title: ORSAM19578-1

source_name: adipose-10% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1


title: H5N1.018_d000_00h_14F05

status: Public on Nov 05 2024

type: RNA

city: Bethesda

first: Foo

last: Cheung

address: Bethesda

country: USA

institute: NIH

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-018

hyb_protocol: Biotin-labeled sample was well mixed with hybridization master mix denatured and then hybridized onto Affymetrix miRNA 3.0 array at  at 48 C and 60 rpm for  18 hours

scan_protocol: Affymetrix scanner 3000

data_processing:
Expression Console 1.2  (RMA+DABG)  software package was used for data summarization
normalization and quality control. Cel files are used for further analysis.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Individual H5N1-018

label_protocol:
Five hundred nanogram of total RNA was poly A tailed
then biotinated using Affymetrix FlashTag Biotin HSR RNA Labeling kit (P/N 703095 v1)

extract_protocol: Total RNA including small RNA is isolated and purified using Qiagen miRNeasy mini kit (Cat #: 217004)

tag: time point


title: H5N1.016_d100_14E05

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-016

source_name: Individual H5N1-016


title: H5N1.018_d000_12h_14G05


title: H5N1.018_d022_14C06


title: ORSAM19577-1

type: SRA

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38

organism: Mus musculus

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

treatment_protocol: Adipose, liver, and skeletal muscle tissue from 6-month and 12-month CC-RIX cohorts underwent transcriptomic profiling. CC-RIX cohorts were exposed to sensitizer (HFHS diet) and a widely used pharmaceutical intervention (metformin). Chow (control) or high fat high sugar (HFHS) diet started at 6 weeks of age.. At six months of age, a subset of mice from each chow group and of each sex were euthanized for tissue collection.  At 7 months of age, half of the remaining mice in each diet treatment group will receive metformin treatment.  In a subset of the 12 month cohort animals, metformin (5 mg/mL) was delivered ad libitum in the drinking water (Chang, Moro et al. 2018). Terminal phenotyping and tissue collection was done at 12 months of age.  These animals also underwent metabolic phenotyping.

tag: tissue

value: gonadal fat pad

tag: Sex

value: male

tag: strain

value: CC042/GeniUncJ x CC040/TauUncJ)F1

tag: genotype

value: Outbred

tag: treatment

value: Metformin

tag: diet

value: 10% fat + fiber

tag: sequencing id


title: H5N1.016_d022_14D05


title: H5N1.016_d021_12h_14C05


title: H5N1.016_d021_00h_14B05


title: H5N1.016_d001_14A05


title: ORSAM19576-1


title: ORSAM19575-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -Metformin-rep1

value: female


title: ORSAM19574-1


title: H5N1.016_d000_12h_14H04


title: ORSAM19572-1

source_name: adipose-10% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1


title: H5N1.021_d000_12h_14G06

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-021

source_name: Individual H5N1-021


title: ORSAM19568-1

source_name: adipose-10% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: H5N1.018_d021_12h_14B06


title: H5N1.012_d100_14F04

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-012

source_name: Individual H5N1-012


title: ORSAM19567-1


title: ORSAM19217-1

source_name: adipose-44% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1

value: 44% fat + fiber


title: ORSAM19220-1

source_name: adipose-10% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: ORSAM19223-1


title: ORSAM19573-1


title: ORSAM19208-1

source_name: adipose-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: H5N1.012_d042_14E04


title: H5N1.012_d021_12h_14D04


title: ORSAM19207-1

source_name: adipose-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1


title: H5N1.012_d001_14B04


title: H5N1.012_d021_00h_14C04


title: H5N1.016_d000_00h_14G04


title: H5N1.011_d001_14B03

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-011

source_name: Individual H5N1-011


title: H5N1.012_d000_00h_14H03


title: ORSAM19204-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: ORSAM19222-1


title: H5N1.008_d100_14G02

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-008

source_name: Individual H5N1-008


title: H5N1.011_d022_14E03


title: H5N1.012_d000_12h_14A04


title: H5N1.011_d021_12h_14D03


title: H5N1.011_d021_00h_14C03


title: H5N1.011_d100_14F03


title: ORSAM19215-1

source_name: adipose-44% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: H5N1.011_d000_12h_14A03


title: ORSAM19203-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: CC051/TauUncJ x CC060/UncJ)F1


title: ORSAM19214-1


title: H5N1.011_d000_00h_14H02


title: ORSAM19202-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM19201-1


title: ORSAM19199-1

source_name: adipose-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC075/UncJ x CC042/GeniUncJ)F1


title: ORSAM19205-1


title: H5N1.008_d022_14F02


title: H5N1.008_d021_00h_14D02


title: ORSAM19198-1


title: H5N1.008_d001_14C02


title: ORSAM19197-1

source_name: adipose-44% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM19194-1

source_name: adipose-10% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM19193-1


title: ORSAM19043-1

source_name: adipose-44% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM19045-1


title: ORSAM19040-1

source_name: adipose-10% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM19192-1


title: ORSAM19044-1


title: ORSAM19042-1


title: ORSAM19038-1

source_name: adipose-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM19037-1


title: ORSAM19036-1


title: H5N1.008_d000_12h_14B02


title: H5N1.001_d022_14F01

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-001

source_name: Individual H5N1-001


title: H5N1.001_d001_14C01


title: H5N1.008_d021_12h_14E02


title: H5N1.001_d021_12h_14E01


title: H5N1.035_d100_13A12

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-035

source_name: Individual H5N1-035


title: H5N1.001_d000_12h_14B01


title: ORSAM19035-1

source_name: adipose-10% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: H5N1.001_d021_00h_14D01


title: ORSAM19034-1


title: H5N1.008_d000_00h_14A02


title: H5N1.001_d100_14G01


title: H5N1.001_d000_00h_14A01


title: ORSAM19039-1


title: H5N1.035_d021_12h_13G11


title: H5N1.035_d000_12h_13D11


title: ORSAM19033-1

source_name: adipose-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: ORSAM19032-1


title: H5N1.035_d022_13H11


title: ORSAM19031-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: H5N1.035_d021_00h_13F11


title: ORSAM19030-1


title: H5N1.035_d000_00h_13C11


title: H5N1.034_d100_13B11

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-034

source_name: Individual H5N1-034


title: H5N1.035_d001_13E11


title: ORSAM19022-1

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1


title: ORSAM19024-1


title: H5N1.034_d021_00h_13G10


title: ORSAM19025-1


title: H5N1.034_d001_13F10


title: ORSAM19020-1

source_name: adipose-44% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC012/GeniUncJ x CC002/UncJ)F1


title: H5N1.034_d022_13A11


title: ORSAM19018-1

source_name: adipose-10% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: gonadal fat pad


title: ORSAM19016-1

source_name: adipose-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: male


title: ORSAM19015-1


title: ORSAM19014-1


title: H5N1.021_d022_14C07

source_name: Individual H5N1-021


title: H5N1.034_d000_12h_13E10


title: H5N1.034_d000_00h_13D10


title: H5N1.032_d022_13B10

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-032

source_name: Individual H5N1-032


title: H5N1.032_d000_00h_13E09


title: H5N1.032_d021_00h_13H09


title: H5N1.032_d021_12h_13A10


title: ORSAM19012-1

source_name: adipose-10% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: H5N1.034_d021_12h_13H10


title: H5N1.032_d001_13G09


title: H5N1.030_d022_13A09

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-030

source_name: Individual H5N1-030


title: ORSAM19011-1


title: ORSAM19579-1

source_name: adipose-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1


title: ORSAM19010-1

value: Outbred


title: ORSAM18718-1

source_name: adipose-10% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: ORSAM18717-1

source_name: adipose-44% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: H5N1.032_d100_13C10


title: H5N1.030_d100_13B09


title: ORSAM18715-1

value: Metformin


title: H5N1.032_d000_12h_13F09


title: H5N1.030_d021_12h_13H08


title: ORSAM18714-1


title: ORSAM18713-1

source_name: adipose-44% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: ORSAM18712-1


title: ORSAM18710-1


title: ORSAM18707-1

source_name: adipose-44% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: H5N1.030_d000_12h_13E08


title: ORSAM18706-1


title: H5N1.030_d000_00h_13D08


title: H5N1.030_d001_13F08


title: ORSAM18702-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1


title: H5N1.028_d100_13C08

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-028

source_name: Individual H5N1-028


title: H5N1.030_d021_00h_13G08


title: H5N1.028_d022_13B08


title: H5N1.028_d021_12h_13A08


title: ORSAM18701-1


title: ORSAM18700-1


title: ORSAM18697-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1

value: 10% fat + fiber


title: ORSAM18696-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1

value: female


title: ORSAM18695-1


title: H5N1.028_d021_00h_13H07


title: ORSAM18693-1


title: ORSAM18422-1


title: ORSAM18421-1


title: H5N1.028_d001_13G07


title: ORSAM18419-1

source_name: adipose-10% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: H5N1.028_d000_00h_13E07


title: H5N1.028_d000_12h_13F07


title: H5N1.026_d100_13D07

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-026

source_name: Individual H5N1-026


title: H5N1.026_d021_12h_13B07


title: ORSAM18420-1


title: H5N1.026_d001_13H06


title: ORSAM18416-1

source_name: adipose-10% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: H5N1.020_d022_13D06

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-020

source_name: Individual H5N1-020


title: H5N1.020_d100_13E06


title: H5N1.026_d000_12h_13G06


title: ORSAM18414-1

source_name: adipose-10% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: H5N1.026_d000_00h_13F06


title: H5N1.026_d021_00h_13A07


title: H5N1.026_d022_13C07


title: ORSAM18413-1


title: ORSAM19013-1

source_name: adipose-44% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: H5N1.020_d001_13A06


title: ORSAM18418-1


title: ORSAM18417-1


title: H5N1.020_d021_00h_13B06


title: ORSAM18412-1


title: ORSAM18411-1

source_name: adipose-44% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: H5N1.020_d000_00h_13G05


title: H5N1.020_d000_12h_13H05


title: H5N1.017_d100_13E05

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-017

source_name: Individual H5N1-017


title: ORSAM18410-1


title: H5N1.017_d022_13D05


title: ORSAM18409-1


title: ORSAM18407-1

source_name: adipose-10% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: ORSAM18400-1

source_name: adipose-44% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1


title: ORSAM18401-1

value: 44% fat + fiber


title: H5N1.017_d021_12h_13C05


title: H5N1.017_d021_00h_13B05


title: ORSAM18399-1


title: ORSAM18396-1

source_name: adipose-44% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM18397-1


title: H5N1.017_d001_13A05


title: H5N1.017_d000_00h_13G04


title: ORSAM17863-1

source_name: adipose-44% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: ORSAM18395-1


title: H5N1.015_d100_13E04

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-015

source_name: Individual H5N1-015


title: ORSAM17861-1

source_name: adipose-10% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: H5N1.015_d022_13D04


title: H5N1.017_d000_12h_13H04


title: ORSAM17862-1


title: ORSAM17859-1


title: ORSAM17857-1

source_name: adipose-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: CC019/TauUncJ x CC075/UncJ)F1


title: H5N1.015_d021_12h_13C04


title: ORSAM17855-1

source_name: adipose-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: H5N1.015_d000_12h_13H03


