genomic alignment were used for subsequent analyses. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq, the same protocol mentioned above for ribo-seq analysis was followed.
The sequenced CAGE reads of each sample were aligned to the reference genome of S. cerevisiae S288c (Assembly version: sacCer3) using HISAT2. CAGE reads mapped to rRNA genes were identified using rRNAdust (http://fantom.gsc.riken.jp/5/sstar/Protocols:rRNAdust), and were excluded from subsequent TSS analyses. CAGE reads with a mapping quality score (MAPQ) > 20 were considered uniquely mapped reads and were used for subsequent analyses. CAGE signals of biological replicates were then merged as a single sample. The transcription abundance of each TSS was quantified as the numbers of CAGE tags/reads supporting the TSS per million mapped reads (TPM). For RNA-Seq samples in parallel with CAGE-Seq, Fastq files after passing the QC and the adapter content check they were mapped to yeast genome (sacCer3) with STAR aligner, then PCR duplicates were removed by samtools.
Assembly: sacCer3
Supplementary files format and content: Processed data (csv) files contain raw reads for each file. For ribosome profiling and parallel RNA-Sequencing, Raw_counts_Ribo (Ribo-sequencing) and Raw_counts_RNA (RNA-sequencing), each file contains five columns providing: systemmatic gene name (Gene_ID), total reads (trx), reads in CDS, reads in 5' UTR and reads in 3' UTR. Foe CAGE-sequencing and parallel RNA-Sequencing, each file contains two columns providing: systemmatic gene name (Gene_ID), total reads.
Library strategy: Ribosome profiling

molecule: polyA RNA

extract_protocol: Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "Reprogramming of translation in yeast cells impaired for ribosome recycling favors short, efficiently translated mRNAs" Gaikwad, Ghobakhlou, et al. eLife 2021;10:e64


title: Cal51_ctrl

description: Cal51 control

source_name: Cal51, control


title: Stage E6.5 embryo 1 section 1 region A/P


title: Stage E7.5 embryo 6 section 9 region MA

description: E7.5_E7_all.samples.genes.revise.fpkm.txt

value: Late-gastrulation embryo (E7.5)


title: Ribo_dcp2-EE_Replicate_1


title: Stage E7.5 embryo 6 section 9 region MP


title: Nalm6_apo_E_extra_1

description: extra sample

source_name: Nalm6, extra

value: RPMI-1640 with 10% FCS, 1% L-Glutamin, 100 U/ml Penicillin, and 100 μg/ml Streptomycin


title: Stage E7.5 embryo 6 section 9 region EP


title: Ribo_dcp2D_Replicate_2


title: Cal51_apo_E

description: Cal51 early apoptosis

source_name: Cal51, BH3 mims, 10h


title: Stage E6.5 embryo 1 section 7 region P


title: Renal Control group replicate3

type: RNA

city: 泉州

first: 清石

last: 陈

state: 福建省

address: 福建省泉州市鲤城区中山北路34号

institute: 医科大学附属第二医院

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: renal tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: We placed mice assigned to receive CIH in a specially designed chamber, which contained oxygen sensors for measuring the concentration of O2 in the chamber. Cages were connected to a gas regulator that controls the infusion of sufficient nitrogen to reduce O2 to 6% for 60 seconds, after which the gas control system allows for a rapid replacement of oxygen leading to a quick restoration of O2 to 21% for another 60 seconds. This 2-minutes CIH cycle was repeated 30 times per h, 8 h/day, for a total duration of 8 weeks.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tissues from pancreatic tissues and promptly cooled at -80℃ refrigerator.

tag: tissue

value: kidney

tag: strain

value: BALB/c


title: Stage E7.5 embryo 6 section 9 region P


title: Renal Control group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: Ribo_dcp2D_Replicate_1


title: Stage E7.5 embryo 6 section 9 region D2


title: Renal Control group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: Stage E6.5 embryo 2 section 5 region A


title: Stage E7.5 embryo 6 section 9 region C1


title: Stage E6.5 embryo 1 section 6 region P


title: Stage E7.5 embryo 6 section 9 region D1


title: HeLa_apo_E

description: HeLa early apoptosis

source_name: HeLa, BH3 mims, 6h

value: HelaS3 (CVCL_0058; DSMZ ACC 161)


title: Stage E7.5 embryo 6 section 9 region EA


title: Stage E7.5 embryo 6 section 9 region C2


title: Ribo_WT_Replicate_2


title: Renal CIH groupn replicate3

address: 福建省泉州市鲤城区中山北路34号


title: Stage E7.5 embryo 6 section 8 region PE


title: Stage E7.5 embryo 6 section 9 region A


title: Nalm6_apo_L_extra_2

description: extra sample


title: SAM3

city: Jinan

first: Shan

last: Han

address: Wenhua West road

institute: Shandong University

data_processing:
BGISEQ software used for basecalling.
We used Bowtie2 to align Clean reads to the reference gene sequence and then used RSEM to calculate gene expression levels for individual samples.
The DEseq2 method is based on the principle of negative binomial distribution and this project is based on the method described in Michael I, et al for differential gene DEG.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with raw gene counts for every gene and every sample

extract_protocol:
1 μg of total RNA was subjected to library synthesis using RNeasy Mini Kit (Qiagen, Hiden,  Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pancreas beta cell line Min6

value: Thada-activated


title: Ribo_WT_Replicate_1


title: Stage E7.5 embryo 6 section 8 region P


title: Stage E7.5 embryo 6 section 8 region MA


title: Renal CIH group replicate2

address: 福建省泉州市鲤城区中山北路34号


title: Renal CIH group replicate1

address: 福建省泉州市鲤城区中山北路34号


title: SAMP-1138: Pre-T2D

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: Genomic DNA extracted from human islet was genotyped using InfiniumOmni2-5-8v1-4 Genotyping BeadChips (Illumina).

hyb_protocol: 200-500ng DNA was genotyped using InfiniumOmni2-5-8v Genotyping BeadChips (Illumina).

scan_protocol: not provided

data_processing: Genotypes were called with GenomeStudio (v.2.0.4) using default settings. Genotypes that passed quality filters (missing<0.05, minor allele frequency (MAF>0.01), non-ambiguous alleles defined by AT/GC variants with MAF>40%) were exported.

label: Cy3, Cy5

source_name: Islets

label_protocol: not provided

extract_protocol: Genomic DNA was extracted from human islets using Dneasy Blood & Tissue Kit (QIAGEN) with RNase A treatment.

tag: disease state

tag: ID

tag: age

tag: gender

value: M

tag: race

value: Caucasian

tag: bmi

tag: islet index

tag: purity

value: islets


title: SAMP-1611: T2D

value: F

value: Hispanic


title: SAM1


title: Stage E7.5 embryo 6 section 8 region EP


title: Stage E7.5 embryo 6 section 8 region MP


title: SAMP-1097: T2D


title: SAM2


title: Stage E7.5 embryo 6 section 8 region EA


title: Stage E7.5 embryo 6 section 7 region P


title: CON3

value: control


title: SAMP-692: Non-diabetic

value: Non-diabetic


title: Stage E7.5 embryo 6 section 7 region PE


title: CON2


title: A0015: Pre-T2D

description: Genomic DNA extracted from human islet was genotyped using InfiniumOmni2-5-8v1-5 Genotyping BeadChips (Illumina).


title: Stage E7.5 embryo 6 section 7 region MP


title: Stage E7.5 embryo 6 section 7 region MA


title: A0007: Non-diabetic


title: Stage E7.5 embryo 6 section 7 region EP


title: Stage E7.5 embryo 6 section 7 region EA


title: CON1


title: SAMP-1143: T2D

value: Asian


title: Stage E7.5 embryo 6 section 6 region EP


title: Stage E7.5 embryo 6 section 6 region P


title: SAMP-1697: Non-diabetic

value: Hispanic/Latino


title: SAMP-1696: Non-diabetic

value: White


title: Stage E7.5 embryo 6 section 6 region MA

value: Late-gastrulation embryo (E7.5)


title: Stage E7.5 embryo 6 section 7 region EA suppl


title: Stage E7.5 embryo 6 section 6 region EA


title: Stage E7.5 embryo 6 section 6 region D2


title: T_RNA_WT_Replicate_1


title: REF strain (rep1)

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent) and for 1 min  with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Log-phase rep1

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Precultures of boron stress resistant Saccharomyces cerevisiae (BA8) mutant strain and reference strain were prepared in yeast minimal medium (2% glucose and 0.67% yeast nitrogen base without amino acid (Difco)) by incubating at 30°C and 150 rpm for about 16 hours. Precultures were inoculated into fresh yeast minimal medium to an initial OD600 of 0.1. Cultures were then incubated at 30°C and 150 rpm. When the OD600 values of the cultures reached about 1.0 (corresponding to mid-exponential phase), cells were harvested and total RNA extraction was done.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: There is no treatment protocol in this study.

value: Reference strain


title: Stage E6.5 embryo 1 section 5 region P

value: Early-gastrulation embryo (E6.5)


title: Stage E7.5 embryo 6 section 6 region D1


title: REF strain (rep2)

source_name: Log-phase rep2


title: Stage E7.5 embryo 6 section 6 region C2


title: REF strain (rep3)

source_name: Log-phase rep3


title: SAMP-1606: Non-diabetic


title: Stage E7.5 embryo 6 section 5 region P


title: Stage E7.5 embryo 6 section 6 region A


title: Stage E7.5 embryo 6 section 6 region C1


title: Stage E7.5 embryo 6 section 6 region MP


title: Stage E7.5 embryo 6 section 5 region MP


title: Stage E7.5 embryo 6 section 5 region MA


title: SAMP-1503: T2D


title: BA8-mutant Log phase-Rep 3

description: Gene expression in the log phase of cell growth

source_name: Boron resistant Saccharomyces cerevisiae, log. Phase, replicate 3

value: CEN.PK 113.7D (MATa)


title: Stage E7.5 embryo 6 section 5 region EA


title: SAMP-1498: Pre-T2D

value: Hispanic Latino


title: BA8-mutant Log phase-Rep 2

source_name: Boron resistant Saccharomyces cerevisiae, log. Phase, replicate 2


title: BA8-mutant Log phase-Rep 1

source_name: Boron resistant Saccharomyces cerevisiae, log. Phase, replicate 1


title: Stage E7.5 embryo 6 section 4 region P


title: SAMP-1695: Non-diabetic


title: Stage E6.5 embryo 2 section 3 region A


title: Stage E7.5 embryo 6 section 4 region MP


title: S1C_047

city: Beijing

first: Jiaqi

last: Xin

address: No.11 Xitoutiao outside You’anmen

institute: CCMU

data_processing:
DSP sequencing data were processed with the GeoMx NGS Pipeline (DND). After sequencing, reads were trimmed, merged, and aligned to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicates and duplicate reads, thus converting reads into digital counts. The limit of quantitation (LOQ) was estimated as the geometric mean of the negative control probes plus 2 geometric standard deviations of the negative control probes. Targets were removed that consistently fell below the LOQ, and the datasets were normalized using upper quartile (Q3) normalization.
Assembly: Readout Tag Sequence ID of the probes can be aligned back to gene target via .pkc file
Supplementary files format and content: .dcc: quantitative results of the probe of each ROI

source_name: zone 1 of sham group

growth_protocol: 6-8weeks male C57BL/6J mice were housed in specific pathogen-free animal facility with free access to water and diet.

