title: WT-Zymosan-3hr-biol rep 3


title: WT-Zymosan-3hr-biol rep 2

status: Public on Apr 19 2023

type: SRA

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

country: USA

institute: University of Virginia

library_source: transcriptomic

data_processing:
Bulk RNAseq analysis: On average we received 30 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: BMDMs

extract_protocol:
Cell pellets (10^6 cells) were sent to Genewiz, Azenta Life Sciences for extraction and sequencing
Library was constructed at Genewiz, Azenta Life Sciences

tag: tissue

value: BMDMs

tag: cell type

value: Macrophage

tag: genotype

value: WT

tag: treatment

value: Zymosan 3hrs


title: WT-Zymosan-3hr-biol rep 1


title: WT-Zymosan-BAPTA-3hr-biol rep 1

value: Zymosan 3hrs + BAPTA


title: KO-Zymosan-3hr-biol rep 1

value: Mcu-/-


title: KO-Zymosan-3hr-biol rep 2


title: 32128, Cerebral cortex, +/+

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCm38.p6 GENCODE r25
Supplementary files format and content: RawCounts.csv

source_name: Cerebral cortex

extract_protocol:
RNA was extracted by using an miRNeasy mini kit.
RNA-Seq libraries were prepared from 500 ng total RNA by using an RNA HyperPrep Kit along with RiboErase (HMR) kit.

value: Cerebral cortex

tag: Sex

value: Male


title: KO-Untreated-biol rep 4

value: Untreated


title: KO-Untreated-biol rep 3


title: KO-Untreated-biol rep 1


title: Feces, TAA, replicate 4

city: Hangzhou

first: Yuchong

last: Wang

address: Xiacheng district

country: China

institute: Zhejiang University

data_processing:
Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean tags according to the fqtrim(v0.94).
Chimeric sequences were filtered using Vsearch software(v2.3.4).
After dereplication using DADA2,we obtained feature table and feature sequence.Alpha diversity and beta diversity were calculated by normalized to the same sequences randomly.Then according to SILVA(release 138) classifier, feature abundance was normalized using relative abundance of each sample.
Alpha diversity and beta diversity were analyzed using QIIME2, and pictures were created using R package (v3.5.2).
Blast was used for sequence alignment, and the feature sequences were annotated with SILVA database for each representative sequence.
Library strategy: 16s rRNA-seq

source_name: Feces

extract_protocol:
DNA from different samples was extracted using the CTAB according to manufacturer ’s instructions.
The PCR products were purifyied by AMPure XT beads (Beckman Coulter Genomics, Danvers, MA, USA) and quantified by Qubit( Invitrogen, USA). The amplicon pools were prepared for sequencing and the size and quantity of the amplicon library were assessed on Agilent 2100 Bioanalyzer (Agilent, USA) and with the Library Quantification Kit for Illumina (Kapa Biosciences, Woburn, MA, USA), respectively.The libraries were sequenced on NovaSeq PE250 platform.

value: Feces

value: TAA


title: Feces, TAA, replicate 3


title: Feces, TAA, replicate 6


title: Feces, TAA, replicate 5


title: Feces, TAA, replicate 2


title: Feces, control, replicate 6

value: control


title: Feces, control, replicate 5


title: Feces, TAA, replicate 1


title: Feces, control, replicate 4


title: Feces, control, replicate 3


title: Feces, control, replicate 2


title: KO-Untreated-biol rep 2


title: 19132X30 Serum Deprived + Metformin + Leucine 6

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

description: 4d differentiated myotubes followed by 4d of serum deprivation with 100 nM metformin + 500 nM leucine

data_processing:
The mouse GRCm38 genome and gene annotation files were downloaded from Ensembl release 102
A reference database was created using STAR version 2.7.6a with splice junctions optimized for 150 base pair reads
Optical duplicates were removed using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Assembly: GRCm38
Supplementary files format and content: Feature count output files combined into a single tab-delimited matrix