title: H5N1.015_d021_00h_13B04


title: H5N1.015_d000_00h_13G03


title: H5N1.015_d001_13A04


title: ORSAM17850-1

source_name: adipose-10% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: ORSAM17860-1


title: ORSAM17849-1


title: ORSAM17843-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -Metformin-rep1

value: CC051/TauUncJ x CC059/TauUncJ)F1


title: ORSAM17848-1


title: ORSAM17846-1

source_name: adipose-44% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: H5N1.020_d021_12h_13C06


title: ORSAM17856-1


title: H5N1.009_d022_13E03

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-009

source_name: Individual H5N1-009


title: H5N1.009_d021_12h_13D03


title: H5N1.009_d001_13B03


title: H5N1.009_d000_12h_13A03


title: H5N1.009_d000_00h_13H02


title: ORSAM17842-1


title: H5N1.004_d022_13E02

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-004

source_name: Individual H5N1-004


title: H5N1.004_d001_13B02


title: H5N1.004_d021_12h_13D02


title: H5N1.004_d100_13F02


title: ORSAM17839-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1


title: ORSAM17844-1


title: ORSAM17485-1

source_name: adipose-44% fat + fiber-male-CC024/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC024/GeniUncJ x CC002/UncJ)F1


title: ORSAM17837-1


title: ORSAM17484-1


title: H5N1.009_d100_13F03


title: ORSAM17479-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC051/TauUncJ x CC019/TauUncJ)F1


title: ORSAM19029-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: ORSAM17840-1


title: ORSAM17475-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1


title: ORSAM17483-1


title: ORSAM17476-1


title: H5N1.004_d021_00h_13C02


title: H5N1.009_d021_00h_13C03


title: ORSAM17472-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1


title: ORSAM17473-1


title: H5N1.002_d022_13F01

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-002

source_name: Individual H5N1-002


title: H5N1.002_d021_00h_13D01


title: H5N1.002_d100_13G01


title: H5N1.004_d000_00h_13H01


title: H5N1.002_d001_13C01


title: ORSAM17470-1


title: H5N1.002_d021_12h_13E01


title: H5N1.002_d000_00h_13A01


title: ORSAM17459-1

source_name: adipose-10% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -Metformin-rep1


title: H5N1.002_d000_12h_13B01


title: ORSAM17457-1

source_name: adipose-44% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1


title: H5N1.004_d000_12h_13A02


title: H5N1.036_d021_12h_12G11

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-036

source_name: Individual H5N1-036


title: ORSAM17454-1


title: ORSAM17474-1


title: H5N1.036_d001_12E11


title: H5N1.036_d021_00h_12F11


title: H5N1.036_d022_12H11


title: ORSAM17453-1


title: H5N1.036_d000_12h_12D11


title: ORSAM17089-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1


title: H5N1.036_d000_00h_12C11


title: H5N1.033_d100_12B11

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-033

source_name: Individual H5N1-033


title: ORSAM17086-1


title: ORSAM17088-1


title: ORSAM17084-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC059/TauUncJ)F1 -None-rep1


title: ORSAM17083-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1


title: ORSAM17082-1


title: H5N1.036_d100_12A12


title: H5N1.033_d021_12h_12H10


title: H5N1.033_d021_00h_12G10


title: H5N1.033_d022_12A11


title: H5N1.033_d001_12F10


title: H5N1.033_d000_00h_12D10


title: H5N1.031_d100_12C10

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-031

source_name: Individual H5N1-031


title: ORSAM17081-1


title: ORSAM17080-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -Metformin-rep1


title: ORSAM17079-1


title: ORSAM17078-1


title: ORSAM17077-1


title: ORSAM17076-1


title: ORSAM17085-1


title: H5N1.031_d021_12h_12A10


title: ORSAM17074-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: ORSAM17073-1


title: H5N1.033_d000_12h_12E10


title: ORSAM17071-1

source_name: adipose-10% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC011/UncJ)F1


title: ORSAM17069-1

source_name: adipose-10% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1


title: H5N1.031_d022_12B10


title: H5N1.031_d021_00h_12H09


title: ORSAM17065-1

source_name: adipose-44% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1

value: CC011/UncJ x CC005/TauUncJ)F1


title: ORSAM17063-1

source_name: adipose-10% fat + fiber-male-CC002/UncJ x CC075/UncJ)F1 -None-rep1

value: CC002/UncJ x CC075/UncJ)F1


title: H5N1.031_d001_12G09


title: ORSAM17060-1

source_name: adipose-10% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -None-rep1

value: gonadal fat pad


title: H5N1.025_d100_12D09

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-025

source_name: Individual H5N1-025


title: H5N1.031_d000_00h_12E09


title: H5N1.025_d021_00h_12A09


title: H5N1.025_d022_12C09


title: H5N1.031_d000_12h_12F09


title: H5N1.025_d021_12h_12B09


title: ORSAM17057-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: male


title: ORSAM17075-1


title: ORSAM17056-1


title: ORSAM17055-1


title: ORSAM17053-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC019/TauUncJ)F1 -None-rep1


title: H5N1.025_d001_12H08


title: ORSAM17050-1


title: ORSAM16493-1

source_name: adipose-44% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -Metformin-rep1


title: H5N1.024_d100_12E08

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-024

source_name: Individual H5N1-024


title: H5N1.025_d000_12h_12G08


title: H5N1.024_d021_00h_12B08


title: H5N1.024_d001_12A08


title: H5N1.024_d021_12h_12C08


title: H5N1.024_d000_12h_12H07


title: H5N1.024_d022_12D08


title: H5N1.025_d000_00h_12F08


title: H5N1.024_d000_00h_12G07


title: ORSAM16489-1

source_name: adipose-10% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -Metformin-rep1


title: ORSAM16488-1


title: H5N1.022_d022_12D07

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-022

source_name: Individual H5N1-022


title: ORSAM16486-1


title: ORSAM16491-1


title: ORSAM16485-1

source_name: adipose-10% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -Metformin-rep1


title: ORSAM17051-1


title: ORSAM16483-1


title: ORSAM16484-1


title: H5N1.022_d021_12h_12C07


title: H5N1.022_d021_00h_12B07


title: ORSAM16482-1

source_name: adipose-44% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -Metformin-rep1


title: H5N1.022_d000_12h_12H06


title: H5N1.022_d000_00h_12G06


title: H5N1.022_d100_12E07


title: ORSAM16490-1


title: H5N1.019_d021_12h_12D06

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-019

source_name: Individual H5N1-019


title: ORSAM16480-1


title: ORSAM16477-1

source_name: adipose-44% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1


title: ORSAM16479-1


title: ORSAM16476-1


title: ORSAM16475-1


title: ORSAM16471-1

source_name: adipose-44% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -Metformin-rep1


title: ORSAM16470-1


title: ORSAM16469-1

source_name: adipose-10% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1


title: ORSAM16468-1


title: ORSAM16465-1


title: H5N1.019_d100_12F06


title: ORSAM16463-1


title: H5N1.022_d001_12A07


title: H5N1.019_d022_12E06


title: H5N1.013_d022_12F05

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-013

source_name: Individual H5N1-013


title: H5N1.019_d000_12h_12A06


title: H5N1.019_d021_00h_12C06


title: H5N1.013_d100_12G05


title: H5N1.019_d001_12B06


title: H5N1.019_d000_00h_12H05


title: H5N1.013_d021_12h_12E05


title: H5N1.013_d001_12C05


title: H5N1.013_d000_12h_12B05


title: ORSAM16334-1

source_name: adipose-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: ORSAM16473-1

value: Outbred


title: H5N1.013_d021_00h_12D05


title: H5N1.013_d000_00h_12A05


title: ORSAM16332-1


title: ORSAM16326-1

source_name: adipose-44% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1


title: ORSAM16325-1


title: H5N1.010_d100_12H04

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-010

source_name: Individual H5N1-010


title: H5N1.010_d000_12h_12C04


title: ORSAM16337-1

source_name: adipose-44% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM16324-1


title: ORSAM16322-1

source_name: adipose-10% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC060/UncJ)F1


title: H5N1.010_d021_12h_12F04


title: H5N1.010_d022_12G04


title: H5N1.010_d001_12D04


title: H5N1.010_d021_00h_12E04


title: ORSAM16320-1

source_name: adipose-44% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: H5N1.010_d000_00h_12B04


title: ORSAM16318-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1

value: 10% fat + fiber


title: ORSAM16319-1

value: female


title: ORSAM16317-1


title: H5N1.007_d022_12H03

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-007

source_name: Individual H5N1-007


title: ORSAM16311-1

source_name: adipose-44% fat + fiber-female-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1


title: ORSAM16315-1


title: ORSAM16310-1

source_name: adipose-10% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1


title: ORSAM16313-1


title: H5N1.007_d021_12h_12G03


title: ORSAM16307-1


title: H5N1.007_d001_12E03


title: H5N1.007_d000_12h_12D03


title: H5N1.007_d000_00h_12C03


title: H5N1.007_d021_00h_12F03


title: H5N1.006_d021_00h_12H02

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-006

source_name: Individual H5N1-006


title: H5N1.006_d022_12B03


title: ORSAM16188-1

source_name: adipose-44% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1

value: Metformin


title: H5N1.007_d100_12A04


title: H5N1.006_d001_12G02


title: H5N1.006_d021_12h_12A03


title: ORSAM16187-1

value: 44% fat + fiber


title: ORSAM16186-1


title: ORSAM16184-1

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1


title: ORSAM16183-1


title: ORSAM16182-1


title: ORSAM16178-1

source_name: adipose-44% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -Metformin-rep1

value: CC011/UncJ x CC027/GeniUncJ)F1


title: ORSAM16179-1

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -Metformin-rep1


title: ORSAM16305-1


title: ORSAM16181-1


title: H5N1.005_d021_12h_12C02

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-005

source_name: Individual H5N1-005


title: H5N1.006_d000_12h_12F02


title: H5N1.005_d022_12D02


title: H5N1.005_d001_12A02


title: H5N1.005_d000_00h_12G01


title: H5N1.005_d000_12h_12H01


title: H5N1.005_d021_00h_12B02


title: H5N1.006_d000_00h_12E02


title: H5N1.003_d022_12F01

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-003

source_name: Individual H5N1-003


title: ORSAM16174-1

source_name: adipose-44% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -Metformin-rep1


title: ORSAM16172-1

source_name: adipose-10% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1


title: ORSAM16170-1

source_name: adipose-44% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1


title: ORSAM16169-1


title: H5N1.003_d021_00h_12D01


title: ORSAM16167-1


title: ORSAM16177-1


title: ORSAM16165-1

source_name: adipose-44% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: ORSAM16176-1


title: ORSAM16173-1


title: Stage4_PDA_R3

city: East Lansing

first: Frances

last: Trail

state: Michigan

address: 612 Wilson Road

department: Plant Biology

institute: Michigan State University

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. The low-quality reads were removed using the read filtering tool, Trimmomatic, Version 0.39. The 3’ ends of NovaSeq6000 single-end 100 bp reads were trimmed to 50 bp reads (keeping the first 50 bp) using Trimmomatic Version 0.39.
The trimmed reads were mapped to the indexed M. anisopliae reference sequences using HISAT 2.2.1.
The HISAT alignments in SAM format were then sorted and converted to BAM format using SAM tools.
Count files were then generated using HTSeq Version 0.11.1.
The DESeq2 package Version 1.30.1 in R was used to normalize the read counts and to perform differential expression analysis.
Assembly: The reference sequence used for the alignment is  Metarhizium anisopliae ARSEF 549 (GCA_000814975.1)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Metarhizium anisopliae

source_name: Germinated conidia

growth_protocol: For total RNA extraction of each germination stage on standard medium (potato dextrose agar), a 200 µL aliquot of the conidial suspension (1 x 106 conidia/mL) of each species was inoculated onto a sterile cellophane sheet overlaid on PDA in a Petri dish (60 x 15 mm). Petri dishes containing inoculated sheets were then incubated at RT in continuous light till the conidia reached respective germination stages. The barley roots were used to examine conidial developmental stages on the host.

