title: RNA-seq of Mus musculus: iKlf5_D5_CHIR_LIF_rep2

city: Shen Zhen

first: Xinyu

last: Wu

address: BGI Space-Time Research Center

institute: BGI

data_processing:
For bulk RNA-seq analysis, reads from the RNA-seq data were aligned to the Ensembl v76 (mm10) transcript annotations using STAR (v.2.7.3a) with default parameter. Gene counts and TPM (Transcript per million) were calculated using RSEM (v1.3.1).For CUT&Tag, reads were trimmed of adapters and low-quality reads were removed by fastp ref (v0.12.4) with default parameter. Trimmed data was proceeded as previously described ref. Brieﬂy reads were first aligned to the mm10 assembly using Bowtie2 (v2.4.4) with the settings --local --very-sensitive-local --no-unal --nomixed --no-discordant --phred33 -I 10 -X 700. Low quality mapped reads were removed using Samtools(v1.9)61 with the settings -q 30. Duplicated reads were collapsed using sambamba (v0.8.0). CUT&Tag sample were called peaks using MACS2 (v2.2.7.1) with the settings -f BAMPE -g mm --SPMR --nomodel --keep-dup 1 --extsize 200 -q 1e-05 .
Assembly: mm10
Supplementary files format and content: For bulk RNA-seq all sample were normolized by TPM.For CUT&Tag the BigWig files were generated using deeptools (v3.4.3) bamCoverage tools with the settings --normalizeUsing RPKM

source_name: cell line

extract_protocol:
For RNA-seq cells were lysed by RNAzol®RT (MRC) and total RNA was extracted following the manufacturer’s instructions.
For RNA-seq extracted RNA was sent to BGI Genomics, where library construction and sequencing were performed.For CUT&Tag library construction, NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit for Illumina (Novoprotein) was used. In brief, 105 cells were incubated 10min at room temperature with Concanavalin A-coated magnetic beads. Bead bound cells were collected by placing a tube on a magnetic stand and removing the clear liquid. The bead-bound cells were resuspended in primary antibody buffer and incubated 2h at room temperature. Tubes were placed on a magnetic rack to remove the supernatants. Secondary antibodies were added and samples were incubated at room temperature for 1h. After placing the tubes on the magnetic rack and removing the supernatants, a mixture of pA-Tn5 were added to the bead-bound cells, vortexed gently, and incubated at RT for 1 h. After removed unbound pA-Tn5 protein, the cells were resuspended in tagmentation buffer and incubated at 37 °C for 1 h. One microliter of 10% SDS was added to stop tagmentation and incubated at 55 °C for 1 h. DNA was then extracted using magnetic beads. Purified DNA fragments were amplified by PCR for 15–20 cycles and the PCR products were purified following the kit’s instructions. CUT&Tag library construction were performed in duplicate. Libraries were sequenced by Berry Genomics Co. Ltd. (Beijing, China). Primary antibodies used were anti-KLF5 (R&D Systems).

value: cell line


title: NR_SK_3_002_Visit1_Involved_Nick_Reynolds_S75

status: Public on Jun 01 2025

type: SRA

city: Newcastle upon Tyne

first: Simon

middle: Joseph

last: Cockell

address: Framlington Place

department: School of Biomedical, Nutritional and Sport Sciences

country: United Kingdom

institute: Newcastle University

description: Library name: Sample_3

library_source: transcriptomic

data_processing:
Reads were quantified to Ensembl (rel91) using Kallisto (v0.46.0)
Transcript level counts were aggrgated to the gene level using tximport.
Data was analysed using Limma
Assembly: GRCh38, Ensembl release 91
Supplementary files format and content: txt files with transcript-level counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Involved

extract_protocol:
RNA was extracted following the Qiagen AllPrep kit’s protocol.  RNA concentration/integrity was checked using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano assay (Agilent: 5067-1511); only samples with an RNA integrity number (RIN) of 8 or more were sequenced.
RNA library preparation from total RNA was conducted following the manufacturer’s protocol for the Kapa mRNA HyperPrep Kit.

treatment_protocol: The subject group were treated with oral methotrexate (10mg for the first week, 15mg/week thereafter, increased incrementally to maximum dose 25mg/week if suboptimal response).

tag: tissue

value: skin biopsy

tag: patient

tag: visit

value: Involved

tag: easi


title: RNA-seq of Mus musculus: iEmpty_D5_CHIR_LIF_rep2

country: China

molecule: total RNA

organism: Mus musculus


title: NR_SK_30_006_Baseline_Involved_Nick_Reynolds_S101

description: Library name: Sample_30

value: Baseline


title: Control (PBS treated) Embryonic day 18 male biological rep 2, image 2

type: RNA

city: Boston

first: Brian

last: Kalish

state: MA

address: 220 Longwood Ave

department: Neurobiology

country: USA

institute: Boston Children's Hospital

description:
E18M_4
mouse brain gene panel

hyb_protocol: A total of 500 genes were selected and assigned a 20-bit binary barcode which was used for generating MERFISH probes. Slides were prepared as per Vizgen protocol, briefly, slides were washed with 1x PBS followed by Sample Prep Wash Buffer (Vizgen, PN 20300001). Slides were incubated in Formamide Wash Buffer (Vizgen, PN 20300002) for 30 min at 37°C, then gene panel mix was spread on the section and incubated for 42-46 hr at 37°C in a humidified incubator. Slides were then incubated two times in Formamide Wash Buffer for 30 min each at 47°C, and washed with sample prep wash buffer for at least 2 min. Sections were coated in gel embedding solution (0.05% w/v ammonium persulfate, 0.05% v/v N,N,N’,N'-tetramethylethylenediamine in Gel Embedding Premix (Vizgen, PN 20300004)) and incubated at RT for 1.5 hr, tissue was cleared in 1:100 proteinase K in Clearing Premix (Vizgen, PN 20300003) at 37°C overnight or for a maximum of 7 days to clear lipids and proteins that may contribute to auto-fluorescence background noise. Prior to imaging, sections were washed two times with Sample Prep Wash Buffer, incubated in DAPI and PolyT Staining Reagent (Vizgen, PN 20300021) for 15 min on a rocking platform, incubated in Formamide Wash Buffer for 10 min, and washed again with Sample Prep Wash Buffer.

scan_protocol: Imaging was performed on the MERSCOPE platform (Vizgen, Cat: 10000001) according to manufacturer instructions.

data_processing: Transcript barcodes were read and matched assigned to the correct gene. MERFISH images were segmented using Vizgen's post-processing tool and Cellpose v2. DAPI and PolyT signals were used to delinate the cell boundaries. Individual RNA molecules were assigned to a cell based on whether they were positioned within the marked boundary. Anatomical segmentation was performed using the MERSCOPE Visualizer software. Cells for MERFISH were processed using the Seurat V5 package in R.

label: Gene targeting probes

source_name: Whole embryonic brain, Control (PBS)

label_protocol: Single-cell spatial RNA imaging  was performed using a gene panel targeting 500 transcripts.

extract_protocol: Fresh frozen brain were cryo-sectioned at 10 μm thickness at -21°C, and mounted onto MERSCOPE beaded slides. Sections were allowed to refreeze, and then fixed for 15 minutes in 4% paraformaldehyde prepared in 1x PBS, followed by 3 washings with 1x PBS for 5 minutes each and stored in 70% ethanol overnight.

value: Whole embryonic brain

tag: treatment

value: Control (PBS treated)

value: Embryonic day 18

tag: Sex

value: male


title: RNA-seq of Mus musculus: iKlf5_D5_CHIR_LIF_rep1


title: Brain stem, D4 post-infection, rep3

city: Aarhus

first: Soren

last: Paludan

address: CF Møllers Alle 6, Building 1115

department: Biomedicine

country: Denmark

institute: Aarhus university

description:
Library name: Sample3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads demultiplexed from the DNBSEQ-G400 were mapped to a composite reference genome consisting of the mouse genome (GRCm39) and the HSV-1 genome (JX142173) using Cell Ranger v6.1 from 10x Genomics.
Assembly: GRCm39
Supplementary files format and content: gene expression value in HDF5 files

source_name: Brain stem

extract_protocol:
Brain stems were harvested from animals sedated with ketamine and xylazine and thoroughly perfused with a minimum of 25 ml of PBS. Brain stems were cut into pieces and digested for 40 min at 37 °C with 5% CO2 in PBS supplemented with 1.6 IU ml-1 Collagenase/Dispase (Roche) and 0.5 mg ml-1 DNase I (Sigma-Aldrich). 20 μl of sterile EDTA was added to each sample and incubated at 37°C for another 5 min. Tissues were then mechanically disrupted through a 70um cell strainer into a single-cell suspension. Single-cell suspensions were washed with 25ml 2% FCS-HBSS (Thermo Fisher Scientific), centrifuged, and resuspended in a mixture of PBS with 0.5% BSA (VWR) and Debris Removal Solution (Miltenyi Biotec). After overlaying PBS with 0.5% BSA, suspensions were centrifuged, resuspended, and adjust the cell count to 106 cells ml-1.
Single cell suspensions were converted to barcoded scRNAseq libraries following the manufacturer’s instructions of Chromium Single Cell 3’ Library, Gel bead & index kit and Chip G Kit (v3.1, 10x Genomics), aiming for recovering 10,000 cells per library. Quality control of libraries were performed with Tapestation 4200. After QC, libraries were sequenced on an MGI DNBSEQ-G400 sequencer.