growth_protocol: Cells were grown in high glucose DMEM (4.5 g/L) with 10% fetal bovine serum until reaching 95-100% confleunce in which cells were switched to low glucose DMEM (1 g/L) with 2% horse serum (differentiation media) for 4 days

extract_protocol:
Total RNA was isolated by homogenizing myotubes in Qiazol Lysis Reagent (Qiagen, cat# 79306). The RNA was separated and precipitated using chloroform and isopropanol. Extracted RNA was washed with ethanol then suspended in nuclease-free water.
Libraries were prepared with Illumina Stranded Total RNA Library Prep Ribo-Zero Gold Plus and RNA was sequenced using Illumina NovaSeq S4 Reagent Kit v1.5 150x150 bp Sequencing

treatment_protocol: After 4 days in differentiation media cells either remained on media with 2% horse serum or were serum deprived (no serum) for 4 days with or without metformin, leucine, or metformin + leucine combination

tag: time

value: 8 days

tag: cell line

value: Skeletal Muscle Myotubes

value: Low glucose DMEM no horse serum + Metformin + Leucine


title: 19132X20 Serum Deprived + Leucine 2

description: 4d differentiated myotubes followed by 4d of serum deprivation with 500 nM leucine

value: Low glucose DMEM no horse serum + Leucine


title: 19132X25 Serum Deprived + Metformin + Leucine 1


title: 19132X24 Serum Deprived + Leucine 6


title: 19132X17 Serum Deprived + Metformin 5

description: 4d differentiated myotubes followed by 4d of serum deprivation with 100 nM metformin

value: Low glucose DMEM no horse serum + Metformin


title: 19132X21 Serum Deprived + Leucine 3


title: 19132X28 Serum Deprived + Metformin + Leucine 4


title: 19132X22 Serum Deprived + Leucine 4


title: 19132X15 Serum Deprived + Metformin 3


title: Feces, control, replicate 1


title: 19132X23 Serum Deprived + Leucine 5


title: 19132X29 Serum Deprived + Metformin + Leucine 5


title: 19132X14 Serum Deprived + Metformin 2


title: 19132X10 Serum Deprived 4

description: 4d differentiated myotubes followed by 4d of serum deprivation

value: Low glucose DMEM no horse serum


title: 19132X11 Serum Deprived 5


title: 19132X26 Serum Deprived + Metformin + Leucine 2


title: 19132X9 Serum Deprived 3


title: 19132X13 Serum Deprived + Metformin 1


title: 19132X16 Serum Deprived + Metformin 4


title: 19132X27 Serum Deprived + Metformin + Leucine 3


title: 19132X12 Serum Deprived 6


title: 19132X8 Serum Deprived 2


title: 19132X5 Control 5

description: 4d differentiated myotubes followed by 4d differentiation media (with 2% horse serum)