extract_protocol:
Total RNA of M. anisopliae from cellophane membranes and infected host tissue was isolated using Trizol reagent. RNA was treated with RNase-Free DNase (Qiagen), purified further using RNA Clean and ConcentratorTM - 5 (ZymoResearch)
Libraries were prepared using the Illumina Stranded mRNA Prep - Ligation kit with IDT for Illumina RNA UD Indexes.

value: Germinated conidia

value: WT

value: 28 hours on PDA


title: ORSAM16162-1

source_name: adipose-44% fat + fiber-female-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: H5N1.003_d001_12C01


title: ORSAM15720-1

source_name: adipose-44% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC011/UncJ)F1


title: Stage4_PDA_R2


title: Stage4_PDA_R1


title: ORSAM15719-1

value: gonadal fat pad


title: H5N1.014_d021_12h_11E05

description: Gene expression data from PAX Tubes extracted from individual from individual H5N1-014

source_name: Individual H5N1-014


title: H5N1.003_d000_00h_12A01


title: H5N1.003_d021_12h_12E01


title: ORSAM15718-1

value: male


title: H5N1.014_d100_11G05


title: H5N1.014_d001_11C05


title: H5N1.014_d000_12h_11B05


title: ORSAM16166-1


title: H5N1.003_d000_12h_12B01


title: Stage3_PDA_R3

value: 19 hours on PDA


title: H5N1.014_d021_00h_11D05


title: ORSAM15717-1

source_name: adipose-44% fat + fiber-female-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: Outbred


title: Stage3_PDA_R2


title: H5N1.014_d000_00h_11A05


title: Stage3_PDA_R1


title: ORSAM15716-1


title: Stage2_PDA_R3

value: 10 hours on PDA


title: ORSAM15715-1


title: Stage2_PDA_R2


title: ORSAM16164-1


title: ORSAM15714-1

source_name: adipose-10% fat + fiber-male-CC043/GeniUncJ x CC011/UncJ)F1 -None-rep1

value: 10% fat + fiber


title: Stage4_Barley_R3

value: 26 hours on barley roots


title: Stage2_PDA_R1


title: Stage4_Barley_R2


title: ORSAM15713-1


title: Stage3_Barley_R3

value: 15 hours on barley roots


title: Stage4_Barley_R1


title: ORSAM15712-1

source_name: adipose-10% fat + fiber-male-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC001/UncJ x CC042/GeniUncJ)F1


title: Stage3_Barley_R2


title: Stage1_PDA_R3

source_name: Conidia

value: Conidia

value: 30 minutes on PDA


title: Stage1_PDA_R1

source_name: Condia

value: Condia


title: Stage2_Barley_R1

value: 7 hours on barley roots


title: ORSAM15710-1

source_name: adipose-10% fat + fiber-female-CC001/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: female


title: Stage1_PDA_R2

value: WT


title: Stage2_Barley_R2

value: Germinated conidia


title: Stage2_Barley_R3


title: ORSAM15711-1


title: Stage1_Barley_R3

value: 30 minutes on barley roots


title: ORSAM15708-1

value: gonadal fat pad


title: Stage3_Barley_R1


title: Stage1_Barley_R1


title: ORSAM15709-1


title: ΔManS-ManNAc-R2

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

country: China

institute: Fudan University

description: ManS-deleted  Salmonella strain were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Biological repeat 2.

data_processing:
RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine.
SOAP (v2.21, -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).The rest reads with adaptor，or with unknown bases more than 5%  ,or with more than 20% low-quality bases were cleared by a software developed by BGI group. After, clear reads were mapped to reference genome with Bowtie2： v2.2.5 -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --), and expression value was caculated  (http://deweylab.biostat.wisc.edu/RSEM）
Assembly: Salmonella Typhimurium LT2 Genome  (NC_003197) Chromosome (https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2) and plasmid (https://www.ncbi.nlm.nih.gov/nuccore/NC_003277.2)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: M9CA broth plus 0.1% ManNAc

extract_protocol:
Bacterial total RNA was isolated using the hot phenol method. Briefly, Cells were resuspended in lysozyme, 10% SDS and 3M sodium acetate (pH5.2). The cleared lysate was mixed with saturated phenol (pH4.5) and incubated at 64°C for 6 min with shaking. After mixing with chloroform and centrifugation in a Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech), the aqueous phase was collected and mixed the with 30:1 ethanol: sodium acetate (pH 6.5) and precipitated at -80°C overnight. RNA pellets were washed with 80% ethanol and dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and the RNA concentration was determined using NanoDrop 2000.
Ribosomal RNAs was removed by Biotin-labeled rRNA probe. RNA was fragmented with BGI fragmentation buffer and was reverse transcribed with random hexamer. Double chain cDNA was then blunted and phosphorylated for the 5’ end, and overhang A base in the 3’ end and ligated with T-overhang adapter. After PCR application, samples were sequenced in BGISeq-500 platform

tag: cell type

value: ManS-deleted


title: ΔManS-ManNAc-R3

description: ManS-deleted  Salmonella strain were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Biological repeat 3.

source_name: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344


title: H5N1.014_d022_11F05


title: NCI-BL1437

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

description:
Illumina HiScanSQ
Noguera-Castells_Average_Beta_Homo_Sapiens.csv

hyb_protocol: Illumina HIIScanSQ with Autoloader system

data_processing:
Data was processed using sesame package pipeline in R environment
hg19 and mm10
.csv format containing Average Beta value and detection P.value

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Ilumina methylation microarrays

extract_protocol: Genomic DNA was extracted and purified from the different cell lines using Qiagen DNeasy Kit according to standard instructions

tag: cell line

value: Hematologic cell line


title: NCI-BL2126

scan_protocol: Illumina HIIScanSQ with Autoloader system


title: ARH-77


title: GM11407


title: ORSAM15707-1

source_name: adipose-44% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

value: male

value: CC002/UncJ x CC043/GeniUncJ)F1

value: Outbred

value: 44% fat + fiber


title: WT-ManNAc-R3

description: Wild-type Salmonella strain were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Biological repeat 3.

value: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

value: Wild-type


title: ΔManS-ManNAc-R1

description: ManS-deleted Salmonella strain were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Biological repeat 1.


title: WT-ManNAc-R2

description: Wild-type Salmonella strain were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Biological repeat 2.


title: ORSAM15705-1


title: IM-9


title: Stage1_Barley_R2

value: Conidia


title: WT-ManNAc-R1

description: Wild-type Salmonella strain were grown in M9CA medium supplemented with 0.1% ManNAc to an OD600 of ~0.5. Biological repeat 1.


title: ORSAM15699-1

source_name: adipose-10% fat + fiber-male-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC012/GeniUncJ x CC002/UncJ)F1

value: 10% fat + fiber


title: SD-1


title: EHEB

source_name: EHEB


title: RPMI-6666


title: SU-DHL-1


title: DEL

source_name: DEL


title: ORSAM15698-1


title: SR

source_name: SR


title: Hs 445


title: ΔManS + pBAD-Ctr R2

description: The ManS-deleted strain carrying the pBAD empty plasmid was grown in M9CA medium supplemented with 0.1% ManNAc until reaching an OD600 of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression, and incubation was continued for 10 minutes. Biological repeat 2."


title: ORSAM15697-1

source_name: adipose-44% fat + fiber-male-CC002/UncJ x CC075/UncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC075/UncJ)F1

value: Metformin


title: ΔManS + pBAD-Ctr R1

description: The ManS-deleted strain carrying the pBAD empty plasmid was grown in M9CA medium supplemented with 0.1% ManNAc until reaching an OD600 of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression, and incubation was continued for 10 minutes. Biological repeat 1."


title: ORSAM15706-1


title: KARPAS-299


title: HH

source_name: HH


title: ORSAM15696-1


title: ΔManS + pBAD-ManS R2

description: The ManS-deleted strain carrying the pBAD-ManS  plasmid was grown in M9CA medium supplemented with 0.1% ManNAc until reaching an OD600 of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression, and incubation was continued for 10 minutes. Biological repeat 2."


title: ORSAM15701-1


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 40hpi (hours post invasion); replicate 2 input

city: State College

first: Manuel

last: Llinás

state: Pennsylvania

address: W122 Millennium Science Complex, Pollock Road

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

library_source: genomic

data_processing:
Raw sequencing reads were trimmed (Trimmomatic v0.32.3) to remove Illumina adaptor sequences and low-quality reads below 30 Phred (Single-end options - "SE ILLUMINACLIP:TrueSeq3-SE:2:30:10 SLIDINGWINDOW:4:30"). FastQC (v0.11.9) was used to check the quality after trimming. The output file format being FASTQ.
Processed reads were then mapped to the P. falciparum genome (PlasmoDB.org; Plasmodium falciparum 3D7 strain; version 3; release 57) using BWA-MEM (v0.7.17.2) simple Illumina mode. Multiple mapped reads filtered out using SamTools (v1.1.2) with option "-q 1" (MAPQ=1). The output file format being BAM.
Aligned BAM files were displayed using DeepTools BAMCompare (v3.3.2.0.0) with options "--binSize 20 --scaleFactorsMethod readCount --operation log2 --pseudocount 1 --smoothLength 60". The output file format being BIGWIG.
Once the sequences were mapped, MACS2 (v2.2.7.1) was used to call peaks with each biological replicate and its paired input sample using a standard significance cut-off (q-value=0.01). Using BedTools Multiple Intersect (v2.29.2), the narrow peak output file for each replicate was overlapped to identify the significant peaks in the overlap between both ChIP-seq biological replicates.
The overlapping regions were then used to identify an enriched DNA motif (STREME Meme Suite: (Bailey 2021), and putative gene targets of PfMORC were defined as genes with peaks within 2 kb upstream of the gene target ATG start codon or peaks within gene bodies. In a situation with any peaks between gene targets in a head-to-head orientation, the closest gene was chosen.
Assembly: Plasmodium falciparum genome (strain 3D7; version 3; release 57)
Supplementary files format and content: BIGWIG: DeepTools BAMCompare output files for Log2(IP/Input) sample display
Supplementary files format and content: BED: MACS2 outfile of ChIP-seq peak summits

organism: Plasmodium falciparum 3D7

source_name: Schizont Stage (40hpi) Parasitized Erythrocyte Cells

growth_protocol: Wild type and PfMORC+3xHA modified parasites (3D7 strain) were cultured under standard P. falciparum culturing conditions (5% O2, 7% CO2, 37°C, RPMI 1640 media with 0.5% AlbumaxII and hypoaxanthine). No additional drug selection added to PfMORC+3xHA modified parasites after transfection.