extract_protocol:
The left lateral liver lobes were extracted and prepared for FFPE slides. The slides were processed following Manual RNA Slide Preparation Protocol (NanoString, MAN-10115-05 for software v2.3). Briefly, the slides were baked at 60°C for 30min before deparaffinization, rehydration and target retrieval. To expose tissue RNA targets, slides were incubated with 1 ug/mL proteinase K (Ambion, 2546) and the Whole Transcriptome Atlas (WTA) probe reagent at 37°C in a humidified HybEZ II System for 15h. The following day, the optimal diluted solutions of morphology markers, including panCK, CD45 and nuclear staining SYTO13 (Nanostring), were used for distinguishing cell types and degrees of damage. After selecting ROIs, the bound RNA probes were photocleaved and individual segmented areas were collected for sequencing before amplifying Illumina sequencing libraries.
AMPure XP beads (Beckman Coulter, A63880) were used to purify PCR reactions at a 1.2× bead-to-sample ratio. DNA high sensitivity bioanalyzer assay (Agilent Technologies) and Qubit dsDNA high sensitivity assay (Thermo Fisher Scientific) were used to evaluate the size and concentration of the sequencing library. Total target counts were calculated from the total sampled areas (μm2) and the sequencing depths were 100 counts / μm2. All sequencing libraries were generated with index uniquely, which were allowed to be pooled together for sequencing.
After loaded at a concentration of 365 pM with 5% PhiX, WTA libraries were sequenced with an Illumina NovaSeq 6000 platform under the following parameters: read 1, 27 cycles; read 2, 27 cycles; index 1, 8 cycles; index 2, 8 cycles.

treatment_protocol: The mice were laparotomized and a microvascular clamp was placed on the left and middle portal vein branches in the liver to interrupt blood flow to the left and middle liver lobes. Reperfusion was achieved by removing the clamp 1h after clamping. The mice were sacrificed 6h after reperfusion and liver samples were collected. Celastrol-treated mice were intraperitoneally injected with 0.3 mg/kg celastrol for one week and underwent the above I/R treatment.

value: liver

value: wild type

value: sham


title: S3C_046

source_name: zone 3 of sham group


title: Stage E7.5 embryo 6 section 4 region MA

source_name: Mouse embryonic cells


title: SAMP-1608: T2D

value: M


title: SAMP-1605: T2D

value: islets


title: Stage E7.5 embryo 6 section 4 region EP


title: SAMP-1150: T2D

value: F


title: Stage E7.5 embryo 6 section 4 region EA


title: S2C_045

source_name: zone 2 of sham group


title: C3_001

source_name: zone 3 of celastrol group

value: 0.3 mg/kg celastrol-treated for one week before 1h ischemia and 6h reperfusion


title: Stage E7.5 embryo 6 section 3 region MP


title: Stage E7.5 embryo 6 section 3 region P


title: S1C_043


title: SAMP-1137: Non-diabetic


title: Stage E7.5 embryo 6 section 3 region MA


title: Stage E7.5 embryo 6 section 3 region EP


title: SAMP-1148: T2D

value: Black or African American


title: RNA_dcp2-EE_Replicate_1

source_name: Whole cells


title: S2C_042


title: Stage E7.5 embryo 6 section 5 region EP


title: S3C_044


title: Stage E7.5 embryo 6 section 3 region D1


title: Stage E7.5 embryo 6 section 3 region D2


title: SAMP-1142: Pre-T2D


title: S3C_041


title: Stage E7.5 embryo 6 section 3 region C2


title: S1C_040


title: SAMP-1141: Pre-T2D


title: Stage E7.5 embryo 6 section 3 region A


title: Stage E7.5 embryo 6 section 3 region C1


title: SAMP-1607: T2D


title: Stage E7.5 embryo 6 section 2 region MA


title: S2C_039


title: SAMP-1149: T2D


title: S1C_038


title: Stage E7.5 embryo 6 section 2 region MP


title: SAMP-1501: Non-diabetic

value: Non-diabetic

value: Caucasian


title: S3C_037


title: Stage E7.5 embryo 6 section 2 region EP


title: Stage E7.5 embryo 6 section 3 region EA


title: SAMP-1499: T2D


title: SAMP-1139: Pre-T2D

value: Hispanic


title: Stage E7.5 embryo 6 section 10 region MP


title: SAMP-1500: Pre-T2D


title: Stage E7.5 embryo 6 section 1 region P


title: Stage E7.5 embryo 6 section 10 region MA


title: Stage E7.5 embryo 6 section 1 region EA/EP


title: Stage E7.5 embryo 6 section 10 region P


title: SAMP-1136: Non-diabetic


title: Stage E7.5 embryo 6 section 10 region EP


title: Stage E7.5 embryo 6 section 2 region EA


title: SAMP-1612: Non-diabetic


title: Stage E7.5 embryo 6 section 10 region EA


title: S2C_036


title: S1C_034


title: S3C_035


title: S2C_033


title: Stage E7.5 embryo 6 section 2 region P


title: SAMP-1145: T2D

value: White


title: S1C_032


title: S3C_031


title: Stage E7.5 embryo 5 section 9 region EA

value: Late-gastrulation embryo (E7.5)


title: Stage E7.5 embryo 5 section 9 region EP


title: Stage E7.5 embryo 5 section 9 region D2


title: S2C_030


title: Stage E7.5 embryo 5 section 9 region P


title: Stage E7.5 embryo 5 section 9 region A


title: Stage E7.5 embryo 5 section 9 region D1


title: SAMP-1135: Non-diabetic


title: S1C_028


title: Stage E7.5 embryo 5 section 9 region C2


title: SAMP-1144: T2D


title: S3C_029


title: SAMP-1609: Pre-T2D


title: Stage E7.5 embryo 5 section 9 region MP


title: Stage E7.5 embryo 5 section 9 region MA


title: Stage E7.5 embryo 5 section 9 region C1


title: Stage E7.5 embryo 5 section 8 region MA


title: S2C_027


title: Stage E7.5 embryo 5 section 8 region EP


title: Stage E7.5 embryo 5 section 8 region P


title: Stage E7.5 embryo 5 section 7 region P


title: Stage E7.5 embryo 5 section 7 region MP


title: SAMP-1610: T2D


title: S3C_026


title: Stage E7.5 embryo 5 section 8 region EA


title: SAMP-1134: Non-diabetic


title: TXNIP-null in MB135 cells, rep 2

city: Salt Lake City

first: Donald

last: Ayer

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
STAR was used to align the reads to GRCh38/hg38. FeatureCounts was used to obtain read counts for each gene.
Assembly: hg38
Supplementary files format and content: counts

growth_protocol: Parental HCC70 and HCC70:TKO cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 Medium (Thermo Fisher Scientific; 11875119) with 10% Fetal Bovine Serum (FBS) (Gibco; A3160506), 10 mM N-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid (HEPES) (Thermo Fisher Scientific; 15630080) and 1 mM sodium pyruvate (Invitrogen; 11360070). MB135 [33] and MB135:TKO cells were cultured in Ham’s F10 with L-glutamine (ThermoFisher; 11550043) with 20% FBS (Gibco; A3160506), 1X Penicillin-streptomycin (Gibco; 15140148), 10ng/ml recombinant human Fibroblast Growth Factor (Promega; G5071) and 1 µM dexamethasone (Sigma-Aldrich; D4902 ). For differentiation, MB135 and MB135:TKO cells were cultured in Ham’s F10 with L-glutamine (ThermoFisher; 11550043), 1X heat-inactivated horse serum (Sigma-Aldrich; H1270), 1X Penicillin-streptomycin (Gibco; 15140148), 10 µg/ml insulin from bovine pancreas (Sigma-Aldrich; I-1882) and 10 µg/ml transferrin (Sigma-Aldrich; T-0665).

extract_protocol:
Total RNA was extracted from 3X106 cells using the Zymo Research Quick RNA miniprep kit (Zymo Research; R1055).
500 ng of total RNA was used to capture mRNA and construct library using KAPA Stranded mRNA-Seq Kit (KAPA Biosystems; KK8420) according to the manufacturer’s protocol. Briefly, after mRNA capturing and fragmentation, cDNA was synthesized. Sequencing adaptors were ligated to the cDNA fragments. The adaptor-ligated cDNA fragments were amplified with library PCR primers that contain barcodes for about 10 cycles.

treatment_protocol: HCC70:TKO and MB135:TKO cells were generated using human TXNIP CRISPR/Cas9 KO plasmid, three TXNIP-specific guide RNA sequences from GeCKO (v2) library (Santa Cruz; sc-400664) and a homology-directed repair (HDR) construct containing a puromycin-resistance cassette (Santa Cruz; sc-400664-HDR). TKO cells were isolated following selection of cells in 2.5 µg/mL puromycin. Loss of TXNIP was verified by immunoblotting.