value: 2% Horse Serum


title: 19132X6 Control 6

value: WT


title: 19132X7 Serum Deprived 1


title: 19132X4 Control 4


title: 19132X18 Serum Deprived + Metformin 6


title: 19132X19 Serum Deprived + Leucine 1


title: 19132X3 Control 3


title: 11B_M_999

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain

value: male


title: 11B_M_997


title: 11B_M_998


title: 11B_M_995


title: 11B_M_994


title: 11B_M_990


title: 11B_M_988


title: 19132X2 Control 2


title: 11B_M_982


title: 11B_M_989


title: 11B_M_979


title: 11B_M_981


title: 11B_M_983


title: 11B_M_976


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title: 11B_M_975


title: 11B_M_972


title: 11B_M_971


title: 11B_M_97


title: 11B_M_969


title: 19132X1 Control 1


title: 11B_M_992


title: 11B_M_985


title: 11B_M_991


title: 11B_M_984


title: 11B_M_968


title: 11B_M_965


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title: 11A_M_927


title: 11A_M_925


title: 11A_M_924


title: 11A_M_92


title: 11A_M_917


title: 11A_M_919


title: 11A_M_922


title: 11A_M_913


title: 11A_M_914


title: 11A_M_923


title: 11A_M_912


title: 11A_M_928


title: 11A_M_921


title: 11A_M_911


title: 11A_M_909


title: 11A_M_907


title: 11A_M_91


title: 11A_M_910


title: 11A_M_918


title: 11A_M_908


title: 11A_M_904


title: 11A_M_906


title: 11A_M_905


title: 11A_M_920


title: 11A_M_915


title: 11A_M_903


title: 11A_M_9


title: 11A_M_902


title: 11A_M_901


title: 11A_M_90


title: 11A_M_897


title: 11A_M_916


title: 11A_M_898


title: 11A_M_896


title: 11A_M_900


title: 11A_M_895


title: 11A_M_899


title: 11A_M_894


title: 11A_M_893


title: 11A_M_890


title: 11A_M_892


title: 11A_M_891


title: 11A_M_886


title: 11A_M_883


title: 11A_M_884


title: 11A_M_882


title: 11A_M_887


title: 11A_M_888


title: 11A_M_881


title: 11A_M_889


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title: 11A_M_879


title: 11A_M_885


title: 11A_M_880


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title: 11A_M_874


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title: 11A_M_869


title: 11A_M_868


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title: 11A_M_855


title: 11A_M_858


title: 11A_M_856


title: 11A_M_857


title: 11A_M_851


title: 11A_M_853


title: 11A_M_852


title: 11A_M_870


title: 11A_M_85


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title: 11A_M_848


title: 11A_M_844


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title: 11A_M_846


title: 11A_M_843


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title: 11A_M_840


title: 11A_M_841


title: 11A_M_842


title: 11A_M_84


title: 11A_M_839


title: 11A_M_838


title: 11A_M_837


title: 11A_M_833


title: 11A_M_835


title: 11A_M_836


title: 11A_M_834


title: 11A_M_830


title: 11A_M_832


title: 11A_M_850


title: 11A_M_83


title: 11A_M_829


title: 11A_M_831


title: 11A_M_827


title: 11A_M_845


title: 11A_M_828


title: 11A_M_820


title: 11A_M_821


title: 11A_M_825


title: 11A_M_82


title: 11A_M_824


title: 11A_M_822


title: 11A_M_818


title: 11A_M_819


title: 11A_M_816


title: 11A_M_817


title: 11A_M_815


title: 11A_M_814


title: 11A_M_812


title: 11A_M_811


title: 11A_M_809


title: 11A_M_81


title: 11A_M_807


title: 11A_M_826


title: 11A_M_804


title: 11A_M_806


title: 11A_M_808


title: 11A_M_805


title: 11A_M_823


title: 11A_M_802


title: 11A_M_801


title: 11A_M_800


title: 11A_M_80


title: 11A_M_796


title: 11A_M_799


title: 11A_M_8


title: 11A_M_797


title: 11A_M_803


title: 11A_M_793


title: 11A_M_794


title: 11A_M_810


title: 11A_M_795


title: 11A_M_791


title: 11A_M_79


title: 11A_M_789


title: 11A_M_787


title: Feces_CHB_rep2

type: RNA

description: miRNA expression in human feces

hyb_protocol: The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v14.9 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

organism: Homo sapiens

label_protocol: Sample labeling and array hybridization were performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase.