extract_protocol:
PfMORC ChIP-seq was performed similarly to previously published ChIP-seq experiments in Plasmodium falciparum (Josling et al. 2020, Singh et al. 2021, Russell et al. 2022). Five samples in total were collected: biological duplicates using the PfMORC+HA parasite line at the trophozoite stage [30 hpi], biological duplicates using the PfMORC+HA parasite line at the schizont stage [40 hpi], and a single replicate using the PfMORC+GFP parasite line at the schizont stage [40 hpi]. In brief, the protocol includes five steps: (1) Treated with 1% formaldehyde to crosslink the suspended PfMORC+HA (or PfMORC+GFP) parasite cultures (at least 10^8 trophozoite- or schizont-stage parasites synchronized with 10% sorbitol more than one cycle prior) at 37°C for 10 minutes; (2) Collected parasite nuclei using prechilled glass dounce homogenizer for 100 strokes per 10^9 trophozoites/schizonts; (3) Lysed parasite nuclei and mechanically sheared chromatin until sufficiently sheared using Covaris Focus-Ultrasonicator M220 (5% duty cycle, 75 W peak incident power, 200 cycles per burst, 7°C, for 5 minutes). (4) We collected 10% of each sample for the nonimmunoprecipitated “input” control and then immunoprecipitated the remaining 90% of each sample. The remaining 90% of each sample was immunoprecipitated with 1:1000 anti-HA antibody (0.5 mg/mL Roche Rat Anti-HA High Affinity [11867423001]) or 1:1000 anti-GFP antibody (0.1 mg/mL Abcam Rabbit Anti-GFP [Ab290]) overnight at 4°C with rotation. (5) DNA was purified after reverse crosslinking using a MinElute column (Qiagen) as directed and quantified by a Qubit fluorometer (Invitrogen).
The PfMORC ChIP-seq libraries were performed similarly to previously published ChIP-seq experiments in Plasmodium falciparum (Josling et al. 2020, Singh et al. 2021, Russell et al. 2022). DNA sequencing libraries were prepared for high-throughput Illumina sequencing on the NextSeq 2000 with the 150 x 150 single-end mode. The library prep underwent 12 rounds of amplification using KAPA HiFi polymerase. Completed libraries were quantified using the Qubit fluorometer (Invitrogen) for high-sensitivity DNA and library sequence length by the Agilent TapeStation 4150.

treatment_protocol: At least 10^8 30hpi or 40hpi (hours post invasion) parasites synchronized with 10% Sorbitol more than one cycle prior.

value: 3D7 strain background

value: 3xHA-tagged PfMORC (C-terminal) in 3D7 strain background

value: No Treatment


title: H9


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 40hpi (hours post invasion); replicate 2 IP

value: Schizont Stage (40hpi) Parasitized Erythrocyte Cells


title: ORSAM15695-1

value: gonadal fat pad


title: ORSAM15693-1

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -Metformin-rep1

value: female


title: DND-41

value: Hematologic cell line


title: Loucy

source_name: Loucy


title: C8166


title: HAL-01


title: ORSAM15692-1


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 40hpi (hours post invasion); replicate 1 IP


title: KAI3


title: PF-382


title: MOLT-4


title: J.RT3-T3.5


title: ORSAM14946-1

source_name: adipose-44% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: male

value: CC051/TauUncJ x CC060/UncJ)F1


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 30hpi (hours post invasion); replicate 2 IP

source_name: Trophozoite Stage (30hpi) Parasitized Erythrocyte Cells


title: Karpas-45


title: ORSAM14941-1

source_name: adipose-44% fat + fiber-male-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: Outbred

value: 44% fat + fiber


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 40hpi (hours post invasion); replicate 1 input


title: SUP-T1


title: ΔManS + pBAD-ManS R1

description: The ManS-deleted strain carrying the pBAD-ManS plasmid was grown in M9CA medium supplemented with 0.1% ManNAc until reaching an OD600 of approximately 0.5. L-arabinose was then added to a final concentration of 0.2% (w/v) to induce expression, and incubation was continued for 10 minutes. Biological repeat 1."

value: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344


title: P12-Ichikawa


title: HuT 78

source_name: HuT 78


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 30hpi (hours post invasion); replicate 2 input

value: Trophozoite Stage (30hpi) Parasitized Erythrocyte Cells


title: ORSAM14940-1


title: MOLT-16


title: MOLT-13


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 30hpi (hours post invasion); replicate 1 IP


title: CEM/C1


title: Jurkat

source_name: Jurkat


title: ORSAM14938-1

source_name: adipose-44% fat + fiber-male-CC042/GeniUncJ x CC060/UncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC060/UncJ)F1


title: ChIP-seq on PfMORC in a PfMORC+3xHA parasite line at 30hpi (hours post invasion); replicate 1 input


title: KE-37


title: ORSAM14937-1


title: SARC_102_EWING

city: Campinas

first: Felipe

last: Silva

address: R. Márcia Mendes, 506

country: Brazil

institute: Boldrini

data_processing:
Transcriptome raw data quality was verified with FASTQC . We used STAR-fusion to identify and annotate fusion transcripts based on discordant read alignments with default configurations. Alinment against GRCh38.primary_assembly.genome.fa and assigned mapped reads from genomic RNA sequencing to genomic features were performed using Rsubread package (v  2.18.0)
Assembly: GRCh38
Supplementary files format and content: A csv  file corresponding to gene count matrix containing assigned mapped reads from genomic RNA sequencing to genomic features

source_name: Tumour tissue

extract_protocol:
RNA was extracted with RNeasy Kit (QIAGEN, Hilden, Germany; cat. ID: 74106) and quantified with High Sensitivity Qubit™ RNA Assay Kits (Invitrogen™, Waltham, MA, USA; cat. ID: Q32855).
Transcriptome assay was performed using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Illumina, San Diego, CA, USA) and sequenced on the NextSeq550 or NOVAseqX (Illumina Inc, San Diego, CA, USA). Paired-end runs were sequenced in 74 cycles per read (2 X 74), with an average of 41.5 million reads per sample.

value: Tumour tissue

value: EWING


title: ORSAM14934-1

source_name: adipose-44% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1


title: CCRF-CEM

source_name: CCRF-CEM


title: BE-13


title: VL51


title: SARC_99_EWING


title: ORSAM14933-1

source_name: adipose-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: BCP-1


title: CRO-AP2


title: BC-1


title: ORSAM14930-1

source_name: adipose-10% fat + fiber-male-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: 10% fat + fiber


title: KHYG-1


title: HK2 cells, hypoxia, solvent control, biol rep 3, RNA 33

city: Berlin

first: Pratik

middle: Hemant

last: Khedkar

address: Charitéplatz 1

department: Institute of Translational Physiology

country: Germany

institute: Charité - Universitätsmedizin Berlin

data_processing:
Sequence reads were mapped to Homo sapiens GRCh38 111 using salmon with --gcBias and --validateMappings flags
Extraction of read counts and summarizing on gene level was performed using tximeta
Normalization of count data and statistical analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: Tab delimited text file containing gene level summarized raw counts for each sample

growth_protocol: HK-2 cells were maintained in DMEM/F-12 (1:1) supplemented with 10% fetal bovine serum, 1% gluatmine and antiobiotics in a humidified environment with 5% carbon dioxide.

extract_protocol:
Total RNA was extracted using the RNA STAT-60 reagent. The extracted RNA was then purified using the NucleoSpin kit, following the manufacturer's protocol.
Libraries were constructed using the NEBNext Ultra II Poly(A) mRNA Kit with 400 ng total RNA following the manufacturers protocol

treatment_protocol: Cells were seeded onto 6-well plates (9 × 10^5 per well) and allowed to adhere for 6h. Cells were serum-deprived overnight and treated with BAY 60-2770 (1 mM, final concentration) or TGF-β1 (2 ng/mL) or both. Control cells were treated with the solvents used to dissolve the substances, namely 0.0001% DMSO, 4 µM HCl + 0.0001% BSA. Cells were incubated under hypoxia (0.3% oxygen) or normoxia for 24h.

value: solvent control, hypoxia


title: ORSAM14924-1


title: HK2 cells, hypoxia, solvent control, biol rep 2, RNA 32


title: HK2 cells, hypoxia, solvent control, biol rep 1, RNA 31


title: YT

source_name: YT


title: ME-1


title: NCI-H929


title: CTV-1


title: JJN-3


title: EJM

source_name: EJM


title: ATN-1


title: HK2 cells, hypoxia, sGC activator, biol rep 3, RNA 23

value: sGC activator, hypoxia


title: ORSAM14919-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: gonadal fat pad


title: AMO1


title: HK2 cells, hypoxia, sGC activator, biol rep 2, RNA 22


title: ORSAM14918-1

source_name: adipose-44% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: female


title: BC-3

value: Hematologic cell line


title: ORSAM14926-1

source_name: adipose-10% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1


title: HK2 cells, hypoxia, sGC activator, biol rep 1, RNA 21


title: SK-MM-2


title: SARC_92_EWING


title: MM.1


title: L-363


title: ORSAM14917-1


title: ORSAM14916-1


title: HK2 cells, normoxia, solvent control, biol rep 5, RNA 18

value: solvent control, normoxia


title: KMS-12-BM


title: MM1.S


title: U266B1


title: MM1.R


title: ORSAM14863-1

source_name: adipose-10% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC075/UncJ)F1

value: Metformin


title: RPMI-8226


title: HK2 cells, normoxia, TGF-β1+ sGC activator, biol rep 5, RNA 17

value: TGF-β1+ sGC activator, normoxia


title: ORSAM14922-1

source_name: adipose-44% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1

value: male

value: CC011/UncJ x CC005/TauUncJ)F1

value: Outbred

value: 44% fat + fiber


title: HK2 cells, normoxia, TGF-β1+ sGC activator, biol rep 4, RNA 16


title: ORSAM14861-1


title: OPM-2


title: HK2 cells, normoxia, TGF-β1+ sGC activator, biol rep 3, RNA 15


title: Granta-519


title: Mino

source_name: Mino


title: ORSAM14860-1


title: UPN-2


title: JeKo-1


title: HK2 cells, normoxia, TGF-β1+ sGC activator, biol rep 2, RNA 14


title: JVM-2


title: ORSAM14858-1

source_name: adipose-10% fat + fiber-male-CC002/UncJ x CC075/UncJ)F1 -Metformin-rep1


title: HK2 cells, normoxia, TGF-β1+ sGC activator, biol rep 1, RNA 13


title: Z-138


title: HDLM-2


title: REC-1


title: ORSAM14856-1


title: L-1236


title: HK2 cells, normoxia, TGF-β1, biol rep 4, RNA 11

value: TGF-β1, normoxia


title: KM-H2


title: ORSAM14855-1

source_name: adipose-10% fat + fiber-female-CC002/UncJ x CC075/UncJ)F1 -None-rep1