tag: cell type

value: human myoblast

value: TXNIP knockout


title: SAMP-1613: Pre-T2D


title: Stage E7.5 embryo 5 section 7 region MA


title: S1_024

tag: genotype


title: S1C_025


title: Stage E7.5 embryo 5 section 8 region MP

tag: developmental stage


title: SAMP-1151: T2D


title: Stage E7.5 embryo 5 section 6 region P

tag: tag


title: Stage E7.5 embryo 5 section 7 region EA


title: S2_023


title: Stage E7.5 embryo 5 section 6 region MA


title: parental MB135 cells, rep 2

tag: cell line

value: wild-type


title: Stage E7.5 embryo 5 section 6 region EP


title: Stage E7.5 embryo 5 section 6 region D1


title: S2_021


title: S1_019


title: Stage E7.5 embryo 5 section 6 region D2


title: Stage E7.5 embryo 5 section 7 region EP


title: Stage E7.5 embryo 5 section 6 region A


title: parental MB135 cells, rep 1


title: Stage E7.5 embryo 5 section 6 region C2


title: TXNIP-null in HCC70 cells, rep 3

value: triple-negative breast cancer


title: Stage E7.5 embryo 5 section 6 region EA


title: Stage E7.5 embryo 5 section 5 region P


title: S1_018

value: liver


title: Stage E7.5 embryo 5 section 6 region C1


title: S2_017

value: wild type


title: TXNIP-null in HCC70 cells, rep 1


title: Stage E7.5 embryo 5 section 5 region MA


title: TXNIP-null in HCC70 cells, rep 2


title: TXNIP-null in MB135 cells, rep 1


title: Stage E7.5 embryo 5 section 6 region MP


title: S3_022

value: sham


title: parental HCC70 cells, rep 3


title: Stage E7.5 embryo 5 section 5 region EP


title: S3_020


title: Stage E7.5 embryo 5 section 5 region EA


title: parental HCC70 cells, rep 2


title: S3_016


title: Stage E7.5 embryo 5 section 4 region P


title: S3_015


title: Stage E7.5 embryo 5 section 4 region EP


title: S2_014


title: parental HCC70 cells, rep 1


title: Stage E7.5 embryo 5 section 3 region MP


title: Stage E7.5 embryo 5 section 4 region EA


title: Stage E7.5 embryo 5 section 4 region MA


title: Stage E7.5 embryo 5 section 3 region P


title: Stage E7.5 embryo 5 section 3 region EP


title: Stage E7.5 embryo 5 section 3 region EA


title: S1_012


title: Stage E7.5 embryo 5 section 4 region MP


title: 79_79_GBF2021_G-15min-79

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

description: 79_79_GBF2021_G-15min-79_S79_R1_001_val_1.fqAligned.sortedByCoord.out.bam

data_processing:
demultiplexing with standard Illumina tool
trimming with TrimGalore 0.6.5
aligning with STAR 2.7.3a
featureCounts 2.0.1
DESeq2 1.28.1
Assembly: hg38
Supplementary files format and content: featureCounts output, raw counts in a table

source_name: in vitro immortalized cells

growth_protocol: Jurkat T cells (ATCC Manassas, USA, Clone E6-1, TIB152™) were cultured in RPMI 1640 (Biochrom, Berlin, Germany Cat. Nr FG1215) medium, supplemented with 10% FCS and 1% Pen/Strep. Split every second day.

extract_protocol:
Elusion/addition of RLT buffer, RNA extraction with commercial RNEasy Mini-kit
E7400X,  NEBNext rRNA Depletion Kit v2, E7765L NEBNext Ultra II Directional RNA Library Prep with Beads
Depletion of rRNA but covering nascent transcripts

value: in vitro immortalized cells

value: T lymphocyte

value: Jurkat T cells

tag: centrifuge


title: 77_77_GBF2021_G-15min-77

description: 77_77_GBF2021_G-15min-77_S77_R1_001_val_1.fqAligned.sortedByCoord.out.bam

tag: treatment


title: Stage E7.5 embryo 5 section 3 region D2


title: Stage E7.5 embryo 5 section 3 region MA


title: S3_010

tag: tissue


title: 80_80_GBF2021_G-15min-80

description: 80_80_GBF2021_G-15min-80_S80_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 5 section 5 region MP


title: 78_78_GBF2021_G-15min-78

description: 78_78_GBF2021_G-15min-78_S78_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 76_76_GBF2021_G-15min-76

description: 76_76_GBF2021_G-15min-76_S76_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 5 section 3 region D1


title: S3_009

tag: strain


title: Stage E7.5 embryo 5 section 3 region C2


title: Stage E7.5 embryo 5 section 3 region C1


title: Stage E7.5 embryo 5 section 3 region A


title: 75_75_GBF2021_G-15min-75

description: 75_75_GBF2021_G-15min-75_S75_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: S1_013


title: S2_008


title: Stage E7.5 embryo 5 section 2 region P


title: S2_011


title: Stage E7.5 embryo 5 section 2 region MP


title: Stage E7.5 embryo 5 section 2 region MA


title: Stage E7.5 embryo 5 section 2 region EP


title: S3_006


title: Stage E7.5 embryo 5 section 2 region EA


title: S1_005


title: Stage E7.5 embryo 5 section 1 region P


title: Stage E7.5 embryo 5 section 1 region EA/EP


title: 71_71_GBF2021_G-3min-71

description: 71_71_GBF2021_G-3min-71_S71_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 5 section 10 region MP


title: 70_70_GBF2021_G-3min-70

description: 70_70_GBF2021_G-3min-70_S70_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: S2_004


title: Stage E7.5 embryo 5 section 10 region P


title: S3_003


title: 69_69_GBF2021_G-3min-69

description: 69_69_GBF2021_G-3min-69_S69_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 5 section 10 region EP


title: Stage E7.5 embryo 5 section 10 region MA


title: 74_74_GBF2021_G-3min-74

description: 74_74_GBF2021_G-3min-74_S74_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 5 section 10 region EA


title: S2_002


title: Stage E7.5 embryo 4 section 9 region P


title: S1_007


title: S1_001


title: 68_68_GBF2021-Achilles_A-heat-68

description: 68_68_GBF2021-Achilles_A-heat-68_S68_R1_001_val_1.fqAligned.sortedByCoord.out.bam

value: heat


title: Stage E7.5 embryo 4 section 9 region M1


title: 73_73_GBF2021_G-3min-73

description: 73_73_GBF2021_G-3min-73_S73_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 72_72_GBF2021_G-3min-72

description: 72_72_GBF2021_G-3min-72_S72_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 67_67_GBF2021-Achilles_A-heat-67

description: 67_67_GBF2021-Achilles_A-heat-67_S67_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 9 region E2


title: Stage E7.5 embryo 4 section 9 region D2


title: Stage E7.5 embryo 4 section 9 region E1


title: V2C_068

source_name: zone 2 of I/R group

value: 1h ischemia and 6h reperfusion


title: V3C_067

source_name: zone 3 of I/R group


title: Stage E7.5 embryo 4 section 9 region D1


title: Stage E7.5 embryo 4 section 9 region C2


title: Stage E7.5 embryo 4 section 9 region C1


title: Stage E7.5 embryo 4 section 9 region A


title: V3C_065


title: Stage E7.5 embryo 4 section 9 region M2


title: V2C_064


title: V1C_063

source_name: zone 1 of I/R group


title: Stage E7.5 embryo 4 section 8 region E2


title: Stage E7.5 embryo 4 section 8 region M1


title: Stage E7.5 embryo 4 section 8 region P


title: Stage E7.5 embryo 4 section 8 region M2


title: Stage E7.5 embryo 4 section 8 region E1


title: V2C_062


title: Stage E7.5 embryo 4 section 7 region P


title: Stage E7.5 embryo 4 section 7 region M2


title: Stage E7.5 embryo 4 section 7 region M1


title: Stage E7.5 embryo 4 section 7 region E1


title: Stage E7.5 embryo 4 section 7 region E2


title: V1C_066


title: V3C_061


title: V1C_060


title: 63_63_GBF2021-Achilles_A-15min-63

description: 63_63_GBF2021-Achilles_A-15min-63_S63_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 60_60_GBF2021-Achilles_A-4min-60

description: 60_60_GBF2021-Achilles_A-1min-60_S60_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 66_66_GBF2021-Achilles_A-heat-66

description: 66_66_GBF2021-Achilles_A-heat-66_S66_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 62_62_GBF2021-Achilles_A-15min-62

description: 62_62_GBF2021-Achilles_A-15min-62_S62_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 64_64_GBF2021-Achilles_A-15min-64

description: 64_64_GBF2021-Achilles_A-15min-64_S64_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 65_65_GBF2021-Achilles_A-heat-65

description: 65_65_GBF2021-Achilles_A-heat-65_S65_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 58_58_GBF2021-Achilles_A-4min-58

description: 58_58_GBF2021-Achilles_A-1min-58_S58_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 61_61_GBF2021-Achilles_A-15min-61

description: 61_61_GBF2021-Achilles_A-15min-61_S61_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 59_59_GBF2021-Achilles_A-4min-59

description: 59_59_GBF2021-Achilles_A-1min-59_S59_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 6 region M2


title: Stage E7.5 embryo 4 section 6 region M1


title: Stage E7.5 embryo 4 section 6 region P


title: 57_57_GBF2021-Achilles_A-4min-57

description: 57_57_GBF2021-Achilles_A-1min-57_S57_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 6 region E2


title: V3C_058


title: 56_56_GBF2021-Achilles_A-1min-56

description: 56_56_GBF2021-Achilles_A-instant-56_S56_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V1C_057


title: Stage E7.5 embryo 4 section 6 region E1


title: Stage E7.5 embryo 4 section 6 region D1


title: Stage E7.5 embryo 4 section 6 region D2


title: 55_55_GBF2021-Achilles_A-1min-55

description: 55_55_GBF2021-Achilles_A-instant-55_S55_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 6 region C2


title: V2C_056


title: Stage E7.5 embryo 4 section 6 region C1


title: Stage E7.5 embryo 4 section 6 region A


title: 54_54_GBF2021-Achilles_A-1min-54

description: 54_54_GBF2021-Achilles_A-instant-54_S54_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 5 region M2


title: 52_52_GBF2021-Achilles_A-Ctrl-52

description: 52_52_GBF2021-Achilles_A-Ctrl-52_S52_R1_001_val_1.fqAligned.sortedByCoord.out.bam

value: Ctrl


title: 53_53_GBF2021-Achilles_A-1min-53

description: 53_53_GBF2021-Achilles_A-instant-53_S53_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 51_51_GBF2021-Achilles_A-Ctrl-51

description: 51_51_GBF2021-Achilles_A-Ctrl-51_S51_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 5 region E2


title: V2C_059


title: Stage E7.5 embryo 4 section 5 region M1


title: V1C_054


title: V3C_055


title: Stage E7.5 embryo 4 section 5 region P


title: Stage E7.5 embryo 4 section 4 region P


title: Stage E7.5 embryo 4 section 4 region M1


title: V2C_053


title: Stage E7.5 embryo 4 section 4 region M2


title: V1C_051


title: V3C_052


title: Stage E7.5 embryo 4 section 4 region E2


title: V2C_050


title: Stage E7.5 embryo 4 section 3 region M2


title: Stage E7.5 embryo 4 section 3 region P


title: Stage E7.5 embryo 4 section 4 region E1


title: 49_49_GBF2021-Achilles_A-Ctrl-49

description: 49_49_GBF2021-Achilles_A-Ctrl-49_S49_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 48_48_GBF2021_G-60min-48

description: 48_48_GBF2021_G-60min-48_S48_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 3 region M1


title: 47_47_GBF2021_G-60min-47

description: 47_47_GBF2021_G-60min-47_S47_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 5 region E1


title: V3C_049


title: Stage E7.5 embryo 4 section 3 region E2


title: V1C_048


title: 46_46_GBF2021_G-60min-46

description: 46_46_GBF2021_G-60min-46_S46_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V2_047