extract_protocol: Total miRNA was isolated from fecal specimens using a miRNA isolation kit (Vazyme, China). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: sample type

value: feces

tag: gender


title: 11A_M_788


title: 11A_M_785


title: 11A_M_786


title: Feces_HE_rep2

description: miRNA expression in human feces


title: 11A_M_783


title: 11A_M_784


title: 11A_M_798


title: Feces_CHB_rep1

description: miRNA expression in human feces


title: 11A_M_780


title: 11A_M_782


title: 11A_M_781


title: 11A_M_776


title: Feces_HE_rep1

description: miRNA expression in human feces


title: 11A_M_792


title: 11A_M_790


title: 11A_M_770


title: 11A_M_775


title: 11A_M_772


title: 11A_M_779


title: 11A_M_773


title: 11A_M_774


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title: 11A_M_771


title: 11A_M_769


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title: 11A_M_767


title: 11A_M_763


title: 11A_M_764


title: 11A_M_762


title: 11A_M_766


title: 11A_M_765


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title: 11A_M_778


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title: 11A_M_757


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title: 11A_M_234


title: 11A_M_233


title: 11A_M_229


title: 11A_M_23


title: 11A_M_228


title: 11A_M_230


title: 11A_M_227


title: 11A_M_247


title: 11A_M_225


title: 11A_M_224


title: 11A_M_223


title: 11A_M_222


title: 11A_M_221


title: 11A_M_220


title: 11A_M_219


title: 11A_M_22


title: 11A_M_217


title: 11A_M_215


title: 11A_M_231


title: 11A_M_213


title: 11A_M_218


title: 11A_M_212


title: 11A_M_214


title: 11A_M_209


title: 11A_M_211


title: 11A_M_210


title: 11A_M_208


title: 11A_M_203


title: 11A_M_207


title: 11A_M_206


title: 11A_M_226


title: 11A_M_204


title: 11A_M_21


title: 11A_M_194


title: 11A_M_199


title: 11A_M_192


title: 11A_M_205


title: 11A_M_19


title: 11A_M_216


title: 11A_M_189


title: 11A_M_188


title: 11A_M_200


title: 11A_M_202


title: 11A_M_201


title: 11A_M_20


title: 11A_M_197


title: 11A_M_183


title: 11A_M_198


title: 11A_M_196


title: 11A_M_193


title: 11A_M_2


title: 11A_M_187


title: 11A_M_190


title: 11A_M_184


title: 11A_M_191


title: 11A_M_186


title: 11A_M_181


title: 11A_M_179


title: 11A_M_182


title: 11A_M_180


title: 11A_M_195


title: 11A_M_177


title: 11A_M_175


title: 11A_M_176


title: 11A_M_167


title: 11A_M_166


title: 11A_M_165


title: 11A_M_164


title: 11A_M_162


title: 11A_M_173


title: 11A_M_171


title: 11A_M_185


title: 11A_M_17


title: 11A_M_178


title: 11A_M_168


title: 11A_M_170


title: 11A_M_174


title: 11A_M_160


title: 11A_M_18


title: 11A_M_163


title: 11A_M_158


title: 11A_M_157


title: 11A_M_155


title: 11A_M_159


title: 11A_M_161


title: 11A_M_16


title: SAMPLE 26_SD_5

city: Frederiksberg C

first: Lisbeth Høier

last: Olsen

address: Ridebanevej 9

department: Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

data_processing:
Data were pre-processed using the GenEx Pro software version 6.1. Briefly, data were corrected for PCR efficiency (assays with an efficiency of 90-110% and R2≥ 0.98 were accepted), ACBT, TBP and RPL4 were the most stable reference genes and were used to normalize the qPCR data. Subsequently, relative expression (or fold changes) for each assay was calculated scaling all samples to the SD diet group. Data were log2 transformed prior to statistical analysis.
fold_change.txt reports test/control (i.e., FFC or FFC-DIA/SD) ratios.

label: Eva Green

organism: Sus scrofa

source_name: Kidney tissue

label_protocol: Five-hundred ng of total RNA were used to perform cDNA synthesis. qPCR was carried out using 2X SsoFast EvaGreen Supermix with low ROX (Bio-Rad), primer pairs, 2X Assay Loading Reagent (Fluidigm) and 20X DNA Binding Dye (Fluidigm) according to manufacturer’s protocol.