title: ORSAM14853-1


title: SUP-HD1


title: Hs 611.T


title: HK2 cells, normoxia, TGF-β1, biol rep 2, RNA 09


title: L-428


title: ORSAM14686-1

source_name: adipose-44% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1

value: CC011/UncJ x CC027/GeniUncJ)F1


title: HK2 cells, normoxia, TGF-β1, biol rep 1, RNA 08


title: BONNA-12


title: Mo-T

source_name: Mo-T


title: ORSAM14685-1


title: ORSAM14859-1


title: OCI-LY3


title: HK2 cells, normoxia, solvent control, biol rep 4, RNA 07


title: Sc-1


title: ORSAM14684-1


title: U-2932


title: PFEIFFER

source_name: PFEIFFER


title: HK2 cells, normoxia, TGF-β1, biol rep 5, RNA 12


title: ORSAM14682-1

source_name: adipose-10% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -Metformin-rep1


title: HK2 cells, normoxia, solvent control, biol rep 2, RNA 05


title: ORSAM14681-1


title: MD-901


title: HK2 cells, normoxia, TGF-β1, biol rep 3, RNA 10


title: HK2 cells, normoxia, solvent control, biol rep 3, RNA 06


title: L-540


title: Farage

source_name: Farage


title: HK2 cells, normoxia, sGC activator, biol rep 3, RNA 03

value: sGC activator, normoxia


title: ORSAM14680-1

value: 10% fat + fiber


title: HK2 cells, normoxia, solvent control, biol rep 1, RNA 04


title: HK2 cells, normoxia, sGC activator, biol rep 2, RNA 02


title: ORSAM14679-1

source_name: adipose-10% fat + fiber-male-CC011/UncJ x CC027/GeniUncJ)F1 -Metformin-rep1


title: WSU-DLCL2


title: VAL

source_name: VAL


title: RC-K8


title: ORSAM14677-1


title: SU-DHL-5


title: ORSAM14676-1


title: HK2 cells, normoxia, sGC activator, biol rep 1, RNA 01


title: RL

source_name: RL


title: CTB-1


title: ORSAM14674-1

source_name: adipose-10% fat + fiber-female-CC011/UncJ x CC027/GeniUncJ)F1 -None-rep1


title: Ri-1


title: HT

source_name: HT


title: ORSAM14673-1


title: ORSAM14672-1


title: SU-DHL-8


title: Kidney, control 70 yo, glomerulus, ROI 1

city: New York

first: Miguel

last: Fribourg

state: NY

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

description: ROI, column N1_1 in GeoMX_TrACR_Q3Matrix

data_processing:
Data processing was performed in R v4.2.1. The RNA count of the negative probes was used to evaluate the limit of quantification (LOQ); in brief the median and standard deviation of the negative probe counts were calculated and we defined the LOQ to be three standard deviations above the median of the negative probe counts. RNA counts below this threshold were converted in missing values. Then the count data was Q3 normalized using .
save-interim-files=false, quality-trim-score=20,2color-trimming=True, adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length=10, adapter-trim-max-mismatch=3,barcode-max-mismatch=1,stitching-max-mismatch=2,dedup-hd=1,threads=4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_TAP_H_WTA_V1.0.pkc)
Supplementary files format and content: Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Supplementary files format and content: Q3 normalized counts
Library strategy: Spatial Transcriptomics

source_name: Kidney

extract_protocol:
Serially prepared sections (previously hybridized with Whole Transcriptome Assay (WTA) probes) were also immunostained with CD3, Ki-67, alpha-Smooth Muscle Actin and SYTO83 to help with region of interest (ROI) selection. Briefly, Morphology Marker Solution was prepared in the following proportions per slide: 22ul SYTO (Thermo Fisher Scientific, Cat#S11364), 5.5 ul a-Smooth Muscle Actin (NanoString Technologies), 5.5 ul CD3 (NanoString Technologies), 5.5 ul Ki-67 (NanoString Technologies), and 181.5 ul Buffer W for a total volume of 220 ul/slide. Slides were incubated in this solution at room temperature for 1 hour followed by successive 2x SSC washes, after which, the slides were loaded into the NanoString GeoMx Digital Spatial Profiler (DSP) where overview scans were captured at 20x to guide the selection of ROIs. Slides were prepared for hybridization following a modified RNA FFPE BOND RX Slide Preparation Protocol in the GeoMx NGS Slide Preparation User Manual (NanoString Technologies, MAN-10115). Briefly, deparaffinization, antigen retrieval, and Proteinase K digestion was performed on a Leica BOND-RX instrument with Bond Dewax Solution, Bond Epitope Retrieval Solution 2, and a 37°C Proteinase K digest at 1mg/ml. Human Whole Transcriptome Assay (WTA) probes (NanoString Technologies, Cat#121401102) hybridized at 4nM each in Buffer R, and incubated in a hybridization chamber for 16 hrs at 37°C. Two washes in 50% Formamide/2x SSC (ThermoFisher, Cat#AM9342 / Sigma-Aldrich, Cat#S6639) at 37°C washed non-specifically-bound probes from the slides, which were then blocked prior to antibody staining with 200 ul Buffer W (Nanostring). Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: Kidney


title: Karpas-422


title: SU-DHL-10


title: Kidney, control 70 yo, glomerulus, ROI 3

description: ROI, column N1_3 in GeoMX_TrACR_Q3Matrix


title: SU-DHL-6


title: SU-DHL-4


title: Kidney, control 70 yo, glomerulus, ROI 2

description: ROI, column N1_2 in GeoMX_TrACR_Q3Matrix


title: ORSAM14669-1

source_name: adipose-10% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -Metformin-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1


title: DoHH-2


title: Kidney, ACR, glomerulus, ROI 3


title: ORSAM14668-1

value: gonadal fat pad


title: DB

source_name: DB


title: EM-2


title: A3-KAW


title: Kidney, ACR, glomerulus, ROI 2


title: Kidney, ACR, glomerulus, ROI 1


title: ORSAM14667-1


title: LAMA-84


title: ORSAM14665-1

source_name: adipose-10% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -Metformin-rep1

value: female


title: RPMI-8866

value: Hematologic cell line


title: Kidney, control 6 yo, glomerulus, ROI 3


title: WSU-NHL

source_name: WSU-NHL


title: Karpas-231


title: Kidney, control 6 yo, glomerulus, ROI 2


title: Ku812


title: CML-T1


title: ORSAM14664-1


title: K-562


title: MEG-01


title: ORSAM14660-1

source_name: adipose-10% fat + fiber-female-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: ORSAM14663-1


title: Kidney, ACR, tubulues, RO1 5

description: ROI, column T1_8 in GeoMX_TrACR_Q3Matrix


title: RAMOS

source_name: RAMOS


title: Kidney, control 6 yo, glomerulus, ROI 1


title: Kidney, ACR, tubulues, RO1 4

description: ROI, column T1_7in GeoMX_TrACR_Q3Matrix


title: Daudi

source_name: Daudi


title: Ramos-2G6-4C10


title: P32/ISH


title: ORSAM14659-1


title: MN-60


title: Kidney, ACR, tubulues, RO1 2

description: ROI, column T1_5 in GeoMX_TrACR_Q3Matrix


title: ORSAM14658-1


title: Jiyoye

source_name: Jiyoye


title: BV-173


title: Kidney, ACR, tubulues, RO1 3

description: ROI, column T1_6 in GeoMX_TrACR_Q3Matrix


title: EB2


title: ORSAM14655-1

source_name: adipose-44% fat + fiber-female-CC030/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1


title: DG-75


title: CA46


title: ORSAM14654-1


title: Raji

source_name: Raji


title: Kidney, ACR, tubulues, RO1 1

description: ROI, column T1_4 in GeoMX_TrACR_Q3Matrix


title: ST486


title: Kidney, control 6 yo, tubules, ROI 5

description: ROI, column N1_18 in GeoMX_TrACR_Q3Matrix


title: ORSAM14652-1

source_name: adipose-44% fat + fiber-female-CC030/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: Namalwa

description:
Illumina HiScanSQ
Noguera-Castells_Average_Beta_Homo_Sapiens.csv

source_name: Namalwa


title: ORSAM14651-1


title: SU-DHL-16


title: EB-3


title: Kidney, control 6 yo, tubules, ROI 3

description: ROI, column N1_9 in GeoMX_TrACR_Q3Matrix


title: GA-10


title: Kidney, control 6 yo, tubules, ROI 4

description: ROI, column N1_8 in GeoMX_TrACR_Q3Matrix


title: ORSAM14650-1


title: ORSAM14099-1

source_name: adipose-44% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: SCC-3


title: MHH-PREB-1


title: MEC-1


title: ORSAM14098-1


title: NALM-20


title: ORSAM14097-1


title: JVM-3


title: ORSAM14090-1

source_name: adipose-44% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: CC019/TauUncJ x CC075/UncJ)F1


title: BLaER1


title: SEM

source_name: SEM


title: RCH-ACV

source_name: RCH-ACV


title: ORSAM14089-1


title: ROS-50


title: HeLa 3hpi

city: Seoul

first: Dohoon

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

department: Bioinformatics Institute

country: South Korea

institute: Seoul National University

data_processing:
Processed reads were aligned to the hg38 reference genome with GENCODE v37 gene annotation using STAR v2.7.3a
Gene expression quantification was performed using RSEM v1.3.1
To quantify the expression levels of transposable elements, we used TEtranscripts v2.2.1.
Assembly: hg38
Supplementary files format and content: genes.results - Gene expression quantification table from RSEM

source_name: HeLa

extract_protocol:
Total RNA material were prepared by conventional phenol extraction (Trizol)
By using the manufacturer's instruction of TruSeq Stranded mRNA Library Prep Kit

value: HeLa

value: infected with VSV-G-pseudotyped HIV-1-EGFP

tag: time (hpi)


title: HeLa 12hpi


title: U-698-M


title: HeLa 48hpi


title: HeLa 6hpi


title: Kidney, control 6 yo, tubules, ROI 2

description: ROI, column N1_16 in GeoMX_TrACR_Q3Matrix

source_name: Kidney

value: male


title: MHH-CALL-4


title: RS4;11


title: MHH-CALL-2


title: ORSAM14087-1

source_name: adipose-10% fat + fiber-male-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: Outbred


title: ORSAM14088-1


title: ALL-PO

source_name: ALL-PO


title: MC116


title: ORSAM14086-1

source_name: adipose-44% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: 44% fat + fiber


title: OE-H3

city: Jinan

first: Yujia

last: Li

address: 44#, Wenhua Xi Road

institute: Shandong University

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by using Seqtk.
The sample was mapped using Hisat2（version:2.0.4)
The quantification of transcripts expressed for each sequenced samples was performed using Stringtie（version:1.3.0）
Differentially expressed genes were identified using edgeR
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: Human podocyte

extract_protocol:
RNA was harvested using MJzol animal RNA Extraction Kit (MagBeads). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring negative control or Gpr124 for 48h.

value: Human podocyte

value: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring Gpr124 for 50h.