title: Stage E7.5 embryo 4 section 3 region E1


title: 50_50_GBF2021-Achilles_A-Ctrl-50

description: 50_50_GBF2021-Achilles_A-Ctrl-50_S50_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 3 region D2


title: Stage E7.5 embryo 4 section 3 region C1


title: Stage E7.5 embryo 4 section 2 region P


title: Stage E7.5 embryo 4 section 3 region D1


title: 45_45_GBF2021_G-60min-45

description: 45_45_GBF2021_G-60min-45_S45_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 44_44_GBF2021_G-60min-44

description: 44_44_GBF2021_G-60min-44_S44_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 43_43_GBF2021_G-60min-43

description: 43_43_GBF2021_G-60min-43_S43_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 3 region A


title: V3_046


title: Stage E7.5 embryo 4 section 3 region C2


title: Stage E7.5 embryo 4 section 2 region M2


title: V1_045


title: V2_044


title: Stage E7.5 embryo 4 section 2 region M1


title: Stage E7.5 embryo 4 section 2 region E1


title: 42_42_GBF2021_G-9min-42

description: 42_42_GBF2021_G-9min-42_S42_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 41_41_GBF2021_G-9min-41

description: 41_41_GBF2021_G-9min-41_S41_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V3_043


title: V1_042


title: Stage E7.5 embryo 4 section 1 region P


title: 40_40_GBF2021_G-9min-40

description: 40_40_GBF2021_G-9min-40_S40_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 4 section 10 region P


title: Stage E7.5 embryo 4 section 10 region M2


title: V2_041


title: Stage E7.5 embryo 4 section 10 region E2


title: 39_39_GBF2021_G-9min-39

description: 39_39_GBF2021_G-9min-39_S39_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 9 region R2


title: Stage E7.5 embryo 3 section 9 region R1


title: Stage E7.5 embryo 4 section 10 region E1


title: 38_38_GBF2021_G-9min-38

description: 38_38_GBF2021_G-9min-38_S38_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 37_37_GBF2021_G-9min-37

description: 37_37_GBF2021_G-9min-37_S37_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 9 region L2


title: Stage E7.5 embryo 3 section 9 region L1


title: 36_36_GBF2021_G-7min-36

description: 36_36_GBF2021_G-7min-36_S36_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 9 region A


title: V2_029


title: Stage E7.5 embryo 3 section 9 region P


title: 35_35_GBF2021_G-7min-35

description: 35_35_GBF2021_G-7min-35_S35_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V1_040


title: Stage E7.5 embryo 3 section 8 region R2


title: V1_027


title: V3_039


title: Stage E7.5 embryo 4 section 2 region E2


title: V3_028


title: Stage E7.5 embryo 3 section 8 region R1


title: 34_34_GBF2021_G-7min-34

description: 34_34_GBF2021_G-7min-34_S34_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V3_026


title: Stage E7.5 embryo 4 section 10 region M1


title: 33_33_GBF2021_G-7min-33

description: 33_33_GBF2021_G-7min-33_S33_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 8 region L2


title: V1_025


title: Stage E7.5 embryo 3 section 8 region A


title: 32_32_GBF2021_G-7min-32

description: 32_32_GBF2021_G-7min-32_S32_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 7 region R2


title: Stage E7.5 embryo 3 section 7 region R1


title: V3_014


title: Stage E7.5 embryo 3 section 7 region L2


title: 31_31_GBF2021_G-7min-31

description: 31_31_GBF2021_G-7min-31_S31_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 7 region L1


title: V2_015


title: V1_013


title: 30_30_GBF2021_G-5min-30

description: 30_30_GBF2021_G-5min-30_S30_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 6 region R2


title: 29_29_GBF2021_G-5min-29

description: 29_29_GBF2021_G-5min-29_S29_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 6 region R1


title: 28_28_GBF2021_G-5min-28

description: 28_28_GBF2021_G-5min-28_S28_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V2_009


title: Stage E7.5 embryo 3 section 7 region A


title: Stage E7.5 embryo 3 section 8 region P


title: 27_27_GBF2021_G-5min-27

description: 27_27_GBF2021_G-5min-27_S27_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 8 region L1


title: V3_008


title: Stage E7.5 embryo 3 section 6 region L2


title: Stage E7.5 embryo 3 section 6 region L1


title: Stage E7.5 embryo 3 section 6 region A


title: Stage E7.5 embryo 3 section 5 region R2


title: V1_007


title: 26_26_GBF2021_G-5min-26

description: 26_26_GBF2021_G-5min-26_S26_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 7 region P


title: 25_25_GBF2021_G-5min-25

description: 25_25_GBF2021_G-5min-25_S25_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 5 region P


title: V3_005


title: Stage E7.5 embryo 3 section 6 region P


title: Stage E7.5 embryo 3 section 5 region L2


title: 24_24_GBF2021_G-75s-24

description: 24_24_GBF2021_G-75s-24_S24_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V1_004


title: Stage E7.5 embryo 3 section 5 region L1


title: 23_23_GBF2021_G-75s-23

description: 23_23_GBF2021_G-75s-23_S23_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 5 region A


title: Stage E7.5 embryo 3 section 4 region R2


title: Stage E7.5 embryo 3 section 5 region R1


title: V2_006


title: 21_21_GBF2021_G-75s-21

description: 21_21_GBF2021_G-75s-21_S21_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V2_003


title: Stage E7.5 embryo 3 section 4 region P


title: Stage E7.5 embryo 3 section 3 region R2


title: Stage E7.5 embryo 3 section 4 region L1


title: 20_20_GBF2021_G-75s-20

description: 20_20_GBF2021_G-75s-20_S20_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: V1_001


title: Stage E7.5 embryo 3 section 4 region A


title: V3_002


title: Stage E7.5 embryo 3 section 4 region L2


title: Stage E7.5 embryo 3 section 4 region R1


title: 19_19_GBF2021_G-75s-19

description: 19_19_GBF2021_G-75s-19_S19_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 3 region P


title: C3C_047

value: 0.3 mg/kg celastrol-treated for one week before 1h ischemia and 6h reperfusion


title: Stage E7.5 embryo 3 section 3 region R1


title: Stage E7.5 embryo 3 section 3 region L2


title: C1C_046

source_name: zone 1 of celastrol group


title: 18_18_GBF2021_G-20s-18

description: 18_18_GBF2021_G-20s-18_S18_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: C2C_045

source_name: zone 2 of celastrol group


title: 22_22_GBF2021_G-75s-22

description: 22_22_GBF2021_G-75s-22_S22_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 3 region L1


title: Stage E7.5 embryo 3 section 3 region A


title: Stage E7.5 embryo 3 section 2 region R


title: C3C_044


title: Stage E7.5 embryo 3 section 2 region P


title: Stage E7.5 embryo 3 section 2 region L


title: C1C_043


title: 16_16_GBF2021_G-20s-16

description: 16_16_GBF2021_G-20s-16_S16_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 2 region A


title: 15_15_GBF2021_G-20s-15

description: 15_15_GBF2021_G-20s-15_S15_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 1 region P


title: Stage E7.5 embryo 3 section 1 region A


title: Stage E7.5 embryo 3 section 10 region L


title: C3C_041


title: Stage E7.5 embryo 3 section 10 region A


title: C1C_040


title: Stage E7.5 embryo 3 section 10 region P


title: 13_13_GBF2021_G-20s-13

description: 13_13_GBF2021_G-20s-13_S13_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 12_12_GBF2021_G-Ctrl60-12

description: 12_12_GBF2021_G-Ctrl_plus_HEPES-12_S12_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.5 embryo 3 section 10 region R


title: Stage E7.0 embryo 2 section 9 region P

value: Mid-gastrulation embryo (E7.0)


title: 11_11_GBF2021_G-Ctrl60-11

description: 11_11_GBF2021_G-Ctrl_plus_HEPES-11_S11_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 9 region M


title: Stage E7.0 embryo 2 section 9 region R


title: Stage E7.0 embryo 2 section 9 region L


title: C3C_038


title: 10_10_GBF2021_G-Ctrl60-10

description: 10_10_GBF2021_G-Ctrl_plus_HEPES-10_S10_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 9 region EP


title: C1C_037


title: Stage E7.0 embryo 2 section 9 region EA


title: 17_17_GBF2021_G-20s-17

description: 17_17_GBF2021_G-20s-17_S17_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: 09_9_GBF2021_G-Ctrl60-09

description: 09_9_GBF2021_G-Ctrl_plus_HEPES-09_S9_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: C2C_042


title: 14_14_GBF2021_G-20s-14

description: 14_14_GBF2021_G-20s-14_S14_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: C2C_036


title: C2C_039


title: 08_8_GBF2021_G-Ctrl60-08

description: 08_8_GBF2021_G-Ctrl_plus_HEPES-08_S8_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 8 region M


title: Stage E7.0 embryo 2 section 8 region P


title: Stage E7.0 embryo 2 section 8 region EP


title: Stage E7.0 embryo 2 section 7 region M


title: Stage E7.0 embryo 2 section 7 region P


title: 06_6_GBF2021_G-Ctrl-06

description: 06_6_GBF2021_G-Ctrl-06_S6_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 8 region EA


title: C1C_034


title: C2C_033


title: Stage E7.0 embryo 2 section 7 region EP


title: Stage E7.0 embryo 2 section 7 region EA


title: 05_5_GBF2021_G-Ctrl-05

description: 05_5_GBF2021_G-Ctrl-05_S5_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 6 region R


title: Stage E7.0 embryo 2 section 6 region P


title: 04_4_GBF2021_G-Ctrl-04

description: 04_4_GBF2021_G-Ctrl-04_S4_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 6 region M


title: 03_3_GBF2021_G-Ctrl-03

description: 03_3_GBF2021_G-Ctrl-03_S3_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 9 region A


title: Stage E7.0 embryo 2 section 6 region L


title: Stage E7.0 embryo 2 section 6 region EP


title: C2C_030


title: 02_2_GBF2021_G-Ctrl-02

description: 02_2_GBF2021_G-Ctrl-02_S2_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: C1C_029


title: 07_7_GBF2021_G-Ctrl60-07

description: 07_7_GBF2021_G-Ctrl_plus_HEPES-07_S7_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: C3C_035


title: 01_1_GBF2021_G-Ctrl-01

description: 01_1_GBF2021_G-Ctrl-01_S1_R1_001_val_1.fqAligned.sortedByCoord.out.bam