extract_protocol: Sixty mg of kidney tissue per sample were homogenized in a GentleMACSTM Octo Dissociator machine (Miltenyi Biotec) using the RNeasy® Mini Kit (Qiagen) with DNase digestion

value: Male, castrated

value: Göttingen Minipigs

tag: developmental stage

value: Adult

value: Fed standard diet (SD)

value: kidney


title: SAMPLE 27_SD_6


title: 11A_M_156


title: 11A_M_169


title: SAMPLE 25_SD_4


title: 11A_M_172


title: SAMPLE 28_SD_7


title: 11A_M_154


title: 11A_M_153


title: 11A_M_152


title: 11A_M_1515


title: 11A_M_1517


title: SAMPLE 21_FFC_13

value: Fed high fat/fructose/cholesterol diet (FFC)


title: SAMPLE 23_SD_2


title: SAMPLE 22_SD_1


title: 11A_M_1513


title: SAMPLE 20_FFC_12


title: SAMPLE 16_FFC_8


title: 11A_M_1511


title: 11A_M_1512


title: SAMPLE 19_FFC_11


title: SAMPLE 15_FFC_7


title: 11A_M_151


title: SAMPLE 14_FFC_6


title: 11A_M_1516


title: 11A_M_1510


title: 11A_M_1508


title: 11A_M_1507


title: 11A_M_1509


title: SAMPLE 24_SD_3


title: SAMPLE 12_FFC_4


title: SAMPLE 10_FFC_2


title: 11A_M_1514


title: SAMPLE 11_FFC_3


title: SAMPLE 9_FFC_1


title: SAMPLE 13_FFC_5


title: SAMPLE 17_FFC_9


title: 11A_M_1505


title: 11A_M_1506


title: 11A_M_1504


title: 11A_M_1502


title: SAMPLE 7_FFC-DIA_7

value: Fed high fat/fructose/cholesterol diet (FFC) and diabetic (DIA)


title: SAMPLE 8_FFC-DIA_8


title: SAMPLE 6_FFC-DIA_6


title: SAMPLE 5_FFC-DIA_5


title: 11A_M_1501


title: SAMPLE 4_FFC-DIA_4


title: 11A_M_150


title: SAMPLE 3_FFC-DIA_3


title: SAMPLE 2_FFC-DIA_2


title: 11A_M_15


title: SAMPLE 1_FFC-DIA_1


title: 11A_M_1499


title: 11A_M_1498


title: 11A_M_1497


title: 11A_M_1496


title: 11A_M_1494


title: 11A_M_1503


title: T47D_Y537S_clone2_ER_knock_down_neg_ctrl_miRNA_expression

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

hyb_protocol: Hybridization of nCounter Reporter Probes was performed per manufacturer's instructions using the NanoString nCounter platform with the human v3 miRNA panel.

scan_protocol: Sample scans were performed on the nCounterTM Digital Analyzer (NanoString Technologies).

data_processing: NanoString miRNA expression assay results in the form of raw counts were analyzed using NanoString’s nSolver software. Raw counts were normalized using two approaches. The first approach used the geometric mean for each sample of the top 100 highest expressed miRNAs across all samples to determine a normalization factor for each sample. The second approach used the geometric mean for each sample of the five spike-in miRNAs profiled for the assay to generate the normalization factors. Normalized counts were then log-scaled and used to perform t test to identify significantly differentially expressed miRNAs.

source_name: mammary gland ductal carcinoma

label_protocol: Samples were prepared per manufacturer's instructions using the NanoString human v3 miRNA panel (Catalog # CSO-MIR3-12).