title: Kidney, control 6 yo, tubules, ROI 1

description: ROI, column N1_17 in GeoMX_TrACR_Q3Matrix


title: OE-H2

value: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring Gpr124 for 49h.


title: SUP-B15


title: TOM-1


title: OE-H1

value: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring Gpr124 for 48h.


title: ORSAM14085-1


title: 697


title: BALL-1


title: ORSAM14083-1

source_name: adipose-44% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1


title: LC4-1


title: OE-C3

value: Overexpression GPR124 in HPC by adenovirus infection harboring Gpr126


title: HeLa 0hpi

value: not infected


title: KOPN-8


title: ORSAM14082-1

value: gonadal fat pad


title: P30/OHK

value: Hematologic cell line


title: OE-C1

value: Overexpression GPR124 in HPC by adenovirus infection harboring Gpr124


title: ORSAM14081-1

source_name: adipose-44% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: female


title: NC-H3

value: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring negative control for 50h.


title: NALM-6


title: Tanoue

source_name: Tanoue


title: REH

source_name: REH


title: ORSAM14080-1

value: CC019/TauUncJ x CC075/UncJ)F1


title: F36-P


title: UKE1


title: SUP-B8


title: NC-H2

value: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring negative control for 49h.


title: GR-ST

source_name: GR-ST


title: ORSAM14077-1

source_name: adipose-10% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: 10% fat + fiber


title: NB4


title: ORSAM14079-1

source_name: adipose-10% fat + fiber-female-CC019/TauUncJ x CC075/UncJ)F1 -None-rep1

value: Outbred


title: KG1A


title: NC-H1

value: Human podocyte

value: High glucose (30 mM D-Glucose) treated HPC with adenovirus infection harboring negative control for 48h.


title: ORSAM14076-1

source_name: adipose-44% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC012/GeniUncJ x CC002/UncJ)F1

value: 44% fat + fiber


title: MOLM-13


title: NC-C3

value: HPC with adenovirus infection harboring negative control


title: OE-C2

value: Overexpression GPR124 in HPC by adenovirus infection harboring Gpr125


title: MV4-11


title: NC-C2


title: OCI-M1


title: TUR

source_name: TUR


title: ORSAM14074-1

source_name: adipose-10% fat + fiber-female-CC012/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: NC-C1

value: HPC with adenovirus infection harboring negative control，


title: P31/FUJ


title: ML-2


title: U-937


title: KO52


title: NOMO-1


title: QIMR-WIL

source_name: QIMR-WIL


title: ORSAM14070-1

source_name: adipose-44% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

value: gonadal fat pad

value: male

value: CC002/UncJ x CC043/GeniUncJ)F1


title: ORSAM14068-1

source_name: adipose-10% fat + fiber-male-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1


title: HL-60

value: Hematologic cell line


title: CESS

source_name: CESS


title: hPSC RNA-seq ActD 4h shLUC Repeat #1

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

data_processing:
STAR --readFilesCommand zcat --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outMultimapperOrder Random --runRNGseed 777 --outSAMmultNmax 1 --outSAMtype BAM Unsorted --twopassMode Basic --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --genomeDir hg38_gencode_v32_starsolo/SAindex --sjdbGTFfile gencode.v32.annotation.gtf --runThreadN 24 --readFilesIn ${p1} ${p2} --outFileNamePrefix ${out} --outTmpDir ${out}
te_count -g hg38 -i ${out}Aligned.out.bam --o ${out}tecount.tsv -m genes_tes
Tag counts were GC normalised with EDASeq
Assembly: hg38
Supplementary files format and content: genes_ntc_expression.tsv.gz: TSV file containing ensembl gene number, gene symbol, and the mean of the normalised tag count for replicate samples
Supplementary files format and content: genes_ntc_expression_nonmerged.tsv.gz:  TSV file containing ensembl gene number, gene symbol, and the merged normalised tag count for replicate samples
Supplementary files format and content: genes_fc_expression.tsv.gz contains fold-change values relative to the 0 hour sample

source_name: cell line

growth_protocol: The cell line used in this study was hESCs H1 cell line. hESCs were grown in mTeSR1 (Stemcell technologies: 85850) on pre-coated Matrigel plates (Corning: 354277). The medium was replaced every day. Cells were passaged by single-cell digestion with Accutase (SIGMA: A6964) every 4-5 days.

extract_protocol:
RNA was isolated using RNAzol RT (MRC, RN190) according to the manufacturer’s protocol and prepared for sequencing with RNA-seq NEB Next Ultra RNA Library Prep Kit (NEB, #7530). RNA quality was tested using an Agilent 2100 and a minimum RIN score of 8.0 was required for sequencing. Samples were sequenced on an Illumina Novaseq 6000.
RNA-seq NEB Next Ultra RNA Library Prep Kit   cat.7530

treatment_protocol: The shRNA virus was packaged using PMD2G, PsPAX2 and target plasmid co-transfected into 293T cells. After 36 hours virus was collected, and purified. Two days later puromycin was used to select transfected cells.

value: cell line

value: hPSCs H1

value: Pluripotent Stem Cells

value: shRNA targetting HNRNPU


title: ORSAM14073-1

value: female

value: 10% fat + fiber


title: ORSAM14027-1

value: Outbred


title: THP-1


title: SKM-1


title: hPSC RNA-seq ActD 4h shLUC Repeat #2


title: ORSAM14025-1


title: Mono-Mac-6


title: ORSAM14075-1


title: KMOE-2


title: ORSAM14024-1


title: KY821


title: hPSC RNA-seq ActD 2h shLUC Repeat #1


title: hPSC RNA-seq ActD 2h shLUC Repeat #2


title: ORSAM14022-1

source_name: adipose-10% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1


title: TF-1


title: KG-1


title: HL-60/MX2


title: hPSC RNA-seq ActD 1h shLUC Repeat #2


title: NKM-1


title: ORSAM14021-1


title: SET-2


title: hPSC RNA-seq ActD 1h shLUC Repeat #1


title: OCI-AML-5


title: MUTZ-8


title: ORSAM13865-1

source_name: adipose-44% fat + fiber-female-CC024/GeniUncJ x CC002/UncJ)F1 -Metformin-rep1

value: CC024/GeniUncJ x CC002/UncJ)F1

value: Metformin


title: OCI-AML-3


title: ORSAM14020-1


title: hPSC RNA-seq ActD 0h shLUC Repeat #2


title: HD-MY-Z

source_name: HD-MY-Z


title: hPSC RNA-seq ActD 4h shHNRNPU Repeat #2


title: HEL

source_name: HEL


title: ORSAM13864-1

value: 44% fat + fiber


title: ORSAM13863-1


title: Kasumi-1


title: hPSC RNA-seq ActD 4h shHNRNPU Repeat #1


title: ORSAM13861-1

source_name: adipose-10% fat + fiber-female-CC024/GeniUncJ x CC002/UncJ)F1 -None-rep1


title: hPSC RNA-seq ActD 2h shHNRNPU Repeat #2


title: in_vivo_Red5

city: Vienna

first: Esther

last: Uijttewaal

address: Dr Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
For data analysis, BAM files were retrieved from Illumina and different samples were demultiplexed using the distinct experimental indices. Furthermore, sgRNAs and UMI sequences were identified using Bowtie, SAMtools, FASTX-Toolkit. Read 1 (R1) contained the sgRNA sequence and to confirm an active or inactive sgRNA, we assessed for each Read 1 sequence the last 6 bases. Reads that contained ‘TTTT’ in the end were assigned as inactive sgRNA and ‘CAGC’ containing reads were marked as active sgRNAs. Read 2 (R2) contained the UMI barcode sequence.
Subsequently, data were processed in R studio
Assembly: mm10
Supplementary files format and content: txt file containing read counts per sgRNA-UMI
Library strategy: custom sequencing strategy

source_name: Tumor tissue

extract_protocol:
DNA was extracted from lysed cell or tumor samples by phenol-chloroform extraction and precipitated with isopropanol.
Samples were individually amplified by PCR with barcded primers and purified.

value: Tumor tissue

value: Melanoma


title: ORSAM13860-1


title: in_vivo_Red2


title: hPSC RNA-seq ActD 2h shHNRNPU Repeat #1


title: in_vivo_Red1


title: in_vivo_Red3


title: ORSAM13859-1

source_name: adipose-10% fat + fiber-male-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1

value: CC011/UncJ x CC005/TauUncJ)F1


title: in_vivo_Green5


title: hPSC RNA-seq ActD 1h shHNRNPU Repeat #2


title: in_vivo_Green4


title: OCI-AML-2


title: hPSC RNA-seq ActD 0h shLUC Repeat #1


title: ORSAM13858-1

value: gonadal fat pad


title: in_vivo_Red6


title: in_vivo_Green2


title: hPSC RNA-seq ActD 0h shHNRNPU Repeat #2


title: hPSC RNA-seq ActD 1h shHNRNPU Repeat #1


title: in_vivo_Green3


title: in_vivo_Green1


title: in_vivo_Red4


title: in_vivo_Blue6


title: ORSAM13857-1

value: male


title: hPSC RNA-seq ActD 0h shHNRNPU Repeat #1


title: in_vivo_Blue5


title: ORSAM13854-1

source_name: adipose-10% fat + fiber-female-CC011/UncJ x CC005/TauUncJ)F1 -None-rep1


title: in_vivo_Blue4


title: ORSAM13850-1

source_name: adipose-44% fat + fiber-female-CC002/UncJ x CC043/GeniUncJ)F1 -None-rep1

value: CC002/UncJ x CC043/GeniUncJ)F1


title: AR-97Q_4

city: Nagoya

first: Madoka

last: Iida

state: Aichi

address: 65 Tsurumai-cho Showa-ku

department: Neurology department

country: Japan

institute: Nagoya University

data_processing:
The quality of the raw paired-end sequence reads was assessed with Fast QC (Version 0.11.5; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned to the reference genome using RNA-Seq aligner HISAT2 (Version 2.1.0). The HISAT2-resultant .sam files were converted into .bam files with samtools and used to estimate the abundance of uniquely mapped reads with featureCounts (Version 1.6.3). The raw counts were normalized with transcripts per million (TPM).
Assembly: mm10
Supplementary files format and content: excel file

source_name: C2C12 cell

growth_protocol: C2C12 cells were seeded at a cell density of 6.0 x 104 cells/well in 24-well plates. The medium was changed to the differentiation medium on day 2. Ten nM of DHT was added on day 3 and RNA was extracted on day 4.

extract_protocol:
Total RNA was extracted from the C2C12 cell model of SBMA and control using the RNeasy Mini Kit (QIAGEN). The quality and quantity of the RNA obtained was checked using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, United States), and analyzed with the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc).
A library was independently prepared with 1ug of total RNA for each sample by Illumina Stranded mRNA Sample Prep Kit (Illumina, Inc.)