value: Brain stem

value: Infected


title: RNA-seq of Mus musculus: iKlf5_D5_LIF_rep2


title: RNA-seq of Mus musculus: iEmpty_D5_CHIR_LIF_rep1


title: NR_SK_29_005_Visit2_Uninvolved_Nick_Reynolds_S116

description: Library name: Sample_29

source_name: Uninvolved

value: Uninvolved


title: RNA-seq of Mus musculus: iKlf5_D5_LIF_rep1


title: AS, replicate1, scRNAseq

city: GuangZhou

first: bian

last: zhenhua

state: GuangDong

address: Panyu University Town

institute: South China University of Technology

data_processing:
The raw sequencing data of gene expression were aligned with the Macaca fascicularis reference genome (Macaca6), and subjected to barcodes assignment and unique molecular identifier (UMI) counting using the CellRanger V6.1.2 pipeline (10X genomics).
To acquire the dataset, genes with low detected cell number (less than 3) and cells with low detected genes (less than 200) were excluded with Seurat package (V4.0.0). Also, single cells with 200-4000 genes and less than 20000 reads counts were retained to ensure the quality of datasets and most of the heterogeneous cell types were included for downstream analyses. The transcriptome expression matrix were firstly natural-log transformed as log1p values. The top 2000 highly variable genes were selected for downstream principal component analysis. To integrated the six samples together, we used harmony package to remove the batch effects. The top 30 harmony principal components were used for cluster (resolution for 0.2), UAMP projection and visualization. The cluster-specific expressed genes were extracted for each cluster to annotate the cell types.
Assembly: Macaca fascicularis 6
Supplementary files format and content: h5

organism: Macaca fascicularis

source_name: Bone marrow

extract_protocol:
First, 3 mL of Ficoll solution (Lymphoprep, Stemcell Technology) was added to a 15 mL centrifuge tube. The centrifuge tube was tilted, and the bone marrow (less than 3 mL) was transferred to the top of the Ficoll solution against the wall of the centrifuge tube. Next, the centrifuge tube was centrifuged at 800 × g for 20 minutes (acceleration 6, brake 2) at room temperature. Finally, the BMMC at the interface were carefully harvested.
The isolation BMMC were captured by the 10X genomics chromium Single Cell 5’ solution. Then, reverse transcription was performed on drops and the cDNA was amplified following multiple amplification schemes from 10X genomics, including extension, purification, adapter connection. Sequencing libraries were quantified using the Qubit High Sensitivity DNA assay and NGS3K assay. The library was sequenced by Novaseq illumina (Illumina, San Diego, CA) on a 150 bp paired-end run. All the single cell library preparation was according to the 10X genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index).

value: Bone marrow

tag: cell type

value: immune cells

tag: disease state

value: Ankylosing Spondylitis-like disease

tag: age

value: 10.3 years


title: Control (PBS treated) Embryonic day 18 male biological rep 2, image 1

description:
E18M_3
mouse brain gene panel


title: RNA-seq of Mus musculus: iEmpty_D5_LIF_rep1


title: Control (PBS treated) Embryonic day 18 male biological rep 1, image 2

description:
E18M_2
mouse brain gene panel


title: Control (PBS treated) Embryonic day 14 male biological rep 1, image 2

description:
E14M_2
mouse brain gene panel

value: Embryonic day 14


title: Control (PBS treated) Embryonic day 18 male biological rep 1, image 1

description:
E18M_1
mouse brain gene panel


title: RNA-seq of Mus musculus: iKlf5_D2_CHIR_LIF_rep2


title: AS, replicate3, scRNAseq

value: 11.8 years


title: Control (PBS treated) Embryonic day 18 male biological rep 3, image 1

description:
E18M_5
mouse brain gene panel


title: NR_SK_26_005_Baseline_Uninvolved_Nick_Reynolds_S98

description: Library name: Sample_26


title: Myometrium from testosterone treated patient (MyoT), patient MP565

type: genomic

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw idat files were processed into beta values in R  using the openSesame pipeline from Sesame (version  1.23.6). Beta values were then batch corrected using ChAMP (version 2.36.0)
Batch corrected beta values using ChAMP, following initial openSesame pipeline using Sesame.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: myometrium

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using colums from the Qiagen DNEasy Blood and Tissue kit

value: myometrium

tag: race/ethnicity

value: C

tag: batch


title: RNA-seq of Mus musculus: iEmpty_D2_CHIR_LIF_rep1

value: cell line


title: RNA-seq of Mus musculus: iKlf5_D2_CHIR_LIF_rep1


title: NR_SK_25_005_Baseline_Involved_Nick_Reynolds_S97

description: Library name: Sample_25

value: skin biopsy

value: Baseline

value: Involved


title: RNA-seq of Mus musculus: iKlf5_D2_LIF_rep2


title: RNA-seq of Mus musculus: iEmpty_D2_LIF_rep2


title: RNA-seq of Mus musculus: iEmpty_D2_LIF_rep1


title: RNA-seq of Mus musculus: iEmpty_D5_LIF_rep2


title: NR_SK_28_005_Visit2_Involved_Nick_Reynolds_S100

description: Library name: Sample_28


title: Myometrium from testosterone treated patient (MyoT), patient MP554


title: NR_SK_24_015_Baseline_Uninvolved_Nick_Reynolds_S96

description: Library name: Sample_24


title: RNA-seq of Mus musculus: iTSC_OC-Epi_No2_rep1


title: NR_SK_23_015_Baseline_Involved_Nick_Reynolds_S95

description: Library name: Sample_23


title: RNA-seq of Mus musculus: iTSC_OC-Epi_No2_rep2


title: Myometrium from testosterone treated patient (MyoT), patient MP551


title: RNA-seq of Mus musculus: iTSC_Epi2-1_No5_rep2


title: NR_SK_27_005_Visit1_Involved_Nick_Reynolds_S99

description: Library name: Sample_27


title: RNA-seq of Mus musculus: iEmpty_D2_CHIR_LIF_rep2


title: NR_SK_22_012_Visit2_Uninvolved_Nick_Reynolds_S94

description: Library name: Sample_22


title: B16-F10 cells, sgCtrl treated with Decitabine, rep2

city: tianjin

first: junying

last: ma

address: Heping District Meteorological Observatory Road

institute: Tianjin Medical University

data_processing:
Paired-end sequencing reads were meticulously trimmed and filtered using fastp (v0.23.4) employing its default settings. Subsequently, these reads were aligned to the mouse mm10 reference genome utilizing STAR (v2.7.5c), with the parameters set to "--outSAMtype BAM SortedByCoordinate --twopassMode Basic --outFilterMismatchNmax 2 --outFilterMultimapNmax 1". Gene expression quantification was accurately calculated using featureCounts from the Rsubread package (v2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw count of each gene for each sample.

source_name: B16-F10 cells

extract_protocol:
Total RNA was extracted using the Trizol method, followed by purification and concentration with an RNA Clean & Concentrator kit. mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads, ensuring enrichment of polyadenylated mRNA transcripts.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: B16-F10 cells


title: RNA-seq of Mus musculus: ESC_Klf5_KO_rep1


title: RNA-seq of Mus musculus: iTSC_Epi2-1_No5_rep1


title: Myometrium from testosterone treated patient (MyoT), patient MP542


title: NR_SK_2_002_Baseline_Uninvolved_Nick_Reynolds_S74

description: Library name: Sample_2


title: RNA-seq of Mus musculus: ESC_WT_rep2


title: RNA-seq of Mus musculus: TSC_WT_rep1


title: Myometrium from testosterone treated patient (MyoT), patient MP545


title: NR_SK_19_012_Baseline_Uninvolved_Nick_Reynolds_S91

description: Library name: Sample_19


title: Myometrium from testosterone treated patient (MyoT), patient MP550


title: RNA-seq of Mus musculus: ESC_Klf5_KO_rep2


title: RNA-seq of Mus musculus: ESC_WT_rep1


title: NR_SK_20_012_Visit1_Involved_Nick_Reynolds_S92

description: Library name: Sample_20


title: RNA-seq of Mus musculus: EpiSCs_WT_rep2


title: RNA-seq of Mus musculus: TSC_WT_rep2


title: snRNAseq AAV-Ant1

city: Philadelphia

first: Joseph

middle: W

last: Guarnieri

state: PA

address: 3501 Civic Center Blvd

department: Center for Mitochondrial and Epigenomic Medicine

institute: Children's Hosptial of Philadelphia

description:
Code_0215
snRNAseq-integration.rds

data_processing:
Sequencing data was aligned using the Ion Torrent S5 ampliSeqRNA and coverageAnalysis plugins.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Heart

extract_protocol:
RNA was collected using TRIzol™ Reagent (Invitrogen, 15596026) from heart samples.
The RNA was assessed by NanoDrop spectrophotometer (ThermoFisher Scientific) and quantified by Qubit Flex (Thermofisher Scientific) using the Qubit RNA HS Assay Kit (Thermofisher Scientific, Q32855).
The RNA was diluted to 1.43 ng/ul and reverse transcribed into cDNA using the Ion Torrent™ NGS Reverse Transcription Kit (Cat. No. A45003). The RNA library was prepared using the Ion Torrent S5 Chef and Ion AmpliSeq Kit for Chef DL8 (Thermofisher Scientific, A29024) and sequenced using the Ion Torrent S5 Sequencer and Ion 540 Kit (Thermofisher Scientific, A30011).
For snRNA-seq, isolated nuclei were processed using the Chromium Single Cell 3ʹ Reagent V3.1 kit from 10X Genomics. A total of 8,000 nuclei per sample were loaded into a Chip G. Barcoding, cDNA amplification, and library construction were performed according to the Chromium 3ʹ V3.1 protocol. Sequencing was performed on a DNBSEQ-T7 platform targeting 20,000 reads per nucleus.

treatment_protocol: Bulk RNA sequencing and single nucleus RNA Sequencing (snRNA-seq) analysis on C57BL/6JEiJ, C57BL/6JEiJ Ant1-/-, and C57BL/6JEiJ Ant1-/- ND6P25L mice (WT, ANT1, ANT1 ND6), pericardially injected with 2.5x10^11 vg AAV2/9Des-Gfp-mAnt1 or 2.5x10^11 vg AAV2/9Des-Gfp .