growth_protocol: Cells were cultured in RPMI1640 Media (ThermoFisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol: Cells were washed with phosphate-buffered saline (PBS; ThermoFisher Scientific) and treated with RLT plus (Qiagen) lysis buffer with 1% beta-mercaptoethanol (BME; Sigma-Aldrich) for cell lysis. Cells were passed through a 21-gauge needle (Sigma-Aldrich) to facilitate genomic DNA lysis. For PDX lines, tissue samples were used from seven PDX lines (WT: HCI-003 and HCI-011; L536P: HCI-005, HCI-006, HCI-007; Y537S: HCI-013, HCI-013EI). Approximately 20mg of tissue per sample was homogenized in RLT plus lysis buffer with 1% beta-mercaptoethanol using gentleMACS M-tubes and a gentleMACS Octo Dissociator (Miltenyi Biotec). RNA extraction for both T-47D and PDX samples was performed using a Quick-RNA RNA Miniprep kit (Zymo Research), and RNA was measured using a Qubit fluorometer.

treatment_protocol: ER mutant or WT T-47D cells were plated in 100mm dishes and grown in estrogen-deprived media for four days prior to treatment with DMSO (0.1%) for 8 hours. For ESR1 knock-down experiments, cells were treated with DMSO (0.1%) and transfected with siRNAs targeting ESR1 or a non-targeting siRNA control for 48 hours prior to RNA harvest. PDX samples were surgically removed from mice and flash frozen. PDX samples were not treated.

tag: model

value: T-47D cell line

tag: esr1 genotype

tag: condition

value: ESR1 knock-down

value: mammary gland ductal carcinoma


title: T47D_D538G_clone2_ER_knock_down_neg_ctrl_miRNA_expression


title: T47D_Y537S_clone1_ER_knock_down_neg_ctrl_miRNA_expression


title: T47D_D583G_clone2_ER_knock_down_miRNA_expression


title: T47D_D538G_clone1_ER_knock_down_neg_ctrl_miRNA_expression


title: T47D_Y537S_clone1_ER_knock_down_miRNA_expression


title: 11A_M_1493


title: 11A_M_1492


title: 11A_M_1500


title: T47D_D538G_clone1_ER_knock_down_miRNA_expression


title: SAMPLE 18_FFC_10


title: 11A_M_1491


title: 11A_M_149


title: T47D_WT_clone1_25day_E2_miRNA_expression

value: ESR1 WT


title: 11A_M_1490


title: T47D_WT_clone2_25day_E2_miRNA_expression


title: 11A_M_1489


title: EM42_glucose+methanol_biol rep 3

city: Kongens Lyngby

first: Oscar

last: Puiggene

address: Kemitorvet 220

department: DTU Biosustain

institute: Novo Nordisk Foundation Center for Biosustainability

data_processing:
(Performed by BGI)
By using the internal software SOAPnuke to filter reads removed the reads mapped to rRNAs and get rawdata, they  filtered the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
By using HISAT2, they mapped the clean reads to the reference genome "NC_002947.4" and by using Bowtie2
the gene expression level for each sample was calculated with RSEM
(Performed by the authors) RNA-Seq data were analyzed using VisomX version 0.0.0.9 which namely relies on the DESeq2 package
Assembly: NC_002947.4
Supplementary files format and content: tab-delimited files include FPKM values for each Sample

organism: Pseudomonas putida

source_name: genome-reduced derivative of KT2440

growth_protocol: De Bont medium was used for all cultivations with 20 mM of glucose and when stated, 1M methanol or 240 mM formate from an initial OD of 0.1 until mid-exponential phase (ca. OD 0.5) at 30°C and 250 rpm in 250 mL flasks with 50 ml media.