value: C2C12 cell


title: AR-97Q_3


title: ORSAM13849-1

source_name: adipose-10% fat + fiber-male-CC030/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: CC030/GeniUncJ x CC002/UncJ)F1


title: in_vivo_Blue3


title: hPSC MAR-seq shLUC Repeat #1

data_processing:
cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff 10 -m 50 -o ${bn}.trim.p1.fq.gz -p ${bn}.trim.p2.fq.gz ${p1} ${p2}
bowtie2 $opts -x /export/genomic/hg38/bowtie2-indeces/hg38 -1 ${p1} -2 ${p2} | grep -E -v 'chrM|chrUn|random|RANDOM|alt' | samtools view -b -q 20 -F 1804 -f 2 | samtools sort -n >${out}.bam
macs2 callpeak -q 0.05 -t ${f} -n ${bn} -g hs -f BEDPE # &>${bn}.err
redefine_peaks() from glbase3
bamCoverage -p 4 --normalizeUsing CPM --minMappingQuality 30 --ignoreDuplicates -b ${in} -o ${out}
Assembly: hg38
Supplementary files format and content: Processed files are BED format data, containing hg38 genome coordinates for the two samples after redefine_peaks was used

extract_protocol:
Briefly, 90% confluence cells were washed 3 time with DPBS on the cell culture plate. We using the cytoskeletal (CSK) extraction buffer (100 mM NaCl, 1 mM EGTA, 10 mM PIPES pH 6.8, 3 mM MgCl2, 300 mM sucrose, 0.5% v/v Triton X-100) isolate the unclears in the plate. Nuclear was crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclear was digest with MspI, HaeIII, RsaI, AluI, BamHI, PvuII restriction enzymes. The nuclear was reverse crosslinked by incubate in 65 degrees overnight. DNA was extracted from the isolated nuclear matrix and the input sample. DNA was recovered by extraction with phenol: chloroform: isoamyl alcohol (25:24:1) and ethanol precipitation. The isolated input DNA was fragmented by using a Bioruptor®Plus sonication device (Diagenode) to obtain the desired DNA fragment size (enriched at 300 bp). The libraries were sequenced at Novogene via a Novaseq instrument in 150bp paired-end mode.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

treatment_protocol: No special treatment was performed

value: cell line

value: hPSCs H1

value: shRNA targetting LUC


title: in_vivo_Blue2


title: ORSAM13848-1


title: AR-97Q_2


title: hPSC MAR-seq shHNRNPU Repeat #2

value: Pluripotent Stem Cells

value: shRNA targetting HNRNPU


title: AR-97Q_1


title: in_vivo_Blue1


title: in_vitro_Red


title: hPSC MAR-seq shHNRNPU Repeat #1


title: ORSAM13846-1

source_name: adipose-10% fat + fiber-female-CC030/GeniUncJ x CC002/UncJ)F1 -None-rep1

value: female

value: Outbred

value: 10% fat + fiber


title: AR-24Q_4


title: POLIIS2P (CUT&TAG) shLUC repeat 2

data_processing:
cutadapt -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff 10 -m 50 -o ${bn}.trim.p1.fq.gz -p ${bn}.trim.p2.fq.gz ${p1} ${p2}
bowtie2 $opts -x /export/genomic/hg38/bowtie2-indeces/hg38 -1 ${p1} -2 ${p2} | grep -E -v 'chrM|chrUn|random|RANDOM|alt' | samtools view -b -q 20 -F 1804 -f 2 | samtools sort -n >${out}.bam
macs2 callpeak -q 0.05 -t ${f} -n ${bn} -g hs -f BEDPE # &>${bn}.err
bamCoverage -p 4 --normalizeUsing CPM --minMappingQuality 30 --ignoreDuplicates -b ${in} -o ${out}
Assembly: hg38
Supplementary files format and content: Processed files are BED format data, containing hg38 genome coordinates for peaks in the indicated sample

extract_protocol:
Briefly, 1 × 105 cells were washed twice with wash buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 0.5 mM spermidine and 1× protease inhibitors). Then cells were bound to concanavalin A beads (Bangs Laboratories, BP531) followed by activated with binding buffer (20 mM Tris-HCl pH 7.4, 10 mM KCl, 1 mM CaCl2 and 1mM MnCl2). The bead-bound cells were wash once with wash buffer containing 0.01% digitonin, and primary antibodies were added to bead-bound cells in antibody buffer (4 mM EDTA and 0.2% BSA in wash buffer containing 0.01% digitonin) and rotated overnight at 4 °C. The primary antibodies used: anti-HNPNPU (Abcam, ab172608), anti-MATR3 (Abcam, ab264136), anti-H3K27ac (Abcam, ab4279), anti-H3K27me3 (Millipore, 07-449,) Then, secondary antibody (Antibodies-Online, ABIN101961) was added to bead-cells-antibody in wash buffer and further incubated at RT for 1h. pG-Tn5 (Vazyme, S603-02) was add to cells in 300-wash buffer (20 mM Tris-HCl pH 7.4, 300 mM NaCl, 0.5 mM spermidine and 1× protease inhibitors, 0.01% digitonin) at RT for 1h. The Tn5 was activated with 300-wash buffer supplemented with 10 mM MgCl2 and washed five times with 500 ul 300-wash buffer. To stop the Tn5 reaction, 10 ul of 0.5 M EDTA, 3 ul of 10% SDS and 1.5 ul of proteinase K (20 mg/ml) were added 55°C for 1 h. DNA fragments were extracted and PCR amplification using NEBNext HiFi 2× PCR Master mix (NEB, M0541L) with the conditions: 72°C, 5 min, 98°C, 30s and 12-14 cycle for 98°C, 10s, 63°C, 10s and 72°C, 30s. The 300-500bp DNA fragments were purified with the VAHTS DNA Clean Beads (Vazyme, N411-02). Libraries were sequenced by an Illumina sequencer.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina


title: POLIIS2P (CUT&TAG) shLUC repeat 1


title: ORSAM13845-1


title: AR-24Q_3


title: in_vitro_Blue


title: ORSAM13844-1


title: hPSC MAR-seq shLUC Repeat #2


title: AR-24Q_1


title: ORSAM13735-1

source_name: adipose-44% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC075/UncJ x CC042/GeniUncJ)F1

value: 44% fat + fiber


title: POLIIS2P (CUT&TAG) shHNRNPU#1 repeat 1


title: Lane2_in_vivo_Red3

extract_protocol:
DNA was extracted from lysed cell or tumor samples by phenol-chloroform extraction and precipitated with isopropanol.
Samples were individually amplified by PCR with barcoded primers and purified.

value: Tumor tissue

value: Melanoma


title: Lane2_in_vivo_Red2


title: OVCAR3-KRAB sgXIST9 hypoxia rep3

city: Irvine

first: Sha

last: Sun

state: CA

address: 4232 McGaugh Hall

department: Development and cell biology

institute: University of california Irvine

data_processing:
Fastq files were trimmed using Trimmomatic package, and quality was checked using Fastqc package. Reads were aligned using hisat2 package using hg38 human genome as a reference. Counts were generated using feature counts, and Differential expression was performed with DeSeq2 packag
Assembly: hg38
Supplementary files format and content: tax-delimited text include raw count for each sample

growth_protocol: OVCAR3 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics

extract_protocol:
RNA was extract with Trizol following the manufacteur instruction
TruSeq Stranded Total RNA following manufacturer's protocol

treatment_protocol: during hypoxia treament cell were put in hypoxia chamber with 1% Oxygen for 24h

value: ovarian cancer cell

value: sgXIST

value: hypoxia

tag: time


title: ORSAM13734-1

source_name: adipose-10% fat + fiber-male-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

value: gonadal fat pad

value: male

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: OVCAR3-KRAB sgXIST9 hypoxia rep2


title: P2001 LN_01

first: Hae-Ock

address: 222 Banpo-daero, Seocho-gu

department: Department of Microbiology

institute: College of Medicine, The Catholic University of Korea

description:
LN_01
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were mapped to the GRCh38 human reference genome using the Cell Ranger toolkit (version 5.0.0).
Assembly: GRCh38
Supplementary files format and content: R object file

source_name: Normal LN

extract_protocol:
Single-cell isolation was performed differently depending on the samples. (1) Biopsy samples and normal lymph node tissues were chopped into 2-4mm pieces and dissociated in an enzyme solution containing collagenase/hyaluronidase (STEMCELL Technologies, Vancouver, Canada) and DNase I, RNase-Free (lyophilized) (QIAGEN, Hilden, Germany) at 37 °C for 1 h. Tissue pieces were re-mixed by gentle pipetting at 20 min intervals during the incubation. (2) Tumor and normal lung tissue dissociation was performed using a tumor dissociation kit (Miltenyi Biotech, Germany) following the manufacturer’s instructions. Briefly, tissue was cut into 2–4 mm pieces and transferred to a C tube containing the enzyme mix (enzymes H, R, and A in RPMI1640 medium). The GentleMACS programs h_tumor_01, h_tumor_02, and h_tumor_02 were run with two 30-min incubations on the MACSmix tube rotator at 37 °C. (3) Brain tissue was chopped into 2–4 mm pieces and incubated in an enzyme solution (collagenase (Gibco, Waltham, MA, USA), DNase I (Roche, Basel, Switzerland), and Dispase I (Gibco, Waltham, MA, USA) in DMEM) at 37 °C for 1 hour. Tissue pieces were re-mixed by gentle pipetting at 15 min intervals during the incubation. (4) Pleural fluids were transferred to a 50-ml tube, and cells spun down at 300 g.  Each cell suspension was transferred to a new 50 ml (15 ml for biopsy samples) tube through a 70-µm strainer. The volume in the tube was readjusted to 50 ml (or 15 ml) with RPMI1640 medium, and spun down to remove the enzymes. The supernatant was aspirated out, the cell pellet was resuspended in 4 ml of RPMI1640 medium, and dead cells were removed using Ficoll-Paque PLUS (GE Healthcare, Chicago, IL, USA) separation.   For the samples subjected to a multiplexing, dissociated cells were cryopreserved in CELLBANKER1 (Zenogen, Fukushima, Japan) and thawed for pooling.
Single-cell suspensions were loaded into the Chromium system (10x Genomics, Pleasanton, CA, USA). Following the manufacturer’s instructions, 3’ scRNA-seq libraries for fourteen samples were generated using Chromium Single Cell 3′ v2 Reagent Kits. The 3’ library preparation for a sample (EBUS_119) used Chromium Single Cell 3′ v3 Reagent Kits. The 5’ scRNA-seq libraries for twelve individual and two pooled samples were generated using Chromium Single Cell 5′ v2 Reagent Kit. Libraries were then sequenced on an Illumina HiSeq 2500 for 3’ scRNA-seq and an Illumina NovaSeq 6000 for 5’ scRNA-seq.