title: Stage E7.0 embryo 2 section 6 region A


title: Stage E7.0 embryo 2 section 5 region P


title: Stage E7.0 embryo 2 section 5 region M


title: Stage E7.0 embryo 2 section 6 region EA


title: Stage E7.0 embryo 2 section 5 region EA


title: Stage E7.0 embryo 2 section 5 region EP


title: C2C_027


title: Stage E7.0 embryo 2 section 4 region P


title: C3C_028


title: WT, monolayer cells, exp15

city: Badalona

first: Lucia

last: Gutierrez-Chamorro

address: Ctra/ del Canyet

country: Spain

institute: IrsiCaixa

description:
In title file exp15 refers to replicate 2
cellsWT15

data_processing:
Mapping was performed with HISAT2 against GRCh38
Transcript was assembled with StringTie
Assembly: GRCh38_NCBI_109.20200522
Supplementary files format and content: Counts.txt (raw counts)

source_name: T47D cell line

extract_protocol:
Maxwell® HT simplyRNA Kit
TruSeq Stranded mRNA LT Sample Prep Kit

tag: culture model

value: Monolayer

tag: samhd1 status


title: C1C_032


title: C3C_031


title: Stage E7.0 embryo 2 section 4 region EP


title: Stage E7.0 embryo 2 section 4 region M


title: Stage E7.0 embryo 2 section 4 region EA


title: C1C_025


title: Stage E7.0 embryo 2 section 3 region P


title: SAMHD1  KO, monolayer cells, clone A2, exp16

description:
In title file exp16 refers to replicate 2
cellsA2_16

value: knock-out


title: Stage E7.0 embryo 2 section 3 region R


title: C2_024


title: SAMHD1  KO, monolayer cells, clone A2, exp15

description:
In title file exp15 refers to replicate 1
cellsA2_15


title: C3_023


title: Stage E7.0 embryo 2 section 3 region M


title: SAMHD1  KO, monolayer cells, clone A1, exp16

description:
In title file exp16 refers to replicate 3
cellsA1_16


title: WT, monolayer cells, exp16

description:
In title file exp16 refers to replicate 3
cellsWT16


title: C1_022


title: SAMHD1  KO, monolayer cells, clone A1, exp15

description:
In title file exp15 refers to replicate 2
cellsA1_15


title: C3C_026


title: Stage E7.0 embryo 2 section 3 region L


title: C2_021


title: Stage E7.0 embryo 2 section 3 region EP


title: Stage E7.0 embryo 2 section 3 region EA


title: C3_019


title: WT, monolayer cells, exp0

description:
In title file exp0 refers to replicate 1
cellsWT


title: Notochord 2

city: Boston

first: Stefan

last: Halvorsen

state: MA

address: 185 Cambridge Street

department: Center for Computational and Integrative Biology

institute: Massachusetts General Hospital

hyb_protocol: cRNA was hybridized on GeneChip Human Genome U133 Plus 2.0 Array according to manufacturer directions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: CEL files were read into R using the bioconductor affy package. Expression values were calculated using the mas5 algorithm in the affy package.

label: biotin

source_name: Notochord

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Notochord samples were prepared by laser capture microdissection and RNA extracted using Arcturus PicoPure RNA Isolation kit.

value: Notochord


title: Stage E7.0 embryo 2 section 3 region A


title: C2_018


title: Stage E7.0 embryo 2 section 2 region P


title: C1_020


title: Notochord 1-1


title: C3_017


title: Stage E7.0 embryo 2 section 2 region M


title: UCH1

source_name: UCH1 cell line


title: C1_016


title: Stage E7.0 embryo 2 section 2 region EA


title: SAMHD1 KO, monolayer cells, clone A1, exp0

description:
In title file exp0 refers to replicate 1
cellsA1


title: Chordoma 4

source_name: Chordoma Tumor

value: Chordoma Tumor


title: CH22-3

source_name: CH22 cell line


title: Chordoma 98


title: Stage E7.0 embryo 2 section 1 region EA/EP


title: C1_013


title: Stage E7.0 embryo 2 section 1 region P


title: C2_015


title: C2_012


title: C3_014


title: Stage E7.0 embryo 2 section 1 region A


title: Stage E7.0 embryo 2 section 2 region EP


title: Stage E7.0 embryo 2 section 11 region P


title: HNSCC_primary tumor_071

first: Xun

last: Qu

address: 107 Wenhuaxi Road

institute: Qilu Hospital of Shandong University

data_processing:
Raw sequencing files were converted to FASTQ files using base calling analysis.
FastQC (version 0.11.7) was used for quality control metrics.
The FASTQ files were filtered using fastp software.
Reads were mapped to the reference genome (GRCh38) using HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) software.
StringTie was used to quantify the abundance of the transcripts and genes. TMM (trimmed mean of M values) algorithm was used for normalization. Fragments per kilobase of transcript per million mapped reads (FPKM) was applied to evaluate the expression levels of individual genes.
Assembly: HG38
Supplementary files format and content: Tab-delimited text files include FPKM and count values for each sample

source_name: Primary tumor tissue of HNSCC

extract_protocol:
Formalin-fixed and paraffin-embedded tumor samples of head and neck squamous cell carcinoma were subjected to total RNA extraction using RecoverAllTM Total Nucleic Acid Isolation Kit (Invitrogen, USA) according to the manufacturer’s instructions. The concentration and the quantity of RNA samples were determined using Qubit®3.0 Fluorometer (Life Technologies, USA) and NanoDrop One spectrophotometer (Thermo Fisher Scientific Inc., USA).
Total RNA was processed for high-throughput sequencing using VAHTS® Total RNA-seq (H/M/R) Library Prep Kit (Vazyme, China) according to the manufacturer’s instructionsthe. Following mRNA generation, fragmentation, and cDNA synthesis, adaptor barcodes were ligated and final cDNA libraries were amplified by PCR and assessed for quality and concentration. Purified libraries were quantified and validated by Qubit® 3.0 Fluorometer and Agilent 2100 bioanalyzer to confirm the insert size and the concentration. The cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on Illumina NovaSeq 6000 platform (Illumina, USA). The library construction and sequencing were performed by Sinotech Genomics Co., Ltd (Shanghai, China).

value: Head and neck squamous cell carcinoma

value: Primary tumor tissue of HNSCC

tag: age

value: Male

tag: smoking

value: No

tag: drinking

tag: tumor site

value: Oral cavity

tag: tnm stage

value: II

tag: grade

value: High

tag: p16 status

value: Positive

tag: radiotherapy

value: Yes

tag: chemotherapy

tag: os event

value: Dead

tag: os month


title: HNSCC_primary tumor_072

tag: cell type

tag: gender

value: Female

value: Pharynx

value: Iva

value: Low


title: C3_011

tag: tissue

value: liver

tag: genotype

value: wild type

tag: treatment

value: 0.3 mg/kg celastrol-treated for one week before 1h ischemia and 6h reperfusion


title: Notochord 1-2

value: Notochord


title: Stage E7.0 embryo 2 section 11 region M

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: C1_010

tag: strain


title: Fetal Spine

source_name: Fetal Spin Tissue

value: Fetal Spinal Tissue


title: HNSCC_primary tumor_074

value: Head and neck squamous cell carcinoma

value: Primary tumor tissue of HNSCC

tag: age

value: Male

tag: smoking

tag: drinking

value: No


title: Chordoma 3

value: Chordoma Tumor


title: Chordoma 10


title: CH22-2

tag: cell line


title: HNSCC_primary tumor_067

tag: tumor site

tag: tnm stage

tag: grade

value: Intermediate

tag: p16 status

value: Positive

value: Yes


title: C2_009


title: HNSCC_primary tumor_006

value: Oral cavity

value: II

value: High

tag: radiotherapy

tag: chemotherapy

tag: os event

value: Dead

tag: os month


title: HNSCC_primary tumor_009

tag: cell type

tag: tissue

tag: gender

value: Negative


title: C3_008

value: liver

tag: genotype

value: wild type

tag: treatment

value: 0.3 mg/kg celastrol-treated for one week before 1h ischemia and 6h reperfusion


title: C1_007

tag: strain


title: HNSCC_primary tumor_054

tag: age

tag: smoking

value: Iva

value: Alive


title: Stage E7.0 embryo 2 section 10 region P

source_name: Mouse embryonic cells

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: Stage E7.0 embryo 2 section 11 region EA


title: HNSCC_primary tumor_035

value: Head and neck squamous cell carcinoma

value: Primary tumor tissue of HNSCC

value: Male

tag: drinking

tag: tumor site

tag: tnm stage

value: I

value: Low


title: Stage E7.0 embryo 2 section 11 region EP


title: HNSCC_primary tumor_024

value: Female

value: No

tag: grade

tag: p16 status

tag: radiotherapy


title: C2_006


title: Stage E7.0 embryo 2 section 10 region M


title: C1_005


title: Stage E7.0 embryo 2 section 10 region EP


title: C2_003


title: HNSCC_primary tumor_002

value: Yes

value: Oral cavity

value: II

tag: chemotherapy

tag: os event

tag: os month


title: Stage E7.0 embryo 2 section 10 region EA


title: Stage E7.0 embryo 1 section 9 region R


title: Stage E7.0 embryo 1 section 9 region P


title: C1_002

tag: tissue


title: HNSCC_primary tumor_019

tag: cell type

tag: gender

value: Intermediate-low

value: Negative


title: HNSCC_primary tumor_168

value: III

value: High

value: Positive


title: Stage E7.0 embryo 1 section 9 region M


title: HNSCC_primary tumor_018

value: High-intermediate

value: Alive


title: HNSCC_primary tumor_021

value: Head and neck squamous cell carcinoma

value: Dead


title: Stage E7.0 embryo 1 section 9 region L

value: Mid-gastrulation embryo (E7.0)


title: C3_004

value: liver

tag: strain

tag: genotype

value: wild type

tag: treatment

value: 0.3 mg/kg celastrol-treated for one week before 1h ischemia and 6h reperfusion


title: intima HCD rep 5

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Assembly: mm10
Supplementary files format and content: intima_reads_count.xlsx: Excel file includes count values for each Sample.

source_name: Intima

growth_protocol: 3-week-old LDLR-/- male mice were fed a low cholesterol or high cholesterol diet for 9 weeks.