extract_protocol:
(Performed by BGI) undisclosed details
(Performed by BGI) Total RNA: (1) mRNA fragmentation, (2) Oligo dT based mRNA enrichment, (3) Random N6 primer Reverse transcription, (4) Bubble adapter ligation, (5) PCR, (6) Heat separation, (7) single-strand circularization, (8) DNB-Seq

treatment_protocol: For treated samples, media was supplemented with 1M methanol or 240 mM formate

value: genome-reduced derivative of KT2440

value: Glucose+Methanol


title: EM42_glucose+methanol_biol rep 2


title: EM42_glucose+methanol_biol rep 1


title: 11A_M_1495


title: EM42 ∆∆FDH_glucose+formate_biol rep 3

value: dfdoGHI-fdhE dfmdEFGH

value: Glucose+Formate


title: EM42 ∆∆FDH_glucose+formate_biol rep 2


title: 11A_M_1486

value: male


title: 11A_M_1487


title: EM42 ∆∆FDH_glucose+formate_biol rep 1


title: 11A_M_1488


title: 11A_M_1485


title: EM42_glucose+formate_biol rep 3

value: WT


title: T47D_Y537S_clone2_ER_knock_down_miRNA_expression


title: EM42_glucose+formate_biol rep 2


title: EM42_glucose+formate_biol rep 1


title: 11A_M_1483


title: EM42_glucose (control)_biol rep 3

value: Glucose (control)


title: 11A_M_1482


title: 11A_M_1484


title: EM42_glucose (control)_biol rep 2


title: EM42_glucose (control)_biol rep 1


title: 11A_M_1480


title: 11A_M_148


title: 11A_M_1477


title: 11A_M_1475


title: 11A_M_1474


title: 11A_M_1473


title: 11A_M_1471


title: 11A_M_1472


title: 11A_M_1470


title: BaF3_gp130_IL11R_LIFR_IL11_d

city: Düsseldorf

first: Puyan

last: Rafii

state: NRW

address: Universitätsstraß 1

department: Biochemistry & Molecularbiology

country: Germany

institute: Heinrich-Heine-University

data_processing:
Illumina DRAGEN FASTQ Generation tool (version 3.8.4) was used for basecalling.
Data analyses on fastq files were conducted with CLC Genomics Workbench (version 22.0.2, QIAGEN, Venlo. NL).
After UMI (Unique Molecular Identifier) filtering, all remaining reads of all probes were adapter trimmed and quality trimmed (Illumina Adapter: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA)
Mapping was done against the Mus musculus (mm39; GRCm39.107) (July 20, 2022) genome sequence.
After grouping of samples (for biological replicates each) according to their respective experimental condition, the statistical differential expression was determined using the Differential Expression for RNA-Seq tool (version 2.7). The Resulting 𝑃 values were corrected for multiple testing by FDR and Bonferroni-correction. A 𝑃 value of ≤0.05 was considered significant.
Assembly: mm 39 (107)
Supplementary files format and content: xlsx file matrix with raw counts; gene IDs as lines and samples as columns

growth_protocol: All cells were grown at 37°C with 5% CO2 in a water-saturated atmosphere in Dulbecco`s modified Eagle`s medium (DMEM) high-glucose culture medium (GIBCO®, Life Technologies, Darmstadt, Germany) with 10% fetal calf serum (GIBCO®, Life Technologies) and 60 mg/l penicillin and 100 mg/l streptomycin (Genaxxon Bioscience GmbH, Ulm, Germany). Murine Ba/F3-gp130 cells were obtained from Immunex (Seattle, WA, USA) and grown in the presence of HIL-6. 0.2% (10ng/ml) conditioned medium from a stable clone of CHO-K1 cells secreting HIL-6 in the supernatant

extract_protocol:
mRNA was isolated with NucleoSpin RNA (Macherey-Nagel, Düren, Germany; cat. no. 740955.250) according to vendor’s manual. DNase digested total RNA samples used for 3´-RNA Seq analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific) and quality measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA standard Sensitivity Assay’ (Agilent Technologies, Inc. Santa Clara, USA). All samples in this study showed very high quality RNA Quality Numbers (RQN; mean = 10.0).
The library preparation was performed according to the manufacturer’s protocol using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD from Lexogen®. Input mount was 200 ng totalRNA. Bead purified libraries were normalized and finally sequenced on the NextSeq2000 system (Illumina Inc. San Diego, USA) with a read setup of SR 1x100 bp.