tag: patient

value: Normal LN

tag: tumor stage

value: IIB

tag: cancer subtype

value: ADC

tag: recist

value: PR

tag: platform

value: Single Cell 3'


title: ORSAM13847-1

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38

value: CC030/GeniUncJ x CC002/UncJ)F1

value: Outbred


title: OVCAR3-KRAB sgXIST9 hypoxia rep1


title: Lane2_in_vivo_Red1


title: ORSAM13733-1

value: 10% fat + fiber


title: Lane2_in_vivo_Green3


title: P0031 LUNG_N31

description:
LUNG_N31
10x Genomics

source_name: Normal Lung

value: Normal Lung

value: IIIA

value: NE


title: OVCAR3-KRAB sgXIST9 normoxia rep3

value: ovarian cancer cell


title: Lane2_in_vivo_Green2

value: Tumor tissue

value: Melanoma


title: ORSAM13730-1

source_name: adipose-10% fat + fiber-female-CC043/GeniUncJ x CC042/GeniUncJ)F1 -None-rep1

value: gonadal fat pad

value: female


title: AR-24Q_2

value: C2C12 cell


title: in_vitro_Green


title: OVCAR3-KRAB sgXIST9 normoxia rep2

value: sgXIST


title: ORSAM13732-1

value: male

value: CC043/GeniUncJ x CC042/GeniUncJ)F1


title: P1025 EBUS_25

description:
EBUS_25
10x Genomics

source_name: LN

value: LN

value: IV

value: SCLC

value: PD


title: Lane2_in_vivo_Green1


title: ORSAM13729-1

source_name: adipose-44% fat + fiber-female-CC019/TauUncJ x CC042/GeniUncJ)F1 -None-rep1

value: CC019/TauUncJ x CC042/GeniUncJ)F1

value: Outbred

value: 44% fat + fiber


title: OVCAR3-KRAB sgXIST9 normoxia rep1


title: P1056 LM_56

description:
LM_56
10x Genomics

source_name: Liver

value: Liver

value: NUT

value: SD

value: Single Cell 3'


title: P1015 EBUS_15

description:
EBUS_15
10x Genomics

value: IIIA

value: ADC


title: ORSAM13728-1

value: gonadal fat pad

value: female


title: Lane2_in_vivo_Blue2

value: Tumor tissue

value: Melanoma


title: ORSAM13726-1


title: OVCAR3-KRAB sgXIST7 hypoxia rep3

value: ovarian cancer cell

value: sgXIST

value: hypoxia


title: P1115 LM_115

description:
LM_115
10x Genomics

value: ED

value: SCLC

value: PR


title: P1056 EBUS_56

description:
EBUS_56
10x Genomics

value: LN

value: IV


title: ORSAM13725-1

source_name: adipose-44% fat + fiber-female-CC042/GeniUncJ x CC040/TauUncJ)F1 -None-rep1

value: CC042/GeniUncJ x CC040/TauUncJ)F1

value: Outbred

value: 44% fat + fiber


title: OVCAR3-KRAB sgXIST7 hypoxia rep1


title: P0031 LUNG_T31

description:
LUNG_T31
10x Genomics

source_name: Lung

value: Lung

value: IIIA

value: NE

value: Single Cell 3'


title: Lane1_in_vivo_Red3

source_name: Tumor tissue

value: Tumor tissue


title: OVCAR3-KRAB sgXIST7 hypoxia rep2


title: P1119 EBUS_119

description:
EBUS_119
10x Genomics

value: ADC

value: PD


title: ORSAM13724-1

source_name: adipose-44% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: gonadal fat pad

value: male

value: CC004/TauUncJ x CC019/TauUncJ)F1


title: Lane1_in_vivo_Red2

value: Melanoma


title: OVCAR3-KRAB sgXIST7 normoxia rep3

value: ovarian cancer cell

value: sgXIST


title: P1089 EBUS_89

description:
EBUS_89
10x Genomics

value: LN

value: IV


title: OVCAR3-KRAB sgXIST7 normoxia rep2


title: ORSAM13723-1

source_name: adipose-10% fat + fiber-female-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1

value: female

value: CC051/TauUncJ x CC060/UncJ)F1

value: Outbred

value: 10% fat + fiber


title: Lane1_in_vivo_Red1


title: Lane2_in_vivo_Blue3


title: OVCAR3-KRAB sgXIST7 normoxia rep1


title: Lane1_in_vivo_Green3


title: ORSAM13722-1

source_name: adipose-10% fat + fiber-male-CC051/TauUncJ x CC060/UncJ)F1 -None-rep1


title: P1076 NECK_05

description:
NECK_05
10x Genomics


title: P1037 EBUS_37

description:
EBUS_37
10x Genomics

value: IVA

value: SQ

value: PR


title: OVCAR3-KRAB sgControl hypoxia rep3

value: sgControl

value: hypoxia


title: Lane1_in_vivo_Green2

value: Tumor tissue


title: Lane2_in_vivo_Blue1


title: ORSAM13720-1

source_name: adipose-10% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: gonadal fat pad

value: male

value: CC075/UncJ x CC042/GeniUncJ)F1


title: OVCAR3-KRAB sgControl hypoxia rep2

value: ovarian cancer cell


title: P1006 EFFUSION_06

description:
EFFUSION_06
10x Genomics

source_name: Effusion

value: Effusion

value: ADC

value: Single Cell 3'


title: Lane1_in_vivo_Green1

value: Melanoma


title: ORSAM13715-1

source_name: adipose-10% fat + fiber-female-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: female

value: CC004/TauUncJ x CC019/TauUncJ)F1


title: OVCAR3-KRAB sgControl hypoxia rep1


title: P1006 EBUS_06

description:
EBUS_06
10x Genomics

value: Lung

value: IV


title: Lane1_in_vivo_Blue3


title: ORSAM13714-1

value: Outbred

value: 10% fat + fiber


title: OVCAR3-KRAB sgControl normoxia rep3

value: sgControl


title: OVCAR3-KRAB sgControl normoxia rep2


title: Lane1_in_vivo_Blue2


title: ORSAM13713-1


title: OVCAR3-KRAB sgControl normoxia rep1


title: P1076 EBUS_76

description:
EBUS_76
10x Genomics

value: LN

value: PD


title: RNA2_U251_NSFD_5DPT

city: DALLAS

first: jianjing

last: Yang

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Reads were aligned to the human reference sequence GRCh37/hg19 with the TopHat (version 1.4.1) algorithm and transcript assembly performed with Cufflinks (version 2.1.0). Expression levels of RefSeq-annotated genes were calculated in units of fragments per kilobase of exon per million mapped fragments (FPKM) and differential expression analysis was performed with Cuffdiff (version 2.1.0). Genes were defined as significant if the following three criteria were satisfied: Student’s t-test p value ≥0.05, at least 2-fold gene expression change relative to the GFP-transduced control, and the triplicate average of ln(FPKM) ≥1 in either the experimental condition or fibroblast control. Gene ontology analysis was performed using the DAVID Functional Annotation Tool (version 6.7).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Differential expression file (.xlsx) was generated using Cuffdiff (version 2.1.0).

source_name: U-251 Glioblastoma Cell

extract_protocol:
After cell sorting, we acquired nearly 5×10^5 U251 cells. RNA isolation was performed by TRIZOL (Life Technologies, 15596-018) followed by chloroform extraction and column-based purification kit (Zymo Research, R1016). Total RNA samples were submitted and analyzed with bioanalyzer to check RNA concentration and RNA integrity number (RIN).
1ug total RNA has been used for library preparation (Illumina, RS-122-2201)

value: Glioblastoma

tag: over-expression

value: NEUROG2 and SOX11

tag: media

value: Neuron induction medium supplemented with 10 microMolar forskolin and 1 microMolar dorsomorphin


title: RNA1_U251_NSFD_5DPT


title: ORSAM13712-1

tag: tissue

value: gonadal fat pad

tag: Sex


title: ORSAM13710-1

source_name: adipose-44% fat + fiber-male-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: male

tag: strain

value: CC075/UncJ x CC042/GeniUncJ)F1

tag: genotype

value: 44% fat + fiber


title: Lane1_in_vitro_Green

value: Melanoma


title: STSW5_S4_L002

city: Chicago

first: Christopher

last: Felicelli

state: Illinois

address: 303 East Chicago Avenue

department: Pathology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Raw sequencing data, in base call format (.bcl) were demultiplexed using Space Ranger (version 2.0.0) from 10x Genomics, converting the raw data into FASTQ format.
The images were processed and manually aligned using the Loupe Browser (version 5.1.0).
pace Ranger was also used for alignment of the FASTQ files to the human probe set version 2 and to count the number of reads from each cell that aligned to each probe.
The resulting matrix files, which summarize the alignment results, were imported to Seurat (Satija Lab, NYGC) for further analysis. In Seurat, each individual sample was preprocessed, normalized, and scaled.
ll samples were then combined into a single dataset using the IntegrateData function in Seurat, adding metadata with the original sample information.
All UMAPs, Violin plots, spatial feature expression plots, and heatmaps were generated using Seurat tools. Cell types were automatically assigned using the R package scType.
Assembly: hq38
Library strategy: Spatial Transcriptomics

source_name: Uterus

growth_protocol: N/A-FFPE

extract_protocol:
1-2 curls (10um thickness each) were used for RNA extraction using Qiagen RNeasy FFPE kit (Qiagen 73504) according to manufactures’ protocol. Extracted RNA was examined by Agilent Bioanalyzer RNA pico chip to confirm the DV200 >30%.  For each FFPE sample, 1 section (5um thickness) was placed on Leica Bond plus slides. Each slide was incubated at 42°C for 3 hours followed by overnight room temperature incubation. Slides were stored in desiccated slide holders until proceeding to deparaffinization. The deparaffinization, HE stains and imaging and decrosslinking of tissue slides were performed according to 10x Genomics protocol (CG000520 Rev B) specific for Visium CytAssist spatial gene expression for FFPE kit.
he deparaffinization, HE stains and imaging and decrosslinking of tissue slides were performed according to 10x Genomics protocol (CG000520 Rev B) specific for Visium CytAssist spatial gene expression for FFPE kit. Then, the slides were proceeded to human probe (v2) hybridization and ligation using 10x Genomics Visium CytAssist spatial gene expression FFPE, human transcriptome, 6.5mm kit (10x Genomics, PN-1000520). The probes were released from tissue slide and transferred to barcoded visium slide using Visium CytAssist instrument followed by probe extension. Sequencing libraries were prepared according to manufacturer’s protocol. Multiplexed libraries were pooled and sequenced on Novaseq6000 S2 flowcell 100 cycles kit with following parameter: 28nt for Read 1 and 90nt for Read 2. The visium slide processing, library preparation and sequencing was done at Northwestern University NUseq facility core.

treatment_protocol: regions of LMBN vs LMS

value: Uterus

value: Mesenchymal

value: LMBN/LMS


title: ORSAM13719-1

first: Gary

address: 600 Main St

institute: The Jackson Laboratory

tag: treatment

tag: diet


title: RNA3_U251_NSFD_5DPT

tag: cell type


title: Lane1_in_vitro_Red

tag: cell line


title: ORSAM13717-1

source_name: adipose-10% fat + fiber-male-CC004/TauUncJ x CC019/TauUncJ)F1 -None-rep1

value: CC004/TauUncJ x CC019/TauUncJ)F1

tag: sequencing id


title: RNA3_U251_NSFD_3DPT


title: Lane1_in_vitro_Blue


title: ORSAM13709-1

value: Outbred


title: STSW3_S3_L002


title: STSW2_S2_L002


title: SARC_77_CSA_MES

source_name: Tumour tissue

value: Tumour tissue

value: Mesenchymal chondrosarcoma


title: ORSAM13708-1

source_name: adipose-44% fat + fiber-female-CC075/UncJ x CC042/GeniUncJ)F1 -None-rep1

value: female