value: Heart

tag: genotype

value: C57BL/6JEiJ ANT1 -/-

value: 2.5x10^11 vg AAV2/9Des-Gfp-mAnt1


title: RNA-seq of Mus musculus: EpiSCs_WT_rep1


title: NR_SK_18_012_Baseline_Involved_Nick_Reynolds_S90

description: Library name: Sample_18


title: Myometrium from fibroid patient (MyoF), patient MP295

value: AA


title: NR_SK_21_012_Visit2_Involved_Nick_Reynolds_S93

description: Library name: Sample_21


title: snRNAseq WT

description:
Code_0213
snRNAseq-integration.rds

value: 0 vg AAV2/9Des-Gfp-mAnt1


title: Myometrium from fibroid patient (MyoF), patient MP411


title: Myometrium from fibroid patient (MyoF), patient MP456

value: A


title: NR_SK_16_008_Visit2_Involved_Nick_Reynolds_S88

description: Library name: Sample_16


title: iK2_PNT_D5：D5_K2_rep2

data_processing:
Raw sequencing reads were filtered and demultiplexed using PISA (v0.2) (https://github.com/shiquan/PISA). Filtered reads were aligned to mm10 genome reference using STAR ref (v2.7.3a) and sorted by sambamba (v0.7.0)ref. Cell versus gene UMIs (Unique Molecular Identifiers) count matrices were generated by PISA. Doublets were estimation and removal by R package DoubletFinderref (v2.0.3) with the default parameter. The cell free mRNA contamination were estimation and removal by R package SoupX (v1.6.1).
Assembly: mm10
Supplementary files format and content: Processed data files were removed doublets and free mRNA contamination

source_name: blastocyst

extract_protocol:
Cells were dissociated into single cells with Accutase Solution. After passing through 40 μM cell strainers, cell suspensions were converted to barcoded scRNA-seq libraries according to the manufacturer’s protocol.
scRNA-seq libraries were prepared using a DNBelab C Series Single-Cell Library Prep set

value: blastocyst

value: OG2 EpiSCs

value: iPSC


title: iK4_PNT_D5：D5_K4_rep1


title: NR_SK_15_008_Visit1_Involved_Nick_Reynolds_S87

description: Library name: Sample_15


title: iK5_PNT_D0-5：D5_K5_rep3


title: NR_SK_17_008_Visit2_Uninvolved_Nick_Reynolds_S89

description: Library name: Sample_17

value: Uninvolved


title: iK2_PNT_D5：D5_K2_rep1


title: iK5_PNT_D0-5：D5_K5_rep2


title: Myometrium from fibroid patient (MyoF), patient HF33

value: myometrium


title: snRNAseq Ant1-/-

description:
Code_0214
snRNAseq-integration.rds


title: iK5_PNT_D0-5：D4_K5_rep2


title: NR_SK_14_008_Baseline_Uninvolved_Nick_Reynolds_S86

description: Library name: Sample_14


title: iK5_PNT_D0-5：D5_K5_rep1


title: Myometrium from fibroid patient (MyoF), patient HF29


title: iK5_PNT_D0-5：D4_K5_rep1


title: NR_SK_13_008_Baseline_Involved_Nick_Reynolds_S85

description: Library name: Sample_13


title: Myometrium from fibroid patient (MyoF), patient MP142

value: C


title: NR_SK_12_013_Baseline_Uninvolved_Nick_Reynolds_S84

description: Library name: Sample_12


title: Myometrium from fibroid patient (MyoF), patient HF28


title: NR_SK_11_013_Baseline_Involved_Nick_Reynolds_S83

description: Library name: Sample_11


title: iK5_PNT_D0-5：D2_K5_rep2


title: Myometrium from fibroid patient (MyoF), patient HF27


title: iK5_PNT_D0-5：EpiSCs

value: EpiSCs


title: NR_SK_1_002_Baseline_Involved_Nick_Reynolds_S73

description: Library name: Sample_1

value: skin biopsy


title: Myometrium from fibroid patient (MyoF), patient HF25

value: Multi


title: iK5_PNT_D0-5：D1_K5_rep2


title: NR_SK_10_003_Visit2_Uninvolved_Nick_Reynolds_S82

description: Library name: Sample_10


title: iK5_PNT_D0-5：D1_K5_rep1


title: Myometrium from fibroid patient (MyoF), patient MP278


title: Myometrium from fibroid patient (MyoF), patient HF24


title: sample120, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep10

city: Cambridge

first: Mary

last: Piper

state: Massachusetts

address: 1 Portland St

institute: Pfizer Inc

description:
RBI-0000097122
Original Plate name: RSA-0000111806_S60
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

data_processing:
Raw FASTQ files were processed using an internal pipeline, Rnaseq Experiment DAshboard, utilizing STAR (v2.7.3a) and Salmon (v1.5.2) to map reads to the rat genome and transcriptome (mRatBN7.2, Ensembl release 106), respectively, with ERCC spike-in sequences included. Quality of the samples was assessed using FastQC (v0.11.9), Picard Tools CollectRnaSeqMetrics (v 2.26.0), and MultiQC (v1.11) to explore base quality, rRNA content, intronic percentages, and mapping rates.  R2 FASTQ files exhibited poor quality, so downstream analysis was performed with R1 reads
The Salmon transcript abundance estimates were aggregated to the gene level using tximport (v1.22.0).
Quality control assessment was performed on the gene-level counts using principal component analysis. Several samples across tissues were removed due to failed sequencing runs and low numbers of reads (<1,000,000). For the kidney tissue, one additional sample was removed as an outlier based on PCA and hierarchical clustering analysis. Differential expression analysis was performed with DESeq2 (v1.34.0) with design: ~ sequencing batch + condition. Over-representation analysis and gene set enrichment analysis (GSEA) of the differential expression results was executed using clusterProfiler (v4.2.2) with GO, KEGG, and MSigDB gene sets. GSEA was performed on the apeglm (v1.16.0)-shrunken log2 fold changes output from DESeq2.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each sample for kidney
Supplementary files format and content: tab-delimited text file includes raw counts for each sample for heart
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for kidney for obese vs lean
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for kidney for obese BT2 vs vehicle
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for kidney for obese Empagliflozin vs vehicle
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for kidney for obese Empagliflozin-BT2 combo treatment vs vehicle
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for heart for obese vs lean
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for heart for obese BT2 vs vehicle
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for heart for obese Empagliflozin vs vehicle
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample combined with the differential expression results for heart for obese Empagliflozin-BT2 combo treatment vs vehicle

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Extraction was performed using the RNeasy Plus Universal Mini Kit (Qiagen) on approximately 50mg of frozen tissue.
Total RNA was evaluated for quality (RIN scores ≥ 7) by 4200 TapeStation System (Agilent) using RNA ScreenTape (cat. 5067-5576, Agilent). The concentrations were measured by High Lunatic plate (cat. 7012000, Unchained Labs). 400 ng total RNA was used as input for the mRNA-Seq library preparation using the TruSeq Stranded mRNA Library Prep Kit (cat. 20020594, Illumina). Poly-A containing mRNA was purified using poly-dT beads, fragmentation of RNA, first strand synthesis, second strand cDNA synthesis and End repairing, A-tailing, Adapter ligation, followed by PCR amplification with 15 PCR cycles to generate final cDNA libraries. The final libraries were then evaluated for quality by 4200 TapeStation System (Agilent) using D1000 ScreenTape (cat. 5067-5582, Agilent). The concentrations were measured using Qubit 1X dsDNA HS Assay Kit (cat. Q33231, Invitrogen-Life Technologies Corporation). The libraries were then normalized to 4 nM and re-quantitated using Qubit 1X dsDNA HS Assay Kit (cat. Q33231, Invitrogen- Life Technologies Corporation) and then pooled into two pools for sequencing. The pools were loaded on two NextSeq2000 sequencers for 75 Paired End run using P3 200 cycle kit (cat. 20040560, Illumina).

treatment_protocol: Compounds were administered in rodent chow.

value: heart

value: ZSF1 Obese

value: BT2 + Empagliflozin


title: sample119, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep9

description:
RBI-0000097121
Original Plate name: RSA-0000111805_S59
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: iK5_PNT_D0-5：D3_K5_rep2


title: Myometrium from fibroid patient (MyoF), patient HF23


title: sample118, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep8

description:
RBI-0000097120
Original Plate name: RSA-0000111804_S58
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Myometrium from fibroid patient (MyoF), patient HF19


title: KASUMI-1 cells, USP6

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

data_processing:
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4)
The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software
Assembly: Ensembl v101
Supplementary files format and content: text file includes FPKM values and raw counts for each Sample

source_name: Blood

growth_protocol: KASUMI-1 cells were maintained in PRMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

treatment_protocol: KASUMI-1 cells infected with lentivirus-pccl or USP6

value: Blood

value: AML


title: iK5_PNT_D0-5：D3_K5_rep1


title: sample117, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep7

description:
RBI-0000097119
Original Plate name: RSA-0000111803_S57
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Myometrium from fibroid patient (MyoF), patient HF18

value: AA


title: sample113, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep3

description:
RBI-0000097105
Original Plate name: RSA-0000111749_S83
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: KASUMI-1 cells, pccl

value: pccl


title: sample116, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep6

description:
RBI-0000097118
Original Plate name: RSA-0000111812_S56
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample114, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep4

description:
RBI-0000097106
Original Plate name: RSA-0000111750_S84
Repeat Plate name: RSA-0000111879_S32
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample115, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep5

description:
RBI-0000097107
Original Plate name: RSA-0000111751_S85
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp03B CD8 T cells, GEX