extract_protocol:
Total RNA was isolated from the intima by flushed the aorta with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Intima

value: LDLRKO

tag: Sex

value: Male

value: high-cholesterol diet

tag: time

value: 9 weeks


title: HNSCC_primary tumor_161

value: Primary tumor tissue of HNSCC

tag: age

tag: smoking

value: Yes

tag: drinking

value: Oral cavity

value: II

value: Negative

value: No


title: intima HCD rep 3


title: Stage E7.0 embryo 1 section 9 region EP

tag: developmental stage

tag: tag


title: HNSCC_primary tumor_158

value: Head and neck squamous cell carcinoma

tag: tumor site

tag: tnm stage

tag: grade

value: High-intermediate

tag: p16 status

tag: radiotherapy

value: Alive


title: Stage E7.0 embryo 1 section 9 region EA

value: Mid-gastrulation embryo (E7.0)


title: intima HCD rep 4

tag: tissue


title: intima HCD rep 2


title: intima HCD rep 1


title: HNSCC_primary tumor_156

tag: cell type

tag: gender

value: Female

value: Pharynx

value: III

value: Low

value: Positive

tag: chemotherapy

tag: os event

tag: os month


title: HNSCC_primary tumor_147

value: I

value: High


title: intima LCD rep 5

value: Intima

tag: genotype

value: LDLRKO

tag: Sex

value: Male

tag: treatment

value: low-cholesterol diet

tag: time

value: 9 weeks


title: PFC Control Rep 2 [CTRL22_24h]

city: Brescia

first: Paolo

last: Martini

address: viale Europa 11

department: Department of Molecular and Translational Medicine

country: Italy

institute: University of Brescia

hyb_protocol: 5.5 µg ssDNA was fragmented, terminally labeled with biotin, hybridized

scan_protocol: Chips were scanned with the GeneChip Scanner 3000 7G.  Fluorescent signals were acquired by Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Gene expression was read and quantified from CEL files using oligo R package (version 1.58.0). Data were normalized using the rma function from the oligo R package. Probe set has been annotated using ragene10sttranscriptcluster.db R package (version 8.8.0).

organism: Rattus norvegicus

source_name: Prefrontal cortex

label_protocol: 250 ng of total RNA, for each samples were processed using Ambion WT Expression Kits for ampliﬁcation and using Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Kit (Life Technologies) to prepare the adequate amount of labeled target for hybridization

extract_protocol: Total RNA from rat PFC was isolated by single-step extraction using TRIzol Reagent (Life Technologies), according to the manufacturer’s instructions

treatment_protocol: 40 min FS stress: 0.8 mA, 20 min total of actual shock with random inter-shock length between 2–8 sec)

tag: group

value: Control

value: Prefrontal cortex


title: PFC Stress Rep 3 [STRESS11_2h]

value: Stress


title: PFC Stress Rep 1 [STRESS21_24h]


title: HNSCC_primary tumor_143

value: Head and neck squamous cell carcinoma

value: Primary tumor tissue of HNSCC

tag: age

tag: smoking

value: No

tag: drinking

value: Oral cavity

value: Yes

value: Alive


title: PFC Stress Rep 2 [STRESS22_24h]


title: intima LCD rep 4


title: PFC Stress Rep 4 [STRESS24_24h]


title: PFC Control Rep 3 [CTRL23_24h]


title: PFC Stress Rep 3 [STRESS23_24h]


title: PFC Control Rep 4 [CTRL24_24h]


title: PFC Stress Rep 2 [STRESS10_2h]


title: PFC Stress Rep 4 [STRESS12_2h]


title: PFC Control Rep 5 [CTRL25_24h]


title: Stage E7.0 embryo 1 section 8 region P

extract_protocol:
According to Geo-seq (Chen et al., 2017), RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)

tag: tag


title: Stage E7.0 embryo 1 section 8 region M


title: Stage E7.0 embryo 1 section 9 region A


title: PFC Stress Rep 6 [STRESS14_2h]


title: PFC Stress Rep 1 [STRESS9_2h]


title: PFC Stress Rep 5 [STRESS13_2h]


title: HNSCC_primary tumor_142

tag: tumor site

value: Pharynx

tag: tnm stage

value: I

tag: grade

tag: p16 status

value: Positive

tag: radiotherapy


title: intima LCD rep 3

tag: tissue

value: Intima

value: LDLRKO


title: PFC Control Rep 5 [CTRL13_2h]


title: Stage E7.0 embryo 1 section 8 region EP


title: HNSCC_primary tumor_014

tag: cell type

tag: gender

value: Male

value: High

value: Negative

tag: chemotherapy

tag: os event

value: Dead

tag: os month


title: PFC Control Rep 6 [CTRL14_2h]

tag: group

value: Control

value: Prefrontal cortex


title: PFC Control Rep 1 [CTRL21_24h]


title: intima LCD rep 2

tag: genotype

tag: Sex

tag: treatment

value: low-cholesterol diet

tag: time

value: 9 weeks


title: Stage E7.0 embryo 1 section 8 region EA

tag: developmental stage

tag: tag


title: PFC Control Rep 4 [CTRL12_2h]


title: HNSCC_primary tumor_139

value: Head and neck squamous cell carcinoma

value: Primary tumor tissue of HNSCC

tag: age

value: Female

tag: smoking

value: No

tag: drinking

tag: tumor site

value: Oral cavity

tag: tnm stage


title: HNSCC_primary tumor_137

tag: cell type

tag: tissue

value: II

tag: grade

value: Low

tag: p16 status

tag: radiotherapy

value: Alive


title: intima LCD rep 1

value: Intima

value: LDLRKO


title: Stage E7.0 embryo 1 section 7 region P

value: Mid-gastrulation embryo (E7.0)


title: Stage E7.0 embryo 1 section 7 region M


title: PFC Stress Rep 5 [STRESS25_24h]

tag: group

value: Stress


title: WGBS, LdlrHR1ex

first: Yuta

last: Takahashi

address: 10010 N Tottey Pines Rd

institute: Salk Institute

library_source: genomic

data_processing:
FastQC was used to get a basic statistics of the raw reads
C is transformed to T and G is transformed to A (reverse complementary) in sequence reads and reference genome via Bismark, and then these sequencing reads are aligned to similarly converted versions of the genome separately.
Assembly: mm10
Supplementary files format and content: The bw format files containing mapping results, corresponding reference genome and gene annotation files are provided

extract_protocol:
Genomic DNA was purified from the mouse ESCs using DNeasy Blood & Tissue Kits (Qiagen).
Firstly, the genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treated to generate single strand DNA (ssDNA). During the bisulfite conversion, unmethylated cytosine were converted into uracil, while methylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. The library was ready after size selection and PCR amplification. Library construction was performed in Novogene Company (Beijing, China)

tag: cell line

value: ESC


title: WGBS, AnkrdHR1ex


title: HNSCC_primary tumor_013

tag: gender

value: Male

value: Negative

value: Yes

tag: chemotherapy

tag: os event

value: Dead

tag: os month


title: WGBS, WT_mESC


title: HNSCC_primary tumor_135

value: Head and neck squamous cell carcinoma

value: High-intermediate

value: Positive


title: HNSCC_primary tumor_122

value: Primary tumor tissue of HNSCC

value: No

value: I

value: High


title: Stage E7.0 embryo 1 section 7 region EP

tag: developmental stage

tag: tag


title: WGS, AnkrdHR1ex

data_processing:
Raw data are stored in FASTQ (.fq) format files, which contain sequencing reads and corresponding base quality.
The sequencing error rate is examined by e, and Illumina sequencing quality by Qphred.
The effective sequencing data was aligned with the reference sequence through BWA software (parameters: mem -t 4 -k 32 -M).
We sequenced the whole genome from mouse ESCs transfected with CRISPR or not. In order to search for offtarget-cleavage, we searched potential sites by sequence homology with gRNA and then performed visual inspection of mapped reads in BAM files with IGV to find mutations.  In such a case, BAM data is the only processed data available.
Assembly: mm10
Library strategy: Whole genome sequencing

extract_protocol:
Genomic DNA was purified from the mouse ESCs using DNeasy Blood & Tissue Kits (Qiagen).
Library construction was performed in Novogene Company (Beijing, China)


title: Stage E7.0 embryo 1 section 7 region EA

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo


title: HNSCC_primary tumor_011

tag: age

tag: smoking

value: Oral cavity

value: II


title: Stage E7.0 embryo 1 section 6 region P


title: PFC Control Rep 3 [CTRL11_2h]

value: Control

value: Prefrontal cortex


title: WGS, LdlrHR1ex


title: PFC Control Rep 1 [CTRL9_2h]


title: parental 231 cells, siMyc, rep 3

growth_protocol: Parental MDA-MB-231 and TXNIP knockout MDA-MB-231 (TKO) cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco; 1195073) with 10% Fetal Bovine Serum (FBS) (Gibco; A3160506), 1X MEM Non-Essential Amino Acids Solution (Gibco; 11140076) and 1X Penicillin-streptomycin (Gibco; 15140148).

treatment_protocol: 231:TKO cells were generated using human TXNIP CRISPR/Cas9 KO plasmid with TXNIP-specific guide RNA sequences from GeCKO (v2) library (Santa Cruz; sc-400664). Myc was knocked down in parental 231 and 231:TKO cells using siRNA approach for 48 hours.

value: triple-negative breast cancer

tag: genotype

value: wild-type

tag: treatment

value: Myc knockdown

tag: time

value: 48 hours


title: Stage E7.0 embryo 1 section 6 region L

value: Mid-gastrulation embryo (E7.0)


title: Stage E7.0 embryo 1 section 6 region EP


title: Stage E7.0 embryo 1 section 6 region EA


title: HNSCC_primary tumor_010

tag: cell type

tag: tissue

value: Female

tag: drinking

tag: tumor site

tag: tnm stage

value: Negative

value: Alive


title: PFC Control Rep 2 [CTRL10_2h]

tag: group


title: PFC Control Rep 8 [CTRL8_0h]


title: PFC Control Rep 7 [CTRL7_0h]


title: WGS, Ankrd_SL_HR1ex

tag: cell line

value: ESC


title: Day28_1%O2_r2

city: Stanford

first: Kyomi

middle: J

last: Igarashi

address: 265 Campus Drive

department: Genetics

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
Fastq files were processed with cellranger (3.1.0) using the cellranger mm10 3.0.0 reference with default parameters. For each sample the expected cell number was set to 10000.
Assembly: mm10
Supplementary files format and content: Annotated, filtered (default cellranger setting) cell x gene matrices in .h5 format (cellranger output file)

source_name: Hematopoietic stem and progenitor cells

growth_protocol: Immunophenotypic CD150+CD34-/loc-Kit+Sca1+Lineage- HSCs from C57BL/6 mice were cultured in Ham’s F12 media (Gibco) supplemented with 1X penicillin-streptomycin-glutamine (Gibco), 1X HEPES (Gibco), 1X insulin-transferrin-selenium-ethanolamine (Gibco), 1 mg/ml polyvinyl alcohol (Sigma), 100 ng/ml recombinant mouse thrombopoietin (Peprotech), and 10 ng/ml recombinant mouse stem cell factor (Peprotech) for 4-weeks on Fibronectin-coated plates at 37C and 10% carbon dioxide.

extract_protocol:
scRNA-seq analysis was performed using a Gene Expression kit (10X Genomics) according to the manufacturer’s protocol
scRNA-seq analysis was performed using a Gene Expression kit (10X Genomics) according to the manufacturer’s protocol

treatment_protocol: HSCs were cultured at 20%, 5% or 1% oxygen. For one sample, fresh c-Kit+ bone marrow was used.