treatment_protocol: Ba/F3 cells expressing the appropriate receptors were stimulated with synthetic and control cytokines for 40 min at 37°C.


title: BaF3_gp130_IL11R_LIFR_LIF_d


title: 11A_M_1481


title: 11A_M_147


title: RAW 264 cells_BTEE pre-treatment 24h_LPS induction 17h_rep2

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description: Gene expression data from RAW264 cells, pre-treated with BTEE for 24 h and then LPS-induced for 17h

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, mouse; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CHP files ).

label: biotin

organism: Mus

source_name: RAW264 cells were treated with 0.2 mg/mL BTEE for 24 h and then induced with LPS solution (1 ng/mL) for 17 h

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: RAW264 cells derived from a murine macrophage cell line (Resource No. RCB0535) were purchased from RIKEN BioResource Center (RIKEN BRC, Tsukuba, Ibaraki, Japan). RAW264 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Merck KGaA, Darmstadt, Germany) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Bio West, Nuaillé, France) and 1penicillin-streptomycin solution (Merck KGaA) at 37ºC in a humidified incubator containing 5% CO2 using 75cm2 flask (BD FALCON, Corning, NY, USA)

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Lyophilized powder of Botryococcus terribilis TEPMO-26 (100 mg) was extracted with 70% Ethanol (1 mL) at room temperature under the dark for 2 weeks. After the extraction was completed, it was centrifuged at 1000 xg for 10 minutes and collected the supernatant. The supernatant of the extracted sample was filtered by using a 0.22 µm filter unit and stored at -20 ºC in the dark until use. Lipopolysaccharide (LPS; E. coli O111:B4) was purchased from EMD Millipore Co. (Billerica, MA USA). 5 mg of LPS was dissolved in 2 ml of PBS (-), and stored at -80 ℃ under the dark until use. RAW264 cells were seeded into a 96-well plate at density of 2.0×105 cells/mL and incubated at 37 °C for 24 h. The cells were treated with or without BTEE at 37 °C for 24 h. After the BTEE treatment, the LPS solution (1 ng/ml) was added to each well and incubated for 6h and 17 h at 37 °C.

value: RAW264 cells (Resource No. RCB0535, RIKEN BRC, Tsukuba, Ibaraki, Japan)


title: RAW 264 cells_BTEE pre-treatment 24h_LPS induction 17h_rep1


title: 11A_M_1469


title: 11A_M_1468


title: RAW 264 cells_No pre-treatment_LPS induction 17h_rep2

description: Gene expression data from RAW264 cells, maintained in culture medium for 24 h and then LPS-induced for 17h

source_name: RAW264 cells were maintained in culture medium for 24h and then induced with LPS solution (1 ng/mL) for 17 h


title: 11A_M_1478


title: BaF3_gp130_IL6R_LIFR_IL6_d


title: BaF3_gp130_IL11R_LIFR_NC_d

description: untreated control


title: RAW 264 cells_No pre-treatment_LPS induction 17h_rep1


title: 11A_M_1467


title: 11A_M_1466


title: BaF3_gp130_IL6R_LIFR_GIO6_d


title: RAW 264 cells_BTEE pre-treatment 24h_LPS induction 6h_rep2

description: Gene expression data from RAW264 cells, pre-treated with BTEE for 24 h and then LPS-induced for 6h

source_name: RAW264 cells were treated with 0.2 mg/mL BTEE for 24 h and then induced with LPS solution (1 ng/mL) for 6 h


title: 11A_M_1465


title: 11A_M_1476


title: RAW 264 cells_BTEE pre-treatment 24h_LPS induction 6h_rep1


title: BaF3_gp130_IL6R_LIFR_GIL6_d