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
We use Cell Ranger 6.1.2 to align reads to GRCh38 human genome. Cell Ranger multi is used to quantify libraries of antibody-derived tags (ADT) and to identify hashtagged samples from pooled CITE-seq libraries. Downstream analysis is performed using the custom scripts for antigen demultiplexing and CITE-seq pipeline described in Seurat v4.2.1.
Poor quality cells are excluded based on the following criteria: cells with < 200 or more than 4000 genes, > 10% reads mapping to mitochondria and having > 20K ADT UMIs. We use DoubletFinder to remove cell doublets. Samples are individually normalized using SCTransform regressing out mitochondrial genes.
For ADT counts we use centralized log ratio transformation along with reciprocal PCA. Then, samples in different experiments are integrated using the diagonalized canonical correlation analysis to identify mutual nearest neighbor.
For Antigen we have used Antigen specificity score to identify the Antigen specific cells using custom scripts.
Assembly: GRCh38
Supplementary files format and content: CellRanger Output Files (filtered_gene_bc_matrices): Exp01_matrix.mtx.gz, Exp01_features.tsv.gz, Exp01_barcodes.tsv.gz.
Supplementary files format and content: CellRanger Output Files (filtered_gene_bc_matrices): Exp02_matrix.mtx.gz, Exp02_features.tsv.gz, Exp02_barcodes.tsv.gz.
Supplementary files format and content: CellRanger Output Files (filtered_gene_bc_matrices): Exp03_matrix.mtx.gz, Exp03_features.tsv.gz, Exp03_barcodes.tsv.gz.
Supplementary files format and content: Comma-separated files: Exp01_feature_reference.csv, Exp02_feature_reference.csv, Exp03_feature_reference.csv.
Supplementary files format and content: Comma-separated files: Exp01_filtered_contig_annotations.csv, Exp02_filtered_contig_annotations.csv, Exp03_filtered_contig_annotations.csv.
Supplementary files format and content: Comma-separated files: Exp01_antigen_specificity_scores.csv, Exp02_antigen_specificity_scores.csv, Exp03_antigen_specificity_scores.csv.
Supplementary files format and content: Comma-separated files: Exp01_cellbarcode_samplename.csv, Exp02_cellbarcode_samplename.csv, Exp03_cellbarcode_samplename.csv.
Supplementary files format and content: RDS files: CD8_Antigen_memory_BEAM_T.RDS, CD8_Antigen_BEAM_T.RDS, CD8_bulk_BEAM_T.RDS.
Library strategy: CITE-seq

extract_protocol:
MACS-purified CD8+ T cells from peripheral blood were subjected to BEAM-T staining (Chromium Human MHC Class I A*02:01 Monomer Kit, 10x Genomics, #1000542 and Chromium Single Cell 5' BEAM Core Kit PE, 10x Genomics, #1000539) and flow cytometry antibody staining according to the manufacturer’s instructions. Four to five individuals per experiment (3 experiments total) were processed. Live, single CD3+ CD8+ PE+ cells representing BEAM-T+ antigen-specific cells and PE– cells representing total CD8+ T cells were sorted. After FACS, cells were counted and equal cell numbers of PE+ and PE– cells from all individuals were pooled, if possible. The pooled sample was then stained with diluted TotalSeq-C cell surface marker antibodies (BioLegend). Cell viability was determined with Trypan Blue and was consistently >90%. Cells were subjected to high-throughput single cell capture via the Chromium X controller (10x genomics) and Chromium Next GEM Single Cell 5' HT Kit v2 (Dual Index, 10x genomics, #PN-1000374). About 40,000 cells were targeted for cell capture for each side of the HT chip.
Four libraries were generated from each captured sample: 5’ gene expression, feature barcodes (for TotalSeq-C antibodies including hashtag antibodies and cell surface marker), TCR (T cell receptor) sequences (Chromium Single Cell V(D)J Amplification kit, 10x Genomics, #PN-1000252) and BEAM-T antigen specificity. All captured samples and libraries were sequenced in one flow cell using a 100 cycle kit (paired-end) on a NovaSeq 6000 S4 (Illumina) targeting 20,000 read pairs/cell for gene expression, 5,000 read pairs/cell for feature barcodes, 5,000 read pairs/cell for TCR sequences, and 5,000 read pairs/cell for BEAM-T.

value: CD8 T cells

tag: library type

value: GEX


title: sample112, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep2

description:
RBI-0000097104
Original Plate name: RSA-0000111748_S82
Repeat Plate name: RSA-0000111878_S31
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp03B CD8 T cells, TCR

value: TCR


title: sample111, heart, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep1

description:
RBI-0000097103
Original Plate name: RSA-0000111747_S81
Repeat Plate name: RSA-0000111877_S30
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample110, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep10

description:
RBI-0000097092
Original Plate name: RSA-0000111822_S55
Repeat Plate name: RSA-0000111911_S20
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: Empagliflozin


title: Myometrium from fibroid patient (MyoF), patient HF15


title: Myometrium from fibroid patient (MyoF), patient HF17


title: sample109, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep9

description:
RBI-0000097091
Original Plate name: RSA-0000111824_S54
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Myometrium from testosterone treated patient (MyoT), patient MP562


title: Exp03B CD8 T cells, BEAM

library_source: other

molecule: other

value: BEAM


title: Myometrium from fibroid patient (MyoF), patient HF14

value: myometrium


title: sample107, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep7

description:
RBI-0000097089
Original Plate name: RSA-0000111826_S52
Repeat Plate name: RSA-0000111910_S19
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample108, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep8

description:
RBI-0000097090
Original Plate name: RSA-0000111825_S53
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample106, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep6

description:
RBI-0000097088
Original Plate name: RSA-0000111827_S51
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp03A CD8 T cells, GEX


title: Exp03A CD8 T cells, TCR


title: Myometrium from fibroid patient (MyoF), patient HF13


title: sample104, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep4

description:
RBI-0000097076
Original Plate name: RSA-0000111735_S69
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Myometrium from fibroid patient (MyoF), patient HF9


title: sample105, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep5

description:
RBI-0000097077
Original Plate name: RSA-0000111736_S70
Repeat Plate name: RSA-0000111876_S29
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp03A CD8 T cells, CITE

molecule: protein

value: CITE


title: Exp03A CD8 T cells, BEAM


title: sample102, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep2

description:
RBI-0000097074
Original Plate name: RSA-0000111733_S67
Repeat Plate name: RSA-0000111875_S28
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample101, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep1

description:
RBI-0000097073
Original Plate name: RSA-0000111732_S66
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample100, heart, ZSF1 Obese, Vehicle, 4 Study B, rep10

description:
RBI-0000097062
Original Plate name: RSA-0000111838_S50
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: Vehicle


title: Myometrium from fibroid patient (MyoF), patient HF8


title: sample103, heart, ZSF1 Obese, Empagliflozin, 5 Study B, rep3

description:
RBI-0000097075
Original Plate name: RSA-0000111734_S68
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample98, heart, ZSF1 Obese, Vehicle, 4 Study B, rep8

description:
RBI-0000097060
Original Plate name: RSA-0000111840_S48
Repeat Plate name: RSA-0000111909_S18
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp02B CD8 T cells, TCR


title: Myometrium from fibroid patient (MyoF), patient HF10

value: C


title: sample97, heart, ZSF1 Obese, Vehicle, 4 Study B, rep7

description:
RBI-0000097059
Original Plate name: RSA-0000111841_S47
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample99, heart, ZSF1 Obese, Vehicle, 4 Study B, rep9

description:
RBI-0000097061
Original Plate name: RSA-0000111839_S49
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample96, heart, ZSF1 Obese, Vehicle, 4 Study B, rep6

description:
RBI-0000097058
Original Plate name: RSA-0000111842_S46
original_plate2_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp02B CD8 T cells, GEX


title: iK5_PNT_D0-5：D2_K5_rep1

value: blastocyst

value: OG2 EpiSCs

value: iPSC


title: Myometrium from fibroid patient (MyoF), patient HF12


title: sample95, heart, ZSF1 Obese, Vehicle, 4 Study B, rep5

description:
RBI-0000097047
Original Plate name: RSA-0000111721_S55
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: heart

value: ZSF1 Obese


title: Myometrium from fibroid patient (MyoF), patient HF3


title: sample94, heart, ZSF1 Obese, Vehicle, 4 Study B, rep4

description:
RBI-0000097046
Original Plate name: RSA-0000111720_S54
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp02B CD8 T cells, BEAM

value: Blood


title: sample93, heart, ZSF1 Obese, Vehicle, 4 Study B, rep3

description:
RBI-0000097045
Original Plate name: RSA-0000111719_S53
original_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp03B CD8 T cells, CITE


title: Myometrium from fibroid patient (MyoF), patient HF2


title: sample91, heart, ZSF1 Obese, Vehicle, 4 Study B, rep1

description:
RBI-0000097043
Original Plate name: RSA-0000111717_S51
Repeat Plate name: RSA-0000111863_S16
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp02A CD8 T cells, TCR


title: Myometrium from fibroid patient (MyoF), patient HF1

value: AA


title: sample90, heart, ZSF1 Obese, BT2, 3 Study A, rep10

description:
RBI-0000097032
Original Plate name: RSA-0000111797_S45
Repeat Plate name: RSA-0000111896_S17
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Myometrium from fibroid patient (MyoF), patient HF4


title: Myometrium from fibroid-free patient (MyoN), patient MP561


title: Exp02A CD8 T cells, CITE


title: sample87, heart, ZSF1 Obese, BT2, 3 Study A, rep7

description:
RBI-0000097029
Original Plate name: RSA-0000111794_S42
Repeat Plate name: RSA-0000111895_S16
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample89, heart, ZSF1 Obese, BT2, 3 Study A, rep9

description:
RBI-0000097031
Original Plate name: RSA-0000111796_S44
original_plate2_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample88, heart, ZSF1 Obese, BT2, 3 Study A, rep8

description:
RBI-0000097030
Original Plate name: RSA-0000111795_S43
original_plate2_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Myometrium from fibroid-free patient (MyoN), patient MP552


title: sample86, heart, ZSF1 Obese, BT2, 3 Study A, rep6

description:
RBI-0000097028
Original Plate name: RSA-0000111793_S41
original_plate2_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp02B CD8 T cells, CITE


title: Myometrium from fibroid-free patient (MyoN), patient MP506


title: sample85, heart, ZSF1 Obese, BT2, 3 Study A, rep5

description:
RBI-0000097017
Original Plate name: RSA-0000111706_S40
Repeat Plate name: RSA-0000111862_S15
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: iK4_PNT_D5：D5_K4_rep2


title: Exp01B CD8 T cells, TCR


title: sample92, heart, ZSF1 Obese, Vehicle, 4 Study B, rep2

description:
RBI-0000097044
Original Plate name: RSA-0000111718_S52
Repeat Plate name: RSA-0000111864_S17
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt
Heart_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp02A CD8 T cells, BEAM


title: sample82, heart, ZSF1 Obese, BT2, 3 Study A, rep2

description:
RBI-0000097014
Original Plate name: RSA-0000111703_S37
Repeat Plate name: RSA-0000111859_S12
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample84, heart, ZSF1 Obese, BT2, 3 Study A, rep4

description:
RBI-0000097016
Original Plate name: RSA-0000111705_S39
Repeat Plate name: RSA-0000111861_S14
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample80, heart, ZSF1 Obese, Vehicle, 2 Study A, rep10