tag: strain

value: 1% oxygen culture


title: Day28_1%O2_r1


title: parental 231 cells, siMyc, rep 1


title: PFC Control Rep 6 [CTRL6_0h]


title: parental 231 cells, si non-targeting, rep 3

value: non-targeting knockdown


title: Day28_5%O2_r2

value: 5% oxygen culture


title: WGS, WT_mESC


title: Stage E7.0 embryo 1 section 6 region M


title: parental 231 cells, si non-targeting, rep 2


title: PFC Stress Rep 1 [STRESS1_0h]

value: 40 min FS stress


title: Stage E7.0 embryo 1 section 5 region P


title: PFC Control Rep 5 [CTRL5_0h]


title: Stage E7.0 embryo 1 section 6 region A


title: PFC Control Rep 4 [CTRL4_0h]


title: Stage E7.0 embryo 1 section 5 region M


title: PFC Control Rep 3 [CTRL3_0h]


title: Day28_5%O2_r1


title: parental 231 cells, siMyc, rep 2


title: parental 231 cells, si non-targeting, rep 1


title: PFC Stress Rep 8 [STRESS8_0h]


title: Stage E7.0 embryo 1 section 5 region EP


title: TKO cells, siMyc, rep 3

value: TXNIP knockout


title: Day28_20%O2

value: 20% oxygen culture


title: pHPC_20%O2_r3

data_processing:
basecalling and trim adaptor sequences
Sequencing reads screened for quality using fastQC (v0.11.9) using parameters -t 2
sequencing reads were aligned to the GRCm39 mouse genome using STAR (v2.7.8a) with parameters --runThreadN 4 --sjdbOverhang 49 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard
raw gene counts were generated using subread featureCounts (v2.0.0) with parameters -T 10 -p -t exon -g gene_id
gene counts were passed into DESeq2  workflow for normalization
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Cultured hematopoietic progenitor cells

extract_protocol:
RNA was extracted from sorted cells using the Qiagen RNeasy Micro Kit
RNA libraries were prepared by Novogene using standard Illumina protocols

treatment_protocol: HSCs were cultured at 20%, 5% or 1% oxygen for 28-days and then sorted for either CD201+CD150+cKit+Sca1+Lineage- cells or cKit+Sca1-Lineage- cells

value: Day-28 20% oxygen culture


title: Stage E7.0 embryo 1 section 4 region M


title: Fresh_cKit+

value: Fresh bone marrow


title: TKO cells, siMyc, rep 1

value: triple-negative breast cancer


title: TKO cells, siMyc, rep 2


title: TKO cells, si non-targeting, rep 3


title: Stage E7.0 embryo 1 section 5 region EA


title: Stage E7.0 embryo 1 section 4 region P


title: pHPC_20%O2_r1


title: Stage E7.0 embryo 1 section 4 region EP


title: TKO cells, si non-targeting, rep 2


title: pHPC_20%O2_r2


title: Stage E7.0 embryo 1 section 4 region EA


title: pHSC_20%O2_r3

source_name: Cultured hematopoietic stem cells


title: TKO cells, si non-targeting, rep 1


title: Stage E7.0 embryo 1 section 3 region R


title: PFC Stress Rep 7 [STRESS7_0h]

value: Prefrontal cortex


title: PFC Control Rep 2 [CTRL2_0h]

value: Control


title: A-431 vaginal epithelial cells replicate 2

city: Orono

first: Benjamin

middle: L

last: King

state: ME

address: 5735 Hitchner Hall

department: Molecular and Biomedical Sciences

institute: University of Maine

data_processing:
Inspected read quality with FastQC and MultQC in Galaxy.
Read trimming using Trimmomatic in Galaxy.
Read alignment to GRCh38 using HISAT2 in Galaxy.
Read counts per gene using Htseq-count with Ensembl version 102 annotation in Galaxy.
Lists of differentially expressed genes using R/DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include read count values for each sample.

source_name: cell line

extract_protocol:
Modified protocols developed by EuroFins Genomics (Konstanz, Germany) based on RNeasy kit (QIAGEN).
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: cell line

value: vaginal epithelial cells

value: control


title: PFC Stress Rep 3 [STRESS3_0h]


title: N2_nhr-86_RNAi_PCN_3

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

data_processing:
Raw fastq reads were evaluated by FastQC (version 0.11.5), clean reads were aligned to the C. elegans reference genome (WBcel235) and quantified using Kallisto (version 0.45.0). Differentially expressed genes were identified using Sleuth (version 0.30.0).
Assembly: WBcel235
Supplementary files format and content: tsv files include TPM transcript abundance values for each sample

organism: Caenorhabditis elegans

source_name: Whole animal

extract_protocol:
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Synchronized L1 staged C. elegans wild-type and nhr-8 loss of function animals were grown to L4, transferred to P. aeruginosa or E. coli and incubated at 25°C for 4 hours..

tag: bacterial exposure

tag: chemical treatment

value: PCN


title: PFC Stress Rep 4 [STRESS4_0h]


title: pHSC_20%O2_r1


title: Stage E7.0 embryo 1 section 3 region P

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

institute: Chinese Academy of Sciences

tag: developmental stage

value: Mid-gastrulation embryo (E7.0)


title: PFC Stress Rep 6 [STRESS6_0h]


title: PFC Stress Rep 2 [STRESS2_0h]


title: pHSC_20%O2_r2


title: N2_nhr-86_RNAi_PCN_2


title: N2_nhr-86_RNAi_PCN_1


title: A-431 vaginal epithelial cells challenged with a colonizing strain (CA14314) replicate 2

value: challenged with Candida albicans colonizing strain CA14314


title: PFC Stress Rep 5 [STRESS5_0h]


title: Stage E7.0 embryo 1 section 3 region M

tag: tag


title: pHSC_5%O2_r3

value: Day-28 5% oxygen culture


title: pHSC_5%O2_r2


title: N2_nhr-86_RNAi_DMSO_3

value: DMSO


title: Stage E7.0 embryo 1 section 3 region L


title: A-431 vaginal epithelial cells challenged with a VVC strain (CA01887) replicate 2

value: challenged with Candida albicans VVC strain CA01887


title: pHSC_5%O2_r1


title: N2_nhr-86_RNAi_DMSO_2


title: N2_nhr-86_RNAi_DMSO_1


title: Stage E7.0 embryo 1 section 3 region EP


title: pHSC_1%O2_r3

value: Day-28 1% oxygen culture


title: A-431 vaginal epithelial cells replicate 1


title: A-431 vaginal epithelial cells challenged with a VVC strain (CA01887) replicate 1


title: Stage E7.0 embryo 1 section 3 region EA


title: Stage E7.0 embryo 1 section 3 region A


title: N2_L4440_PCN_3


title: INPUT_siNS

city: Cleveland

first: Ruth

last: Keri

state: OHIO

address: 9500 Euclid Ave

institute: Cleveland Clinic

data_processing:
Libraries were pooled and sequenced with Illumina technology with paired-end reads of 50bp length.
ChIP-seq reads were trimmed using TrimGalore!
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA software v.0.7.5a and samples were filtered for regions blacklisted by the ENCODE project.
PCR duplicates and multimapping reads were removed using samtools
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bed files containing peaks (except for Input sample)

growth_protocol: MDA-MB-453 cell line was maintained according to ATCC

extract_protocol:
Cells were fixed and immunopreciptated using Diagenode iDeal ChIP-seq kit for Transcription Factors per the manufacturers’ instructions. Cells were crosslinked using Diagenode ChIP Cross-link Gold prior to formaldehyde fixation.
Library preparation was performed by Diagenode. Briefly, libraries were prepared using IP-Star Compact Automated System from both INPUT and ChIP DNA samples (starting amount of 3µg for IP and 1.5µg for INPUT) with the MIcroPlex Library Preparation Kit v2 (Diagenode #C05010013). Library amplification was assessed by qPCR, purified, and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher Q32854). Fragment size was analyzed using High Sensitivity NGS Fragment Analysis Kit on an Agilent Fragment Analyzer.

value: Human breast epithelial

tag: chip antibody


title: PFC Control Rep 1 [CTRL1_0h]


title: N2_L4440_PCN_2


title: Stage E7.0 embryo 1 section 2 region P

city: Guangzhou


title: pHSC_1%O2_r1


title: siNS_2_biol_rep2

value: TLE3 (Proteintech (#11372-1AP)


title: N2_L4440_PCN_1


title: Low_3_S24

city: Aurora

first: Linda

middle: A

last: Barlow

state: CO

address: 12801 East 17th Ave

department: Cell&Dev Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
For differential expression analysis, fastq were quantified at the transcript level via Salmon (v1.4.0) with GENCODE vM26 genome. Abundance was summarized at the gene level using tximport (v1.16.1) and DESeq2 (v1.28.1).
Assembly: mm39 (GENCODE vM26)
Supplementary files format and content: TSV count matrices of Salmon abundance and estimated counts

source_name: circumvallate papilla epithelium

extract_protocol:
Collagenase (2mg/mL) and Dispase (5mg/mL) in PBS was injected beneath and beside the CVP, the epithelium peeled and then dissociated for 45 min in Collagenase (2mg/mL), Dispase (5mg/mL), and Elastase (2mg/mL) at 37°C. Cells were centrifuged (2000 RPM 4°C), the pellet resuspended in FACS buffer (1mM EDTA, 25mM HEPES pH 7.0, 1% FBS, 1x Ca2+/Mg2+-free dPBS), passed through a 30µm cell strainer and subjected to FACS for GFP signal. GFPneg cells were discarded
PolyA selection was performed and sequencing libraries were synthesized using NuGen Universal Plus mRNA-Seq with NuQuant kit at the University of Colorado Genomics and Microarray Core. Libraries were sequenced on an Illumina NovaSeq6000.

value: Adult (11-12 week)

tag: gfp expression

value: Low

value: circumvallate papilla epithelium


title: Stage E7.0 embryo 1 section 2 region EP


title: INPUT_siFOXA1


title: siNS_1_biol_rep1


title: N2_L4440_DMSO_3


title: Low_2_S23

tag: genotype


title: Low_1_S22


title: N2_L4440_DMSO_1


title: pHSC_1%O2_r2

tag: treatment


title: N2_PA14_delta_phz_PCN_3


title: MedLow_2_S20

value: MedLow


title: Stage E7.0 embryo 1 section 1 region EA


title: siFOXA1_1_biol_rep1


title: MedLow_1_S19


title: Stage E7.0 embryo 1 section 11 region P


title: Stage E7.0 embryo 1 section 2 region M


title: N2_PA14_delta_phz_PCN_1


title: Stage E7.0 embryo 1 section 11 region M


title: HiMed_3_S18

value: HiMed


title: MDA-MB-453 siFOXA1 biol rep 2

description:
M45FOXA2
M45FOXAvsM45NS_DEG.xls

data_processing:
A non-directional, polyA selection library preparation was performed using NEBNext Ultra II RNA Library Prep Kit for Illumina
paired end, cleaned reads were aligned to human genome (version hg19) using STAR (v2.5)
HTSeq v0.6.1 was used to count the read numbers mapped of each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis between groups was preformed using DESeq2 (2_1.6.3). Genes considered signifcantly differentially expressed were determined by a corrected p-value of 0.05 (Benjamini & Hochberg method) and absolute fold change of 1
Assembly: hg19

source_name: Breast, Mammary Gland

growth_protocol: Cell lines were maintained as recommended by ATCC.