description:
RBI-0000097002
Original Plate name: RSA-0000111782_S40
Repeat Plate name: RSA-0000111894_S15
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample83, heart, ZSF1 Obese, BT2, 3 Study A, rep3

description:
RBI-0000097015
Original Plate name: RSA-0000111704_S38
Repeat Plate name: RSA-0000111860_S13
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Exp01B CD8 T cells, GEX


title: Exp02A CD8 T cells, GEX


title: Exp01B CD8 T cells, CITE


title: sample78, heart, ZSF1 Obese, Vehicle, 2 Study A, rep8

description:
RBI-0000097000
Original Plate name: RSA-0000111780_S38
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: DRGs from KPC- Grin2d +/+ Mouse Nr 1

city: Munich

first: Rouzanna

last: Istvánffy

address: Ismaningerstr. 22

department: Department of Surgery

country: Germany

institute: Klinikum rechts der Isar

description: Library name: MDRG1

data_processing:
Data Quality Control: Raw reads were processed using fastp to remove adapter-containing reads, poly-N reads, and low-quality reads, resulting in clean reads. Q20, Q30, and GC content were calculated for the clean data.
Ribosomal RNA Removal: Ribosomal RNA sequences were removed by aligning reads to the Silva database using Bowtie2 v2.3.4.3.
Gene Expression Quantification: Gene expression levels were quantified using the featureCounts tool in the Subread package. Reads with mapping quality scores below 10, unpaired reads, and reads mapped to multiple genomic regions were filtered out. Final expression values were normalized to FPKM by accounting for sequencing depth and gene length.
The data were normalized using quantile normalization with Illumina GUI in R.
Assembly: Genome Alignment: Clean reads were aligned to the reference genome using HISAT2 v2.0.5 for accurate mapping.  The reference genome used was GRCh38/hg38
Supplementary files format and content: txt file includes FPKMs for all samples

source_name: dorsal root ganglions (T8-T12)

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries were generated using the SMARTer mRNA-Seq Library Preparation Kit (Takara Bio), following the manufacturer's instructions.
Eukaryotic 250~300 bp insert cDNA library
Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection
Illumina NovaSeq X Plus sequencer and 25B sequencing flow cell, the sequencing strategy employed is PE150.

value: dorsal root ganglions (T8-T12)

value: primary cells

value: Neural cells

value: wt

value: untreated


title: DRGs from KPC- Grin2d +/+  Mouse Nr 2

description: Library name: MDRG2


title: sample79, heart, ZSF1 Obese, Vehicle, 2 Study A, rep9

description:
RBI-0000097001
Original Plate name: RSA-0000111781_S39
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample74, heart, ZSF1 Obese, Vehicle, 2 Study A, rep4

description:
RBI-0000096986
Original Plate name: RSA-0000111690_S24
Repeat Plate name: RSA-0000111857_S10
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample75, heart, ZSF1 Obese, Vehicle, 2 Study A, rep5

description:
RBI-0000096987
Original Plate name: RSA-0000111691_S25
original_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample77, heart, ZSF1 Obese, Vehicle, 2 Study A, rep7

description:
RBI-0000096999
Original Plate name: RSA-0000111779_S37
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample76, heart, ZSF1 Obese, Vehicle, 2 Study A, rep6

description:
RBI-0000096998
Original Plate name: RSA-0000111778_S36
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: RNA-seq of Mus musculus: iKlf5_D2_LIF_rep1

value: cell line


title: Exp01A CD8 T cells, TCR

value: CD8 T cells

value: TCR


title: Exp01B CD8 T cells, BEAM

value: BEAM


title: DRGs from KPC- Grin2d -/- Mouse Nr 3

description: Library name: MKPC3


title: sample73, heart, ZSF1 Obese, Vehicle, 2 Study A, rep3

description:
RBI-0000096985
Original Plate name: RSA-0000111689_S23
Repeat Plate name: RSA-0000111856_S9
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: Vehicle


title: DRGs from KPC- Grin2d +/+ Mouse Nr 3

description: Library name: MDRG3


title: Exp01A CD8 T cells, GEX

value: GEX


title: sample71, heart, ZSF1 Obese, Vehicle, 2 Study A, rep1

description:
RBI-0000096983
Original Plate name: RSA-0000111687_S21
Repeat Plate name: RSA-0000111855_S8
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: DRGs from KPC- Grin2d -/-  Mouse Nr 1

description: Library name: MKPC1


title: DRGs from KPC- Grin2d -/- Mouse Nr 2

description: Library name: MKPC2


title: sample69, heart, ZSF1 Lean, Vehicle, 1 Study A, rep9

description:
RBI-0000096971
Original Plate name: RSA-0000111766_S34
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt

value: ZSF1 Lean


title: sample72, heart, ZSF1 Obese, Vehicle, 2 Study A, rep2

description:
RBI-0000096984
Original Plate name: RSA-0000111688_S22
original_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample70, heart, ZSF1 Lean, Vehicle, 1 Study A, rep10

description:
RBI-0000096972
Original Plate name: RSA-0000111767_S35
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: Exp01A CD8 T cells, CITE

value: CITE


title: Exp01A CD8 T cells, BEAM


title: Cancer cells from KPC- Grin2d +/+  Mouse Nr 3

description: Library name: WT3

source_name: pancreas tumour

value: pancreas tumour

value: Cancer cells


title: sample68, heart, ZSF1 Lean, Vehicle, 1 Study A, rep8

description:
RBI-0000096970
Original Plate name: RSA-0000111765_S33
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt

value: heart


title: SARC

city: Guangzhou

first: Zikun

last: Liao

address: 63 Duobao Road, Liwan District

institute: The Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Hisat2（version:2.0.4）to map the cleaned reads to the GRCh38 reference genome with two mismatches.
After genome mapping, Stringtie（version:1.3.0）  was run with a reference annotation to generate FPKM values for known gene models.
Differentially expressed genes were identified using Stringtie]. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR) . The fold-changes were also estimated according to the FPKM in each sample.
The differentially expressed genes were selected using the following filter criteria: FDR ≤0.05 and fold-change ≥2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

source_name: Sarcoma vertebral metastases

extract_protocol:
Total RNA was isolated using MJzol animal RNA Extraction Kit (MagBeads) #T02096  (MJzol, China).
Paired-end libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.

value: Sarcoma vertebral metastases


title: Cancer cells from KPC- Grin2d +/+ Mouse Nr 1

description: Library name: WT1


title: Cancer cells from KPC- Grin2d +/+ Mouse Nr 2

description: Library name: WT2


title: sample66, heart, ZSF1 Lean, Vehicle, 1 Study A, rep6

description:
RBI-0000096968
Original Plate name: RSA-0000111763_S31
original_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample67, heart, ZSF1 Lean, Vehicle, 1 Study A, rep7

description:
RBI-0000096969
Original Plate name: RSA-0000111764_S32
Repeat Plate name: RSA-0000111893_S14
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: Cancer cells from KPC- Grin2d -/-  Mouse Nr 21

description: Library name: KO21


title: sample65, heart, ZSF1 Lean, Vehicle, 1 Study A, rep5

description:
RBI-0000096957
Original Plate name: RSA-0000111676_S10
Repeat Plate name: RSA-0000111854_S7
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: Myometrium from fibroid patient (MyoF), patient HFBN

value: myometrium

value: A


title: sample64, heart, ZSF1 Lean, Vehicle, 1 Study A, rep4

description:
RBI-0000096956
Original Plate name: RSA-0000111675_S9
original_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample60, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep10

description:
RBI-0000097117
Original Plate name: RSA-0000111813_S30
Repeat Plate name: RSA-0000111908_S13
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

source_name: kidney

value: kidney

value: ZSF1 Obese

value: BT2 + Empagliflozin


title: sample63, heart, ZSF1 Lean, Vehicle, 1 Study A, rep3

description:
RBI-0000096955
Original Plate name: RSA-0000111674_S8
Repeat Plate name: RSA-0000111853_S6
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: Cancer cells from KPC- Grin2d -/-  Mouse Nr 18

description: Library name: KO18

value: primary cells

value: untreated


title: sample61, heart, ZSF1 Lean, Vehicle, 1 Study A, rep1

description:
RBI-0000096953
Original Plate name: RSA-0000111672_S6
original_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample81, heart, ZSF1 Obese, BT2, 3 Study A, rep1

description:
RBI-0000097013
Original Plate name: RSA-0000111702_S36
Repeat Plate name: RSA-0000111858_S11
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Heart_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: PRAD

source_name: Prostate adenocarcinoma vertebral metastases


title: sample62, heart, ZSF1 Lean, Vehicle, 1 Study A, rep2

description:
RBI-0000096954
Original Plate name: RSA-0000111673_S7
original_plate1_gene_counts.csv.gz
Heart_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample58, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep8

description:
RBI-0000097115
Original Plate name: RSA-0000111815_S28
Repeat Plate name: RSA-0000111907_S12
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: LUAD2

source_name: Lung adenocarcinoma vertebral metastases


title: Ai39 x BAC-AT1A-Cre, Female, control treatment, housed at 30°C, replicate 4

city: Milwaukee

first: Justin

middle: L

last: Grobe

state: WI

address: 8701 W Watertown Plank Road

department: Physiology

institute: Medical College of Wisconsin

description: Library name: G24_30C_Control_Female_rep4

data_processing:
Raw reads were demuliplexed and quality of pre-aligned data was computed by CASAVA base recognition
Reads were aligned to the reference genome (GRCm39/mm39) with HISAT2
Differential gene expression was tested in R using the package DESeq2. Pairwise comparisons between treatment and temperature groups were done by the Wald test, and LFC estimates were shrunk using the "apeglm" option.
Assembly: GRCm39/mm39
Supplementary files format and content: Excel file (.xlsx) with individual raw counts and individual FPKM values

source_name: liver

growth_protocol: All mice were housed in a temperature and humidity-controlled facility with ad libitum access to 2029x Teklad diet and water.

extract_protocol:
RNA was isolated in TRIzol using a bead mill, chloroform was added, and aqueous phase was transferred to Invitrogen PureLink RNA Mini Kit (per manufacture instructions), gDNA was removed with on-column treatment with PureLink Dnase
poly-A enrichment, random hexamer primers with first strand cDNA synthesis, Illumina standard prepartion kit

value: liver

value: Cre+ Halo+/-

value: Control, 30°C


title: LUAD4

value: Lung adenocarcinoma vertebral metastases


title: sample56, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep6

description:
RBI-0000097113
Original Plate name: RSA-0000111817_S26
Repeat Plate name: RSA-0000111905_S10
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample57, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep7

description:
RBI-0000097114
Original Plate name: RSA-0000111816_S27
Repeat Plate name: RSA-0000111906_S11
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: MCF7 cells : Palbociclib-Resistant 100nM (+ JQ1 Treatment)

first: Renyan

last: Liu

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

data_processing:
The final pool was sequenced with paired-end 150bp reads on an Illumina NovaSeq 6000
Assembly: Sequenced reads were aligned to the UCSC hg38 reference genome assembly and gene counts were quantified using STAR (v2.7.3a)
Supplementary files format and content: MR100_GeneCounts.txt

source_name: Breast; Mammary gland

growth_protocol: Standard culture conditions

extract_protocol:
total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol
Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation reagents on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance

treatment_protocol: Control samples are Palbociclib Resistant (100nM). Treated samples are Palcociblib-Resistant (100nM) treated with JQ1 300nM 24h

value: Breast; Mammary gland

value: epithelial

value: Palbociclib-Resistant (100nM) + JQ1 300nM 24h


title: Ai39 x BAC-AT1A-Cre, Male, control treatment, housed at 30°C, replicate 2

description: Library name: G23_30C_Control_Male_rep2


title: sample55, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep5

description:
RBI-0000097102
Original Plate name: RSA-0000111746_S80
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: MCF7 cells : Palbociclib-Resistant 100nM (Control)

value: Palbociclib-Resistant (100nM)


title: Cancer cells from KPC- Grin2d -/-  Mouse Nr 23

description: Library name: KO23

value: pancreas tumour

value: Cancer cells


title: sample54, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep4

description:
RBI-0000097101
Original Plate name: RSA-0000111745_S79
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: LIHC

source_name: Liver hepatocellular carcinoma vertebral metastases


title: BAC-AT1A-Cre, Female, control treatment, housed at 30°C, replicate 3

description: Library name: G22_30C_Control_Female_rep3

value: Cre-


title: sample48, ZSF1 Obese, Empagliflozin, 5 Study B, rep8

description:
RBI-0000097085
Original Plate name: RSA-0000111830_S23
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: Empagliflozin


title: BAC-AT1A-Cre, Male, control treatment, housed at 30°C, replicate 1

description: Library name: G21_30C_Control_Male_rep1

value: Cre+


title: sample46, ZSF1 Obese, Empagliflozin, 5 Study B, rep6

description:
RBI-0000097083
Original Plate name: RSA-0000111832_S21
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: kidney

value: ZSF1 Obese


title: THYM

source_name: Thymoma vertebral metastases

value: Thymoma vertebral metastases


title: sample53, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep3

description:
RBI-0000097100
Original Plate name: RSA-0000111744_S78
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: BT2 + Empagliflozin


title: sample44, ZSF1 Obese, Empagliflozin, 5 Study B, rep4

description:
RBI-0000097071
Original Plate name: RSA-0000111730_S64
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample49, ZSF1 Obese, Empagliflozin, 5 Study B, rep9

description:
RBI-0000097086
Original Plate name: RSA-0000111829_S24
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample45, ZSF1 Obese, Empagliflozin, 5 Study B, rep5

description:
RBI-0000097072
Original Plate name: RSA-0000111731_S65
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: SCKM

source_name: Skin Cutaneous Melanoma vertebral metastases


title: sample47, ZSF1 Obese, Empagliflozin, 5 Study B, rep7

description:
RBI-0000097084
Original Plate name: RSA-0000111831_S22
Repeat Plate name: RSA-0000111903_S8
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Ai9 x BAC-AT1A-Cre, Female, ablated treatment, housed at 30°C, replicate 3

description: Library name: G19_30C_Ablated_Female_rep3

value: liver

value: Cre+ R+/-

value: Ablated, 30°C


title: Ai9 x BAC-AT1A-Cre, Male, ablated treatment, housed at 30°C, replicate 2

description: Library name: G18_30C_Ablated_Male_rep2

value: Cre+ R+/+


title: sample52, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep2

description:
RBI-0000097099
Original Plate name: RSA-0000111743_S77
Repeat Plate name: RSA-0000111886_S39
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample50, ZSF1 Obese, Empagliflozin, 5 Study B, rep10

description:
RBI-0000097087
Original Plate name: RSA-0000111828_S25
Repeat Plate name: RSA-0000111904_S9
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Ai39 x BAC-AT1A-Cre, Female, control treatment, housed at 30°C, replicate 2

description: Library name: G17_30C_Control_Female_rep2

value: Cre- Halo+/-

value: Control, 30°C


title: sample43, ZSF1 Obese, Empagliflozin, 5 Study B, rep3

description:
RBI-0000097070
Original Plate name: RSA-0000111729_S63
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: LUAD1

value: Lung adenocarcinoma vertebral metastases


title: BRCA

source_name: Breast invasive carcinoma vertebral metastases


title: Ai39 x BAC-AT1A-Cre, Female, ablated treatment, housed at 30°C, replicate 2

description: Library name: G16_30C_Ablated_Female_rep2

value: Cre+ Halo+/-


title: sample42, ZSF1 Obese, Empagliflozin, 5 Study B, rep2

description:
RBI-0000097069
Original Plate name: RSA-0000111728_S62
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample41, ZSF1 Obese, Empagliflozin, 5 Study B, rep1

description:
RBI-0000097068
Original Plate name: RSA-0000111727_S61
Repeat Plate name: RSA-0000111874_S27
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHIDA2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

source_name: Mononuclear cells separated from the AML patient's bone marrow

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AML cells


title: sample40, ZSF1 Obese, Vehicle, 4 Study B, rep10

description:
RBI-0000097057
Original Plate name: RSA-0000111843_S20
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: Vehicle


title: sample37, ZSF1 Obese, Vehicle, 4 Study B, rep7

description:
RBI-0000097054
Original Plate name: RSA-0000111846_S17
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHCOM3

value: Mononuclear cells separated from the AML patient's bone marrow

value: 5uM ANA+0.005uM IDA, 72h


title: Ai39 x BAC-AT1A-Cre, Female, ablated treatment, housed at 30°C, replicate 1

description: Library name: G15_30C_Ablated_Female_rep1


title: GBHIDA1


title: sample36, ZSF1 Obese, Vehicle, 4 Study B, rep6

description:
RBI-0000097053
Original Plate name: RSA-0000111847_S16
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Ai39 x BAC-AT1A-Cre, Female, control treatment, housed at 30°C, replicate 1

description: Library name: G14_30C_Control_Female_rep1


title: sample35, ZSF1 Obese, Vehicle, 4 Study B, rep5

description:
RBI-0000097042
Original Plate name: RSA-0000111716_S50
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHCOM2


title: sample33, ZSF1 Obese, Vehicle, 4 Study B, rep3

description:
RBI-0000097040
Original Plate name: RSA-0000111714_S48
Repeat Plate name: RSA-0000111852_S5
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample38, ZSF1 Obese, Vehicle, 4 Study B, rep8

description:
RBI-0000097055
Original Plate name: RSA-0000111845_S18
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Ai39 x BAC-AT1A-Cre, Female, control treatment, housed at 22°C, replicate 3

description: Library name: G12_22C_Control_Female_rep3

value: Control, 22°C


title: GBHIDA3


title: Ai39 x BAC-AT1A-Cre, Male, ablated treatment, housed at 30°C, replicate 1

description: Library name: G13_30C_Ablated_Male_rep1


title: sample29, ZSF1 Obese, BT2, 3 Study A, rep9

description:
RBI-0000097026
Original Plate name: RSA-0000111791_S14
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: kidney


title: Ai39 x BAC-AT1A-Cre, Female, ablated treatment, housed at 22°C, replicate 3

description: Library name: G11_22C_Ablated_Female_rep3

value: Ablated, 22°C


title: GBHNC3

value: DMSO, 72h


title: sample39, ZSF1 Obese, Vehicle, 4 Study B, rep9

description:
RBI-0000097056
Original Plate name: RSA-0000111844_S19
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: ZSF1 Obese


title: sample30, ZSF1 Obese, BT2, 3 Study A, rep10

description:
RBI-0000097027
Original Plate name: RSA-0000111792_S15
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample32, ZSF1 Obese, Vehicle, 4 Study B, rep2

description:
RBI-0000097039
Original Plate name: RSA-0000111713_S47
Repeat Plate name: RSA-0000111851_S4
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample31, ZSF1 Obese, Vehicle, 4 Study B, rep1

description:
RBI-0000097038
Original Plate name: RSA-0000111712_S46
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHCOM1


title: sample34, ZSF1 Obese, Vehicle, 4 Study B, rep4

description:
RBI-0000097041
Original Plate name: RSA-0000111715_S49
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_emp_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHNC2


title: sample28, ZSF1 Obese, BT2, 3 Study A, rep8

description:
RBI-0000097025
Original Plate name: RSA-0000111790_S13
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHNC1


title: Ai39 x BAC-AT1A-Cre, Female, ablated treatment, housed at 22°C, replicate 1

description: Library name: G7_22C_Ablated_Female_rep1

value: liver


title: Ai39 x BAC-AT1A-Cre, Female, control treatment, housed at 22°C, replicate 1

description: Library name: G8_22C_Control_Female_rep1


title: BAC-AT1A-Cre, Male, ablated treatment, housed at 30°C, replicate 3

description: Library name: G20_30C_Ablated_Male_rep3

value: Cre+


title: sample51, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep1

description:
RBI-0000097098
Original Plate name: RSA-0000111742_S76
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: BT2 + Empagliflozin


title: sample21, ZSF1 Obese, BT2, 3 Study A, rep1

description:
RBI-0000097008
Original Plate name: RSA-0000111697_S31
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHANA1

value: 5uM, ANA, 72h


title: sample23, ZSF1 Obese, BT2, 3 Study A, rep3

description:
RBI-0000097010
Original Plate name: RSA-0000111699_S33
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample18, ZSF1 Obese, Vehicle, 2 Study A, rep8