extract_protocol: RNA was isolated using the Rneasy Plus Mini Kit (Qiagen) and processed as per manufacturer's instructions

treatment_protocol: cell were reverse transfected with either non-targting siRNA (siNS) or SMARTPOOL siRNAs targeting either TLE3 or FOXA1

value: Breast, Mammary Gland

value: Breast epithelial


title: MDA-MB-453 siFOXA1 biol rep 1

description:
M45FOXA1
M45FOXAvsM45NS_DEG.xls


title: N2_L4440_DMSO_2


title: N2_PA14_PCN_3


title: HiMed_2_S17


title: MDA-MB-453 siTLE3 biol rep 3

description:
M45TLE3
M45TLEvsM45NS_DEG.xls


title: HiMed_1_S16


title: siFOXA1_2_biol_rep2


title: MDA-MB-453 siTLE3 biol rep 2

description:
M45TLE2
M45TLEvsM45NS_DEG.xls


title: MedLow_3_S21


title: Stage E7.0 embryo 1 section 2 region EA


title: Stage E7.0 embryo 1 section 1 region P


title: N2_PA14_PCN_1


title: MDA-MB-453 siFOXA1 biol rep 3

description:
M45FOXA3
M45FOXAvsM45NS_DEG.xls


title: N2_PA14_delta_phz_PCN_2


title: N2_PA14_PCN_2


title: High_3_S15

value: High


title: Stage E7.0 embryo 1 section 10 region P


title: N2_OP50_PCN_3

value: PCN


title: MDA-MB-453 siTLE3 biol rep 1

description:
M45TLE1
M45TLEvsM45NS_DEG.xls


title: High_2_S14


title: Stage E7.0 embryo 1 section 10 region M

value: Mid-gastrulation embryo (E7.0)


title: MDA-MB-453 siNS biol rep 3


title: N2_OP50_PCN_2


title: Stage E7.0 embryo 1 section 11 region EP


title: High_1_S13


title: Stage E7.0 embryo 1 section 10 region EP


title: Stage E7.0 embryo 1 section 11 region EA


title: N2_OP50_PCN_1


title: Stage E7.0 embryo 1 section 10 region EA


title: MDA-MB-453 siNS biol rep 2


title: N2_PA14_delta_phz_DMSO_2


title: Ly6Cpos.Mo.WT_R2

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

data_processing:
Sequence alignment with the mouse genome, sequence counting and quality control were performed using the nf-core/rnaseq pipeline. RNA-seq data were analyzed using R Bioconductor (3.5.1) and DESeq2 package (version 1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Text counts table: scaled counts length
Supplementary_files_format_and_content: Text counts table: scaled gene counts
Supplementary_files_format_and_content: Text counts table: gene counts
Supplementary_files_format_and_content: Text counts table: scaled gene tpm length
Supplementary_files_format_and_content: DE_refilled_vs_control_in_IMs.txt (DE genes comparing refilled to control IMs)
Supplementary_files_format_and_content: metadata_all_samples.csv (Metadata for all the samples)
Supplementary_files_format_and_content: normalized_expression.csv (Normalized expression (counts by salmon) in all samples)

source_name: Ly6C+ Mo

extract_protocol:
For bulk mRNA-sequencing (RNA-seq), lungs from IM-depleted and control mice were isolated, chopped and incubated with collagenase I and DNaseI at 37 degrees for 30 minutes. Mononuclear cells were released and purified by gredient centrifugation with Percoll. Alveoloar macrophages (AM), CD206+ interstitial macrophages (CD206+ IM) and CD206- IM were FACS-sorted into Trizol. Total RNA was extracted with standard Trizol RNA extraction protocole. RNA quality and quantity were evaluated using a 2100 bioanalyzer (Agilent) and the Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher).
One hundred nano-grams of RNA was used to generate the libraries using the Truseq stranded mRNA kit (Illumina). These libraries were sequenced on an Illumina Novaseq sequencer on a SP flow cell.

treatment_protocol: IM-depleted mice were IM-DTR mice that had been treated with 50ng diphtheria toxin (DT) i.p. and sacrificed 14 days later. Control mice were the litermate of IM-DTR mice without DT treatment.

value: control

tag: cell type 1

value: Mo

tag: cell type 2

tag: cell type 3

value: Ly6Cpos Mo


title: N2_PA14_delta_phz_DMSO_3

value: DMSO


title: Ly6Cpos.Mo.WT_R1


title: Ly6Cpos.Mo.WT_R3


title: SKBR3 siFOXA1 biol rep 3

description:
SKBFOXA3
SKBFOXAvsSKBNS_DEG.xls

tag: tissue

tag: cell type


title: SKBR3 siFOXA1 biol rep 2

description:
SKBFOXA2
SKBFOXAvsSKBNS_DEG.xls


title: Stage E6.5 embryo 6 section 8 region EP

value: Early-gastrulation embryo (E6.5)


title: N2_PA14_delta_phz_DMSO_1


title: CD206pos.IM.WT_R3

source_name: CD206+ control IM

value: Mac

value: IM

value: CD206pos IM


title: Stage E6.5 embryo 6 section 8 region P


title: Stage E6.5 embryo 6 section 8 region EA


title: SKBR3 siFOXA1 biol rep 1

description:
SKBFOXA1
SKBFOXAvsSKBNS_DEG.xls


title: N2_PA14_DMSO_3


title: SKBR3 siTLE3 biol rep 3

description:
SKBTLE3
SKBTLEvsSKBNS_DEG.xls


title: Stage E6.5 embryo 6 section 8 region A


title: CD206pos.IM.WT_R2


title: Stage E6.5 embryo 6 section 7 region P


title: CD206pos.IM.WT_R1


title: N2_PA14_DMSO_2


title: SKBR3 siTLE3 biol rep 2

description:
SKBTLE2
SKBTLEvsSKBNS_DEG.xls


title: N2_PA14_DMSO_1


title: N2_OP50_DMSO_3


title: CD206pos.IM.CRE_R2

source_name: CD206+ refilled IM

value: Cx3cr1-LSL-DTR Tmem119-Cre

value: refilled


title: MDA-MB-453 siNS biol rep 1


title: Stage E6.5 embryo 6 section 7 region EP


title: SKBR3 siTLE3 biol rep 1

description:
SKBTLE1
SKBTLEvsSKBNS_DEG.xls


title: SKBR3 siNS biol rep 3


title: N2_OP50_DMSO_2


title: SKBR3 siNS biol rep 2


title: N2_OP50_DMSO_1


title: Stage E6.5 embryo 6 section 7 region A


title: CD206neg.IM.WT_R3

source_name: CD206- control IM

value: CD206neg IM


title: Stage E6.5 embryo 6 section 6 region P


title: CD206pos.IM.CRE_R1


title: G401 F2 TAZ BiolRep 3

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

data_processing:
Reads were adaptor and quality trimmed using ‘trim_galore’ (v0.4.4_dev)
Reads were mapped to hg19 using STAR v2.6.0a using default parameters.
Read counts were extracted using HTSeq.
Read counts tables were normalized using DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing normalized read counts

growth_protocol: G401 malignant rhabdoid tumor cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and penicillin/streptomycin s in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using RNeasy Mini, according to manufacturer’s instructions (Qiagen). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 149-500ng of total RNA underwent Poly(A) selection
TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR
Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina)

treatment_protocol: 10µM tazemetostat or equivalent volume of DMSO for 11 days

value: Malignant Rhabdoid Tumor

value: RB1 knockout

tag: clone

value: 10µM tazemetostat


title: SKBR3 siNS biol rep 1

value: Breast, Mammary Gland

value: Breast epithelial


title: G401 F2 TAZ BiolRep 2


title: A-431 vaginal epithelial cells challenged with a colonizing strain (CA14314) replicate 1

value: cell line

value: vaginal epithelial cells

value: challenged with Candida albicans colonizing strain CA14314


title: CD206neg.IM.WT_R1

value: control


title: CD206neg.IM.WT_R2


title: Stage E6.5 embryo 6 section 6 region EA


title: Stage E6.5 embryo 6 section 6 region EP


title: T47D siFOXA1 biol rep 2

description:
T47FOXA2
T47FOXAvsT47NS_DEG.xls


title: G401 F2 TAZ BiolRep 1


title: CD206pos.IM.CRE_R3


title: CD206neg.IM.CRE_R3

source_name: CD206- refilled IM


title: Stage E6.5 embryo 6 section 6 region A


title: T47D siFOXA1 biol rep 1

description:
T47FOXA1
T47FOXAvsT47NS_DEG.xls


title: Stage E6.5 embryo 6 section 7 region EA


title: G401 F2 DMSO BiolRep 3

value: DMSO


title: CD206neg.IM.CRE_R2


title: Stage E6.5 embryo 6 section 5 region P

value: Early-gastrulation embryo (E6.5)


title: T47D siTLE3 biol rep 3

description:
T47TLE3
T47TLEvsT47NS_DEG.xls


title: G401 F2 DMSO BiolRep 2


title: Stage E6.5 embryo 6 section 5 region EP


title: G401 F2 DMSO BiolRep 1


title: Stage E6.5 embryo 6 section 5 region EA


title: T47D siFOXA1 biol rep 3

description:
T47FOXA3
T47FOXAvsT47NS_DEG.xls


title: AM.WT_R3

source_name: AM

value: Mac

value: AM


title: CD206neg.IM.CRE_R1

value: IM


title: G401 E1 TAZ BiolRep 3


title: T47D siTLE3 biol rep 1

description:
T47TLE1
T47TLEvsT47NS_DEG.xls


title: AM.WT_R2


title: Stage E6.5 embryo 6 section 5 region A


title: T47D siNS biol rep 3


title: AM.WT_R1


title: G401 E1 TAZ BiolRep 2


title: G401 E1 TAZ BiolRep 1


title: Stage E6.5 embryo 6 section 4 region P


title: Stage E6.5 embryo 6 section 4 region EP


title: G401 E1 DMSO BiolRep 3


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