description:
RBI-0000096995
Original Plate name: RSA-0000111775_S8
Repeat Plate name: RSA-0000111891_S5
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample27, ZSF1 Obese, BT2, 3 Study A, rep7

description:
RBI-0000097024
Original Plate name: RSA-0000111789_S12
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample26, ZSF1 Obese, BT2, 3 Study A, rep6

description:
RBI-0000097023
Original Plate name: RSA-0000111788_S111
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: GBHANA3


title: sample25, ZSF1 Obese, BT2, 3 Study A, rep5

description:
RBI-0000097012
Original Plate name: RSA-0000111701_S35
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Ai39 x BAC-AT1A-Cre, Male, control treatment, housed at 22°C, replicate 3

description: Library name: G6_22C_Control_Male_rep3

value: Cre- Halo+/-


title: Ai39 x BAC-AT1A-Cre, Male, control treatment, housed at 22°C, replicate 1

description: Library name: G4_22C_Control_Male_rep1


title: sample19, ZSF1 Obese, Vehicle, 2 Study A, rep9

description:
RBI-0000096996
Original Plate name: RSA-0000111776_S9
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample17, ZSF1 Obese, Vehicle, 2 Study A, rep7

description:
RBI-0000096994
Original Plate name: RSA-0000111774_S7
Repeat Plate name: RSA-0000111890_S4
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: Ai39 x BAC-AT1A-Cre, Male, control treatment, housed at 22°C, replicate 2

description: Library name: G5_22C_Control_Male_rep2


title: Ai39 x BAC-AT1A-Cre, Female, ablated treatment, housed at 22°C, replicate 2

description: Library name: G10_22C_Ablated_Female_rep2


title: Ai39 x BAC-AT1A-Cre, Male, ablated treatment, housed at 22°C, replicate 3

description: Library name: G3_22C_Ablated_Male_rep3


title: GBHANA2


title: CIC_SB_3

city: Zhanjiang

first: wei

last: yisheng

address: No. 57 South Renmin Avenue, Xiashan District

institute: The Affiliated Hospital of Guangdong Medical University

data_processing:
Read aligment: featureCounts v1.5.0-p3
Assembly: Homo Sapiens (GRCh38/hg38)
Supplementary files format and content: xsl file; Gene ID; RPKM;

source_name: colon

extract_protocol:
trizol
NEBNext® Ultra RNA Library Prep Kit for Illumina®

value: colon

value: Ileocecal colorectal adenocarcinoma

value: WT


title: sample16, ZSF1 Obese, Vehicle, 2 Study A, rep6

description:
RBI-0000096993
Original Plate name: RSA-0000111773_S6
Repeat Plate name: RSA-0000111889_S3
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: CIC_SB_1


title: sample15, ZSF1 Obese, Vehicle, 2 Study A, rep5

description:
RBI-0000096982
Original Plate name: RSA-0000111686_S20
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample22, ZSF1 Obese, BT2, 3 Study A, rep2

description:
RBI-0000097009
Original Plate name: RSA-0000111698_S32
Repeat Plate name: RSA-0000111850_S3
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample20, ZSF1 Obese, Vehicle, 2 Study A, rep10

description:
RBI-0000096997
Original Plate name: RSA-0000111777_S10
Repeat Plate name: RSA-0000111892_S6
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: CIC_SB_2


title: sample24, ZSF1 Obese, BT2, 3 Study A, rep4

description:
RBI-0000097011
Original Plate name: RSA-0000111700_S34
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample13, ZSF1 Obese, Vehicle, 2 Study A, rep3

description:
RBI-0000096980
Original Plate name: RSA-0000111684_S18
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: CIC_3

value: untreated


title: Ai39 x BAC-AT1A-Cre, Female, control treatment, housed at 22°C, replicate 2

description: Library name: G9_22C_Control_Female_rep2


title: sample11, ZSF1 Obese, Vehicle, 2 Study A, rep1

description:
RBI-0000096978
Original Plate name: RSA-0000111682_S16
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: Vehicle


title: Ai39 x BAC-AT1A-Cre, Male, ablated treatment, housed at 22°C, replicate 2

description: Library name: G2_22C_Ablated_Male_rep2

value: Cre+ Halo+/-


title: sample59, ZSF1 Obese, BT2 + Empagliflozin, 6 Study B, rep9

description:
RBI-0000097116
Original Plate name: RSA-0000111814_S29
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_emp_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: C2C12 cells,siFAM129B-4

city: Wuhan

first: Yushen

last: Lu

state: Hubei

address: Donghu Road 115

institute: Wuhan University

data_processing:
R4.2.2 and Rstudio
Assembly: mm9
Supplementary files format and content: excel file includes raw counts for each sample

growth_protocol: C2C12 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) andantibiotics in humidified atmosphere with 5% CO2 at 37 °C for proliferation and in DMEM with 2% horse serum (Gibco,USA) at the same condition for differentiation.

extract_protocol:
RNA was harvested using Trizol Reagent,1.3ug of total RNA was used for the construction of sequencing libraries
mRNA was purified from total RNA  using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was  reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and  second strand cDNA synthesis was subsequently performed. Remaining overhangs of  double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the  cDNA and the library fragments were purified. The template was enriched by PCR, and the  PCR product was purified to obtain the final library

treatment_protocol: Transfections were carried out using Lipofectamine RNAiMAX for siRNA

value: muscle differentiation


title: sample9, ZSF1 Lean, Vehicle, 1 Study A, rep9

description:
RBI-0000096966
Original Plate name: RSA-0000111761_S4
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt

value: ZSF1 Lean


title: LUAD3

value: Lung adenocarcinoma vertebral metastases


title: CIC_1


title: C2C12 cells,siFAM129B-3


title: C2C12 cells,siFAM129B-1


title: HEK-3

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

data_processing:
Cutadapt 2.5 used for adapter trimming
BWA-MEM 0.7.12-r1039 used for mapping
PRIMseqTools used for downstream processing
Assembly: hg38
Supplementary files format and content: chimeric read pairs for RPA identification
Library strategy: PRIM-seq

growth_protocol: Ligation of Total RNA to Interaction Linker: Purified total RNA was fragmented with the NEBNext® Magnesium RNA Fragmentation Module (NEB, E6150S) for 2 minutes at 94 °C. The fragmented RNA was purified with a RNeasy Mini Column (Qiagen, 74104). The ends of the 200 pmols of RNA were repaired in a 200 μLs reaction containing 100 U Quick CIP (NEB, M0525S) and 1x rCutSmart buffer (B6004S). The reaction was incubated at 37 °C for 1 hour and then purified with RNeasy Mini Columns (Qiagen, 74104). To ligate the interaction linker to the total RNA, a 200 μLs reaction was mixed containing 400 pmols of App-interaction linker, 200 pmols of fragmented total RNA, 4,000 U T4 RNA Ligase 2, truncated KQ (NEB, M0373S), 1x T4 RNA Ligase buffer (NEB, M0373S), and 15% PEG 8000 (NEB, M0373S). This reaction was incubated at 16 °C overnight and then purified with RNeasy Mini Columns (Qiagen, 74104). The bottom strand of the interaction linker was added to the purified sample in a 1:1 molar ratio in 1x Annealing buffer [10x: 100 mM Tris-HCI Buffer, pH 7.5 (Invitrogen, 15567027), 500 mM NaCl (Thermo Scientific, AM9759), 10 mM EDTA pH 8.0 (Invitrogen™, AM9260G)]. The solution was heated to 75°C for 5 minutes and cooled to 25°C at 0.1°C per second.

extract_protocol:
The DNA was released from the beads with the NEBNext® Ultra™ II FS DNA Module (NEB, E7810S) using twice the reaction volume and a fragmentation time of 10 minutes. The end-repair step was not performed. Libraries were then generated with the NEBNext Ultra™ II DNA Library Kit (NEB, E7805S) without purification. After ligated with adaptors, DNA fragments are selected with 20 μLs of Streptavidin T1 beads (Invitrogen™, 65602) by incubation at room temperature for 1h with agitation. The beads were washed 3 times each with: Low Salt wash buffer [0.1% SDS (Invitrogen™, AM9820), 0.1% Triton X-100 (Sigma-Aldrich, T8787-50ML), 2 mM EDTA pH 8.0 (Invitrogen™, AM9260G), 20 mM Tris-HCl pH 8.0 (Invitrogen™, 15568025), 150 mM NaCl (Thermo Fisher Scientific, AM9759)], 1x B&W buffer (5 mM Tris-HCl pH 7.5 (Invitrogen™, 15567027), 0.5 mM EDTA pH 8.0 (Invitrogen™, AM9260G), 1M NaCl (Thermo Fisher Scientific, AM9759)), and 1x PBS pH 7.4 (Gibco™, 70011044) with 0.1% Triton X-100 (Sigma-Aldrich, T8787-50ML). 50 μLs of the pre-mixed reagents (NEB, E7805S) including 25 μLs of 2x PCR Master Mix, 5 μLs of Universal Primer, and 5 μLs of Primer Mix-Index 1 from the NEBNext Ultra II Single Indexing Kit (NEB, E7335S) were added to the beads.
The amplification was conducted with an initial denaturation of 95°C for 2 minutes then cycled 15 times with a 98°C -denaturation step for 10 seconds and a 68°C combined annealing and extension step for 90 seconds. PCR products were purified with 0.75x AMPure XP Beads (Beckman, A63880), eluted in 20 μLs of UltraPure™ DNase/RNase-Free distilled water (Thermo Scientific, 10977023), and quantified with the Qubit dsDNA HS Assay Kit (Invitrogen™, Q32851). Each library was paired-end sequenced for 150 cycles on each end on an Illumina NovaSeq 6000.

treatment_protocol: The first step is the incubation of the SMART-display protein library with an RNA library. In this step, displayed protein libraries are pulled down onto streptavidin magnetic T1 beads, and their mRNA tags are stabilized by reverse transcription to convert to double-stranded cDNA using a template-switching oligo (TSO) containing a non-palindromic restriction enzyme (BbvCI) site. Next, free biotin is added to the protein population to block the remaining binding sites on the streptavidin beads and prevent non-specific binding. Subsequently, an RNA library ligated with a biotin ligation linker (gray bars, Figure 2) designed with complementary sticky ends to the BbvCI restriction site was prepared and added to the protein library allowing the formation of RNA-protein associations. Then, the double-stranded cDNA barcode is treated with a BbvCI to generate sticky ends. The second step is to ligate the barcodes from interacting RNA-protein pairs. In this step, the interacting RNA-protein pairs will be cross-linked. Stringent washes will be applied to remove non-specifically bound proteins or RNAs. The biotin ligation linker-containing ends of the RNA library are then ligated to the sticky end of the interacting protein library. The use of a non-palindromic restriction enzyme prevents the self-ligation of the cDNA or the self-ligation of the linker sequence. At this point, RNA-protein associations have been recorded by chimeric sequences of the form cDNA-linker-RNA. The third step is to construct the sequencing library. The RNA is converted to double-stranded cDNA, allowing the chimeric sequences to transfer into the form of cDNA1-linker-cDNA2 where the cDNA1 comes from the protein and cDNA2 comes from the RNA end. The cDNAs, including those that have been ligated (cDNA1-linker-cDNA2), are subjected to enzymatic fragmentation (NEBNext Ultra II FS) and the addition of sequencing adapters. The chimeric sequences (cDNA1-linker-cDNA2) are selected for using the biotin on the linker sequence. The resulting library is amplified and subjected to paired-end sequencing. Taken together, SMART-display and REILIS constitute the entire PRIM-seq experimental pipeline.


title: K562-2


title: sample5, ZSF1 Lean, Vehicle, 1 Study A, rep5

description:
RBI-0000096952
Original Plate name: RSA-0000111671_S5
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt

value: kidney


title: sample7, ZSF1 Lean, Vehicle, 1 Study A, rep7

description:
RBI-0000096964
Original Plate name: RSA-0000111759_S2
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample14, ZSF1 Obese, Vehicle, 2 Study A, rep4

description:
RBI-0000096981
Original Plate name: RSA-0000111685_S19
Repeat Plate name: RSA-0000111849_S2
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt


title: sample10, ZSF1 Lean, Vehicle, 1 Study A, rep10

description:
RBI-0000096967
Original Plate name: RSA-0000111762_S5
Repeat Plate name: RSA-0000111888_S2
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample2, ZSF1 Lean, Vehicle, 1 Study A, rep2

description:
RBI-0000096949
Original Plate name: RSA-0000111668_S2
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample6, ZSF1 Lean, Vehicle, 1 Study A, rep6

description:
RBI-0000096963
Original Plate name: RSA-0000111758_S1
original_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: C2C12 cells,siFAM129B-2


title: sample4, ZSF1 Lean, Vehicle, 1 Study A, rep4

description:
RBI-0000096951
Original Plate name: RSA-0000111670_S4
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: K562-1


title: ΔdamΔdcm RDM logarithmic rep 2 - RNA-seq

city: Ann Arbor

first: Lydia

last: Freddolino

state: Michigan

address: 1150 W. Medical Center Dr., Room 3315 MSRB III

institute: University of Michigan

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 3.5
Read ends were trimmed using Trimmomatic 0.39 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.4.4 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were processed using Rockhopper to detect transcripts and respective expression levels, as well as significance of mutant versus wild-type expression change. The IPOD pipeline up to the alignment step was also used to quantify the number of RNA reads at each basepair position.
Assembly: E. coli U00096.3
Supplementary files format and content: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript. The .bedgraph file extension refers to a 5 basepair graphing of occupancy scores, where the first column indicates the chromosome, while the second and third columns indicate the left and right, respectively, basepair positions of the 5 basepair bin a genomic position and the fourth a corresponding signal. chip_vs_inp.bedgraph files – RNA polymerase occupancy given as a log_2 ratio of extracted to input, z-scored and then used to calculate enrichment p values as described in the text. rzchipsub.bedgraph files – ChIP-subtracted IPOD-HR occupancy, z-scored and then used to calculate enrichment p values as described in the text. rockhopper_summary.txt - summary of transcript information, mutant vs wt log2(fold change) and qvalue as calculated by Rockhopper from RNAseq data. rna_positive_reads_ptmr.bedgraph - RNAseq reads per tens of millions of reads within each replicate, then the mean of replicates is calculated.  rna_negative_reads_ptmr.bedgraph - RNAseq reads per tens of millions of reads within each replicate, then the mean of replicates is calculated, and signed negative to indicate strandedness.

organism: Escherichia coli

source_name: Culture lysate

extract_protocol:
DNA samples: When resuspending frozen cell pellets, two pellets (taken from a single biological replicate) of each sample were separately resuspended with spike-in, sonicated, and then combined into one tube immediately after sonication. Individual frozen C. crescentus spike-in cell pellets were resuspended in 600 µL of 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free, Roche Diagnostics GmbH, Mannheim, Germany) and 1.5 µL of ready-lyse (Epicentre, Madison, WI). The spike-in resuspension was used to resuspend one of the sample cell pellets, and then the resuspended cells were incubated for 15 minutes in a 30°C water bath. Sonication was then performed on all samples using a Branson digital sonifier with a microtip at 25% amplitude for four pulses of 5 seconds with a 5 second rest between each pulse; samples were kept in an ice/water bath during sonication. The two separate tubes for each biological sample were then combined. DNA digestion was performed by adding to the sonicated lysates 120 μg RNase A (Thermo Fisher Scientific, Waltham, MA), 12 μL DNase I (Fisher product #89835), 10.8 μL 100 mM MnCl2, and 9 μL 100 mM CaCl2, and then incubating on ice for 30 minutes. The digestion was quenched with 100 μL of 500 mM EDTA (pH 8.0), followed by clarification by centrifuge for 10 minutes at 13,000 rpm at 4°C. Aliquots were taken from the clarified lysate for IPOD-HR interface extraction, RNA polymerase chromatin immunoprecipitation, and cross-linking reversal and recovery of DNA as previously described in (Freddolino et al., 2021). The procedures described in that reference were replicated here, apart from all the 2-minute centrifuging steps instead being done in 4 minutes. For DNA recovery, standard phenol-chloroform extraction as ethanol precipitation as described in (Ausubel F, 1998), where we used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA and the dried DNA was resuspended in 100 μL of TEe (10 mM Tris pH 8.0; 0.1 mM EDTA pH 8.0) for input samples, 20 μL of TEe for RNAP-ChIP samples, and 50 μL of TEe for IPOD samples. RNA samples: RNA pellets were removed from -80°C and then immediately resuspended in 100 μL TE buffer (10 mM Tris pH 8.0; 1 mM EDTA pH 7.0). The resuspended pellet was treated with 1 μL lysozyme (Ready-Lyse; Lucigen, Ltd.) and incubated for 10 minutes at 4°C, followed by treatment with 10 μL proteinase K and incubation for 10 minutes at room temperature with vortexing every 2 minutes. RNA was then isolated using a Zymo RNA Clean and Concentrate 5 Kit twice for each sample, with a DNase digestion (25 μL eluate from first Zymo clean-up, 58 μL nuclease-free water, 10 μL 10X DNase Reaction Buffer, 2 μL RNase inhibitor, 5 μL Baseline Zero DNase) at 37°C for 30 minutes in-between Zymo kit clean-ups. Samples were then ribo-depleted using a NEBNext rRNA Depletion (Bacteria) Kit according to manufacturer’s instructions – with the exception that 10 μL of RNA sample, containing 1 μg of RNA, was used for probe hybridization. Following ribo-depletion, samples were again cleaned-up with the Zymo Clean and Concentrate 5 Kit and then prepared for sequencing using the NEBNext Ultra II Directional RNA Sequencing Kit
DNA samples: NEB Nebnext Ultra 2 DNA kit RNA samples: NEBNext Ultra 2 Directional RNA kit

tag: strain

value: {delta}dam{delta}dcm

tag: media

value: MOPS Rich Defined Media (RDM) + glucose

tag: time of_harvest

value: logarithmic phase


title: sample8, ZSF1 Lean, Vehicle, 1 Study A, rep8

description:
RBI-0000096965
Original Plate name: RSA-0000111760_S3
Repeat Plate name: RSA-0000111887_S1
original_plate2_gene_counts.csv.gz
repeat_plate2_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt

tag: tissue


title: C2C12 cells,siNC-3


title: C2C12 cells,siNC-4


title: ΔdamΔdcm RDM logarithmic rep 1 -RNA-seq


title: CIC_2


title: sample1, ZSF1 Lean, Vehicle, 1 Study A, rep1

description:
RBI-0000096948
Original Plate name: RSA-0000111667_S1
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: Ai39 x BAC-AT1A-Cre, Male, ablated treatment, housed at 22°C, replicate 1

description: Library name: G1_22C_Ablated_Male_rep1

value: liver

value: Ablated, 22°C


title: ΔdamΔdcm RDM logarithmic rep 3 - RNA-seq


title: Sample12_HEL,COM,rep3

source_name: HEL

value: HEL

value: AML cells

value: 1 μM ANA + 0.005 μM IDA, 72h


title: C2C12 cells,siNC-2


title: Δdcm RDM logarithmic rep 2 - RNA-seq

value: {delta}dcm


title: HEK-2


title: sample3, ZSF1 Lean, Vehicle, 1 Study A, rep3

description:
RBI-0000096950
Original Plate name: RSA-0000111669_S3
original_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt


title: sample12, ZSF1 Obese, Vehicle, 2 Study A, rep2

description:
RBI-0000096979
Original Plate name: RSA-0000111683_S17
Repeat Plate name: RSA-0000111848_S1
original_plate1_gene_counts.csv.gz
repeat_plate1_gene_counts.csv.gz
Kidney_ZSF1_obese_vs_lean_all_DE_results_with_norm_counts.txt
Kidney_ZSF1_bt2_vs_Vehicle_all_DE_results_with_norm_counts.txt

value: ZSF1 Obese


title: C2C12 cells,siNC-1


title: Δdam RDM logarithmic rep 3 - RNA-seq

value: {delta}dam


title: Δdam RDM logarithmic rep 2 - RNA-seq


title: Δdcm RDM logarithmic rep 3 - RNA-seq